From 9161ac66c247d3a2998218b17acb19e161ddf969 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 19 Oct 2021 18:32:07 -0700 Subject: [PATCH 001/368] some refactoring --- src/combinators/power.jl | 2 +- src/combinators/product.jl | 13 +++++++++++-- src/combinators/smart-constructors.jl | 23 ++++++++++++++++------- 3 files changed, 28 insertions(+), 10 deletions(-) diff --git a/src/combinators/power.jl b/src/combinators/power.jl index 58fe8ac9..15ad1c57 100644 --- a/src/combinators/power.jl +++ b/src/combinators/power.jl @@ -75,7 +75,7 @@ end # Same as PowerMeasure @inline function _basemeasure(d::ProductMeasure{F,S,<:Fill}, b::FactoredBase) where {F,S} n = length(d.pars) - inbounds(x) = all(xj -> b.inbounds(xj), x) + inbounds(x) = all(b.inbounds, x) constℓ = n * b.constℓ varℓ() = n * b.varℓ() base = b.base ^ size(d.pars) diff --git a/src/combinators/product.jl b/src/combinators/product.jl index c4a3df22..b812b491 100644 --- a/src/combinators/product.jl +++ b/src/combinators/product.jl @@ -95,13 +95,22 @@ end ############################################################################### # I <: AbstractArray -marginals(d::ProductMeasure{F,A}) where {F,A<:AbstractArray} = mappedarray(d.f, d.pars) +marginals(d::ProductMeasure{F,S,A}) where {F,S,A<:AbstractArray} = mappedarray(d.f, d.pars) + +function marginals(d::ProductMeasure{<:Returns, S, A}) where {F,S,A<:AbstractArray} + Fill(d.f.f.value, size(d.pars)) + # mappedarray(d.f.f, d.pars) +end function logdensity(d::ProductMeasure, x) mapreduce(logdensity, +, marginals(d), x) end -function Base.show(io::IO, d::ProductMeasure{F,A}) where {F,A<:AbstractArray} +function logdensity(d::ProductMeasure{<:Returns}, x) + sum(x -> logdensity(d.f.f.value, x), x) +end + +function Base.show(io::IO, d::ProductMeasure{F,S,A}) where {F,S,A<:AbstractArray} io = IOContext(io, :compact => true) print(io, "For(") print(io, d.f, ", ") diff --git a/src/combinators/smart-constructors.jl b/src/combinators/smart-constructors.jl index c525fdee..17200b22 100644 --- a/src/combinators/smart-constructors.jl +++ b/src/combinators/smart-constructors.jl @@ -54,19 +54,21 @@ end ############################################################################### # PowerMeaure -function powermeasure(μ::M, dims::NTuple{N,I}) where {M<:AbstractMeasure,N,I<:Integer} +function powermeasure(μ::M, dims::NTuple{N,I}) where {M<:AbstractMeasure,N,I} productmeasure(Returns(μ), identity, CartesianIndices(dims)) end -function powermeasure(μ::M, dims::Tuple{I}) where {M<:AbstractMeasure,N,I<:Integer} +function powermeasure(μ::M, dims::Tuple{I}) where {M<:AbstractMeasure,N,I} productmeasure(Returns(μ), identity, 1:first(dims)) end -function powermeasure(μ::WeightedMeasure, dims::NTuple{N,I}) where {N,I<:Integer} +function powermeasure(μ::WeightedMeasure, dims::NTuple{N,I}) where {N,I} k = prod(dims) * μ.logweight return weightedmeasure(k, μ.base^dims) end + + ############################################################################### # ProductMeasure @@ -76,15 +78,22 @@ productmeasure(f, pars) = productmeasure(f, identity, pars) productmeasure(μs::Tuple) = TupleProductMeasure(μs) -productmeasure(f::Returns, ::typeof(identity), pars) = ProductMeasure(kernel(f, identity), pars) +productmeasure(f::Returns, ops, pars) = ProductMeasure(kernel(f, identity), pars) productmeasure(k::Kernel, pars) = productmeasure(k.f, k.ops, pars) productmeasure(nt::NamedTuple) = productmeasure(identity, nt) - -productmeasure(f::Returns, ops, pars) = productmeasure(f, identity, pars) - +function productmeasure(f::Returns{FB}, ops, pars) where {FB<:FactoredBase} + fb = f.value + dims = size(pars) + n = prod(dims) + inbounds(x) = all(fb.inbounds, x) + constℓ = n * fb.constℓ + varℓ() = n * fb.varℓ() + base = fb.base ^ dims + FactoredBase(inbounds, constℓ, varℓ, base) +end function productmeasure(f::Returns{W}, ::typeof(identity), pars) where {W <: WeightedMeasure} ℓ = f.value.logweight From 681dbcd7dbf4ba816b7a674cd94e3131c67857eb Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 25 Oct 2021 16:00:36 -0700 Subject: [PATCH 002/368] pretty printing --- Project.toml | 2 ++ src/MeasureBase.jl | 3 ++ src/combinators/affine.jl | 2 ++ src/combinators/for.jl | 2 +- src/combinators/power.jl | 10 +++--- src/combinators/product.jl | 45 +++++++++------------------ src/combinators/smart-constructors.jl | 2 +- src/combinators/superpose.jl | 17 +++++++++- src/density.jl | 12 +++---- src/domains.jl | 2 +- src/kernel.jl | 7 +++++ src/primitives/dirac.jl | 5 +++ src/primitives/lebesgue.jl | 9 +++--- src/primitives/trivial.jl | 2 ++ src/thunks.jl | 2 +- src/utils.jl | 11 +++++++ 16 files changed, 81 insertions(+), 52 deletions(-) diff --git a/Project.toml b/Project.toml index 11142182..51ea2e1e 100644 --- a/Project.toml +++ b/Project.toml @@ -12,6 +12,7 @@ LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" LogExpFunctions = "2ab3a3ac-af41-5b50-aa03-7779005ae688" MLStyle = "d8e11817-5142-5d16-987a-aa16d5891078" MappedArrays = "dbb5928d-eab1-5f90-85c2-b9b0edb7c900" +PrettyPrinting = "54e16d92-306c-5ea0-a30b-337be88ac337" Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" Tricks = "410a4b4d-49e4-4fbc-ab6d-cb71b17b3775" @@ -23,6 +24,7 @@ KeywordCalls = "0.2" LogExpFunctions = "0.3" MLStyle = "0.4" MappedArrays = "0.4" +PrettyPrinting = "0.3" Tricks = "0.1" julia = "1.3" diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index 6b2a87a3..cdc6c906 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -16,6 +16,9 @@ export AbstractMeasure abstract type AbstractMeasure end +import PrettyPrinting as Pretty + + sampletype(μ::AbstractMeasure) = typeof(testvalue(μ)) # sampletype(μ::AbstractMeasure) = sampletype(basemeasure(μ)) diff --git a/src/combinators/affine.jl b/src/combinators/affine.jl index a13c9bcb..88f5639d 100644 --- a/src/combinators/affine.jl +++ b/src/combinators/affine.jl @@ -4,6 +4,8 @@ using LinearAlgebra par::NamedTuple{N,T} end +quoteof(f::AffineTransform) = :(AffineTransform($(quoteof(f.par)))) + params(f::AffineTransform) = getfield(f, :par) @inline Base.getproperty(d::AffineTransform, s::Symbol) = getfield(getfield(d, :par), s) diff --git a/src/combinators/for.jl b/src/combinators/for.jl index 1996df38..27c58d62 100644 --- a/src/combinators/for.jl +++ b/src/combinators/for.jl @@ -79,7 +79,7 @@ For(f, dims...) = productmeasure(i -> f(i...), zip(dims...)) For(f, inds::AbstractArray) = productmeasure(f, inds) -For(f, n::Int) = productmeasure(f, 1:n) +For(f, n::Int) = productmeasure(f, Base.OneTo(n)) For(f, dims::Int...) = productmeasure(i -> f(Tuple(i)...), CartesianIndices(dims)) diff --git a/src/combinators/power.jl b/src/combinators/power.jl index 15ad1c57..6258830d 100644 --- a/src/combinators/power.jl +++ b/src/combinators/power.jl @@ -42,14 +42,12 @@ function Base.:^(μ::M, dims::NTuple{N,I}) where {M<:AbstractMeasure,N,I<:Intege end # Same as PowerMeasure -function Base.show(io::IO, d::ProductMeasure{Returns{T},I,C}) where {T,I,C<:CartesianIndices} - io = IOContext(io, :compact => true) - print(io, d.f.f.value, " ^ ", size(d.pars)) +function Pretty.tile(d::ProductMeasure{Returns{T},I,C}) where {T,I,C<:CartesianIndices} + Pretty.pair_layout(Pretty.tile(d.f.f.value), Pretty.tile(size(d.pars)); sep=" ^ ") end -function Base.show(io::IO, d::ProductMeasure{R,I,V}) where {R<:Returns,I,V<:AbstractVector} - io = IOContext(io, :compact => true) - print(io, d.f.f.value, " ^ ", length(d.pars)) +function Pretty.tile(d::ProductMeasure{R,I,V}) where {R<:Returns,I,V<:AbstractVector} + Pretty.pair_layout(Pretty.tile(d.f.f.value), Pretty.tile(length(d.pars)); sep=" ^ ") end # sampletype(d::PowerMeasure{M,N}) where {M,N} = @inbounds Array{sampletype(first(marginals(d))), N} diff --git a/src/combinators/product.jl b/src/combinators/product.jl index b812b491..48250f40 100644 --- a/src/combinators/product.jl +++ b/src/combinators/product.jl @@ -49,24 +49,12 @@ end testvalue(d::ProductMeasure) = map(testvalue, marginals(d)) -function Base.show(io::IO, μ::ProductMeasure{F,S,NamedTuple{N,T}}) where {F,S,N,T} - io = IOContext(io, :compact => true) - print(io, "Product(",μ.data, ")") -end - -function Base.show_unquoted(io::IO, μ::ProductMeasure, indent::Int, prec::Int) - io = IOContext(io, :compact => true) - if Base.operator_precedence(:*) ≤ prec - print(io, "(") - show(io, μ) - print(io, ")") - else - show(io, μ) - end - return nothing +function Pretty.tile(μ::ProductMeasure{F,S,NamedTuple{N,T}}) where {F,S,N,T} + result = Pretty.literal("Product(") + result *= Pretty.pair_layout(μ.f, μ.pars; sep=", ") + result *= Pretty.literal(")") end - ############################################################################### # I <: Tuple @@ -79,9 +67,9 @@ export ⊗ marginals(d::TupleProductMeasure{T}) where {F, T<:Tuple} = d.pars -function Base.show(io::IO, μ::TupleProductMeasure{T}) where {F,T <: Tuple} - io = IOContext(io, :compact => true) - print(io, join(string.(marginals(μ)), " ⊗ ")) +function Pretty.tile(μ::TupleProductMeasure{T}) where {F,T <: Tuple} + mar = marginals(μ) + Pretty.list_layout(Pretty.Layout[Pretty.tile.(mar)...]; sep=" ⊗ ") end @inline function logdensity(d::TupleProductMeasure, x::Tuple) where {T<:Tuple} @@ -110,23 +98,20 @@ function logdensity(d::ProductMeasure{<:Returns}, x) sum(x -> logdensity(d.f.f.value, x), x) end -function Base.show(io::IO, d::ProductMeasure{F,S,A}) where {F,S,A<:AbstractArray} - io = IOContext(io, :compact => true) - print(io, "For(") - print(io, d.f, ", ") - print(io, d.pars, ")") +function Pretty.tile(d::ProductMeasure{F,S,A}) where {F,S,A} + result = Pretty.literal("For(") + result *= Pretty.pair_layout(Pretty.tile(d.f), Pretty.tile(d.pars); sep=", ") + result *= Pretty.literal(")") end ############################################################################### # I <: CartesianIndices -function Base.show(io::IO, d::ProductMeasure{F,S,I}) where {F, S, I<:CartesianIndices} - io = IOContext(io, :compact => true) - print(io, "For(") - print(io, d.f, ", ") - join(io, size(d.pars), ", ") - print(io, ")") +function Pretty.tile(d::ProductMeasure{F,S,I}) where {F, S, I<:CartesianIndices} + result = Pretty.literal("For(") + result *= Pretty.pair_layout(Pretty.tile(d.f), Pretty.tile(size(d.pars)); sep=", ") + result *= Pretty.literal(")") end diff --git a/src/combinators/smart-constructors.jl b/src/combinators/smart-constructors.jl index 17200b22..c9d333f7 100644 --- a/src/combinators/smart-constructors.jl +++ b/src/combinators/smart-constructors.jl @@ -59,7 +59,7 @@ function powermeasure(μ::M, dims::NTuple{N,I}) where {M<:AbstractMeasure,N,I} end function powermeasure(μ::M, dims::Tuple{I}) where {M<:AbstractMeasure,N,I} - productmeasure(Returns(μ), identity, 1:first(dims)) + productmeasure(Returns(μ), identity, Base.OneTo(first(dims))) end function powermeasure(μ::WeightedMeasure, dims::NTuple{N,I}) where {N,I} diff --git a/src/combinators/superpose.jl b/src/combinators/superpose.jl index 4edbe268..3a824be3 100644 --- a/src/combinators/superpose.jl +++ b/src/combinators/superpose.jl @@ -1,6 +1,6 @@ export SuperpositionMeasure -""" +@doc raw""" struct SuperpositionMeasure{X,NT} <: AbstractMeasure components :: NT end @@ -10,11 +10,26 @@ The superposition of two measures μ and ν can be more concisely written as μ Superposition measures satisfy basemeasure(μ + ν) == basemeasure(μ) + basemeasure(ν) + + +```math + \begin{aligned}\frac{\mathrm{d}(\mu+\nu)}{\mathrm{d}(\alpha+\beta)} & =\frac{f\,\mathrm{d}\alpha+g\,\mathrm{d}\beta}{\mathrm{d}\alpha+\mathrm{d}\beta}\\ + & =\frac{f\,\mathrm{d}\alpha}{\mathrm{d}\alpha+\mathrm{d}\beta}+\frac{g\,\mathrm{d}\beta}{\mathrm{d}\alpha+\mathrm{d}\beta}\\ + & =\frac{f}{1+\frac{\mathrm{d}\beta}{\mathrm{d}\alpha}}+\frac{g}{\frac{\mathrm{d}\alpha}{\mathrm{d}\beta}+1}\\ + & =\frac{f}{1+\left(\frac{\mathrm{d}\alpha}{\mathrm{d}\beta}\right)^{-1}}+\frac{g}{\frac{\mathrm{d}\alpha}{\mathrm{d}\beta}+1}\ . + \end{aligned} +``` """ struct SuperpositionMeasure{NT} <: AbstractMeasure components :: NT end +function Pretty.tile(d::SuperpositionMeasure) + result = Pretty.literal("SuperpositionMeasure(") + result *= Pretty.list_layout([Pretty.tile.(d.components)...]) + result *= Pretty.literal(")") +end + testvalue(μ::SuperpositionMeasure) = testvalue(first(μ.components)) # SuperpositionMeasure(ms :: AbstractMeasure...) = SuperpositionMeasure{X,length(ms)}(ms) diff --git a/src/density.jl b/src/density.jl index 9979cbbc..c300b84d 100644 --- a/src/density.jl +++ b/src/density.jl @@ -54,12 +54,12 @@ struct DensityMeasure{F,B,L} <: AbstractMeasure log :: L end -function Base.show(io::IO, μ::DensityMeasure{F,B,Val{L}}) where {F,B,L} - io = IOContext(io, :compact => true) - print(io, "DensityMeasure ") - print(io, "∫(", μ.f) - print(io, ", ", μ.base) - print(io, "; log = ", L, ")") +function Pretty.tile(μ::DensityMeasure{F,B,Val{L}}) where {F,B,L} + result = Pretty.literal("DensityMeasure ∫(") + result *= Pretty.pair_layout(Pretty.tile(μ.f), Pretty.tile(μ.base); sep=", ") + result *= Pretty.literal("; log = ") + result *= Pretty.tile(L) + result *= Pretty.literal(")") end function Base.rand(rng::AbstractRNG, T::Type, d::DensityMeasure) diff --git a/src/domains.jl b/src/domains.jl index f25fc099..e5d48124 100644 --- a/src/domains.jl +++ b/src/domains.jl @@ -26,7 +26,7 @@ macro domain(name, T) struct $T <: AbstractDomain end export $name const $name = $T() - Base.show(io::IO, ::$T) = print(io, $sname) + Pretty.tile(::$T) = Pretty.literal($sname) end end diff --git a/src/kernel.jl b/src/kernel.jl index c688c69f..72cbb5de 100644 --- a/src/kernel.jl +++ b/src/kernel.jl @@ -3,6 +3,7 @@ export Kernel abstract type AbstractKernel <: AbstractMeasure end + struct Kernel{F,S} <: AbstractKernel f::F ops::S @@ -11,6 +12,12 @@ struct Kernel{F,S} <: AbstractKernel Kernel(f::F, ops::S) where {F,S} = new{F, S}(f,ops) end +function Pretty.quoteof(k::Kernel) + qf = Pretty.quoteof(k.f) + qops = Pretty.quoteof(k.ops) + :(Kernel($qf, $qops)) +end + """ kernel(f, M) kernel((f1, f2, ...), M) diff --git a/src/primitives/dirac.jl b/src/primitives/dirac.jl index 88501d58..b4e0a9e2 100644 --- a/src/primitives/dirac.jl +++ b/src/primitives/dirac.jl @@ -5,6 +5,11 @@ struct Dirac{X} <: PrimitiveMeasure x::X end +function Pretty.quoteof(d::Dirac) + q = Pretty.quoteof(d.x) + :(Dirac($q)) +end + sampletype(μ::Dirac{X}) where {X} = X function (μ::Dirac{X})(s) where {X} diff --git a/src/primitives/lebesgue.jl b/src/primitives/lebesgue.jl index 72a1017f..e66dd4ab 100644 --- a/src/primitives/lebesgue.jl +++ b/src/primitives/lebesgue.jl @@ -4,11 +4,10 @@ export Lebesgue struct Lebesgue{X} <: PrimitiveMeasure end -function Base.show(io::IO, μ::Lebesgue{X}) where X - io = IOContext(io, :compact => true) - print(io, "Lebesgue(") - print(io, X) - print(io, ")") +function Pretty.tile(::Lebesgue{X}) where X + result = Pretty.literal("Lebesgue(") + result *= Pretty.tile(X) + result *= Pretty.literal(")") end Lebesgue(X) = Lebesgue{X}() diff --git a/src/primitives/trivial.jl b/src/primitives/trivial.jl index affb5d1f..5e4ec260 100644 --- a/src/primitives/trivial.jl +++ b/src/primitives/trivial.jl @@ -3,3 +3,5 @@ export TrivialMeasure struct TrivialMeasure <: PrimitiveMeasure end sampletype(::TrivialMeasure) = Nothing + +Pretty.quoteof(::TrivialMeasure) = :(TrivialMeasure()) diff --git a/src/thunks.jl b/src/thunks.jl index 6b729c39..b56f757d 100644 --- a/src/thunks.jl +++ b/src/thunks.jl @@ -14,7 +14,7 @@ # end # function reduce_step(thunk :: LogdensityThunk, callback=Returns(nothing)) - + # reduce_step(LogdensityThunk{M,B,X,L}, callback=Returns(nothing)) -> Union{LogdensityThunk, L} diff --git a/src/utils.jl b/src/utils.jl index 1f7dfc2e..f079f327 100644 --- a/src/utils.jl +++ b/src/utils.jl @@ -1,5 +1,10 @@ const EmptyNamedTuple = NamedTuple{(),Tuple{}} +function Base.show(io::IO, μ::AbstractMeasure) + io = IOContext(io, :compact => true) + Pretty.pprint(io, μ) +end + showparams(io::IO, ::EmptyNamedTuple) = print(io, "()") showparams(io::IO, nt::NamedTuple) = print(io, nt) @@ -51,3 +56,9 @@ functioninstance(::Type{F}) where {F<:Function} = F.instance # See https://github.com/cscherrer/KeywordCalls.jl/issues/22 @inline instance_type(f::F) where {F<:Function} = F @inline instance_type(f::UnionAll) = Type{f} + +using MLStyle + +macro quoteof(ex) + +end From a330c5ed69136627036f8c25d0e2eb7bb4df2a77 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Fri, 29 Oct 2021 11:09:29 -0700 Subject: [PATCH 003/368] some updates for resettablerng --- src/resettablerng.jl | 32 +++++++++++++++++++++++++++++--- 1 file changed, 29 insertions(+), 3 deletions(-) diff --git a/src/resettablerng.jl b/src/resettablerng.jl index 1b3079e6..13841ace 100644 --- a/src/resettablerng.jl +++ b/src/resettablerng.jl @@ -13,6 +13,7 @@ function Base.show(io::IO, r::ResettableRNG) end function reset!(r::ResettableRNG) + @info "Calling reset!" Random.seed!(r.rng, r.seed) end @@ -42,9 +43,26 @@ end # Base.rand(r::ResettableRNG, d::AbstractMeasure) = rand(r.rng, d) # Base.rand(r::ResettableRNG, ::Type{T}, d::AbstractMeasure) where {T} = rand(r.rng, T, d) # Base.rand(r::ResettableRNG) = rand(r.rng, Float64) -Base.rand(r::ResettableRNG, ::Type{T}) where {T} = rand(r.rng, T) -Base.randn(r::ResettableRNG, ::Type{T}) where {T} = randn(r.rng, T) -Base.randn(r::ResettableRNG, ::Type{Float64}) where {T} = randn(r.rng, Float64) + +import Random +using Random: randexp + +for T in isbits_subtypes(Real) + @eval begin + + function Base.rand(r::ResettableRNG, ::Type{$T}) + rand(r.rng, $T) + end + + function Base.randn(r::ResettableRNG, ::Type{$T}) + randn(r.rng, $T) + end + + function Random.randexp(r::ResettableRNG, ::Type{$T}) + randexp(r.rng, $T) + end + end +end function Base.iterate(r::ResettableRNG) reset!(r) @@ -53,3 +71,11 @@ end Base.iterate(r::ResettableRNG, _) = (rand(r), nothing) Base.IteratorSize(r::ResettableRNG) = Base.IsInfinite() + +function Random.Sampler(r::Type{R}, s::Random.Sampler, rep::Random.Repetition) where {R<:ResettableRNG} + return Random.Sampler(r.rng, s, r) +end + +function Base.rand(r::ResettableRNG, sp::Random.Sampler) + rand(r.rng, sp) +end From 77d7232b1ebe599536b45073599bea6d208ff466 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 1 Nov 2021 07:40:49 -0700 Subject: [PATCH 004/368] deepcopy on iterate --- src/resettablerng.jl | 1 + 1 file changed, 1 insertion(+) diff --git a/src/resettablerng.jl b/src/resettablerng.jl index 13841ace..89c444cd 100644 --- a/src/resettablerng.jl +++ b/src/resettablerng.jl @@ -65,6 +65,7 @@ for T in isbits_subtypes(Real) end function Base.iterate(r::ResettableRNG) + r = deepcopy(r) reset!(r) return (rand(r), nothing) end From fadc3f483b3240f90bf6f3b82acd7a14ac8c145a Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 2 Nov 2021 14:45:30 -0700 Subject: [PATCH 005/368] Move ResettableRNG to MeasureTheory --- src/MeasureBase.jl | 1 - src/combinators/product.jl | 22 +++++----- src/resettablerng.jl | 82 -------------------------------------- 3 files changed, 9 insertions(+), 96 deletions(-) diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index cdc6c906..40bec62e 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -60,7 +60,6 @@ include("domains.jl") include("utils.jl") include("absolutecontinuity.jl") include("macros.jl") -include("resettablerng.jl") include("primitive.jl") include("primitives/counting.jl") diff --git a/src/combinators/product.jl b/src/combinators/product.jl index 48250f40..1e899042 100644 --- a/src/combinators/product.jl +++ b/src/combinators/product.jl @@ -55,6 +55,14 @@ function Pretty.tile(μ::ProductMeasure{F,S,NamedTuple{N,T}}) where {F,S,N,T} result *= Pretty.literal(")") end +function Base.rand(rng::AbstractRNG, ::Type{T}, d::ProductMeasure) where {T} + _rand(rng, T, d, marginals(d)) +end + +function _rand(rng::AbstractRNG, ::Type{T}, d::ProductMeasure, mar) where {T} + (rand(rng, T, m) for m in mar) +end + ############################################################################### # I <: Tuple @@ -132,14 +140,7 @@ function logdensity(d::ProductMeasure{F,S,I}, x) where {F, S, I<:Base.Generator} end -function Base.rand(rng::AbstractRNG, ::Type{T}, d::ProductMeasure{F,S,I}) where {T,F,S,I<:Base.Generator} - mar = marginals(d) - elT = typeof(rand(rng, T, first(mar))) - sz = size(mar) - r = ResettableRNG(rng, rand(rng, UInt)) - Base.Generator(s -> rand(r, d.pars.f(s)), d.pars.iter) -end @propagate_inbounds function Random.rand!(rng::AbstractRNG, d::ProductMeasure, x::AbstractArray) @@ -154,13 +155,8 @@ end export rand! using Random: rand!, GLOBAL_RNG, AbstractRNG -function Base.rand(rng::AbstractRNG, ::Type{T}, d::ProductMeasure) where {T} - d1 = d.f(first(d.pars)) - rand(rng, T, d, d1) -end -function Base.rand(rng::AbstractRNG, ::Type{T}, d::ProductMeasure, d1::AbstractMeasure) where {T} - mar = marginals(d) +function _rand(rng::AbstractRNG, ::Type{T}, d::ProductMeasure, mar::AbstractArray) where {T} elT = typeof(rand(rng, T, first(mar))) sz = size(mar) diff --git a/src/resettablerng.jl b/src/resettablerng.jl index 89c444cd..e69de29b 100644 --- a/src/resettablerng.jl +++ b/src/resettablerng.jl @@ -1,82 +0,0 @@ -using Random -export ResettableRNG - -export reset! -struct ResettableRNG{R,S} <: Random.AbstractRNG - rng::R - seed::S -end - -function Base.show(io::IO, r::ResettableRNG) - io = IOContext(io, :compact => true) - print(io, "ResettableRNG(::", constructor(r.rng), ", ", r.seed, ")") -end - -function reset!(r::ResettableRNG) - @info "Calling reset!" - Random.seed!(r.rng, r.seed) -end - - -# for f in [ -# :(Base.rand) -# :(Base.randn) -# :(Random.rand!) -# :(Random.randcycle) -# :(Random.randcycle!) -# :(Random.randexp) -# :(Random.randexp!) -# :(Random.randn!) -# :(Random.randperm) -# :(Random.randperm!) -# :(Random.randstring) -# :(Random.randsubseq) -# :(Random.randsubseq!) -# :(Random.shuffle) -# :(Random.shuffle!) -# :(Random.seed!) -# ] -# @eval $f(r::ResettableRNG, args...) = $f(r.rng, args...) -# end - - -# Base.rand(r::ResettableRNG, d::AbstractMeasure) = rand(r.rng, d) -# Base.rand(r::ResettableRNG, ::Type{T}, d::AbstractMeasure) where {T} = rand(r.rng, T, d) -# Base.rand(r::ResettableRNG) = rand(r.rng, Float64) - -import Random -using Random: randexp - -for T in isbits_subtypes(Real) - @eval begin - - function Base.rand(r::ResettableRNG, ::Type{$T}) - rand(r.rng, $T) - end - - function Base.randn(r::ResettableRNG, ::Type{$T}) - randn(r.rng, $T) - end - - function Random.randexp(r::ResettableRNG, ::Type{$T}) - randexp(r.rng, $T) - end - end -end - -function Base.iterate(r::ResettableRNG) - r = deepcopy(r) - reset!(r) - return (rand(r), nothing) -end - -Base.iterate(r::ResettableRNG, _) = (rand(r), nothing) -Base.IteratorSize(r::ResettableRNG) = Base.IsInfinite() - -function Random.Sampler(r::Type{R}, s::Random.Sampler, rep::Random.Repetition) where {R<:ResettableRNG} - return Random.Sampler(r.rng, s, r) -end - -function Base.rand(r::ResettableRNG, sp::Random.Sampler) - rand(r.rng, sp) -end From f022c665ffe4c863553c8abb03d037ce71edd943 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 2 Nov 2021 14:49:32 -0700 Subject: [PATCH 006/368] Make Pretty a const --- src/MeasureBase.jl | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index 40bec62e..59b1c309 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -16,7 +16,10 @@ export AbstractMeasure abstract type AbstractMeasure end -import PrettyPrinting as Pretty +import PrettyPrinting + +const Pretty = PrettyPrinting + sampletype(μ::AbstractMeasure) = typeof(testvalue(μ)) From d338774d2cb002bc86b3f7e61daca9b952e46f7d Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 2 Nov 2021 16:40:51 -0700 Subject: [PATCH 007/368] drop extra spaces --- src/MeasureBase.jl | 3 --- 1 file changed, 3 deletions(-) diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index 59b1c309..608ac1a6 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -20,8 +20,6 @@ import PrettyPrinting const Pretty = PrettyPrinting - - sampletype(μ::AbstractMeasure) = typeof(testvalue(μ)) # sampletype(μ::AbstractMeasure) = sampletype(basemeasure(μ)) @@ -43,7 +41,6 @@ Methods for computing density relative to other measures will be """ function logdensity end - if VERSION < v"1.7.0-beta1.0" @eval begin struct Returns{T} From b56e8013c7b4d81e6cdd642aae543b654fa0066c Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 2 Nov 2021 16:51:39 -0700 Subject: [PATCH 008/368] formatting --- src/combinators/affine.jl | 80 ++++++++++++++------------- src/combinators/likelihood.jl | 10 ++-- src/combinators/pointwise.jl | 6 +- src/combinators/product.jl | 36 ++++++------ src/combinators/smart-constructors.jl | 27 ++++----- 5 files changed, 85 insertions(+), 74 deletions(-) diff --git a/src/combinators/affine.jl b/src/combinators/affine.jl index 88f5639d..eca08c42 100644 --- a/src/combinators/affine.jl +++ b/src/combinators/affine.jl @@ -10,23 +10,24 @@ params(f::AffineTransform) = getfield(f, :par) @inline Base.getproperty(d::AffineTransform, s::Symbol) = getfield(getfield(d, :par), s) -Base.propertynames(d::AffineTransform{N}) where {N} = N +Base.propertynames(d::AffineTransform{N}) where {N} = N -@inline Base.inv(f::AffineTransform{(:μ,:σ)}) = AffineTransform((μ = -(f.σ \ f.μ), ω = f.σ)) -@inline Base.inv(f::AffineTransform{(:μ,:ω)}) = AffineTransform((μ = - f.ω * f.μ, σ = f.ω)) +@inline Base.inv(f::AffineTransform{(:μ, :σ)}) = + AffineTransform((μ = -(f.σ \ f.μ), ω = f.σ)) +@inline Base.inv(f::AffineTransform{(:μ, :ω)}) = AffineTransform((μ = -f.ω * f.μ, σ = f.ω)) @inline Base.inv(f::AffineTransform{(:σ,)}) = AffineTransform((ω = f.σ,)) @inline Base.inv(f::AffineTransform{(:ω,)}) = AffineTransform((σ = f.ω,)) @inline Base.inv(f::AffineTransform{(:μ,)}) = AffineTransform((μ = -f.μ,)) # `size(f) == (m,n)` means `f : ℝⁿ → ℝᵐ` -Base.size(f::AffineTransform{(:μ,:σ)}) = size(f.σ) -Base.size(f::AffineTransform{(:μ,:ω)}) = size(f.ω) -Base.size(f::AffineTransform{(:σ,)}) = size(f.σ) -Base.size(f::AffineTransform{(:ω,)}) = size(f.ω) +Base.size(f::AffineTransform{(:μ, :σ)}) = size(f.σ) +Base.size(f::AffineTransform{(:μ, :ω)}) = size(f.ω) +Base.size(f::AffineTransform{(:σ,)}) = size(f.σ) +Base.size(f::AffineTransform{(:ω,)}) = size(f.ω) function Base.size(f::AffineTransform{(:μ,)}) (n,) = size(f.μ) - return (n,n) + return (n, n) end Base.size(f::AffineTransform, n::Int) = @inbounds size(f)[n] @@ -34,11 +35,11 @@ Base.size(f::AffineTransform, n::Int) = @inbounds size(f)[n] (f::AffineTransform{(:μ,)})(x) = x + f.μ (f::AffineTransform{(:σ,)})(x) = f.σ * x (f::AffineTransform{(:ω,)})(x) = f.ω \ x -(f::AffineTransform{(:μ,:σ)})(x) = f.σ * x + f.μ -(f::AffineTransform{(:μ,:ω)})(x) = f.ω \ x + f.μ +(f::AffineTransform{(:μ, :σ)})(x) = f.σ * x + f.μ +(f::AffineTransform{(:μ, :ω)})(x) = f.ω \ x + f.μ rowsize(x) = () -rowsize(x::AbstractArray) = (size(x,1),) +rowsize(x::AbstractArray) = (size(x, 1),) function rowsize(f::AffineTransform) size_f = size(f) @@ -48,7 +49,7 @@ function rowsize(f::AffineTransform) end colsize(x) = () -colsize(x::AbstractArray) = (size(x,2),) +colsize(x::AbstractArray) = (size(x, 2),) function colsize(f::AffineTransform) size_f = size(f) @@ -67,7 +68,7 @@ end return x end -@inline function apply!(x, f::AffineTransform{(:ω,), Tuple{F}}, z) where {F<:Factorization} +@inline function apply!(x, f::AffineTransform{(:ω,),Tuple{F}}, z) where {F<:Factorization} ldiv!(x, f.ω, z) return x end @@ -77,20 +78,20 @@ end return x end -@inline function apply!(x, f::AffineTransform{(:μ,:σ)}, z) +@inline function apply!(x, f::AffineTransform{(:μ, :σ)}, z) apply!(x, AffineTransform((σ = f.σ,)), z) apply!(x, AffineTransform((μ = f.μ,)), x) return x end -@inline function apply!(x, f::AffineTransform{(:μ,:ω)}, z) +@inline function apply!(x, f::AffineTransform{(:μ, :ω)}, z) apply!(x, AffineTransform((ω = f.ω,)), z) apply!(x, AffineTransform((μ = f.μ,)), x) return x end -function logjac(x::AbstractMatrix) - (m,n) = size(x) +function logjac(x::AbstractMatrix) + (m, n) = size(x) m == n && return first(logabsdet(x)) # Equivalent to sum(log, svdvals(x)), but much faster @@ -101,8 +102,8 @@ end logjac(x::Number) = log(abs(x)) # TODO: `log` doesn't work for the multivariate case, we need the log absolute determinant -logjac(f::AffineTransform{(:μ,:σ)}) = logjac(f.σ) -logjac(f::AffineTransform{(:μ,:ω)}) = -logjac(f.ω) +logjac(f::AffineTransform{(:μ, :σ)}) = logjac(f.σ) +logjac(f::AffineTransform{(:μ, :ω)}) = -logjac(f.ω) logjac(f::AffineTransform{(:σ,)}) = logjac(f.σ) logjac(f::AffineTransform{(:ω,)}) = -logjac(f.ω) logjac(f::AffineTransform{(:μ,)}) = 0.0 @@ -132,16 +133,16 @@ function params(μ::Affine) return merge(nt1, nt2) end -function paramnames(::Type{A}) where {N,M, A<:Affine{N,M}} +function paramnames(::Type{A}) where {N,M,A<:Affine{N,M}} tuple(union(N, paramnames(M))...) end -Base.propertynames(d::Affine{N}) where {N} = N ∪ (:parent,:f) +Base.propertynames(d::Affine{N}) where {N} = N ∪ (:parent, :f) -@inline function Base.getproperty(d::Affine, s::Symbol) +@inline function Base.getproperty(d::Affine, s::Symbol) if s === :parent return getfield(d, :parent) - elseif s === :f + elseif s === :f return getfield(d, :f) else return getproperty(getfield(d, :f), s) @@ -168,18 +169,18 @@ end function logdensity(d::Affine{(:μ,)}, x) z = x - d.μ - logdensity(d.parent, z) + logdensity(d.parent, z) end -function logdensity(d::Affine{(:μ,:σ)}, x) +function logdensity(d::Affine{(:μ, :σ)}, x) z = d.σ \ (x - d.μ) - logdensity(d.parent, z) + logdensity(d.parent, z) end -function logdensity(d::Affine{(:μ,:ω)}, x) +function logdensity(d::Affine{(:μ, :ω)}, x) z = d.ω * (x - d.μ) logdensity(d.parent, z) -end +end # # logdensity(d::Affine{(:μ,:ω)}, x) = logdensity(d.parent, d.σ \ (x - d.μ)) # @inline function logdensity(d::Affine{(:μ,:σ), P, Tuple{V,M}}, x) where {P, V<:AbstractVector, M<:AbstractMatrix} @@ -192,7 +193,7 @@ end # end # sum(zⱼ -> logdensity(d.parent, zⱼ), z) # end - + # # logdensity(d::Affine{(:μ,:ω)}, x) = logdensity(d.parent, d.ω * (x - d.μ)) # @inline function logdensity(d::Affine{(:μ,:ω), P,Tuple{V,M}}, x) where {P,V<:AbstractVector, M<:AbstractMatrix} # z = x - d.μ @@ -204,15 +205,20 @@ basemeasure(d::Affine) = affine(getfield(d, :f), basemeasure(d.parent)) # We can't do this until we know we're working with Lebesgue measure, since for # example it wouldn't make sense to apply a log-Jacobian to a point measure -basemeasure(d::Affine{N,L}) where {N, L<:Lebesgue} = weightedmeasure(-logjac(d), d.parent) +basemeasure(d::Affine{N,L}) where {N,L<:Lebesgue} = weightedmeasure(-logjac(d), d.parent) -function basemeasure(d::Affine{N,M}) where {N,L<:Lebesgue, M<:ProductMeasure{Returns{L}}} +function basemeasure(d::Affine{N,M}) where {N,L<:Lebesgue,M<:ProductMeasure{Returns{L}}} weightedmeasure(-logjac(d), d.parent) end logjac(d::Affine) = logjac(getfield(d, :f)) -function Random.rand!(rng::Random.AbstractRNG, d::Affine, x::AbstractVector{T}, z=Vector{T}(undef, size(getfield(d,:f),2))) where {T} +function Random.rand!( + rng::Random.AbstractRNG, + d::Affine, + x::AbstractVector{T}, + z = Vector{T}(undef, size(getfield(d, :f), 2)), +) where {T} rand!(rng, parent(d), z) f = getfield(d, :f) apply!(x, f, z) @@ -227,8 +233,8 @@ end # return z # end -supportdim(nt::NamedTuple{(:μ,:σ)}) = colsize(nt.σ) -supportdim(nt::NamedTuple{(:μ,:ω)}) = rowsize(nt.ω) -supportdim(nt::NamedTuple{(:σ,)}) = colsize(nt.σ) -supportdim(nt::NamedTuple{(:ω,)}) = rowsize(nt.ω) -supportdim(nt::NamedTuple{(:μ,)}) = size(nt.μ) +supportdim(nt::NamedTuple{(:μ, :σ)}) = colsize(nt.σ) +supportdim(nt::NamedTuple{(:μ, :ω)}) = rowsize(nt.ω) +supportdim(nt::NamedTuple{(:σ,)}) = colsize(nt.σ) +supportdim(nt::NamedTuple{(:ω,)}) = rowsize(nt.ω) +supportdim(nt::NamedTuple{(:μ,)}) = size(nt.μ) diff --git a/src/combinators/likelihood.jl b/src/combinators/likelihood.jl index 7a033915..87cf99c1 100644 --- a/src/combinators/likelihood.jl +++ b/src/combinators/likelihood.jl @@ -106,17 +106,17 @@ struct Likelihood{F,S,X} x::X end -Likelihood(μ::AbstractMeasure, x) = Likelihood(kernel(μ),x) +Likelihood(μ::AbstractMeasure, x) = Likelihood(kernel(μ), x) -Likelihood(::Type{M}, x) where {M<:AbstractMeasure} = Likelihood(kernel(M),x) +Likelihood(::Type{M}, x) where {M<:AbstractMeasure} = Likelihood(kernel(M), x) -function Base.show(io::IO, ℓ::Likelihood) +function Base.show(io::IO, ℓ::Likelihood) io = IOContext(io, :compact => true) k, x = ℓ.k, ℓ.x - print(io, "Likelihood(",k,", ", x, ")") + print(io, "Likelihood(", k, ", ", x, ")") end -function logdensity(ℓ::Likelihood, p) +function logdensity(ℓ::Likelihood, p) return logdensity(ℓ.k(p), ℓ.x) end diff --git a/src/combinators/pointwise.jl b/src/combinators/pointwise.jl index ca751927..2cb57966 100644 --- a/src/combinators/pointwise.jl +++ b/src/combinators/pointwise.jl @@ -1,7 +1,7 @@ export ⊙ @concrete terse struct PointwiseProductMeasure{T} <: AbstractMeasure - data :: T + data::T end Base.size(μ::PointwiseProductMeasure) = size(μ.data) @@ -31,8 +31,8 @@ Base.length(m::PointwiseProductMeasure{T}) where {T} = length(m.data) sum((logdensity(dⱼ, x) for dⱼ in d.data)) end -function sampletype(d::PointwiseProductMeasure) +function sampletype(d::PointwiseProductMeasure) @inbounds sampletype(first(d.data)) end -basemeasure(d::PointwiseProductMeasure) = @inbounds basemeasure(first(d.data)) +basemeasure(d::PointwiseProductMeasure) = @inbounds basemeasure(first(d.data)) diff --git a/src/combinators/product.jl b/src/combinators/product.jl index 1e899042..e8fe7515 100644 --- a/src/combinators/product.jl +++ b/src/combinators/product.jl @@ -51,7 +51,7 @@ testvalue(d::ProductMeasure) = map(testvalue, marginals(d)) function Pretty.tile(μ::ProductMeasure{F,S,NamedTuple{N,T}}) where {F,S,N,T} result = Pretty.literal("Product(") - result *= Pretty.pair_layout(μ.f, μ.pars; sep=", ") + result *= Pretty.pair_layout(μ.f, μ.pars; sep = ", ") result *= Pretty.literal(")") end @@ -73,11 +73,11 @@ end export ⊗ ⊗(μs::AbstractMeasure...) = productmeasure(μs) -marginals(d::TupleProductMeasure{T}) where {F, T<:Tuple} = d.pars +marginals(d::TupleProductMeasure{T}) where {F,T<:Tuple} = d.pars -function Pretty.tile(μ::TupleProductMeasure{T}) where {F,T <: Tuple} +function Pretty.tile(μ::TupleProductMeasure{T}) where {F,T<:Tuple} mar = marginals(μ) - Pretty.list_layout(Pretty.Layout[Pretty.tile.(mar)...]; sep=" ⊗ ") + Pretty.list_layout(Pretty.Layout[Pretty.tile.(mar)...]; sep = " ⊗ ") end @inline function logdensity(d::TupleProductMeasure, x::Tuple) where {T<:Tuple} @@ -93,7 +93,7 @@ end marginals(d::ProductMeasure{F,S,A}) where {F,S,A<:AbstractArray} = mappedarray(d.f, d.pars) -function marginals(d::ProductMeasure{<:Returns, S, A}) where {F,S,A<:AbstractArray} +function marginals(d::ProductMeasure{<:Returns,S,A}) where {F,S,A<:AbstractArray} Fill(d.f.f.value, size(d.pars)) # mappedarray(d.f.f, d.pars) end @@ -108,7 +108,7 @@ end function Pretty.tile(d::ProductMeasure{F,S,A}) where {F,S,A} result = Pretty.literal("For(") - result *= Pretty.pair_layout(Pretty.tile(d.f), Pretty.tile(d.pars); sep=", ") + result *= Pretty.pair_layout(Pretty.tile(d.f), Pretty.tile(d.pars); sep = ", ") result *= Pretty.literal(")") end @@ -116,9 +116,9 @@ end ############################################################################### # I <: CartesianIndices -function Pretty.tile(d::ProductMeasure{F,S,I}) where {F, S, I<:CartesianIndices} +function Pretty.tile(d::ProductMeasure{F,S,I}) where {F,S,I<:CartesianIndices} result = Pretty.literal("For(") - result *= Pretty.pair_layout(Pretty.tile(d.f), Pretty.tile(size(d.pars)); sep=", ") + result *= Pretty.pair_layout(Pretty.tile(d.f), Pretty.tile(size(d.pars)); sep = ", ") result *= Pretty.literal(")") end @@ -135,7 +135,7 @@ export rand! using Random: rand!, GLOBAL_RNG, AbstractRNG -function logdensity(d::ProductMeasure{F,S,I}, x) where {F, S, I<:Base.Generator} +function logdensity(d::ProductMeasure{F,S,I}, x) where {F,S,I<:Base.Generator} sum((logdensity(dj, xj) for (dj, xj) in zip(marginals(d), x))) end @@ -143,10 +143,14 @@ end -@propagate_inbounds function Random.rand!(rng::AbstractRNG, d::ProductMeasure, x::AbstractArray) +@propagate_inbounds function Random.rand!( + rng::AbstractRNG, + d::ProductMeasure, + x::AbstractArray, +) # TODO: Generalize this T = Float64 - for(j,m) in zip(eachindex(x), marginals(d)) + for (j, m) in zip(eachindex(x), marginals(d)) @inbounds x[j] = rand(rng, T, m) end return x @@ -160,7 +164,7 @@ function _rand(rng::AbstractRNG, ::Type{T}, d::ProductMeasure, mar::AbstractArra elT = typeof(rand(rng, T, first(mar))) sz = size(mar) - x = Array{elT, length(sz)}(undef, sz) + x = Array{elT,length(sz)}(undef, sz) rand!(rng, d, x) end @@ -178,12 +182,12 @@ end # return rand(Random.GLOBAL_RNG, T, d) # end -function sampletype(d::ProductMeasure{A}) where {T,N,A <: AbstractArray{T,N}} +function sampletype(d::ProductMeasure{A}) where {T,N,A<:AbstractArray{T,N}} S = @inbounds sampletype(marginals(d)[1]) - Array{S, N} + Array{S,N} end -function sampletype(d::ProductMeasure{<: Tuple}) +function sampletype(d::ProductMeasure{<:Tuple}) Tuple{sampletype.(marginals(d))...} end @@ -192,7 +196,7 @@ end # μ.data # end -function ConstructionBase.constructorof(::Type{P}) where {F,S,I,P <: ProductMeasure{F,S,I}} +function ConstructionBase.constructorof(::Type{P}) where {F,S,I,P<:ProductMeasure{F,S,I}} p -> productmeasure(d.f, p) end diff --git a/src/combinators/smart-constructors.jl b/src/combinators/smart-constructors.jl index c9d333f7..2a6c9bfb 100644 --- a/src/combinators/smart-constructors.jl +++ b/src/combinators/smart-constructors.jl @@ -31,7 +31,10 @@ half(μ::AbstractMeasure) = Half(μ) pointwiseproduct(μ::AbstractMeasure...) = PointwiseProductMeasure(μ) -function pointwiseproduct(μ::PointwiseProductMeasure{X}, ν::PointwiseProductMeasure{Y}) where {X,Y} +function pointwiseproduct( + μ::PointwiseProductMeasure{X}, + ν::PointwiseProductMeasure{Y}, +) where {X,Y} data = (μ.data..., ν.data...) pointwiseproduct(data...) end @@ -41,7 +44,7 @@ function pointwiseproduct(μ::AbstractMeasure, ν::PointwiseProductMeasure) return pointwiseproduct(data...) end -function pointwiseproduct(μ::PointwiseProductMeasure, ν::N) where {N <: AbstractMeasure} +function pointwiseproduct(μ::PointwiseProductMeasure, ν::N) where {N<:AbstractMeasure} data = (μ.data..., ν) return pointwiseproduct(data...) end @@ -67,8 +70,6 @@ function powermeasure(μ::WeightedMeasure, dims::NTuple{N,I}) where {N,I} return weightedmeasure(k, μ.base^dims) end - - ############################################################################### # ProductMeasure @@ -91,11 +92,11 @@ function productmeasure(f::Returns{FB}, ops, pars) where {FB<:FactoredBase} inbounds(x) = all(fb.inbounds, x) constℓ = n * fb.constℓ varℓ() = n * fb.varℓ() - base = fb.base ^ dims + base = fb.base^dims FactoredBase(inbounds, constℓ, varℓ, base) end -function productmeasure(f::Returns{W}, ::typeof(identity), pars) where {W <: WeightedMeasure} +function productmeasure(f::Returns{W}, ::typeof(identity), pars) where {W<:WeightedMeasure} ℓ = f.value.logweight base = f.value.base newbase = productmeasure(Returns(base), identity, pars) @@ -127,11 +128,11 @@ end function weightedmeasure(ℓ::R, b::M) where {R,M} WeightedMeasure{R,M}(ℓ, b) -end +end function weightedmeasure(ℓ, b::WeightedMeasure) weightedmeasure(ℓ + b.logweight, b.base) -end +end ############################################################################### # Kernel @@ -140,22 +141,22 @@ kernel(μ, ops...) = Kernel(μ, ops) kernel(μ, op) = Kernel(μ, op) # kernel(Normal(μ=2)) -function kernel(μ::P) where {P <: AbstractMeasure} +function kernel(μ::P) where {P<:AbstractMeasure} (f, ops) = kernelfactor(μ) - kernel(f,ops) + kernel(f, ops) end # kernel(Normal{(:μ,), Tuple{Int64}}) -function kernel(::Type{P}) where {P <: AbstractMeasure} +function kernel(::Type{P}) where {P<:AbstractMeasure} (f, ops) = kernelfactor(P) - kernel(f,ops) + kernel(f, ops) end # kernel(::Type{P}, op::O) where {O, N, P<:ParameterizedMeasure{N}} = kernel{constructorof(P),O}(op) function kernel(::Type{M}; ops...) where {M} nt = NamedTuple(ops) - kernel(M,nt) + kernel(M, nt) end kernel(f::Returns, op::typeof(identity)) = Kernel(f, op) From c5aa0ebcf72f83216d35b94b030676cc9e91cb9d Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 2 Nov 2021 16:54:39 -0700 Subject: [PATCH 009/368] formatting --- src/combinators/superpose.jl | 4 ++-- src/combinators/weighted.jl | 14 +++++++------- src/density.jl | 22 +++++++++++----------- src/resettablerng.jl | 0 4 files changed, 20 insertions(+), 20 deletions(-) delete mode 100644 src/resettablerng.jl diff --git a/src/combinators/superpose.jl b/src/combinators/superpose.jl index 3a824be3..75bb135a 100644 --- a/src/combinators/superpose.jl +++ b/src/combinators/superpose.jl @@ -21,7 +21,7 @@ Superposition measures satisfy ``` """ struct SuperpositionMeasure{NT} <: AbstractMeasure - components :: NT + components::NT end function Pretty.tile(d::SuperpositionMeasure) @@ -58,7 +58,7 @@ function Base.:+(μ::AbstractMeasure, ν::AbstractMeasure) superpose(components) end -logdensity(μ::SuperpositionMeasure, x) = logsumexp((logdensity(m,x) for m in μ.components)) +logdensity(μ::SuperpositionMeasure, x) = logsumexp((logdensity(m, x) for m in μ.components)) basemeasure(μ::SuperpositionMeasure) = superpose(map(basemeasure, μ.components)) diff --git a/src/combinators/weighted.jl b/src/combinators/weighted.jl index 6f8f294f..a48617cb 100644 --- a/src/combinators/weighted.jl +++ b/src/combinators/weighted.jl @@ -20,8 +20,8 @@ end ############################################################################### struct WeightedMeasure{R,M} <: AbstractWeightedMeasure - logweight :: R - base :: M + logweight::R + base::M end function Base.show(io::IO, μ::WeightedMeasure) @@ -41,9 +41,9 @@ function Base.show_unquoted(io::IO, μ::WeightedMeasure, indent::Int, prec::Int) return nothing end -function Base.:*(k::T, m::AbstractMeasure) where {T <: Number} +function Base.:*(k::T, m::AbstractMeasure) where {T<:Number} logk = log(k) - return weightedmeasure(logk,m) + return weightedmeasure(logk, m) end Base.:*(m::AbstractMeasure, k::Real) = k * m @@ -51,12 +51,12 @@ Base.:*(m::AbstractMeasure, k::Real) = k * m ≪(::M, ::WeightedMeasure{R,M}) where {R,M} = true ≪(::WeightedMeasure{R,M}, ::M) where {R,M} = true -sampletype(μ:: WeightedMeasure) = sampletype(μ.base) +sampletype(μ::WeightedMeasure) = sampletype(μ.base) ############################################################################### export ParamWeightedMeasure -struct ParamWeightedMeasure{L,N,T,B} <: AbstractWeightedMeasure +struct ParamWeightedMeasure{L,N,T,B} <: AbstractWeightedMeasure ℓ::L par::NamedTuple{N,T} base::B @@ -64,7 +64,7 @@ end function Base.show(io::IO, d::ParamWeightedMeasure) io = IOContext(io, :compact => true) - print(io, "ParamWeighted(",d.ℓ, ", ", d.par,", ", d.base, ")") + print(io, "ParamWeighted(", d.ℓ, ", ", d.par, ", ", d.base, ")") end basemeasure(d::ParamWeightedMeasure) = d.base diff --git a/src/density.jl b/src/density.jl index c300b84d..abde04c5 100644 --- a/src/density.jl +++ b/src/density.jl @@ -30,7 +30,7 @@ log𝒹(μ, base) = Density(μ, base, Val{true}()) Compute the Radom-Nikodym derivative (or its log, if `log=false`) of μ with respect to `base`. """ -function 𝒹(μ::AbstractMeasure, base::AbstractMeasure; log=false) +function 𝒹(μ::AbstractMeasure, base::AbstractMeasure; log = false) return Density(μ, base, Val(log)) end @@ -49,14 +49,14 @@ A `DensityMeasure` is a measure defined by a density with respect to some other "base" measure """ struct DensityMeasure{F,B,L} <: AbstractMeasure - f :: F - base :: B - log :: L + f::F + base::B + log::L end function Pretty.tile(μ::DensityMeasure{F,B,Val{L}}) where {F,B,L} result = Pretty.literal("DensityMeasure ∫(") - result *= Pretty.pair_layout(Pretty.tile(μ.f), Pretty.tile(μ.base); sep=", ") + result *= Pretty.pair_layout(Pretty.tile(μ.f), Pretty.tile(μ.base); sep = ", ") result *= Pretty.literal("; log = ") result *= Pretty.tile(L) result *= Pretty.literal(")") @@ -73,7 +73,7 @@ logdensity(μ::DensityMeasure{F,B,Val{true}}, x) where {F,B} = μ.f(x) density(μ::DensityMeasure{F,B,Val{false}}, x) where {F,B} = μ.f(x) -logdensity(μ::DensityMeasure{F,B,Val{false}}, x) where {F,B} = log(density(μ,x)) +logdensity(μ::DensityMeasure{F,B,Val{false}}, x) where {F,B} = log(density(μ, x)) export ∫ @@ -94,13 +94,13 @@ export ∫exp Define a new measure in terms of a density `f` over some measure `base`. """ -∫exp(f,μ) = DensityMeasure(f,μ,Val{true}()) +∫exp(f, μ) = DensityMeasure(f, μ, Val{true}()) # TODO: `density` and `logdensity` functions for `DensityMeasure` @inline function logdensity(μ::T, ν::T, x) where {T<:AbstractMeasure} - μ==ν && return 0.0 - invoke(logdensity, Tuple{AbstractMeasure, AbstractMeasure, typeof(x)}, μ, ν, x) + μ == ν && return 0.0 + invoke(logdensity, Tuple{AbstractMeasure,AbstractMeasure,typeof(x)}, μ, ν, x) end @inline function logdensity(μ::AbstractMeasure, ν::AbstractMeasure, x) @@ -109,7 +109,7 @@ end # If α===μ and β===ν, The recursive call would be exactly the same as the # original one. We need to break the recursion. - if α===μ && β===ν + if α === μ && β === ν @warn """ No method found for logdensity(μ, ν, x) where typeof(μ) == $(typeof(μ)) @@ -139,7 +139,7 @@ function logpdf(d::AbstractMeasure, x) _logpdf(d, basemeasure(d), x) end -@inline function _logpdf(d::AbstractMeasure, β::AbstractMeasure, x, ℓ=zero(Float64)) +@inline function _logpdf(d::AbstractMeasure, β::AbstractMeasure, x, ℓ = zero(Float64)) # @show d # @show x Δℓ = logdensity(d, x) diff --git a/src/resettablerng.jl b/src/resettablerng.jl deleted file mode 100644 index e69de29b..00000000 From 44a5860c34fb07e171ae82bffa529287124aa201 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 2 Nov 2021 17:07:27 -0700 Subject: [PATCH 010/368] formatting --- src/combinators/affine.jl | 3 +-- src/combinators/factoredbase.jl | 8 +++--- src/combinators/for.jl | 2 -- src/combinators/likelihood.jl | 1 - src/combinators/mapsto.jl | 4 +-- src/combinators/power.jl | 12 ++++----- src/combinators/product.jl | 15 +---------- src/combinators/smart-constructors.jl | 5 +--- src/combinators/spikemixture.jl | 6 ++--- src/combinators/weighted.jl | 1 - src/density.jl | 2 -- src/domains.jl | 20 +++++++-------- src/exp.jl | 2 -- src/integration.jl | 8 +++--- src/kernel.jl | 16 +++++------- src/macros.jl | 37 ++++++++++++--------------- src/parameterized.jl | 26 ++++++++++--------- src/primitives/dirac.jl | 6 ++--- src/primitives/lebesgue.jl | 5 +--- src/testvalues.jl | 1 + src/utils.jl | 8 +++--- 21 files changed, 76 insertions(+), 112 deletions(-) diff --git a/src/combinators/affine.jl b/src/combinators/affine.jl index eca08c42..f453c8f4 100644 --- a/src/combinators/affine.jl +++ b/src/combinators/affine.jl @@ -217,7 +217,7 @@ function Random.rand!( rng::Random.AbstractRNG, d::Affine, x::AbstractVector{T}, - z = Vector{T}(undef, size(getfield(d, :f), 2)), + z = Vector{T}(undef, size(getfield(d, :f), 2)) ) where {T} rand!(rng, parent(d), z) f = getfield(d, :f) @@ -225,7 +225,6 @@ function Random.rand!( return x end - # function Base.rand(rng::Random.AbstractRNG, ::Type{T}, d::Affine) where {T} # f = getfield(d, :f) # z = rand(rng, T, parent(d)) diff --git a/src/combinators/factoredbase.jl b/src/combinators/factoredbase.jl index ac17be0b..6a922dff 100644 --- a/src/combinators/factoredbase.jl +++ b/src/combinators/factoredbase.jl @@ -1,10 +1,10 @@ export FactoredBase struct FactoredBase{R,C,V,B} <: AbstractMeasure - inbounds :: R - constℓ :: C - varℓ :: V - base :: B + inbounds::R + constℓ::C + varℓ::V + base::B end @inline function logdensity(d::FactoredBase, x) diff --git a/src/combinators/for.jl b/src/combinators/for.jl index 27c58d62..780863c0 100644 --- a/src/combinators/for.jl +++ b/src/combinators/for.jl @@ -3,7 +3,6 @@ export For using Random import Base - """ For(f, base...) @@ -82,7 +81,6 @@ For(f, inds::AbstractArray) = productmeasure(f, inds) For(f, n::Int) = productmeasure(f, Base.OneTo(n)) For(f, dims::Int...) = productmeasure(i -> f(Tuple(i)...), CartesianIndices(dims)) - function Base.eltype(d::ProductMeasure{F,I}) where {F,I<:AbstractArray} return eltype(d.f(first(d.pars))) end diff --git a/src/combinators/likelihood.jl b/src/combinators/likelihood.jl index 87cf99c1..878a9172 100644 --- a/src/combinators/likelihood.jl +++ b/src/combinators/likelihood.jl @@ -116,7 +116,6 @@ function Base.show(io::IO, ℓ::Likelihood) print(io, "Likelihood(", k, ", ", x, ")") end - function logdensity(ℓ::Likelihood, p) return logdensity(ℓ.k(p), ℓ.x) end diff --git a/src/combinators/mapsto.jl b/src/combinators/mapsto.jl index 11edd740..09147bc8 100644 --- a/src/combinators/mapsto.jl +++ b/src/combinators/mapsto.jl @@ -5,9 +5,9 @@ end export ↦, mapsto -mapsto(x,y) = x ↦ y +mapsto(x, y) = x ↦ y -↦(x::X,y::Y) where {X,Y} = MapsTo{X,Y}(x,y) +↦(x::X, y::Y) where {X,Y} = MapsTo{X,Y}(x, y) Base.first(t::MapsTo) = t.x Base.last(t::MapsTo) = t.y diff --git a/src/combinators/power.jl b/src/combinators/power.jl index 6258830d..c8622e53 100644 --- a/src/combinators/power.jl +++ b/src/combinators/power.jl @@ -34,7 +34,7 @@ const PowerMeasure{F,S,T,N,A} = ProductMeasure{F,S,Fill{T,N,A}} Base.:^(μ::AbstractMeasure, ::Tuple{}) = μ function Base.:^(μ::AbstractMeasure, dims::Integer...) - return μ ^ dims + return μ^dims end function Base.:^(μ::M, dims::NTuple{N,I}) where {M<:AbstractMeasure,N,I<:Integer} @@ -43,17 +43,15 @@ end # Same as PowerMeasure function Pretty.tile(d::ProductMeasure{Returns{T},I,C}) where {T,I,C<:CartesianIndices} - Pretty.pair_layout(Pretty.tile(d.f.f.value), Pretty.tile(size(d.pars)); sep=" ^ ") + Pretty.pair_layout(Pretty.tile(d.f.f.value), Pretty.tile(size(d.pars)); sep = " ^ ") end function Pretty.tile(d::ProductMeasure{R,I,V}) where {R<:Returns,I,V<:AbstractVector} - Pretty.pair_layout(Pretty.tile(d.f.f.value), Pretty.tile(length(d.pars)); sep=" ^ ") + Pretty.pair_layout(Pretty.tile(d.f.f.value), Pretty.tile(length(d.pars)); sep = " ^ ") end # sampletype(d::PowerMeasure{M,N}) where {M,N} = @inbounds Array{sampletype(first(marginals(d))), N} - - params(d::ProductMeasure{F,S,<:Fill}) where {F,S} = params(first(marginals(d))) params(::Type{P}) where {F,S,P<:ProductMeasure{F,S,<:Fill}} = params(D) @@ -67,7 +65,7 @@ end # Same as PowerMeasure @inline function _basemeasure(d::ProductMeasure{F,S,<:Fill}, b) where {F,S} - b ^ size(d.pars) + b^size(d.pars) end # Same as PowerMeasure @@ -76,7 +74,7 @@ end inbounds(x) = all(b.inbounds, x) constℓ = n * b.constℓ varℓ() = n * b.varℓ() - base = b.base ^ size(d.pars) + base = b.base^size(d.pars) FactoredBase(inbounds, constℓ, varℓ, base) end diff --git a/src/combinators/product.jl b/src/combinators/product.jl index e8fe7515..44f96f12 100644 --- a/src/combinators/product.jl +++ b/src/combinators/product.jl @@ -7,13 +7,11 @@ using FillArrays abstract type AbstractProductMeasure <: AbstractMeasure end - struct ProductMeasure{F,S,I} <: AbstractProductMeasure f::Kernel{F,S} pars::I end - # TODO: Test for equality without traversal, probably by first converting to a # canonical form function Base.:(==)(a::ProductMeasure, b::ProductMeasure) @@ -112,7 +110,6 @@ function Pretty.tile(d::ProductMeasure{F,S,A}) where {F,S,A} result *= Pretty.literal(")") end - ############################################################################### # I <: CartesianIndices @@ -122,7 +119,6 @@ function Pretty.tile(d::ProductMeasure{F,S,I}) where {F,S,I<:CartesianIndices} result *= Pretty.literal(")") end - # function Base.rand(rng::AbstractRNG, ::Type{T}, d::ProductMeasure{F,S,I}) where {T,F,I<:CartesianIndices} # end @@ -130,23 +126,17 @@ end ############################################################################### # I <: Base.Generator - export rand! using Random: rand!, GLOBAL_RNG, AbstractRNG - function logdensity(d::ProductMeasure{F,S,I}, x) where {F,S,I<:Base.Generator} sum((logdensity(dj, xj) for (dj, xj) in zip(marginals(d), x))) end - - - - @propagate_inbounds function Random.rand!( rng::AbstractRNG, d::ProductMeasure, - x::AbstractArray, + x::AbstractArray ) # TODO: Generalize this T = Float64 @@ -159,7 +149,6 @@ end export rand! using Random: rand!, GLOBAL_RNG, AbstractRNG - function _rand(rng::AbstractRNG, ::Type{T}, d::ProductMeasure, mar::AbstractArray) where {T} elT = typeof(rand(rng, T, first(mar))) @@ -191,7 +180,6 @@ function sampletype(d::ProductMeasure{<:Tuple}) Tuple{sampletype.(marginals(d))...} end - # function logdensity(μ::ProductMeasure{Aμ}, x::Ax) where {Aμ <: MappedArray, Ax <: AbstractArray} # μ.data # end @@ -204,7 +192,6 @@ end # setproperties(d, NamedTuple{N}(p...)) # end - # function Accessors.set(d::ProductMeasure{F,T}, ::typeof(params), p::Tuple) where {F, T<:Tuple} # set.(marginals(d), params, p) # end diff --git a/src/combinators/smart-constructors.jl b/src/combinators/smart-constructors.jl index 2a6c9bfb..6a78b7ea 100644 --- a/src/combinators/smart-constructors.jl +++ b/src/combinators/smart-constructors.jl @@ -20,7 +20,6 @@ function affine(f::AffineTransform, parent::FactoredBase) FactoredBase(Returns(true), constℓ, varℓ, base) end - ############################################################################### # Half @@ -33,7 +32,7 @@ pointwiseproduct(μ::AbstractMeasure...) = PointwiseProductMeasure(μ) function pointwiseproduct( μ::PointwiseProductMeasure{X}, - ν::PointwiseProductMeasure{Y}, + ν::PointwiseProductMeasure{Y} ) where {X,Y} data = (μ.data..., ν.data...) pointwiseproduct(data...) @@ -103,8 +102,6 @@ function productmeasure(f::Returns{W}, ::typeof(identity), pars) where {W<:Weigh weightedmeasure(length(pars) * ℓ, newbase) end - - ############################################################################### # RestrictedMeasure diff --git a/src/combinators/spikemixture.jl b/src/combinators/spikemixture.jl index 98b1fdeb..beedfb34 100644 --- a/src/combinators/spikemixture.jl +++ b/src/combinators/spikemixture.jl @@ -11,14 +11,14 @@ SpikeMixture(m, w) = SpikeMixture(m, w, one(w)) function Base.show(io::IO, μ::SpikeMixture) io = IOContext(io, :compact => true) - print(io, "(", μ.s*μ.w, "*", string(μ.m), " + ", μ.s*(1-μ.w), "Dirac(0))") + print(io, "(", μ.s * μ.w, "*", string(μ.m), " + ", μ.s * (1 - μ.w), "Dirac(0))") end function basemeasure(μ::SpikeMixture) # Compare formula (1.4) in Joris Bierkens, Sebastiano Grazzi, Frank van der Meulen, Moritz Schauer: # Sticky PDMP samplers for sparse and local inference problems. 2020. [https://arxiv.org/abs/2103.08478]. - ki = (1/μ.w - 1)/density(μ.m, 0) - SpikeMixture(basemeasure(μ.m), 1/(1+ki), μ.s*(1+ki)) + ki = (1 / μ.w - 1) / density(μ.m, 0) + SpikeMixture(basemeasure(μ.m), 1 / (1 + ki), μ.s * (1 + ki)) end function logdensity(μ::SpikeMixture, x) diff --git a/src/combinators/weighted.jl b/src/combinators/weighted.jl index a48617cb..06fee4b9 100644 --- a/src/combinators/weighted.jl +++ b/src/combinators/weighted.jl @@ -7,7 +7,6 @@ export WeightedMeasure, AbstractWeightedMeasure end """ - abstract type AbstractWeightedMeasure <: AbstractMeasure end logweight(μ::AbstractWeightedMeasure) = μ.logweight diff --git a/src/density.jl b/src/density.jl index abde04c5..b63691d2 100644 --- a/src/density.jl +++ b/src/density.jl @@ -36,7 +36,6 @@ end (f::Density{M,B,Val{true}})(x) where {M,B} = logdensity(f.μ, f.base, x) - (f::Density{M,B,Val{false}})(x) where {M,B} = density(f.μ, f.base, x) """ @@ -86,7 +85,6 @@ Define a new measure in terms of a density `f` over some measure `base`. ∫(μ::AbstractMeasure, base::AbstractMeasure) = ∫exp(log𝒹(μ, base), base) - export ∫exp """ diff --git a/src/domains.jl b/src/domains.jl index e5d48124..41ec4c2c 100644 --- a/src/domains.jl +++ b/src/domains.jl @@ -20,7 +20,7 @@ For example, `@domain ℝ RealNumbers` is equivalent to """ macro domain(name, T) sname = String(name) - + name = esc(name) quote struct $T <: AbstractDomain end @@ -38,30 +38,28 @@ end @domain ℤ Integers - ########################################################### # Integer ranges -struct IntegerRange{lo, hi} <: AbstractDomain end +struct IntegerRange{lo,hi} <: AbstractDomain end -Base.minimum(::IntegerRange{lo, hi}) where {lo, hi} = lo -Base.maximum(::IntegerRange{lo, hi}) where {lo, hi} = hi +Base.minimum(::IntegerRange{lo,hi}) where {lo,hi} = lo +Base.maximum(::IntegerRange{lo,hi}) where {lo,hi} = hi -Base.iterate(r::IntegerRange{lo, hi}) where {lo, hi} = iterate(lo:hi) +Base.iterate(r::IntegerRange{lo,hi}) where {lo,hi} = iterate(lo:hi) function Base.getindex(::Integers, r::AbstractUnitRange) - IntegerRange{minimum(r), maximum(r)}() + IntegerRange{minimum(r),maximum(r)}() end -function Base.show(io::IO, r::IntegerRange{lo, hi}) where {lo, hi} +function Base.show(io::IO, r::IntegerRange{lo,hi}) where {lo,hi} io = IOContext(io, :compact => true) print(io, "ℤ[", lo, ":", hi, "]") end -testvalue(::IntegerRange{lo, hi}) where {lo, hi} = lo +testvalue(::IntegerRange{lo,hi}) where {lo,hi} = lo ########################################################### # Real intervals - -struct RealInterval{lo, hi} <: AbstractDomain end +struct RealInterval{lo,hi} <: AbstractDomain end diff --git a/src/exp.jl b/src/exp.jl index 879dd16c..7a67c15f 100644 --- a/src/exp.jl +++ b/src/exp.jl @@ -29,8 +29,6 @@ Base.promote_rule(::Type{Exp}, T::Type{<:Real}) = T Base.convert(::Type{<:Real}, x::Exp) = exp(log(x)) - - # Exp(3) / Exp(2) # Exp(3) * Exp(2) diff --git a/src/integration.jl b/src/integration.jl index 7bc3c4a7..44266738 100644 --- a/src/integration.jl +++ b/src/integration.jl @@ -1,15 +1,17 @@ import Distributions -const Dists=Distributions +const Dists = Distributions struct Integral{F,M} f::F μ::M end -∫(μ) = ∫(identity,μ) +∫(μ) = ∫(identity, μ) ∫(f, μ) = Integral(f, μ) ∫(::typeof(identity), ::Dists.Distribution) = 1.0 -∫(Dists.Normal()) do x x^2 end \ No newline at end of file +∫(Dists.Normal()) do x + x^2 +end diff --git a/src/kernel.jl b/src/kernel.jl index 72cbb5de..a940f3c3 100644 --- a/src/kernel.jl +++ b/src/kernel.jl @@ -3,13 +3,12 @@ export Kernel abstract type AbstractKernel <: AbstractMeasure end - struct Kernel{F,S} <: AbstractKernel f::F ops::S - Kernel(::Type{T}, ops::S) where {T,S} = new{Type{T}, S}(T,ops) - Kernel(f::F, ops::S) where {F,S} = new{F, S}(f,ops) + Kernel(::Type{T}, ops::S) where {T,S} = new{Type{T},S}(T, ops) + Kernel(f::F, ops::S) where {F,S} = new{F,S}(f, ops) end function Pretty.quoteof(k::Kernel) @@ -38,7 +37,6 @@ function kernel end export kernel - # kernel(Normal) do x # (μ=x,σ=x^2) # end @@ -50,15 +48,15 @@ mapcall(t, x) = map(func -> func(x), t) # (k::Kernel{Type{P},<:Tuple})(x) where {P<:ParameterizedMeasure} = k.f(mapcall(k.ops, x)...) -(k::Kernel{M,<:NamedTuple})(x) where {M} = k.f(;mapcall(k.ops, x)...) +(k::Kernel{M,<:NamedTuple})(x) where {M} = k.f(; mapcall(k.ops, x)...) -(k::Kernel{F,S})(x...) where {F, N, S<:NTuple{N,Symbol}} = k(x) +(k::Kernel{F,S})(x...) where {F,N,S<:NTuple{N,Symbol}} = k(x) -function (k::Kernel{F,S})(x::Tuple) where {F, N, S<:NTuple{N,Symbol}} +function (k::Kernel{F,S})(x::Tuple) where {F,N,S<:NTuple{N,Symbol}} k.f(NamedTuple{k.ops}(x)) end -(k::Kernel)(x) = k.f(k.ops(x)) +(k::Kernel)(x) = k.f(k.ops(x)) """ For any `k::Kernel`, `basekernel` is expected to satisfy @@ -73,14 +71,12 @@ basemeasure(d::ProductMeasure) = productmeasure(basekernel(d.f), d.pars) """ function basekernel end - # TODO: Find a way to do better than this basekernel(f) = basemeasure ∘ f basekernel(k::Kernel) = kernel(basekernel(k.f), k.ops) basekernel(f::Returns) = Returns(basemeasure(f.value)) - # export kernelize # function kernelize(μ::M) where {N, M <: ParameterizedMeasure{N}} diff --git a/src/macros.jl b/src/macros.jl index 9197cb9c..e54f6236 100644 --- a/src/macros.jl +++ b/src/macros.jl @@ -18,7 +18,7 @@ function foldast(leaf, branch; kwargs...) end function replace(p, f, expr) - leaf(s) = p(s) ? f(s) : s + leaf(s) = p(s) ? f(s) : s branch(head, newargs) = Expr(head, newargs...) foldast(leaf, branch)(expr) end @@ -27,11 +27,11 @@ end function capture(template, ex, action) let template = Expr(:quote, template) quote - @match $ex begin + @match $ex begin $template => $action _ => nothing end - end + end end end @@ -39,8 +39,6 @@ macro capture(template, ex, action) capture(template, ex, action) |> esc end - - function _parameterized(__module__, expr) @capture ($op($μ($(p...)), $base)) expr begin @assert op ∈ [:<<, :≪, :≃] @@ -52,19 +50,19 @@ function _parameterized(__module__, expr) # @gensym basename q = quote struct $μ{N,T} <: MeasureBase.ParameterizedMeasure{N} - par :: NamedTuple{N,T} + par::NamedTuple{N,T} end - + const $μbase = $base MeasureBase.basemeasure(::$μ) = $μbase - end - + end + if !isempty(p) # e.g. Normal(μ,σ) = Normal((μ=μ, σ=σ)) pnames = QuoteNode.(p) push!(q.args, :($μ($(p...)) = $μ(NamedTuple{($(pnames...),)}(($(p...),))))) end - + return q end @@ -73,16 +71,16 @@ function _parameterized(__module__, expr) q = quote struct $μ{N,T} <: MeasureBase.ParameterizedMeasure{N} - par :: NamedTuple{N,T} + par::NamedTuple{N,T} end - end - + end + if !isempty(p) # e.g. Normal(μ,σ) = Normal((μ=μ, σ=σ)) pnames = QuoteNode.(p) push!(q.args, :($μ($(p...)) = $μ(NamedTuple{($(pnames...),)}(($(p...),))))) end - + return q end @@ -91,16 +89,16 @@ function _parameterized(__module__, expr) q = quote struct $μ{N,T} <: MeasureBase.ParameterizedMeasure{N} - par :: NamedTuple{N,T} + par::NamedTuple{N,T} end - end - + end + if !isempty(p) # e.g. Normal(μ,σ) = Normal((μ=μ, σ=σ)) pnames = QuoteNode.(p) push!(q.args, :($μ($(p...)) = $μ(NamedTuple{($(pnames...),)}(($(p...),))))) end - + return q end end @@ -130,7 +128,6 @@ macro parameterized(expr) _parameterized(__module__, expr) end - """ @half dist([paramnames]) @@ -156,7 +153,7 @@ function _half(__module__, ex) dist = esc(dist) quote $halfdist(args...) = half($dist(args...)) - $halfdist(;kwargs...) = half($dist(;kwargs...)) + $halfdist(; kwargs...) = half($dist(; kwargs...)) end end end diff --git a/src/parameterized.jl b/src/parameterized.jl index 779b69a3..69bacd55 100644 --- a/src/parameterized.jl +++ b/src/parameterized.jl @@ -12,7 +12,7 @@ function Base.propertynames(μ::ParameterizedMeasure{N}) where {N} return N end -function Base.show(io::IO, μ::ParameterizedMeasure{()}) +function Base.show(io::IO, μ::ParameterizedMeasure{()}) io = IOContext(io, :compact => true) print(io, nameof(typeof(μ)), "()") end @@ -20,24 +20,26 @@ end function Base.show(io::IO, μ::ParameterizedMeasure{N}) where {N} io = IOContext(io, :compact => true) print(io, nameof(typeof(μ))) - print(io, getfield(μ,:par)) + print(io, getfield(μ, :par)) end - # Allow things like # # julia> Normal{(:μ,)}(2) # Normal(μ = 2,) # -function (::Type{P})(args...) where {N, P <: ParameterizedMeasure{N}} +function (::Type{P})(args...) where {N,P<:ParameterizedMeasure{N}} C = constructorof(P) return C(NamedTuple{N}(args...)) end -(::Type{P})(;kwargs...) where {P <: ParameterizedMeasure} = P(NamedTuple(kwargs)) +(::Type{P})(; kwargs...) where {P<:ParameterizedMeasure} = P(NamedTuple(kwargs)) -function ConstructionBase.setproperties(d::P, nt::NamedTuple) where {P<:ParameterizedMeasure} - return constructorof(P)(merge(params(d), nt)) +function ConstructionBase.setproperties( + d::P, + nt::NamedTuple +) where {P<:ParameterizedMeasure} + return constructorof(P)(merge(params(d), nt)) end ############################################################################### @@ -47,7 +49,7 @@ export params params(μ::ParameterizedMeasure) = getfield(μ, :par) -function params(μ::AbstractMeasure, constraints::NamedTuple{C}) where {C} +function params(μ::AbstractMeasure, constraints::NamedTuple{C}) where {C} NamedTuple{paramnames(μ, constraints)}(params(μ)) end @@ -60,11 +62,11 @@ export paramnames paramnames(μ) = paramnames(typeof(μ)) -paramnames(::Type{PM}) where {N, PM<:ParameterizedMeasure{N}} = N +paramnames(::Type{PM}) where {N,PM<:ParameterizedMeasure{N}} = N paramnames(μ::AbstractMeasure) = propertynames(μ) -params(::Type{PM}) where {N, PM<:ParameterizedMeasure{N}} = N +params(::Type{PM}) where {N,PM<:ParameterizedMeasure{N}} = N function paramnames(μ, constraints::NamedTuple{N}) where {N} tuple((k for k in paramnames(μ) if k ∉ N)...) @@ -73,10 +75,10 @@ end ############################################################################### # kernelfactor -function kernelfactor(::Type{P}) where {N, P <: ParameterizedMeasure{N}} +function kernelfactor(::Type{P}) where {N,P<:ParameterizedMeasure{N}} (constructorof(P), N) end -function kernelfactor(::P) where {N, P <: ParameterizedMeasure{N}} +function kernelfactor(::P) where {N,P<:ParameterizedMeasure{N}} (constructorof(P), N) end diff --git a/src/primitives/dirac.jl b/src/primitives/dirac.jl index b4e0a9e2..2e870d4f 100644 --- a/src/primitives/dirac.jl +++ b/src/primitives/dirac.jl @@ -21,16 +21,14 @@ density(μ::Dirac, x) = x == μ.x logdensity(μ::Dirac, x) = (x == μ.x) ? 0.0 : -Inf - Base.rand(::Random.AbstractRNG, T::Type, μ::Dirac) = μ.x - export dirac dirac(d::AbstractMeasure) = Dirac(rand(d)) -function logdensity(μ::Dirac{M}, ν::Dirac{M}, x) where {M} - logdensity(μ,x) - logdensity(ν,x) +function logdensity(μ::Dirac{M}, ν::Dirac{M}, x) where {M} + logdensity(μ, x) - logdensity(ν, x) end testvalue(d::Dirac) = d.x diff --git a/src/primitives/lebesgue.jl b/src/primitives/lebesgue.jl index e66dd4ab..a866413c 100644 --- a/src/primitives/lebesgue.jl +++ b/src/primitives/lebesgue.jl @@ -4,7 +4,7 @@ export Lebesgue struct Lebesgue{X} <: PrimitiveMeasure end -function Pretty.tile(::Lebesgue{X}) where X +function Pretty.tile(::Lebesgue{X}) where {X} result = Pretty.literal("Lebesgue(") result *= Pretty.tile(X) result *= Pretty.literal(")") @@ -12,7 +12,6 @@ end Lebesgue(X) = Lebesgue{X}() - sampletype(::Lebesgue{ℝ}) = Float64 sampletype(::Lebesgue{ℝ₊}) = Float64 sampletype(::Lebesgue{𝕀}) = Float64 @@ -24,6 +23,4 @@ testvalue(::Lebesgue{<:Real}) = 0.0 logdensity(::Lebesgue, x) = zero(x) - - Base.:∘(::typeof(basemeasure), ::Type{Lebesgue}) = Lebesgue diff --git a/src/testvalues.jl b/src/testvalues.jl index e69de29b..8b137891 100644 --- a/src/testvalues.jl +++ b/src/testvalues.jl @@ -0,0 +1 @@ + diff --git a/src/utils.jl b/src/utils.jl index f079f327..c225abca 100644 --- a/src/utils.jl +++ b/src/utils.jl @@ -12,7 +12,7 @@ showparams(io::IO, nt::NamedTuple) = print(io, nt) y = f(x) # Workaround bug https://github.com/JuliaLang/julia/issues/42615 while x !== y - (x,y) = (y, f(y)) + (x, y) = (y, f(y)) end return y @@ -49,7 +49,8 @@ rootmeasure(μ::AbstractMeasure) = fix(basemeasure, μ) using Tricks struct Iterable end struct NonIterable end -isiterable(::Type{T}) where T = static_hasmethod(iterate, Tuple{T}) ? Iterable() : NonIterable() +isiterable(::Type{T}) where {T} = + static_hasmethod(iterate, Tuple{T}) ? Iterable() : NonIterable() functioninstance(::Type{F}) where {F<:Function} = F.instance @@ -59,6 +60,5 @@ functioninstance(::Type{F}) where {F<:Function} = F.instance using MLStyle -macro quoteof(ex) - +macro quoteof(ex) end From 20152cdd79f2883b1f4b52678b1e6243c64c68b8 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 9 Nov 2021 14:26:42 -0800 Subject: [PATCH 011/368] add DensityInterface dependency --- Project.toml | 1 + 1 file changed, 1 insertion(+) diff --git a/Project.toml b/Project.toml index 8e954f73..181fcaaa 100644 --- a/Project.toml +++ b/Project.toml @@ -6,6 +6,7 @@ version = "0.5.1" [deps] ConcreteStructs = "2569d6c7-a4a2-43d3-a901-331e8e4be471" ConstructionBase = "187b0558-2788-49d3-abe0-74a17ed4e7c9" +DensityInterface = "b429d917-457f-4dbc-8f4c-0cc954292b1d" FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b" KeywordCalls = "4d827475-d3e4-43d6-abe3-9688362ede9f" LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" From 94589d65c850e5ec0ea509770cef011c4d5209aa Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Fri, 12 Nov 2021 13:49:36 -0800 Subject: [PATCH 012/368] faster `rootmeasure` --- src/utils.jl | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/src/utils.jl b/src/utils.jl index 9da9c94d..8032d09a 100644 --- a/src/utils.jl +++ b/src/utils.jl @@ -43,7 +43,12 @@ It's sometimes important to be able to find the fix point of a measure under `basemeasure`. That is, to start with some measure and apply `basemeasure` repeatedly until there's no change. That's what this does. """ -rootmeasure(μ::AbstractMeasure) = fix(basemeasure, μ) +@inline function rootmeasure(μ) + α = basemeasure(μ) + μ === α && return α + return rootmeasure(α) +end + # Base on the Tricks.jl README using Tricks From 4b9162ef00c29e87d9122f4f446985b6f359859b Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 15 Nov 2021 09:13:08 -0800 Subject: [PATCH 013/368] updates --- Project.toml | 3 +- src/MeasureBase.jl | 4 +- src/combinators/affine.jl | 80 +++++++++++++++++++++++++++++---- src/combinators/half.jl | 2 +- src/combinators/likelihood.jl | 2 +- src/combinators/mapsto.jl | 4 ++ src/combinators/pointwise.jl | 2 +- src/combinators/product.jl | 6 +-- src/combinators/restricted.jl | 2 + src/combinators/spikemixture.jl | 6 ++- src/combinators/weighted.jl | 4 +- src/density.jl | 35 ++++++++++----- src/primitives/dirac.jl | 2 +- src/utils.jl | 33 ++++++++++++++ 14 files changed, 151 insertions(+), 34 deletions(-) diff --git a/Project.toml b/Project.toml index 8e954f73..18b4e6a4 100644 --- a/Project.toml +++ b/Project.toml @@ -4,7 +4,6 @@ authors = ["Chad Scherrer and contributors"] version = "0.5.1" [deps] -ConcreteStructs = "2569d6c7-a4a2-43d3-a901-331e8e4be471" ConstructionBase = "187b0558-2788-49d3-abe0-74a17ed4e7c9" FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b" KeywordCalls = "4d827475-d3e4-43d6-abe3-9688362ede9f" @@ -14,10 +13,10 @@ MLStyle = "d8e11817-5142-5d16-987a-aa16d5891078" MappedArrays = "dbb5928d-eab1-5f90-85c2-b9b0edb7c900" PrettyPrinting = "54e16d92-306c-5ea0-a30b-337be88ac337" Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" +Static = "aedffcd0-7271-4cad-89d0-dc628f76c6d3" Tricks = "410a4b4d-49e4-4fbc-ab6d-cb71b17b3775" [compat] -ConcreteStructs = "0.2" ConstructionBase = "1.3" FillArrays = "0.12" KeywordCalls = "0.2" diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index 608ac1a6..5294f849 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -6,8 +6,8 @@ using Random import Random: rand! using FillArrays -using ConcreteStructs using MLStyle +using Static export ≪ export sampletype @@ -57,11 +57,11 @@ include("combinators/mapsto.jl") include("combinators/half.jl") include("exp.jl") include("domains.jl") +include("primitive.jl") include("utils.jl") include("absolutecontinuity.jl") include("macros.jl") -include("primitive.jl") include("primitives/counting.jl") include("primitives/lebesgue.jl") include("primitives/dirac.jl") diff --git a/src/combinators/affine.jl b/src/combinators/affine.jl index f453c8f4..82102fcd 100644 --- a/src/combinators/affine.jl +++ b/src/combinators/affine.jl @@ -1,10 +1,25 @@ export Affine, AffineTransform using LinearAlgebra -@concrete terse struct AffineTransform{N,T} + + +const AFFINEPARS = [ + (:μ,:σ) + (:μ,:ω) + (:σ,) + (:ω,) + (:μ,) +] + +struct AffineTransform{N,T} par::NamedTuple{N,T} end -quoteof(f::AffineTransform) = :(AffineTransform($(quoteof(f.par)))) +function Base.show(io::IO, f::AffineTransform) + io = IOContext(io, :compact => true) + Pretty.pprint(io, f) +end + +Pretty.quoteof(f::AffineTransform) = :(AffineTransform($(Pretty.quoteof(params(f))))) params(f::AffineTransform) = getfield(f, :par) @@ -110,11 +125,13 @@ logjac(f::AffineTransform{(:μ,)}) = 0.0 ############################################################################### -@concrete terse struct Affine{N,M,T} <: AbstractMeasure +struct Affine{N,M,T} <: AbstractMeasure f::AffineTransform{N,T} parent::M end +Pretty.quoteof(μ::Affine) = :(Affine($(Pretty.quoteof(params(μ.f))), $(Pretty.quoteof(μ.parent)))) + function testvalue(d::Affine) f = getfield(d, :f) z = testvalue(parent(d)) @@ -155,33 +172,76 @@ Base.size(d::Affine{(:ω,)}) = (size(d.ω, 2),) logdensity(d::Affine, x::MapsTo) = logdensity(d.parent, x.x) -function logdensity(d::Affine{(:σ,)}, x) +@inline function logdensity(d::Affine{(:σ,)}, x) z = d.σ \ x # @show z # println() logdensity(d.parent, z) end -function logdensity(d::Affine{(:ω,)}, x) +@inline function logdensity(d::Affine{(:ω,)}, x) z = d.ω * x logdensity(d.parent, z) end -function logdensity(d::Affine{(:μ,)}, x) +@inline function logdensity(d::Affine{(:μ,)}, x) z = x - d.μ logdensity(d.parent, z) end -function logdensity(d::Affine{(:μ, :σ)}, x) +@inline function logdensity(d::Affine{(:μ, :σ)}, x) z = d.σ \ (x - d.μ) logdensity(d.parent, z) end -function logdensity(d::Affine{(:μ, :ω)}, x) +@inline function logdensity(d::Affine{(:μ, :ω)}, x) z = d.ω * (x - d.μ) logdensity(d.parent, z) end + + + + + +@inline function logdensity_tuple(d::Affine{(:σ,)}, x) + z = d.σ \ x + # @show z + # println() + (logdensity(d.parent, z), basemeasure(d), z ↦ x) +end + +@inline function logdensity_tuple(d::Affine{(:ω,)}, x) + z = d.ω * x + (logdensity(d.parent, z), basemeasure(d), z ↦ x) +end + +@inline function logdensity_tuple(d::Affine{(:μ,)}, x) + z = x - d.μ + (logdensity(d.parent, z), basemeasure(d), z ↦ x) +end + +@inline function logdensity_tuple(d::Affine{(:μ, :σ)}, x) + z = d.σ \ (x - d.μ) + (logdensity(d.parent, z), basemeasure(d), z ↦ x) +end + +@inline function logdensity_tuple(d::Affine{(:μ, :ω)}, x) + z = d.ω * (x - d.μ) + (logdensity(d.parent, z), basemeasure(d), z ↦ x) +end + + + +for p in AFFINEPARS + @eval begin + @inline function logdensity_tuple(d::Affine{$p}, (z,x)::MapsTo) + (logdensity(d.parent, z), basemeasure(d), z ↦ x) + end + end +end + + # # logdensity(d::Affine{(:μ,:ω)}, x) = logdensity(d.parent, d.σ \ (x - d.μ)) # @inline function logdensity(d::Affine{(:μ,:σ), P, Tuple{V,M}}, x) where {P, V<:AbstractVector, M<:AbstractMatrix} # z = x - d.μ @@ -207,10 +267,12 @@ basemeasure(d::Affine) = affine(getfield(d, :f), basemeasure(d.parent)) # example it wouldn't make sense to apply a log-Jacobian to a point measure basemeasure(d::Affine{N,L}) where {N,L<:Lebesgue} = weightedmeasure(-logjac(d), d.parent) -function basemeasure(d::Affine{N,M}) where {N,L<:Lebesgue,M<:ProductMeasure{Returns{L}}} +@inline function basemeasure(d::Affine{N,M}) where {N,L<:Lebesgue,M<:ProductMeasure{Returns{L}}} weightedmeasure(-logjac(d), d.parent) end +basemeasure_depth(::Type{Affine{N,M}}) where {N, M<:Lebesgue} = static(1) + logjac(d::Affine) = logjac(getfield(d, :f)) function Random.rand!( diff --git a/src/combinators/half.jl b/src/combinators/half.jl index 8ef257a4..c5224021 100644 --- a/src/combinators/half.jl +++ b/src/combinators/half.jl @@ -11,7 +11,7 @@ end unhalf(μ::Half) = μ.parent -function basemeasure(μ::Half) +@inline function basemeasure(μ::Half) inbounds(x) = x > 0 constℓ = logtwo varℓ() = 0.0 diff --git a/src/combinators/likelihood.jl b/src/combinators/likelihood.jl index 878a9172..f4b14f47 100644 --- a/src/combinators/likelihood.jl +++ b/src/combinators/likelihood.jl @@ -116,6 +116,6 @@ function Base.show(io::IO, ℓ::Likelihood) print(io, "Likelihood(", k, ", ", x, ")") end -function logdensity(ℓ::Likelihood, p) +@inline function logdensity(ℓ::Likelihood, p) return logdensity(ℓ.k(p), ℓ.x) end diff --git a/src/combinators/mapsto.jl b/src/combinators/mapsto.jl index 09147bc8..7477d553 100644 --- a/src/combinators/mapsto.jl +++ b/src/combinators/mapsto.jl @@ -17,3 +17,7 @@ Base.Pair(t::MapsTo) = t.x => t.y Base.show(io::IO, t::MapsTo) = print(t.x, " ↦ ", t.y) logdensity(d, t::MapsTo) = logdensity(d, t.y) + +Base.iterate(m::MapsTo) = (first(m), 1) +Base.iterate(m::MapsTo, ::Int) = (last(m), nothing) +Base.iterate(m::MapsTo, ::Nothing) = nothing \ No newline at end of file diff --git a/src/combinators/pointwise.jl b/src/combinators/pointwise.jl index 2cb57966..12f88bb1 100644 --- a/src/combinators/pointwise.jl +++ b/src/combinators/pointwise.jl @@ -1,6 +1,6 @@ export ⊙ -@concrete terse struct PointwiseProductMeasure{T} <: AbstractMeasure +struct PointwiseProductMeasure{T} <: AbstractMeasure data::T end diff --git a/src/combinators/product.jl b/src/combinators/product.jl index 44f96f12..e9e912de 100644 --- a/src/combinators/product.jl +++ b/src/combinators/product.jl @@ -96,11 +96,11 @@ function marginals(d::ProductMeasure{<:Returns,S,A}) where {F,S,A<:AbstractArray # mappedarray(d.f.f, d.pars) end -function logdensity(d::ProductMeasure, x) +@inline function logdensity(d::ProductMeasure, x) mapreduce(logdensity, +, marginals(d), x) end -function logdensity(d::ProductMeasure{<:Returns}, x) +@inline function logdensity(d::ProductMeasure{<:Returns}, x) sum(x -> logdensity(d.f.f.value, x), x) end @@ -129,7 +129,7 @@ end export rand! using Random: rand!, GLOBAL_RNG, AbstractRNG -function logdensity(d::ProductMeasure{F,S,I}, x) where {F,S,I<:Base.Generator} +@inline function logdensity(d::ProductMeasure{F,S,I}, x) where {F,S,I<:Base.Generator} sum((logdensity(dj, xj) for (dj, xj) in zip(marginals(d), x))) end diff --git a/src/combinators/restricted.jl b/src/combinators/restricted.jl index 5500405a..76afa3af 100644 --- a/src/combinators/restricted.jl +++ b/src/combinators/restricted.jl @@ -14,3 +14,5 @@ function density(d::RestrictedMeasure, x) end basemeasure(μ::RestrictedMeasure) = μ.base + +basemeasure_depth(::Type{RestrictedMeasure{F,M}}) where {F,M} = static(1) + basemeasure_depth(M) \ No newline at end of file diff --git a/src/combinators/spikemixture.jl b/src/combinators/spikemixture.jl index beedfb34..a623faab 100644 --- a/src/combinators/spikemixture.jl +++ b/src/combinators/spikemixture.jl @@ -14,14 +14,16 @@ function Base.show(io::IO, μ::SpikeMixture) print(io, "(", μ.s * μ.w, "*", string(μ.m), " + ", μ.s * (1 - μ.w), "Dirac(0))") end -function basemeasure(μ::SpikeMixture) +@inline function basemeasure(μ::SpikeMixture) # Compare formula (1.4) in Joris Bierkens, Sebastiano Grazzi, Frank van der Meulen, Moritz Schauer: # Sticky PDMP samplers for sparse and local inference problems. 2020. [https://arxiv.org/abs/2103.08478]. ki = (1 / μ.w - 1) / density(μ.m, 0) SpikeMixture(basemeasure(μ.m), 1 / (1 + ki), μ.s * (1 + ki)) end -function logdensity(μ::SpikeMixture, x) +basemeasure_depth(::Type{SpikeMixture{T,S}}) where {T,S} = static(1) + basemeasure_depth(T) + +@inline function logdensity(μ::SpikeMixture, x) return log(μ.w) + logdensity(μ.m, x) end diff --git a/src/combinators/weighted.jl b/src/combinators/weighted.jl index 06fee4b9..3823d1c6 100644 --- a/src/combinators/weighted.jl +++ b/src/combinators/weighted.jl @@ -12,7 +12,7 @@ abstract type AbstractWeightedMeasure <: AbstractMeasure end logweight(μ::AbstractWeightedMeasure) = μ.logweight basemeasure(μ::AbstractWeightedMeasure) = μ.base -function logdensity(sm::AbstractWeightedMeasure, x) +@inline function logdensity(sm::AbstractWeightedMeasure, x) logdensity(sm.base, x) + sm.logweight end @@ -23,6 +23,8 @@ struct WeightedMeasure{R,M} <: AbstractWeightedMeasure base::M end +basemeasure_depth(::Type{WeightedMeasure{R,M}}) where {R, M} = static(1) + basemeasure_depth(M) + function Base.show(io::IO, μ::WeightedMeasure) io = IOContext(io, :compact => true) print(io, exp(μ.logweight), " * ", μ.base) diff --git a/src/density.jl b/src/density.jl index b63691d2..bc7cdcc6 100644 --- a/src/density.jl +++ b/src/density.jl @@ -68,6 +68,8 @@ end basemeasure(μ::DensityMeasure) = μ.base +basemeasure_depth(::Type{DensityMeasure{F,B,L}}) where {F,B,L} = static(1) + basemeasure_depth(B) + logdensity(μ::DensityMeasure{F,B,Val{true}}, x) where {F,B} = μ.f(x) density(μ::DensityMeasure{F,B,Val{false}}, x) where {F,B} = μ.f(x) @@ -125,7 +127,7 @@ end # computation to "fall through" in these cases. # TODO: Add tests to check that NaN cases work properly ℓ = logdensity(α, β, x) - isfinite(ℓ) || return ℓ + isnan(ℓ) && return ℓ ℓ += logdensity(μ, x) ℓ -= logdensity(ν, x) @@ -133,18 +135,29 @@ end return ℓ end -function logpdf(d::AbstractMeasure, x) - _logpdf(d, basemeasure(d), x) +@inline function logpdf(μ, x) + n = basemeasure_depth(μ) + (ℓ, β, y) = logdensity_tuple(μ, x) + return _logpdf(β, y, ℓ, static(n)) end -@inline function _logpdf(d::AbstractMeasure, β::AbstractMeasure, x, ℓ = zero(Float64)) - # @show d - # @show x - Δℓ = logdensity(d, x) - newℓ = ℓ + Δℓ - d == β && return newℓ - # @show Δℓ, d - _logpdf(β, basemeasure(β), x, newℓ) + + +@generated function _logpdf(μ, x, ℓ, ::StaticInt{n}) where {n} + quote + # $(Expr(:meta,:inline)) + Base.Cartesian.@nexprs $n i -> begin + (Δℓ, μ, x) = logdensity_tuple(μ, x) + ℓ += Δℓ + end + return ℓ + end + # # @show μ + # (Δℓ, β, y) = logdensity_tuple(μ, x) + # β === μ && return ℓ + # # @show Δℓ + # ℓ += Δℓ + # return _logpdf(β, y, ℓ) end logdensity(::Lebesgue, ::Lebesgue, x) = 0.0 diff --git a/src/primitives/dirac.jl b/src/primitives/dirac.jl index 2e870d4f..d6091b47 100644 --- a/src/primitives/dirac.jl +++ b/src/primitives/dirac.jl @@ -27,7 +27,7 @@ export dirac dirac(d::AbstractMeasure) = Dirac(rand(d)) -function logdensity(μ::Dirac{M}, ν::Dirac{M}, x) where {M} +@inline function logdensity(μ::Dirac{M}, ν::Dirac{M}, x) where {M} logdensity(μ, x) - logdensity(ν, x) end diff --git a/src/utils.jl b/src/utils.jl index 8032d09a..8bd3ab29 100644 --- a/src/utils.jl +++ b/src/utils.jl @@ -1,5 +1,17 @@ const EmptyNamedTuple = NamedTuple{(),Tuple{}} +""" + function proxy end + +It's often useful to delegate methods like `logdensity` and `basemeasure` to +those of a different measure. For example, a `Normal{(:μ,:σ)}` is equivalent to +an affine transformation of a `Normal{()}`. + +We _could_ just have calls like `Normal(μ=2,σ=4)` directly construct a +transformed measure, but this would make dispatch awkward. +""" +proxy(μ) = μ + function Base.show(io::IO, μ::AbstractMeasure) io = IOContext(io, :compact => true) Pretty.pprint(io, μ) @@ -36,6 +48,8 @@ testvalue(μ::AbstractMeasure) = testvalue(basemeasure(μ)) export rootmeasure +basemeasure(μ, x) = basemeasure(μ) + """ rootmeasure(μ::AbstractMeasure) @@ -64,3 +78,22 @@ functioninstance(::Type{F}) where {F<:Function} = F.instance @inline instance_type(f::UnionAll) = Type{f} using MLStyle + +export basemeasure_depth + +basemeasure_depth(μ::M) where {M<:AbstractMeasure} = basemeasure_depth(M) + +@inline function basemeasure_depth(μ::M) where {M} + static(1) + basemeasure_depth(basemeasure(μ)) +end + +@inline basemeasure_depth(::PrimitiveMeasure) = static(0) + +export logdensity_tuple + +logdensity_tuple(d, x) = logdensity_tuple(MeasureBase.proxy(d), x) + +function logdensity_tuple(d, (z,x)::MapsTo) + prox = MeasureBase.proxy(d) + return (logdensity(prox, x), basemeasure(prox, x), z ↦ x) +end \ No newline at end of file From 148412ab5f6b5068d8847779892ba60e59abce98 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 15 Nov 2021 10:55:17 -0800 Subject: [PATCH 014/368] primitive measure docs --- src/primitive.jl | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/src/primitive.jl b/src/primitive.jl index 781defe8..5e1a5b84 100644 --- a/src/primitive.jl +++ b/src/primitive.jl @@ -1,5 +1,18 @@ export PrimitiveMeasure +""" + abstract type PrimitiveMeasure <: AbstractMeasure end + +In the MeasureTheory ecosystem, a _primitive_ measure is a measure for which the +definition and construction do not depend on any other measure. Primitive +measures satisfy the following laws: + + basemeasure(μ::PrimitiveMeasure) = μ + + logdensity(μ::PrimitiveMeasure, x) = 0.0 + + logdensity(μ::M, ν::M, x) where {M<:PrimitiveMeasure} = 0.0 +""" abstract type PrimitiveMeasure <: AbstractMeasure end basemeasure(μ::PrimitiveMeasure) = μ From a48f6dab2fc2f3b5802f6dc3ad70ac155bbc0947 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 15 Nov 2021 13:08:08 -0800 Subject: [PATCH 015/368] get tests passing --- Project.toml | 1 + src/MeasureBase.jl | 1 + src/combinators/affine.jl | 3 ++- src/combinators/power.jl | 9 +++++++++ src/combinators/weighted.jl | 2 ++ src/density.jl | 4 ++-- src/proxies.jl | 17 +++++++++++++++++ src/rand.jl | 2 ++ src/utils.jl | 31 +++++++++++++------------------ 9 files changed, 49 insertions(+), 21 deletions(-) create mode 100644 src/proxies.jl diff --git a/Project.toml b/Project.toml index 18b4e6a4..20752075 100644 --- a/Project.toml +++ b/Project.toml @@ -24,6 +24,7 @@ LogExpFunctions = "0.3" MLStyle = "0.4" MappedArrays = "0.4" PrettyPrinting = "0.3" +Static = "0.4" Tricks = "0.1" julia = "1.3" diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index 5294f849..935fd659 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -51,6 +51,7 @@ if VERSION < v"1.7.0-beta1.0" end end +include("proxies.jl") include("kernel.jl") include("parameterized.jl") include("combinators/mapsto.jl") diff --git a/src/combinators/affine.jl b/src/combinators/affine.jl index 82102fcd..22765df6 100644 --- a/src/combinators/affine.jl +++ b/src/combinators/affine.jl @@ -271,7 +271,8 @@ basemeasure(d::Affine{N,L}) where {N,L<:Lebesgue} = weightedmeasure(-logjac(d), weightedmeasure(-logjac(d), d.parent) end -basemeasure_depth(::Type{Affine{N,M}}) where {N, M<:Lebesgue} = static(1) +basemeasure_depth(::Affine{N,M,T}) where {N, M, T} = static(1) + basemeasure_depth(M) +basemeasure_depth(::Type{Affine{N,M,T}}) where {N, M, T} = static(1) + basemeasure_depth(M) logjac(d::Affine) = logjac(getfield(d, :f)) diff --git a/src/combinators/power.jl b/src/combinators/power.jl index c8622e53..70b78afe 100644 --- a/src/combinators/power.jl +++ b/src/combinators/power.jl @@ -78,6 +78,15 @@ end FactoredBase(inbounds, constℓ, varℓ, base) end + +function basemeasure_depth(d::P) where {M, P<:ProductMeasure{Returns{M}}} + return static(1) + basemeasure_depth(M) +end + +function basemeasure_depth(::Type{P}) where {M, P<:ProductMeasure{Returns{M}}} + return static(1) + basemeasure_depth(M) +end + # Same as PowerMeasure @inline function logdensity(d::ProductMeasure{F,S,<:Fill}, x) where {F,S} d1 = d.f(first(d.pars)) diff --git a/src/combinators/weighted.jl b/src/combinators/weighted.jl index 3823d1c6..4b1e7a45 100644 --- a/src/combinators/weighted.jl +++ b/src/combinators/weighted.jl @@ -23,6 +23,8 @@ struct WeightedMeasure{R,M} <: AbstractWeightedMeasure base::M end + +basemeasure_depth(::WeightedMeasure{R,M}) where {R, M} = static(1) + basemeasure_depth(M) basemeasure_depth(::Type{WeightedMeasure{R,M}}) where {R, M} = static(1) + basemeasure_depth(M) function Base.show(io::IO, μ::WeightedMeasure) diff --git a/src/density.jl b/src/density.jl index bc7cdcc6..c9f8dc50 100644 --- a/src/density.jl +++ b/src/density.jl @@ -68,6 +68,8 @@ end basemeasure(μ::DensityMeasure) = μ.base +basemeasure_depth(::DensityMeasure{F,B,L}) where {F,B,L} = static(1) + basemeasure_depth(B) + basemeasure_depth(::Type{DensityMeasure{F,B,L}}) where {F,B,L} = static(1) + basemeasure_depth(B) logdensity(μ::DensityMeasure{F,B,Val{true}}, x) where {F,B} = μ.f(x) @@ -160,8 +162,6 @@ end # return _logpdf(β, y, ℓ) end -logdensity(::Lebesgue, ::Lebesgue, x) = 0.0 - # logdensity(::Lebesgue{ℝ}, ::Lebesgue{ℝ}, x) = zero(x) export density diff --git a/src/proxies.jl b/src/proxies.jl new file mode 100644 index 00000000..28a301f1 --- /dev/null +++ b/src/proxies.jl @@ -0,0 +1,17 @@ + +""" +function proxy end + +It's often useful to delegate methods like `logdensity` and `basemeasure` to +those of a different measure. For example, a `Normal{(:μ,:σ)}` is equivalent to +an affine transformation of a `Normal{()}`. + +We _could_ just have calls like `Normal(μ=2,σ=4)` directly construct a +transformed measure, but this would make dispatch awkward. +""" +function proxy end + +proxy(μ) = μ + +proxy(f, μ) = proxy(μ) + diff --git a/src/rand.jl b/src/rand.jl index 7144524a..8955a271 100644 --- a/src/rand.jl +++ b/src/rand.jl @@ -6,6 +6,8 @@ Base.rand(T::Type, μ::AbstractMeasure) = rand(Random.GLOBAL_RNG, T, μ) Base.rand(rng::AbstractRNG, d::AbstractMeasure) = rand(rng, Float64, d) +Base.rand(rng::AbstractRNG, ::Type{T}, d::AbstractMeasure) where {T} = rand(rng, T, proxy(rand, d)) + @inline Random.rand!(d::AbstractMeasure, args...) = rand!(GLOBAL_RNG, d, args...) function Base.rand(rng::Random.AbstractRNG, ::Type{T}, d::Affine) where {T} diff --git a/src/utils.jl b/src/utils.jl index 8bd3ab29..63a859ee 100644 --- a/src/utils.jl +++ b/src/utils.jl @@ -1,17 +1,5 @@ const EmptyNamedTuple = NamedTuple{(),Tuple{}} -""" - function proxy end - -It's often useful to delegate methods like `logdensity` and `basemeasure` to -those of a different measure. For example, a `Normal{(:μ,:σ)}` is equivalent to -an affine transformation of a `Normal{()}`. - -We _could_ just have calls like `Normal(μ=2,σ=4)` directly construct a -transformed measure, but this would make dispatch awkward. -""" -proxy(μ) = μ - function Base.show(io::IO, μ::AbstractMeasure) io = IOContext(io, :compact => true) Pretty.pprint(io, μ) @@ -81,19 +69,26 @@ using MLStyle export basemeasure_depth -basemeasure_depth(μ::M) where {M<:AbstractMeasure} = basemeasure_depth(M) - -@inline function basemeasure_depth(μ::M) where {M} +@inline function basemeasure_depth(μ::M) where {M<:AbstractMeasure} + @info """ + Add a method for better performance: + + basemeasure_depth(::$M) + + """ static(1) + basemeasure_depth(basemeasure(μ)) end @inline basemeasure_depth(::PrimitiveMeasure) = static(0) +@inline basemeasure_depth(::Type{M}) where {M<:PrimitiveMeasure} = static(0) + export logdensity_tuple -logdensity_tuple(d, x) = logdensity_tuple(MeasureBase.proxy(d), x) +function logdensity_tuple(d, x) + return (logdensity(d, x), basemeasure(d, x), x) +end function logdensity_tuple(d, (z,x)::MapsTo) - prox = MeasureBase.proxy(d) - return (logdensity(prox, x), basemeasure(prox, x), z ↦ x) + return (logdensity(d, x), basemeasure(d, x), z ↦ x) end \ No newline at end of file From f688c9489568c40a716256a005d339a874799d79 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 15 Nov 2021 14:37:11 -0800 Subject: [PATCH 016/368] cleaning up --- src/density.jl | 10 ++-------- 1 file changed, 2 insertions(+), 8 deletions(-) diff --git a/src/density.jl b/src/density.jl index c9f8dc50..5887c8bd 100644 --- a/src/density.jl +++ b/src/density.jl @@ -140,26 +140,20 @@ end @inline function logpdf(μ, x) n = basemeasure_depth(μ) (ℓ, β, y) = logdensity_tuple(μ, x) - return _logpdf(β, y, ℓ, static(n)) + return _logpdf(β, y, ℓ, n) end @generated function _logpdf(μ, x, ℓ, ::StaticInt{n}) where {n} quote - # $(Expr(:meta,:inline)) + $(Expr(:meta,:inline)) Base.Cartesian.@nexprs $n i -> begin (Δℓ, μ, x) = logdensity_tuple(μ, x) ℓ += Δℓ end return ℓ end - # # @show μ - # (Δℓ, β, y) = logdensity_tuple(μ, x) - # β === μ && return ℓ - # # @show Δℓ - # ℓ += Δℓ - # return _logpdf(β, y, ℓ) end # logdensity(::Lebesgue{ℝ}, ::Lebesgue{ℝ}, x) = zero(x) From 2dcf56ce11332b6ba4c83dd3030fc8cadbe20ca9 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 16 Nov 2021 09:08:28 -0800 Subject: [PATCH 017/368] formatting --- .JuliaFormatter.toml | 20 ++++++ src/combinators/affine.jl | 28 +++----- src/combinators/mapsto.jl | 2 +- src/combinators/power.jl | 5 +- src/combinators/product.jl | 2 +- src/combinators/restricted.jl | 3 +- src/combinators/smart-constructors.jl | 2 +- src/combinators/weighted.jl | 6 +- src/density.jl | 9 ++- src/parameterized.jl | 2 +- src/proxies.jl | 1 - src/rand.jl | 2 - src/utils.jl | 13 ++-- test/runtests.jl | 96 +++++++++++++++------------ 14 files changed, 104 insertions(+), 87 deletions(-) create mode 100644 .JuliaFormatter.toml diff --git a/.JuliaFormatter.toml b/.JuliaFormatter.toml new file mode 100644 index 00000000..154894d0 --- /dev/null +++ b/.JuliaFormatter.toml @@ -0,0 +1,20 @@ +indent = 4 +margin = 92 +always_for_in = true +whitespace_typedefs = false +whitespace_ops_in_indices = false +remove_extra_newlines = true +import_to_using = false +pipe_to_function_call = false +short_to_long_function_def = false +always_use_return = false +whitespace_in_kwargs = true +annotate_untyped_fields_with_any = false +format_docstrings = false +align_struct_field = true +align_conditional = true +align_assignment = true +align_pair_arrow = true +conditional_to_if = true +normalize_line_endings = "unix" +align_matrix = false \ No newline at end of file diff --git a/src/combinators/affine.jl b/src/combinators/affine.jl index 22765df6..1d113def 100644 --- a/src/combinators/affine.jl +++ b/src/combinators/affine.jl @@ -1,10 +1,9 @@ export Affine, AffineTransform using LinearAlgebra - const AFFINEPARS = [ - (:μ,:σ) - (:μ,:ω) + (:μ, :σ) + (:μ, :ω) (:σ,) (:ω,) (:μ,) @@ -130,7 +129,8 @@ struct Affine{N,M,T} <: AbstractMeasure parent::M end -Pretty.quoteof(μ::Affine) = :(Affine($(Pretty.quoteof(params(μ.f))), $(Pretty.quoteof(μ.parent)))) +Pretty.quoteof(μ::Affine) = + :(Affine($(Pretty.quoteof(params(μ.f))), $(Pretty.quoteof(μ.parent)))) function testvalue(d::Affine) f = getfield(d, :f) @@ -199,11 +199,6 @@ end logdensity(d.parent, z) end - - - - - @inline function logdensity_tuple(d::Affine{(:σ,)}, x) z = d.σ \ x # @show z @@ -231,17 +226,14 @@ end (logdensity(d.parent, z), basemeasure(d), z ↦ x) end - - for p in AFFINEPARS @eval begin - @inline function logdensity_tuple(d::Affine{$p}, (z,x)::MapsTo) + @inline function logdensity_tuple(d::Affine{$p}, (z, x)::MapsTo) (logdensity(d.parent, z), basemeasure(d), z ↦ x) end end end - # # logdensity(d::Affine{(:μ,:ω)}, x) = logdensity(d.parent, d.σ \ (x - d.μ)) # @inline function logdensity(d::Affine{(:μ,:σ), P, Tuple{V,M}}, x) where {P, V<:AbstractVector, M<:AbstractMatrix} # z = x - d.μ @@ -267,12 +259,14 @@ basemeasure(d::Affine) = affine(getfield(d, :f), basemeasure(d.parent)) # example it wouldn't make sense to apply a log-Jacobian to a point measure basemeasure(d::Affine{N,L}) where {N,L<:Lebesgue} = weightedmeasure(-logjac(d), d.parent) -@inline function basemeasure(d::Affine{N,M}) where {N,L<:Lebesgue,M<:ProductMeasure{Returns{L}}} +@inline function basemeasure( + d::Affine{N,M}, +) where {N,L<:Lebesgue,M<:ProductMeasure{Returns{L}}} weightedmeasure(-logjac(d), d.parent) end -basemeasure_depth(::Affine{N,M,T}) where {N, M, T} = static(1) + basemeasure_depth(M) -basemeasure_depth(::Type{Affine{N,M,T}}) where {N, M, T} = static(1) + basemeasure_depth(M) +basemeasure_depth(::Affine{N,M,T}) where {N,M,T} = static(1) + basemeasure_depth(M) +basemeasure_depth(::Type{Affine{N,M,T}}) where {N,M,T} = static(1) + basemeasure_depth(M) logjac(d::Affine) = logjac(getfield(d, :f)) @@ -280,7 +274,7 @@ function Random.rand!( rng::Random.AbstractRNG, d::Affine, x::AbstractVector{T}, - z = Vector{T}(undef, size(getfield(d, :f), 2)) + z = Vector{T}(undef, size(getfield(d, :f), 2)), ) where {T} rand!(rng, parent(d), z) f = getfield(d, :f) diff --git a/src/combinators/mapsto.jl b/src/combinators/mapsto.jl index 7477d553..9e59642a 100644 --- a/src/combinators/mapsto.jl +++ b/src/combinators/mapsto.jl @@ -20,4 +20,4 @@ logdensity(d, t::MapsTo) = logdensity(d, t.y) Base.iterate(m::MapsTo) = (first(m), 1) Base.iterate(m::MapsTo, ::Int) = (last(m), nothing) -Base.iterate(m::MapsTo, ::Nothing) = nothing \ No newline at end of file +Base.iterate(m::MapsTo, ::Nothing) = nothing diff --git a/src/combinators/power.jl b/src/combinators/power.jl index 70b78afe..bfd0887a 100644 --- a/src/combinators/power.jl +++ b/src/combinators/power.jl @@ -78,12 +78,11 @@ end FactoredBase(inbounds, constℓ, varℓ, base) end - -function basemeasure_depth(d::P) where {M, P<:ProductMeasure{Returns{M}}} +function basemeasure_depth(d::P) where {M,P<:ProductMeasure{Returns{M}}} return static(1) + basemeasure_depth(M) end -function basemeasure_depth(::Type{P}) where {M, P<:ProductMeasure{Returns{M}}} +function basemeasure_depth(::Type{P}) where {M,P<:ProductMeasure{Returns{M}}} return static(1) + basemeasure_depth(M) end diff --git a/src/combinators/product.jl b/src/combinators/product.jl index e9e912de..6b0959e4 100644 --- a/src/combinators/product.jl +++ b/src/combinators/product.jl @@ -136,7 +136,7 @@ end @propagate_inbounds function Random.rand!( rng::AbstractRNG, d::ProductMeasure, - x::AbstractArray + x::AbstractArray, ) # TODO: Generalize this T = Float64 diff --git a/src/combinators/restricted.jl b/src/combinators/restricted.jl index 76afa3af..a55768f0 100644 --- a/src/combinators/restricted.jl +++ b/src/combinators/restricted.jl @@ -15,4 +15,5 @@ end basemeasure(μ::RestrictedMeasure) = μ.base -basemeasure_depth(::Type{RestrictedMeasure{F,M}}) where {F,M} = static(1) + basemeasure_depth(M) \ No newline at end of file +basemeasure_depth(::Type{RestrictedMeasure{F,M}}) where {F,M} = + static(1) + basemeasure_depth(M) diff --git a/src/combinators/smart-constructors.jl b/src/combinators/smart-constructors.jl index 6a78b7ea..c890d488 100644 --- a/src/combinators/smart-constructors.jl +++ b/src/combinators/smart-constructors.jl @@ -32,7 +32,7 @@ pointwiseproduct(μ::AbstractMeasure...) = PointwiseProductMeasure(μ) function pointwiseproduct( μ::PointwiseProductMeasure{X}, - ν::PointwiseProductMeasure{Y} + ν::PointwiseProductMeasure{Y}, ) where {X,Y} data = (μ.data..., ν.data...) pointwiseproduct(data...) diff --git a/src/combinators/weighted.jl b/src/combinators/weighted.jl index 4b1e7a45..5220fc39 100644 --- a/src/combinators/weighted.jl +++ b/src/combinators/weighted.jl @@ -23,9 +23,9 @@ struct WeightedMeasure{R,M} <: AbstractWeightedMeasure base::M end - -basemeasure_depth(::WeightedMeasure{R,M}) where {R, M} = static(1) + basemeasure_depth(M) -basemeasure_depth(::Type{WeightedMeasure{R,M}}) where {R, M} = static(1) + basemeasure_depth(M) +basemeasure_depth(::WeightedMeasure{R,M}) where {R,M} = static(1) + basemeasure_depth(M) +basemeasure_depth(::Type{WeightedMeasure{R,M}}) where {R,M} = + static(1) + basemeasure_depth(M) function Base.show(io::IO, μ::WeightedMeasure) io = IOContext(io, :compact => true) diff --git a/src/density.jl b/src/density.jl index 5887c8bd..8c6d09bb 100644 --- a/src/density.jl +++ b/src/density.jl @@ -70,7 +70,8 @@ basemeasure(μ::DensityMeasure) = μ.base basemeasure_depth(::DensityMeasure{F,B,L}) where {F,B,L} = static(1) + basemeasure_depth(B) -basemeasure_depth(::Type{DensityMeasure{F,B,L}}) where {F,B,L} = static(1) + basemeasure_depth(B) +basemeasure_depth(::Type{DensityMeasure{F,B,L}}) where {F,B,L} = + static(1) + basemeasure_depth(B) logdensity(μ::DensityMeasure{F,B,Val{true}}, x) where {F,B} = μ.f(x) @@ -143,17 +144,15 @@ end return _logpdf(β, y, ℓ, n) end - - @generated function _logpdf(μ, x, ℓ, ::StaticInt{n}) where {n} quote - $(Expr(:meta,:inline)) + $(Expr(:meta, :inline)) Base.Cartesian.@nexprs $n i -> begin (Δℓ, μ, x) = logdensity_tuple(μ, x) ℓ += Δℓ end return ℓ - end + end end # logdensity(::Lebesgue{ℝ}, ::Lebesgue{ℝ}, x) = zero(x) diff --git a/src/parameterized.jl b/src/parameterized.jl index 69bacd55..ca89e627 100644 --- a/src/parameterized.jl +++ b/src/parameterized.jl @@ -37,7 +37,7 @@ end function ConstructionBase.setproperties( d::P, - nt::NamedTuple + nt::NamedTuple, ) where {P<:ParameterizedMeasure} return constructorof(P)(merge(params(d), nt)) end diff --git a/src/proxies.jl b/src/proxies.jl index 28a301f1..dc85196e 100644 --- a/src/proxies.jl +++ b/src/proxies.jl @@ -14,4 +14,3 @@ function proxy end proxy(μ) = μ proxy(f, μ) = proxy(μ) - diff --git a/src/rand.jl b/src/rand.jl index 8955a271..7144524a 100644 --- a/src/rand.jl +++ b/src/rand.jl @@ -6,8 +6,6 @@ Base.rand(T::Type, μ::AbstractMeasure) = rand(Random.GLOBAL_RNG, T, μ) Base.rand(rng::AbstractRNG, d::AbstractMeasure) = rand(rng, Float64, d) -Base.rand(rng::AbstractRNG, ::Type{T}, d::AbstractMeasure) where {T} = rand(rng, T, proxy(rand, d)) - @inline Random.rand!(d::AbstractMeasure, args...) = rand!(GLOBAL_RNG, d, args...) function Base.rand(rng::Random.AbstractRNG, ::Type{T}, d::Affine) where {T} diff --git a/src/utils.jl b/src/utils.jl index 63a859ee..fd123a2a 100644 --- a/src/utils.jl +++ b/src/utils.jl @@ -51,7 +51,6 @@ repeatedly until there's no change. That's what this does. return rootmeasure(α) end - # Base on the Tricks.jl README using Tricks struct Iterable end @@ -71,10 +70,10 @@ export basemeasure_depth @inline function basemeasure_depth(μ::M) where {M<:AbstractMeasure} @info """ - Add a method for better performance: - - basemeasure_depth(::$M) - + Add methods for better performance: + + basemeasure_depth(::$M) + basemeasure_depth(::Type{$M}) """ static(1) + basemeasure_depth(basemeasure(μ)) end @@ -89,6 +88,6 @@ function logdensity_tuple(d, x) return (logdensity(d, x), basemeasure(d, x), x) end -function logdensity_tuple(d, (z,x)::MapsTo) +function logdensity_tuple(d, (z, x)::MapsTo) return (logdensity(d, x), basemeasure(d, x), z ↦ x) -end \ No newline at end of file +end diff --git a/test/runtests.jl b/test/runtests.jl index 64bf3cf2..9f9707a6 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -7,7 +7,7 @@ using MeasureBase using MeasureBase: logpdf using Aqua -Aqua.test_all(MeasureBase; ambiguities=false, unbound_args=false) +Aqua.test_all(MeasureBase; ambiguities = false, unbound_args = false) d = ∫exp(x -> -x^2, Lebesgue(ℝ)) @@ -19,7 +19,7 @@ d = ∫exp(x -> -x^2, Lebesgue(ℝ)) # @test_nodispatch density(Dirac(0), 0.3) # @test_nodispatch density(Dirac(0), 0) - + # @test_nodispatch density(d, 3) # @test_nodispatch basemeasure(d) @@ -43,10 +43,14 @@ end test_measures = [ # Chain(x -> Normal(μ=x), Normal(μ=0.0)) - For(3) do j Dirac(j) end - For(2,3) do i,j Dirac(i) + Dirac(j) end - Lebesgue(ℝ) ^ 3 - Lebesgue(ℝ) ^ (2,3) + For(3) do j + Dirac(j) + end + For(2, 3) do i, j + Dirac(i) + Dirac(j) + end + Lebesgue(ℝ)^3 + Lebesgue(ℝ)^(2, 3) 3 * Lebesgue(ℝ) Dirac(π) Lebesgue(ℝ) @@ -60,7 +64,6 @@ testbroken_measures = [ # MvNormal(I(3)) # Entirely broken for now CountingMeasure(Float64) Likelihood - TrivialMeasure() ] @@ -74,10 +77,8 @@ testbroken_measures = [ @info "testing $μ" @test_broken test_testvalue(μ) end - end - # @testset "Kernel" begin # κ = MeasureBase.kernel(MeasureBase.Dirac, identity) # @test rand(κ(1.1)) == 1.1 @@ -86,12 +87,12 @@ end @testset "SpikeMixture" begin @test rand(SpikeMixture(Dirac(0), 0.5)) == 0 @test rand(SpikeMixture(Dirac(1), 1.0)) == 1 - w = 1/3 + w = 1 / 3 m = SpikeMixture(d, w) bm = basemeasure(m) - @test (bm.s*bm.w)*bm.m == 1.0*basemeasure(d) - @test density(m, 1.0)*(bm.s*bm.w) ≈ w*density(d,1.0) - @test density(m, 0)*(bm.s*(1-bm.w)) ≈ (1-w) + @test (bm.s * bm.w) * bm.m == 1.0 * basemeasure(d) + @test density(m, 1.0) * (bm.s * bm.w) ≈ w * density(d, 1.0) + @test density(m, 0) * (bm.s * (1 - bm.w)) ≈ (1 - w) end @testset "Dirac" begin @@ -101,36 +102,36 @@ end end @testset "AffineTransform" begin - f = AffineTransform((μ=3,σ=2)) + f = AffineTransform((μ = 3, σ = 2)) @test f(inv(f)(1)) == 1 @test inv(f)(f(1)) == 1 - - f = AffineTransform((μ=3,ω=2)) + + f = AffineTransform((μ = 3, ω = 2)) @test f(inv(f)(1)) == 1 @test inv(f)(f(1)) == 1 - f = AffineTransform((σ=2,)) + f = AffineTransform((σ = 2,)) @test f(inv(f)(1)) == 1 @test inv(f)(f(1)) == 1 - f = AffineTransform((ω=2,)) + f = AffineTransform((ω = 2,)) @test f(inv(f)(1)) == 1 @test inv(f)(f(1)) == 1 - f = AffineTransform((μ=3,)) + f = AffineTransform((μ = 3,)) @test f(inv(f)(1)) == 1 @test inv(f)(f(1)) == 1 end @testset "Affine" begin - unif = ∫(x -> 0 0 < x < 1, Lebesgue(ℝ)) + f1 = AffineTransform((μ = 3.0, σ = 2.0)) + f2 = AffineTransform((μ = 3.0, ω = 2.0)) + f3 = AffineTransform((μ = 3.0,)) + f4 = AffineTransform((σ = 2.0,)) + f5 = AffineTransform((ω = 2.0,)) + + for f in [f1, f2, f3, f4, f5] par = getfield(f, :par) @test Affine(par)(unif) == Affine(f, unif) @test density(Affine(f, Affine(inv(f), unif)), 0.5) == 1 @@ -139,35 +140,45 @@ end d = ∫exp(x -> -x^2, Lebesgue(ℝ)) μ = randn(3) - σ = LowerTriangular(randn(3,3)) + σ = LowerTriangular(randn(3, 3)) ω = inv(σ) x = randn(3) - @test logdensity(Affine((μ=μ,σ=σ), d^3), x) ≈ logdensity(Affine((μ=μ,ω=ω), d^3), x) - @test logdensity(Affine((σ=σ,), d^3), x) ≈ logdensity(Affine((ω=ω,), d^3), x) - @test logdensity(Affine((μ=μ,), d^3), x) ≈ logdensity(d^3, x-μ) - + @test logdensity(Affine((μ = μ, σ = σ), d^3), x) ≈ + logdensity(Affine((μ = μ, ω = ω), d^3), x) + @test logdensity(Affine((σ = σ,), d^3), x) ≈ logdensity(Affine((ω = ω,), d^3), x) + @test logdensity(Affine((μ = μ,), d^3), x) ≈ logdensity(d^3, x - μ) d = ∫exp(x -> -x^2, Lebesgue(ℝ)) - a = Affine((σ=[1 0]',), d^1) + a = Affine((σ = [1 0]',), d^1) x = randn(2) y = randn(1) @test logpdf(a, x) ≈ logpdf(d, inv(a.f)(x)[1]) @test logpdf(a, a.f(y)) ≈ logpdf(d^1, y) - b = Affine((ω=[1 0]'',), d^1) + b = Affine((ω = [1 0]'',), d^1) @test logpdf(b, x) ≈ logpdf(d, inv(b.f)(x)[1]) @test logpdf(b, b.f(y)) ≈ logpdf(d^1, y) end @testset "For" begin FORDISTS = [ - For(1:10) do j Dirac(j) end - For(4,3) do i,j Dirac(i) ⊗ Dirac(j) end - For(1:4, 1:4) do i,j Dirac(i) ⊗ Dirac(j) end - For(eachrow(rand(4,2))) do x Dirac(x[1]) ⊗ Dirac(x[2]) end - For(rand(4), rand(4)) do i,j Dirac(i) ⊗ Dirac(j) end + For(1:10) do j + Dirac(j) + end + For(4, 3) do i, j + Dirac(i) ⊗ Dirac(j) + end + For(1:4, 1:4) do i, j + Dirac(i) ⊗ Dirac(j) + end + For(eachrow(rand(4, 2))) do x + Dirac(x[1]) ⊗ Dirac(x[2]) + end + For(rand(4), rand(4)) do i, j + Dirac(i) ⊗ Dirac(j) + end ] for d in FORDISTS @@ -184,7 +195,6 @@ end @test density(HalfNormal(), Lebesgue(ℝ), 0.2) ≈ 2 * density(Normal(), Lebesgue(ℝ), 0.2) end - # import MeasureBase.:⋅ # function ⋅(μ::Normal, kernel) # m = kernel(μ) @@ -197,7 +207,6 @@ end # (a::AffineMap)(x) = a.B*x + a.β # (a::AffineMap)(p::Normal) = Normal(μ = a.B*mean(p) + a.β, σ = sqrt(a.B*p.σ^2*a.B')) - # @testset "Likelihood" begin # dps = [ # (Normal() , 2.0 ) @@ -216,7 +225,6 @@ end # end # end - # @testset "ProductMeasure" begin # d = For(1:10) do j Poisson(exp(j)) end # x = Vector{Int16}(undef, 10) @@ -240,8 +248,8 @@ end @testset "Show methods" begin @testset "PowerMeasure" begin - @test repr(Lebesgue(ℝ) ^ 5) == "Lebesgue(ℝ) ^ 5" - @test repr(Lebesgue(ℝ) ^ (3, 2)) == "Lebesgue(ℝ) ^ (3, 2)" + @test repr(Lebesgue(ℝ)^5) == "Lebesgue(ℝ) ^ 5" + @test repr(Lebesgue(ℝ)^(3, 2)) == "Lebesgue(ℝ) ^ (3, 2)" end end From c1679fdbbb1d53c25c71edd7cffad9ef7346e011 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 22 Nov 2021 09:58:08 -0800 Subject: [PATCH 018/368] drop some unneeded methods --- src/combinators/smart-constructors.jl | 18 ------------------ 1 file changed, 18 deletions(-) diff --git a/src/combinators/smart-constructors.jl b/src/combinators/smart-constructors.jl index c890d488..36566172 100644 --- a/src/combinators/smart-constructors.jl +++ b/src/combinators/smart-constructors.jl @@ -30,24 +30,6 @@ half(μ::AbstractMeasure) = Half(μ) pointwiseproduct(μ::AbstractMeasure...) = PointwiseProductMeasure(μ) -function pointwiseproduct( - μ::PointwiseProductMeasure{X}, - ν::PointwiseProductMeasure{Y}, -) where {X,Y} - data = (μ.data..., ν.data...) - pointwiseproduct(data...) -end - -function pointwiseproduct(μ::AbstractMeasure, ν::PointwiseProductMeasure) - data = (μ, ν.data...) - return pointwiseproduct(data...) -end - -function pointwiseproduct(μ::PointwiseProductMeasure, ν::N) where {N<:AbstractMeasure} - data = (μ.data..., ν) - return pointwiseproduct(data...) -end - function pointwiseproduct(μ::AbstractMeasure, ℓ::Likelihood) data = (μ, ℓ) return PointwiseProductMeasure(data) From 836fb19068e7c85638896fb351c19adcae758a32 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 23 Nov 2021 06:15:11 -0800 Subject: [PATCH 019/368] update for DensityInterface --- Project.toml | 6 +- src/MeasureBase.jl | 18 ++-- src/combinators/affine.jl | 56 +++++------ src/combinators/factoredbase.jl | 2 +- src/combinators/for.jl | 8 +- src/combinators/half.jl | 2 +- src/combinators/likelihood.jl | 28 +++--- src/combinators/mapsto.jl | 2 +- src/combinators/pointwise.jl | 8 +- src/combinators/power.jl | 14 +-- src/combinators/product.jl | 56 +++-------- src/combinators/restricted.jl | 4 +- src/combinators/spikemixture.jl | 10 +- src/combinators/superpose.jl | 8 +- src/combinators/weighted.jl | 8 +- src/density.jl | 69 +++++++------- src/domains.jl | 49 +++++++++- src/kernel.jl | 6 -- src/macros.jl | 160 -------------------------------- src/modified_gram_schmitt.jl | 85 +++++++++++++++++ src/primitive.jl | 8 +- src/primitives/counting.jl | 10 +- src/primitives/dirac.jl | 15 +-- src/primitives/lebesgue.jl | 8 +- src/primitives/trivial.jl | 4 +- src/thunks.jl | 2 +- src/utils.jl | 11 +-- test/runtests.jl | 54 +++++------ 28 files changed, 300 insertions(+), 411 deletions(-) create mode 100644 src/modified_gram_schmitt.jl diff --git a/Project.toml b/Project.toml index 20752075..f8187589 100644 --- a/Project.toml +++ b/Project.toml @@ -5,13 +5,12 @@ version = "0.5.1" [deps] ConstructionBase = "187b0558-2788-49d3-abe0-74a17ed4e7c9" +DensityInterface = "b429d917-457f-4dbc-8f4c-0cc954292b1d" FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b" KeywordCalls = "4d827475-d3e4-43d6-abe3-9688362ede9f" LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" LogExpFunctions = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -MLStyle = "d8e11817-5142-5d16-987a-aa16d5891078" MappedArrays = "dbb5928d-eab1-5f90-85c2-b9b0edb7c900" -PrettyPrinting = "54e16d92-306c-5ea0-a30b-337be88ac337" Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" Static = "aedffcd0-7271-4cad-89d0-dc628f76c6d3" Tricks = "410a4b4d-49e4-4fbc-ab6d-cb71b17b3775" @@ -21,11 +20,8 @@ ConstructionBase = "1.3" FillArrays = "0.12" KeywordCalls = "0.2" LogExpFunctions = "0.3" -MLStyle = "0.4" MappedArrays = "0.4" -PrettyPrinting = "0.3" Static = "0.4" -Tricks = "0.1" julia = "1.3" [extras] diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index 935fd659..ff5ce71d 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -4,25 +4,28 @@ const logtwo = log(2.0) using Random import Random: rand! +import Random: gentype +import DensityInterface: logdensityof +import DensityInterface: densityof +import DensityInterface: DensityKind +using DensityInterface: HasDensity, IsDensity using FillArrays -using MLStyle using Static export ≪ -export sampletype +export gentype export AbstractMeasure abstract type AbstractMeasure end -import PrettyPrinting +@inline DensityKind(::AbstractMeasure) = HasDensity() -const Pretty = PrettyPrinting +gentype(μ::AbstractMeasure) = typeof(testvalue(μ)) -sampletype(μ::AbstractMeasure) = typeof(testvalue(μ)) -# sampletype(μ::AbstractMeasure) = sampletype(basemeasure(μ)) +# gentype(μ::AbstractMeasure) = gentype(basemeasure(μ)) export logdensity export basemeasure @@ -31,7 +34,7 @@ export basekernel using LogExpFunctions: logsumexp """ - logdensity(μ::AbstractMeasure{X}, x::X) + logdensity_def(μ::AbstractMeasure{X}, x::X) Compute the logdensity of the measure μ at the point x. This is the standard way to define `logdensity` for a new measure. the base measure is implicit here, and @@ -61,7 +64,6 @@ include("domains.jl") include("primitive.jl") include("utils.jl") include("absolutecontinuity.jl") -include("macros.jl") include("primitives/counting.jl") include("primitives/lebesgue.jl") diff --git a/src/combinators/affine.jl b/src/combinators/affine.jl index 1d113def..d65fc728 100644 --- a/src/combinators/affine.jl +++ b/src/combinators/affine.jl @@ -13,13 +13,6 @@ struct AffineTransform{N,T} par::NamedTuple{N,T} end -function Base.show(io::IO, f::AffineTransform) - io = IOContext(io, :compact => true) - Pretty.pprint(io, f) -end - -Pretty.quoteof(f::AffineTransform) = :(AffineTransform($(Pretty.quoteof(params(f))))) - params(f::AffineTransform) = getfield(f, :par) @inline Base.getproperty(d::AffineTransform, s::Symbol) = getfield(getfield(d, :par), s) @@ -129,9 +122,6 @@ struct Affine{N,M,T} <: AbstractMeasure parent::M end -Pretty.quoteof(μ::Affine) = - :(Affine($(Pretty.quoteof(params(μ.f))), $(Pretty.quoteof(μ.parent)))) - function testvalue(d::Affine) f = getfield(d, :f) z = testvalue(parent(d)) @@ -170,72 +160,72 @@ Base.size(d::Affine) = size(d.μ) Base.size(d::Affine{(:σ,)}) = (size(d.σ, 1),) Base.size(d::Affine{(:ω,)}) = (size(d.ω, 2),) -logdensity(d::Affine, x::MapsTo) = logdensity(d.parent, x.x) +logdensity_def(d::Affine, x::MapsTo) = logdensity_def(d.parent, x.x) -@inline function logdensity(d::Affine{(:σ,)}, x) +@inline function logdensity_def(d::Affine{(:σ,)}, x) z = d.σ \ x # @show z # println() - logdensity(d.parent, z) + logdensity_def(d.parent, z) end -@inline function logdensity(d::Affine{(:ω,)}, x) +@inline function logdensity_def(d::Affine{(:ω,)}, x) z = d.ω * x - logdensity(d.parent, z) + logdensity_def(d.parent, z) end -@inline function logdensity(d::Affine{(:μ,)}, x) +@inline function logdensity_def(d::Affine{(:μ,)}, x) z = x - d.μ - logdensity(d.parent, z) + logdensity_def(d.parent, z) end -@inline function logdensity(d::Affine{(:μ, :σ)}, x) +@inline function logdensity_def(d::Affine{(:μ, :σ)}, x) z = d.σ \ (x - d.μ) - logdensity(d.parent, z) + logdensity_def(d.parent, z) end -@inline function logdensity(d::Affine{(:μ, :ω)}, x) +@inline function logdensity_def(d::Affine{(:μ, :ω)}, x) z = d.ω * (x - d.μ) - logdensity(d.parent, z) + logdensity_def(d.parent, z) end @inline function logdensity_tuple(d::Affine{(:σ,)}, x) z = d.σ \ x # @show z # println() - (logdensity(d.parent, z), basemeasure(d), z ↦ x) + (logdensity_def(d.parent, z), basemeasure(d), z ↦ x) end @inline function logdensity_tuple(d::Affine{(:ω,)}, x) z = d.ω * x - (logdensity(d.parent, z), basemeasure(d), z ↦ x) + (logdensity_def(d.parent, z), basemeasure(d), z ↦ x) end @inline function logdensity_tuple(d::Affine{(:μ,)}, x) z = x - d.μ - (logdensity(d.parent, z), basemeasure(d), z ↦ x) + (logdensity_def(d.parent, z), basemeasure(d), z ↦ x) end @inline function logdensity_tuple(d::Affine{(:μ, :σ)}, x) z = d.σ \ (x - d.μ) - (logdensity(d.parent, z), basemeasure(d), z ↦ x) + (logdensity_def(d.parent, z), basemeasure(d), z ↦ x) end @inline function logdensity_tuple(d::Affine{(:μ, :ω)}, x) z = d.ω * (x - d.μ) - (logdensity(d.parent, z), basemeasure(d), z ↦ x) + (logdensity_def(d.parent, z), basemeasure(d), z ↦ x) end for p in AFFINEPARS @eval begin @inline function logdensity_tuple(d::Affine{$p}, (z, x)::MapsTo) - (logdensity(d.parent, z), basemeasure(d), z ↦ x) + (logdensity_def(d.parent, z), basemeasure(d), z ↦ x) end end end -# # logdensity(d::Affine{(:μ,:ω)}, x) = logdensity(d.parent, d.σ \ (x - d.μ)) -# @inline function logdensity(d::Affine{(:μ,:σ), P, Tuple{V,M}}, x) where {P, V<:AbstractVector, M<:AbstractMatrix} +# # logdensity_def(d::Affine{(:μ,:ω)}, x) = logdensity_def(d.parent, d.σ \ (x - d.μ)) +# @inline function logdensity_def(d::Affine{(:μ,:σ), P, Tuple{V,M}}, x) where {P, V<:AbstractVector, M<:AbstractMatrix} # z = x - d.μ # σ = d.σ # if σ isa Factorization @@ -243,14 +233,14 @@ end # else # ldiv!(factorize(σ), z) # end -# sum(zⱼ -> logdensity(d.parent, zⱼ), z) +# sum(zⱼ -> logdensity_def(d.parent, zⱼ), z) # end -# # logdensity(d::Affine{(:μ,:ω)}, x) = logdensity(d.parent, d.ω * (x - d.μ)) -# @inline function logdensity(d::Affine{(:μ,:ω), P,Tuple{V,M}}, x) where {P,V<:AbstractVector, M<:AbstractMatrix} +# # logdensity_def(d::Affine{(:μ,:ω)}, x) = logdensity_def(d.parent, d.ω * (x - d.μ)) +# @inline function logdensity_def(d::Affine{(:μ,:ω), P,Tuple{V,M}}, x) where {P,V<:AbstractVector, M<:AbstractMatrix} # z = x - d.μ # lmul!(d.ω, z) -# logdensity(d.parent, z) +# logdensity_def(d.parent, z) # end basemeasure(d::Affine) = affine(getfield(d, :f), basemeasure(d.parent)) diff --git a/src/combinators/factoredbase.jl b/src/combinators/factoredbase.jl index 6a922dff..2747d419 100644 --- a/src/combinators/factoredbase.jl +++ b/src/combinators/factoredbase.jl @@ -7,7 +7,7 @@ struct FactoredBase{R,C,V,B} <: AbstractMeasure base::B end -@inline function logdensity(d::FactoredBase, x) +@inline function logdensity_def(d::FactoredBase, x) d.inbounds(x) || return -Inf d.constℓ + d.varℓ() end diff --git a/src/combinators/for.jl b/src/combinators/for.jl index 780863c0..121519a9 100644 --- a/src/combinators/for.jl +++ b/src/combinators/for.jl @@ -105,13 +105,13 @@ end # rand!(rng, x, μ) # end -# function logdensity(μ::ForArray{D,N,T,F}, x) -# getℓ(θⱼ, xⱼ) = logdensity(μ.f(θⱼ), xⱼ) +# function logdensity_def(μ::ForArray{D,N,T,F}, x) +# getℓ(θⱼ, xⱼ) = logdensity_def(μ.f(θⱼ), xⱼ) # ℓ = mappedarray(getℓ, μ.θ, x) -# _logdensity(μ, x, indexstyle(μ.θ, x), result_type) +# _logdensity_def(μ, x, indexstyle(μ.θ, x), result_type) # end -# function _logdensity(μ::ForArray{D,N,T,F}, x, ::IndexLinear, ::Type{R}) where {R<:AbstractFloat} +# function _logdensity_def(μ::ForArray{D,N,T,F}, x, ::IndexLinear, ::Type{R}) where {R<:AbstractFloat} # ℓ = zero(R) # μ.f(μ.θ) # end diff --git a/src/combinators/half.jl b/src/combinators/half.jl index c5224021..4b843e59 100644 --- a/src/combinators/half.jl +++ b/src/combinators/half.jl @@ -23,4 +23,4 @@ function Base.rand(rng::AbstractRNG, T::Type, μ::Half) return abs(rand(rng, T, unhalf(μ))) end -logdensity(μ::Half, x) = logdensity(unhalf(μ), x) +logdensity_def(μ::Half, x) = logdensity_def(unhalf(μ), x) diff --git a/src/combinators/likelihood.jl b/src/combinators/likelihood.jl index f4b14f47..9ca93317 100644 --- a/src/combinators/likelihood.jl +++ b/src/combinators/likelihood.jl @@ -23,19 +23,19 @@ For example, julia> ℓ = Likelihood(Normal{(:μ,)}, 2.0) Likelihood(Normal{(:μ,), T} where T, 2.0) - julia> density(ℓ, (μ=2.0,)) + julia> density_def(ℓ, (μ=2.0,)) 1.0 - julia> logdensity(ℓ, (μ=2.0,)) + julia> logdensity_def(ℓ, (μ=2.0,)) -0.0 If, as above, the measure includes the parameter information, we can optionally leave it out of the second argument in the call to `density` or `logdensity`. - julia> density(ℓ, 2.0) + julia> density_def(ℓ, 2.0) 1.0 - julia> logdensity(ℓ, 2.0) + julia> logdensity_def(ℓ, 2.0) -0.0 With several parameters, things work as expected: @@ -43,13 +43,13 @@ With several parameters, things work as expected: julia> ℓ = Likelihood(Normal{(:μ,:σ)}, 2.0) Likelihood(Normal{(:μ, :σ), T} where T, 2.0) - julia> logdensity(ℓ, (μ=2, σ=3)) + julia> logdensity_def(ℓ, (μ=2, σ=3)) -1.0986122886681098 - julia> logdensity(ℓ, (2,3)) + julia> logdensity_def(ℓ, (2,3)) -1.0986122886681098 - julia> logdensity(ℓ, [2, 3]) + julia> logdensity_def(ℓ, [2, 3]) -1.0986122886681098 --------- @@ -65,16 +65,16 @@ the three-argument form, where the second argument is a constraint. For example, Similarly to the above, we have - julia> density(ℓ, (μ=2.0,)) + julia> density_def(ℓ, (μ=2.0,)) 0.3333333333333333 - julia> logdensity(ℓ, (μ=2.0,)) + julia> logdensity_def(ℓ, (μ=2.0,)) -1.0986122886681098 - julia> density(ℓ, 2.0) + julia> density_def(ℓ, 2.0) 0.3333333333333333 - julia> logdensity(ℓ, 2.0) + julia> logdensity_def(ℓ, 2.0) -1.0986122886681098 ----------------------- @@ -98,7 +98,7 @@ and we observe `x=3`. We can compute the posterior measure on `μ` as julia> post = Normal() ⊙ Likelihood(Normal{(:μ, :σ)}, (σ=1,), 3) Normal() ⊙ Likelihood(Normal{(:μ, :σ), T} where T, (σ = 1,), 3) - julia> logdensity(post, 2) + julia> logdensity_def(post, 2) -2.5 """ struct Likelihood{F,S,X} @@ -116,6 +116,6 @@ function Base.show(io::IO, ℓ::Likelihood) print(io, "Likelihood(", k, ", ", x, ")") end -@inline function logdensity(ℓ::Likelihood, p) - return logdensity(ℓ.k(p), ℓ.x) +@inline function logdensity_def(ℓ::Likelihood, p) + return logdensity_def(ℓ.k(p), ℓ.x) end diff --git a/src/combinators/mapsto.jl b/src/combinators/mapsto.jl index 9e59642a..e5e75323 100644 --- a/src/combinators/mapsto.jl +++ b/src/combinators/mapsto.jl @@ -16,7 +16,7 @@ Base.Pair(t::MapsTo) = t.x => t.y Base.show(io::IO, t::MapsTo) = print(t.x, " ↦ ", t.y) -logdensity(d, t::MapsTo) = logdensity(d, t.y) +logdensity_def(d, t::MapsTo) = logdensity_def(d, t.y) Base.iterate(m::MapsTo) = (first(m), 1) Base.iterate(m::MapsTo, ::Int) = (last(m), nothing) diff --git a/src/combinators/pointwise.jl b/src/combinators/pointwise.jl index 12f88bb1..0a0b0e97 100644 --- a/src/combinators/pointwise.jl +++ b/src/combinators/pointwise.jl @@ -27,12 +27,12 @@ Base.length(m::PointwiseProductMeasure{T}) where {T} = length(m.data) ⊙(args...) = pointwiseproduct(args...) -@inline function logdensity(d::PointwiseProductMeasure, x) - sum((logdensity(dⱼ, x) for dⱼ in d.data)) +@inline function logdensity_def(d::PointwiseProductMeasure, x) + sum((logdensity_def(dⱼ, x) for dⱼ in d.data)) end -function sampletype(d::PointwiseProductMeasure) - @inbounds sampletype(first(d.data)) +function gentype(d::PointwiseProductMeasure) + @inbounds gentype(first(d.data)) end basemeasure(d::PointwiseProductMeasure) = @inbounds basemeasure(first(d.data)) diff --git a/src/combinators/power.jl b/src/combinators/power.jl index bfd0887a..aaf2bdf1 100644 --- a/src/combinators/power.jl +++ b/src/combinators/power.jl @@ -41,16 +41,8 @@ function Base.:^(μ::M, dims::NTuple{N,I}) where {M<:AbstractMeasure,N,I<:Intege powermeasure(μ, dims) end -# Same as PowerMeasure -function Pretty.tile(d::ProductMeasure{Returns{T},I,C}) where {T,I,C<:CartesianIndices} - Pretty.pair_layout(Pretty.tile(d.f.f.value), Pretty.tile(size(d.pars)); sep = " ^ ") -end - -function Pretty.tile(d::ProductMeasure{R,I,V}) where {R<:Returns,I,V<:AbstractVector} - Pretty.pair_layout(Pretty.tile(d.f.f.value), Pretty.tile(length(d.pars)); sep = " ^ ") -end -# sampletype(d::PowerMeasure{M,N}) where {M,N} = @inbounds Array{sampletype(first(marginals(d))), N} +# gentype(d::PowerMeasure{M,N}) where {M,N} = @inbounds Array{gentype(first(marginals(d))), N} params(d::ProductMeasure{F,S,<:Fill}) where {F,S} = params(first(marginals(d))) @@ -87,7 +79,7 @@ function basemeasure_depth(::Type{P}) where {M,P<:ProductMeasure{Returns{M}}} end # Same as PowerMeasure -@inline function logdensity(d::ProductMeasure{F,S,<:Fill}, x) where {F,S} +@inline function logdensity_def(d::ProductMeasure{F,S,<:Fill}, x) where {F,S} d1 = d.f(first(d.pars)) - sum(xj -> logdensity(d1, xj), x) + sum(xj -> logdensity_def(d1, xj), x) end diff --git a/src/combinators/product.jl b/src/combinators/product.jl index 6b0959e4..679e5be0 100644 --- a/src/combinators/product.jl +++ b/src/combinators/product.jl @@ -47,12 +47,6 @@ end testvalue(d::ProductMeasure) = map(testvalue, marginals(d)) -function Pretty.tile(μ::ProductMeasure{F,S,NamedTuple{N,T}}) where {F,S,N,T} - result = Pretty.literal("Product(") - result *= Pretty.pair_layout(μ.f, μ.pars; sep = ", ") - result *= Pretty.literal(")") -end - function Base.rand(rng::AbstractRNG, ::Type{T}, d::ProductMeasure) where {T} _rand(rng, T, d, marginals(d)) end @@ -73,12 +67,7 @@ export ⊗ marginals(d::TupleProductMeasure{T}) where {F,T<:Tuple} = d.pars -function Pretty.tile(μ::TupleProductMeasure{T}) where {F,T<:Tuple} - mar = marginals(μ) - Pretty.list_layout(Pretty.Layout[Pretty.tile.(mar)...]; sep = " ⊗ ") -end - -@inline function logdensity(d::TupleProductMeasure, x::Tuple) where {T<:Tuple} +@inline function logdensity_def(d::TupleProductMeasure, x::Tuple) where {T<:Tuple} mapreduce(logdensity, +, d.pars, x) end @@ -96,27 +85,12 @@ function marginals(d::ProductMeasure{<:Returns,S,A}) where {F,S,A<:AbstractArray # mappedarray(d.f.f, d.pars) end -@inline function logdensity(d::ProductMeasure, x) +@inline function logdensity_def(d::ProductMeasure, x) mapreduce(logdensity, +, marginals(d), x) end -@inline function logdensity(d::ProductMeasure{<:Returns}, x) - sum(x -> logdensity(d.f.f.value, x), x) -end - -function Pretty.tile(d::ProductMeasure{F,S,A}) where {F,S,A} - result = Pretty.literal("For(") - result *= Pretty.pair_layout(Pretty.tile(d.f), Pretty.tile(d.pars); sep = ", ") - result *= Pretty.literal(")") -end - -############################################################################### -# I <: CartesianIndices - -function Pretty.tile(d::ProductMeasure{F,S,I}) where {F,S,I<:CartesianIndices} - result = Pretty.literal("For(") - result *= Pretty.pair_layout(Pretty.tile(d.f), Pretty.tile(size(d.pars)); sep = ", ") - result *= Pretty.literal(")") +@inline function logdensity_def(d::ProductMeasure{<:Returns}, x) + sum(x -> logdensity_def(d.f.f.value, x), x) end # function Base.rand(rng::AbstractRNG, ::Type{T}, d::ProductMeasure{F,S,I}) where {T,F,I<:CartesianIndices} @@ -129,8 +103,8 @@ end export rand! using Random: rand!, GLOBAL_RNG, AbstractRNG -@inline function logdensity(d::ProductMeasure{F,S,I}, x) where {F,S,I<:Base.Generator} - sum((logdensity(dj, xj) for (dj, xj) in zip(marginals(d), x))) +@inline function logdensity_def(d::ProductMeasure{F,S,I}, x) where {F,S,I<:Base.Generator} + sum((logdensity_def(dj, xj) for (dj, xj) in zip(marginals(d), x))) end @propagate_inbounds function Random.rand!( @@ -159,7 +133,7 @@ end # TODO: # function Base.rand(rng::AbstractRNG, d::ProductMeasure) -# return rand(rng, sampletype(d), d) +# return rand(rng, gentype(d), d) # end # function Base.rand(T::Type, d::ProductMeasure) @@ -167,20 +141,20 @@ end # end # function Base.rand(d::ProductMeasure) -# T = sampletype(d) +# T = gentype(d) # return rand(Random.GLOBAL_RNG, T, d) # end -function sampletype(d::ProductMeasure{A}) where {T,N,A<:AbstractArray{T,N}} - S = @inbounds sampletype(marginals(d)[1]) +function gentype(d::ProductMeasure{A}) where {T,N,A<:AbstractArray{T,N}} + S = @inbounds gentype(marginals(d)[1]) Array{S,N} end -function sampletype(d::ProductMeasure{<:Tuple}) - Tuple{sampletype.(marginals(d))...} +function gentype(d::ProductMeasure{<:Tuple}) + Tuple{gentype.(marginals(d))...} end -# function logdensity(μ::ProductMeasure{Aμ}, x::Ax) where {Aμ <: MappedArray, Ax <: AbstractArray} +# function logdensity_def(μ::ProductMeasure{Aμ}, x::Ax) where {Aμ <: MappedArray, Ax <: AbstractArray} # μ.data # end @@ -196,9 +170,9 @@ end # set.(marginals(d), params, p) # end -# function logdensity(μ::ProductMeasure, ν::ProductMeasure, x) +# function logdensity_def(μ::ProductMeasure, ν::ProductMeasure, x) # sum(zip(marginals(μ), marginals(ν), x)) do μ_ν_x -# logdensity(μ_ν_x...) +# logdensity_def(μ_ν_x...) # end # end diff --git a/src/combinators/restricted.jl b/src/combinators/restricted.jl index a55768f0..d0e8ba57 100644 --- a/src/combinators/restricted.jl +++ b/src/combinators/restricted.jl @@ -3,12 +3,12 @@ struct RestrictedMeasure{F,M} <: AbstractMeasure base::M end -@inline function logdensity(d::RestrictedMeasure, x) +@inline function logdensity_def(d::RestrictedMeasure, x) d.f(x) || return -Inf return 0.0 end -function density(d::RestrictedMeasure, x) +function density_def(d::RestrictedMeasure, x) d.f(x) || return 0.0 return 1.0 end diff --git a/src/combinators/spikemixture.jl b/src/combinators/spikemixture.jl index a623faab..3d6c2b43 100644 --- a/src/combinators/spikemixture.jl +++ b/src/combinators/spikemixture.jl @@ -17,18 +17,18 @@ end @inline function basemeasure(μ::SpikeMixture) # Compare formula (1.4) in Joris Bierkens, Sebastiano Grazzi, Frank van der Meulen, Moritz Schauer: # Sticky PDMP samplers for sparse and local inference problems. 2020. [https://arxiv.org/abs/2103.08478]. - ki = (1 / μ.w - 1) / density(μ.m, 0) + ki = (1 / μ.w - 1) / density_def(μ.m, 0) SpikeMixture(basemeasure(μ.m), 1 / (1 + ki), μ.s * (1 + ki)) end basemeasure_depth(::Type{SpikeMixture{T,S}}) where {T,S} = static(1) + basemeasure_depth(T) -@inline function logdensity(μ::SpikeMixture, x) - return log(μ.w) + logdensity(μ.m, x) +@inline function logdensity_def(μ::SpikeMixture, x) + return log(μ.w) + logdensity_def(μ.m, x) end -function sampletype(μ::SpikeMixture) - sampletype(μ.m) +function gentype(μ::SpikeMixture) + gentype(μ.m) end function Base.rand(rng::AbstractRNG, T::Type, μ::SpikeMixture) diff --git a/src/combinators/superpose.jl b/src/combinators/superpose.jl index 75bb135a..ae9c942c 100644 --- a/src/combinators/superpose.jl +++ b/src/combinators/superpose.jl @@ -24,12 +24,6 @@ struct SuperpositionMeasure{NT} <: AbstractMeasure components::NT end -function Pretty.tile(d::SuperpositionMeasure) - result = Pretty.literal("SuperpositionMeasure(") - result *= Pretty.list_layout([Pretty.tile.(d.components)...]) - result *= Pretty.literal(")") -end - testvalue(μ::SuperpositionMeasure) = testvalue(first(μ.components)) # SuperpositionMeasure(ms :: AbstractMeasure...) = SuperpositionMeasure{X,length(ms)}(ms) @@ -58,7 +52,7 @@ function Base.:+(μ::AbstractMeasure, ν::AbstractMeasure) superpose(components) end -logdensity(μ::SuperpositionMeasure, x) = logsumexp((logdensity(m, x) for m in μ.components)) +logdensity_def(μ::SuperpositionMeasure, x) = logsumexp((logdensity_def(m, x) for m in μ.components)) basemeasure(μ::SuperpositionMeasure) = superpose(map(basemeasure, μ.components)) diff --git a/src/combinators/weighted.jl b/src/combinators/weighted.jl index 5220fc39..fb419db2 100644 --- a/src/combinators/weighted.jl +++ b/src/combinators/weighted.jl @@ -12,8 +12,8 @@ abstract type AbstractWeightedMeasure <: AbstractMeasure end logweight(μ::AbstractWeightedMeasure) = μ.logweight basemeasure(μ::AbstractWeightedMeasure) = μ.base -@inline function logdensity(sm::AbstractWeightedMeasure, x) - logdensity(sm.base, x) + sm.logweight +@inline function logdensity_def(sm::AbstractWeightedMeasure, x) + logdensity_def(sm.base, x) + sm.logweight end ############################################################################### @@ -54,7 +54,7 @@ Base.:*(m::AbstractMeasure, k::Real) = k * m ≪(::M, ::WeightedMeasure{R,M}) where {R,M} = true ≪(::WeightedMeasure{R,M}, ::M) where {R,M} = true -sampletype(μ::WeightedMeasure) = sampletype(μ.base) +gentype(μ::WeightedMeasure) = gentype(μ.base) ############################################################################### @@ -72,4 +72,4 @@ end basemeasure(d::ParamWeightedMeasure) = d.base -logdensity(d::ParamWeightedMeasure, x) = d.ℓ(d.par) +logdensity_def(d::ParamWeightedMeasure, x) = d.ℓ(d.par) diff --git a/src/density.jl b/src/density.jl index 8c6d09bb..bfdd632d 100644 --- a/src/density.jl +++ b/src/density.jl @@ -15,29 +15,21 @@ representation to allow comptuational flexibilty. struct Density{M,B,L} μ::M base::B - log::L end -export 𝒹 - -export log𝒹 +@inline DensityKind(::Density) = IsDensity() -log𝒹(μ, base) = Density(μ, base, Val{true}()) +export 𝒹 """ - 𝒹(μ::AbstractMeasure, base::AbstractMeasure; log=false) + 𝒹(μ::AbstractMeasure, base::AbstractMeasure) -Compute the Radom-Nikodym derivative (or its log, if `log=false`) of μ with -respect to `base`. +Compute the Radom-Nikodym derivative of μ with respect to `base`. """ -function 𝒹(μ::AbstractMeasure, base::AbstractMeasure; log = false) - return Density(μ, base, Val(log)) +function 𝒹(μ::AbstractMeasure, base::AbstractMeasure) + return Density(μ, base) end -(f::Density{M,B,Val{true}})(x) where {M,B} = logdensity(f.μ, f.base, x) - -(f::Density{M,B,Val{false}})(x) where {M,B} = density(f.μ, f.base, x) - """ struct DensityMeasure{F,B} <: AbstractMeasure density :: F @@ -50,15 +42,18 @@ A `DensityMeasure` is a measure defined by a density with respect to some other struct DensityMeasure{F,B,L} <: AbstractMeasure f::F base::B - log::L end -function Pretty.tile(μ::DensityMeasure{F,B,Val{L}}) where {F,B,L} - result = Pretty.literal("DensityMeasure ∫(") - result *= Pretty.pair_layout(Pretty.tile(μ.f), Pretty.tile(μ.base); sep = ", ") - result *= Pretty.literal("; log = ") - result *= Pretty.tile(L) - result *= Pretty.literal(")") +densitymeasure(f, base) = _densitymeasure(f, base, DensityKind(f)) + +_densitymeasure(f, base, ::IsDensity) = DensityMeasure(f, base) + +function _densitymeasure(f, base, _) + @error """ + The first argument of `DensityMeasure`" must be `::IsDensity`. To pass a + function, first wrap it in `DensityInterface.funcdensity` or + `DensityInterface.logfuncdensity`. + """ end function Base.rand(rng::AbstractRNG, T::Type, d::DensityMeasure) @@ -73,11 +68,11 @@ basemeasure_depth(::DensityMeasure{F,B,L}) where {F,B,L} = static(1) + basemeasu basemeasure_depth(::Type{DensityMeasure{F,B,L}}) where {F,B,L} = static(1) + basemeasure_depth(B) -logdensity(μ::DensityMeasure{F,B,Val{true}}, x) where {F,B} = μ.f(x) +logdensity_def(μ::DensityMeasure{F,B,Val{true}}, x) where {F,B} = μ.f(x) -density(μ::DensityMeasure{F,B,Val{false}}, x) where {F,B} = μ.f(x) +density_def(μ::DensityMeasure{F,B,Val{false}}, x) where {F,B} = μ.f(x) -logdensity(μ::DensityMeasure{F,B,Val{false}}, x) where {F,B} = log(density(μ, x)) +logdensity_def(μ::DensityMeasure{F,B,Val{false}}, x) where {F,B} = log(density_def(μ, x)) export ∫ @@ -101,12 +96,12 @@ Define a new measure in terms of a density `f` over some measure `base`. # TODO: `density` and `logdensity` functions for `DensityMeasure` -@inline function logdensity(μ::T, ν::T, x) where {T<:AbstractMeasure} +@inline function logdensity_def(μ::T, ν::T, x) where {T<:AbstractMeasure} μ == ν && return 0.0 invoke(logdensity, Tuple{AbstractMeasure,AbstractMeasure,typeof(x)}, μ, ν, x) end -@inline function logdensity(μ::AbstractMeasure, ν::AbstractMeasure, x) +@inline function logdensity_def(μ::AbstractMeasure, ν::AbstractMeasure, x) α = basemeasure(μ) β = basemeasure(ν) @@ -114,12 +109,12 @@ end # original one. We need to break the recursion. if α === μ && β === ν @warn """ - No method found for logdensity(μ, ν, x) where + No method found for logdensity_def(μ, ν, x) where typeof(μ) == $(typeof(μ)) typeof(ν) == $(typeof(ν)) Returning NaN. If this is incorrect, please add a method - logdensity(μ::$(typeof(μ)), ν::$(typeof(ν)), x) + logdensity_def(μ::$(typeof(μ)), ν::$(typeof(ν)), x) """ return NaN end @@ -129,22 +124,22 @@ end # measures first is often much cheaper, and allows the numerically-intensive # computation to "fall through" in these cases. # TODO: Add tests to check that NaN cases work properly - ℓ = logdensity(α, β, x) + ℓ = logdensity_def(α, β, x) isnan(ℓ) && return ℓ - ℓ += logdensity(μ, x) - ℓ -= logdensity(ν, x) + ℓ += logdensity_def(μ, x) + ℓ -= logdensity_def(ν, x) return ℓ end -@inline function logpdf(μ, x) +@inline function logdensityof(μ, x) n = basemeasure_depth(μ) (ℓ, β, y) = logdensity_tuple(μ, x) - return _logpdf(β, y, ℓ, n) + return _logdensityof(β, y, ℓ, n) end -@generated function _logpdf(μ, x, ℓ, ::StaticInt{n}) where {n} +@generated function _logdensityof(μ, x, ℓ, ::StaticInt{n}) where {n} quote $(Expr(:meta, :inline)) Base.Cartesian.@nexprs $n i -> begin @@ -155,10 +150,10 @@ end end end -# logdensity(::Lebesgue{ℝ}, ::Lebesgue{ℝ}, x) = zero(x) +# logdensity_def(::Lebesgue{ℝ}, ::Lebesgue{ℝ}, x) = zero(x) export density -density(μ, ν::AbstractMeasure, x) = exp(logdensity(μ, ν, x)) +density_def(μ, ν::AbstractMeasure, x) = exp(logdensity_def(μ, ν, x)) -density(μ, x) = exp(logdensity(μ, x)) +density_def(μ, x) = exp(logdensity_def(μ, x)) diff --git a/src/domains.jl b/src/domains.jl index 41ec4c2c..1c011154 100644 --- a/src/domains.jl +++ b/src/domains.jl @@ -26,7 +26,7 @@ macro domain(name, T) struct $T <: AbstractDomain end export $name const $name = $T() - Pretty.tile(::$T) = Pretty.literal($sname) + Base.show(io::IO, ::$T) = Pretty.literal($sname) end end @@ -63,3 +63,50 @@ testvalue(::IntegerRange{lo,hi}) where {lo,hi} = lo # Real intervals struct RealInterval{lo,hi} <: AbstractDomain end + + +struct Simplex{D} <: AbstractDomain + dim::D # dimensionality as a manifold +end + +projectto!(x, ::Simplex) = normalize!(x, 1) + +struct Sphere{D} <: AbstractDomain + dim::D # dimensionality as a manifold +end + + +projectto!(x, ::Sphere) = normalize!(x, 2) +struct ZeroSet{F, G} <: AbstractDomain + f::F + ∇f::G +end + +function zeroset(::Simplex) + f(x::AbstractVector{T}) where {T} = sum(x) - one(T) + ∇f(x::AbstractVector{T}) where {T} = Fill(one(T), axes(x)) + ZeroSet(f, ∇f) +end + +function zeroset(::Sphere) + f(x::AbstractVector{T}) where {T} = (sum(xⱼ -> xⱼ^2, x) - one(T)) / 2 + ∇f(x::AbstractVector{T}) where {T} = x + ZeroSet(f, ∇f) +end + +struct LebesgueCodimOne{D,T,O} <: AbstractMeasure + ndims ::D + ortho ::O +end + +function logdensityof(d::Density{L1, L2}, x) where {L1<:LebesgueCodimOne, L2<:LebesgueCodimOne} + μ = d.μ + ν = d.base + μ.ndims == ν.ndims || return NaN + rank([μ.ortho ν.ortho]) == 1 || return NaN + return 0.0 +end + +struct LebesgueSimplex <: AbstractMeasure end + +basemeasure(::LebesgueSimplex, x) \ No newline at end of file diff --git a/src/kernel.jl b/src/kernel.jl index a940f3c3..67bc5129 100644 --- a/src/kernel.jl +++ b/src/kernel.jl @@ -11,12 +11,6 @@ struct Kernel{F,S} <: AbstractKernel Kernel(f::F, ops::S) where {F,S} = new{F,S}(f, ops) end -function Pretty.quoteof(k::Kernel) - qf = Pretty.quoteof(k.f) - qops = Pretty.quoteof(k.ops) - :(Kernel($qf, $qops)) -end - """ kernel(f, M) kernel((f1, f2, ...), M) diff --git a/src/macros.jl b/src/macros.jl index e54f6236..e69de29b 100644 --- a/src/macros.jl +++ b/src/macros.jl @@ -1,160 +0,0 @@ - -using MLStyle -using Random: AbstractRNG -using KeywordCalls -using ConstructionBase -export @parameterized, @half - -# A fold over ASTs. Example usage in `replace` -function foldast(leaf, branch; kwargs...) - function go(ast) - MLStyle.@match ast begin - Expr(head, args...) => branch(head, map(go, args); kwargs...) - x => leaf(x; kwargs...) - end - end - - return go -end - -function replace(p, f, expr) - leaf(s) = p(s) ? f(s) : s - branch(head, newargs) = Expr(head, newargs...) - foldast(leaf, branch)(expr) -end - -# from https://thautwarm.github.io/MLStyle.jl/latest/tutorials/capture.html -function capture(template, ex, action) - let template = Expr(:quote, template) - quote - @match $ex begin - $template => $action - _ => nothing - end - end - end -end - -macro capture(template, ex, action) - capture(template, ex, action) |> esc -end - -function _parameterized(__module__, expr) - @capture ($op($μ($(p...)), $base)) expr begin - @assert op ∈ [:<<, :≪, :≃] - μbase = Symbol(:__, μ, :_base) - - μ = esc(μ) - base = esc(base) - - # @gensym basename - q = quote - struct $μ{N,T} <: MeasureBase.ParameterizedMeasure{N} - par::NamedTuple{N,T} - end - - const $μbase = $base - MeasureBase.basemeasure(::$μ) = $μbase - end - - if !isempty(p) - # e.g. Normal(μ,σ) = Normal((μ=μ, σ=σ)) - pnames = QuoteNode.(p) - push!(q.args, :($μ($(p...)) = $μ(NamedTuple{($(pnames...),)}(($(p...),))))) - end - - return q - end - - @capture $μ($(p...)) expr begin - μ = esc(μ) - - q = quote - struct $μ{N,T} <: MeasureBase.ParameterizedMeasure{N} - par::NamedTuple{N,T} - end - end - - if !isempty(p) - # e.g. Normal(μ,σ) = Normal((μ=μ, σ=σ)) - pnames = QuoteNode.(p) - push!(q.args, :($μ($(p...)) = $μ(NamedTuple{($(pnames...),)}(($(p...),))))) - end - - return q - end - - @capture $μ($(p...)) expr begin - μ = esc(μ) - - q = quote - struct $μ{N,T} <: MeasureBase.ParameterizedMeasure{N} - par::NamedTuple{N,T} - end - end - - if !isempty(p) - # e.g. Normal(μ,σ) = Normal((μ=μ, σ=σ)) - pnames = QuoteNode.(p) - push!(q.args, :($μ($(p...)) = $μ(NamedTuple{($(pnames...),)}(($(p...),))))) - end - - return q - end -end - -""" - @parameterized - -The gives a measure and its default parameters, and specifies -its relation to its base measure. For example, - - @parameterized Normal(μ,σ) - -declares the `Normal` is a measure with default parameters `μ and σ`. The result is equivalent to -``` -struct Normal{N,T} <: ParameterizedMeasure{N} - par :: NamedTuple{N,T} -end - -KeywordCalls.@kwstruct Normal(μ,σ) - -Normal(μ,σ) = Normal((μ=μ, σ=σ)) -``` - -See [KeywordCalls.jl](https://github.com/cscherrer/KeywordCalls.jl) for details on `@kwstruct`. -""" -macro parameterized(expr) - _parameterized(__module__, expr) -end - -""" - @half dist([paramnames]) - -Starting from a symmetric univariate measure `dist ≪ Lebesgue(ℝ)`, create a new -measure `Halfdist ≪ Lebesgue(ℝ₊)`. For example, - - @half Normal() - -creates `HalfNormal()`, and - - @half StudentT(ν) - -creates `HalfStudentT(ν)`. -""" -macro half(ex) - _half(__module__, ex) -end - -function _half(__module__, ex) - @match ex begin - :($dist) => begin - halfdist = esc(Symbol(:Half, dist)) - dist = esc(dist) - quote - $halfdist(args...) = half($dist(args...)) - $halfdist(; kwargs...) = half($dist(; kwargs...)) - end - end - end -end diff --git a/src/modified_gram_schmitt.jl b/src/modified_gram_schmitt.jl new file mode 100644 index 00000000..2adcdf72 --- /dev/null +++ b/src/modified_gram_schmitt.jl @@ -0,0 +1,85 @@ +using LinearAlgebra + +# Modify column jᵥ to be orthogonal to column jᵤ +function ortho!(A::AbstractMatrix, jᵥ, jᵤ; startat=1) + # v ← v - projᵤ(v) + nrows = size(A,1) + u_v = 0.0 + u_u = 0.0 + @inbounds for i in startat:nrows + u_v += A[i,jᵤ] * A[i,jᵥ] + u_u += A[i,jᵤ] ^ 2 + end + + k = u_v / u_u + + @inbounds for i in startat:nrows + A[i, jᵥ] = A[i, jᵥ] - k * A[i, jᵤ] + end + + return A +end + +function ortho!(A::AbstractMatrix, triangular=false) + for j2 in size(A,2):-1:1 + for j1 in 1:(j2-1) + ortho!(A, j1, j2) + end + end + + for col in eachcol(A) + normalize!(col) + end + + return A +end + +function makelower!(A) + for jᵥ in 2:size(A,2) + @inbounds for jᵤ in 1:(jᵥ-1) + k = A[jᵤ, jᵥ] / A[jᵤ, jᵤ] + + A[jᵤ,jᵥ] = 0.0 + + @inbounds for i in (jᵤ+1):size(A,1) + A[i,jᵥ] = A[i, jᵥ] - k * A[i, jᵤ] + end + end + end + + for j in 1:size(A,2) + @inbounds if A[j,j] < 0.0 + view(A, :, j) .*= -1 + end + end + + return A + +end + + + + +function WtoV(W) + # make columns orthogonal + for j2 in size(W,2):-1:1 + for j1 in 1:(j2-1) + ortho!(W, j1, j2; startat=j2) + end + end + + for col in eachcol(W) + normalize!(col) + end + + return W +end + +W = [I; randn(5,5) ./ randn(5,5)] + +using BenchmarkTools +@btime WtoV(W) + + + +W' * W \ No newline at end of file diff --git a/src/primitive.jl b/src/primitive.jl index 5e1a5b84..a8f679a5 100644 --- a/src/primitive.jl +++ b/src/primitive.jl @@ -9,14 +9,14 @@ measures satisfy the following laws: basemeasure(μ::PrimitiveMeasure) = μ - logdensity(μ::PrimitiveMeasure, x) = 0.0 + logdensity_def(μ::PrimitiveMeasure, x) = 0.0 - logdensity(μ::M, ν::M, x) where {M<:PrimitiveMeasure} = 0.0 + logdensity_def(μ::M, ν::M, x) where {M<:PrimitiveMeasure} = 0.0 """ abstract type PrimitiveMeasure <: AbstractMeasure end basemeasure(μ::PrimitiveMeasure) = μ -logdensity(μ::PrimitiveMeasure, x) = 0.0 +logdensity_def(μ::PrimitiveMeasure, x) = 0.0 -logdensity(μ::M, ν::M, x) where {M<:PrimitiveMeasure} = 0.0 +logdensity_def(μ::M, ν::M, x) where {M<:PrimitiveMeasure} = 0.0 diff --git a/src/primitives/counting.jl b/src/primitives/counting.jl index 502c9689..769abb07 100644 --- a/src/primitives/counting.jl +++ b/src/primitives/counting.jl @@ -9,14 +9,14 @@ end CountingMeasure(X) = CountingMeasure{X}() -# sampletype(::CountingMeasure{ℝ}) = Float64 -# sampletype(::CountingMeasure{ℝ₊}) = Float64 -# sampletype(::CountingMeasure{𝕀}) = Float64 +# gentype(::CountingMeasure{ℝ}) = Float64 +# gentype(::CountingMeasure{ℝ₊}) = Float64 +# gentype(::CountingMeasure{𝕀}) = Float64 -sampletype(::CountingMeasure) = Int +gentype(::CountingMeasure) = Int testvalue(μ::CountingMeasure{X}) where {X} = testvalue(X) -logdensity(::CountingMeasure, x) = zero(float(x)) +logdensity_def(::CountingMeasure, x) = zero(float(x)) # (::CountingMeaure)(s) = length(Set(s)) diff --git a/src/primitives/dirac.jl b/src/primitives/dirac.jl index d6091b47..80cd4a93 100644 --- a/src/primitives/dirac.jl +++ b/src/primitives/dirac.jl @@ -5,21 +5,16 @@ struct Dirac{X} <: PrimitiveMeasure x::X end -function Pretty.quoteof(d::Dirac) - q = Pretty.quoteof(d.x) - :(Dirac($q)) -end - -sampletype(μ::Dirac{X}) where {X} = X +gentype(μ::Dirac{X}) where {X} = X function (μ::Dirac{X})(s) where {X} μ.x ∈ s && return 1 return 0 end -density(μ::Dirac, x) = x == μ.x +density_def(μ::Dirac, x) = x == μ.x -logdensity(μ::Dirac, x) = (x == μ.x) ? 0.0 : -Inf +logdensity_def(μ::Dirac, x) = (x == μ.x) ? 0.0 : -Inf Base.rand(::Random.AbstractRNG, T::Type, μ::Dirac) = μ.x @@ -27,8 +22,8 @@ export dirac dirac(d::AbstractMeasure) = Dirac(rand(d)) -@inline function logdensity(μ::Dirac{M}, ν::Dirac{M}, x) where {M} - logdensity(μ, x) - logdensity(ν, x) +@inline function logdensity_def(μ::Dirac{M}, ν::Dirac{M}, x) where {M} + logdensity_def(μ, x) - logdensity_def(ν, x) end testvalue(d::Dirac) = d.x diff --git a/src/primitives/lebesgue.jl b/src/primitives/lebesgue.jl index a866413c..a11f6ad5 100644 --- a/src/primitives/lebesgue.jl +++ b/src/primitives/lebesgue.jl @@ -4,12 +4,6 @@ export Lebesgue struct Lebesgue{X} <: PrimitiveMeasure end -function Pretty.tile(::Lebesgue{X}) where {X} - result = Pretty.literal("Lebesgue(") - result *= Pretty.tile(X) - result *= Pretty.literal(")") -end - Lebesgue(X) = Lebesgue{X}() sampletype(::Lebesgue{ℝ}) = Float64 @@ -21,6 +15,6 @@ testvalue(::Lebesgue{𝕀}) = 0.5 testvalue(::Lebesgue{ℝ₊}) = 1.0 testvalue(::Lebesgue{<:Real}) = 0.0 -logdensity(::Lebesgue, x) = zero(x) +logdensity_def(::Lebesgue, x) = zero(x) Base.:∘(::typeof(basemeasure), ::Type{Lebesgue}) = Lebesgue diff --git a/src/primitives/trivial.jl b/src/primitives/trivial.jl index 5e4ec260..48165254 100644 --- a/src/primitives/trivial.jl +++ b/src/primitives/trivial.jl @@ -2,6 +2,4 @@ export TrivialMeasure struct TrivialMeasure <: PrimitiveMeasure end -sampletype(::TrivialMeasure) = Nothing - -Pretty.quoteof(::TrivialMeasure) = :(TrivialMeasure()) +gentype(::TrivialMeasure) = Nothing diff --git a/src/thunks.jl b/src/thunks.jl index b56f757d..1d88420c 100644 --- a/src/thunks.jl +++ b/src/thunks.jl @@ -19,7 +19,7 @@ # reduce_step(LogdensityThunk{M,B,X,L}, callback=Returns(nothing)) -> Union{LogdensityThunk, L} -# function logdensity(μ, b, x; cb=Returns(nothing)) +# function logdensity_def(μ, b, x; cb=Returns(nothing)) # f(thunk) = reduce_step(thunk, cb) # fix(f, LogdensityThunk(μ, b, x, zero(Float64))) # end diff --git a/src/utils.jl b/src/utils.jl index fd123a2a..c4f90690 100644 --- a/src/utils.jl +++ b/src/utils.jl @@ -1,10 +1,5 @@ const EmptyNamedTuple = NamedTuple{(),Tuple{}} -function Base.show(io::IO, μ::AbstractMeasure) - io = IOContext(io, :compact => true) - Pretty.pprint(io, μ) -end - showparams(io::IO, ::EmptyNamedTuple) = print(io, "()") showparams(io::IO, nt::NamedTuple) = print(io, nt) @@ -64,8 +59,6 @@ functioninstance(::Type{F}) where {F<:Function} = F.instance @inline instance_type(f::F) where {F<:Function} = F @inline instance_type(f::UnionAll) = Type{f} -using MLStyle - export basemeasure_depth @inline function basemeasure_depth(μ::M) where {M<:AbstractMeasure} @@ -85,9 +78,9 @@ end export logdensity_tuple function logdensity_tuple(d, x) - return (logdensity(d, x), basemeasure(d, x), x) + return (logdensity_def(d, x), basemeasure(d, x), x) end function logdensity_tuple(d, (z, x)::MapsTo) - return (logdensity(d, x), basemeasure(d, x), z ↦ x) + return (logdensity_def(d, x), basemeasure(d, x), z ↦ x) end diff --git a/test/runtests.jl b/test/runtests.jl index 9f9707a6..3ef8d4ae 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -4,7 +4,7 @@ using Random using LinearAlgebra using MeasureBase -using MeasureBase: logpdf +using MeasureBase: logdensityof using Aqua Aqua.test_all(MeasureBase; ambiguities = false, unbound_args = false) @@ -15,16 +15,16 @@ d = ∫exp(x -> -x^2, Lebesgue(ℝ)) # @eval using JETTest # @eval begin -# @test_nodispatch density(Lebesgue(ℝ), 0.3) +# @test_nodispatch density_def(Lebesgue(ℝ), 0.3) -# @test_nodispatch density(Dirac(0), 0.3) -# @test_nodispatch density(Dirac(0), 0) +# @test_nodispatch density_def(Dirac(0), 0.3) +# @test_nodispatch density_def(Dirac(0), 0) -# @test_nodispatch density(d, 3) +# @test_nodispatch density_def(d, 3) # @test_nodispatch basemeasure(d) -# @test_nodispatch logdensity(For(3) do j Dirac(j) end, [1,2,3]) +# @test_nodispatch logdensity_def(For(3) do j Dirac(j) end, [1,2,3]) # end # end @@ -38,7 +38,7 @@ d = ∫exp(x -> -x^2, Lebesgue(ℝ)) # end function test_testvalue(μ) - logdensity(μ, testvalue(μ)) isa AbstractFloat + logdensity_def(μ, testvalue(μ)) isa AbstractFloat end test_measures = [ @@ -91,14 +91,14 @@ end m = SpikeMixture(d, w) bm = basemeasure(m) @test (bm.s * bm.w) * bm.m == 1.0 * basemeasure(d) - @test density(m, 1.0) * (bm.s * bm.w) ≈ w * density(d, 1.0) - @test density(m, 0) * (bm.s * (1 - bm.w)) ≈ (1 - w) + @test density_def(m, 1.0) * (bm.s * bm.w) ≈ w * density_def(d, 1.0) + @test density_def(m, 0) * (bm.s * (1 - bm.w)) ≈ (1 - w) end @testset "Dirac" begin @test rand(Dirac(0.2)) == 0.2 - @test logdensity(Dirac(0.3), 0.3) == 0.0 - @test logdensity(Dirac(0.3), 0.4) == -Inf + @test logdensity_def(Dirac(0.3), 0.3) == 0.0 + @test logdensity_def(Dirac(0.3), 0.4) == -Inf end @testset "AffineTransform" begin @@ -134,7 +134,7 @@ end for f in [f1, f2, f3, f4, f5] par = getfield(f, :par) @test Affine(par)(unif) == Affine(f, unif) - @test density(Affine(f, Affine(inv(f), unif)), 0.5) == 1 + @test density_def(Affine(f, Affine(inv(f), unif)), 0.5) == 1 end d = ∫exp(x -> -x^2, Lebesgue(ℝ)) @@ -145,21 +145,21 @@ end x = randn(3) - @test logdensity(Affine((μ = μ, σ = σ), d^3), x) ≈ - logdensity(Affine((μ = μ, ω = ω), d^3), x) - @test logdensity(Affine((σ = σ,), d^3), x) ≈ logdensity(Affine((ω = ω,), d^3), x) - @test logdensity(Affine((μ = μ,), d^3), x) ≈ logdensity(d^3, x - μ) + @test logdensity_def(Affine((μ = μ, σ = σ), d^3), x) ≈ + logdensity_def(Affine((μ = μ, ω = ω), d^3), x) + @test logdensity_def(Affine((σ = σ,), d^3), x) ≈ logdensity_def(Affine((ω = ω,), d^3), x) + @test logdensity_def(Affine((μ = μ,), d^3), x) ≈ logdensity_def(d^3, x - μ) d = ∫exp(x -> -x^2, Lebesgue(ℝ)) a = Affine((σ = [1 0]',), d^1) x = randn(2) y = randn(1) - @test logpdf(a, x) ≈ logpdf(d, inv(a.f)(x)[1]) - @test logpdf(a, a.f(y)) ≈ logpdf(d^1, y) + @test logdensityof(a, x) ≈ logdensityof(d, inv(a.f)(x)[1]) + @test logdensityof(a, a.f(y)) ≈ logdensityof(d^1, y) b = Affine((ω = [1 0]'',), d^1) - @test logpdf(b, x) ≈ logpdf(d, inv(b.f)(x)[1]) - @test logpdf(b, b.f(y)) ≈ logpdf(d^1, y) + @test logdensityof(b, x) ≈ logdensityof(d, inv(b.f)(x)[1]) + @test logdensityof(b, b.f(y)) ≈ logdensityof(d^1, y) end @testset "For" begin @@ -183,16 +183,16 @@ end for d in FORDISTS @info "testing $d" - @test logdensity(d, rand(d)) isa Float64 + @test logdensity_def(d, rand(d)) isa Float64 end end @testset "Half" begin Normal() = ∫exp(x -> -0.5x^2, Lebesgue(ℝ)) @half Normal - @test logdensity(HalfNormal(), Lebesgue(ℝ), -0.2) == -Inf - @test logdensity(HalfNormal(), 0.2) == logdensity(Normal(), 0.2) - @test density(HalfNormal(), Lebesgue(ℝ), 0.2) ≈ 2 * density(Normal(), Lebesgue(ℝ), 0.2) + @test logdensity_def(HalfNormal(), Lebesgue(ℝ), -0.2) == -Inf + @test logdensity_def(HalfNormal(), 0.2) == logdensity_def(Normal(), 0.2) + @test density_def(HalfNormal(), Lebesgue(ℝ), 0.2) ≈ 2 * density_def(Normal(), Lebesgue(ℝ), 0.2) end # import MeasureBase.:⋅ @@ -220,7 +220,7 @@ end # for (d,p) in dps # for ℓ in ℓs -# @test logdensity(d ⊙ ℓ, p) == logdensity(d, p) + logdensity(ℓ, p) +# @test logdensity_def(d ⊙ ℓ, p) == logdensity_def(d, p) + logdensity_def(ℓ, p) # end # end # end @@ -256,7 +256,7 @@ end # @testset "Density measures and Radon-Nikodym" begin # x = randn() # let d = ∫(𝒹(Cauchy(), Normal()), Normal()) -# @test logdensity(d, x) ≈ logdensity(Cauchy(), x) +# @test logdensity_def(d, x) ≈ logdensity_def(Cauchy(), x) # end # let f = 𝒹(∫(x -> x^2, Normal()), Normal()) @@ -264,7 +264,7 @@ end # end # let d = ∫exp(log𝒹(Cauchy(), Normal()), Normal()) -# @test logdensity(d, x) ≈ logdensity(Cauchy(), x) +# @test logdensity_def(d, x) ≈ logdensity_def(Cauchy(), x) # end # let f = log𝒹(∫exp(x -> x^2, Normal()), Normal()) From 26aa0b95dff98e93ff95c180d596178e459f9e79 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 23 Nov 2021 06:54:45 -0800 Subject: [PATCH 020/368] updating densities to DensityInterface approach --- src/density.jl | 21 +++++++-------------- 1 file changed, 7 insertions(+), 14 deletions(-) diff --git a/src/density.jl b/src/density.jl index bfdd632d..dfc10f47 100644 --- a/src/density.jl +++ b/src/density.jl @@ -56,11 +56,6 @@ function _densitymeasure(f, base, _) """ end -function Base.rand(rng::AbstractRNG, T::Type, d::DensityMeasure) - x = rand(rng, T, d.base) - WeightedMeasure(d.f(x), Dirac(x)) -end - basemeasure(μ::DensityMeasure) = μ.base basemeasure_depth(::DensityMeasure{F,B,L}) where {F,B,L} = static(1) + basemeasure_depth(B) @@ -68,11 +63,9 @@ basemeasure_depth(::DensityMeasure{F,B,L}) where {F,B,L} = static(1) + basemeasu basemeasure_depth(::Type{DensityMeasure{F,B,L}}) where {F,B,L} = static(1) + basemeasure_depth(B) -logdensity_def(μ::DensityMeasure{F,B,Val{true}}, x) where {F,B} = μ.f(x) +logdensity_def(μ::DensityMeasure, x) = logdensityof(μ.f, x) -density_def(μ::DensityMeasure{F,B,Val{false}}, x) where {F,B} = μ.f(x) - -logdensity_def(μ::DensityMeasure{F,B,Val{false}}, x) where {F,B} = log(density_def(μ, x)) +density_def(μ::DensityMeasure, x) = densityof(μ.f, x) export ∫ @@ -81,18 +74,18 @@ export ∫ Define a new measure in terms of a density `f` over some measure `base`. """ -∫(f, base::AbstractMeasure) = DensityMeasure(f, base, Val(false)) +∫(f, base::AbstractMeasure) = DensityMeasure(funcdensity(f), base) -∫(μ::AbstractMeasure, base::AbstractMeasure) = ∫exp(log𝒹(μ, base), base) +# ∫(μ::AbstractMeasure, base::AbstractMeasure) = ∫(𝒹(μ, base), base) export ∫exp """ - ∫exp(f, base::AbstractMeasure; log=false) + ∫exp(f, base::AbstractMeasure) -Define a new measure in terms of a density `f` over some measure `base`. +Define a new measure in terms of a log-density `f` over some measure `base`. """ -∫exp(f, μ) = DensityMeasure(f, μ, Val{true}()) +∫exp(f, μ) = ∫(logfuncdensity(f), μ) # TODO: `density` and `logdensity` functions for `DensityMeasure` From 3a5cc8b0ac566e5d15a25dfc0ccc5fcd2fdbac86 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 23 Nov 2021 13:58:19 -0800 Subject: [PATCH 021/368] update domains --- src/domains.jl | 47 ++++++++++++++++++++++++----------------------- 1 file changed, 24 insertions(+), 23 deletions(-) diff --git a/src/domains.jl b/src/domains.jl index 1c011154..73461d68 100644 --- a/src/domains.jl +++ b/src/domains.jl @@ -2,41 +2,42 @@ export IntegerRange abstract type AbstractDomain end -""" - @domain(name, T) +struct RealBounds{L,U} <: AbstractDomain + lower :: L + upper :: U +end + +Base.in(x, b::RealBounds) = b.lower ≤ x ≤ b.upper + -Defines a new singleton struct `T`, and a value `name` for building values of -that type. +const ℝ = RealBounds(static(-Inf), static(Inf)) -For example, `@domain ℝ RealNumbers` is equivalent to +const ℝ₊ = RealBounds(static(0.0), static(Inf)) - struct RealNumbers <: AbstractDomain end +const 𝕀 = RealBounds(static(0.0), static(1.0)) - export ℝ +Base.minimum(b::RealBounds) = b.lower +Base.maximum(b::RealBounds) = b.upper - ℝ = RealNumbers() +Base.show(io::IO, ::typeof(ℝ)) = print(io, "ℝ") +Base.show(io::IO, ::typeof(ℝ₊)) = print(io, "ℝ₊") +Base.show(io::IO, ::typeof(𝕀)) = print(io, "𝕀") - Base.show(io::IO, ::RealNumbers) = print(io, "ℝ") -""" -macro domain(name, T) - sname = String(name) +testvalue(::typeof(ℝ)) = 0.0 +testvalue(::typeof(ℝ₊)) = 1.0 +testvalue(::typeof(𝕀)) = 0.5 - name = esc(name) - quote - struct $T <: AbstractDomain end - export $name - const $name = $T() - Base.show(io::IO, ::$T) = Pretty.literal($sname) - end +struct IntegerBounds{L,U} <: AbstractDomain + lower :: L + upper :: U end -@domain ℝ RealNumbers +Base.in(x, b::IntegerBounds) = b.lower ≤ x ≤ b.upper -@domain ℝ₊ PositiveReals +const ℤ = IntegerBounds(static(-Inf), static(Inf)) -@domain 𝕀 UnitInterval +Base.show(io::IO, ::typeof(ℤ)) = print(io, "ℤ") -@domain ℤ Integers ########################################################### # Integer ranges From cbf40d102f65734af18c91e8e016660e31709576 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 23 Nov 2021 15:38:35 -0800 Subject: [PATCH 022/368] moving things around --- Project.toml | 3 +-- src/MeasureBase.jl | 2 +- src/domains.jl | 15 --------------- src/primitives/lebesgue.jl | 22 +++++++++++++++++++--- 4 files changed, 21 insertions(+), 21 deletions(-) diff --git a/Project.toml b/Project.toml index 97c63877..c9bf24fb 100644 --- a/Project.toml +++ b/Project.toml @@ -22,9 +22,8 @@ FillArrays = "0.12" KeywordCalls = "0.2" LogExpFunctions = "0.3" MappedArrays = "0.4" -PrettyPrinting = "0.3" -Tricks = "0.1" Static = "0.4" +Tricks = "0.1" julia = "1.3" [extras] diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index ff5ce71d..bd1310e2 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -64,6 +64,7 @@ include("domains.jl") include("primitive.jl") include("utils.jl") include("absolutecontinuity.jl") +include("density.jl") include("primitives/counting.jl") include("primitives/lebesgue.jl") @@ -85,6 +86,5 @@ include("combinators/smart-constructors.jl") include("rand.jl") -include("density.jl") end diff --git a/src/domains.jl b/src/domains.jl index 02fae5ec..591af940 100644 --- a/src/domains.jl +++ b/src/domains.jl @@ -94,19 +94,4 @@ function zeroset(::Sphere) ZeroSet(f, ∇f) end -struct LebesgueCodimOne{D,T,O} <: AbstractMeasure - ndims ::D - ortho ::O -end - -function logdensityof(d::Density{L1, L2}, x) where {L1<:LebesgueCodimOne, L2<:LebesgueCodimOne} - μ = d.μ - ν = d.base - μ.ndims == ν.ndims || return NaN - rank([μ.ortho ν.ortho]) == 1 || return NaN - return 0.0 -end - -struct LebesgueSimplex <: AbstractMeasure end -basemeasure(::LebesgueSimplex, x) diff --git a/src/primitives/lebesgue.jl b/src/primitives/lebesgue.jl index a11f6ad5..36ddb200 100644 --- a/src/primitives/lebesgue.jl +++ b/src/primitives/lebesgue.jl @@ -6,9 +6,9 @@ struct Lebesgue{X} <: PrimitiveMeasure end Lebesgue(X) = Lebesgue{X}() -sampletype(::Lebesgue{ℝ}) = Float64 -sampletype(::Lebesgue{ℝ₊}) = Float64 -sampletype(::Lebesgue{𝕀}) = Float64 +gentype(::Lebesgue{ℝ}) = Float64 +gentype(::Lebesgue{ℝ₊}) = Float64 +gentype(::Lebesgue{𝕀}) = Float64 testvalue(::Lebesgue{ℝ}) = 0.0 testvalue(::Lebesgue{𝕀}) = 0.5 @@ -18,3 +18,19 @@ testvalue(::Lebesgue{<:Real}) = 0.0 logdensity_def(::Lebesgue, x) = zero(x) Base.:∘(::typeof(basemeasure), ::Type{Lebesgue}) = Lebesgue + + +struct LebesgueCodimOne{D,T,O} <: AbstractMeasure + ndims ::D + ortho ::O +end + +function logdensityof(d::Density{L1, L2}, x) where {L1<:LebesgueCodimOne, L2<:LebesgueCodimOne} + μ = d.μ + ν = d.base + μ.ndims == ν.ndims || return NaN + rank([μ.ortho ν.ortho]) == 1 || return NaN + return 0.0 +end + +struct LebesgueSimplex <: AbstractMeasure end From 5491ba70501214d9a813eda32a1b09635e118aba Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 24 Nov 2021 13:53:52 -0800 Subject: [PATCH 023/368] updates to IntegerBounds --- src/domains.jl | 29 ++++++++++++----------------- 1 file changed, 12 insertions(+), 17 deletions(-) diff --git a/src/domains.jl b/src/domains.jl index 73461d68..9918cd7c 100644 --- a/src/domains.jl +++ b/src/domains.jl @@ -32,39 +32,34 @@ struct IntegerBounds{L,U} <: AbstractDomain upper :: U end -Base.in(x, b::IntegerBounds) = b.lower ≤ x ≤ b.upper +Base.in(x, b::IntegerBounds) = isinteger(x) && b.lower ≤ x ≤ b.upper const ℤ = IntegerBounds(static(-Inf), static(Inf)) Base.show(io::IO, ::typeof(ℤ)) = print(io, "ℤ") +Base.minimum(::IntegerBounds{lo,hi}) where {lo,hi} = lo +Base.maximum(::IntegerBounds{lo,hi}) where {lo,hi} = hi -########################################################### -# Integer ranges - -struct IntegerRange{lo,hi} <: AbstractDomain end +function Base.show(io::IO, b::IntegerBounds) + io = IOContext(io, :compact => true) + print(io, "ℤ[", b.lower, ":", b.upper, "]") +end -Base.minimum(::IntegerRange{lo,hi}) where {lo,hi} = lo -Base.maximum(::IntegerRange{lo,hi}) where {lo,hi} = hi +testvalue(::IntegerBounds) = min(b.lower, 0) Base.iterate(r::IntegerRange{lo,hi}) where {lo,hi} = iterate(lo:hi) -function Base.getindex(::Integers, r::AbstractUnitRange) - IntegerRange{minimum(r),maximum(r)}() +function Base.getindex(::typeof(ℤ), r::AbstractUnitRange) + IntegerBounds(extrema(r)...) end -function Base.show(io::IO, r::IntegerRange{lo,hi}) where {lo,hi} - io = IOContext(io, :compact => true) - print(io, "ℤ[", lo, ":", hi, "]") -end -testvalue(::IntegerRange{lo,hi}) where {lo,hi} = lo -########################################################### -# Real intervals -struct RealInterval{lo,hi} <: AbstractDomain end +########################################################### +# Simplex struct Simplex{D} <: AbstractDomain dim::D # dimensionality as a manifold From 7207b35f886991b208fca5dcefd6ff06617f41b3 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 24 Nov 2021 14:29:47 -0800 Subject: [PATCH 024/368] more domain mucking --- src/domains.jl | 131 ++++++++++++++++++++++++++++--------------------- 1 file changed, 75 insertions(+), 56 deletions(-) diff --git a/src/domains.jl b/src/domains.jl index 9918cd7c..9ae44e5a 100644 --- a/src/domains.jl +++ b/src/domains.jl @@ -2,24 +2,37 @@ export IntegerRange abstract type AbstractDomain end -struct RealBounds{L,U} <: AbstractDomain +abstract type RealDomain <: AbstractDomain end + +struct RealNumbers <: RealDomain end + +const ℝ = RealNumbers() + +Base.minimum(::RealNumbers) = static(-Inf) +Base.maximum(::RealNumbers) = static(Inf) + +Base.in(x, ::RealNumbers) = isreal(x) + +Base.show(io::IO, ::typeof(ℝ)) = print(io, "ℝ") + +struct BoundedReals{L,U} <: RealDomain lower :: L upper :: U end -Base.in(x, b::RealBounds) = b.lower ≤ x ≤ b.upper +Base.in(x, b::BoundedReals) = b.lower ≤ x ≤ b.upper -const ℝ = RealBounds(static(-Inf), static(Inf)) +export ℝ, ℝ₊, 𝕀 -const ℝ₊ = RealBounds(static(0.0), static(Inf)) -const 𝕀 = RealBounds(static(0.0), static(1.0)) +const ℝ₊ = BoundedReals(static(0.0), static(Inf)) +const 𝕀 = BoundedReals(static(0.0), static(1.0)) + +Base.minimum(b::BoundedReals) = b.lower +Base.maximum(b::BoundedReals) = b.upper -Base.minimum(b::RealBounds) = b.lower -Base.maximum(b::RealBounds) = b.upper -Base.show(io::IO, ::typeof(ℝ)) = print(io, "ℝ") Base.show(io::IO, ::typeof(ℝ₊)) = print(io, "ℝ₊") Base.show(io::IO, ::typeof(𝕀)) = print(io, "𝕀") @@ -27,31 +40,37 @@ testvalue(::typeof(ℝ)) = 0.0 testvalue(::typeof(ℝ₊)) = 1.0 testvalue(::typeof(𝕀)) = 0.5 -struct IntegerBounds{L,U} <: AbstractDomain - lower :: L - upper :: U -end +abstract type IntegerDomain <: AbstractDomain end + +struct IntegerNumbers <: IntegerDomain end -Base.in(x, b::IntegerBounds) = isinteger(x) && b.lower ≤ x ≤ b.upper +Base.in(x, ::IntegerNumbers) = isinteger(x) -const ℤ = IntegerBounds(static(-Inf), static(Inf)) +const ℤ = IntegerNumbers() Base.show(io::IO, ::typeof(ℤ)) = print(io, "ℤ") -Base.minimum(::IntegerBounds{lo,hi}) where {lo,hi} = lo -Base.maximum(::IntegerBounds{lo,hi}) where {lo,hi} = hi +Base.minimum(::IntegerNumbers) = static(-Inf) +Base.maximum(::IntegerNumbers) = static(Inf) +struct BoundedInts{L,U} <: IntegerDomain + lower :: L + upper :: U +end + +Base.in(x, b::BoundedInts) = x ∈ ℤ && b.lower ≤ x ≤ b.upper -function Base.show(io::IO, b::IntegerBounds) +Base.minimum(b::BoundedInts) = b.lower +Base.maximum(b::BoundedInts) = b.upper + +function Base.show(io::IO, b::BoundedInts) io = IOContext(io, :compact => true) print(io, "ℤ[", b.lower, ":", b.upper, "]") end -testvalue(::IntegerBounds) = min(b.lower, 0) - -Base.iterate(r::IntegerRange{lo,hi}) where {lo,hi} = iterate(lo:hi) +testvalue(::BoundedInts) = min(b.lower, 0) function Base.getindex(::typeof(ℤ), r::AbstractUnitRange) - IntegerBounds(extrema(r)...) + BoundedInts(extrema(r)...) end @@ -61,48 +80,48 @@ end ########################################################### # Simplex -struct Simplex{D} <: AbstractDomain - dim::D # dimensionality as a manifold -end +# struct Simplex{D} <: AbstractDomain +# dim::D # dimensionality as a manifold +# end -projectto!(x, ::Simplex) = normalize!(x, 1) +# projectto!(x, ::Simplex) = normalize!(x, 1) -struct Sphere{D} <: AbstractDomain - dim::D # dimensionality as a manifold -end +# struct Sphere{D} <: AbstractDomain +# dim::D # dimensionality as a manifold +# end -projectto!(x, ::Sphere) = normalize!(x, 2) -struct ZeroSet{F, G} <: AbstractDomain - f::F - ∇f::G -end +# projectto!(x, ::Sphere) = normalize!(x, 2) +# struct ZeroSet{F, G} <: AbstractDomain +# f::F +# ∇f::G +# end -function zeroset(::Simplex) - f(x::AbstractVector{T}) where {T} = sum(x) - one(T) - ∇f(x::AbstractVector{T}) where {T} = Fill(one(T), axes(x)) - ZeroSet(f, ∇f) -end +# function zeroset(::Simplex) +# f(x::AbstractVector{T}) where {T} = sum(x) - one(T) +# ∇f(x::AbstractVector{T}) where {T} = Fill(one(T), axes(x)) +# ZeroSet(f, ∇f) +# end -function zeroset(::Sphere) - f(x::AbstractVector{T}) where {T} = (sum(xⱼ -> xⱼ^2, x) - one(T)) / 2 - ∇f(x::AbstractVector{T}) where {T} = x - ZeroSet(f, ∇f) -end +# function zeroset(::Sphere) +# f(x::AbstractVector{T}) where {T} = (sum(xⱼ -> xⱼ^2, x) - one(T)) / 2 +# ∇f(x::AbstractVector{T}) where {T} = x +# ZeroSet(f, ∇f) +# end -struct LebesgueCodimOne{D,T,O} <: AbstractMeasure - ndims ::D - ortho ::O -end +# struct LebesgueCodimOne{D,T,O} <: AbstractMeasure +# ndims ::D +# ortho ::O +# end -function logdensityof(d::Density{L1, L2}, x) where {L1<:LebesgueCodimOne, L2<:LebesgueCodimOne} - μ = d.μ - ν = d.base - μ.ndims == ν.ndims || return NaN - rank([μ.ortho ν.ortho]) == 1 || return NaN - return 0.0 -end +# function logdensityof(d::Density{L1, L2}, x) where {L1<:LebesgueCodimOne, L2<:LebesgueCodimOne} +# μ = d.μ +# ν = d.base +# μ.ndims == ν.ndims || return NaN +# rank([μ.ortho ν.ortho]) == 1 || return NaN +# return 0.0 +# end -struct LebesgueSimplex <: AbstractMeasure end +# struct LebesgueSimplex <: AbstractMeasure end -basemeasure(::LebesgueSimplex, x) \ No newline at end of file +# basemeasure(::LebesgueSimplex, x) \ No newline at end of file From af9e113ddab520865797cb470f9e0b13b8654515 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 24 Nov 2021 14:32:45 -0800 Subject: [PATCH 025/368] fix some exports --- src/density.jl | 3 ++- src/domains.jl | 4 +--- 2 files changed, 3 insertions(+), 4 deletions(-) diff --git a/src/density.jl b/src/density.jl index dfc10f47..dc3ae34b 100644 --- a/src/density.jl +++ b/src/density.jl @@ -145,7 +145,8 @@ end # logdensity_def(::Lebesgue{ℝ}, ::Lebesgue{ℝ}, x) = zero(x) -export density +export densityof +export logdensityof density_def(μ, ν::AbstractMeasure, x) = exp(logdensity_def(μ, ν, x)) diff --git a/src/domains.jl b/src/domains.jl index 9ae44e5a..a0d68af9 100644 --- a/src/domains.jl +++ b/src/domains.jl @@ -1,5 +1,3 @@ -export IntegerRange - abstract type AbstractDomain end abstract type RealDomain <: AbstractDomain end @@ -23,7 +21,7 @@ end Base.in(x, b::BoundedReals) = b.lower ≤ x ≤ b.upper -export ℝ, ℝ₊, 𝕀 +export ℝ, ℝ₊, 𝕀, ℤ const ℝ₊ = BoundedReals(static(0.0), static(Inf)) From e3f41ccd2c2b80bd25aefcbb411edaf00d45dbef Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 24 Nov 2021 14:32:54 -0800 Subject: [PATCH 026/368] update deps --- Project.toml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Project.toml b/Project.toml index f8187589..08dc2ad0 100644 --- a/Project.toml +++ b/Project.toml @@ -7,7 +7,6 @@ version = "0.5.1" ConstructionBase = "187b0558-2788-49d3-abe0-74a17ed4e7c9" DensityInterface = "b429d917-457f-4dbc-8f4c-0cc954292b1d" FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b" -KeywordCalls = "4d827475-d3e4-43d6-abe3-9688362ede9f" LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" LogExpFunctions = "2ab3a3ac-af41-5b50-aa03-7779005ae688" MappedArrays = "dbb5928d-eab1-5f90-85c2-b9b0edb7c900" @@ -17,11 +16,12 @@ Tricks = "410a4b4d-49e4-4fbc-ab6d-cb71b17b3775" [compat] ConstructionBase = "1.3" +DensityInterface = "0.4" FillArrays = "0.12" -KeywordCalls = "0.2" LogExpFunctions = "0.3" MappedArrays = "0.4" Static = "0.4" +Tricks = "0.1" julia = "1.3" [extras] From 7acbed44665428b39ba1acf84f0232a80e19f572 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 24 Nov 2021 14:40:04 -0800 Subject: [PATCH 027/368] update `using` --- src/MeasureBase.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index ff5ce71d..3eb8da5b 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -8,7 +8,7 @@ import Random: gentype import DensityInterface: logdensityof import DensityInterface: densityof import DensityInterface: DensityKind -using DensityInterface: HasDensity, IsDensity +using DensityInterface using FillArrays using Static From 21b728e41292e4165c79adece19fa0cdf039162c Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 24 Nov 2021 15:59:53 -0800 Subject: [PATCH 028/368] working on tests --- src/combinators/product.jl | 4 ++-- src/density.jl | 16 +++++++++++----- src/primitives/counting.jl | 8 +------- src/primitives/dirac.jl | 13 ++++++++----- test/runtests.jl | 6 +++--- 5 files changed, 25 insertions(+), 22 deletions(-) diff --git a/src/combinators/product.jl b/src/combinators/product.jl index 679e5be0..279112dd 100644 --- a/src/combinators/product.jl +++ b/src/combinators/product.jl @@ -68,7 +68,7 @@ export ⊗ marginals(d::TupleProductMeasure{T}) where {F,T<:Tuple} = d.pars @inline function logdensity_def(d::TupleProductMeasure, x::Tuple) where {T<:Tuple} - mapreduce(logdensity, +, d.pars, x) + mapreduce(logdensity_def, +, d.pars, x) end function Base.rand(rng::AbstractRNG, ::Type{T}, d::TupleProductMeasure) where {T} @@ -86,7 +86,7 @@ function marginals(d::ProductMeasure{<:Returns,S,A}) where {F,S,A<:AbstractArray end @inline function logdensity_def(d::ProductMeasure, x) - mapreduce(logdensity, +, marginals(d), x) + mapreduce(logdensity_def, +, marginals(d), x) end @inline function logdensity_def(d::ProductMeasure{<:Returns}, x) diff --git a/src/density.jl b/src/density.jl index dc3ae34b..9785c001 100644 --- a/src/density.jl +++ b/src/density.jl @@ -39,7 +39,7 @@ end A `DensityMeasure` is a measure defined by a density with respect to some other "base" measure """ -struct DensityMeasure{F,B,L} <: AbstractMeasure +struct DensityMeasure{F,B} <: AbstractMeasure f::F base::B end @@ -58,9 +58,9 @@ end basemeasure(μ::DensityMeasure) = μ.base -basemeasure_depth(::DensityMeasure{F,B,L}) where {F,B,L} = static(1) + basemeasure_depth(B) +basemeasure_depth(::DensityMeasure{F,B}) where {F,B} = static(1) + basemeasure_depth(B) -basemeasure_depth(::Type{DensityMeasure{F,B,L}}) where {F,B,L} = +basemeasure_depth(::Type{DensityMeasure{F,B}}) where {F,B} = static(1) + basemeasure_depth(B) logdensity_def(μ::DensityMeasure, x) = logdensityof(μ.f, x) @@ -74,7 +74,13 @@ export ∫ Define a new measure in terms of a density `f` over some measure `base`. """ -∫(f, base::AbstractMeasure) = DensityMeasure(funcdensity(f), base) +∫(f::Function, base::AbstractMeasure) = DensityMeasure(funcdensity(f), base) + +∫(f, base::AbstractMeasure) = _densitymeasure(f, base, DensityKind(f)) + +_densitymeasure(f, base, ::IsDensity) = DensityMeasure(f, base) + +_densitymeasure(f, base, _) = @error "DensityInterface.DensityKind($f) ≠ DensityInterface.IsDensity()" # ∫(μ::AbstractMeasure, base::AbstractMeasure) = ∫(𝒹(μ, base), base) @@ -85,7 +91,7 @@ export ∫exp Define a new measure in terms of a log-density `f` over some measure `base`. """ -∫exp(f, μ) = ∫(logfuncdensity(f), μ) +∫exp(f::Function, μ) = ∫(logfuncdensity(f), μ) # TODO: `density` and `logdensity` functions for `DensityMeasure` diff --git a/src/primitives/counting.jl b/src/primitives/counting.jl index 769abb07..943eb45d 100644 --- a/src/primitives/counting.jl +++ b/src/primitives/counting.jl @@ -1,13 +1,8 @@ export CountingMeasure -struct CountingMeasure{X} <: PrimitiveMeasure end +struct CountingMeasure <: PrimitiveMeasure end -function Base.show(io::IO, μ::CountingMeasure{X}) where {X} - io = IOContext(io, :compact => true) - print(io, "CountingMeasure(", X, ")") -end -CountingMeasure(X) = CountingMeasure{X}() # gentype(::CountingMeasure{ℝ}) = Float64 # gentype(::CountingMeasure{ℝ₊}) = Float64 @@ -15,7 +10,6 @@ CountingMeasure(X) = CountingMeasure{X}() gentype(::CountingMeasure) = Int -testvalue(μ::CountingMeasure{X}) where {X} = testvalue(X) logdensity_def(::CountingMeasure, x) = zero(float(x)) diff --git a/src/primitives/dirac.jl b/src/primitives/dirac.jl index 80cd4a93..2ac3fbed 100644 --- a/src/primitives/dirac.jl +++ b/src/primitives/dirac.jl @@ -1,7 +1,7 @@ export Dirac -struct Dirac{X} <: PrimitiveMeasure +struct Dirac{X} <: AbstractMeasure x::X end @@ -12,6 +12,13 @@ function (μ::Dirac{X})(s) where {X} return 0 end +basemeasure(d::Dirac) = CountingMeasure() + +basemeasure_depth(::Dirac) = static(1) +basemeasure_depth(::Type{D}) where {D<:Dirac} = static(1) + + + density_def(μ::Dirac, x) = x == μ.x logdensity_def(μ::Dirac, x) = (x == μ.x) ? 0.0 : -Inf @@ -22,8 +29,4 @@ export dirac dirac(d::AbstractMeasure) = Dirac(rand(d)) -@inline function logdensity_def(μ::Dirac{M}, ν::Dirac{M}, x) where {M} - logdensity_def(μ, x) - logdensity_def(ν, x) -end - testvalue(d::Dirac) = d.x diff --git a/test/runtests.jl b/test/runtests.jl index 3ef8d4ae..f9d488e1 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -4,7 +4,7 @@ using Random using LinearAlgebra using MeasureBase -using MeasureBase: logdensityof +using MeasureBase: logdensityof, logdensity_def using Aqua Aqua.test_all(MeasureBase; ambiguities = false, unbound_args = false) @@ -56,13 +56,13 @@ test_measures = [ Lebesgue(ℝ) Dirac(0.0) + Lebesgue(ℝ) SpikeMixture(Lebesgue(ℝ), 2) - d ⊙ d + # d ⊙ d ] testbroken_measures = [ # InverseGamma(2) # Not defined yet # MvNormal(I(3)) # Entirely broken for now - CountingMeasure(Float64) + CountingMeasure() Likelihood TrivialMeasure() ] From b1b992d6153a344cb07dacf4559d66b2732ef953 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 24 Nov 2021 19:20:09 -0800 Subject: [PATCH 029/368] Working toward tests passing --- src/combinators/power.jl | 26 ++++++++++++-------------- src/combinators/product.jl | 27 +++++++++++---------------- src/combinators/smart-constructors.jl | 26 +++++++++++++++----------- src/density.jl | 3 --- src/kernel.jl | 5 +++++ src/primitives/lebesgue.jl | 16 +++++++--------- test/runtests.jl | 4 ++-- 7 files changed, 52 insertions(+), 55 deletions(-) diff --git a/src/combinators/power.jl b/src/combinators/power.jl index aaf2bdf1..c1432572 100644 --- a/src/combinators/power.jl +++ b/src/combinators/power.jl @@ -29,7 +29,7 @@ using FillArrays: Fill export PowerMeasure -const PowerMeasure{F,S,T,N,A} = ProductMeasure{F,S,Fill{T,N,A}} +const PowerMeasure{M,N,R} = ProductMeasure{KernelReturns{M}, CartesianIndices{N, R}} Base.:^(μ::AbstractMeasure, ::Tuple{}) = μ @@ -37,31 +37,29 @@ function Base.:^(μ::AbstractMeasure, dims::Integer...) return μ^dims end -function Base.:^(μ::M, dims::NTuple{N,I}) where {M<:AbstractMeasure,N,I<:Integer} - powermeasure(μ, dims) -end - +Base.show(io::IO, d::PowerMeasure) = print(io, d.f.value, " ^ ", size(d.pars)) +Base.show(io::IO, d::PowerMeasure{M,1}) where {M} = print(io, d.f.value, " ^ ", length(d.pars)) # gentype(d::PowerMeasure{M,N}) where {M,N} = @inbounds Array{gentype(first(marginals(d))), N} -params(d::ProductMeasure{F,S,<:Fill}) where {F,S} = params(first(marginals(d))) +params(d::PowerMeasure) = params(first(marginals(d))) -params(::Type{P}) where {F,S,P<:ProductMeasure{F,S,<:Fill}} = params(D) +params(::Type{P}) where {K,P<:PowerMeasure} = params(D) # basemeasure(μ::PowerMeasure) = @inbounds basemeasure(first(μ.data))^size(μ.data) # Same as PowerMeasure -@inline function basemeasure(d::ProductMeasure{F,S,<:Fill}) where {F,S} +@inline function basemeasure(d::PowerMeasure) _basemeasure(d, (basemeasure(d.f(first(d.pars))))) end # Same as PowerMeasure -@inline function _basemeasure(d::ProductMeasure{F,S,<:Fill}, b) where {F,S} - b^size(d.pars) +@inline function _basemeasure(d::PowerMeasure, b) + b ^ size(d.pars) end # Same as PowerMeasure -@inline function _basemeasure(d::ProductMeasure{F,S,<:Fill}, b::FactoredBase) where {F,S} +@inline function _basemeasure(d::PowerMeasure, b::FactoredBase) n = length(d.pars) inbounds(x) = all(b.inbounds, x) constℓ = n * b.constℓ @@ -70,16 +68,16 @@ end FactoredBase(inbounds, constℓ, varℓ, base) end -function basemeasure_depth(d::P) where {M,P<:ProductMeasure{Returns{M}}} +function basemeasure_depth(d::PowerMeasure) return static(1) + basemeasure_depth(M) end -function basemeasure_depth(::Type{P}) where {M,P<:ProductMeasure{Returns{M}}} +function basemeasure_depth(::Type{P}) where {P<:PowerMeasure} return static(1) + basemeasure_depth(M) end # Same as PowerMeasure -@inline function logdensity_def(d::ProductMeasure{F,S,<:Fill}, x) where {F,S} +@inline function logdensity_def(d::PowerMeasure, x) d1 = d.f(first(d.pars)) sum(xj -> logdensity_def(d1, xj), x) end diff --git a/src/combinators/product.jl b/src/combinators/product.jl index 279112dd..cc61a67a 100644 --- a/src/combinators/product.jl +++ b/src/combinators/product.jl @@ -7,8 +7,8 @@ using FillArrays abstract type AbstractProductMeasure <: AbstractMeasure end -struct ProductMeasure{F,S,I} <: AbstractProductMeasure - f::Kernel{F,S} +struct ProductMeasure{K,I} <: AbstractProductMeasure + f::K pars::I end @@ -22,7 +22,7 @@ end Base.size(μ::ProductMeasure) = size(marginals(μ)) -Base.length(m::ProductMeasure{T}) where {T} = length(marginals(μ)) +Base.length(m::ProductMeasure) = length(marginals(μ)) basemeasure(d::ProductMeasure) = productmeasure(basekernel(d.f), d.pars) @@ -33,7 +33,7 @@ basemeasure(d::ProductMeasure) = productmeasure(basekernel(d.f), d.pars) export marginals -function marginals(d::ProductMeasure{F,S,I}) where {F,S,I} +function marginals(d::ProductMeasure{K,I}) where {K,I} _marginals(d, isiterable(I)) end @@ -41,7 +41,7 @@ function _marginals(d::ProductMeasure, ::Iterable) return (d.f(i) for i in d.pars) end -function _marginals(d::ProductMeasure{F,S,I}, ::NonIterable) where {F,S,I} +function _marginals(d::ProductMeasure{K,I}, ::NonIterable) where {K,I} error("Type $I is not iterable. Add an `iterate` or `marginals` method to fix.") end @@ -78,12 +78,7 @@ end ############################################################################### # I <: AbstractArray -marginals(d::ProductMeasure{F,S,A}) where {F,S,A<:AbstractArray} = mappedarray(d.f, d.pars) - -function marginals(d::ProductMeasure{<:Returns,S,A}) where {F,S,A<:AbstractArray} - Fill(d.f.f.value, size(d.pars)) - # mappedarray(d.f.f, d.pars) -end +marginals(d::ProductMeasure{K,A}) where {K,A<:AbstractArray} = mappedarray(d.f, d.pars) @inline function logdensity_def(d::ProductMeasure, x) mapreduce(logdensity_def, +, marginals(d), x) @@ -93,7 +88,7 @@ end sum(x -> logdensity_def(d.f.f.value, x), x) end -# function Base.rand(rng::AbstractRNG, ::Type{T}, d::ProductMeasure{F,S,I}) where {T,F,I<:CartesianIndices} +# function Base.rand(rng::AbstractRNG, ::Type{T}, d::ProductMeasure{K,I}) where {T,F,I<:CartesianIndices} # end @@ -103,7 +98,7 @@ end export rand! using Random: rand!, GLOBAL_RNG, AbstractRNG -@inline function logdensity_def(d::ProductMeasure{F,S,I}, x) where {F,S,I<:Base.Generator} +@inline function logdensity_def(d::ProductMeasure{K,I}, x) where {K,I<:Base.Generator} sum((logdensity_def(dj, xj) for (dj, xj) in zip(marginals(d), x))) end @@ -158,7 +153,7 @@ end # μ.data # end -function ConstructionBase.constructorof(::Type{P}) where {F,S,I,P<:ProductMeasure{F,S,I}} +function ConstructionBase.constructorof(::Type{P}) where {K,I,P<:ProductMeasure{K,I}} p -> productmeasure(d.f, p) end @@ -176,11 +171,11 @@ end # end # end -function kernelfactor(μ::ProductMeasure{F,S,<:Fill}) where {F,S} +function kernelfactor(μ::ProductMeasure{K,<:Fill}) where {K} k = kernel(first(marginals(μ))) (p -> k.f(p)^size(μ), k.ops) end -function kernelfactor(μ::ProductMeasure{F,S,A}) where {F,S,A<:AbstractArray} +function kernelfactor(μ::ProductMeasure{K,A}) where {K,A<:AbstractArray} (p -> set.(marginals(μ), params, p), μ.pars) end diff --git a/src/combinators/smart-constructors.jl b/src/combinators/smart-constructors.jl index 36566172..3666b6ab 100644 --- a/src/combinators/smart-constructors.jl +++ b/src/combinators/smart-constructors.jl @@ -38,15 +38,15 @@ end ############################################################################### # PowerMeaure -function powermeasure(μ::M, dims::NTuple{N,I}) where {M<:AbstractMeasure,N,I} - productmeasure(Returns(μ), identity, CartesianIndices(dims)) +function Base.:^(μ::M, dims::NTuple{N,I}) where {M<:AbstractMeasure,N,I} + productmeasure(KernelReturns(μ), CartesianIndices(dims)) end -function powermeasure(μ::M, dims::Tuple{I}) where {M<:AbstractMeasure,N,I} - productmeasure(Returns(μ), identity, Base.OneTo(first(dims))) -end +# function Base.:^(μ::M, dims::Tuple{I}) where {M<:AbstractMeasure,N,I} +# productmeasure(KernelReturns(μ), Base.OneTo(first(dims))) +# end -function powermeasure(μ::WeightedMeasure, dims::NTuple{N,I}) where {N,I} +function Base.:^(μ::WeightedMeasure, dims::NTuple{N,I}) where {N,I} k = prod(dims) * μ.logweight return weightedmeasure(k, μ.base^dims) end @@ -54,13 +54,14 @@ end ############################################################################### # ProductMeasure -productmeasure(f, ops, pars) = ProductMeasure(kernel(f, ops), pars) -productmeasure(f, pars) = productmeasure(f, identity, pars) +productmeasure(f::AbstractKernel, pars) = ProductMeasure(f, pars) + +productmeasure(f, ops, pars) = ProductMeasure(kernel(f, ops), pars) productmeasure(μs::Tuple) = TupleProductMeasure(μs) -productmeasure(f::Returns, ops, pars) = ProductMeasure(kernel(f, identity), pars) +productmeasure(f::Returns, ops, pars) = ProductMeasure(KernelReturns(f.value), pars) productmeasure(k::Kernel, pars) = productmeasure(k.f, k.ops, pars) @@ -138,5 +139,8 @@ function kernel(::Type{M}; ops...) where {M} kernel(M, nt) end -kernel(f::Returns, op::typeof(identity)) = Kernel(f, op) -kernel(f::Returns, op) = kernel(f, identity) +kernel(f::Returns, op) = KernelReturns(f.value) +kernel(f, op::Returns) = KernelReturns(f(op.value)) + +# Just to avoid dispatch ambiguity +kernel(f::Returns, op::Returns) = KernelReturns(f.value) \ No newline at end of file diff --git a/src/density.jl b/src/density.jl index 9785c001..dd2d5260 100644 --- a/src/density.jl +++ b/src/density.jl @@ -78,9 +78,6 @@ Define a new measure in terms of a density `f` over some measure `base`. ∫(f, base::AbstractMeasure) = _densitymeasure(f, base, DensityKind(f)) -_densitymeasure(f, base, ::IsDensity) = DensityMeasure(f, base) - -_densitymeasure(f, base, _) = @error "DensityInterface.DensityKind($f) ≠ DensityInterface.IsDensity()" # ∫(μ::AbstractMeasure, base::AbstractMeasure) = ∫(𝒹(μ, base), base) diff --git a/src/kernel.jl b/src/kernel.jl index 67bc5129..b1d6dfb4 100644 --- a/src/kernel.jl +++ b/src/kernel.jl @@ -3,6 +3,11 @@ export Kernel abstract type AbstractKernel <: AbstractMeasure end +struct KernelReturns{M} <: AbstractKernel + value::M +end + +(k::KernelReturns)(_) = k.value struct Kernel{F,S} <: AbstractKernel f::F ops::S diff --git a/src/primitives/lebesgue.jl b/src/primitives/lebesgue.jl index a11f6ad5..35f6b022 100644 --- a/src/primitives/lebesgue.jl +++ b/src/primitives/lebesgue.jl @@ -2,19 +2,17 @@ export Lebesgue -struct Lebesgue{X} <: PrimitiveMeasure end +struct Lebesgue{T} <: PrimitiveMeasure + support::T +end -Lebesgue(X) = Lebesgue{X}() -sampletype(::Lebesgue{ℝ}) = Float64 -sampletype(::Lebesgue{ℝ₊}) = Float64 -sampletype(::Lebesgue{𝕀}) = Float64 +sampletype(::Lebesgue) = Float64 -testvalue(::Lebesgue{ℝ}) = 0.0 -testvalue(::Lebesgue{𝕀}) = 0.5 -testvalue(::Lebesgue{ℝ₊}) = 1.0 -testvalue(::Lebesgue{<:Real}) = 0.0 +testvalue(d::Lebesgue) = testvalue(d.support) logdensity_def(::Lebesgue, x) = zero(x) Base.:∘(::typeof(basemeasure), ::Type{Lebesgue}) = Lebesgue + +Base.show(io::IO, d::Lebesgue) = print("Lebesgue(",d.support,")") \ No newline at end of file diff --git a/test/runtests.jl b/test/runtests.jl index f9d488e1..2826aa83 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -4,7 +4,7 @@ using Random using LinearAlgebra using MeasureBase -using MeasureBase: logdensityof, logdensity_def +using MeasureBase: logdensityof, logdensity_def, density_def, densityof using Aqua Aqua.test_all(MeasureBase; ambiguities = false, unbound_args = false) @@ -189,7 +189,7 @@ end @testset "Half" begin Normal() = ∫exp(x -> -0.5x^2, Lebesgue(ℝ)) - @half Normal + HalfNormal() = Half(Normal()) @test logdensity_def(HalfNormal(), Lebesgue(ℝ), -0.2) == -Inf @test logdensity_def(HalfNormal(), 0.2) == logdensity_def(Normal(), 0.2) @test density_def(HalfNormal(), Lebesgue(ℝ), 0.2) ≈ 2 * density_def(Normal(), Lebesgue(ℝ), 0.2) From 16e66fa3348f3fd4b29f39b7ad9617da30d69ada Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Sun, 28 Nov 2021 14:40:52 -0800 Subject: [PATCH 030/368] some refactoring --- src/MeasureBase.jl | 4 +-- src/combinators/affine.jl | 3 +- src/combinators/for.jl | 6 ++-- src/combinators/power.jl | 26 +++++++-------- src/combinators/product.jl | 48 +++++++++++++++------------ src/combinators/restricted.jl | 5 +-- src/combinators/smart-constructors.jl | 32 +++++++++--------- src/combinators/spikemixture.jl | 3 ++ src/combinators/weighted.jl | 4 +-- src/density.jl | 7 ++-- src/domains.jl | 2 +- src/kernel.jl | 37 ++++++++++++--------- src/parameterized.jl | 8 ++--- src/primitive.jl | 2 +- src/primitives/dirac.jl | 7 ++-- src/primitives/lebesgue.jl | 20 ++++++++--- src/primitives/trivial.jl | 2 ++ src/utils.jl | 20 ++++++----- 18 files changed, 128 insertions(+), 108 deletions(-) diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index 3eb8da5b..70ac0650 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -27,7 +27,7 @@ gentype(μ::AbstractMeasure) = typeof(testvalue(μ)) # gentype(μ::AbstractMeasure) = gentype(basemeasure(μ)) -export logdensity +export logdensity_def export basemeasure export basekernel @@ -42,7 +42,7 @@ is understood to be `basemeasure(μ)`. Methods for computing density relative to other measures will be """ -function logdensity end +function logdensity_def end if VERSION < v"1.7.0-beta1.0" @eval begin diff --git a/src/combinators/affine.jl b/src/combinators/affine.jl index d65fc728..afdd3e27 100644 --- a/src/combinators/affine.jl +++ b/src/combinators/affine.jl @@ -255,8 +255,7 @@ basemeasure(d::Affine{N,L}) where {N,L<:Lebesgue} = weightedmeasure(-logjac(d), weightedmeasure(-logjac(d), d.parent) end -basemeasure_depth(::Affine{N,M,T}) where {N,M,T} = static(1) + basemeasure_depth(M) -basemeasure_depth(::Type{Affine{N,M,T}}) where {N,M,T} = static(1) + basemeasure_depth(M) +basemeasure_type(::Type{Affine{N,M,T}}) where {N,M,T} = M logjac(d::Affine) = logjac(getfield(d, :f)) diff --git a/src/combinators/for.jl b/src/combinators/for.jl index 121519a9..107cf6a2 100644 --- a/src/combinators/for.jl +++ b/src/combinators/for.jl @@ -78,11 +78,11 @@ For(f, dims...) = productmeasure(i -> f(i...), zip(dims...)) For(f, inds::AbstractArray) = productmeasure(f, inds) -For(f, n::Int) = productmeasure(f, Base.OneTo(n)) -For(f, dims::Int...) = productmeasure(i -> f(Tuple(i)...), CartesianIndices(dims)) +For(f, n::Integer) = productmeasure(f, Base.OneTo(n)) +For(f, dims::Integer...) = productmeasure(i -> f(Tuple(i)...), CartesianIndices(dims)) function Base.eltype(d::ProductMeasure{F,I}) where {F,I<:AbstractArray} - return eltype(d.f(first(d.pars))) + return eltype(d.f(first(d.xs))) end # """ diff --git a/src/combinators/power.jl b/src/combinators/power.jl index c1432572..7503d3e6 100644 --- a/src/combinators/power.jl +++ b/src/combinators/power.jl @@ -29,7 +29,7 @@ using FillArrays: Fill export PowerMeasure -const PowerMeasure{M,N,R} = ProductMeasure{KernelReturns{M}, CartesianIndices{N, R}} +const PowerMeasure{M,N,R} = ProductMeasure{Kernel{Returns{M}, typeof(identity)}, CartesianIndices{N, R}} Base.:^(μ::AbstractMeasure, ::Tuple{}) = μ @@ -37,47 +37,45 @@ function Base.:^(μ::AbstractMeasure, dims::Integer...) return μ^dims end -Base.show(io::IO, d::PowerMeasure) = print(io, d.f.value, " ^ ", size(d.pars)) -Base.show(io::IO, d::PowerMeasure{M,1}) where {M} = print(io, d.f.value, " ^ ", length(d.pars)) +Base.show(io::IO, d::PowerMeasure) = print(io, d.f.f.value, " ^ ", size(d.xs)) +Base.show(io::IO, d::PowerMeasure{M,1}) where {M} = print(io, d.f.f.value, " ^ ", length(d.xs)) # gentype(d::PowerMeasure{M,N}) where {M,N} = @inbounds Array{gentype(first(marginals(d))), N} params(d::PowerMeasure) = params(first(marginals(d))) -params(::Type{P}) where {K,P<:PowerMeasure} = params(D) - # basemeasure(μ::PowerMeasure) = @inbounds basemeasure(first(μ.data))^size(μ.data) # Same as PowerMeasure @inline function basemeasure(d::PowerMeasure) - _basemeasure(d, (basemeasure(d.f(first(d.pars))))) + _basemeasure(d, (basemeasure(d.f(first(d.xs))))) end # Same as PowerMeasure @inline function _basemeasure(d::PowerMeasure, b) - b ^ size(d.pars) + b ^ size(d.xs) end # Same as PowerMeasure @inline function _basemeasure(d::PowerMeasure, b::FactoredBase) - n = length(d.pars) + n = length(d.xs) inbounds(x) = all(b.inbounds, x) constℓ = n * b.constℓ varℓ() = n * b.varℓ() - base = b.base^size(d.pars) + base = b.base^size(d.xs) FactoredBase(inbounds, constℓ, varℓ, base) end -function basemeasure_depth(d::PowerMeasure) - return static(1) + basemeasure_depth(M) +function basemeasure_depth(d::PowerMeasure{M,N,R}) where {M,N,R} + return basemeasure_depth(M) end -function basemeasure_depth(::Type{P}) where {P<:PowerMeasure} - return static(1) + basemeasure_depth(M) +function basemeasure_type(::Type{P}) where {M,N,R,P<:PowerMeasure{M,N,R}} + return PowerMeasure{basemeasure_type(M), N, R} end # Same as PowerMeasure @inline function logdensity_def(d::PowerMeasure, x) - d1 = d.f(first(d.pars)) + d1 = d.f(first(d.xs)) sum(xj -> logdensity_def(d1, xj), x) end diff --git a/src/combinators/product.jl b/src/combinators/product.jl index cc61a67a..899f17a0 100644 --- a/src/combinators/product.jl +++ b/src/combinators/product.jl @@ -9,27 +9,27 @@ abstract type AbstractProductMeasure <: AbstractMeasure end struct ProductMeasure{K,I} <: AbstractProductMeasure f::K - pars::I + xs::I end # TODO: Test for equality without traversal, probably by first converting to a # canonical form function Base.:(==)(a::ProductMeasure, b::ProductMeasure) - all(zip(a.pars, b.pars)) do (aᵢ, bᵢ) + all(zip(a.xs, b.xs)) do (aᵢ, bᵢ) a.f(aᵢ) == b.f(bᵢ) end end Base.size(μ::ProductMeasure) = size(marginals(μ)) -Base.length(m::ProductMeasure) = length(marginals(μ)) +Base.length(μ::ProductMeasure) = length(marginals(μ)) -basemeasure(d::ProductMeasure) = productmeasure(basekernel(d.f), d.pars) +basemeasure(d::ProductMeasure) = productmeasure(basekernel(d.f), d.xs) # TODO: Do we need these methods? -# basemeasure(d::ProductMeasure) = ProductMeasure(basemeasure ∘ d.f, d.pars) -# basemeasure(d::ProductMeasure{typeof(identity)}) = ProductMeasure(identity, map(basemeasure, d.pars)) -# basemeasure(d::ProductMeasure{typeof(identity), <:FillArrays.Fill}) = ProductMeasure(identity, map(basemeasure, d.pars)) +# basemeasure(d::ProductMeasure) = ProductMeasure(basemeasure ∘ d.f, d.xs) +# basemeasure(d::ProductMeasure{typeof(identity)}) = ProductMeasure(identity, map(basemeasure, d.xs)) +# basemeasure(d::ProductMeasure{typeof(identity), <:FillArrays.Fill}) = ProductMeasure(identity, map(basemeasure, d.xs)) export marginals @@ -38,7 +38,7 @@ function marginals(d::ProductMeasure{K,I}) where {K,I} end function _marginals(d::ProductMeasure, ::Iterable) - return (d.f(i) for i in d.pars) + return (d.f(i) for i in d.xs) end function _marginals(d::ProductMeasure{K,I}, ::NonIterable) where {K,I} @@ -59,26 +59,26 @@ end # I <: Tuple struct TupleProductMeasure{T} <: AbstractProductMeasure - pars::T + components::T end export ⊗ ⊗(μs::AbstractMeasure...) = productmeasure(μs) -marginals(d::TupleProductMeasure{T}) where {F,T<:Tuple} = d.pars +marginals(d::TupleProductMeasure{T}) where {F,T<:Tuple} = d.components @inline function logdensity_def(d::TupleProductMeasure, x::Tuple) where {T<:Tuple} - mapreduce(logdensity_def, +, d.pars, x) + mapreduce(logdensity_def, +, d.components, x) end function Base.rand(rng::AbstractRNG, ::Type{T}, d::TupleProductMeasure) where {T} - rand.(d.pars) + rand.(d.components) end ############################################################################### # I <: AbstractArray -marginals(d::ProductMeasure{K,A}) where {K,A<:AbstractArray} = mappedarray(d.f, d.pars) +marginals(d::ProductMeasure{K,A}) where {K,A<:AbstractArray} = mappedarray(d.f, d.xs) @inline function logdensity_def(d::ProductMeasure, x) mapreduce(logdensity_def, +, marginals(d), x) @@ -98,8 +98,11 @@ end export rand! using Random: rand!, GLOBAL_RNG, AbstractRNG -@inline function logdensity_def(d::ProductMeasure{K,I}, x) where {K,I<:Base.Generator} - sum((logdensity_def(dj, xj) for (dj, xj) in zip(marginals(d), x))) + +function logdensity_def(μ::AbstractProductMeasure, x) + mapreduce(+, μ.xs, x) do (j,x) + logdensity_def(μ.f(j), x) + end end @propagate_inbounds function Random.rand!( @@ -153,9 +156,10 @@ end # μ.data # end -function ConstructionBase.constructorof(::Type{P}) where {K,I,P<:ProductMeasure{K,I}} - p -> productmeasure(d.f, p) -end +# # FIXME +# function ConstructionBase.constructorof(::Type{P}) where {K,I,P<:ProductMeasure{K,I}} +# p -> productmeasure(d.f, p) +# end # function Accessors.set(d::ProductMeasure{N}, ::typeof(params), p) where {N} # setproperties(d, NamedTuple{N}(p...)) @@ -173,9 +177,9 @@ end function kernelfactor(μ::ProductMeasure{K,<:Fill}) where {K} k = kernel(first(marginals(μ))) - (p -> k.f(p)^size(μ), k.ops) + (p -> k.f(p)^size(μ), k.param_maps) end -function kernelfactor(μ::ProductMeasure{K,A}) where {K,A<:AbstractArray} - (p -> set.(marginals(μ), params, p), μ.pars) -end +# function kernelfactor(μ::ProductMeasure{K,A}) where {K,A<:AbstractArray} +# (p -> set.(marginals(μ), params, p), μ.xs) +# end diff --git a/src/combinators/restricted.jl b/src/combinators/restricted.jl index d0e8ba57..bd444532 100644 --- a/src/combinators/restricted.jl +++ b/src/combinators/restricted.jl @@ -15,5 +15,6 @@ end basemeasure(μ::RestrictedMeasure) = μ.base -basemeasure_depth(::Type{RestrictedMeasure{F,M}}) where {F,M} = - static(1) + basemeasure_depth(M) +basemeasure_type(::Type{RestrictedMeasure{F,M}}) where {F,M} = M + +insupport(μ::RestrictedMeasure, x) = μ.f(x) && insupport(μ.base, x) \ No newline at end of file diff --git a/src/combinators/smart-constructors.jl b/src/combinators/smart-constructors.jl index 3666b6ab..f66c8fdc 100644 --- a/src/combinators/smart-constructors.jl +++ b/src/combinators/smart-constructors.jl @@ -39,7 +39,7 @@ end # PowerMeaure function Base.:^(μ::M, dims::NTuple{N,I}) where {M<:AbstractMeasure,N,I} - productmeasure(KernelReturns(μ), CartesianIndices(dims)) + productmeasure(Kernel(Returns(μ), identity), CartesianIndices(dims)) end # function Base.:^(μ::M, dims::Tuple{I}) where {M<:AbstractMeasure,N,I} @@ -57,17 +57,15 @@ end productmeasure(f::AbstractKernel, pars) = ProductMeasure(f, pars) -productmeasure(f, ops, pars) = ProductMeasure(kernel(f, ops), pars) +productmeasure(f, param_maps, pars) = ProductMeasure(kernel(f, param_maps), pars) productmeasure(μs::Tuple) = TupleProductMeasure(μs) -productmeasure(f::Returns, ops, pars) = ProductMeasure(KernelReturns(f.value), pars) - -productmeasure(k::Kernel, pars) = productmeasure(k.f, k.ops, pars) +productmeasure(k::ParameterizedKernel, pars) = productmeasure(k.f, k.param_maps, pars) productmeasure(nt::NamedTuple) = productmeasure(identity, nt) -function productmeasure(f::Returns{FB}, ops, pars) where {FB<:FactoredBase} +function productmeasure(f::Returns{FB}, param_maps, pars) where {FB<:FactoredBase} fb = f.value dims = size(pars) n = prod(dims) @@ -117,30 +115,32 @@ end ############################################################################### # Kernel -kernel(μ, ops...) = Kernel(μ, ops) +kernel(f) = kernel(f, identity) + +kernel(μ, op1, op2, param_maps...) = Kernel(μ, op1, op2, param_maps...) kernel(μ, op) = Kernel(μ, op) # kernel(Normal(μ=2)) function kernel(μ::P) where {P<:AbstractMeasure} - (f, ops) = kernelfactor(μ) - kernel(f, ops) + (f, param_maps) = kernelfactor(μ) + kernel(f, param_maps) end # kernel(Normal{(:μ,), Tuple{Int64}}) function kernel(::Type{P}) where {P<:AbstractMeasure} - (f, ops) = kernelfactor(P) - kernel(f, ops) + (f, param_maps) = kernelfactor(P) + kernel(f, param_maps) end # kernel(::Type{P}, op::O) where {O, N, P<:ParameterizedMeasure{N}} = kernel{constructorof(P),O}(op) -function kernel(::Type{M}; ops...) where {M} - nt = NamedTuple(ops) +function kernel(::Type{M}; param_maps...) where {M} + nt = NamedTuple(param_maps) kernel(M, nt) end -kernel(f::Returns, op) = KernelReturns(f.value) -kernel(f, op::Returns) = KernelReturns(f(op.value)) +kernel(f::Returns, op) = Kernel(f, identity) +kernel(f, op::Returns) = Kernel(Returns(f(op.value)), identity) # Just to avoid dispatch ambiguity -kernel(f::Returns, op::Returns) = KernelReturns(f.value) \ No newline at end of file +kernel(f::Returns, op::Returns) = Kernel(Returns(f.value), identity) \ No newline at end of file diff --git a/src/combinators/spikemixture.jl b/src/combinators/spikemixture.jl index 3d6c2b43..1d8c8ad1 100644 --- a/src/combinators/spikemixture.jl +++ b/src/combinators/spikemixture.jl @@ -14,6 +14,7 @@ function Base.show(io::IO, μ::SpikeMixture) print(io, "(", μ.s * μ.w, "*", string(μ.m), " + ", μ.s * (1 - μ.w), "Dirac(0))") end +# TODO: Should this base measure be local? @inline function basemeasure(μ::SpikeMixture) # Compare formula (1.4) in Joris Bierkens, Sebastiano Grazzi, Frank van der Meulen, Moritz Schauer: # Sticky PDMP samplers for sparse and local inference problems. 2020. [https://arxiv.org/abs/2103.08478]. @@ -23,6 +24,8 @@ end basemeasure_depth(::Type{SpikeMixture{T,S}}) where {T,S} = static(1) + basemeasure_depth(T) +# basemeasure_type(::Type{SpikeMixture{T,S}}) where {T,S} = SpikeMixture{} + @inline function logdensity_def(μ::SpikeMixture, x) return log(μ.w) + logdensity_def(μ.m, x) end diff --git a/src/combinators/weighted.jl b/src/combinators/weighted.jl index fb419db2..1ac61a46 100644 --- a/src/combinators/weighted.jl +++ b/src/combinators/weighted.jl @@ -23,9 +23,7 @@ struct WeightedMeasure{R,M} <: AbstractWeightedMeasure base::M end -basemeasure_depth(::WeightedMeasure{R,M}) where {R,M} = static(1) + basemeasure_depth(M) -basemeasure_depth(::Type{WeightedMeasure{R,M}}) where {R,M} = - static(1) + basemeasure_depth(M) +basemeasure_type(::Type{WeightedMeasure{R,M}}) where {R,M} = M function Base.show(io::IO, μ::WeightedMeasure) io = IOContext(io, :compact => true) diff --git a/src/density.jl b/src/density.jl index dd2d5260..ca71b6b6 100644 --- a/src/density.jl +++ b/src/density.jl @@ -58,10 +58,7 @@ end basemeasure(μ::DensityMeasure) = μ.base -basemeasure_depth(::DensityMeasure{F,B}) where {F,B} = static(1) + basemeasure_depth(B) - -basemeasure_depth(::Type{DensityMeasure{F,B}}) where {F,B} = - static(1) + basemeasure_depth(B) +basemeasure_type(::Type{DensityMeasure{F,B}}) where {F,B} = B logdensity_def(μ::DensityMeasure, x) = logdensityof(μ.f, x) @@ -94,7 +91,7 @@ Define a new measure in terms of a log-density `f` over some measure `base`. @inline function logdensity_def(μ::T, ν::T, x) where {T<:AbstractMeasure} μ == ν && return 0.0 - invoke(logdensity, Tuple{AbstractMeasure,AbstractMeasure,typeof(x)}, μ, ν, x) + invoke(logdensity_def, Tuple{AbstractMeasure,AbstractMeasure,typeof(x)}, μ, ν, x) end @inline function logdensity_def(μ::AbstractMeasure, ν::AbstractMeasure, x) diff --git a/src/domains.jl b/src/domains.jl index a0d68af9..38655ba1 100644 --- a/src/domains.jl +++ b/src/domains.jl @@ -65,7 +65,7 @@ function Base.show(io::IO, b::BoundedInts) print(io, "ℤ[", b.lower, ":", b.upper, "]") end -testvalue(::BoundedInts) = min(b.lower, 0) +testvalue(b::BoundedInts) = min(b.lower, 0) function Base.getindex(::typeof(ℤ), r::AbstractUnitRange) BoundedInts(extrema(r)...) diff --git a/src/kernel.jl b/src/kernel.jl index b1d6dfb4..083e750e 100644 --- a/src/kernel.jl +++ b/src/kernel.jl @@ -3,17 +3,21 @@ export Kernel abstract type AbstractKernel <: AbstractMeasure end -struct KernelReturns{M} <: AbstractKernel - value::M +struct Kernel{F,G} <: AbstractKernel + f::F + g::G + + Kernel(::Type{T}, g::G) where {T,G} = new{Type{T},G}(T, g) + Kernel(f::F, g::G) where {F,G} = new{F,G}(f, g) end -(k::KernelReturns)(_) = k.value -struct Kernel{F,S} <: AbstractKernel + +struct ParameterizedKernel{F,N,T} <: AbstractKernel f::F - ops::S + param_maps::NamedTuple{N,T} - Kernel(::Type{T}, ops::S) where {T,S} = new{Type{T},S}(T, ops) - Kernel(f::F, ops::S) where {F,S} = new{F,S}(f, ops) + ParameterizedKernel(::Type{F}, param_maps::NamedTuple{N,T}) where {F,N,T} = new{Type{F},N,T}(F, param_maps) + ParameterizedKernel(f::F, param_maps::NamedTuple{N,T}) where {F,N,T} = new{F,N,T}(f, param_maps) end """ @@ -45,17 +49,17 @@ kernel(f, ::Type{M}) where {M} = kernel(M, f) # TODO: Would this benefit from https://github.com/tisztamo/FunctionWranglers.jl? mapcall(t, x) = map(func -> func(x), t) -# (k::Kernel{Type{P},<:Tuple})(x) where {P<:ParameterizedMeasure} = k.f(mapcall(k.ops, x)...) +# (k::Kernel{Type{P},<:Tuple})(x) where {P<:ParameterizedMeasure} = k.f(mapcall(k.param_maps, x)...) -(k::Kernel{M,<:NamedTuple})(x) where {M} = k.f(; mapcall(k.ops, x)...) +(k::ParameterizedKernel)(x) where {M} = k.f(; mapcall(k.param_maps, x)...) -(k::Kernel{F,S})(x...) where {F,N,S<:NTuple{N,Symbol}} = k(x) +(k::ParameterizedKernel)(x...) = k(x) -function (k::Kernel{F,S})(x::Tuple) where {F,N,S<:NTuple{N,Symbol}} - k.f(NamedTuple{k.ops}(x)) +function (k::ParameterizedKernel)(x::Tuple) + k.f(NamedTuple{k.param_maps}(x)) end -(k::Kernel)(x) = k.f(k.ops(x)) +(k::Kernel)(x) = (k.f ∘ k.g)(x) """ For any `k::Kernel`, `basekernel` is expected to satisfy @@ -65,7 +69,7 @@ basemeasure(k(p)) == basekernel(k)(p) The main purpose of `basekernel` is to make it efficient to compute ``` -basemeasure(d::ProductMeasure) = productmeasure(basekernel(d.f), d.pars) +basemeasure(d::ProductMeasure) = productmeasure(basekernel(d.f), d.xs) ``` """ function basekernel end @@ -73,7 +77,10 @@ function basekernel end # TODO: Find a way to do better than this basekernel(f) = basemeasure ∘ f -basekernel(k::Kernel) = kernel(basekernel(k.f), k.ops) +basekernel(k::ParameterizedKernel) = kernel(basekernel(k.f), k.param_maps) + +basekernel(k::Kernel) = kernel(basekernel(k.f), k.g) + basekernel(f::Returns) = Returns(basemeasure(f.value)) # export kernelize diff --git a/src/parameterized.jl b/src/parameterized.jl index ca89e627..9e5c627c 100644 --- a/src/parameterized.jl +++ b/src/parameterized.jl @@ -29,7 +29,7 @@ end # Normal(μ = 2,) # function (::Type{P})(args...) where {N,P<:ParameterizedMeasure{N}} - C = constructorof(P) + C = constructor(P) return C(NamedTuple{N}(args...)) end @@ -39,7 +39,7 @@ function ConstructionBase.setproperties( d::P, nt::NamedTuple, ) where {P<:ParameterizedMeasure} - return constructorof(P)(merge(params(d), nt)) + return constructor(P)(merge(params(d), nt)) end ############################################################################### @@ -76,9 +76,9 @@ end # kernelfactor function kernelfactor(::Type{P}) where {N,P<:ParameterizedMeasure{N}} - (constructorof(P), N) + (constructor(P), N) end function kernelfactor(::P) where {N,P<:ParameterizedMeasure{N}} - (constructorof(P), N) + (constructor(P), N) end diff --git a/src/primitive.jl b/src/primitive.jl index a8f679a5..61feacc6 100644 --- a/src/primitive.jl +++ b/src/primitive.jl @@ -17,6 +17,6 @@ abstract type PrimitiveMeasure <: AbstractMeasure end basemeasure(μ::PrimitiveMeasure) = μ -logdensity_def(μ::PrimitiveMeasure, x) = 0.0 +logdensity_def(μ::PrimitiveMeasure, x) = static(0.0) logdensity_def(μ::M, ν::M, x) where {M<:PrimitiveMeasure} = 0.0 diff --git a/src/primitives/dirac.jl b/src/primitives/dirac.jl index 2ac3fbed..49bdb25d 100644 --- a/src/primitives/dirac.jl +++ b/src/primitives/dirac.jl @@ -14,10 +14,7 @@ end basemeasure(d::Dirac) = CountingMeasure() -basemeasure_depth(::Dirac) = static(1) -basemeasure_depth(::Type{D}) where {D<:Dirac} = static(1) - - +basemeasure_type(::Type{Dirac}) = CountingMeasure density_def(μ::Dirac, x) = x == μ.x @@ -30,3 +27,5 @@ export dirac dirac(d::AbstractMeasure) = Dirac(rand(d)) testvalue(d::Dirac) = d.x + +insupport(d::Dirac, x) = x == d.x \ No newline at end of file diff --git a/src/primitives/lebesgue.jl b/src/primitives/lebesgue.jl index 35f6b022..dd15f028 100644 --- a/src/primitives/lebesgue.jl +++ b/src/primitives/lebesgue.jl @@ -2,17 +2,27 @@ export Lebesgue -struct Lebesgue{T} <: PrimitiveMeasure +struct LebesgueMeasure <: PrimitiveMeasure end + +testvalue(::LebesgueMeasure) = 0.0 + + +struct Lebesgue{T} <: AbstractMeasure support::T end +Lebesgue() = Lebesgue(ℝ) -sampletype(::Lebesgue) = Float64 +gentype(::Lebesgue) = Float64 testvalue(d::Lebesgue) = testvalue(d.support) -logdensity_def(::Lebesgue, x) = zero(x) +proxy(d::Lebesgue) = restrict(in(d.support), LebesgueMeasure()) + +Base.:∘(::typeof(basemeasure), ::Type{Lebesgue}) = LebesgueMeasure() + +Base.show(io::IO, d::Lebesgue) = print("Lebesgue(",d.support,")") -Base.:∘(::typeof(basemeasure), ::Type{Lebesgue}) = Lebesgue +insupport(μ::Lebesgue, x) = x ∈ μ.support -Base.show(io::IO, d::Lebesgue) = print("Lebesgue(",d.support,")") \ No newline at end of file +insupport(::Lebesgue{RealNumbers}, ::Real) = static(true) \ No newline at end of file diff --git a/src/primitives/trivial.jl b/src/primitives/trivial.jl index 48165254..ed4f8572 100644 --- a/src/primitives/trivial.jl +++ b/src/primitives/trivial.jl @@ -3,3 +3,5 @@ export TrivialMeasure struct TrivialMeasure <: PrimitiveMeasure end gentype(::TrivialMeasure) = Nothing + +insupport(::TrivialMeasure, x) = False \ No newline at end of file diff --git a/src/utils.jl b/src/utils.jl index c4f90690..77aaef9f 100644 --- a/src/utils.jl +++ b/src/utils.jl @@ -3,15 +3,15 @@ const EmptyNamedTuple = NamedTuple{(),Tuple{}} showparams(io::IO, ::EmptyNamedTuple) = print(io, "()") showparams(io::IO, nt::NamedTuple) = print(io, nt) -@inline function fix(f, x) - y = f(x) - # Workaround bug https://github.com/JuliaLang/julia/issues/42615 - while x !== y - (x, y) = (y, f(y)) - end - - return y -end +# @inline function fix(f, x) +# y = f(x) +# # Workaround bug https://github.com/JuliaLang/julia/issues/42615 +# while x !== y +# (x, y) = (y, f(y)) +# end + +# return y +# end # function constructorof(::Type{T}) where {T} # C = T @@ -71,6 +71,8 @@ export basemeasure_depth static(1) + basemeasure_depth(basemeasure(μ)) end +@inline basemeasure_depth(::Type{M}) where {M} = static(1) + basemeasure_depth(basemeasure_type(M)) + @inline basemeasure_depth(::PrimitiveMeasure) = static(0) @inline basemeasure_depth(::Type{M}) where {M<:PrimitiveMeasure} = static(0) From 0c5527f357262b8365007739dbeba8332d9164e9 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 29 Nov 2021 08:03:30 -0800 Subject: [PATCH 031/368] working on tests --- src/combinators/for.jl | 8 ++++---- src/combinators/power.jl | 4 ++++ src/primitive.jl | 5 +++++ src/primitives/lebesgue.jl | 2 ++ src/proxies.jl | 7 +++++++ src/utils.jl | 10 +--------- 6 files changed, 23 insertions(+), 13 deletions(-) diff --git a/src/combinators/for.jl b/src/combinators/for.jl index 107cf6a2..df3b8d60 100644 --- a/src/combinators/for.jl +++ b/src/combinators/for.jl @@ -74,12 +74,12 @@ julia> For(eachrow(rand(4,2))) do x Normal(x[1], x[2]) end |> marginals |> colle ``` """ -For(f, dims...) = productmeasure(i -> f(i...), zip(dims...)) +For(f, dims::Integer...) = productmeasure(kernel(i -> f(i...)), zip(dims...)) -For(f, inds::AbstractArray) = productmeasure(f, inds) +For(k::AbstractKernel, inds::AbstractArray) = productmeasure(k, inds) -For(f, n::Integer) = productmeasure(f, Base.OneTo(n)) -For(f, dims::Integer...) = productmeasure(i -> f(Tuple(i)...), CartesianIndices(dims)) +For(l::AbstractKernel, n::Integer) = productmeasure(k, Base.OneTo(n)) +For(l::AbstractKernel, dims::Integer...) = productmeasure(i -> k(Tuple(i)...), CartesianIndices(dims)) function Base.eltype(d::ProductMeasure{F,I}) where {F,I<:AbstractArray} return eltype(d.f(first(d.xs))) diff --git a/src/combinators/power.jl b/src/combinators/power.jl index 7503d3e6..76e41aa6 100644 --- a/src/combinators/power.jl +++ b/src/combinators/power.jl @@ -74,6 +74,10 @@ function basemeasure_type(::Type{P}) where {M,N,R,P<:PowerMeasure{M,N,R}} return PowerMeasure{basemeasure_type(M), N, R} end +function basemeasure_depth(::Type{P}) where {M<:PrimitiveMeasure,N,R,P<:PowerMeasure{M,N,R}} + return static(0) +end + # Same as PowerMeasure @inline function logdensity_def(d::PowerMeasure, x) d1 = d.f(first(d.xs)) diff --git a/src/primitive.jl b/src/primitive.jl index 61feacc6..a442c980 100644 --- a/src/primitive.jl +++ b/src/primitive.jl @@ -17,6 +17,11 @@ abstract type PrimitiveMeasure <: AbstractMeasure end basemeasure(μ::PrimitiveMeasure) = μ +basemeasure_type(::Type{M}) where {M<:PrimitiveMeasure} = M + +@inline basemeasure_depth(::PrimitiveMeasure) = static(0) +@inline basemeasure_depth(::Type{M}) where {M<:PrimitiveMeasure} = static(0) + logdensity_def(μ::PrimitiveMeasure, x) = static(0.0) logdensity_def(μ::M, ν::M, x) where {M<:PrimitiveMeasure} = 0.0 diff --git a/src/primitives/lebesgue.jl b/src/primitives/lebesgue.jl index dd15f028..a6a64cd7 100644 --- a/src/primitives/lebesgue.jl +++ b/src/primitives/lebesgue.jl @@ -13,6 +13,8 @@ end Lebesgue() = Lebesgue(ℝ) +basemeasure_type(::Type{L}) where {L<:Lebesgue}= LebesgueMeasure + gentype(::Lebesgue) = Float64 testvalue(d::Lebesgue) = testvalue(d.support) diff --git a/src/proxies.jl b/src/proxies.jl index dc85196e..fbd93b18 100644 --- a/src/proxies.jl +++ b/src/proxies.jl @@ -14,3 +14,10 @@ function proxy end proxy(μ) = μ proxy(f, μ) = proxy(μ) + +logdensity_def(μ, x) = logdensity_def(proxy(μ), x) + + +basemeasure(μ, x) = basemeasure(proxy(μ), x) + +basemeasure(μ) = basemeasure(proxy(μ)) diff --git a/src/utils.jl b/src/utils.jl index 77aaef9f..24aa404c 100644 --- a/src/utils.jl +++ b/src/utils.jl @@ -62,19 +62,11 @@ functioninstance(::Type{F}) where {F<:Function} = F.instance export basemeasure_depth @inline function basemeasure_depth(μ::M) where {M<:AbstractMeasure} - @info """ - Add methods for better performance: - - basemeasure_depth(::$M) - basemeasure_depth(::Type{$M}) - """ - static(1) + basemeasure_depth(basemeasure(μ)) + basemeasure_depth(M) end @inline basemeasure_depth(::Type{M}) where {M} = static(1) + basemeasure_depth(basemeasure_type(M)) -@inline basemeasure_depth(::PrimitiveMeasure) = static(0) - @inline basemeasure_depth(::Type{M}) where {M<:PrimitiveMeasure} = static(0) export logdensity_tuple From b611f6204d8432cb94573c3e27f890df03e0f15e Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 29 Nov 2021 12:01:42 -0800 Subject: [PATCH 032/368] cleaning up --- src/combinators/for.jl | 11 ++++++++--- src/combinators/power.jl | 8 ++------ src/combinators/product.jl | 26 +++++++++++++++----------- src/combinators/smart-constructors.jl | 2 +- src/proxies.jl | 1 - src/utils.jl | 2 -- 6 files changed, 26 insertions(+), 24 deletions(-) diff --git a/src/combinators/for.jl b/src/combinators/for.jl index df3b8d60..2129be51 100644 --- a/src/combinators/for.jl +++ b/src/combinators/for.jl @@ -74,12 +74,17 @@ julia> For(eachrow(rand(4,2))) do x Normal(x[1], x[2]) end |> marginals |> colle ``` """ -For(f, dims::Integer...) = productmeasure(kernel(i -> f(i...)), zip(dims...)) +For(f::Function, args...) = productmeasure(kernel(f), zip(args...)) + +For(f::Function, n::Integer) = productmeasure(kernel(f), Base.OneTo(n)) + +For(f::Function, dims::Integer...) = productmeasure(kernel(i -> f(Tuple(i)...)), CartesianIndices(dims)) For(k::AbstractKernel, inds::AbstractArray) = productmeasure(k, inds) -For(l::AbstractKernel, n::Integer) = productmeasure(k, Base.OneTo(n)) -For(l::AbstractKernel, dims::Integer...) = productmeasure(i -> k(Tuple(i)...), CartesianIndices(dims)) +For(k::AbstractKernel, n::Integer) = productmeasure(k, Base.OneTo(n)) + +For(k::AbstractKernel, dims::Integer...) = productmeasure(kernel(i -> k(Tuple(i)...)), CartesianIndices(dims)) function Base.eltype(d::ProductMeasure{F,I}) where {F,I<:AbstractArray} return eltype(d.f(first(d.xs))) diff --git a/src/combinators/power.jl b/src/combinators/power.jl index 76e41aa6..8978ea9b 100644 --- a/src/combinators/power.jl +++ b/src/combinators/power.jl @@ -29,7 +29,7 @@ using FillArrays: Fill export PowerMeasure -const PowerMeasure{M,N,R} = ProductMeasure{Kernel{Returns{M}, typeof(identity)}, CartesianIndices{N, R}} +const PowerMeasure{M,N,R} = ProductMeasure{M,Kernel{Returns{M}, typeof(identity)}, LinearIndices{N, R}} Base.:^(μ::AbstractMeasure, ::Tuple{}) = μ @@ -46,17 +46,14 @@ params(d::PowerMeasure) = params(first(marginals(d))) # basemeasure(μ::PowerMeasure) = @inbounds basemeasure(first(μ.data))^size(μ.data) -# Same as PowerMeasure @inline function basemeasure(d::PowerMeasure) - _basemeasure(d, (basemeasure(d.f(first(d.xs))))) + _basemeasure(d, basemeasure(d.f.f.value)) end -# Same as PowerMeasure @inline function _basemeasure(d::PowerMeasure, b) b ^ size(d.xs) end -# Same as PowerMeasure @inline function _basemeasure(d::PowerMeasure, b::FactoredBase) n = length(d.xs) inbounds(x) = all(b.inbounds, x) @@ -78,7 +75,6 @@ function basemeasure_depth(::Type{P}) where {M<:PrimitiveMeasure,N,R,P<:PowerMea return static(0) end -# Same as PowerMeasure @inline function logdensity_def(d::PowerMeasure, x) d1 = d.f(first(d.xs)) sum(xj -> logdensity_def(d1, xj), x) diff --git a/src/combinators/product.jl b/src/combinators/product.jl index 899f17a0..995bcc25 100644 --- a/src/combinators/product.jl +++ b/src/combinators/product.jl @@ -7,9 +7,15 @@ using FillArrays abstract type AbstractProductMeasure <: AbstractMeasure end -struct ProductMeasure{K,I} <: AbstractProductMeasure +struct ProductMeasure{M,K<:AbstractKernel,I} <: AbstractProductMeasure f::K xs::I + + function ProductMeasure(f::K, xs::I) where {K,I} + μ₁ = f(first(xs)) + M = typeof(μ₁) + new{M,K,I}(f, xs) + end end # TODO: Test for equality without traversal, probably by first converting to a @@ -26,6 +32,8 @@ Base.length(μ::ProductMeasure) = length(marginals(μ)) basemeasure(d::ProductMeasure) = productmeasure(basekernel(d.f), d.xs) +basemeasure_depth(μ::ProductMeasure) = basemeasure_depth(first(marginals(μ))) + # TODO: Do we need these methods? # basemeasure(d::ProductMeasure) = ProductMeasure(basemeasure ∘ d.f, d.xs) # basemeasure(d::ProductMeasure{typeof(identity)}) = ProductMeasure(identity, map(basemeasure, d.xs)) @@ -33,7 +41,7 @@ basemeasure(d::ProductMeasure) = productmeasure(basekernel(d.f), d.xs) export marginals -function marginals(d::ProductMeasure{K,I}) where {K,I} +function marginals(d::ProductMeasure{M,K,I}) where {M,K,I} _marginals(d, isiterable(I)) end @@ -41,11 +49,7 @@ function _marginals(d::ProductMeasure, ::Iterable) return (d.f(i) for i in d.xs) end -function _marginals(d::ProductMeasure{K,I}, ::NonIterable) where {K,I} - error("Type $I is not iterable. Add an `iterate` or `marginals` method to fix.") -end - -testvalue(d::ProductMeasure) = map(testvalue, marginals(d)) +testvalue(d::AbstractProductMeasure) = map(testvalue, marginals(d)) function Base.rand(rng::AbstractRNG, ::Type{T}, d::ProductMeasure) where {T} _rand(rng, T, d, marginals(d)) @@ -78,7 +82,7 @@ end ############################################################################### # I <: AbstractArray -marginals(d::ProductMeasure{K,A}) where {K,A<:AbstractArray} = mappedarray(d.f, d.xs) +marginals(d::ProductMeasure{M,K,A}) where {M,K,A<:AbstractArray} = mappedarray(d.f, d.xs) @inline function logdensity_def(d::ProductMeasure, x) mapreduce(logdensity_def, +, marginals(d), x) @@ -88,7 +92,7 @@ end sum(x -> logdensity_def(d.f.f.value, x), x) end -# function Base.rand(rng::AbstractRNG, ::Type{T}, d::ProductMeasure{K,I}) where {T,F,I<:CartesianIndices} +# function Base.rand(rng::AbstractRNG, ::Type{T}, d::ProductMeasure{M,K,I}) where {T,F,I<:CartesianIndices} # end @@ -157,7 +161,7 @@ end # end # # FIXME -# function ConstructionBase.constructorof(::Type{P}) where {K,I,P<:ProductMeasure{K,I}} +# function ConstructionBase.constructorof(::Type{P}) where {K,I,P<:ProductMeasure{M,K,I}} # p -> productmeasure(d.f, p) # end @@ -175,7 +179,7 @@ end # end # end -function kernelfactor(μ::ProductMeasure{K,<:Fill}) where {K} +function kernelfactor(μ::ProductMeasure{M,K,<:Fill}) where {M,K} k = kernel(first(marginals(μ))) (p -> k.f(p)^size(μ), k.param_maps) end diff --git a/src/combinators/smart-constructors.jl b/src/combinators/smart-constructors.jl index f66c8fdc..cf44fd0c 100644 --- a/src/combinators/smart-constructors.jl +++ b/src/combinators/smart-constructors.jl @@ -39,7 +39,7 @@ end # PowerMeaure function Base.:^(μ::M, dims::NTuple{N,I}) where {M<:AbstractMeasure,N,I} - productmeasure(Kernel(Returns(μ), identity), CartesianIndices(dims)) + productmeasure(Kernel(Returns(μ), identity), LinearIndices(dims)) end # function Base.:^(μ::M, dims::Tuple{I}) where {M<:AbstractMeasure,N,I} diff --git a/src/proxies.jl b/src/proxies.jl index fbd93b18..6112f747 100644 --- a/src/proxies.jl +++ b/src/proxies.jl @@ -18,6 +18,5 @@ proxy(f, μ) = proxy(μ) logdensity_def(μ, x) = logdensity_def(proxy(μ), x) -basemeasure(μ, x) = basemeasure(proxy(μ), x) basemeasure(μ) = basemeasure(proxy(μ)) diff --git a/src/utils.jl b/src/utils.jl index 24aa404c..3fd5fe28 100644 --- a/src/utils.jl +++ b/src/utils.jl @@ -67,8 +67,6 @@ end @inline basemeasure_depth(::Type{M}) where {M} = static(1) + basemeasure_depth(basemeasure_type(M)) -@inline basemeasure_depth(::Type{M}) where {M<:PrimitiveMeasure} = static(0) - export logdensity_tuple function logdensity_tuple(d, x) From 38f230bd30cec8e351bd07d5a460e3ebf1e2691a Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 29 Nov 2021 12:36:06 -0800 Subject: [PATCH 033/368] get tests to pass --- src/combinators/for.jl | 2 +- src/combinators/power.jl | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/combinators/for.jl b/src/combinators/for.jl index 2129be51..279724c1 100644 --- a/src/combinators/for.jl +++ b/src/combinators/for.jl @@ -74,7 +74,7 @@ julia> For(eachrow(rand(4,2))) do x Normal(x[1], x[2]) end |> marginals |> colle ``` """ -For(f::Function, args...) = productmeasure(kernel(f), zip(args...)) +For(f::Function, args...) = productmeasure(kernel(i -> f(Tuple(i)...)), zip(args...)) For(f::Function, n::Integer) = productmeasure(kernel(f), Base.OneTo(n)) diff --git a/src/combinators/power.jl b/src/combinators/power.jl index 8978ea9b..9cfd1510 100644 --- a/src/combinators/power.jl +++ b/src/combinators/power.jl @@ -29,7 +29,7 @@ using FillArrays: Fill export PowerMeasure -const PowerMeasure{M,N,R} = ProductMeasure{M,Kernel{Returns{M}, typeof(identity)}, LinearIndices{N, R}} +const PowerMeasure{M,N,R} = ProductMeasure{M, Kernel{Returns{M}, typeof(identity)}, LinearIndices{N, R}} Base.:^(μ::AbstractMeasure, ::Tuple{}) = μ From a60a4fa621cd95ce324096009e1ba37ab94013b4 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 29 Nov 2021 12:36:18 -0800 Subject: [PATCH 034/368] tests passing --- src/primitives/lebesgue.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/primitives/lebesgue.jl b/src/primitives/lebesgue.jl index a6a64cd7..dee50e33 100644 --- a/src/primitives/lebesgue.jl +++ b/src/primitives/lebesgue.jl @@ -23,7 +23,7 @@ proxy(d::Lebesgue) = restrict(in(d.support), LebesgueMeasure()) Base.:∘(::typeof(basemeasure), ::Type{Lebesgue}) = LebesgueMeasure() -Base.show(io::IO, d::Lebesgue) = print("Lebesgue(",d.support,")") +Base.show(io::IO, d::Lebesgue) = print(io, "Lebesgue(",d.support,")") insupport(μ::Lebesgue, x) = x ∈ μ.support From 54adf0d02f3851538be4994e50642402bb9c4992 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 29 Nov 2021 12:55:26 -0800 Subject: [PATCH 035/368] update logdensity_def for pointwise product --- src/combinators/pointwise.jl | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/src/combinators/pointwise.jl b/src/combinators/pointwise.jl index 0a0b0e97..9635f7bf 100644 --- a/src/combinators/pointwise.jl +++ b/src/combinators/pointwise.jl @@ -28,7 +28,9 @@ Base.length(m::PointwiseProductMeasure{T}) where {T} = length(m.data) ⊙(args...) = pointwiseproduct(args...) @inline function logdensity_def(d::PointwiseProductMeasure, x) - sum((logdensity_def(dⱼ, x) for dⱼ in d.data)) + sum(d.data) do dⱼ + logdensity_def(dⱼ, x) + end end function gentype(d::PointwiseProductMeasure) From 2b08bd85bdce8ec402a9030e68467c95ba251783 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 29 Nov 2021 15:24:53 -0800 Subject: [PATCH 036/368] PrettyPrinting + tests --- Project.toml | 1 + src/MeasureBase.jl | 3 +++ src/combinators/power.jl | 12 ++++++++++-- src/combinators/product.jl | 14 ++++++++++++++ src/combinators/superpose.jl | 8 ++++++++ src/density.jl | 6 ++++++ src/kernel.jl | 18 ++++++++++++++++++ src/primitive.jl | 4 ++++ src/primitives/dirac.jl | 5 +++++ src/primitives/lebesgue.jl | 6 +++--- src/utils.jl | 10 ---------- 11 files changed, 72 insertions(+), 15 deletions(-) diff --git a/Project.toml b/Project.toml index c7f0ed55..794897c6 100644 --- a/Project.toml +++ b/Project.toml @@ -21,6 +21,7 @@ DensityInterface = "0.4" FillArrays = "0.12" LogExpFunctions = "0.3" MappedArrays = "0.4" +PrettyPrinting = "0.3" Static = "0.4" Tricks = "0.1" julia = "1.3" diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index 70ac0650..4af36421 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -10,6 +10,9 @@ import DensityInterface: densityof import DensityInterface: DensityKind using DensityInterface +using PrettyPrinting +const Pretty = PrettyPrinting + using FillArrays using Static diff --git a/src/combinators/power.jl b/src/combinators/power.jl index 9cfd1510..d7e190a6 100644 --- a/src/combinators/power.jl +++ b/src/combinators/power.jl @@ -37,8 +37,16 @@ function Base.:^(μ::AbstractMeasure, dims::Integer...) return μ^dims end -Base.show(io::IO, d::PowerMeasure) = print(io, d.f.f.value, " ^ ", size(d.xs)) -Base.show(io::IO, d::PowerMeasure{M,1}) where {M} = print(io, d.f.f.value, " ^ ", length(d.xs)) +function Pretty.tile(d::PowerMeasure{M,1}) where {M} + Pretty.pair_layout(Pretty.tile(d.f.f.value), Pretty.tile(length(d.xs)); sep = " ^ ") +end + +function Pretty.tile(d::PowerMeasure) + Pretty.pair_layout(Pretty.tile(d.f.f.value), Pretty.tile(size(d.xs)); sep = " ^ ") +end + +# Base.show(io::IO, d::PowerMeasure) = print(io, d.f.f.value, " ^ ", size(d.xs)) +# Base.show(io::IO, d::PowerMeasure{M,1}) where {M} = print(io, d.f.f.value, " ^ ", length(d.xs)) # gentype(d::PowerMeasure{M,N}) where {M,N} = @inbounds Array{gentype(first(marginals(d))), N} diff --git a/src/combinators/product.jl b/src/combinators/product.jl index 995bcc25..f6a1fa8a 100644 --- a/src/combinators/product.jl +++ b/src/combinators/product.jl @@ -18,6 +18,13 @@ struct ProductMeasure{M,K<:AbstractKernel,I} <: AbstractProductMeasure end end + +function Pretty.tile(μ::ProductMeasure) + result = Pretty.literal("For(") + result *= Pretty.pair_layout(Pretty.tile(μ.f), Pretty.tile(μ.xs); sep = ", ") + result *= Pretty.literal(")") +end + # TODO: Test for equality without traversal, probably by first converting to a # canonical form function Base.:(==)(a::ProductMeasure, b::ProductMeasure) @@ -66,6 +73,12 @@ struct TupleProductMeasure{T} <: AbstractProductMeasure components::T end + +function Pretty.tile(μ::TupleProductMeasure{T}) where {F,T<:Tuple} + mar = marginals(μ) + Pretty.list_layout(Pretty.Layout[Pretty.tile.(mar)...]; sep = " ⊗ ") +end + export ⊗ ⊗(μs::AbstractMeasure...) = productmeasure(μs) @@ -187,3 +200,4 @@ end # function kernelfactor(μ::ProductMeasure{K,A}) where {K,A<:AbstractArray} # (p -> set.(marginals(μ), params, p), μ.xs) # end + diff --git a/src/combinators/superpose.jl b/src/combinators/superpose.jl index ae9c942c..50862550 100644 --- a/src/combinators/superpose.jl +++ b/src/combinators/superpose.jl @@ -24,6 +24,14 @@ struct SuperpositionMeasure{NT} <: AbstractMeasure components::NT end + +function Pretty.tile(d::SuperpositionMeasure) + result = Pretty.literal("SuperpositionMeasure(") + result *= Pretty.list_layout([Pretty.tile.(d.components)...]) + result *= Pretty.literal(")") +end + + testvalue(μ::SuperpositionMeasure) = testvalue(first(μ.components)) # SuperpositionMeasure(ms :: AbstractMeasure...) = SuperpositionMeasure{X,length(ms)}(ms) diff --git a/src/density.jl b/src/density.jl index ca71b6b6..cc4a7802 100644 --- a/src/density.jl +++ b/src/density.jl @@ -44,6 +44,12 @@ struct DensityMeasure{F,B} <: AbstractMeasure base::B end +function Pretty.tile(μ::DensityMeasure{F,B}) where {F,B} + result = Pretty.literal("DensityMeasure ∫(") + result *= Pretty.pair_layout(Pretty.tile(μ.f), Pretty.tile(μ.base); sep = ", ") + result *= Pretty.literal(")") +end + densitymeasure(f, base) = _densitymeasure(f, base, DensityKind(f)) _densitymeasure(f, base, ::IsDensity) = DensityMeasure(f, base) diff --git a/src/kernel.jl b/src/kernel.jl index 083e750e..e9ad6aac 100644 --- a/src/kernel.jl +++ b/src/kernel.jl @@ -90,4 +90,22 @@ basekernel(f::Returns) = Returns(basemeasure(f.value)) # (Kernel{C,}(NamedTuple{N}, ), values(getfield(μ, :par))) # end +function Base.show(io::IO, μ::AbstractKernel) + io = IOContext(io, :compact => true) + Pretty.pprint(io, μ) +end + + +function Pretty.quoteof(k::Kernel) + qf = Pretty.quoteof(k.f) + qg = Pretty.quoteof(k.g) + :(Kernel($qf, $qg)) +end + +function Pretty.quoteof(k::ParameterizedKernel) + qf = Pretty.quoteof(k.f) + qg = Pretty.quoteof(k.param_maps) + :(Kernel($qf, $qg)) +end + export kernelfactor diff --git a/src/primitive.jl b/src/primitive.jl index a442c980..4841e13b 100644 --- a/src/primitive.jl +++ b/src/primitive.jl @@ -25,3 +25,7 @@ basemeasure_type(::Type{M}) where {M<:PrimitiveMeasure} = M logdensity_def(μ::PrimitiveMeasure, x) = static(0.0) logdensity_def(μ::M, ν::M, x) where {M<:PrimitiveMeasure} = 0.0 + +function Pretty.quoteof(μ::M) where {M<:PrimitiveMeasure} + :($M()) +end \ No newline at end of file diff --git a/src/primitives/dirac.jl b/src/primitives/dirac.jl index 49bdb25d..6008f654 100644 --- a/src/primitives/dirac.jl +++ b/src/primitives/dirac.jl @@ -5,6 +5,11 @@ struct Dirac{X} <: AbstractMeasure x::X end +function Pretty.quoteof(d::Dirac) + q = Pretty.quoteof(d.x) + :(Dirac($q)) +end + gentype(μ::Dirac{X}) where {X} = X function (μ::Dirac{X})(s) where {X} diff --git a/src/primitives/lebesgue.jl b/src/primitives/lebesgue.jl index 89f6d0e5..da2f723f 100644 --- a/src/primitives/lebesgue.jl +++ b/src/primitives/lebesgue.jl @@ -6,14 +6,14 @@ struct LebesgueMeasure <: PrimitiveMeasure end testvalue(::LebesgueMeasure) = 0.0 -gentype(::Lebesgue) = Float64 -gentype(::Lebesgue) = Float64 -gentype(::Lebesgue) = Float64 + struct Lebesgue{T} <: AbstractMeasure support::T end +gentype(::Lebesgue) = Float64 + Lebesgue() = Lebesgue(ℝ) basemeasure_type(::Type{L}) where {L<:Lebesgue}= LebesgueMeasure diff --git a/src/utils.jl b/src/utils.jl index ece2303e..559f9af4 100644 --- a/src/utils.jl +++ b/src/utils.jl @@ -8,16 +8,6 @@ end showparams(io::IO, ::EmptyNamedTuple) = print(io, "()") showparams(io::IO, nt::NamedTuple) = print(io, nt) -# @inline function fix(f, x) -# y = f(x) -# # Workaround bug https://github.com/JuliaLang/julia/issues/42615 -# while x !== y -# (x, y) = (y, f(y)) -# end - -# return y -# end - # function constructorof(::Type{T}) where {T} # C = T # while C isa UnionAll From 88777db322785efec107cabf2929a728bf011526 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 29 Nov 2021 16:05:00 -0800 Subject: [PATCH 037/368] speed up `rootmeasure` --- src/utils.jl | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) diff --git a/src/utils.jl b/src/utils.jl index 559f9af4..b780c4e5 100644 --- a/src/utils.jl +++ b/src/utils.jl @@ -36,11 +36,19 @@ It's sometimes important to be able to find the fix point of a measure under repeatedly until there's no change. That's what this does. """ @inline function rootmeasure(μ) - α = basemeasure(μ) - μ === α && return α - return rootmeasure(α) + n = basemeasure_depth(μ) + _rootmeasure(μ, static(n)) end +@generated function _rootmeasure(μ, ::StaticInt{n}) where {n} + q = quote end + foreach(1:n) do _ + push!(q.args, :(μ = basemeasure(μ))) + end + return q +end + + # Base on the Tricks.jl README using Tricks struct Iterable end From 3a66b604cd2ac895d76b28b01a35763e5fca4393 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 29 Nov 2021 16:05:12 -0800 Subject: [PATCH 038/368] oops didn't mean to include that --- src/modified_gram_schmitt.jl | 85 ------------------------------------ 1 file changed, 85 deletions(-) delete mode 100644 src/modified_gram_schmitt.jl diff --git a/src/modified_gram_schmitt.jl b/src/modified_gram_schmitt.jl deleted file mode 100644 index 2adcdf72..00000000 --- a/src/modified_gram_schmitt.jl +++ /dev/null @@ -1,85 +0,0 @@ -using LinearAlgebra - -# Modify column jᵥ to be orthogonal to column jᵤ -function ortho!(A::AbstractMatrix, jᵥ, jᵤ; startat=1) - # v ← v - projᵤ(v) - nrows = size(A,1) - u_v = 0.0 - u_u = 0.0 - @inbounds for i in startat:nrows - u_v += A[i,jᵤ] * A[i,jᵥ] - u_u += A[i,jᵤ] ^ 2 - end - - k = u_v / u_u - - @inbounds for i in startat:nrows - A[i, jᵥ] = A[i, jᵥ] - k * A[i, jᵤ] - end - - return A -end - -function ortho!(A::AbstractMatrix, triangular=false) - for j2 in size(A,2):-1:1 - for j1 in 1:(j2-1) - ortho!(A, j1, j2) - end - end - - for col in eachcol(A) - normalize!(col) - end - - return A -end - -function makelower!(A) - for jᵥ in 2:size(A,2) - @inbounds for jᵤ in 1:(jᵥ-1) - k = A[jᵤ, jᵥ] / A[jᵤ, jᵤ] - - A[jᵤ,jᵥ] = 0.0 - - @inbounds for i in (jᵤ+1):size(A,1) - A[i,jᵥ] = A[i, jᵥ] - k * A[i, jᵤ] - end - end - end - - for j in 1:size(A,2) - @inbounds if A[j,j] < 0.0 - view(A, :, j) .*= -1 - end - end - - return A - -end - - - - -function WtoV(W) - # make columns orthogonal - for j2 in size(W,2):-1:1 - for j1 in 1:(j2-1) - ortho!(W, j1, j2; startat=j2) - end - end - - for col in eachcol(W) - normalize!(col) - end - - return W -end - -W = [I; randn(5,5) ./ randn(5,5)] - -using BenchmarkTools -@btime WtoV(W) - - - -W' * W \ No newline at end of file From 71af957add56e3b6f8119a53845813a45e3ecb7a Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 29 Nov 2021 16:24:15 -0800 Subject: [PATCH 039/368] tile(::FactoredBase) --- src/combinators/factoredbase.jl | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/src/combinators/factoredbase.jl b/src/combinators/factoredbase.jl index 2747d419..f96911c8 100644 --- a/src/combinators/factoredbase.jl +++ b/src/combinators/factoredbase.jl @@ -12,4 +12,10 @@ end d.constℓ + d.varℓ() end +function Pretty.tile(fb::FactoredBase) + result = Pretty.literal("FactoredBase") + result *= Pretty.list_layout(Pretty.tile.([fb.inbounds, fb.constℓ, fb.varℓ, fb.base])) + result +end + basemeasure(d::FactoredBase) = d.base From f3b3b96102fd942164e3f0e9ec41a0a82bd37439 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 29 Nov 2021 16:34:12 -0800 Subject: [PATCH 040/368] Update Half and FactoredBase --- src/combinators/factoredbase.jl | 2 ++ src/combinators/half.jl | 13 ++++++++++--- test/runtests.jl | 4 ++-- 3 files changed, 14 insertions(+), 5 deletions(-) diff --git a/src/combinators/factoredbase.jl b/src/combinators/factoredbase.jl index f96911c8..aa2467b3 100644 --- a/src/combinators/factoredbase.jl +++ b/src/combinators/factoredbase.jl @@ -19,3 +19,5 @@ function Pretty.tile(fb::FactoredBase) end basemeasure(d::FactoredBase) = d.base + +basemeasure_type(::Type{FactoredBase{R,C,V,B}}) where {R,C,V,B} = B \ No newline at end of file diff --git a/src/combinators/half.jl b/src/combinators/half.jl index 4b843e59..c3cdb6d0 100644 --- a/src/combinators/half.jl +++ b/src/combinators/half.jl @@ -11,14 +11,21 @@ end unhalf(μ::Half) = μ.parent +isnonnegative(x) = x ≥ 0.0 + @inline function basemeasure(μ::Half) - inbounds(x) = x > 0 - constℓ = logtwo - varℓ() = 0.0 + inbounds = isnonnegative + constℓ = static(logtwo) + varℓ = Returns(0.0) base = basemeasure(unhalf(μ)) FactoredBase(inbounds, constℓ, varℓ, base) end +function basemeasure_type(::Type{Half{M}}) where {M} + B = basemeasure_type(M) + FactoredBase{typeof(isnonnegative), StaticFloat64{logtwo}, Returns{Float64}, B} +end + function Base.rand(rng::AbstractRNG, T::Type, μ::Half) return abs(rand(rng, T, unhalf(μ))) end diff --git a/test/runtests.jl b/test/runtests.jl index 2826aa83..5d258647 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -190,9 +190,9 @@ end @testset "Half" begin Normal() = ∫exp(x -> -0.5x^2, Lebesgue(ℝ)) HalfNormal() = Half(Normal()) - @test logdensity_def(HalfNormal(), Lebesgue(ℝ), -0.2) == -Inf + @test logdensityof(HalfNormal(), -0.2) == -Inf @test logdensity_def(HalfNormal(), 0.2) == logdensity_def(Normal(), 0.2) - @test density_def(HalfNormal(), Lebesgue(ℝ), 0.2) ≈ 2 * density_def(Normal(), Lebesgue(ℝ), 0.2) + @test densityof(HalfNormal(), 0.2) ≈ 2 * densityof(Normal(), 0.2) end # import MeasureBase.:⋅ From edd2f0be4be42997429c2df48daf9be6e77492fe Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 29 Nov 2021 16:35:15 -0800 Subject: [PATCH 041/368] drop exp.jl --- src/exp.jl | 44 -------------------------------------------- 1 file changed, 44 deletions(-) delete mode 100644 src/exp.jl diff --git a/src/exp.jl b/src/exp.jl deleted file mode 100644 index 7a67c15f..00000000 --- a/src/exp.jl +++ /dev/null @@ -1,44 +0,0 @@ -struct Exp{X} <: AbstractFloat - log::X -end - -Base.iszero(::Exp) = false - -Base.log(x::Exp) = x.log - -function Base.show(io::IO, x::Exp) - io = IOContext(io, :compact => true) - print(io, "Exp(", log(x), ")") -end - -Base.:*(a::Exp, b::Exp) = Exp(log(a) + log(b)) - -Base.:/(a::Number, b::Exp) = a * Exp(-log(b)) - -Base.inv(a::Exp) = Exp(-log(a)) - -Base.:^(a::Exp, b::Number) = Exp(b * log(a)) - -Base.:^(a::Exp, b::Integer) = Exp(b * log(a)) - -Base.:^(a::Exp, b) = Exp(b * log(a)) -Base.:^(a::Exp, b::Rational) = Exp(b * log(a)) - -Base.promote_rule(T::Type{<:Real}, ::Type{Exp}) = T -Base.promote_rule(::Type{Exp}, T::Type{<:Real}) = T - -Base.convert(::Type{<:Real}, x::Exp) = exp(log(x)) - -# Exp(3) / Exp(2) - -# Exp(3) * Exp(2) - -# 3 + Exp(2) - -# 3 / Exp(4) - -# Exp(2) ^ 3 - -# 1 / Exp(2) - -# 2 + Exp(3) ^ 0 From e5abb39e370acef1b2ea3e64d945bcbf21e93eb8 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 29 Nov 2021 18:22:22 -0800 Subject: [PATCH 042/368] simplify basemeasure --- src/combinators/power.jl | 15 +-------------- 1 file changed, 1 insertion(+), 14 deletions(-) diff --git a/src/combinators/power.jl b/src/combinators/power.jl index d7e190a6..09625716 100644 --- a/src/combinators/power.jl +++ b/src/combinators/power.jl @@ -55,20 +55,7 @@ params(d::PowerMeasure) = params(first(marginals(d))) # basemeasure(μ::PowerMeasure) = @inbounds basemeasure(first(μ.data))^size(μ.data) @inline function basemeasure(d::PowerMeasure) - _basemeasure(d, basemeasure(d.f.f.value)) -end - -@inline function _basemeasure(d::PowerMeasure, b) - b ^ size(d.xs) -end - -@inline function _basemeasure(d::PowerMeasure, b::FactoredBase) - n = length(d.xs) - inbounds(x) = all(b.inbounds, x) - constℓ = n * b.constℓ - varℓ() = n * b.varℓ() - base = b.base^size(d.xs) - FactoredBase(inbounds, constℓ, varℓ, base) + basemeasure(d.f.f.value) ^ size(d.xs) end function basemeasure_depth(d::PowerMeasure{M,N,R}) where {M,N,R} From 869158d11b9272806c559240d3e6d72593108e81 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 29 Nov 2021 18:22:35 -0800 Subject: [PATCH 043/368] drop old `include` --- src/MeasureBase.jl | 1 - 1 file changed, 1 deletion(-) diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index 4af36421..d0bc6f3a 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -62,7 +62,6 @@ include("kernel.jl") include("parameterized.jl") include("combinators/mapsto.jl") include("combinators/half.jl") -include("exp.jl") include("domains.jl") include("primitive.jl") include("utils.jl") From ee7cd0667afd270abbdba5127e78382700430f36 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 30 Nov 2021 06:05:31 -0800 Subject: [PATCH 044/368] drop redundant method --- src/primitives/lebesgue.jl | 2 -- 1 file changed, 2 deletions(-) diff --git a/src/primitives/lebesgue.jl b/src/primitives/lebesgue.jl index da2f723f..fe29246c 100644 --- a/src/primitives/lebesgue.jl +++ b/src/primitives/lebesgue.jl @@ -18,8 +18,6 @@ Lebesgue() = Lebesgue(ℝ) basemeasure_type(::Type{L}) where {L<:Lebesgue}= LebesgueMeasure -gentype(::Lebesgue) = Float64 - testvalue(d::Lebesgue) = testvalue(d.support) proxy(d::Lebesgue) = restrict(in(d.support), LebesgueMeasure()) From 913cb360b837ebbb60afc3ea5988d183b7d0ed6f Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 30 Nov 2021 06:07:44 -0800 Subject: [PATCH 045/368] update compat Returns --- src/MeasureBase.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index d0bc6f3a..e9001ce9 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -53,7 +53,7 @@ if VERSION < v"1.7.0-beta1.0" value::T end - (f::Returns)(x) = f.value + (f::Returns)(args...) = f.value end end From 4291748e842e0c936b1a8cf151c0fcd0f8f63bf8 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 30 Nov 2021 11:44:14 -0800 Subject: [PATCH 046/368] add AbstractDensity --- src/density.jl | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/src/density.jl b/src/density.jl index cc4a7802..b497b855 100644 --- a/src/density.jl +++ b/src/density.jl @@ -1,3 +1,8 @@ +abstract type AbstractDensity end + +@inline DensityKind(::AbstractDensity) = IsDensity() + + """ struct Density{M,B} μ::M @@ -12,12 +17,11 @@ Because this function is often difficult to express in closed form, there are many different ways of computing it. We therefore provide a formal representation to allow comptuational flexibilty. """ -struct Density{M,B,L} +struct Density{M,B,L} <: AbstractDensity μ::M base::B end -@inline DensityKind(::Density) = IsDensity() export 𝒹 From 046dc2fdb339b45b8294eca5a95a02e6a063b55c Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 30 Nov 2021 11:58:04 -0800 Subject: [PATCH 047/368] Move Affine to MeasureTheory --- src/MeasureBase.jl | 1 - src/combinators/affine.jl | 287 -------------------------- src/combinators/smart-constructors.jl | 19 -- src/rand.jl | 6 +- test/runtests.jl | 73 ------- 5 files changed, 1 insertion(+), 385 deletions(-) delete mode 100644 src/combinators/affine.jl diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index e9001ce9..88f0e8fc 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -78,7 +78,6 @@ include("combinators/superpose.jl") include("combinators/product.jl") include("combinators/for.jl") include("combinators/power.jl") -include("combinators/affine.jl") include("combinators/spikemixture.jl") include("combinators/likelihood.jl") include("combinators/pointwise.jl") diff --git a/src/combinators/affine.jl b/src/combinators/affine.jl deleted file mode 100644 index 2072a450..00000000 --- a/src/combinators/affine.jl +++ /dev/null @@ -1,287 +0,0 @@ -export Affine, AffineTransform -using LinearAlgebra - -const AFFINEPARS = [ - (:μ, :σ) - (:μ, :ω) - (:σ,) - (:ω,) - (:μ,) -] - -struct AffineTransform{N,T} - par::NamedTuple{N,T} -end - -quoteof(f::AffineTransform) = :(AffineTransform($(quoteof(f.par)))) - -params(f::AffineTransform) = getfield(f, :par) - -@inline Base.getproperty(d::AffineTransform, s::Symbol) = getfield(getfield(d, :par), s) - -Base.propertynames(d::AffineTransform{N}) where {N} = N - -@inline Base.inv(f::AffineTransform{(:μ, :σ)}) = - AffineTransform((μ = -(f.σ \ f.μ), ω = f.σ)) -@inline Base.inv(f::AffineTransform{(:μ, :ω)}) = AffineTransform((μ = -f.ω * f.μ, σ = f.ω)) -@inline Base.inv(f::AffineTransform{(:σ,)}) = AffineTransform((ω = f.σ,)) -@inline Base.inv(f::AffineTransform{(:ω,)}) = AffineTransform((σ = f.ω,)) -@inline Base.inv(f::AffineTransform{(:μ,)}) = AffineTransform((μ = -f.μ,)) - -# `size(f) == (m,n)` means `f : ℝⁿ → ℝᵐ` -Base.size(f::AffineTransform{(:μ, :σ)}) = size(f.σ) -Base.size(f::AffineTransform{(:μ, :ω)}) = size(f.ω) -Base.size(f::AffineTransform{(:σ,)}) = size(f.σ) -Base.size(f::AffineTransform{(:ω,)}) = size(f.ω) - -function Base.size(f::AffineTransform{(:μ,)}) - (n,) = size(f.μ) - return (n, n) -end - -Base.size(f::AffineTransform, n::Int) = @inbounds size(f)[n] - -(f::AffineTransform{(:μ,)})(x) = x + f.μ -(f::AffineTransform{(:σ,)})(x) = f.σ * x -(f::AffineTransform{(:ω,)})(x) = f.ω \ x -(f::AffineTransform{(:μ, :σ)})(x) = f.σ * x + f.μ -(f::AffineTransform{(:μ, :ω)})(x) = f.ω \ x + f.μ - -rowsize(x) = () -rowsize(x::AbstractArray) = (size(x, 1),) - -function rowsize(f::AffineTransform) - size_f = size(f) - - size_f isa Tuple{} && return 0 - return first(size_f) -end - -colsize(x) = () -colsize(x::AbstractArray) = (size(x, 2),) - -function colsize(f::AffineTransform) - size_f = size(f) - - size_f isa NTuple{2} && return last(size_f) - return 0 -end - -@inline function apply!(x, f::AffineTransform{(:μ,)}, z) - x .= z .+ f.μ - return x -end - -@inline function apply!(x, f::AffineTransform{(:σ,)}, z) - mul!(x, f.σ, z) - return x -end - -@inline function apply!(x, f::AffineTransform{(:ω,),Tuple{F}}, z) where {F<:Factorization} - ldiv!(x, f.ω, z) - return x -end - -@inline function apply!(x, f::AffineTransform{(:ω,)}, z) - ldiv!(x, factorize(f.ω), z) - return x -end - -@inline function apply!(x, f::AffineTransform{(:μ, :σ)}, z) - apply!(x, AffineTransform((σ = f.σ,)), z) - apply!(x, AffineTransform((μ = f.μ,)), x) - return x -end - -@inline function apply!(x, f::AffineTransform{(:μ, :ω)}, z) - apply!(x, AffineTransform((ω = f.ω,)), z) - apply!(x, AffineTransform((μ = f.μ,)), x) - return x -end - -function logjac(x::AbstractMatrix) - (m, n) = size(x) - m == n && return first(logabsdet(x)) - - # Equivalent to sum(log, svdvals(x)), but much faster - m > n && return first(logabsdet(x' * x)) / 2 - return first(logabsdet(x * x')) / 2 -end - -logjac(x::Number) = log(abs(x)) - -# TODO: `log` doesn't work for the multivariate case, we need the log absolute determinant -logjac(f::AffineTransform{(:μ, :σ)}) = logjac(f.σ) -logjac(f::AffineTransform{(:μ, :ω)}) = -logjac(f.ω) -logjac(f::AffineTransform{(:σ,)}) = logjac(f.σ) -logjac(f::AffineTransform{(:ω,)}) = -logjac(f.ω) -logjac(f::AffineTransform{(:μ,)}) = 0.0 - -############################################################################### - -struct Affine{N,M,T} <: AbstractMeasure - f::AffineTransform{N,T} - parent::M -end - -function testvalue(d::Affine) - f = getfield(d, :f) - z = testvalue(parent(d)) - return f(z) -end - -Affine(nt::NamedTuple, μ::AbstractMeasure) = affine(nt, μ) - -Affine(nt::NamedTuple) = affine(nt) - -parent(d::Affine) = getfield(d, :parent) - -function params(μ::Affine) - nt1 = getfield(getfield(μ, :f), :par) - nt2 = params(parent(μ)) - return merge(nt1, nt2) -end - -function paramnames(::Type{A}) where {N,M,A<:Affine{N,M}} - tuple(union(N, paramnames(M))...) -end - -Base.propertynames(d::Affine{N}) where {N} = N ∪ (:parent, :f) - -@inline function Base.getproperty(d::Affine, s::Symbol) - if s === :parent - return getfield(d, :parent) - elseif s === :f - return getfield(d, :f) - else - return getproperty(getfield(d, :f), s) - end -end - -Base.size(d::Affine) = size(d.μ) -Base.size(d::Affine{(:σ,)}) = (size(d.σ, 1),) -Base.size(d::Affine{(:ω,)}) = (size(d.ω, 2),) - -logdensity_def(d::Affine, x::MapsTo) = logdensity_def(d.parent, x.x) - -@inline function logdensity_def(d::Affine{(:σ,)}, x) - z = d.σ \ x - # @show z - # println() - logdensity_def(d.parent, z) -end - -@inline function logdensity_def(d::Affine{(:ω,)}, x) - z = d.ω * x - logdensity_def(d.parent, z) -end - -@inline function logdensity_def(d::Affine{(:μ,)}, x) - z = x - d.μ - logdensity_def(d.parent, z) -end - -@inline function logdensity_def(d::Affine{(:μ, :σ)}, x) - z = d.σ \ (x - d.μ) - logdensity_def(d.parent, z) -end - -@inline function logdensity_def(d::Affine{(:μ, :ω)}, x) - z = d.ω * (x - d.μ) - logdensity_def(d.parent, z) -end - -@inline function logdensity_tuple(d::Affine{(:σ,)}, x) - z = d.σ \ x - # @show z - # println() - (logdensity_def(d.parent, z), basemeasure(d), z ↦ x) -end - -@inline function logdensity_tuple(d::Affine{(:ω,)}, x) - z = d.ω * x - (logdensity_def(d.parent, z), basemeasure(d), z ↦ x) -end - -@inline function logdensity_tuple(d::Affine{(:μ,)}, x) - z = x - d.μ - (logdensity_def(d.parent, z), basemeasure(d), z ↦ x) -end - -@inline function logdensity_tuple(d::Affine{(:μ, :σ)}, x) - z = d.σ \ (x - d.μ) - (logdensity_def(d.parent, z), basemeasure(d), z ↦ x) -end - -@inline function logdensity_tuple(d::Affine{(:μ, :ω)}, x) - z = d.ω * (x - d.μ) - (logdensity_def(d.parent, z), basemeasure(d), z ↦ x) -end - -for p in AFFINEPARS - @eval begin - @inline function logdensity_tuple(d::Affine{$p}, (z, x)::MapsTo) - (logdensity_def(d.parent, z), basemeasure(d), z ↦ x) - end - end -end - -# # logdensity_def(d::Affine{(:μ,:ω)}, x) = logdensity_def(d.parent, d.σ \ (x - d.μ)) -# @inline function logdensity_def(d::Affine{(:μ,:σ), P, Tuple{V,M}}, x) where {P, V<:AbstractVector, M<:AbstractMatrix} -# z = x - d.μ -# σ = d.σ -# if σ isa Factorization -# ldiv!(σ, z) -# else -# ldiv!(factorize(σ), z) -# end -# sum(zⱼ -> logdensity_def(d.parent, zⱼ), z) -# end - -# # logdensity_def(d::Affine{(:μ,:ω)}, x) = logdensity_def(d.parent, d.ω * (x - d.μ)) -# @inline function logdensity_def(d::Affine{(:μ,:ω), P,Tuple{V,M}}, x) where {P,V<:AbstractVector, M<:AbstractMatrix} -# z = x - d.μ -# lmul!(d.ω, z) -# logdensity_def(d.parent, z) -# end - -basemeasure(d::Affine) = affine(getfield(d, :f), basemeasure(d.parent)) - -# We can't do this until we know we're working with Lebesgue measure, since for -# example it wouldn't make sense to apply a log-Jacobian to a point measure -basemeasure(d::Affine{N,L}) where {N,L<:Lebesgue} = weightedmeasure(-logjac(d), d.parent) - -@inline function basemeasure( - d::Affine{N,M}, -) where {N,L<:Lebesgue,M<:ProductMeasure{Returns{L}}} - weightedmeasure(-logjac(d), d.parent) -end - -basemeasure_type(::Type{Affine{N,M,T}}) where {N,M,T} = M - -logjac(d::Affine) = logjac(getfield(d, :f)) - -function Random.rand!( - rng::Random.AbstractRNG, - d::Affine, - x::AbstractVector{T}, - z = Vector{T}(undef, size(getfield(d, :f), 2)), -) where {T} - rand!(rng, parent(d), z) - f = getfield(d, :f) - apply!(x, f, z) - return x -end - -# function Base.rand(rng::Random.AbstractRNG, ::Type{T}, d::Affine) where {T} -# f = getfield(d, :f) -# z = rand(rng, T, parent(d)) -# apply!(x, f, z) -# return z -# end - -supportdim(nt::NamedTuple{(:μ, :σ)}) = colsize(nt.σ) -supportdim(nt::NamedTuple{(:μ, :ω)}) = rowsize(nt.ω) -supportdim(nt::NamedTuple{(:σ,)}) = colsize(nt.σ) -supportdim(nt::NamedTuple{(:ω,)}) = rowsize(nt.ω) -supportdim(nt::NamedTuple{(:μ,)}) = size(nt.μ) diff --git a/src/combinators/smart-constructors.jl b/src/combinators/smart-constructors.jl index cf44fd0c..4bae7b01 100644 --- a/src/combinators/smart-constructors.jl +++ b/src/combinators/smart-constructors.jl @@ -1,24 +1,5 @@ -############################################################################### -# Affine - -affine(f::AffineTransform, μ::AbstractMeasure) = Affine(f, μ) - -affine(nt::NamedTuple, μ::AbstractMeasure) = affine(AffineTransform(nt), μ) - -affine(f) = μ -> affine(f, μ) -function affine(f::AffineTransform, parent::WeightedMeasure) - WeightedMeasure(parent.logweight, affine(f, parent.base)) -end - -function affine(f::AffineTransform, parent::FactoredBase) - constℓ = parent.constℓ - varℓ = parent.varℓ - # Avoid transforming `inbounds`, which is expensive - base = affine(f, restrict(parent.inbounds, parent.base)) - FactoredBase(Returns(true), constℓ, varℓ, base) -end ############################################################################### # Half diff --git a/src/rand.jl b/src/rand.jl index 7144524a..08f3974d 100644 --- a/src/rand.jl +++ b/src/rand.jl @@ -8,11 +8,7 @@ Base.rand(rng::AbstractRNG, d::AbstractMeasure) = rand(rng, Float64, d) @inline Random.rand!(d::AbstractMeasure, args...) = rand!(GLOBAL_RNG, d, args...) -function Base.rand(rng::Random.AbstractRNG, ::Type{T}, d::Affine) where {T} - z = rand(rng, T, parent(d)) - f = getfield(d, :f) - return f(z) -end + # TODO: Make this work # function Base.rand(rng::AbstractRNG, ::Type{T}, d::AbstractMeasure) where {T} diff --git a/test/runtests.jl b/test/runtests.jl index 5d258647..b0510641 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -101,67 +101,6 @@ end @test logdensity_def(Dirac(0.3), 0.4) == -Inf end -@testset "AffineTransform" begin - f = AffineTransform((μ = 3, σ = 2)) - @test f(inv(f)(1)) == 1 - @test inv(f)(f(1)) == 1 - - f = AffineTransform((μ = 3, ω = 2)) - @test f(inv(f)(1)) == 1 - @test inv(f)(f(1)) == 1 - - f = AffineTransform((σ = 2,)) - @test f(inv(f)(1)) == 1 - @test inv(f)(f(1)) == 1 - - f = AffineTransform((ω = 2,)) - @test f(inv(f)(1)) == 1 - @test inv(f)(f(1)) == 1 - - f = AffineTransform((μ = 3,)) - @test f(inv(f)(1)) == 1 - @test inv(f)(f(1)) == 1 -end - -@testset "Affine" begin - unif = ∫(x -> 0 < x < 1, Lebesgue(ℝ)) - f1 = AffineTransform((μ = 3.0, σ = 2.0)) - f2 = AffineTransform((μ = 3.0, ω = 2.0)) - f3 = AffineTransform((μ = 3.0,)) - f4 = AffineTransform((σ = 2.0,)) - f5 = AffineTransform((ω = 2.0,)) - - for f in [f1, f2, f3, f4, f5] - par = getfield(f, :par) - @test Affine(par)(unif) == Affine(f, unif) - @test density_def(Affine(f, Affine(inv(f), unif)), 0.5) == 1 - end - - d = ∫exp(x -> -x^2, Lebesgue(ℝ)) - - μ = randn(3) - σ = LowerTriangular(randn(3, 3)) - ω = inv(σ) - - x = randn(3) - - @test logdensity_def(Affine((μ = μ, σ = σ), d^3), x) ≈ - logdensity_def(Affine((μ = μ, ω = ω), d^3), x) - @test logdensity_def(Affine((σ = σ,), d^3), x) ≈ logdensity_def(Affine((ω = ω,), d^3), x) - @test logdensity_def(Affine((μ = μ,), d^3), x) ≈ logdensity_def(d^3, x - μ) - - d = ∫exp(x -> -x^2, Lebesgue(ℝ)) - a = Affine((σ = [1 0]',), d^1) - x = randn(2) - y = randn(1) - @test logdensityof(a, x) ≈ logdensityof(d, inv(a.f)(x)[1]) - @test logdensityof(a, a.f(y)) ≈ logdensityof(d^1, y) - - b = Affine((ω = [1 0]'',), d^1) - @test logdensityof(b, x) ≈ logdensityof(d, inv(b.f)(x)[1]) - @test logdensityof(b, b.f(y)) ≈ logdensityof(d^1, y) -end - @testset "For" begin FORDISTS = [ For(1:10) do j @@ -195,18 +134,6 @@ end @test densityof(HalfNormal(), 0.2) ≈ 2 * densityof(Normal(), 0.2) end -# import MeasureBase.:⋅ -# function ⋅(μ::Normal, kernel) -# m = kernel(μ) -# Normal(μ = m.μ.μ, σ = sqrt(m.μ.σ^2 + m.σ^2)) -# end -# struct AffineMap{S,T} -# B::S -# β::T -# end -# (a::AffineMap)(x) = a.B*x + a.β -# (a::AffineMap)(p::Normal) = Normal(μ = a.B*mean(p) + a.β, σ = sqrt(a.B*p.σ^2*a.B')) - # @testset "Likelihood" begin # dps = [ # (Normal() , 2.0 ) From 80abcb6f87ca5d044f43335812bc01836a304525 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 30 Nov 2021 12:06:04 -0800 Subject: [PATCH 048/368] drop some old `For` code --- src/combinators/for.jl | 35 ----------------------------------- 1 file changed, 35 deletions(-) diff --git a/src/combinators/for.jl b/src/combinators/for.jl index 279724c1..8ad12c63 100644 --- a/src/combinators/for.jl +++ b/src/combinators/for.jl @@ -89,38 +89,3 @@ For(k::AbstractKernel, dims::Integer...) = productmeasure(kernel(i -> k(Tuple(i) function Base.eltype(d::ProductMeasure{F,I}) where {F,I<:AbstractArray} return eltype(d.f(first(d.xs))) end - -# """ -# indexstyle(a::AbstractArray, b::AbstractArray) - -# Find the best IndexStyle that works for both `a` and `b`. This will return -# `IndexLinear` if both `a` and `b` support it; otherwise it will fall back on `IndexCartesian`. -# """ -# function indexstyle(::A,::B) -# if IndexStyle(A) == IndexStyle(B) == IndexLinear() -# return IndexLinear() -# end - -# return IndexCartesian() -# end - -# function Base.rand(rng::AbstractRNG, μ::ForArray{D,N,T,F}) where {F,T<:AbstractArray,D,X} -# s = size(μ.θ) -# x = Array{X,length(s)}(undef, s...) -# rand!(rng, x, μ) -# end - -# function logdensity_def(μ::ForArray{D,N,T,F}, x) -# getℓ(θⱼ, xⱼ) = logdensity_def(μ.f(θⱼ), xⱼ) -# ℓ = mappedarray(getℓ, μ.θ, x) -# _logdensity_def(μ, x, indexstyle(μ.θ, x), result_type) -# end - -# function _logdensity_def(μ::ForArray{D,N,T,F}, x, ::IndexLinear, ::Type{R}) where {R<:AbstractFloat} -# ℓ = zero(R) -# μ.f(μ.θ) -# end - -# function basemeasure(μ::ForArray{D,N,T,F}) where {F,T<:AbstractArray,D,X} - -# ForGenerator From 1d0964351d70e6b1176fb3a39372f108255aec18 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 30 Nov 2021 15:36:39 -0800 Subject: [PATCH 049/368] update counting measure --- src/primitives/counting.jl | 22 +++++++++++++++------- 1 file changed, 15 insertions(+), 7 deletions(-) diff --git a/src/primitives/counting.jl b/src/primitives/counting.jl index 943eb45d..66a8c268 100644 --- a/src/primitives/counting.jl +++ b/src/primitives/counting.jl @@ -1,16 +1,24 @@ -export CountingMeasure +# Counting measure + +export Counting, CountingMeasure struct CountingMeasure <: PrimitiveMeasure end +struct Counting{T} <: AbstractMeasure + support::T +end + +Counting() = Counting(ℤ) + +basemeasure_type(::Type{C}) where {C<:Counting}= CountingMeasure +testvalue(d::Counting) = testvalue(d.support) -# gentype(::CountingMeasure{ℝ}) = Float64 -# gentype(::CountingMeasure{ℝ₊}) = Float64 -# gentype(::CountingMeasure{𝕀}) = Float64 +proxy(d::Counting) = restrict(in(d.support), CountingMeasure()) -gentype(::CountingMeasure) = Int +Base.:∘(::typeof(basemeasure), ::Type{Counting}) = CountingMeasure() +Base.show(io::IO, d::Counting) = print(io, "Counting(",d.support,")") -logdensity_def(::CountingMeasure, x) = zero(float(x)) +insupport(μ::Counting, x) = x ∈ μ.support -# (::CountingMeaure)(s) = length(Set(s)) From b3c4d920ff6386f62df7e1e19f54e4e4aff6d9f5 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 30 Nov 2021 16:13:48 -0800 Subject: [PATCH 050/368] add testvalue(::Type{T}) --- src/utils.jl | 1 + 1 file changed, 1 insertion(+) diff --git a/src/utils.jl b/src/utils.jl index b780c4e5..cab0ed61 100644 --- a/src/utils.jl +++ b/src/utils.jl @@ -23,6 +23,7 @@ constructor(::Type{T}) where {T} = constructorof(T) export testvalue testvalue(μ::AbstractMeasure) = testvalue(basemeasure(μ)) +testvalue(::Type{T}) where {T} = zero(T) export rootmeasure From 2920ab4dfdf4b4992bcbb816b6f1c5e114975ac3 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 1 Dec 2021 06:04:58 -0800 Subject: [PATCH 051/368] bugfix --- src/MeasureBase.jl | 3 +++ src/parameterized.jl | 2 -- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index 88f0e8fc..8205af71 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -10,6 +10,9 @@ import DensityInterface: densityof import DensityInterface: DensityKind using DensityInterface +import ConstructionBase +using ConstructionBase: constructorof + using PrettyPrinting const Pretty = PrettyPrinting diff --git a/src/parameterized.jl b/src/parameterized.jl index 9e5c627c..7d673277 100644 --- a/src/parameterized.jl +++ b/src/parameterized.jl @@ -1,5 +1,3 @@ -import ConstructionBase - export ParameterizedMeasure abstract type ParameterizedMeasure{N} <: AbstractMeasure end From 877e9a38aa416486450bfb49666f435dad4411b2 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 1 Dec 2021 10:16:19 -0800 Subject: [PATCH 052/368] some dispatch adjustments --- src/combinators/for.jl | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/src/combinators/for.jl b/src/combinators/for.jl index 8ad12c63..dd1961bb 100644 --- a/src/combinators/for.jl +++ b/src/combinators/for.jl @@ -74,17 +74,14 @@ julia> For(eachrow(rand(4,2))) do x Normal(x[1], x[2]) end |> marginals |> colle ``` """ -For(f::Function, args...) = productmeasure(kernel(i -> f(Tuple(i)...)), zip(args...)) - -For(f::Function, n::Integer) = productmeasure(kernel(f), Base.OneTo(n)) - -For(f::Function, dims::Integer...) = productmeasure(kernel(i -> f(Tuple(i)...)), CartesianIndices(dims)) +For(f, args...) = productmeasure(kernel(i -> f(Tuple(i)...)), zip(args...)) For(k::AbstractKernel, inds::AbstractArray) = productmeasure(k, inds) +For(f, n::Integer) = productmeasure(kernel(f), Base.OneTo(n)) For(k::AbstractKernel, n::Integer) = productmeasure(k, Base.OneTo(n)) -For(k::AbstractKernel, dims::Integer...) = productmeasure(kernel(i -> k(Tuple(i)...)), CartesianIndices(dims)) +For(f, dims::Integer...) = productmeasure(kernel(i -> f(Tuple(i)...)), CartesianIndices(dims)) function Base.eltype(d::ProductMeasure{F,I}) where {F,I<:AbstractArray} return eltype(d.f(first(d.xs))) From 3030cc04bf371a63b46204927e7bafd9ee61028a Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 1 Dec 2021 10:31:47 -0800 Subject: [PATCH 053/368] simplify show --- src/kernel.jl | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/src/kernel.jl b/src/kernel.jl index e9ad6aac..1560546c 100644 --- a/src/kernel.jl +++ b/src/kernel.jl @@ -102,6 +102,11 @@ function Pretty.quoteof(k::Kernel) :(Kernel($qf, $qg)) end +function Pretty.quoteof(k::Kernel{F,typeof(identity)}) where {F} + qf = Pretty.quoteof(k.f) + :(Kernel($qf)) +end + function Pretty.quoteof(k::ParameterizedKernel) qf = Pretty.quoteof(k.f) qg = Pretty.quoteof(k.param_maps) From 1bade39fcd8e43174e8ff2a8e71bfa6cd137af0b Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 1 Dec 2021 10:42:24 -0800 Subject: [PATCH 054/368] formatting --- src/MeasureBase.jl | 1 - src/combinators/factoredbase.jl | 2 +- src/combinators/for.jl | 3 ++- src/combinators/half.jl | 2 +- src/combinators/power.jl | 7 ++++--- src/combinators/product.jl | 6 +----- src/combinators/restricted.jl | 2 +- src/combinators/smart-constructors.jl | 5 +---- src/combinators/superpose.jl | 5 ++--- src/density.jl | 7 ++----- src/domains.jl | 18 +++++------------- src/kernel.jl | 10 +++++----- src/macros.jl | 1 + src/primitive.jl | 2 +- src/primitives/counting.jl | 5 ++--- src/primitives/dirac.jl | 2 +- src/primitives/lebesgue.jl | 6 ++---- src/primitives/trivial.jl | 2 +- src/proxies.jl | 2 -- src/rand.jl | 2 -- src/utils.jl | 4 ++-- 21 files changed, 35 insertions(+), 59 deletions(-) diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index 8205af71..52a8933a 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -30,7 +30,6 @@ abstract type AbstractMeasure end gentype(μ::AbstractMeasure) = typeof(testvalue(μ)) - # gentype(μ::AbstractMeasure) = gentype(basemeasure(μ)) export logdensity_def diff --git a/src/combinators/factoredbase.jl b/src/combinators/factoredbase.jl index aa2467b3..0fa1ac42 100644 --- a/src/combinators/factoredbase.jl +++ b/src/combinators/factoredbase.jl @@ -20,4 +20,4 @@ end basemeasure(d::FactoredBase) = d.base -basemeasure_type(::Type{FactoredBase{R,C,V,B}}) where {R,C,V,B} = B \ No newline at end of file +basemeasure_type(::Type{FactoredBase{R,C,V,B}}) where {R,C,V,B} = B diff --git a/src/combinators/for.jl b/src/combinators/for.jl index dd1961bb..ca0d5de1 100644 --- a/src/combinators/for.jl +++ b/src/combinators/for.jl @@ -81,7 +81,8 @@ For(k::AbstractKernel, inds::AbstractArray) = productmeasure(k, inds) For(f, n::Integer) = productmeasure(kernel(f), Base.OneTo(n)) For(k::AbstractKernel, n::Integer) = productmeasure(k, Base.OneTo(n)) -For(f, dims::Integer...) = productmeasure(kernel(i -> f(Tuple(i)...)), CartesianIndices(dims)) +For(f, dims::Integer...) = + productmeasure(kernel(i -> f(Tuple(i)...)), CartesianIndices(dims)) function Base.eltype(d::ProductMeasure{F,I}) where {F,I<:AbstractArray} return eltype(d.f(first(d.xs))) diff --git a/src/combinators/half.jl b/src/combinators/half.jl index c3cdb6d0..fe51693b 100644 --- a/src/combinators/half.jl +++ b/src/combinators/half.jl @@ -23,7 +23,7 @@ end function basemeasure_type(::Type{Half{M}}) where {M} B = basemeasure_type(M) - FactoredBase{typeof(isnonnegative), StaticFloat64{logtwo}, Returns{Float64}, B} + FactoredBase{typeof(isnonnegative),StaticFloat64{logtwo},Returns{Float64},B} end function Base.rand(rng::AbstractRNG, T::Type, μ::Half) diff --git a/src/combinators/power.jl b/src/combinators/power.jl index 09625716..c54f9249 100644 --- a/src/combinators/power.jl +++ b/src/combinators/power.jl @@ -29,7 +29,8 @@ using FillArrays: Fill export PowerMeasure -const PowerMeasure{M,N,R} = ProductMeasure{M, Kernel{Returns{M}, typeof(identity)}, LinearIndices{N, R}} +const PowerMeasure{M,N,R} = + ProductMeasure{M,Kernel{Returns{M},typeof(identity)},LinearIndices{N,R}} Base.:^(μ::AbstractMeasure, ::Tuple{}) = μ @@ -55,7 +56,7 @@ params(d::PowerMeasure) = params(first(marginals(d))) # basemeasure(μ::PowerMeasure) = @inbounds basemeasure(first(μ.data))^size(μ.data) @inline function basemeasure(d::PowerMeasure) - basemeasure(d.f.f.value) ^ size(d.xs) + basemeasure(d.f.f.value)^size(d.xs) end function basemeasure_depth(d::PowerMeasure{M,N,R}) where {M,N,R} @@ -63,7 +64,7 @@ function basemeasure_depth(d::PowerMeasure{M,N,R}) where {M,N,R} end function basemeasure_type(::Type{P}) where {M,N,R,P<:PowerMeasure{M,N,R}} - return PowerMeasure{basemeasure_type(M), N, R} + return PowerMeasure{basemeasure_type(M),N,R} end function basemeasure_depth(::Type{P}) where {M<:PrimitiveMeasure,N,R,P<:PowerMeasure{M,N,R}} diff --git a/src/combinators/product.jl b/src/combinators/product.jl index f6a1fa8a..026b29c1 100644 --- a/src/combinators/product.jl +++ b/src/combinators/product.jl @@ -18,7 +18,6 @@ struct ProductMeasure{M,K<:AbstractKernel,I} <: AbstractProductMeasure end end - function Pretty.tile(μ::ProductMeasure) result = Pretty.literal("For(") result *= Pretty.pair_layout(Pretty.tile(μ.f), Pretty.tile(μ.xs); sep = ", ") @@ -73,7 +72,6 @@ struct TupleProductMeasure{T} <: AbstractProductMeasure components::T end - function Pretty.tile(μ::TupleProductMeasure{T}) where {F,T<:Tuple} mar = marginals(μ) Pretty.list_layout(Pretty.Layout[Pretty.tile.(mar)...]; sep = " ⊗ ") @@ -115,9 +113,8 @@ end export rand! using Random: rand!, GLOBAL_RNG, AbstractRNG - function logdensity_def(μ::AbstractProductMeasure, x) - mapreduce(+, μ.xs, x) do (j,x) + mapreduce(+, μ.xs, x) do (j, x) logdensity_def(μ.f(j), x) end end @@ -200,4 +197,3 @@ end # function kernelfactor(μ::ProductMeasure{K,A}) where {K,A<:AbstractArray} # (p -> set.(marginals(μ), params, p), μ.xs) # end - diff --git a/src/combinators/restricted.jl b/src/combinators/restricted.jl index bd444532..4811a680 100644 --- a/src/combinators/restricted.jl +++ b/src/combinators/restricted.jl @@ -17,4 +17,4 @@ basemeasure(μ::RestrictedMeasure) = μ.base basemeasure_type(::Type{RestrictedMeasure{F,M}}) where {F,M} = M -insupport(μ::RestrictedMeasure, x) = μ.f(x) && insupport(μ.base, x) \ No newline at end of file +insupport(μ::RestrictedMeasure, x) = μ.f(x) && insupport(μ.base, x) diff --git a/src/combinators/smart-constructors.jl b/src/combinators/smart-constructors.jl index 4bae7b01..1f853ae1 100644 --- a/src/combinators/smart-constructors.jl +++ b/src/combinators/smart-constructors.jl @@ -1,6 +1,4 @@ - - ############################################################################### # Half @@ -35,7 +33,6 @@ end ############################################################################### # ProductMeasure - productmeasure(f::AbstractKernel, pars) = ProductMeasure(f, pars) productmeasure(f, param_maps, pars) = ProductMeasure(kernel(f, param_maps), pars) @@ -124,4 +121,4 @@ kernel(f::Returns, op) = Kernel(f, identity) kernel(f, op::Returns) = Kernel(Returns(f(op.value)), identity) # Just to avoid dispatch ambiguity -kernel(f::Returns, op::Returns) = Kernel(Returns(f.value), identity) \ No newline at end of file +kernel(f::Returns, op::Returns) = Kernel(Returns(f.value), identity) diff --git a/src/combinators/superpose.jl b/src/combinators/superpose.jl index 50862550..994703f9 100644 --- a/src/combinators/superpose.jl +++ b/src/combinators/superpose.jl @@ -24,14 +24,12 @@ struct SuperpositionMeasure{NT} <: AbstractMeasure components::NT end - function Pretty.tile(d::SuperpositionMeasure) result = Pretty.literal("SuperpositionMeasure(") result *= Pretty.list_layout([Pretty.tile.(d.components)...]) result *= Pretty.literal(")") end - testvalue(μ::SuperpositionMeasure) = testvalue(first(μ.components)) # SuperpositionMeasure(ms :: AbstractMeasure...) = SuperpositionMeasure{X,length(ms)}(ms) @@ -60,7 +58,8 @@ function Base.:+(μ::AbstractMeasure, ν::AbstractMeasure) superpose(components) end -logdensity_def(μ::SuperpositionMeasure, x) = logsumexp((logdensity_def(m, x) for m in μ.components)) +logdensity_def(μ::SuperpositionMeasure, x) = + logsumexp((logdensity_def(m, x) for m in μ.components)) basemeasure(μ::SuperpositionMeasure) = superpose(map(basemeasure, μ.components)) diff --git a/src/density.jl b/src/density.jl index b497b855..cd52a6a6 100644 --- a/src/density.jl +++ b/src/density.jl @@ -2,7 +2,6 @@ abstract type AbstractDensity end @inline DensityKind(::AbstractDensity) = IsDensity() - """ struct Density{M,B} μ::M @@ -22,7 +21,6 @@ struct Density{M,B,L} <: AbstractDensity base::B end - export 𝒹 """ @@ -58,7 +56,7 @@ densitymeasure(f, base) = _densitymeasure(f, base, DensityKind(f)) _densitymeasure(f, base, ::IsDensity) = DensityMeasure(f, base) -function _densitymeasure(f, base, _) +function _densitymeasure(f, base, _) @error """ The first argument of `DensityMeasure`" must be `::IsDensity`. To pass a function, first wrap it in `DensityInterface.funcdensity` or @@ -70,7 +68,7 @@ basemeasure(μ::DensityMeasure) = μ.base basemeasure_type(::Type{DensityMeasure{F,B}}) where {F,B} = B -logdensity_def(μ::DensityMeasure, x) = logdensityof(μ.f, x) +logdensity_def(μ::DensityMeasure, x) = logdensityof(μ.f, x) density_def(μ::DensityMeasure, x) = densityof(μ.f, x) @@ -85,7 +83,6 @@ Define a new measure in terms of a density `f` over some measure `base`. ∫(f, base::AbstractMeasure) = _densitymeasure(f, base, DensityKind(f)) - # ∫(μ::AbstractMeasure, base::AbstractMeasure) = ∫(𝒹(μ, base), base) export ∫exp diff --git a/src/domains.jl b/src/domains.jl index 38655ba1..a6a41764 100644 --- a/src/domains.jl +++ b/src/domains.jl @@ -14,23 +14,20 @@ Base.in(x, ::RealNumbers) = isreal(x) Base.show(io::IO, ::typeof(ℝ)) = print(io, "ℝ") struct BoundedReals{L,U} <: RealDomain - lower :: L - upper :: U + lower::L + upper::U end Base.in(x, b::BoundedReals) = b.lower ≤ x ≤ b.upper - export ℝ, ℝ₊, 𝕀, ℤ - const ℝ₊ = BoundedReals(static(0.0), static(Inf)) const 𝕀 = BoundedReals(static(0.0), static(1.0)) Base.minimum(b::BoundedReals) = b.lower Base.maximum(b::BoundedReals) = b.upper - Base.show(io::IO, ::typeof(ℝ₊)) = print(io, "ℝ₊") Base.show(io::IO, ::typeof(𝕀)) = print(io, "𝕀") @@ -51,8 +48,8 @@ Base.show(io::IO, ::typeof(ℤ)) = print(io, "ℤ") Base.minimum(::IntegerNumbers) = static(-Inf) Base.maximum(::IntegerNumbers) = static(Inf) struct BoundedInts{L,U} <: IntegerDomain - lower :: L - upper :: U + lower::L + upper::U end Base.in(x, b::BoundedInts) = x ∈ ℤ && b.lower ≤ x ≤ b.upper @@ -71,10 +68,6 @@ function Base.getindex(::typeof(ℤ), r::AbstractUnitRange) BoundedInts(extrema(r)...) end - - - - ########################################################### # Simplex @@ -88,7 +81,6 @@ end # dim::D # dimensionality as a manifold # end - # projectto!(x, ::Sphere) = normalize!(x, 2) # struct ZeroSet{F, G} <: AbstractDomain # f::F @@ -122,4 +114,4 @@ end # struct LebesgueSimplex <: AbstractMeasure end -# basemeasure(::LebesgueSimplex, x) \ No newline at end of file +# basemeasure(::LebesgueSimplex, x) diff --git a/src/kernel.jl b/src/kernel.jl index 1560546c..e3fc539f 100644 --- a/src/kernel.jl +++ b/src/kernel.jl @@ -11,13 +11,14 @@ struct Kernel{F,G} <: AbstractKernel Kernel(f::F, g::G) where {F,G} = new{F,G}(f, g) end - struct ParameterizedKernel{F,N,T} <: AbstractKernel f::F param_maps::NamedTuple{N,T} - ParameterizedKernel(::Type{F}, param_maps::NamedTuple{N,T}) where {F,N,T} = new{Type{F},N,T}(F, param_maps) - ParameterizedKernel(f::F, param_maps::NamedTuple{N,T}) where {F,N,T} = new{F,N,T}(f, param_maps) + ParameterizedKernel(::Type{F}, param_maps::NamedTuple{N,T}) where {F,N,T} = + new{Type{F},N,T}(F, param_maps) + ParameterizedKernel(f::F, param_maps::NamedTuple{N,T}) where {F,N,T} = + new{F,N,T}(f, param_maps) end """ @@ -55,7 +56,7 @@ mapcall(t, x) = map(func -> func(x), t) (k::ParameterizedKernel)(x...) = k(x) -function (k::ParameterizedKernel)(x::Tuple) +function (k::ParameterizedKernel)(x::Tuple) k.f(NamedTuple{k.param_maps}(x)) end @@ -95,7 +96,6 @@ function Base.show(io::IO, μ::AbstractKernel) Pretty.pprint(io, μ) end - function Pretty.quoteof(k::Kernel) qf = Pretty.quoteof(k.f) qg = Pretty.quoteof(k.g) diff --git a/src/macros.jl b/src/macros.jl index e69de29b..8b137891 100644 --- a/src/macros.jl +++ b/src/macros.jl @@ -0,0 +1 @@ + diff --git a/src/primitive.jl b/src/primitive.jl index 4841e13b..e662f27f 100644 --- a/src/primitive.jl +++ b/src/primitive.jl @@ -28,4 +28,4 @@ logdensity_def(μ::M, ν::M, x) where {M<:PrimitiveMeasure} = 0.0 function Pretty.quoteof(μ::M) where {M<:PrimitiveMeasure} :($M()) -end \ No newline at end of file +end diff --git a/src/primitives/counting.jl b/src/primitives/counting.jl index 66a8c268..1fe93229 100644 --- a/src/primitives/counting.jl +++ b/src/primitives/counting.jl @@ -10,7 +10,7 @@ end Counting() = Counting(ℤ) -basemeasure_type(::Type{C}) where {C<:Counting}= CountingMeasure +basemeasure_type(::Type{C}) where {C<:Counting} = CountingMeasure testvalue(d::Counting) = testvalue(d.support) @@ -18,7 +18,6 @@ proxy(d::Counting) = restrict(in(d.support), CountingMeasure()) Base.:∘(::typeof(basemeasure), ::Type{Counting}) = CountingMeasure() -Base.show(io::IO, d::Counting) = print(io, "Counting(",d.support,")") +Base.show(io::IO, d::Counting) = print(io, "Counting(", d.support, ")") insupport(μ::Counting, x) = x ∈ μ.support - diff --git a/src/primitives/dirac.jl b/src/primitives/dirac.jl index 6008f654..b63d6e77 100644 --- a/src/primitives/dirac.jl +++ b/src/primitives/dirac.jl @@ -33,4 +33,4 @@ dirac(d::AbstractMeasure) = Dirac(rand(d)) testvalue(d::Dirac) = d.x -insupport(d::Dirac, x) = x == d.x \ No newline at end of file +insupport(d::Dirac, x) = x == d.x diff --git a/src/primitives/lebesgue.jl b/src/primitives/lebesgue.jl index fe29246c..6054504f 100644 --- a/src/primitives/lebesgue.jl +++ b/src/primitives/lebesgue.jl @@ -6,8 +6,6 @@ struct LebesgueMeasure <: PrimitiveMeasure end testvalue(::LebesgueMeasure) = 0.0 - - struct Lebesgue{T} <: AbstractMeasure support::T end @@ -16,7 +14,7 @@ gentype(::Lebesgue) = Float64 Lebesgue() = Lebesgue(ℝ) -basemeasure_type(::Type{L}) where {L<:Lebesgue}= LebesgueMeasure +basemeasure_type(::Type{L}) where {L<:Lebesgue} = LebesgueMeasure testvalue(d::Lebesgue) = testvalue(d.support) @@ -24,7 +22,7 @@ proxy(d::Lebesgue) = restrict(in(d.support), LebesgueMeasure()) Base.:∘(::typeof(basemeasure), ::Type{Lebesgue}) = LebesgueMeasure() -Base.show(io::IO, d::Lebesgue) = print(io, "Lebesgue(",d.support,")") +Base.show(io::IO, d::Lebesgue) = print(io, "Lebesgue(", d.support, ")") insupport(μ::Lebesgue, x) = x ∈ μ.support diff --git a/src/primitives/trivial.jl b/src/primitives/trivial.jl index ed4f8572..e82b4ffc 100644 --- a/src/primitives/trivial.jl +++ b/src/primitives/trivial.jl @@ -4,4 +4,4 @@ struct TrivialMeasure <: PrimitiveMeasure end gentype(::TrivialMeasure) = Nothing -insupport(::TrivialMeasure, x) = False \ No newline at end of file +insupport(::TrivialMeasure, x) = False diff --git a/src/proxies.jl b/src/proxies.jl index 6112f747..f1073a8a 100644 --- a/src/proxies.jl +++ b/src/proxies.jl @@ -17,6 +17,4 @@ proxy(f, μ) = proxy(μ) logdensity_def(μ, x) = logdensity_def(proxy(μ), x) - - basemeasure(μ) = basemeasure(proxy(μ)) diff --git a/src/rand.jl b/src/rand.jl index 08f3974d..f92cb16a 100644 --- a/src/rand.jl +++ b/src/rand.jl @@ -8,8 +8,6 @@ Base.rand(rng::AbstractRNG, d::AbstractMeasure) = rand(rng, Float64, d) @inline Random.rand!(d::AbstractMeasure, args...) = rand!(GLOBAL_RNG, d, args...) - - # TODO: Make this work # function Base.rand(rng::AbstractRNG, ::Type{T}, d::AbstractMeasure) where {T} # x = testvalue(d) diff --git a/src/utils.jl b/src/utils.jl index cab0ed61..0804eedf 100644 --- a/src/utils.jl +++ b/src/utils.jl @@ -49,7 +49,6 @@ end return q end - # Base on the Tricks.jl README using Tricks struct Iterable end @@ -69,7 +68,8 @@ export basemeasure_depth basemeasure_depth(M) end -@inline basemeasure_depth(::Type{M}) where {M} = static(1) + basemeasure_depth(basemeasure_type(M)) +@inline basemeasure_depth(::Type{M}) where {M} = + static(1) + basemeasure_depth(basemeasure_type(M)) export logdensity_tuple From c69b96edcd7a9ba1513ef3d3197d70034c696f6c Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 1 Dec 2021 17:15:37 -0800 Subject: [PATCH 055/368] transformed measures --- src/MeasureBase.jl | 1 + src/combinators/transformedmeasure.jl | 13 +++++++++++++ 2 files changed, 14 insertions(+) create mode 100644 src/combinators/transformedmeasure.jl diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index 52a8933a..7b5f8955 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -74,6 +74,7 @@ include("primitives/lebesgue.jl") include("primitives/dirac.jl") include("primitives/trivial.jl") +include("combinators/transformedmeasure.jl") include("combinators/factoredbase.jl") include("combinators/weighted.jl") include("combinators/superpose.jl") diff --git a/src/combinators/transformedmeasure.jl b/src/combinators/transformedmeasure.jl new file mode 100644 index 00000000..e4c898ce --- /dev/null +++ b/src/combinators/transformedmeasure.jl @@ -0,0 +1,13 @@ +abstract type AbstractTransformedMeasure <: AbstractMeasure end + +abstract type AbstractPushforward <: AbstractTransformedMeasure end + +abstract type AbstractPullback <: AbstractTransformedMeasure end + +function gettransform(::AbstractTransformedMeasure) end + +function params(::AbstractTransformedMeasure) end + +function paramnames(::AbstractTransformedMeasure) end + +function parent(::AbstractTransformedMeasure) end \ No newline at end of file From c8389f3fcc6505e7b562566eb60eebf254a81834 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 1 Dec 2021 17:15:46 -0800 Subject: [PATCH 056/368] ZeroSets --- src/domains.jl | 107 +++++++++++++++++++++++++++++-------------------- 1 file changed, 63 insertions(+), 44 deletions(-) diff --git a/src/domains.jl b/src/domains.jl index a6a41764..3166d99c 100644 --- a/src/domains.jl +++ b/src/domains.jl @@ -68,50 +68,69 @@ function Base.getindex(::typeof(ℤ), r::AbstractUnitRange) BoundedInts(extrema(r)...) end +########################################################### +# ZeroSet + +struct ZeroSet{F, G} <: AbstractDomain + f::F + ∇f::G +end + +# Based on some quick tests, but may need some adjustment +Base.in(x::AbstractArray{T}, z::ZeroSet) where {T} = abs(z.f(x)) < ldexp(eps(float(T)), 6) + + +########################################################### +# CodimOne + +abstract type CodimOne <: AbstractDomain end + +function tangentat(a::CodimOne, b::CodimOne, x::AbstractArray{T}; tol=ldexp(eps(float(T)), 6)) where {T} + # Sometimes you get lucky + a == b && return true + + # Get the normal vectors + g1 = a.∇f(x) + g2 = b.∇f(x) + + # See if one is a multiple of the other + Statistics.corm(g1, zero(T), g2, zero(T)) > one(T) - tol +end + +function zeroset(::CodimOne)::ZeroSet end + ########################################################### # Simplex -# struct Simplex{D} <: AbstractDomain -# dim::D # dimensionality as a manifold -# end - -# projectto!(x, ::Simplex) = normalize!(x, 1) - -# struct Sphere{D} <: AbstractDomain -# dim::D # dimensionality as a manifold -# end - -# projectto!(x, ::Sphere) = normalize!(x, 2) -# struct ZeroSet{F, G} <: AbstractDomain -# f::F -# ∇f::G -# end - -# function zeroset(::Simplex) -# f(x::AbstractVector{T}) where {T} = sum(x) - one(T) -# ∇f(x::AbstractVector{T}) where {T} = Fill(one(T), axes(x)) -# ZeroSet(f, ∇f) -# end - -# function zeroset(::Sphere) -# f(x::AbstractVector{T}) where {T} = (sum(xⱼ -> xⱼ^2, x) - one(T)) / 2 -# ∇f(x::AbstractVector{T}) where {T} = x -# ZeroSet(f, ∇f) -# end - -# struct LebesgueCodimOne{D,T,O} <: AbstractMeasure -# ndims ::D -# ortho ::O -# end - -# function logdensityof(d::Density{L1, L2}, x) where {L1<:LebesgueCodimOne, L2<:LebesgueCodimOne} -# μ = d.μ -# ν = d.base -# μ.ndims == ν.ndims || return NaN -# rank([μ.ortho ν.ortho]) == 1 || return NaN -# return 0.0 -# end - -# struct LebesgueSimplex <: AbstractMeasure end - -# basemeasure(::LebesgueSimplex, x) +struct Simplex <: CodimOne end + +function zeroset(::Simplex) + f(x::AbstractArray{T}) where {T} = sum(x) - one(T) + ∇f(x::AbstractArray{T}) where {T} = Fill(one(T), size(x)) + ZeroSet(f, ∇f) +end + +function Base.in(x::AbstractArray{T}, ::Simplex) where {T} + x .≥ zero(eltype(x)) || return false + return x ∈ zeroset(Simplex()) +end + +projectto!(x, ::Simplex) = normalize!(x, 1) + +########################################################### +# Sphere + +struct Sphere <: CodimOne end + +function zeroset(::Sphere) + f(x::AbstractArray{T}) where {T} = sum(xⱼ -> xⱼ^2, x) - one(T) + ∇f(x::AbstractArray{T}) where {T} = x + ZeroSet(f, ∇f) +end + +function Base.in(x::AbstractArray{T}, ::Sphere) where {T} + return x ∈ zeroset(Sphere()) +end + +projectto!(x, ::Sphere) = normalize!(x, 2) + From 6c2aa8b471414b0c2635ce60351751b93e7f151d Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Thu, 2 Dec 2021 10:46:38 -0800 Subject: [PATCH 057/368] using LinearAlgebra, Statistics --- Project.toml | 1 + src/MeasureBase.jl | 3 +++ src/domains.jl | 2 +- 3 files changed, 5 insertions(+), 1 deletion(-) diff --git a/Project.toml b/Project.toml index 794897c6..7e24250f 100644 --- a/Project.toml +++ b/Project.toml @@ -13,6 +13,7 @@ MappedArrays = "dbb5928d-eab1-5f90-85c2-b9b0edb7c900" PrettyPrinting = "54e16d92-306c-5ea0-a30b-337be88ac337" Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" Static = "aedffcd0-7271-4cad-89d0-dc628f76c6d3" +Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" Tricks = "410a4b4d-49e4-4fbc-ab6d-cb71b17b3775" [compat] diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index 7b5f8955..03488776 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -5,6 +5,9 @@ const logtwo = log(2.0) using Random import Random: rand! import Random: gentype +using Statistics +using LinearAlgebra + import DensityInterface: logdensityof import DensityInterface: densityof import DensityInterface: DensityKind diff --git a/src/domains.jl b/src/domains.jl index 3166d99c..9669b287 100644 --- a/src/domains.jl +++ b/src/domains.jl @@ -94,7 +94,7 @@ function tangentat(a::CodimOne, b::CodimOne, x::AbstractArray{T}; tol=ldexp(eps( g2 = b.∇f(x) # See if one is a multiple of the other - Statistics.corm(g1, zero(T), g2, zero(T)) > one(T) - tol + one(T) - Statistics.corm(g1, zero(T), g2, zero(T)) < tol end function zeroset(::CodimOne)::ZeroSet end From 93643939e16d8f17c7c684e5cce658bd9db07fac Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Thu, 2 Dec 2021 14:38:55 -0800 Subject: [PATCH 058/368] working on MeasureTheory tests --- src/MeasureBase.jl | 7 +++++++ src/combinators/for.jl | 2 ++ src/combinators/power.jl | 17 ----------------- src/combinators/smart-constructors.jl | 3 +-- 4 files changed, 10 insertions(+), 19 deletions(-) diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index 03488776..dd2752f1 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -29,6 +29,13 @@ export AbstractMeasure abstract type AbstractMeasure end +function Pretty.tile(d::AbstractMeasure) + M = Symbol(constructor(d)) + the_names = fieldnames(typeof(d)) + isempty(the_names) && return Pretty.literal(M) + Pretty.list_layout(Pretty.tile.([getfield(d, n) for n in the_names]); prefix=M) +end + @inline DensityKind(::AbstractMeasure) = HasDensity() gentype(μ::AbstractMeasure) = typeof(testvalue(μ)) diff --git a/src/combinators/for.jl b/src/combinators/for.jl index ca0d5de1..2e50de6b 100644 --- a/src/combinators/for.jl +++ b/src/combinators/for.jl @@ -76,6 +76,8 @@ julia> For(eachrow(rand(4,2))) do x Normal(x[1], x[2]) end |> marginals |> colle """ For(f, args...) = productmeasure(kernel(i -> f(Tuple(i)...)), zip(args...)) +For(f, inds::AbstractArray) = productmeasure(kernel(f), inds) + For(k::AbstractKernel, inds::AbstractArray) = productmeasure(k, inds) For(f, n::Integer) = productmeasure(kernel(f), Base.OneTo(n)) diff --git a/src/combinators/power.jl b/src/combinators/power.jl index c54f9249..af8b1158 100644 --- a/src/combinators/power.jl +++ b/src/combinators/power.jl @@ -10,23 +10,6 @@ using FillArrays: Fill # """ # PowerMeasure{M,N,D} = ProductMeasure{Fill{M,N,D}} -# function Base.show(io::IO, μ::PowerMeasure) -# io = IOContext(io, :compact => true) -# print(io, μ.data.value, " ^ ", size(μ.data)) -# end - -# function Base.show_unquoted(io::IO, μ::PowerMeasure{M,N,D}, indent::Int, prec::Int) where {M,N,D} -# io = IOContext(io, :compact => true) -# if Base.operator_precedence(:^) ≤ prec -# print(io, "(") -# show(io, μ.data.value) -# print(io, ")") -# else -# show(io, size(μ.data)) -# end -# return nothing -# end - export PowerMeasure const PowerMeasure{M,N,R} = diff --git a/src/combinators/smart-constructors.jl b/src/combinators/smart-constructors.jl index 1f853ae1..e91fe724 100644 --- a/src/combinators/smart-constructors.jl +++ b/src/combinators/smart-constructors.jl @@ -106,8 +106,7 @@ end # kernel(Normal{(:μ,), Tuple{Int64}}) function kernel(::Type{P}) where {P<:AbstractMeasure} - (f, param_maps) = kernelfactor(P) - kernel(f, param_maps) + kernel(P, identity) end # kernel(::Type{P}, op::O) where {O, N, P<:ParameterizedMeasure{N}} = kernel{constructorof(P),O}(op) From 398b00102cb042c7685df429407cfdc1198b026e Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Fri, 3 Dec 2021 06:46:54 -0800 Subject: [PATCH 059/368] updates --- src/MeasureBase.jl | 3 +-- src/combinators/mapsto.jl | 23 ---------------------- src/density.jl | 40 +++++++++++++++++++++++++++------------ src/utils.jl | 10 ---------- 4 files changed, 29 insertions(+), 47 deletions(-) delete mode 100644 src/combinators/mapsto.jl diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index dd2752f1..64a39198 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -32,7 +32,7 @@ abstract type AbstractMeasure end function Pretty.tile(d::AbstractMeasure) M = Symbol(constructor(d)) the_names = fieldnames(typeof(d)) - isempty(the_names) && return Pretty.literal(M) + isempty(the_names) && return Pretty.literal(M)*Pretty.literal("()") Pretty.list_layout(Pretty.tile.([getfield(d, n) for n in the_names]); prefix=M) end @@ -72,7 +72,6 @@ end include("proxies.jl") include("kernel.jl") include("parameterized.jl") -include("combinators/mapsto.jl") include("combinators/half.jl") include("domains.jl") include("primitive.jl") diff --git a/src/combinators/mapsto.jl b/src/combinators/mapsto.jl deleted file mode 100644 index e5e75323..00000000 --- a/src/combinators/mapsto.jl +++ /dev/null @@ -1,23 +0,0 @@ -struct MapsTo{X,Y} - x::X - y::Y -end - -export ↦, mapsto - -mapsto(x, y) = x ↦ y - -↦(x::X, y::Y) where {X,Y} = MapsTo{X,Y}(x, y) - -Base.first(t::MapsTo) = t.x -Base.last(t::MapsTo) = t.y - -Base.Pair(t::MapsTo) = t.x => t.y - -Base.show(io::IO, t::MapsTo) = print(t.x, " ↦ ", t.y) - -logdensity_def(d, t::MapsTo) = logdensity_def(d, t.y) - -Base.iterate(m::MapsTo) = (first(m), 1) -Base.iterate(m::MapsTo, ::Int) = (last(m), nothing) -Base.iterate(m::MapsTo, ::Nothing) = nothing diff --git a/src/density.jl b/src/density.jl index cd52a6a6..77c6650e 100644 --- a/src/density.jl +++ b/src/density.jl @@ -16,7 +16,7 @@ Because this function is often difficult to express in closed form, there are many different ways of computing it. We therefore provide a formal representation to allow comptuational flexibilty. """ -struct Density{M,B,L} <: AbstractDensity +struct Density{M,B} <: AbstractDensity μ::M base::B end @@ -32,6 +32,11 @@ function 𝒹(μ::AbstractMeasure, base::AbstractMeasure) return Density(μ, base) end +logdensityof(d::Density, x) = logdensityof(d.μ, d.base, x) + +logdensityof(d::Density, x) = exp(logdensityof(d.μ, d.base, x)) + + """ struct DensityMeasure{F,B} <: AbstractMeasure density :: F @@ -72,6 +77,8 @@ logdensity_def(μ::DensityMeasure, x) = logdensityof(μ.f, x) density_def(μ::DensityMeasure, x) = densityof(μ.f, x) +densityof(μ::AbstractMeasure, ν::AbstractMeasure, x) = exp(logdensityof(μ, ν, x)) + export ∫ """ @@ -96,12 +103,12 @@ Define a new measure in terms of a log-density `f` over some measure `base`. # TODO: `density` and `logdensity` functions for `DensityMeasure` -@inline function logdensity_def(μ::T, ν::T, x) where {T<:AbstractMeasure} +@inline function logdensityof(μ::T, ν::T, x) where {T<:AbstractMeasure} μ == ν && return 0.0 - invoke(logdensity_def, Tuple{AbstractMeasure,AbstractMeasure,typeof(x)}, μ, ν, x) + invoke(logdensityof, Tuple{AbstractMeasure,AbstractMeasure,typeof(x)}, μ, ν, x) end -@inline function logdensity_def(μ::AbstractMeasure, ν::AbstractMeasure, x) +@inline function logdensityof(μ::AbstractMeasure, ν::AbstractMeasure, x) α = basemeasure(μ) β = basemeasure(ν) @@ -124,7 +131,7 @@ end # measures first is often much cheaper, and allows the numerically-intensive # computation to "fall through" in these cases. # TODO: Add tests to check that NaN cases work properly - ℓ = logdensity_def(α, β, x) + ℓ = logdensityof(α, β, x) isnan(ℓ) && return ℓ ℓ += logdensity_def(μ, x) @@ -133,20 +140,29 @@ end return ℓ end -@inline function logdensityof(μ, x) - n = basemeasure_depth(μ) - (ℓ, β, y) = logdensity_tuple(μ, x) - return _logdensityof(β, y, ℓ, n) +@inline logdensityof(μ, x) = first(_logdensityof(μ, x)) + +# Because it's sometimes useful, this returns a pair (ℓ,r) where +# • ℓ is the log-density +# • r is the rootmeasure of μ +@inline function _logdensityof(μ, x) + n = basemeasure_depth(μ) - static(1) + + β = basemeasure(μ, x) + ℓ = logdensity_def(μ, x) + return _logdensityof(β, x, ℓ, n) end @generated function _logdensityof(μ, x, ℓ, ::StaticInt{n}) where {n} + nsteps = max(n, 0) quote $(Expr(:meta, :inline)) - Base.Cartesian.@nexprs $n i -> begin - (Δℓ, μ, x) = logdensity_tuple(μ, x) + Base.Cartesian.@nexprs $nsteps i -> begin + Δℓ = logdensity_def(μ, x) + μ = basemeasure(μ, x) ℓ += Δℓ end - return ℓ + return (ℓ,μ) end end diff --git a/src/utils.jl b/src/utils.jl index 0804eedf..fc16fee0 100644 --- a/src/utils.jl +++ b/src/utils.jl @@ -70,13 +70,3 @@ end @inline basemeasure_depth(::Type{M}) where {M} = static(1) + basemeasure_depth(basemeasure_type(M)) - -export logdensity_tuple - -function logdensity_tuple(d, x) - return (logdensity_def(d, x), basemeasure(d, x), x) -end - -function logdensity_tuple(d, (z, x)::MapsTo) - return (logdensity_def(d, x), basemeasure(d, x), z ↦ x) -end From b3ad3e9ed138a30fb944d128a41b0c5f85b9bb40 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Fri, 3 Dec 2021 09:44:47 -0800 Subject: [PATCH 060/368] updates --- src/MeasureBase.jl | 1 + src/density.jl | 5 ++++- src/help.jl | 14 ++++++++++++++ 3 files changed, 19 insertions(+), 1 deletion(-) create mode 100644 src/help.jl diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index 64a39198..d873d6a7 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -99,5 +99,6 @@ include("combinators/smart-constructors.jl") include("rand.jl") include("density.jl") +include("help.jl") end diff --git a/src/density.jl b/src/density.jl index 77c6650e..3c2c59f9 100644 --- a/src/density.jl +++ b/src/density.jl @@ -146,7 +146,7 @@ end # • ℓ is the log-density # • r is the rootmeasure of μ @inline function _logdensityof(μ, x) - n = basemeasure_depth(μ) - static(1) + n = basemeasure_depth(proxy(μ)) - static(1) β = basemeasure(μ, x) ℓ = logdensity_def(μ, x) @@ -171,6 +171,9 @@ end export densityof export logdensityof +export density_def + + density_def(μ, ν::AbstractMeasure, x) = exp(logdensity_def(μ, ν, x)) density_def(μ, x) = exp(logdensity_def(μ, x)) diff --git a/src/help.jl b/src/help.jl new file mode 100644 index 00000000..db86ca91 --- /dev/null +++ b/src/help.jl @@ -0,0 +1,14 @@ +export help_basemeasure_type + +function help_basemeasure_type(μ::M) where M + b = basemeasure(μ) + B = typeof(b) + println(""" + function basemeasure_type(::Type{$M}) + $B + end + + """ + ) + return B +end From a662ed5cf2fcbf36aeabe653688476a2571730df Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Sun, 5 Dec 2021 07:40:54 -0800 Subject: [PATCH 061/368] typo --- src/density.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/density.jl b/src/density.jl index 3c2c59f9..732e79c7 100644 --- a/src/density.jl +++ b/src/density.jl @@ -34,7 +34,7 @@ end logdensityof(d::Density, x) = logdensityof(d.μ, d.base, x) -logdensityof(d::Density, x) = exp(logdensityof(d.μ, d.base, x)) +densityof(d::Density, x) = exp(logdensityof(d.μ, d.base, x)) """ From 0680126c00a7e60869c36d9758ac654e9015ef69 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Sun, 5 Dec 2021 07:41:11 -0800 Subject: [PATCH 062/368] update default to mimic Base --- src/MeasureBase.jl | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index d873d6a7..fd088fbb 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -29,11 +29,11 @@ export AbstractMeasure abstract type AbstractMeasure end -function Pretty.tile(d::AbstractMeasure) - M = Symbol(constructor(d)) +function Pretty.tile(d::M) where {M<:AbstractMeasure} the_names = fieldnames(typeof(d)) - isempty(the_names) && return Pretty.literal(M)*Pretty.literal("()") - Pretty.list_layout(Pretty.tile.([getfield(d, n) for n in the_names]); prefix=M) + result = Pretty.literal(repr(M)) + isempty(the_names) && return result * Pretty.literal("()") + Pretty.list_layout(Pretty.tile.([getfield(d, n) for n in the_names]); prefix=result) end @inline DensityKind(::AbstractMeasure) = HasDensity() From af78f82c21adae165c0fda9555ea43bd16172ca2 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Sun, 5 Dec 2021 07:59:21 -0800 Subject: [PATCH 063/368] fix tile(::Lebesgue) --- src/primitives/lebesgue.jl | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/src/primitives/lebesgue.jl b/src/primitives/lebesgue.jl index 6054504f..eea02e54 100644 --- a/src/primitives/lebesgue.jl +++ b/src/primitives/lebesgue.jl @@ -10,6 +10,10 @@ struct Lebesgue{T} <: AbstractMeasure support::T end +function Pretty.tile(μ::Lebesgue) + Pretty.list_layout([Pretty.tile(μ.support)]; prefix=:Lebesgue) +end + gentype(::Lebesgue) = Float64 Lebesgue() = Lebesgue(ℝ) From 264fa57664209a5d014a878e95865c4088d70c66 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Sun, 5 Dec 2021 10:42:15 -0800 Subject: [PATCH 064/368] Add test_interface function --- Project.toml | 1 + src/MeasureBase.jl | 1 + src/interface.jl | 29 +++++++++++++++++++++++++++++ 3 files changed, 31 insertions(+) create mode 100644 src/interface.jl diff --git a/Project.toml b/Project.toml index 7e24250f..7478c4e0 100644 --- a/Project.toml +++ b/Project.toml @@ -14,6 +14,7 @@ PrettyPrinting = "54e16d92-306c-5ea0-a30b-337be88ac337" Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" Static = "aedffcd0-7271-4cad-89d0-dc628f76c6d3" Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" +Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" Tricks = "410a4b4d-49e4-4fbc-ab6d-cb71b17b3775" [compat] diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index fd088fbb..30a75ae8 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -100,5 +100,6 @@ include("rand.jl") include("density.jl") include("help.jl") +include("interface.jl") end diff --git a/src/interface.jl b/src/interface.jl new file mode 100644 index 00000000..52b55a49 --- /dev/null +++ b/src/interface.jl @@ -0,0 +1,29 @@ +using Test + +function dynamic_basemeasure_depth(μ) + β = basemeasure(μ) + depth = 0 + while μ ≠ β + (μ, β) = (β, basemeasure(β)) + depth += 1 + end + return depth +end + +function test_interface(μ) + ########################################################################### + # basemeasure_depth + + static_depth = basemeasure_depth(μ) + dynamic_depth = dynamic_basemeasure_depth(μ) + + if static_depth > dynamic_depth + @warn "basemeasure_depth($μ) greater than requirement, could add some overhead" + end + @test static_depth ≥ dynamic_depth + + ########################################################################### + # basemeasure_type + + @test (basemeasure_type ∘ typeof)(μ) == (typeof ∘ basemeasure)(μ) +end \ No newline at end of file From cb5f5a749c8ec62ad7a2fe8d2ce77768fc2e72f1 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 6 Dec 2021 10:31:11 -0800 Subject: [PATCH 065/368] small doc update --- src/kernel.jl | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/src/kernel.jl b/src/kernel.jl index e3fc539f..8959044c 100644 --- a/src/kernel.jl +++ b/src/kernel.jl @@ -47,7 +47,6 @@ export kernel kernel(f, ::Type{M}) where {M} = kernel(M, f) -# TODO: Would this benefit from https://github.com/tisztamo/FunctionWranglers.jl? mapcall(t, x) = map(func -> func(x), t) # (k::Kernel{Type{P},<:Tuple})(x) where {P<:ParameterizedMeasure} = k.f(mapcall(k.param_maps, x)...) @@ -65,7 +64,7 @@ end """ For any `k::Kernel`, `basekernel` is expected to satisfy ``` -basemeasure(k(p)) == basekernel(k)(p) +basekernel(k)(p) == (basemeasure ∘ k)(p) ``` The main purpose of `basekernel` is to make it efficient to compute From f67c7c344f4cb031648b17d77a44285d18363129 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 6 Dec 2021 11:09:32 -0800 Subject: [PATCH 066/368] DensityKind(::Likelihood) --- src/combinators/likelihood.jl | 3 +++ 1 file changed, 3 insertions(+) diff --git a/src/combinators/likelihood.jl b/src/combinators/likelihood.jl index 9ca93317..9593d866 100644 --- a/src/combinators/likelihood.jl +++ b/src/combinators/likelihood.jl @@ -106,6 +106,9 @@ struct Likelihood{F,S,X} x::X end +# Not really a density, but this makes the code work +@inline DensityKind(::Likelihood) = IsDensity() + Likelihood(μ::AbstractMeasure, x) = Likelihood(kernel(μ), x) Likelihood(::Type{M}, x) where {M<:AbstractMeasure} = Likelihood(kernel(M), x) From cbaf9172970f11a9e95105b773165746fd1c9d8b Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 6 Dec 2021 11:09:50 -0800 Subject: [PATCH 067/368] fixing show(::Likelihood) --- src/combinators/likelihood.jl | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/src/combinators/likelihood.jl b/src/combinators/likelihood.jl index 9593d866..64a917a2 100644 --- a/src/combinators/likelihood.jl +++ b/src/combinators/likelihood.jl @@ -113,10 +113,15 @@ Likelihood(μ::AbstractMeasure, x) = Likelihood(kernel(μ), x) Likelihood(::Type{M}, x) where {M<:AbstractMeasure} = Likelihood(kernel(M), x) +function Pretty.quoteof(ℓ::Likelihood) + k = Pretty.quoteof(ℓ.k) + x = Pretty.quoteof(ℓ.x) + :(Likelihood($k, $x)) +end + function Base.show(io::IO, ℓ::Likelihood) io = IOContext(io, :compact => true) - k, x = ℓ.k, ℓ.x - print(io, "Likelihood(", k, ", ", x, ")") + Pretty.pprint(io, ℓ) end @inline function logdensity_def(ℓ::Likelihood, p) From 49062c621bbc052cf44356c44c8af46cf20a1491 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 6 Dec 2021 11:09:56 -0800 Subject: [PATCH 068/368] adding some docs --- src/parameterized.jl | 37 +++++++++++++++++++++++++++++++++++-- 1 file changed, 35 insertions(+), 2 deletions(-) diff --git a/src/parameterized.jl b/src/parameterized.jl index 7d673277..f0c52c9f 100644 --- a/src/parameterized.jl +++ b/src/parameterized.jl @@ -45,20 +45,53 @@ end export params +""" +`params(μ)` returns the parameters of a measure `μ`, as a `NamedTuple`. The +default method is +``` +params(μ) = NamedTuple() +``` + +See also `paramnames` +""" +function params end + params(μ::ParameterizedMeasure) = getfield(μ, :par) function params(μ::AbstractMeasure, constraints::NamedTuple{C}) where {C} NamedTuple{paramnames(μ, constraints)}(params(μ)) end -params(μ::AbstractMeasure) = NamedTuple() +params(μ) = NamedTuple() ############################################################################### # paramnames export paramnames -paramnames(μ) = paramnames(typeof(μ)) +""" +`paramnames(μ)` returns the names of the parameters of `μ`. This is equivalent to +``` +paramnames(μ) == (keys ∘ params)(μ) +``` +but depends only on the type. In particular, the default implementation is +``` +paramnames(μ::M) where {M} = paramnames(M) +``` + +New `ParameterizedMeasure`s will automatically have a `paramnames` method. For +other measures, this method is optional, but can be added by defining +``` +paramnames(::Type{M}) where {M} = ... +``` + +See also `params` +""" +function paramnames end + + + +paramnames(μ::M) where {M} = paramnames(M) paramnames(::Type{PM}) where {N,PM<:ParameterizedMeasure{N}} = N From 31ad304bedc1b65e570750afacb83088cbd9a7e0 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 6 Dec 2021 11:29:59 -0800 Subject: [PATCH 069/368] update `rand` method --- src/combinators/product.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/combinators/product.jl b/src/combinators/product.jl index 026b29c1..84ca941b 100644 --- a/src/combinators/product.jl +++ b/src/combinators/product.jl @@ -87,7 +87,7 @@ marginals(d::TupleProductMeasure{T}) where {F,T<:Tuple} = d.components end function Base.rand(rng::AbstractRNG, ::Type{T}, d::TupleProductMeasure) where {T} - rand.(d.components) + tuple((rand(rng, T, comp) for comp in d.components)...) end ############################################################################### From 488e6a2da0984432277ec2e3c426e27b1efbd490 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 6 Dec 2021 12:21:52 -0800 Subject: [PATCH 070/368] drop old integration code --- src/integration.jl | 17 ----------------- 1 file changed, 17 deletions(-) delete mode 100644 src/integration.jl diff --git a/src/integration.jl b/src/integration.jl deleted file mode 100644 index 44266738..00000000 --- a/src/integration.jl +++ /dev/null @@ -1,17 +0,0 @@ -import Distributions - -const Dists = Distributions - -struct Integral{F,M} - f::F - μ::M -end - -∫(μ) = ∫(identity, μ) -∫(f, μ) = Integral(f, μ) - -∫(::typeof(identity), ::Dists.Distribution) = 1.0 - -∫(Dists.Normal()) do x - x^2 -end From 96c9f4f6393ff5fdb19410054cb43f2f182ed595 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 6 Dec 2021 12:26:34 -0800 Subject: [PATCH 071/368] add `rebase` --- src/density.jl | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/src/density.jl b/src/density.jl index 732e79c7..25b92ede 100644 --- a/src/density.jl +++ b/src/density.jl @@ -177,3 +177,14 @@ export density_def density_def(μ, ν::AbstractMeasure, x) = exp(logdensity_def(μ, ν, x)) density_def(μ, x) = exp(logdensity_def(μ, x)) + +""" + rebase(μ, ν) + +Express `μ` in terms of a density over `ν`. Satisfies +``` +basemeasure(rebase(μ, ν)) == ν +density(rebase(μ, ν)) == 𝒹(μ,ν) +``` +""" +rebase(μ, ν) = ∫(𝒹(μ,ν), ν) \ No newline at end of file From 4ffd5cf5cea4491346e0ba2a1f8cf93d1288fa73 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 6 Dec 2021 12:26:47 -0800 Subject: [PATCH 072/368] export rebase --- src/MeasureBase.jl | 1 + 1 file changed, 1 insertion(+) diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index 30a75ae8..29372194 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -24,6 +24,7 @@ using Static export ≪ export gentype +export rebase export AbstractMeasure From 3a4d90e6e7d20a0ade3496d5913b5b444dcb9c7a Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 6 Dec 2021 12:45:20 -0800 Subject: [PATCH 073/368] =?UTF-8?q?law=20for=20=E2=8A=97?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- src/combinators/product.jl | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/src/combinators/product.jl b/src/combinators/product.jl index 84ca941b..e73df7a6 100644 --- a/src/combinators/product.jl +++ b/src/combinators/product.jl @@ -78,6 +78,16 @@ function Pretty.tile(μ::TupleProductMeasure{T}) where {F,T<:Tuple} end export ⊗ + +""" + ⊗(μs::AbstractMeasure...) + +`⊗` is a binary operator for building product measures. This satisfies the law + +``` +basemeasure(μ + ν) == basemeasure(μ) + basemeasure(ν) +``` +""" ⊗(μs::AbstractMeasure...) = productmeasure(μs) marginals(d::TupleProductMeasure{T}) where {F,T<:Tuple} = d.components From a15993938b1999fd43eb6dc8b2fa1e4c5e979d73 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 6 Dec 2021 12:45:49 -0800 Subject: [PATCH 074/368] typo --- src/combinators/product.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/combinators/product.jl b/src/combinators/product.jl index e73df7a6..bc699478 100644 --- a/src/combinators/product.jl +++ b/src/combinators/product.jl @@ -85,7 +85,7 @@ export ⊗ `⊗` is a binary operator for building product measures. This satisfies the law ``` -basemeasure(μ + ν) == basemeasure(μ) + basemeasure(ν) +basemeasure(μ ⊗ ν) == basemeasure(μ) ⊗ basemeasure(ν) ``` """ ⊗(μs::AbstractMeasure...) = productmeasure(μs) From 5997f5294d95ffd3e069e5b54507928c021f9cff Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 6 Dec 2021 13:41:06 -0800 Subject: [PATCH 075/368] Make Likelihood more flexible --- src/combinators/likelihood.jl | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/combinators/likelihood.jl b/src/combinators/likelihood.jl index 64a917a2..28810052 100644 --- a/src/combinators/likelihood.jl +++ b/src/combinators/likelihood.jl @@ -1,7 +1,7 @@ export Likelihood @doc raw""" - Likelihood(M<:ParameterizedMeasure, x) + Likelihood(k::AbstractKernel, x) "Observe" a value `x`, yielding a function from the parameters to ℝ. @@ -101,8 +101,8 @@ and we observe `x=3`. We can compute the posterior measure on `μ` as julia> logdensity_def(post, 2) -2.5 """ -struct Likelihood{F,S,X} - k::Kernel{F,S} +struct Likelihood{K,X} + k::K x::X end From 9596fd0e01606b0ebe24fe1768c975ad27088293 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 6 Dec 2021 14:11:51 -0800 Subject: [PATCH 076/368] update kernel methods --- src/combinators/smart-constructors.jl | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/src/combinators/smart-constructors.jl b/src/combinators/smart-constructors.jl index e91fe724..f9ca9add 100644 --- a/src/combinators/smart-constructors.jl +++ b/src/combinators/smart-constructors.jl @@ -121,3 +121,7 @@ kernel(f, op::Returns) = Kernel(Returns(f(op.value)), identity) # Just to avoid dispatch ambiguity kernel(f::Returns, op::Returns) = Kernel(Returns(f.value), identity) + +kernel(k::Kernel) = kernel(k.f, k.g) + +kernel(k::ParameterizedKernel) = kernel(k.f, k.param_maps) \ No newline at end of file From 8c73fc93c1aa216a82fc02f8305b7aaddd3ec0b3 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 6 Dec 2021 14:12:09 -0800 Subject: [PATCH 077/368] add Likelihood method (avoid stack overflow) --- src/combinators/likelihood.jl | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/combinators/likelihood.jl b/src/combinators/likelihood.jl index 28810052..786de157 100644 --- a/src/combinators/likelihood.jl +++ b/src/combinators/likelihood.jl @@ -109,6 +109,8 @@ end # Not really a density, but this makes the code work @inline DensityKind(::Likelihood) = IsDensity() +Likelihood(k::K, x::X) where {K<:AbstractKernel,X} = Likelihood{K,X}(k,x) + Likelihood(μ::AbstractMeasure, x) = Likelihood(kernel(μ), x) Likelihood(::Type{M}, x) where {M<:AbstractMeasure} = Likelihood(kernel(M), x) From 18238c0bbf9b8f7470e3a543eeca528e627baf63 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 8 Dec 2021 16:27:58 -0800 Subject: [PATCH 078/368] refactoring --- src/combinators/for.jl | 24 ++-- src/combinators/power.jl | 50 +++++--- src/combinators/product.jl | 164 ++++---------------------- src/combinators/smart-constructors.jl | 31 +---- src/combinators/transformedmeasure.jl | 2 + src/domains.jl | 1 + src/kernel.jl | 30 +---- 7 files changed, 74 insertions(+), 228 deletions(-) diff --git a/src/combinators/for.jl b/src/combinators/for.jl index 2e50de6b..eb0b2704 100644 --- a/src/combinators/for.jl +++ b/src/combinators/for.jl @@ -3,6 +3,11 @@ export For using Random import Base +struct For{F, I} <: AbstractProductMeasure + f::F + inds::I +end + """ For(f, base...) @@ -74,18 +79,7 @@ julia> For(eachrow(rand(4,2))) do x Normal(x[1], x[2]) end |> marginals |> colle ``` """ -For(f, args...) = productmeasure(kernel(i -> f(Tuple(i)...)), zip(args...)) - -For(f, inds::AbstractArray) = productmeasure(kernel(f), inds) - -For(k::AbstractKernel, inds::AbstractArray) = productmeasure(k, inds) - -For(f, n::Integer) = productmeasure(kernel(f), Base.OneTo(n)) -For(k::AbstractKernel, n::Integer) = productmeasure(k, Base.OneTo(n)) - -For(f, dims::Integer...) = - productmeasure(kernel(i -> f(Tuple(i)...)), CartesianIndices(dims)) - -function Base.eltype(d::ProductMeasure{F,I}) where {F,I<:AbstractArray} - return eltype(d.f(first(d.xs))) -end +For(f, inds::AbstractArray...) = productmeasure(mappedarray(f, inds...)) +For(f, n::Integer) = For(f, Base.OneTo(n)) +For(f, inds::Integer...) = For(i -> f(Tuple(i)...), Base.CartesianIndices(inds)) +For(f, gen::Base.Generator) = ProductMeasure(Base.Generator(f ∘ gen.f, gen.iter)) diff --git a/src/combinators/power.jl b/src/combinators/power.jl index af8b1158..5770b3f8 100644 --- a/src/combinators/power.jl +++ b/src/combinators/power.jl @@ -12,25 +12,36 @@ using FillArrays: Fill export PowerMeasure -const PowerMeasure{M,N,R} = - ProductMeasure{M,Kernel{Returns{M},typeof(identity)},LinearIndices{N,R}} - -Base.:^(μ::AbstractMeasure, ::Tuple{}) = μ +struct PowerMeasure{M,A} <: AbstractProductMeasure + parent::M + axes::A +end -function Base.:^(μ::AbstractMeasure, dims::Integer...) - return μ^dims +function Pretty.tile(μ::PowerMeasure) + sz = length.(μ.axes) + arg1 = Pretty.tile(μ.parent) + arg2 = Pretty.tile(length(sz) == 1 ? only(sz) : sz) + return Pretty.pair_layout(arg1, arg2; sep = " ^ ") end -function Pretty.tile(d::PowerMeasure{M,1}) where {M} - Pretty.pair_layout(Pretty.tile(d.f.f.value), Pretty.tile(length(d.xs)); sep = " ^ ") +@inline function powermeasure(x::T, sz::Vararg{<:Integer,N}) where {T, N} + a = axes(Fill{T, N}(x, sz)) + A = typeof(a) + PowerMeasure{T,A}(x,a) end -function Pretty.tile(d::PowerMeasure) - Pretty.pair_layout(Pretty.tile(d.f.f.value), Pretty.tile(size(d.xs)); sep = " ^ ") +@inline function powermeasure(x::T, sz::Tuple{Vararg{<:Any,N}}) where {T, N} + a = axes(Fill{T, N}(x, sz)) + A = typeof(a) + PowerMeasure{T,A}(x,a) end -# Base.show(io::IO, d::PowerMeasure) = print(io, d.f.f.value, " ^ ", size(d.xs)) -# Base.show(io::IO, d::PowerMeasure{M,1}) where {M} = print(io, d.f.f.value, " ^ ", length(d.xs)) +marginals(d::PowerMeasure) = Fill(d.parent, d.axes) + +Base.:^(μ::AbstractMeasure, dims) = powermeasure(μ, dims) + +# Base.show(io::IO, d::PowerMeasure) = print(io, d.parent, " ^ ", size(d.xs)) +# Base.show(io::IO, d::PowerMeasure{M,1}) where {M} = print(io, d.parent, " ^ ", length(d.xs)) # gentype(d::PowerMeasure{M,N}) where {M,N} = @inbounds Array{gentype(first(marginals(d))), N} @@ -39,22 +50,23 @@ params(d::PowerMeasure) = params(first(marginals(d))) # basemeasure(μ::PowerMeasure) = @inbounds basemeasure(first(μ.data))^size(μ.data) @inline function basemeasure(d::PowerMeasure) - basemeasure(d.f.f.value)^size(d.xs) + basemeasure(d.parent) ^ d.axes end -function basemeasure_depth(d::PowerMeasure{M,N,R}) where {M,N,R} +function basemeasure_depth(::PowerMeasure{M}) where {M} return basemeasure_depth(M) end -function basemeasure_type(::Type{P}) where {M,N,R,P<:PowerMeasure{M,N,R}} - return PowerMeasure{basemeasure_type(M),N,R} +function basemeasure_type(::Type{PowerMeasure{M,D}}) where {M,D} + return PowerMeasure{basemeasure_type(M),D} end -function basemeasure_depth(::Type{P}) where {M<:PrimitiveMeasure,N,R,P<:PowerMeasure{M,N,R}} +function basemeasure_depth(::Type{PowerMeasure{M,D}}) where {M<:PrimitiveMeasure,D} return static(0) end @inline function logdensity_def(d::PowerMeasure, x) - d1 = d.f(first(d.xs)) - sum(xj -> logdensity_def(d1, xj), x) + sum(x) do xj + logdensity_def(d.parent, xj) + end end diff --git a/src/combinators/product.jl b/src/combinators/product.jl index bc699478..bfb18ef4 100644 --- a/src/combinators/product.jl +++ b/src/combinators/product.jl @@ -7,74 +7,42 @@ using FillArrays abstract type AbstractProductMeasure <: AbstractMeasure end -struct ProductMeasure{M,K<:AbstractKernel,I} <: AbstractProductMeasure - f::K - xs::I - - function ProductMeasure(f::K, xs::I) where {K,I} - μ₁ = f(first(xs)) - M = typeof(μ₁) - new{M,K,I}(f, xs) - end -end - -function Pretty.tile(μ::ProductMeasure) - result = Pretty.literal("For(") - result *= Pretty.pair_layout(Pretty.tile(μ.f), Pretty.tile(μ.xs); sep = ", ") +function Pretty.tile(μ::AbstractProductMeasure) + result = Pretty.literal("ProductMeasure(") + result *= Pretty.tile(marginals(μ)) result *= Pretty.literal(")") end -# TODO: Test for equality without traversal, probably by first converting to a -# canonical form -function Base.:(==)(a::ProductMeasure, b::ProductMeasure) - all(zip(a.xs, b.xs)) do (aᵢ, bᵢ) - a.f(aᵢ) == b.f(bᵢ) - end -end +export marginals -Base.size(μ::ProductMeasure) = size(marginals(μ)) +function Base.:(==)(a::AbstractProductMeasure, b::AbstractProductMeasure) + marginals(a) == marginals(b) +end +Base.length(μ::AbstractProductMeasure) = length(marginals(μ)) +Base.size(μ::AbstractProductMeasure) = size(marginals(μ)) +basemeasure(d::AbstractProductMeasure) = map(basemeasure, marginals(d)) -Base.length(μ::ProductMeasure) = length(marginals(μ)) +@inline function logdensity_def(d::AbstractProductMeasure, x) + mapreduce(logdensity_def, +, marginals(d), x) +end +struct ProductMeasure{M} <: AbstractProductMeasure + marginals::M +end -basemeasure(d::ProductMeasure) = productmeasure(basekernel(d.f), d.xs) -basemeasure_depth(μ::ProductMeasure) = basemeasure_depth(first(marginals(μ))) -# TODO: Do we need these methods? -# basemeasure(d::ProductMeasure) = ProductMeasure(basemeasure ∘ d.f, d.xs) -# basemeasure(d::ProductMeasure{typeof(identity)}) = ProductMeasure(identity, map(basemeasure, d.xs)) -# basemeasure(d::ProductMeasure{typeof(identity), <:FillArrays.Fill}) = ProductMeasure(identity, map(basemeasure, d.xs)) +marginals(μ::ProductMeasure) = μ.marginals -export marginals -function marginals(d::ProductMeasure{M,K,I}) where {M,K,I} - _marginals(d, isiterable(I)) -end -function _marginals(d::ProductMeasure, ::Iterable) - return (d.f(i) for i in d.xs) -end +basemeasure_depth(μ::ProductMeasure) = basemeasure_depth(first(marginals(μ))) testvalue(d::AbstractProductMeasure) = map(testvalue, marginals(d)) function Base.rand(rng::AbstractRNG, ::Type{T}, d::ProductMeasure) where {T} - _rand(rng, T, d, marginals(d)) -end - -function _rand(rng::AbstractRNG, ::Type{T}, d::ProductMeasure, mar) where {T} - (rand(rng, T, m) for m in mar) -end - -############################################################################### -# I <: Tuple - -struct TupleProductMeasure{T} <: AbstractProductMeasure - components::T -end - -function Pretty.tile(μ::TupleProductMeasure{T}) where {F,T<:Tuple} - mar = marginals(μ) - Pretty.list_layout(Pretty.Layout[Pretty.tile.(mar)...]; sep = " ⊗ ") + map(marginals(d)) do dⱼ + rand(rng, T, dⱼ) + end end export ⊗ @@ -85,50 +53,17 @@ export ⊗ `⊗` is a binary operator for building product measures. This satisfies the law ``` -basemeasure(μ ⊗ ν) == basemeasure(μ) ⊗ basemeasure(ν) + basemeasure(μ ⊗ ν) == basemeasure(μ) ⊗ basemeasure(ν) ``` """ ⊗(μs::AbstractMeasure...) = productmeasure(μs) -marginals(d::TupleProductMeasure{T}) where {F,T<:Tuple} = d.components - -@inline function logdensity_def(d::TupleProductMeasure, x::Tuple) where {T<:Tuple} - mapreduce(logdensity_def, +, d.components, x) -end - -function Base.rand(rng::AbstractRNG, ::Type{T}, d::TupleProductMeasure) where {T} - tuple((rand(rng, T, comp) for comp in d.components)...) -end - -############################################################################### -# I <: AbstractArray - -marginals(d::ProductMeasure{M,K,A}) where {M,K,A<:AbstractArray} = mappedarray(d.f, d.xs) - -@inline function logdensity_def(d::ProductMeasure, x) - mapreduce(logdensity_def, +, marginals(d), x) -end - -@inline function logdensity_def(d::ProductMeasure{<:Returns}, x) - sum(x -> logdensity_def(d.f.f.value, x), x) -end - -# function Base.rand(rng::AbstractRNG, ::Type{T}, d::ProductMeasure{M,K,I}) where {T,F,I<:CartesianIndices} - -# end - ############################################################################### # I <: Base.Generator export rand! using Random: rand!, GLOBAL_RNG, AbstractRNG -function logdensity_def(μ::AbstractProductMeasure, x) - mapreduce(+, μ.xs, x) do (j, x) - logdensity_def(μ.f(j), x) - end -end - @propagate_inbounds function Random.rand!( rng::AbstractRNG, d::ProductMeasure, @@ -152,58 +87,3 @@ function _rand(rng::AbstractRNG, ::Type{T}, d::ProductMeasure, mar::AbstractArra x = Array{elT,length(sz)}(undef, sz) rand!(rng, d, x) end - -# TODO: -# function Base.rand(rng::AbstractRNG, d::ProductMeasure) -# return rand(rng, gentype(d), d) -# end - -# function Base.rand(T::Type, d::ProductMeasure) -# return rand(Random.GLOBAL_RNG, T, d) -# end - -# function Base.rand(d::ProductMeasure) -# T = gentype(d) -# return rand(Random.GLOBAL_RNG, T, d) -# end - -function gentype(d::ProductMeasure{A}) where {T,N,A<:AbstractArray{T,N}} - S = @inbounds gentype(marginals(d)[1]) - Array{S,N} -end - -function gentype(d::ProductMeasure{<:Tuple}) - Tuple{gentype.(marginals(d))...} -end - -# function logdensity_def(μ::ProductMeasure{Aμ}, x::Ax) where {Aμ <: MappedArray, Ax <: AbstractArray} -# μ.data -# end - -# # FIXME -# function ConstructionBase.constructorof(::Type{P}) where {K,I,P<:ProductMeasure{M,K,I}} -# p -> productmeasure(d.f, p) -# end - -# function Accessors.set(d::ProductMeasure{N}, ::typeof(params), p) where {N} -# setproperties(d, NamedTuple{N}(p...)) -# end - -# function Accessors.set(d::ProductMeasure{F,T}, ::typeof(params), p::Tuple) where {F, T<:Tuple} -# set.(marginals(d), params, p) -# end - -# function logdensity_def(μ::ProductMeasure, ν::ProductMeasure, x) -# sum(zip(marginals(μ), marginals(ν), x)) do μ_ν_x -# logdensity_def(μ_ν_x...) -# end -# end - -function kernelfactor(μ::ProductMeasure{M,K,<:Fill}) where {M,K} - k = kernel(first(marginals(μ))) - (p -> k.f(p)^size(μ), k.param_maps) -end - -# function kernelfactor(μ::ProductMeasure{K,A}) where {K,A<:AbstractArray} -# (p -> set.(marginals(μ), params, p), μ.xs) -# end diff --git a/src/combinators/smart-constructors.jl b/src/combinators/smart-constructors.jl index f9ca9add..e9f92443 100644 --- a/src/combinators/smart-constructors.jl +++ b/src/combinators/smart-constructors.jl @@ -17,15 +17,7 @@ end ############################################################################### # PowerMeaure -function Base.:^(μ::M, dims::NTuple{N,I}) where {M<:AbstractMeasure,N,I} - productmeasure(Kernel(Returns(μ), identity), LinearIndices(dims)) -end - -# function Base.:^(μ::M, dims::Tuple{I}) where {M<:AbstractMeasure,N,I} -# productmeasure(KernelReturns(μ), Base.OneTo(first(dims))) -# end - -function Base.:^(μ::WeightedMeasure, dims::NTuple{N,I}) where {N,I} +function powermeasure(μ::WeightedMeasure, dims::NTuple{N,I}) where {N,I} k = prod(dims) * μ.logweight return weightedmeasure(k, μ.base^dims) end @@ -33,15 +25,14 @@ end ############################################################################### # ProductMeasure -productmeasure(f::AbstractKernel, pars) = ProductMeasure(f, pars) +productmeasure(data::AbstractArray) = ProductMeasure(data) +productmeasure(nt::NamedTuple) = ProductMeasure(nt) +productmeasure(tup::Tuple) = ProductMeasure(tup) productmeasure(f, param_maps, pars) = ProductMeasure(kernel(f, param_maps), pars) -productmeasure(μs::Tuple) = TupleProductMeasure(μs) - productmeasure(k::ParameterizedKernel, pars) = productmeasure(k.f, k.param_maps, pars) -productmeasure(nt::NamedTuple) = productmeasure(identity, nt) function productmeasure(f::Returns{FB}, param_maps, pars) where {FB<:FactoredBase} fb = f.value @@ -93,10 +84,7 @@ end ############################################################################### # Kernel -kernel(f) = kernel(f, identity) - -kernel(μ, op1, op2, param_maps...) = Kernel(μ, op1, op2, param_maps...) -kernel(μ, op) = Kernel(μ, op) +kernel(μ, op1, op2, param_maps...) = ParameterizedKernel(μ, op1, op2, param_maps...) # kernel(Normal(μ=2)) function kernel(μ::P) where {P<:AbstractMeasure} @@ -116,12 +104,5 @@ function kernel(::Type{M}; param_maps...) where {M} kernel(M, nt) end -kernel(f::Returns, op) = Kernel(f, identity) -kernel(f, op::Returns) = Kernel(Returns(f(op.value)), identity) - -# Just to avoid dispatch ambiguity -kernel(f::Returns, op::Returns) = Kernel(Returns(f.value), identity) - -kernel(k::Kernel) = kernel(k.f, k.g) -kernel(k::ParameterizedKernel) = kernel(k.f, k.param_maps) \ No newline at end of file +kernel(k::ParameterizedKernel) = k \ No newline at end of file diff --git a/src/combinators/transformedmeasure.jl b/src/combinators/transformedmeasure.jl index e4c898ce..0c497a33 100644 --- a/src/combinators/transformedmeasure.jl +++ b/src/combinators/transformedmeasure.jl @@ -1,3 +1,5 @@ +# TODO: Compare with ChangesOfVariables.jl + abstract type AbstractTransformedMeasure <: AbstractMeasure end abstract type AbstractPushforward <: AbstractTransformedMeasure end diff --git a/src/domains.jl b/src/domains.jl index 9669b287..2af15ea0 100644 --- a/src/domains.jl +++ b/src/domains.jl @@ -2,6 +2,7 @@ abstract type AbstractDomain end abstract type RealDomain <: AbstractDomain end +# TODO: Use IntervalSets struct RealNumbers <: RealDomain end const ℝ = RealNumbers() diff --git a/src/kernel.jl b/src/kernel.jl index 8959044c..34898ea1 100644 --- a/src/kernel.jl +++ b/src/kernel.jl @@ -1,16 +1,6 @@ - -export Kernel - +# TODO: Dangerous to export this - let's not abstract type AbstractKernel <: AbstractMeasure end -struct Kernel{F,G} <: AbstractKernel - f::F - g::G - - Kernel(::Type{T}, g::G) where {T,G} = new{Type{T},G}(T, g) - Kernel(f::F, g::G) where {F,G} = new{F,G}(f, g) -end - struct ParameterizedKernel{F,N,T} <: AbstractKernel f::F param_maps::NamedTuple{N,T} @@ -39,7 +29,6 @@ If the argument is a named tuple `(;a=f1, b=f1)`, `κ(x)` is defined as """ function kernel end -export kernel # kernel(Normal) do x # (μ=x,σ=x^2) @@ -59,7 +48,6 @@ function (k::ParameterizedKernel)(x::Tuple) k.f(NamedTuple{k.param_maps}(x)) end -(k::Kernel)(x) = (k.f ∘ k.g)(x) """ For any `k::Kernel`, `basekernel` is expected to satisfy @@ -79,8 +67,6 @@ basekernel(f) = basemeasure ∘ f basekernel(k::ParameterizedKernel) = kernel(basekernel(k.f), k.param_maps) -basekernel(k::Kernel) = kernel(basekernel(k.f), k.g) - basekernel(f::Returns) = Returns(basemeasure(f.value)) # export kernelize @@ -95,21 +81,11 @@ function Base.show(io::IO, μ::AbstractKernel) Pretty.pprint(io, μ) end -function Pretty.quoteof(k::Kernel) - qf = Pretty.quoteof(k.f) - qg = Pretty.quoteof(k.g) - :(Kernel($qf, $qg)) -end - -function Pretty.quoteof(k::Kernel{F,typeof(identity)}) where {F} - qf = Pretty.quoteof(k.f) - :(Kernel($qf)) -end - function Pretty.quoteof(k::ParameterizedKernel) qf = Pretty.quoteof(k.f) qg = Pretty.quoteof(k.param_maps) - :(Kernel($qf, $qg)) + :(ParameterizedKernel($qf, $qg)) end export kernelfactor + From 77a574d6a599ca84e40721b43ca813aabad895cf Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 8 Dec 2021 16:40:54 -0800 Subject: [PATCH 079/368] compat --- Project.toml | 2 ++ src/MeasureBase.jl | 13 ++++--------- 2 files changed, 6 insertions(+), 9 deletions(-) diff --git a/Project.toml b/Project.toml index 7478c4e0..8d284dd4 100644 --- a/Project.toml +++ b/Project.toml @@ -4,6 +4,7 @@ authors = ["Chad Scherrer and contributors"] version = "0.5.1" [deps] +Compat = "34da2185-b29b-5c13-b0c7-acf172513d20" ConstructionBase = "187b0558-2788-49d3-abe0-74a17ed4e7c9" DensityInterface = "b429d917-457f-4dbc-8f4c-0cc954292b1d" FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b" @@ -18,6 +19,7 @@ Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" Tricks = "410a4b4d-49e4-4fbc-ab6d-cb71b17b3775" [compat] +Compat = "3.35" ConstructionBase = "1.3" DensityInterface = "0.4" FillArrays = "0.12" diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index 29372194..4921bf6b 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -60,15 +60,10 @@ Methods for computing density relative to other measures will be """ function logdensity_def end -if VERSION < v"1.7.0-beta1.0" - @eval begin - struct Returns{T} - value::T - end - - (f::Returns)(args...) = f.value - end -end +using Compat + +const Returns = @compat Returns +const only = @compat only include("proxies.jl") include("kernel.jl") From ff3160381465ff02f6533d35a760547e7c4b8969 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 8 Dec 2021 18:43:46 -0800 Subject: [PATCH 080/368] Maybe Comat just works? --- src/MeasureBase.jl | 3 --- 1 file changed, 3 deletions(-) diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index 4921bf6b..855785bf 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -62,9 +62,6 @@ function logdensity_def end using Compat -const Returns = @compat Returns -const only = @compat only - include("proxies.jl") include("kernel.jl") include("parameterized.jl") From 3fce024e5269212262841b67519de35c2732cc8d Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Thu, 9 Dec 2021 14:18:55 -0800 Subject: [PATCH 081/368] refactoring --- src/MeasureBase.jl | 6 +- src/combinators/likelihood.jl | 8 +-- src/combinators/smart-constructors.jl | 30 ++++----- src/kernel.jl | 91 --------------------------- src/parameterized.jl | 12 +++- test/runtests.jl | 6 +- 6 files changed, 35 insertions(+), 118 deletions(-) delete mode 100644 src/kernel.jl diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index 855785bf..dfd01d78 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -45,7 +45,7 @@ gentype(μ::AbstractMeasure) = typeof(testvalue(μ)) export logdensity_def export basemeasure -export basekernel +export basekleisli using LogExpFunctions: logsumexp @@ -63,7 +63,7 @@ function logdensity_def end using Compat include("proxies.jl") -include("kernel.jl") +include("kleisli.jl") include("parameterized.jl") include("combinators/half.jl") include("domains.jl") @@ -76,6 +76,7 @@ include("primitives/lebesgue.jl") include("primitives/dirac.jl") include("primitives/trivial.jl") +include("combinators/bind.jl") include("combinators/transformedmeasure.jl") include("combinators/factoredbase.jl") include("combinators/weighted.jl") @@ -88,6 +89,7 @@ include("combinators/likelihood.jl") include("combinators/pointwise.jl") include("combinators/restricted.jl") include("combinators/smart-constructors.jl") +include("combinators/conditional.jl") include("rand.jl") diff --git a/src/combinators/likelihood.jl b/src/combinators/likelihood.jl index 786de157..9c9b65fe 100644 --- a/src/combinators/likelihood.jl +++ b/src/combinators/likelihood.jl @@ -1,7 +1,7 @@ export Likelihood @doc raw""" - Likelihood(k::AbstractKernel, x) + Likelihood(k::AbstractKleisli, x) "Observe" a value `x`, yielding a function from the parameters to ℝ. @@ -109,11 +109,11 @@ end # Not really a density, but this makes the code work @inline DensityKind(::Likelihood) = IsDensity() -Likelihood(k::K, x::X) where {K<:AbstractKernel,X} = Likelihood{K,X}(k,x) +Likelihood(k::K, x::X) where {K<:AbstractKleisli,X} = Likelihood{K,X}(k,x) -Likelihood(μ::AbstractMeasure, x) = Likelihood(kernel(μ), x) +Likelihood(μ::AbstractMeasure, x) = Likelihood(askleisli(μ), x) -Likelihood(::Type{M}, x) where {M<:AbstractMeasure} = Likelihood(kernel(M), x) +Likelihood(::Type{M}, x) where {M<:AbstractMeasure} = Likelihood(askleisli(M), x) function Pretty.quoteof(ℓ::Likelihood) k = Pretty.quoteof(ℓ.k) diff --git a/src/combinators/smart-constructors.jl b/src/combinators/smart-constructors.jl index e9f92443..94cb9cfa 100644 --- a/src/combinators/smart-constructors.jl +++ b/src/combinators/smart-constructors.jl @@ -29,9 +29,9 @@ productmeasure(data::AbstractArray) = ProductMeasure(data) productmeasure(nt::NamedTuple) = ProductMeasure(nt) productmeasure(tup::Tuple) = ProductMeasure(tup) -productmeasure(f, param_maps, pars) = ProductMeasure(kernel(f, param_maps), pars) +productmeasure(f, param_maps, pars) = ProductMeasure(kleisli(f, param_maps), pars) -productmeasure(k::ParameterizedKernel, pars) = productmeasure(k.f, k.param_maps, pars) +productmeasure(k::ParameterizedKleisli, pars) = productmeasure(k.f, k.param_maps, pars) function productmeasure(f::Returns{FB}, param_maps, pars) where {FB<:FactoredBase} @@ -82,27 +82,27 @@ function weightedmeasure(ℓ, b::WeightedMeasure) end ############################################################################### -# Kernel +# Kleisli -kernel(μ, op1, op2, param_maps...) = ParameterizedKernel(μ, op1, op2, param_maps...) +kleisli(μ, op1, op2, param_maps...) = ParameterizedKleisli(μ, op1, op2, param_maps...) -# kernel(Normal(μ=2)) -function kernel(μ::P) where {P<:AbstractMeasure} - (f, param_maps) = kernelfactor(μ) - kernel(f, param_maps) +# kleisli(Normal(μ=2)) +function kleisli(μ::P) where {P<:AbstractMeasure} + (f, param_maps) = kleislifactor(μ) + kleisli(f, param_maps) end -# kernel(Normal{(:μ,), Tuple{Int64}}) -function kernel(::Type{P}) where {P<:AbstractMeasure} - kernel(P, identity) +# kleisli(Normal{(:μ,), Tuple{Int64}}) +function kleisli(::Type{P}) where {P<:AbstractMeasure} + kleisli(P, identity) end -# kernel(::Type{P}, op::O) where {O, N, P<:ParameterizedMeasure{N}} = kernel{constructorof(P),O}(op) +# kleisli(::Type{P}, op::O) where {O, N, P<:ParameterizedMeasure{N}} = kleisli{constructorof(P),O}(op) -function kernel(::Type{M}; param_maps...) where {M} +function kleisli(::Type{M}; param_maps...) where {M} nt = NamedTuple(param_maps) - kernel(M, nt) + kleisli(M, nt) end -kernel(k::ParameterizedKernel) = k \ No newline at end of file +kleisli(k::ParameterizedKleisli) = k \ No newline at end of file diff --git a/src/kernel.jl b/src/kernel.jl deleted file mode 100644 index 34898ea1..00000000 --- a/src/kernel.jl +++ /dev/null @@ -1,91 +0,0 @@ -# TODO: Dangerous to export this - let's not -abstract type AbstractKernel <: AbstractMeasure end - -struct ParameterizedKernel{F,N,T} <: AbstractKernel - f::F - param_maps::NamedTuple{N,T} - - ParameterizedKernel(::Type{F}, param_maps::NamedTuple{N,T}) where {F,N,T} = - new{Type{F},N,T}(F, param_maps) - ParameterizedKernel(f::F, param_maps::NamedTuple{N,T}) where {F,N,T} = - new{F,N,T}(f, param_maps) -end - -""" - kernel(f, M) - kernel((f1, f2, ...), M) - -A kernel `κ = kernel(f, m)` returns a wrapper around -a function `f` giving the parameters for a measure of type `M`, -such that `κ(x) = M(f(x)...)` -respective `κ(x) = M(f1(x), f2(x), ...)` - -If the argument is a named tuple `(;a=f1, b=f1)`, `κ(x)` is defined as -`M(;a=f(x),b=g(x))`. - -# Reference - -* https://en.wikipedia.org/wiki/Markov_kernel -""" -function kernel end - - -# kernel(Normal) do x -# (μ=x,σ=x^2) -# end - -kernel(f, ::Type{M}) where {M} = kernel(M, f) - -mapcall(t, x) = map(func -> func(x), t) - -# (k::Kernel{Type{P},<:Tuple})(x) where {P<:ParameterizedMeasure} = k.f(mapcall(k.param_maps, x)...) - -(k::ParameterizedKernel)(x) where {M} = k.f(; mapcall(k.param_maps, x)...) - -(k::ParameterizedKernel)(x...) = k(x) - -function (k::ParameterizedKernel)(x::Tuple) - k.f(NamedTuple{k.param_maps}(x)) -end - - -""" -For any `k::Kernel`, `basekernel` is expected to satisfy -``` -basekernel(k)(p) == (basemeasure ∘ k)(p) -``` - -The main purpose of `basekernel` is to make it efficient to compute -``` -basemeasure(d::ProductMeasure) = productmeasure(basekernel(d.f), d.xs) -``` -""" -function basekernel end - -# TODO: Find a way to do better than this -basekernel(f) = basemeasure ∘ f - -basekernel(k::ParameterizedKernel) = kernel(basekernel(k.f), k.param_maps) - -basekernel(f::Returns) = Returns(basemeasure(f.value)) - -# export kernelize - -# function kernelize(μ::M) where {N, M <: ParameterizedMeasure{N}} -# C = constructorof(M) -# (Kernel{C,}(NamedTuple{N}, ), values(getfield(μ, :par))) -# end - -function Base.show(io::IO, μ::AbstractKernel) - io = IOContext(io, :compact => true) - Pretty.pprint(io, μ) -end - -function Pretty.quoteof(k::ParameterizedKernel) - qf = Pretty.quoteof(k.f) - qg = Pretty.quoteof(k.param_maps) - :(ParameterizedKernel($qf, $qg)) -end - -export kernelfactor - diff --git a/src/parameterized.jl b/src/parameterized.jl index f0c52c9f..4cbd7405 100644 --- a/src/parameterized.jl +++ b/src/parameterized.jl @@ -26,6 +26,12 @@ end # julia> Normal{(:μ,)}(2) # Normal(μ = 2,) # +export kleisli + +function kleisli(::Type{P}) where {N,P<:ParameterizedMeasure{N}} + function(args...) P(args...) end +end + function (::Type{P})(args...) where {N,P<:ParameterizedMeasure{N}} C = constructor(P) return C(NamedTuple{N}(args...)) @@ -104,12 +110,12 @@ function paramnames(μ, constraints::NamedTuple{N}) where {N} end ############################################################################### -# kernelfactor +# kleislifactor -function kernelfactor(::Type{P}) where {N,P<:ParameterizedMeasure{N}} +function kleislifactor(::Type{P}) where {N,P<:ParameterizedMeasure{N}} (constructor(P), N) end -function kernelfactor(::P) where {N,P<:ParameterizedMeasure{N}} +function kleislifactor(::P) where {N,P<:ParameterizedMeasure{N}} (constructor(P), N) end diff --git a/test/runtests.jl b/test/runtests.jl index b0510641..a54d33b6 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -79,8 +79,8 @@ testbroken_measures = [ end end -# @testset "Kernel" begin -# κ = MeasureBase.kernel(MeasureBase.Dirac, identity) +# @testset "Kleisli" begin +# κ = MeasureBase.kleisli(MeasureBase.Dirac, identity) # @test rand(κ(1.1)) == 1.1 # end @@ -142,7 +142,7 @@ end # ℓs = [ # Likelihood(Normal{(:μ,)}, 3.0) -# Likelihood(kernel(Normal, x -> (μ=x, σ=2.0)), 3.0) +# Likelihood(kleisli(Normal, x -> (μ=x, σ=2.0)), 3.0) # ] # for (d,p) in dps From 156c9909341a28229c5298e3356f1b6dfbbf6b43 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Thu, 9 Dec 2021 14:19:07 -0800 Subject: [PATCH 082/368] some new stuff --- src/combinators/bind.jl | 30 ++++++++++++ src/combinators/conditional.jl | 6 +++ src/kleisli.jl | 89 ++++++++++++++++++++++++++++++++++ 3 files changed, 125 insertions(+) create mode 100644 src/combinators/bind.jl create mode 100644 src/combinators/conditional.jl create mode 100644 src/kleisli.jl diff --git a/src/combinators/bind.jl b/src/combinators/bind.jl new file mode 100644 index 00000000..9d3ea89c --- /dev/null +++ b/src/combinators/bind.jl @@ -0,0 +1,30 @@ +struct Bind{M,K} <: AbstractMeasure + μ::M + k::K +end + +export ↣ + +""" +If +- μ is an `AbstractMeasure` or satisfies the Measure interface, and +- k is a function taking values from the support of μ and returning a measure + +Then `μ ↣ k` is a measure, called a *monadic bind*. In a +probabilistic programming language like Soss.jl, this could be expressed as + +Note that bind is usually written `>>=`, but this symbol is unavailable in Julia. + +``` +bind = @model μ,k begin + x ~ μ + y ~ k(x) + return y +end +``` + +See also `bind` and `Bind` +""" +↣(μ, k) = bind(μ, k) + +bind(μ, k) = Bind(μ, k) \ No newline at end of file diff --git a/src/combinators/conditional.jl b/src/combinators/conditional.jl new file mode 100644 index 00000000..ecc1e918 --- /dev/null +++ b/src/combinators/conditional.jl @@ -0,0 +1,6 @@ +struct ConditionalMeasure{M,C} <: AbstractMeasure + parent::M + constraint::C +end + +Base.:|(μ::AbstractMeasure, constraint) = ConditionalMeasure(μ, constraint) \ No newline at end of file diff --git a/src/kleisli.jl b/src/kleisli.jl new file mode 100644 index 00000000..ccf30bcf --- /dev/null +++ b/src/kleisli.jl @@ -0,0 +1,89 @@ +# TODO: Dangerous to export this - let's not +abstract type AbstractKleisli <: AbstractMeasure end + +struct ParameterizedKleisli{F,N,T} <: AbstractKleisli + f::F + param_maps::NamedTuple{N,T} + + ParameterizedKleisli(::Type{F}, param_maps::NamedTuple{N,T}) where {F,N,T} = + new{Type{F},N,T}(F, param_maps) + ParameterizedKleisli(f::F, param_maps::NamedTuple{N,T}) where {F,N,T} = + new{F,N,T}(f, param_maps) +end + +""" + kleisli(f, M) + kleisli((f1, f2, ...), M) + +A kleisli `κ = kleisli(f, m)` returns a wrapper around +a function `f` giving the parameters for a measure of type `M`, +such that `κ(x) = M(f(x)...)` +respective `κ(x) = M(f1(x), f2(x), ...)` + +If the argument is a named tuple `(;a=f1, b=f1)`, `κ(x)` is defined as +`M(;a=f(x),b=g(x))`. + +# Reference + +* https://en.wikipedia.org/wiki/Markov_kleisli +""" +function kleisli end + + +# kleisli(Normal) do x +# (μ=x,σ=x^2) +# end + +kleisli(f, ::Type{M}) where {M} = kleisli(M, f) + +mapcall(t, x) = map(func -> func(x), t) + +# (k::Kleisli{Type{P},<:Tuple})(x) where {P<:ParameterizedMeasure} = k.f(mapcall(k.param_maps, x)...) + +(k::ParameterizedKleisli)(x) where {M} = k.f(; mapcall(k.param_maps, x)...) + +(k::ParameterizedKleisli)(x...) = k(x) + +function (k::ParameterizedKleisli)(x::Tuple) + k.f(NamedTuple{k.param_maps}(x)) +end + + +""" +For any `k::Kleisli`, `basekleisli` is expected to satisfy +``` +basekleisli(k)(p) == (basemeasure ∘ k)(p) +``` + +The main purpose of `basekleisli` is to make it efficient to compute +``` +basemeasure(d::ProductMeasure) = productmeasure(basekleisli(d.f), d.xs) +``` +""" +function basekleisli end + +# TODO: Find a way to do better than this +basekleisli(f) = basemeasure ∘ f + +basekleisli(k::ParameterizedKleisli) = kleisli(basekleisli(k.f), k.param_maps) + +basekleisli(f::Returns) = Returns(basemeasure(f.value)) + +# export kleisliize + +# function kleisliize(μ::M) where {N, M <: ParameterizedMeasure{N}} +# C = constructorof(M) +# (Kleisli{C,}(NamedTuple{N}, ), values(getfield(μ, :par))) +# end + +function Base.show(io::IO, μ::AbstractKleisli) + io = IOContext(io, :compact => true) + Pretty.pprint(io, μ) +end + +function Pretty.quoteof(k::ParameterizedKleisli) + qf = Pretty.quoteof(k.f) + qg = Pretty.quoteof(k.param_maps) + :(ParameterizedKleisli($qf, $qg)) +end + From 931ecb0db62502fd66893d6349362adf08206826 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Thu, 9 Dec 2021 15:07:41 -0800 Subject: [PATCH 083/368] working on tests --- src/combinators/likelihood.jl | 4 ++-- src/combinators/power.jl | 6 ++++++ src/combinators/product.jl | 12 +++++++----- src/combinators/smart-constructors.jl | 11 +++++------ 4 files changed, 20 insertions(+), 13 deletions(-) diff --git a/src/combinators/likelihood.jl b/src/combinators/likelihood.jl index 9c9b65fe..3047a5bc 100644 --- a/src/combinators/likelihood.jl +++ b/src/combinators/likelihood.jl @@ -111,9 +111,9 @@ end Likelihood(k::K, x::X) where {K<:AbstractKleisli,X} = Likelihood{K,X}(k,x) -Likelihood(μ::AbstractMeasure, x) = Likelihood(askleisli(μ), x) +Likelihood(μ::AbstractMeasure, x) = Likelihood(kleisli(μ), x) -Likelihood(::Type{M}, x) where {M<:AbstractMeasure} = Likelihood(askleisli(M), x) +Likelihood(::Type{M}, x) where {M<:AbstractMeasure} = Likelihood(kleisli(M), x) function Pretty.quoteof(ℓ::Likelihood) k = Pretty.quoteof(ℓ.k) diff --git a/src/combinators/power.jl b/src/combinators/power.jl index 5770b3f8..7d96e6c2 100644 --- a/src/combinators/power.jl +++ b/src/combinators/power.jl @@ -24,6 +24,12 @@ function Pretty.tile(μ::PowerMeasure) return Pretty.pair_layout(arg1, arg2; sep = " ^ ") end +function Base.rand(rng::AbstractRNG, ::Type{T}, d::PowerMeasure) where {T} + map(CartesianIndices(d.axes)) do _ + rand(rng, T, d.parent) + end +end + @inline function powermeasure(x::T, sz::Vararg{<:Integer,N}) where {T, N} a = axes(Fill{T, N}(x, sz)) A = typeof(a) diff --git a/src/combinators/product.jl b/src/combinators/product.jl index bfb18ef4..ad51c3c5 100644 --- a/src/combinators/product.jl +++ b/src/combinators/product.jl @@ -22,6 +22,12 @@ Base.length(μ::AbstractProductMeasure) = length(marginals(μ)) Base.size(μ::AbstractProductMeasure) = size(marginals(μ)) basemeasure(d::AbstractProductMeasure) = map(basemeasure, marginals(d)) +function Base.rand(rng::AbstractRNG, ::Type{T}, d::AbstractProductMeasure) where {T} + map(marginals(d)) do dⱼ + rand(rng, T, dⱼ) + end +end + @inline function logdensity_def(d::AbstractProductMeasure, x) mapreduce(logdensity_def, +, marginals(d), x) end @@ -39,11 +45,7 @@ basemeasure_depth(μ::ProductMeasure) = basemeasure_depth(first(marginals(μ))) testvalue(d::AbstractProductMeasure) = map(testvalue, marginals(d)) -function Base.rand(rng::AbstractRNG, ::Type{T}, d::ProductMeasure) where {T} - map(marginals(d)) do dⱼ - rand(rng, T, dⱼ) - end -end + export ⊗ diff --git a/src/combinators/smart-constructors.jl b/src/combinators/smart-constructors.jl index 94cb9cfa..cc12ea0a 100644 --- a/src/combinators/smart-constructors.jl +++ b/src/combinators/smart-constructors.jl @@ -18,7 +18,7 @@ end # PowerMeaure function powermeasure(μ::WeightedMeasure, dims::NTuple{N,I}) where {N,I} - k = prod(dims) * μ.logweight + k = mapreduce(length, *, dims...) * μ.logweight return weightedmeasure(k, μ.base^dims) end @@ -87,14 +87,13 @@ end kleisli(μ, op1, op2, param_maps...) = ParameterizedKleisli(μ, op1, op2, param_maps...) # kleisli(Normal(μ=2)) -function kleisli(μ::P) where {P<:AbstractMeasure} - (f, param_maps) = kleislifactor(μ) - kleisli(f, param_maps) +function kleisli(μ::AbstractMeasure) + constructor(μ) end # kleisli(Normal{(:μ,), Tuple{Int64}}) -function kleisli(::Type{P}) where {P<:AbstractMeasure} - kleisli(P, identity) +function kleisli(::Type{M}) where {M<:AbstractMeasure} + constructor(M) end # kleisli(::Type{P}, op::O) where {O, N, P<:ParameterizedMeasure{N}} = kleisli{constructorof(P),O}(op) From 63898589e5ec8a1ec860f60a4b05dfd6fb19f286 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Thu, 9 Dec 2021 18:45:49 -0800 Subject: [PATCH 084/368] update powermeasure combinator --- src/combinators/power.jl | 12 ++++++------ src/combinators/smart-constructors.jl | 15 +++++++++++++++ src/density.jl | 6 ++++++ 3 files changed, 27 insertions(+), 6 deletions(-) diff --git a/src/combinators/power.jl b/src/combinators/power.jl index 7d96e6c2..a94c9310 100644 --- a/src/combinators/power.jl +++ b/src/combinators/power.jl @@ -30,11 +30,6 @@ function Base.rand(rng::AbstractRNG, ::Type{T}, d::PowerMeasure) where {T} end end -@inline function powermeasure(x::T, sz::Vararg{<:Integer,N}) where {T, N} - a = axes(Fill{T, N}(x, sz)) - A = typeof(a) - PowerMeasure{T,A}(x,a) -end @inline function powermeasure(x::T, sz::Tuple{Vararg{<:Any,N}}) where {T, N} a = axes(Fill{T, N}(x, sz)) @@ -44,7 +39,12 @@ end marginals(d::PowerMeasure) = Fill(d.parent, d.axes) -Base.:^(μ::AbstractMeasure, dims) = powermeasure(μ, dims) +function Base.:^(μ::AbstractMeasure, dims::Tuple{Vararg{<:AbstractArray,N}}) where {N} + powermeasure(μ, dims) +end + +Base.:^(μ::AbstractMeasure, dims::Tuple) = powermeasure(μ, Base.OneTo.(dims)) +Base.:^(μ::AbstractMeasure, n) = powermeasure(μ, (n,)) # Base.show(io::IO, d::PowerMeasure) = print(io, d.parent, " ^ ", size(d.xs)) # Base.show(io::IO, d::PowerMeasure{M,1}) where {M} = print(io, d.parent, " ^ ", length(d.xs)) diff --git a/src/combinators/smart-constructors.jl b/src/combinators/smart-constructors.jl index cc12ea0a..a4097115 100644 --- a/src/combinators/smart-constructors.jl +++ b/src/combinators/smart-constructors.jl @@ -17,6 +17,21 @@ end ############################################################################### # PowerMeaure +function powermeasure(μ::WeightedMeasure, dims::NTuple{N,I}) where {N,I<:AbstractArray} + k = mapreduce(length, *, dims...) * μ.logweight + return weightedmeasure(k, μ.base^dims) +end + +function powermeasure(μ::WeightedMeasure, dims::NTuple{N,I}) where {N,I<:Base.Generator} + k = mapreduce(length, *, dims...) * μ.logweight + return weightedmeasure(k, μ.base^dims) +end + +function powermeasure(μ::WeightedMeasure, dims::NTuple{N,I}) where {N,I} + k = mapreduce(length, *, dims...) * μ.logweight + return weightedmeasure(k, μ.base^dims) +end + function powermeasure(μ::WeightedMeasure, dims::NTuple{N,I}) where {N,I} k = mapreduce(length, *, dims...) * μ.logweight return weightedmeasure(k, μ.base^dims) diff --git a/src/density.jl b/src/density.jl index 25b92ede..2f7b852d 100644 --- a/src/density.jl +++ b/src/density.jl @@ -150,6 +150,9 @@ end β = basemeasure(μ, x) ℓ = logdensity_def(μ, x) + @show μ + @show ℓ + println() return _logdensityof(β, x, ℓ, n) end @@ -159,6 +162,9 @@ end $(Expr(:meta, :inline)) Base.Cartesian.@nexprs $nsteps i -> begin Δℓ = logdensity_def(μ, x) + @show μ + @show Δℓ + println() μ = basemeasure(μ, x) ℓ += Δℓ end From a1ee588af30efa9370cc62122f715deb65648bc4 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Thu, 9 Dec 2021 18:55:17 -0800 Subject: [PATCH 085/368] bugfix --- src/combinators/smart-constructors.jl | 17 +---------------- 1 file changed, 1 insertion(+), 16 deletions(-) diff --git a/src/combinators/smart-constructors.jl b/src/combinators/smart-constructors.jl index a4097115..ddd19a8e 100644 --- a/src/combinators/smart-constructors.jl +++ b/src/combinators/smart-constructors.jl @@ -17,23 +17,8 @@ end ############################################################################### # PowerMeaure -function powermeasure(μ::WeightedMeasure, dims::NTuple{N,I}) where {N,I<:AbstractArray} - k = mapreduce(length, *, dims...) * μ.logweight - return weightedmeasure(k, μ.base^dims) -end - -function powermeasure(μ::WeightedMeasure, dims::NTuple{N,I}) where {N,I<:Base.Generator} - k = mapreduce(length, *, dims...) * μ.logweight - return weightedmeasure(k, μ.base^dims) -end - -function powermeasure(μ::WeightedMeasure, dims::NTuple{N,I}) where {N,I} - k = mapreduce(length, *, dims...) * μ.logweight - return weightedmeasure(k, μ.base^dims) -end - function powermeasure(μ::WeightedMeasure, dims::NTuple{N,I}) where {N,I} - k = mapreduce(length, *, dims...) * μ.logweight + k = mapreduce(length, *, dims) * μ.logweight return weightedmeasure(k, μ.base^dims) end From 59a0e5fb187142160e20c4785755a971d8e89b24 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Thu, 9 Dec 2021 18:56:57 -0800 Subject: [PATCH 086/368] comment out debugging lines --- src/density.jl | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/src/density.jl b/src/density.jl index 2f7b852d..23a77e96 100644 --- a/src/density.jl +++ b/src/density.jl @@ -150,9 +150,9 @@ end β = basemeasure(μ, x) ℓ = logdensity_def(μ, x) - @show μ - @show ℓ - println() + # @show μ + # @show ℓ + # println() return _logdensityof(β, x, ℓ, n) end @@ -162,9 +162,9 @@ end $(Expr(:meta, :inline)) Base.Cartesian.@nexprs $nsteps i -> begin Δℓ = logdensity_def(μ, x) - @show μ - @show Δℓ - println() + # @show μ + # @show Δℓ + # println() μ = basemeasure(μ, x) ℓ += Δℓ end From 0f51fae1fb37da372507a837c9a1570d76997f65 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Fri, 10 Dec 2021 15:17:58 -0800 Subject: [PATCH 087/368] more refactoring --- src/combinators/factoredbase.jl | 2 +- src/combinators/half.jl | 4 ++-- src/combinators/power.jl | 6 +++--- src/combinators/restricted.jl | 2 +- src/combinators/spikemixture.jl | 2 +- src/combinators/weighted.jl | 2 +- src/generated.jl | 24 ++++++++++++++++++++++++ src/help.jl | 2 +- src/interface.jl | 2 +- src/primitive.jl | 4 ++-- src/primitives/counting.jl | 2 +- src/primitives/dirac.jl | 2 +- src/primitives/lebesgue.jl | 5 ++++- src/proxies.jl | 17 ++++++++++------- src/thunks.jl | 25 ------------------------- src/utils.jl | 12 +++++++++--- 16 files changed, 62 insertions(+), 51 deletions(-) create mode 100644 src/generated.jl delete mode 100644 src/thunks.jl diff --git a/src/combinators/factoredbase.jl b/src/combinators/factoredbase.jl index 0fa1ac42..6ed94d3e 100644 --- a/src/combinators/factoredbase.jl +++ b/src/combinators/factoredbase.jl @@ -20,4 +20,4 @@ end basemeasure(d::FactoredBase) = d.base -basemeasure_type(::Type{FactoredBase{R,C,V,B}}) where {R,C,V,B} = B +tbasemeasure_type(::Type{FactoredBase{R,C,V,B}}) where {R,C,V,B} = B diff --git a/src/combinators/half.jl b/src/combinators/half.jl index fe51693b..a1b9a0f2 100644 --- a/src/combinators/half.jl +++ b/src/combinators/half.jl @@ -21,8 +21,8 @@ isnonnegative(x) = x ≥ 0.0 FactoredBase(inbounds, constℓ, varℓ, base) end -function basemeasure_type(::Type{Half{M}}) where {M} - B = basemeasure_type(M) +function tbasemeasure_type(::Type{Half{M}}) where {M} + B = tbasemeasure_type(M) FactoredBase{typeof(isnonnegative),StaticFloat64{logtwo},Returns{Float64},B} end diff --git a/src/combinators/power.jl b/src/combinators/power.jl index a94c9310..4e279b05 100644 --- a/src/combinators/power.jl +++ b/src/combinators/power.jl @@ -63,11 +63,11 @@ function basemeasure_depth(::PowerMeasure{M}) where {M} return basemeasure_depth(M) end -function basemeasure_type(::Type{PowerMeasure{M,D}}) where {M,D} - return PowerMeasure{basemeasure_type(M),D} +function tbasemeasure_type(::Type{PowerMeasure{M,D}}) where {M,D} + return PowerMeasure{tbasemeasure_type(M),D} end -function basemeasure_depth(::Type{PowerMeasure{M,D}}) where {M<:PrimitiveMeasure,D} +function tbasemeasure_depth(::Type{PowerMeasure{M,D}}) where {M<:PrimitiveMeasure,D} return static(0) end diff --git a/src/combinators/restricted.jl b/src/combinators/restricted.jl index 4811a680..9b654734 100644 --- a/src/combinators/restricted.jl +++ b/src/combinators/restricted.jl @@ -15,6 +15,6 @@ end basemeasure(μ::RestrictedMeasure) = μ.base -basemeasure_type(::Type{RestrictedMeasure{F,M}}) where {F,M} = M +tbasemeasure_type(::Type{RestrictedMeasure{F,M}}) where {F,M} = M insupport(μ::RestrictedMeasure, x) = μ.f(x) && insupport(μ.base, x) diff --git a/src/combinators/spikemixture.jl b/src/combinators/spikemixture.jl index 1d8c8ad1..1e5a6197 100644 --- a/src/combinators/spikemixture.jl +++ b/src/combinators/spikemixture.jl @@ -22,7 +22,7 @@ end SpikeMixture(basemeasure(μ.m), 1 / (1 + ki), μ.s * (1 + ki)) end -basemeasure_depth(::Type{SpikeMixture{T,S}}) where {T,S} = static(1) + basemeasure_depth(T) +tbasemeasure_depth(::Type{SpikeMixture{T,S}}) where {T,S} = static(1) + tbasemeasure_depth(T) # basemeasure_type(::Type{SpikeMixture{T,S}}) where {T,S} = SpikeMixture{} diff --git a/src/combinators/weighted.jl b/src/combinators/weighted.jl index 1ac61a46..3277bf37 100644 --- a/src/combinators/weighted.jl +++ b/src/combinators/weighted.jl @@ -23,7 +23,7 @@ struct WeightedMeasure{R,M} <: AbstractWeightedMeasure base::M end -basemeasure_type(::Type{WeightedMeasure{R,M}}) where {R,M} = M +tbasemeasure_type(::Type{WeightedMeasure{R,M}}) where {R,M} = M function Base.show(io::IO, μ::WeightedMeasure) io = IOContext(io, :compact => true) diff --git a/src/generated.jl b/src/generated.jl new file mode 100644 index 00000000..7f1e2c66 --- /dev/null +++ b/src/generated.jl @@ -0,0 +1,24 @@ +@generated function _logdensityof(μ, x, ℓ, ::StaticInt{n}) where {n} + nsteps = max(n, 0) + quote + $(Expr(:meta, :inline)) + Base.Cartesian.@nexprs $nsteps i -> begin + Δℓ = logdensity_def(μ, x) + # @show μ + # @show Δℓ + # println() + μ = basemeasure(μ, x) + ℓ += Δℓ + end + return (ℓ,μ) + end +end + +@generated function _rootmeasure(μ, ::StaticInt{n}) where {n} + q = quote end + foreach(1:n) do _ + push!(q.args, :(μ = basemeasure(μ))) + end + return q +end + diff --git a/src/help.jl b/src/help.jl index db86ca91..b6c4e6f5 100644 --- a/src/help.jl +++ b/src/help.jl @@ -4,7 +4,7 @@ function help_basemeasure_type(μ::M) where M b = basemeasure(μ) B = typeof(b) println(""" - function basemeasure_type(::Type{$M}) + function tbasemeasure_type(::Type{$M}) $B end diff --git a/src/interface.jl b/src/interface.jl index 52b55a49..05123f28 100644 --- a/src/interface.jl +++ b/src/interface.jl @@ -25,5 +25,5 @@ function test_interface(μ) ########################################################################### # basemeasure_type - @test (basemeasure_type ∘ typeof)(μ) == (typeof ∘ basemeasure)(μ) + @test (tbasemeasure_type ∘ typeof)(μ) == (typeof ∘ basemeasure)(μ) end \ No newline at end of file diff --git a/src/primitive.jl b/src/primitive.jl index e662f27f..fd928cf0 100644 --- a/src/primitive.jl +++ b/src/primitive.jl @@ -17,10 +17,10 @@ abstract type PrimitiveMeasure <: AbstractMeasure end basemeasure(μ::PrimitiveMeasure) = μ -basemeasure_type(::Type{M}) where {M<:PrimitiveMeasure} = M +tbasemeasure_type(::Type{M}) where {M<:PrimitiveMeasure} = M @inline basemeasure_depth(::PrimitiveMeasure) = static(0) -@inline basemeasure_depth(::Type{M}) where {M<:PrimitiveMeasure} = static(0) +@inline tbasemeasure_depth(::Type{M}) where {M<:PrimitiveMeasure} = static(0) logdensity_def(μ::PrimitiveMeasure, x) = static(0.0) diff --git a/src/primitives/counting.jl b/src/primitives/counting.jl index 1fe93229..9f12de20 100644 --- a/src/primitives/counting.jl +++ b/src/primitives/counting.jl @@ -10,7 +10,7 @@ end Counting() = Counting(ℤ) -basemeasure_type(::Type{C}) where {C<:Counting} = CountingMeasure +tbasemeasure_type(::Type{C}) where {C<:Counting} = CountingMeasure testvalue(d::Counting) = testvalue(d.support) diff --git a/src/primitives/dirac.jl b/src/primitives/dirac.jl index b63d6e77..c6764275 100644 --- a/src/primitives/dirac.jl +++ b/src/primitives/dirac.jl @@ -19,7 +19,7 @@ end basemeasure(d::Dirac) = CountingMeasure() -basemeasure_type(::Type{Dirac}) = CountingMeasure +tbasemeasure_type(::Type{Dirac}) = CountingMeasure density_def(μ::Dirac, x) = x == μ.x diff --git a/src/primitives/lebesgue.jl b/src/primitives/lebesgue.jl index eea02e54..9db9e51f 100644 --- a/src/primitives/lebesgue.jl +++ b/src/primitives/lebesgue.jl @@ -18,11 +18,14 @@ gentype(::Lebesgue) = Float64 Lebesgue() = Lebesgue(ℝ) -basemeasure_type(::Type{L}) where {L<:Lebesgue} = LebesgueMeasure +# basemeasure(::Lebesgue) = LebesgueMeasure() + +tbasemeasure_type(::Type{<:Lebesgue}) = LebesgueMeasure testvalue(d::Lebesgue) = testvalue(d.support) proxy(d::Lebesgue) = restrict(in(d.support), LebesgueMeasure()) +@useproxy Lebesgue Base.:∘(::typeof(basemeasure), ::Type{Lebesgue}) = LebesgueMeasure() diff --git a/src/proxies.jl b/src/proxies.jl index f1073a8a..0cef6d38 100644 --- a/src/proxies.jl +++ b/src/proxies.jl @@ -11,10 +11,13 @@ transformed measure, but this would make dispatch awkward. """ function proxy end -proxy(μ) = μ - -proxy(f, μ) = proxy(μ) - -logdensity_def(μ, x) = logdensity_def(proxy(μ), x) - -basemeasure(μ) = basemeasure(proxy(μ)) +macro useproxy(M) + M = esc(M) + quote + @inline $__module__.logdensity_def(μ::$M, x) = logdensity_def(proxy(μ), x) + @inline $__module__.basemeasure(μ::$M) = basemeasure(proxy(μ)) + @inline $__module__.basemeasure(μ::$M, x) = basemeasure(proxy(μ), x) + @inline $__module__.basemeasure_type(μ::$M) = basemeasure_type(proxy(μ)) + @inline $__module__.basemeasure_depth(μ::$M) = basemeasure_depth(proxy(μ)) + end +end diff --git a/src/thunks.jl b/src/thunks.jl deleted file mode 100644 index 1d88420c..00000000 --- a/src/thunks.jl +++ /dev/null @@ -1,25 +0,0 @@ -# abstract type LogdensityComputation end - -# struct LogpdfComputation end - -# struct BasemeasureComputation{B} <: LogdensityComputation -# base::B -# end - -# struct LogdensityThunk{C,M,X,L} -# computation::C -# measure::M -# x::X -# ℓ::L -# end - -# function reduce_step(thunk :: LogdensityThunk, callback=Returns(nothing)) - - - -# reduce_step(LogdensityThunk{M,B,X,L}, callback=Returns(nothing)) -> Union{LogdensityThunk, L} - -# function logdensity_def(μ, b, x; cb=Returns(nothing)) -# f(thunk) = reduce_step(thunk, cb) -# fix(f, LogdensityThunk(μ, b, x, zero(Float64))) -# end diff --git a/src/utils.jl b/src/utils.jl index fc16fee0..b47fa06b 100644 --- a/src/utils.jl +++ b/src/utils.jl @@ -64,9 +64,15 @@ functioninstance(::Type{F}) where {F<:Function} = F.instance export basemeasure_depth +@inline function basemeasure_type(μ::M) where {M<:AbstractMeasure} + return tbasemeasure_type(M) +end + @inline function basemeasure_depth(μ::M) where {M<:AbstractMeasure} - basemeasure_depth(M) + return tbasemeasure_depth(M) +end + +@inline function tbasemeasure_depth(::Type{M}) where {M} + static(1) + tbasemeasure_depth(tbasemeasure_type(M)) end -@inline basemeasure_depth(::Type{M}) where {M} = - static(1) + basemeasure_depth(basemeasure_type(M)) From 2735705a32a473774b0bffac12bdf13816c3e901 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Sat, 11 Dec 2021 08:33:34 -0800 Subject: [PATCH 088/368] =?UTF-8?q?test=20@inferred=20basemeasure=5Fdepth(?= =?UTF-8?q?=CE=BC)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- src/interface.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/interface.jl b/src/interface.jl index 05123f28..6ba12876 100644 --- a/src/interface.jl +++ b/src/interface.jl @@ -14,7 +14,7 @@ function test_interface(μ) ########################################################################### # basemeasure_depth - static_depth = basemeasure_depth(μ) + static_depth = @inferred basemeasure_depth(μ) dynamic_depth = dynamic_basemeasure_depth(μ) if static_depth > dynamic_depth From 94bda1bd1e816c40892a59eebf60879ff96274fb Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Sat, 11 Dec 2021 08:50:14 -0800 Subject: [PATCH 089/368] drop `constructor` (just use ConstructionBase.constructorof`) --- src/combinators/smart-constructors.jl | 6 +++--- src/parameterized.jl | 8 ++++---- src/utils.jl | 4 ---- 3 files changed, 7 insertions(+), 11 deletions(-) diff --git a/src/combinators/smart-constructors.jl b/src/combinators/smart-constructors.jl index ddd19a8e..e797005b 100644 --- a/src/combinators/smart-constructors.jl +++ b/src/combinators/smart-constructors.jl @@ -87,13 +87,13 @@ end kleisli(μ, op1, op2, param_maps...) = ParameterizedKleisli(μ, op1, op2, param_maps...) # kleisli(Normal(μ=2)) -function kleisli(μ::AbstractMeasure) - constructor(μ) +function kleisli(μ::M) where {M<:AbstractMeasure} + constructorof(M) end # kleisli(Normal{(:μ,), Tuple{Int64}}) function kleisli(::Type{M}) where {M<:AbstractMeasure} - constructor(M) + constructorof(M) end # kleisli(::Type{P}, op::O) where {O, N, P<:ParameterizedMeasure{N}} = kleisli{constructorof(P),O}(op) diff --git a/src/parameterized.jl b/src/parameterized.jl index 4cbd7405..d7ff7362 100644 --- a/src/parameterized.jl +++ b/src/parameterized.jl @@ -33,7 +33,7 @@ function kleisli(::Type{P}) where {N,P<:ParameterizedMeasure{N}} end function (::Type{P})(args...) where {N,P<:ParameterizedMeasure{N}} - C = constructor(P) + C = constructorof(P) return C(NamedTuple{N}(args...)) end @@ -43,7 +43,7 @@ function ConstructionBase.setproperties( d::P, nt::NamedTuple, ) where {P<:ParameterizedMeasure} - return constructor(P)(merge(params(d), nt)) + return constructorof(P)(merge(params(d), nt)) end ############################################################################### @@ -113,9 +113,9 @@ end # kleislifactor function kleislifactor(::Type{P}) where {N,P<:ParameterizedMeasure{N}} - (constructor(P), N) + (constructorof(P), N) end function kleislifactor(::P) where {N,P<:ParameterizedMeasure{N}} - (constructor(P), N) + (constructorof(P), N) end diff --git a/src/utils.jl b/src/utils.jl index b47fa06b..32b3bee4 100644 --- a/src/utils.jl +++ b/src/utils.jl @@ -17,10 +17,6 @@ showparams(io::IO, nt::NamedTuple) = print(io, nt) # return C.name.wrapper # end -constructor(::T) where {T} = constructor(T) - -constructor(::Type{T}) where {T} = constructorof(T) - export testvalue testvalue(μ::AbstractMeasure) = testvalue(basemeasure(μ)) testvalue(::Type{T}) where {T} = zero(T) From 340cc85128bdbaca4b6d9822c50db2c58138a8d1 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Sat, 11 Dec 2021 09:01:57 -0800 Subject: [PATCH 090/368] debugging --- src/combinators/half.jl | 4 ++-- src/density.jl | 6 ++++-- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/src/combinators/half.jl b/src/combinators/half.jl index a1b9a0f2..9f9ebbd3 100644 --- a/src/combinators/half.jl +++ b/src/combinators/half.jl @@ -16,14 +16,14 @@ isnonnegative(x) = x ≥ 0.0 @inline function basemeasure(μ::Half) inbounds = isnonnegative constℓ = static(logtwo) - varℓ = Returns(0.0) + varℓ = Returns(static(0.0)) base = basemeasure(unhalf(μ)) FactoredBase(inbounds, constℓ, varℓ, base) end function tbasemeasure_type(::Type{Half{M}}) where {M} B = tbasemeasure_type(M) - FactoredBase{typeof(isnonnegative),StaticFloat64{logtwo},Returns{Float64},B} + FactoredBase{typeof(isnonnegative),StaticFloat64{logtwo},Returns{StaticFloat64{0.0}},B} end function Base.rand(rng::AbstractRNG, T::Type, μ::Half) diff --git a/src/density.jl b/src/density.jl index 23a77e96..1b8e9f69 100644 --- a/src/density.jl +++ b/src/density.jl @@ -69,9 +69,11 @@ function _densitymeasure(f, base, _) """ end + + basemeasure(μ::DensityMeasure) = μ.base -basemeasure_type(::Type{DensityMeasure{F,B}}) where {F,B} = B +tbasemeasure_type(::Type{DensityMeasure{F,B}}) where {F,B} = B logdensity_def(μ::DensityMeasure, x) = logdensityof(μ.f, x) @@ -146,7 +148,7 @@ end # • ℓ is the log-density # • r is the rootmeasure of μ @inline function _logdensityof(μ, x) - n = basemeasure_depth(proxy(μ)) - static(1) + n = basemeasure_depth(μ) - static(1) β = basemeasure(μ, x) ℓ = logdensity_def(μ, x) From 1f5ffa913567d71046242b9132fc384c5ab078d7 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Sat, 11 Dec 2021 09:11:27 -0800 Subject: [PATCH 091/368] update help --- src/help.jl | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/help.jl b/src/help.jl index b6c4e6f5..16045852 100644 --- a/src/help.jl +++ b/src/help.jl @@ -1,13 +1,13 @@ -export help_basemeasure_type +export help_tbasemeasure_type -function help_basemeasure_type(μ::M) where M +function help_tbasemeasure_type(μ::M) where M b = basemeasure(μ) B = typeof(b) println(""" function tbasemeasure_type(::Type{$M}) $B end - + """ ) return B From ebcbba099b110fd4b8118629aa4aa3aad8c12ab3 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Sat, 11 Dec 2021 14:01:39 -0800 Subject: [PATCH 092/368] update interface --- src/interface.jl | 19 +++++++++++++++++-- 1 file changed, 17 insertions(+), 2 deletions(-) diff --git a/src/interface.jl b/src/interface.jl index 6ba12876..e0333662 100644 --- a/src/interface.jl +++ b/src/interface.jl @@ -10,11 +10,14 @@ function dynamic_basemeasure_depth(μ) return depth end -function test_interface(μ) +function test_interface(μ::M) where {M} ########################################################################### # basemeasure_depth + @testset "$μ" begin static_depth = @inferred basemeasure_depth(μ) + + @test static_depth == tbasemeasure_depth(M) dynamic_depth = dynamic_basemeasure_depth(μ) if static_depth > dynamic_depth @@ -22,8 +25,20 @@ function test_interface(μ) end @test static_depth ≥ dynamic_depth + ########################################################################### + # testvalue, logdensityof + + x = @inferred testvalue(μ) + β = @inferred basemeasure(μ) + + ℓμ = @inferred logdensityof(μ, x) + ℓβ = @inferred logdensityof(β, x) + @test ℓμ ≈ logdensity_def(μ, x) + ℓβ + ########################################################################### # basemeasure_type - @test (tbasemeasure_type ∘ typeof)(μ) == (typeof ∘ basemeasure)(μ) + @test @inferred tbasemeasure_type(M) == @inferred basemeasure_type(μ) + @test basemeasure_type(μ) == (typeof ∘ basemeasure)(μ) + end end \ No newline at end of file From 9c2fe0c26e66eaa16e1bc1b403accae8d56c1fb7 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Sat, 11 Dec 2021 14:08:38 -0800 Subject: [PATCH 093/368] make tests harder --- test/runtests.jl | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/test/runtests.jl b/test/runtests.jl index a54d33b6..0e4f5ebe 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -4,7 +4,7 @@ using Random using LinearAlgebra using MeasureBase -using MeasureBase: logdensityof, logdensity_def, density_def, densityof +using MeasureBase: test_interface using Aqua Aqua.test_all(MeasureBase; ambiguities = false, unbound_args = false) @@ -37,9 +37,6 @@ d = ∫exp(x -> -x^2, Lebesgue(ℝ)) # return (x,y) # end -function test_testvalue(μ) - logdensity_def(μ, testvalue(μ)) isa AbstractFloat -end test_measures = [ # Chain(x -> Normal(μ=x), Normal(μ=0.0)) @@ -70,7 +67,7 @@ testbroken_measures = [ @testset "testvalue" begin for μ in test_measures @info "testing $μ" - @test test_testvalue(μ) + @test test_interface(μ) end for μ in testbroken_measures From a3fda8194cfbf5b4c4bb3c2f9eb230a133457ae9 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Sun, 12 Dec 2021 07:46:06 -0800 Subject: [PATCH 094/368] fixes --- src/combinators/power.jl | 2 +- src/density.jl | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/combinators/power.jl b/src/combinators/power.jl index 4e279b05..2d7627f4 100644 --- a/src/combinators/power.jl +++ b/src/combinators/power.jl @@ -60,7 +60,7 @@ params(d::PowerMeasure) = params(first(marginals(d))) end function basemeasure_depth(::PowerMeasure{M}) where {M} - return basemeasure_depth(M) + return tbasemeasure_depth(M) end function tbasemeasure_type(::Type{PowerMeasure{M,D}}) where {M,D} diff --git a/src/density.jl b/src/density.jl index 23a77e96..fb32bdc4 100644 --- a/src/density.jl +++ b/src/density.jl @@ -71,7 +71,7 @@ end basemeasure(μ::DensityMeasure) = μ.base -basemeasure_type(::Type{DensityMeasure{F,B}}) where {F,B} = B +tbasemeasure_type(::Type{DensityMeasure{F,B}}) where {F,B} = B logdensity_def(μ::DensityMeasure, x) = logdensityof(μ.f, x) @@ -146,7 +146,7 @@ end # • ℓ is the log-density # • r is the rootmeasure of μ @inline function _logdensityof(μ, x) - n = basemeasure_depth(proxy(μ)) - static(1) + n = basemeasure_depth(μ) - static(1) β = basemeasure(μ, x) ℓ = logdensity_def(μ, x) From 8a1411c163a5c09d85c200b073ebe98ece98784f Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Sun, 12 Dec 2021 07:48:08 -0800 Subject: [PATCH 095/368] Dirac bugfix --- src/primitives/dirac.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/primitives/dirac.jl b/src/primitives/dirac.jl index c6764275..a2330ea0 100644 --- a/src/primitives/dirac.jl +++ b/src/primitives/dirac.jl @@ -19,7 +19,7 @@ end basemeasure(d::Dirac) = CountingMeasure() -tbasemeasure_type(::Type{Dirac}) = CountingMeasure +tbasemeasure_type(::Type{Dirac{X}}) where {X} = CountingMeasure density_def(μ::Dirac, x) = x == μ.x From 49165bc664ff682b310f0085582726cc23599617 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Sun, 12 Dec 2021 09:12:37 -0800 Subject: [PATCH 096/368] formatting --- src/interface.jl | 51 ++++++++++++++++++++++++------------------------ 1 file changed, 25 insertions(+), 26 deletions(-) diff --git a/src/interface.jl b/src/interface.jl index e0333662..74bc92ff 100644 --- a/src/interface.jl +++ b/src/interface.jl @@ -14,31 +14,30 @@ function test_interface(μ::M) where {M} ########################################################################### # basemeasure_depth @testset "$μ" begin - - static_depth = @inferred basemeasure_depth(μ) - - @test static_depth == tbasemeasure_depth(M) - dynamic_depth = dynamic_basemeasure_depth(μ) - - if static_depth > dynamic_depth - @warn "basemeasure_depth($μ) greater than requirement, could add some overhead" - end - @test static_depth ≥ dynamic_depth - - ########################################################################### - # testvalue, logdensityof - - x = @inferred testvalue(μ) - β = @inferred basemeasure(μ) - - ℓμ = @inferred logdensityof(μ, x) - ℓβ = @inferred logdensityof(β, x) - @test ℓμ ≈ logdensity_def(μ, x) + ℓβ - - ########################################################################### - # basemeasure_type - - @test @inferred tbasemeasure_type(M) == @inferred basemeasure_type(μ) - @test basemeasure_type(μ) == (typeof ∘ basemeasure)(μ) + static_depth = @inferred basemeasure_depth(μ) + + @test static_depth == tbasemeasure_depth(M) + dynamic_depth = dynamic_basemeasure_depth(μ) + + if static_depth > dynamic_depth + @warn "basemeasure_depth($μ) greater than requirement, could add some overhead" + end + @test static_depth ≥ dynamic_depth + + ########################################################################### + # testvalue, logdensityof + + x = @inferred testvalue(μ) + β = @inferred basemeasure(μ) + + ℓμ = @inferred logdensityof(μ, x) + ℓβ = @inferred logdensityof(β, x) + @test ℓμ ≈ logdensity_def(μ, x) + ℓβ + + ########################################################################### + # basemeasure_type + + @test @inferred tbasemeasure_type(M) == @inferred basemeasure_type(μ) + @test basemeasure_type(μ) == (typeof ∘ basemeasure)(μ) end end \ No newline at end of file From d0f4766f1d367186591c80c04b0e48202866c3fd Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Sun, 12 Dec 2021 09:12:55 -0800 Subject: [PATCH 097/368] improve type inference --- src/combinators/product.jl | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/src/combinators/product.jl b/src/combinators/product.jl index ad51c3c5..af5e440b 100644 --- a/src/combinators/product.jl +++ b/src/combinators/product.jl @@ -31,17 +31,24 @@ end @inline function logdensity_def(d::AbstractProductMeasure, x) mapreduce(logdensity_def, +, marginals(d), x) end + struct ProductMeasure{M} <: AbstractProductMeasure marginals::M end - marginals(μ::ProductMeasure) = μ.marginals +function tbasemeasure_type(::Type{ProductMeasure{T}}) where {T<:Tuple} + ProductMeasure{Tuple{map(tbasemeasure_type, T.types)...}} +end +# basemeasure_depth(μ::ProductMeasure) = basemeasure_depth(first(marginals(μ))) + +@inline function tbasemeasure_depth(::Type{ProductMeasure{T}}) where {T<:Tuple} + mapreduce(tbasemeasure_depth, max, Tuple(T.types)) +end -basemeasure_depth(μ::ProductMeasure) = basemeasure_depth(first(marginals(μ))) testvalue(d::AbstractProductMeasure) = map(testvalue, marginals(d)) From 49790b233840bdeb8b6a850f630d07988636e850 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Sun, 12 Dec 2021 10:04:10 -0800 Subject: [PATCH 098/368] working on type inference --- src/combinators/product.jl | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/src/combinators/product.jl b/src/combinators/product.jl index af5e440b..1e37914f 100644 --- a/src/combinators/product.jl +++ b/src/combinators/product.jl @@ -20,7 +20,7 @@ function Base.:(==)(a::AbstractProductMeasure, b::AbstractProductMeasure) end Base.length(μ::AbstractProductMeasure) = length(marginals(μ)) Base.size(μ::AbstractProductMeasure) = size(marginals(μ)) -basemeasure(d::AbstractProductMeasure) = map(basemeasure, marginals(d)) +basemeasure(d::AbstractProductMeasure) = productmeasure(map(basemeasure, marginals(d))) function Base.rand(rng::AbstractRNG, ::Type{T}, d::AbstractProductMeasure) where {T} map(marginals(d)) do dⱼ @@ -36,13 +36,22 @@ struct ProductMeasure{M} <: AbstractProductMeasure marginals::M end +@inline function logdensityof(μ::ProductMeasure, x) + mapreduce(logdensityof, +, marginals(μ), x) +end marginals(μ::ProductMeasure) = μ.marginals -function tbasemeasure_type(::Type{ProductMeasure{T}}) where {T<:Tuple} +@generated function tbasemeasure_type(::Type{ProductMeasure{T}}) where {T<:Tuple} ProductMeasure{Tuple{map(tbasemeasure_type, T.types)...}} end +function tbasemeasure_type(::Type{ProductMeasure{A}}) where {M,A<:AbstractArray{M}} + C = constructorof(A) + p = Tuple(A.parameters) + ProductMeasure{C{(tbasemeasure_type(first(p)), Base.tail(p)...)...}} +end + # basemeasure_depth(μ::ProductMeasure) = basemeasure_depth(first(marginals(μ))) @inline function tbasemeasure_depth(::Type{ProductMeasure{T}}) where {T<:Tuple} From 5fc1eeacc089112bd72f6edb47fab6af02e66efd Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Sun, 12 Dec 2021 10:04:41 -0800 Subject: [PATCH 099/368] update interface --- src/interface.jl | 21 ++++++++++++--------- 1 file changed, 12 insertions(+), 9 deletions(-) diff --git a/src/interface.jl b/src/interface.jl index 74bc92ff..436232b1 100644 --- a/src/interface.jl +++ b/src/interface.jl @@ -15,28 +15,31 @@ function test_interface(μ::M) where {M} # basemeasure_depth @testset "$μ" begin static_depth = @inferred basemeasure_depth(μ) - + @test static_depth == tbasemeasure_depth(M) dynamic_depth = dynamic_basemeasure_depth(μ) - + if static_depth > dynamic_depth @warn "basemeasure_depth($μ) greater than requirement, could add some overhead" end @test static_depth ≥ dynamic_depth - + ########################################################################### # testvalue, logdensityof - + x = @inferred testvalue(μ) β = @inferred basemeasure(μ) - - ℓμ = @inferred logdensityof(μ, x) - ℓβ = @inferred logdensityof(β, x) + + @inferred logdensityof(μ, x) + @inferred logdensityof(β, x) + ℓμ = logdensityof(μ, x) + ℓβ = logdensityof(β, x) + @test ℓμ ≈ logdensity_def(μ, x) + ℓβ - + ########################################################################### # basemeasure_type - + @test @inferred tbasemeasure_type(M) == @inferred basemeasure_type(μ) @test basemeasure_type(μ) == (typeof ∘ basemeasure)(μ) end From 971e5ab6d2a3e3568ef1fc90a75e8c7b2841cb21 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 13 Dec 2021 07:30:04 -0800 Subject: [PATCH 100/368] udpates --- src/MeasureBase.jl | 20 +++++++++++++++++++- src/combinators/product.jl | 29 +++++++++++++++++------------ src/combinators/superpose.jl | 8 ++++++-- src/density.jl | 19 ++++++++----------- src/interface.jl | 18 ++++++++++-------- src/utils.jl | 12 +++++++----- 6 files changed, 67 insertions(+), 39 deletions(-) diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index dfd01d78..decd0e60 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -30,6 +30,8 @@ export AbstractMeasure abstract type AbstractMeasure end +using Static: @constprop + function Pretty.tile(d::M) where {M<:AbstractMeasure} the_names = fieldnames(typeof(d)) result = Pretty.literal(repr(M)) @@ -94,7 +96,23 @@ include("combinators/conditional.jl") include("rand.jl") include("density.jl") +module Interface + +using MeasureBase +using MeasureBase:basemeasure_depth, tbasemeasure_depth, basemeasure_type, tbasemeasure_type +using Test + +export test_interface +export tbasemeasure_depth +export tbasemeasure_type +export help_tbasemeasure_type +export basemeasure_depth +export basemeasure_type + include("help.jl") include("interface.jl") +end # module Interface -end +using .Interface + +end # module MeasureBase \ No newline at end of file diff --git a/src/combinators/product.jl b/src/combinators/product.jl index 1e37914f..c3cbf713 100644 --- a/src/combinators/product.jl +++ b/src/combinators/product.jl @@ -35,9 +35,17 @@ end struct ProductMeasure{M} <: AbstractProductMeasure marginals::M end + + +# For tuples, `mapreduce` has trouble with type inference +@inline function logdensity_def(d::ProductMeasure{T}, x) where {T<:Tuple} + ℓs = map(logdensity_def, marginals(d),x) + sum(ℓs) +end -@inline function logdensityof(μ::ProductMeasure, x) - mapreduce(logdensityof, +, marginals(μ), x) +function basemeasure(μ::ProductMeasure{A}) where {T,A<:ReadonlyMappedArray{T}} + mar = marginals(μ) + productmeasure(mappedarray(basekleisli(mar.f), mar.data)) end marginals(μ::ProductMeasure) = μ.marginals @@ -46,19 +54,16 @@ marginals(μ::ProductMeasure) = μ.marginals ProductMeasure{Tuple{map(tbasemeasure_type, T.types)...}} end -function tbasemeasure_type(::Type{ProductMeasure{A}}) where {M,A<:AbstractArray{M}} - C = constructorof(A) +@inline @constprop :aggressive function tbasemeasure_type(::Type{ProductMeasure{A}}) where {M,A<:AbstractArray{M}} p = Tuple(A.parameters) - ProductMeasure{C{(tbasemeasure_type(first(p)), Base.tail(p)...)...}} -end - -# basemeasure_depth(μ::ProductMeasure) = basemeasure_depth(first(marginals(μ))) - -@inline function tbasemeasure_depth(::Type{ProductMeasure{T}}) where {T<:Tuple} - mapreduce(tbasemeasure_depth, max, Tuple(T.types)) + C = constructorof(A) + if isconcretetype(M) + return ProductMeasure{C{(tbasemeasure_type(M), Base.tail(p)...)...}} + else + return ProductMeasure{C{(Any, Base.tail(p)...)...}} + end end - testvalue(d::AbstractProductMeasure) = map(testvalue, marginals(d)) diff --git a/src/combinators/superpose.jl b/src/combinators/superpose.jl index 994703f9..c503ace7 100644 --- a/src/combinators/superpose.jl +++ b/src/combinators/superpose.jl @@ -20,8 +20,8 @@ Superposition measures satisfy \end{aligned} ``` """ -struct SuperpositionMeasure{NT} <: AbstractMeasure - components::NT +struct SuperpositionMeasure{C} <: AbstractMeasure + components::C end function Pretty.tile(d::SuperpositionMeasure) @@ -63,6 +63,10 @@ logdensity_def(μ::SuperpositionMeasure, x) = basemeasure(μ::SuperpositionMeasure) = superpose(map(basemeasure, μ.components)) +tbasemeasure_type(::Type{S}) where {C,S<:SuperpositionMeasure{C}} + SuperpositionMeasure{tmap(tbasemeasure_type, C)} +end + # TODO: Fix `rand` method (this one is wrong) # function Base.rand(μ::SuperpositionMeasure{X,N}) where {X,N} # return rand(rand(μ.components)) diff --git a/src/density.jl b/src/density.jl index 1b8e9f69..792cd859 100644 --- a/src/density.jl +++ b/src/density.jl @@ -142,35 +142,32 @@ end return ℓ end -@inline logdensityof(μ, x) = first(_logdensityof(μ, x)) +@inline logdensityof(μ, x) = _logdensityof(μ, basemeasure(μ), x, logdensity_def(μ, x)) # Because it's sometimes useful, this returns a pair (ℓ,r) where # • ℓ is the log-density # • r is the rootmeasure of μ -@inline function _logdensityof(μ, x) +@inline function _logdensityof(μ, β, x, ℓ) n = basemeasure_depth(μ) - static(1) - - β = basemeasure(μ, x) - ℓ = logdensity_def(μ, x) + iszero(n) && return ℓ # @show μ # @show ℓ # println() - return _logdensityof(β, x, ℓ, n) + return _logdensityof(β, basemeasure(β), x, ℓ, n) end -@generated function _logdensityof(μ, x, ℓ, ::StaticInt{n}) where {n} +@generated function _logdensityof(μ, β, x, ℓ::T, ::StaticInt{n}) where {n,T} nsteps = max(n, 0) quote $(Expr(:meta, :inline)) Base.Cartesian.@nexprs $nsteps i -> begin - Δℓ = logdensity_def(μ, x) - # @show μ + Δℓ = oftype(ℓ, logdensity_def(μ, x)) # @show Δℓ # println() - μ = basemeasure(μ, x) + μ,β = β, basemeasure(μ, x) ℓ += Δℓ end - return (ℓ,μ) + return ℓ end end diff --git a/src/interface.jl b/src/interface.jl index 436232b1..853dae0b 100644 --- a/src/interface.jl +++ b/src/interface.jl @@ -11,9 +11,16 @@ function dynamic_basemeasure_depth(μ) end function test_interface(μ::M) where {M} - ########################################################################### - # basemeasure_depth @testset "$μ" begin + ########################################################################### + # basemeasure_type + + @test @inferred tbasemeasure_type(M) == @inferred basemeasure_type(μ) + + @info typejoin(basemeasure_type(μ), (typeof ∘ basemeasure)(μ)) + + ########################################################################### + # basemeasure_depth static_depth = @inferred basemeasure_depth(μ) @test static_depth == tbasemeasure_depth(M) @@ -37,10 +44,5 @@ function test_interface(μ::M) where {M} @test ℓμ ≈ logdensity_def(μ, x) + ℓβ - ########################################################################### - # basemeasure_type - - @test @inferred tbasemeasure_type(M) == @inferred basemeasure_type(μ) - @test basemeasure_type(μ) == (typeof ∘ basemeasure)(μ) end -end \ No newline at end of file +end diff --git a/src/utils.jl b/src/utils.jl index 32b3bee4..08564311 100644 --- a/src/utils.jl +++ b/src/utils.jl @@ -60,15 +60,17 @@ functioninstance(::Type{F}) where {F<:Function} = F.instance export basemeasure_depth -@inline function basemeasure_type(μ::M) where {M<:AbstractMeasure} +@inline @constprop :aggressive function basemeasure_type(μ::M) where {M<:AbstractMeasure} return tbasemeasure_type(M) end -@inline function basemeasure_depth(μ::M) where {M<:AbstractMeasure} +@inline @constprop :aggressive function basemeasure_depth(μ::M) where {M<:AbstractMeasure} return tbasemeasure_depth(M) end -@inline function tbasemeasure_depth(::Type{M}) where {M} - static(1) + tbasemeasure_depth(tbasemeasure_type(M)) -end +@inline @constprop :aggressive tbasemeasure_depth(::Type{M}) where M = tbasemeasure_depth(M, tbasemeasure_type(M), static(0)) +@inline @constprop :aggressive function tbasemeasure_depth(::Type{M}, ::Type{B}, S::StaticInt) where {M,B} + M === B && return S + return tbasemeasure_depth(B, tbasemeasure_type(B), S + static(1)) +end \ No newline at end of file From de10c90ce23ed562be11d6f8d82a7968e04dc51e Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 13 Dec 2021 10:23:30 -0800 Subject: [PATCH 101/368] get test passing --- src/MeasureBase.jl | 1 + src/combinators/product.jl | 17 ++--------------- src/combinators/spikemixture.jl | 14 +++++++++++--- src/combinators/superpose.jl | 5 +++-- src/density.jl | 4 ++-- src/help.jl | 3 +-- src/tmap.jl | 18 ++++++++++++++++++ src/utils.jl | 6 +++--- test/runtests.jl | 18 ++++++------------ 9 files changed, 47 insertions(+), 39 deletions(-) create mode 100644 src/tmap.jl diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index decd0e60..71fc3f2a 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -96,6 +96,7 @@ include("combinators/conditional.jl") include("rand.jl") include("density.jl") +include("tmap.jl") module Interface using MeasureBase diff --git a/src/combinators/product.jl b/src/combinators/product.jl index c3cbf713..7c18be42 100644 --- a/src/combinators/product.jl +++ b/src/combinators/product.jl @@ -36,7 +36,6 @@ struct ProductMeasure{M} <: AbstractProductMeasure marginals::M end - # For tuples, `mapreduce` has trouble with type inference @inline function logdensity_def(d::ProductMeasure{T}, x) where {T<:Tuple} ℓs = map(logdensity_def, marginals(d),x) @@ -50,24 +49,12 @@ end marginals(μ::ProductMeasure) = μ.marginals -@generated function tbasemeasure_type(::Type{ProductMeasure{T}}) where {T<:Tuple} - ProductMeasure{Tuple{map(tbasemeasure_type, T.types)...}} -end - -@inline @constprop :aggressive function tbasemeasure_type(::Type{ProductMeasure{A}}) where {M,A<:AbstractArray{M}} - p = Tuple(A.parameters) - C = constructorof(A) - if isconcretetype(M) - return ProductMeasure{C{(tbasemeasure_type(M), Base.tail(p)...)...}} - else - return ProductMeasure{C{(Any, Base.tail(p)...)...}} - end +@inline function tbasemeasure_type(::Type{P}) where {P<:ProductMeasure} + tmap(tbasemeasure_type, P) end testvalue(d::AbstractProductMeasure) = map(testvalue, marginals(d)) - - export ⊗ """ diff --git a/src/combinators/spikemixture.jl b/src/combinators/spikemixture.jl index 1e5a6197..8538cad5 100644 --- a/src/combinators/spikemixture.jl +++ b/src/combinators/spikemixture.jl @@ -18,16 +18,24 @@ end @inline function basemeasure(μ::SpikeMixture) # Compare formula (1.4) in Joris Bierkens, Sebastiano Grazzi, Frank van der Meulen, Moritz Schauer: # Sticky PDMP samplers for sparse and local inference problems. 2020. [https://arxiv.org/abs/2103.08478]. - ki = (1 / μ.w - 1) / density_def(μ.m, 0) - SpikeMixture(basemeasure(μ.m), 1 / (1 + ki), μ.s * (1 + ki)) + SpikeMixture(basemeasure(μ.m), μ.w, μ.s) end tbasemeasure_depth(::Type{SpikeMixture{T,S}}) where {T,S} = static(1) + tbasemeasure_depth(T) # basemeasure_type(::Type{SpikeMixture{T,S}}) where {T,S} = SpikeMixture{} +function tbasemeasure_type(::Type{SpikeMixture{M, T}}) where {M,T} + B = tbasemeasure_type(M) + SpikeMixture{B, T} +end + @inline function logdensity_def(μ::SpikeMixture, x) - return log(μ.w) + logdensity_def(μ.m, x) + if iszero(x) + return log1p(-μ.w) + else + return log(μ.w) + logdensity_def(μ.m, x) + end end function gentype(μ::SpikeMixture) diff --git a/src/combinators/superpose.jl b/src/combinators/superpose.jl index c503ace7..ed49bbda 100644 --- a/src/combinators/superpose.jl +++ b/src/combinators/superpose.jl @@ -58,12 +58,13 @@ function Base.:+(μ::AbstractMeasure, ν::AbstractMeasure) superpose(components) end -logdensity_def(μ::SuperpositionMeasure, x) = +function logdensity_def(μ::SuperpositionMeasure, x) logsumexp((logdensity_def(m, x) for m in μ.components)) +end basemeasure(μ::SuperpositionMeasure) = superpose(map(basemeasure, μ.components)) -tbasemeasure_type(::Type{S}) where {C,S<:SuperpositionMeasure{C}} +function tbasemeasure_type(::Type{S}) where {C,S<:SuperpositionMeasure{C}} SuperpositionMeasure{tmap(tbasemeasure_type, C)} end diff --git a/src/density.jl b/src/density.jl index 792cd859..096ead27 100644 --- a/src/density.jl +++ b/src/density.jl @@ -142,7 +142,7 @@ end return ℓ end -@inline logdensityof(μ, x) = _logdensityof(μ, basemeasure(μ), x, logdensity_def(μ, x)) +@inline logdensityof(μ, x) = _logdensityof(μ, basemeasure(μ, x), x, logdensity_def(μ, x)) # Because it's sometimes useful, this returns a pair (ℓ,r) where # • ℓ is the log-density @@ -153,7 +153,7 @@ end # @show μ # @show ℓ # println() - return _logdensityof(β, basemeasure(β), x, ℓ, n) + return _logdensityof(β, basemeasure(β,x), x, ℓ, n) end @generated function _logdensityof(μ, β, x, ℓ::T, ::StaticInt{n}) where {n,T} diff --git a/src/help.jl b/src/help.jl index 16045852..77d37476 100644 --- a/src/help.jl +++ b/src/help.jl @@ -7,8 +7,7 @@ function help_tbasemeasure_type(μ::M) where M function tbasemeasure_type(::Type{$M}) $B end - """ ) - return B + return nothing end diff --git a/src/tmap.jl b/src/tmap.jl new file mode 100644 index 00000000..fc09a9e0 --- /dev/null +++ b/src/tmap.jl @@ -0,0 +1,18 @@ +# A type-level map + +@generated function tmap(f::F, ::Type{T}) where {F,T<:Tuple} + f = functioninstance(F) + Tuple{map(f, T.types)...} +end + +function tmap(f::F, ::Type{A}) where {F,T,A<:AbstractArray{T}} + f = functioninstance(F) + p = Tuple(A.parameters) + C = constructorof(A) + C{(f(T), Base.tail(p)...)...} +end + +function tmap(f::F, ::Type{ProductMeasure{T}}) where {F,T} + f = functioninstance(F) + ProductMeasure{tmap(f, T)} +end diff --git a/src/utils.jl b/src/utils.jl index 08564311..15b18434 100644 --- a/src/utils.jl +++ b/src/utils.jl @@ -70,7 +70,7 @@ end @inline @constprop :aggressive tbasemeasure_depth(::Type{M}) where M = tbasemeasure_depth(M, tbasemeasure_type(M), static(0)) -@inline @constprop :aggressive function tbasemeasure_depth(::Type{M}, ::Type{B}, S::StaticInt) where {M,B} - M === B && return S - return tbasemeasure_depth(B, tbasemeasure_type(B), S + static(1)) +@generated function tbasemeasure_depth(::Type{M}, ::Type{B}, S::StaticInt{N}) where {M,B,N} + M === B && return static(N) + return tbasemeasure_depth(B, tbasemeasure_type(B), static(N+1)) end \ No newline at end of file diff --git a/test/runtests.jl b/test/runtests.jl index 0e4f5ebe..37759614 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -43,16 +43,16 @@ test_measures = [ For(3) do j Dirac(j) end - For(2, 3) do i, j - Dirac(i) + Dirac(j) - end + # For(2, 3) do i, j + # Dirac(i) + Dirac(j) + # end Lebesgue(ℝ)^3 Lebesgue(ℝ)^(2, 3) 3 * Lebesgue(ℝ) Dirac(π) Lebesgue(ℝ) - Dirac(0.0) + Lebesgue(ℝ) - SpikeMixture(Lebesgue(ℝ), 2) + # Dirac(0.0) + Lebesgue(ℝ) + SpikeMixture(Lebesgue(ℝ), 0.2) # d ⊙ d ] @@ -67,7 +67,7 @@ testbroken_measures = [ @testset "testvalue" begin for μ in test_measures @info "testing $μ" - @test test_interface(μ) + test_interface(μ) end for μ in testbroken_measures @@ -84,12 +84,6 @@ end @testset "SpikeMixture" begin @test rand(SpikeMixture(Dirac(0), 0.5)) == 0 @test rand(SpikeMixture(Dirac(1), 1.0)) == 1 - w = 1 / 3 - m = SpikeMixture(d, w) - bm = basemeasure(m) - @test (bm.s * bm.w) * bm.m == 1.0 * basemeasure(d) - @test density_def(m, 1.0) * (bm.s * bm.w) ≈ w * density_def(d, 1.0) - @test density_def(m, 0) * (bm.s * (1 - bm.w)) ≈ (1 - w) end @testset "Dirac" begin From 9fc52d839dce56e2ac30235e6d748b58e79e37ee Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 13 Dec 2021 10:31:35 -0800 Subject: [PATCH 102/368] @test !isabstracttype(typejoin(...)) --- src/interface.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/interface.jl b/src/interface.jl index 853dae0b..9b0e780f 100644 --- a/src/interface.jl +++ b/src/interface.jl @@ -17,7 +17,7 @@ function test_interface(μ::M) where {M} @test @inferred tbasemeasure_type(M) == @inferred basemeasure_type(μ) - @info typejoin(basemeasure_type(μ), (typeof ∘ basemeasure)(μ)) + @test !isabstracttype(typejoin(basemeasure_type(μ), (typeof ∘ basemeasure)(μ))) ########################################################################### # basemeasure_depth From 071fdf7580920401e078f161a93d916a9686ac83 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 13 Dec 2021 12:52:12 -0800 Subject: [PATCH 103/368] work on show methods --- src/combinators/spikemixture.jl | 18 ++++++++++-------- src/primitives/dirac.jl | 5 ++--- src/utils.jl | 8 -------- 3 files changed, 12 insertions(+), 19 deletions(-) diff --git a/src/combinators/spikemixture.jl b/src/combinators/spikemixture.jl index 8538cad5..37ff952b 100644 --- a/src/combinators/spikemixture.jl +++ b/src/combinators/spikemixture.jl @@ -5,20 +5,23 @@ export SpikeMixture struct SpikeMixture{T,S} <: AbstractMeasure m::T # parent w::S # relative weight of parent - s::S # scale end -SpikeMixture(m, w) = SpikeMixture(m, w, one(w)) - -function Base.show(io::IO, μ::SpikeMixture) - io = IOContext(io, :compact => true) - print(io, "(", μ.s * μ.w, "*", string(μ.m), " + ", μ.s * (1 - μ.w), "Dirac(0))") +SpikeMixture(m, w) = SpikeMixture(m, w) + +function Pretty.tile(μ::SpikeMixture) + result = Pretty.tile(μ.w) + result *= Pretty.tile(μ.m) + result *= Pretty.literal(" + ") + result *= Pretty.tile(1 - μ.w) + result *= Pretty.literal("Dirac(0)") + return result end # TODO: Should this base measure be local? @inline function basemeasure(μ::SpikeMixture) # Compare formula (1.4) in Joris Bierkens, Sebastiano Grazzi, Frank van der Meulen, Moritz Schauer: # Sticky PDMP samplers for sparse and local inference problems. 2020. [https://arxiv.org/abs/2103.08478]. - SpikeMixture(basemeasure(μ.m), μ.w, μ.s) + SpikeMixture(basemeasure(μ.m), μ.w) end tbasemeasure_depth(::Type{SpikeMixture{T,S}}) where {T,S} = static(1) + tbasemeasure_depth(T) @@ -43,7 +46,6 @@ function gentype(μ::SpikeMixture) end function Base.rand(rng::AbstractRNG, T::Type, μ::SpikeMixture) - μ.s != 1 && throw(ArgumentError("Not a probability measure")) return (rand(rng, T) < μ.w) * rand(rng, T, μ.m) end diff --git a/src/primitives/dirac.jl b/src/primitives/dirac.jl index a2330ea0..44ee75ff 100644 --- a/src/primitives/dirac.jl +++ b/src/primitives/dirac.jl @@ -5,9 +5,8 @@ struct Dirac{X} <: AbstractMeasure x::X end -function Pretty.quoteof(d::Dirac) - q = Pretty.quoteof(d.x) - :(Dirac($q)) +function Pretty.tile(d::Dirac) + Pretty.literal("Dirac(") * Pretty.tile(d.x) * Pretty.literal(")") end gentype(μ::Dirac{X}) where {X} = X diff --git a/src/utils.jl b/src/utils.jl index 15b18434..fb5b7a33 100644 --- a/src/utils.jl +++ b/src/utils.jl @@ -8,14 +8,6 @@ end showparams(io::IO, ::EmptyNamedTuple) = print(io, "()") showparams(io::IO, nt::NamedTuple) = print(io, nt) -# function constructorof(::Type{T}) where {T} -# C = T -# while C isa UnionAll -# C = C.body -# end - -# return C.name.wrapper -# end export testvalue testvalue(μ::AbstractMeasure) = testvalue(basemeasure(μ)) From b7efac2052a6ea715275d3e56307eb454112511f Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 13 Dec 2021 12:53:03 -0800 Subject: [PATCH 104/368] update CI --- .github/workflows/CI.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index 3fc86d18..a038d474 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -12,8 +12,8 @@ jobs: fail-fast: false matrix: version: - - '1.3' - '1.6' + - '1.7' - 'nightly' os: - ubuntu-latest From 61cf5b51d630d03ec88ebda95c629561d52e1a89 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 13 Dec 2021 13:59:43 -0800 Subject: [PATCH 105/368] remove old code --- src/combinators/spikemixture.jl | 1 - 1 file changed, 1 deletion(-) diff --git a/src/combinators/spikemixture.jl b/src/combinators/spikemixture.jl index 37ff952b..f9111435 100644 --- a/src/combinators/spikemixture.jl +++ b/src/combinators/spikemixture.jl @@ -6,7 +6,6 @@ struct SpikeMixture{T,S} <: AbstractMeasure m::T # parent w::S # relative weight of parent end -SpikeMixture(m, w) = SpikeMixture(m, w) function Pretty.tile(μ::SpikeMixture) result = Pretty.tile(μ.w) From 15cc2a58a201b9be96e8f800b9505fe7be61b269 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 13 Dec 2021 14:00:00 -0800 Subject: [PATCH 106/368] update productmeasure --- src/combinators/smart-constructors.jl | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/src/combinators/smart-constructors.jl b/src/combinators/smart-constructors.jl index e797005b..fbb60d04 100644 --- a/src/combinators/smart-constructors.jl +++ b/src/combinators/smart-constructors.jl @@ -25,7 +25,13 @@ end ############################################################################### # ProductMeasure -productmeasure(data::AbstractArray) = ProductMeasure(data) +productmeasure(mar::Fill) = powermeasure(mar.value, mar.axes) + +function productmeasure(mar::ReadonlyMappedArray{T, N, A, Returns{M}}) where {T,N,A,M} + return powermeasure(mar.f.value, axes(mar.data)) +end + +productmeasure(mar::AbstractArray) = ProductMeasure(mar) productmeasure(nt::NamedTuple) = ProductMeasure(nt) productmeasure(tup::Tuple) = ProductMeasure(tup) From 2979095064fbc7a9595925888fa0859c4c90fa06 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 13 Dec 2021 14:00:12 -0800 Subject: [PATCH 107/368] prettyprinting stuff --- src/combinators/for.jl | 6 ++++++ src/combinators/product.jl | 6 +++++- 2 files changed, 11 insertions(+), 1 deletion(-) diff --git a/src/combinators/for.jl b/src/combinators/for.jl index eb0b2704..11ffb701 100644 --- a/src/combinators/for.jl +++ b/src/combinators/for.jl @@ -8,6 +8,12 @@ struct For{F, I} <: AbstractProductMeasure inds::I end +function Pretty.tile(d::For) + result = Pretty.literal("For(") + result *= Pretty.pair_layout(Pretty.tile(d.f), Pretty.tile(d.inds); sep = ", ") + result *= Pretty.literal(")") +end + """ For(f, base...) diff --git a/src/combinators/product.jl b/src/combinators/product.jl index 7c18be42..822b2549 100644 --- a/src/combinators/product.jl +++ b/src/combinators/product.jl @@ -35,7 +35,11 @@ end struct ProductMeasure{M} <: AbstractProductMeasure marginals::M end - + +function Pretty.tile(d::ProductMeasure{T}) where {T<:Tuple} + Pretty.list_layout(Pretty.tile.([marginals(d)...]), sep=" ⊗ ") +end + # For tuples, `mapreduce` has trouble with type inference @inline function logdensity_def(d::ProductMeasure{T}, x) where {T<:Tuple} ℓs = map(logdensity_def, marginals(d),x) From 42e11a8c683d1139b5f8cf9fb03a926954e1977d Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 13 Dec 2021 15:03:57 -0800 Subject: [PATCH 108/368] Drop te @constprop :aggressive stuff (maybe don't need it?) --- src/utils.jl | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/utils.jl b/src/utils.jl index fb5b7a33..f4ca7a25 100644 --- a/src/utils.jl +++ b/src/utils.jl @@ -52,15 +52,15 @@ functioninstance(::Type{F}) where {F<:Function} = F.instance export basemeasure_depth -@inline @constprop :aggressive function basemeasure_type(μ::M) where {M<:AbstractMeasure} +@inline function basemeasure_type(μ::M) where {M<:AbstractMeasure} return tbasemeasure_type(M) end -@inline @constprop :aggressive function basemeasure_depth(μ::M) where {M<:AbstractMeasure} +@inline function basemeasure_depth(μ::M) where {M<:AbstractMeasure} return tbasemeasure_depth(M) end -@inline @constprop :aggressive tbasemeasure_depth(::Type{M}) where M = tbasemeasure_depth(M, tbasemeasure_type(M), static(0)) +@inline tbasemeasure_depth(::Type{M}) where M = tbasemeasure_depth(M, tbasemeasure_type(M), static(0)) @generated function tbasemeasure_depth(::Type{M}, ::Type{B}, S::StaticInt{N}) where {M,B,N} M === B && return static(N) From 82d174daba33bf7438109873352b7eeccb849de7 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 13 Dec 2021 15:21:12 -0800 Subject: [PATCH 109/368] nerline --- src/combinators/bind.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/combinators/bind.jl b/src/combinators/bind.jl index 9d3ea89c..a15d692d 100644 --- a/src/combinators/bind.jl +++ b/src/combinators/bind.jl @@ -27,4 +27,4 @@ See also `bind` and `Bind` """ ↣(μ, k) = bind(μ, k) -bind(μ, k) = Bind(μ, k) \ No newline at end of file +bind(μ, k) = Bind(μ, k) From 85277ec87b530709d41c9f24adf0af1666abe07e Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 14 Dec 2021 06:35:07 -0800 Subject: [PATCH 110/368] dropping some old code --- src/density.jl | 3 --- 1 file changed, 3 deletions(-) diff --git a/src/density.jl b/src/density.jl index 096ead27..5c3f0288 100644 --- a/src/density.jl +++ b/src/density.jl @@ -32,11 +32,8 @@ function 𝒹(μ::AbstractMeasure, base::AbstractMeasure) return Density(μ, base) end -logdensityof(d::Density, x) = logdensityof(d.μ, d.base, x) - densityof(d::Density, x) = exp(logdensityof(d.μ, d.base, x)) - """ struct DensityMeasure{F,B} <: AbstractMeasure density :: F From 08088d892dc5b4dfc9451f6b74d3afa03e2c3072 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 14 Dec 2021 06:35:31 -0800 Subject: [PATCH 111/368] update tbasemeasure_type(::PowerMeasure) --- src/combinators/power.jl | 16 ++++++++++++++-- 1 file changed, 14 insertions(+), 2 deletions(-) diff --git a/src/combinators/power.jl b/src/combinators/power.jl index 2d7627f4..bc2a9a33 100644 --- a/src/combinators/power.jl +++ b/src/combinators/power.jl @@ -63,10 +63,22 @@ function basemeasure_depth(::PowerMeasure{M}) where {M} return tbasemeasure_depth(M) end -function tbasemeasure_type(::Type{PowerMeasure{M,D}}) where {M,D} - return PowerMeasure{tbasemeasure_type(M),D} +function tbasemeasure_type(::Type{P}) where {M,P<:PowerMeasure{M}} + tbasemeasure_type(P, tbasemeasure_type(M)) end +# This form assumes +# P == typeof(μ) +# B == typeof(basemeasure(parent(μ))) +function tbasemeasure_type(::Type{P},::Type{B}) where {M,D,B,P<:PowerMeasure{M,D}} + return PowerMeasure{B,D} +end + +function tbasemeasure_type(::Type{P},::Type{B}) where {M,T,W,D,B<:WeightedMeasure{W,T},P<:PowerMeasure{M,D}} + return WeightedMeasure{W,PowerMeasure{T,D}} +end + + function tbasemeasure_depth(::Type{PowerMeasure{M,D}}) where {M<:PrimitiveMeasure,D} return static(0) end From 37b9567a64eedd1b618bc575520cf8b254197282 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 14 Dec 2021 13:58:19 -0800 Subject: [PATCH 112/368] moar tests --- test/runtests.jl | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/test/runtests.jl b/test/runtests.jl index 37759614..838c88f0 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -68,6 +68,10 @@ testbroken_measures = [ for μ in test_measures @info "testing $μ" test_interface(μ) + test_interface(μ ^ 3) + test_interface(μ ^ (3,2)) + test_interface(5 * μ) + # test_interface(SpikeMixture(μ, 0.2)) end for μ in testbroken_measures From 61f64408a9596c92545cedaa30e3c10630107557 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 14 Dec 2021 13:58:27 -0800 Subject: [PATCH 113/368] update SpikeMixture --- src/combinators/spikemixture.jl | 26 ++++++++++++-------------- 1 file changed, 12 insertions(+), 14 deletions(-) diff --git a/src/combinators/spikemixture.jl b/src/combinators/spikemixture.jl index f9111435..606d1c94 100644 --- a/src/combinators/spikemixture.jl +++ b/src/combinators/spikemixture.jl @@ -2,39 +2,37 @@ export SpikeMixture # TODO: Add `AbstractSuperposition <: AbstractMeasure`, and make SpikeMixture a # subtype of this -struct SpikeMixture{T,S} <: AbstractMeasure - m::T # parent - w::S # relative weight of parent +struct SpikeMixture{M,W,S} <: AbstractMeasure + m::M # parent + w::W # parent weight + s::S # spike weight end +SpikeMixture(μ,w) = SpikeMixture(μ, w, static(1.0) - w) + function Pretty.tile(μ::SpikeMixture) - result = Pretty.tile(μ.w) - result *= Pretty.tile(μ.m) - result *= Pretty.literal(" + ") - result *= Pretty.tile(1 - μ.w) - result *= Pretty.literal("Dirac(0)") - return result + Pretty.list_layout(Pretty.tile.([μ.m, μ.w]), prefix="SpikeMixture") end # TODO: Should this base measure be local? @inline function basemeasure(μ::SpikeMixture) # Compare formula (1.4) in Joris Bierkens, Sebastiano Grazzi, Frank van der Meulen, Moritz Schauer: # Sticky PDMP samplers for sparse and local inference problems. 2020. [https://arxiv.org/abs/2103.08478]. - SpikeMixture(basemeasure(μ.m), μ.w) + SpikeMixture(basemeasure(μ.m), static(1.0), static(1.0)) end -tbasemeasure_depth(::Type{SpikeMixture{T,S}}) where {T,S} = static(1) + tbasemeasure_depth(T) +# tbasemeasure_depth(::Type{SpikeMixture{M,W}}) where {M,W} = static(1) + tbasemeasure_depth(M) # basemeasure_type(::Type{SpikeMixture{T,S}}) where {T,S} = SpikeMixture{} -function tbasemeasure_type(::Type{SpikeMixture{M, T}}) where {M,T} +function tbasemeasure_type(::Type{SpikeMixture{M,W,S}}) where {M,W,S} B = tbasemeasure_type(M) - SpikeMixture{B, T} + SpikeMixture{B,StaticFloat64{1.0},StaticFloat64{1.0}} end @inline function logdensity_def(μ::SpikeMixture, x) if iszero(x) - return log1p(-μ.w) + return log(μ.s) else return log(μ.w) + logdensity_def(μ.m, x) end From f09a1793087046a63c74c0e366ba301a5a976edb Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 20 Dec 2021 06:44:16 -0800 Subject: [PATCH 114/368] update superpose type parameter name --- src/combinators/superpose.jl | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/src/combinators/superpose.jl b/src/combinators/superpose.jl index 994703f9..e589698f 100644 --- a/src/combinators/superpose.jl +++ b/src/combinators/superpose.jl @@ -20,8 +20,8 @@ Superposition measures satisfy \end{aligned} ``` """ -struct SuperpositionMeasure{NT} <: AbstractMeasure - components::NT +struct SuperpositionMeasure{C} <: AbstractMeasure + components::C end function Pretty.tile(d::SuperpositionMeasure) @@ -63,6 +63,10 @@ logdensity_def(μ::SuperpositionMeasure, x) = basemeasure(μ::SuperpositionMeasure) = superpose(map(basemeasure, μ.components)) +function basemeasure_depth(μ::SuperpositionMeasure{C}) where C + mapreduce(basemeasure_depth, maximum, μ.components) +end + # TODO: Fix `rand` method (this one is wrong) # function Base.rand(μ::SuperpositionMeasure{X,N}) where {X,N} # return rand(rand(μ.components)) From 9b23149b81924532b8bcef9ba2d1b723cb9d03ce Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 20 Dec 2021 06:44:23 -0800 Subject: [PATCH 115/368] drop old tests --- test/runtests.jl | 20 +------------------- 1 file changed, 1 insertion(+), 19 deletions(-) diff --git a/test/runtests.jl b/test/runtests.jl index 0e4f5ebe..71b00216 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -11,23 +11,6 @@ Aqua.test_all(MeasureBase; ambiguities = false, unbound_args = false) d = ∫exp(x -> -x^2, Lebesgue(ℝ)) -# if VERSION ≥ v"1.6" -# @eval using JETTest - -# @eval begin -# @test_nodispatch density_def(Lebesgue(ℝ), 0.3) - -# @test_nodispatch density_def(Dirac(0), 0.3) -# @test_nodispatch density_def(Dirac(0), 0) - -# @test_nodispatch density_def(d, 3) - -# @test_nodispatch basemeasure(d) - -# @test_nodispatch logdensity_def(For(3) do j Dirac(j) end, [1,2,3]) -# end -# end - # function draw2(μ) # x = rand(μ) # y = rand(μ) @@ -118,8 +101,7 @@ end ] for d in FORDISTS - @info "testing $d" - @test logdensity_def(d, rand(d)) isa Float64 + test_interface(d) end end From 7916f6ee5582290d4a16120f88c5f20817c54362 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 20 Dec 2021 12:16:33 -0800 Subject: [PATCH 116/368] func_string --- src/combinators/for.jl | 25 +++++++++++++++++++------ src/utils.jl | 40 +++++++++++++++++++++++++++++++++++++++- 2 files changed, 58 insertions(+), 7 deletions(-) diff --git a/src/combinators/for.jl b/src/combinators/for.jl index 11ffb701..8cc25a89 100644 --- a/src/combinators/for.jl +++ b/src/combinators/for.jl @@ -3,17 +3,30 @@ export For using Random import Base -struct For{F, I} <: AbstractProductMeasure +struct For{T, F, I} <: AbstractProductMeasure f::F inds::I + + function For(f::F, inds::I) where {F,I<:Tuple} + T = Core.Compiler.return_type(f, Tuple{eltype.(inds)...}) + new{T,F,I}(f, inds) + end end -function Pretty.tile(d::For) - result = Pretty.literal("For(") - result *= Pretty.pair_layout(Pretty.tile(d.f), Pretty.tile(d.inds); sep = ", ") +function Pretty.tile(d::For{T}) where {T} + result = Pretty.literal("For{") + result *= Pretty.tile(T) + result *= Pretty.literal("}(") + result *= Pretty.literal(func_string(d.f, Tuple{eltype.(d.inds)...})) + for ind in d.inds + result *= Pretty.literal(", ") + result *= Pretty.tile(ind) + end result *= Pretty.literal(")") end +marginals(d::For) = mappedarray(d.f, d.inds...) + """ For(f, base...) @@ -85,7 +98,7 @@ julia> For(eachrow(rand(4,2))) do x Normal(x[1], x[2]) end |> marginals |> colle ``` """ -For(f, inds::AbstractArray...) = productmeasure(mappedarray(f, inds...)) +For(f, inds::AbstractArray...) = For(f, inds) For(f, n::Integer) = For(f, Base.OneTo(n)) For(f, inds::Integer...) = For(i -> f(Tuple(i)...), Base.CartesianIndices(inds)) -For(f, gen::Base.Generator) = ProductMeasure(Base.Generator(f ∘ gen.f, gen.iter)) +# For(f, gen::Base.Generator) = ProductMeasure(Base.Generator(f ∘ gen.f, gen.iter)) diff --git a/src/utils.jl b/src/utils.jl index f4ca7a25..68e6593c 100644 --- a/src/utils.jl +++ b/src/utils.jl @@ -65,4 +65,42 @@ end @generated function tbasemeasure_depth(::Type{M}, ::Type{B}, S::StaticInt{N}) where {M,B,N} M === B && return static(N) return tbasemeasure_depth(B, tbasemeasure_type(B), static(N+1)) -end \ No newline at end of file +end + +# Adapted from https://github.com/JuliaArrays/MappedArrays.jl/blob/46bf47f3388d011419fe43404214c1b7a44a49cc/src/MappedArrays.jl#L229 +function func_string(f, types) + ft = typeof(f) + mt = ft.name.mt + name = string(mt.name) + if startswith(name, '#') + # This is an anonymous function. See if it can be printed nicely + lwrds = code_lowered(f, types) + if length(lwrds) != 1 + return string(f) + end + lwrd = lwrds[1] + c = lwrd.code + if length(c) == 2 && ((isa(c[2], Expr) && c[2].head === :return) || (isdefined(Core, :ReturnNode) && isa(c[2], Core.ReturnNode))) + # This is a single-line anonymous function, we should handle it + s = lwrd.slotnames[2:end] + result = "" + if length(s) == 1 + result *= string(s[1]) + result *= "->" + else + result *= string(tuple(s...)) + result *= "->" + end + c1 = string(c[1]) + for i = 1:length(s) + c1 = replace(c1, "_"*string(i+1)=>string(s[i])) + end + result *= c1 + return result + else + return string(f) + end + else + return string(f) + end +end From 56b92826503bc584a303a9b98fb84cdd764364d3 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 21 Dec 2021 09:56:34 -0800 Subject: [PATCH 117/368] more updates --- src/combinators/for.jl | 35 ++++++++++++++++++++++++--- src/combinators/product.jl | 32 ++++++++++++++++++++++-- src/combinators/smart-constructors.jl | 1 + src/kleisli.jl | 6 ----- src/tmap.jl | 4 +++ test/runtests.jl | 3 ++- 6 files changed, 69 insertions(+), 12 deletions(-) diff --git a/src/combinators/for.jl b/src/combinators/for.jl index 8cc25a89..25ccecb3 100644 --- a/src/combinators/for.jl +++ b/src/combinators/for.jl @@ -13,6 +13,36 @@ struct For{T, F, I} <: AbstractProductMeasure end end +@useproxy For + +# For(f, gen::Base.Generator) = ProductMeasure(Base.Generator(f ∘ gen.f, gen.iter)) + +function proxy(d::For{T,F,I}) where {T,F,I} + productmeasure(mappedarray(d.f, d.inds...)) +end + +function proxy(d::For{T,F,I}) where {N,T,F,I<:NTuple{N,<:Base.Generator}} + productmeasure(Base.Generator(d.f, zip(d.inds...))) +end + +function tproxy(::Type{For{T,F,I}}) where {N,T,F,I<:NTuple{N,<:Base.Generator}} + ProductMeasure{Base.Generator{F, Iterators.Zip{I}}} +end + +function tproxy(::Type{For{T,F,Tuple{I}}}) where {Ta,N,I<:AbstractArray{Ta,N},T,F} + ProductMeasure{MappedArrays.ReadonlyMappedArray{T, N, I, F}} +end + +function tproxy(::Type{For{T,F,I}}) where {M,Ta,N,T,F,I<:NTuple{M,<:AbstractArray{Ta,N}}} + ProductMeasure{MappedArrays.ReadonlyMultiMappedArray{T, N, I, F}} +end + +# function tproxy(::Type{For{ProductMeasure{T}, F, I}}) where {N,T<:NTuple{N,<:AbstractMeasure},F,I} + +# end + +tbasemeasure_type(::Type{For{T,F,I}}) where {T,F,I} = tbasemeasure_type(tproxy(For{T,F,I})) + function Pretty.tile(d::For{T}) where {T} result = Pretty.literal("For{") result *= Pretty.tile(T) @@ -25,7 +55,7 @@ function Pretty.tile(d::For{T}) where {T} result *= Pretty.literal(")") end -marginals(d::For) = mappedarray(d.f, d.inds...) +marginals(d::For) = marginals(proxy(d)) """ For(f, base...) @@ -98,7 +128,6 @@ julia> For(eachrow(rand(4,2))) do x Normal(x[1], x[2]) end |> marginals |> colle ``` """ -For(f, inds::AbstractArray...) = For(f, inds) +For(f, inds...) = For(f, inds) For(f, n::Integer) = For(f, Base.OneTo(n)) For(f, inds::Integer...) = For(i -> f(Tuple(i)...), Base.CartesianIndices(inds)) -# For(f, gen::Base.Generator) = ProductMeasure(Base.Generator(f ∘ gen.f, gen.iter)) diff --git a/src/combinators/product.jl b/src/combinators/product.jl index 822b2549..be451e11 100644 --- a/src/combinators/product.jl +++ b/src/combinators/product.jl @@ -1,6 +1,7 @@ export ProductMeasure using MappedArrays +using MappedArrays: ReadonlyMultiMappedArray using Base: @propagate_inbounds import Base using FillArrays @@ -46,13 +47,40 @@ end sum(ℓs) end -function basemeasure(μ::ProductMeasure{A}) where {T,A<:ReadonlyMappedArray{T}} +function basemeasure(μ::ProductMeasure{A}) where {T,A<:AbstractMappedArray{T}} mar = marginals(μ) - productmeasure(mappedarray(basekleisli(mar.f), mar.data)) + if static_hasmethod(tbasemeasure_type, Tuple{Type{T}}) + B = tbasemeasure_type(T) + if Base.issingletontype(B) + return B.instance ^ size(mar) + end + end + + return productmeasure(mappedarray(basekleisli(mar.f), mar.data)) end marginals(μ::ProductMeasure) = μ.marginals +@inline function tbasemeasure_type(::Type{P}) where {T,N,A,F,M<:ReadonlyMultiMappedArray{T,N,A,F},P<:ProductMeasure{M}} + if static_hasmethod(tbasemeasure_type, Tuple{Type{T}}) + B = tbasemeasure_type(T) + if Base.issingletontype(B) + return PowerMeasure{B, A} + end + end + tmap(tbasemeasure_type, P) +end + +@inline function tbasemeasure_type(::Type{P}) where {T,N,A,F,M<:ReadonlyMappedArray{T,N,A,F},P<:ProductMeasure{M}} + if static_hasmethod(tbasemeasure_type, Tuple{Type{T}}) + B = tbasemeasure_type(T) + if Base.issingletontype(B) + return PowerMeasure{B, Tuple{A}} + end + end + tmap(tbasemeasure_type, P) +end + @inline function tbasemeasure_type(::Type{P}) where {P<:ProductMeasure} tmap(tbasemeasure_type, P) end diff --git a/src/combinators/smart-constructors.jl b/src/combinators/smart-constructors.jl index fbb60d04..d1029b26 100644 --- a/src/combinators/smart-constructors.jl +++ b/src/combinators/smart-constructors.jl @@ -31,6 +31,7 @@ function productmeasure(mar::ReadonlyMappedArray{T, N, A, Returns{M}}) where {T, return powermeasure(mar.f.value, axes(mar.data)) end +productmeasure(mar::Base.Generator) = ProductMeasure(mar) productmeasure(mar::AbstractArray) = ProductMeasure(mar) productmeasure(nt::NamedTuple) = ProductMeasure(nt) productmeasure(tup::Tuple) = ProductMeasure(tup) diff --git a/src/kleisli.jl b/src/kleisli.jl index ccf30bcf..f79efaf0 100644 --- a/src/kleisli.jl +++ b/src/kleisli.jl @@ -69,12 +69,6 @@ basekleisli(k::ParameterizedKleisli) = kleisli(basekleisli(k.f), k.param_maps) basekleisli(f::Returns) = Returns(basemeasure(f.value)) -# export kleisliize - -# function kleisliize(μ::M) where {N, M <: ParameterizedMeasure{N}} -# C = constructorof(M) -# (Kleisli{C,}(NamedTuple{N}, ), values(getfield(μ, :par))) -# end function Base.show(io::IO, μ::AbstractKleisli) io = IOContext(io, :compact => true) diff --git a/src/tmap.jl b/src/tmap.jl index fc09a9e0..823a9580 100644 --- a/src/tmap.jl +++ b/src/tmap.jl @@ -12,6 +12,10 @@ function tmap(f::F, ::Type{A}) where {F,T,A<:AbstractArray{T}} C{(f(T), Base.tail(p)...)...} end +function tmap(f::F, ::Type{Base.Generator{G,I}}) where {F,G,I} + Base.Generator{ComposedFunction{F,G}, I} +end + function tmap(f::F, ::Type{ProductMeasure{T}}) where {F,T} f = functioninstance(F) ProductMeasure{tmap(f, T)} diff --git a/test/runtests.jl b/test/runtests.jl index 8e61a905..604ff263 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -98,7 +98,8 @@ end end ] - for d in FORDISTS + for (n,d) in enumerate(FORDISTS) + # @show n,d test_interface(d) end end From bf461521755c53d47debfa38c95f5f8eaf2fa345 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 22 Dec 2021 12:16:57 -0800 Subject: [PATCH 118/368] getting closer --- src/combinators/for.jl | 46 +++++++++++++++++++++++++++----------- src/combinators/product.jl | 21 ++++++++++++++--- src/proxies.jl | 2 -- src/tmap.jl | 7 ++---- src/utils.jl | 38 +++++++++++++++++++++++++------ test/runtests.jl | 3 +-- 6 files changed, 85 insertions(+), 32 deletions(-) diff --git a/src/combinators/for.jl b/src/combinators/for.jl index 25ccecb3..762299a0 100644 --- a/src/combinators/for.jl +++ b/src/combinators/for.jl @@ -8,7 +8,7 @@ struct For{T, F, I} <: AbstractProductMeasure inds::I function For(f::F, inds::I) where {F,I<:Tuple} - T = Core.Compiler.return_type(f, Tuple{eltype.(inds)...}) + T = Core.Compiler.return_type(f, Tuple{_eltype.(inds)...}) new{T,F,I}(f, inds) end end @@ -21,33 +21,51 @@ function proxy(d::For{T,F,I}) where {T,F,I} productmeasure(mappedarray(d.f, d.inds...)) end -function proxy(d::For{T,F,I}) where {N,T,F,I<:NTuple{N,<:Base.Generator}} - productmeasure(Base.Generator(d.f, zip(d.inds...))) +function logdensity_def(d::For{T,F,I}, x) where {N,T,F,I<:NTuple{N,<:Base.Generator}} + MeasureBase.logdensity_def(proxy(d), x) end -function tproxy(::Type{For{T,F,I}}) where {N,T,F,I<:NTuple{N,<:Base.Generator}} - ProductMeasure{Base.Generator{F, Iterators.Zip{I}}} +function marginals(d::For{T,F,I}) where {N,T,F,I<:NTuple{N,<:Base.Generator}} + Iterators.map(d.f, d.inds...) end -function tproxy(::Type{For{T,F,Tuple{I}}}) where {Ta,N,I<:AbstractArray{Ta,N},T,F} - ProductMeasure{MappedArrays.ReadonlyMappedArray{T, N, I, F}} +# TODO: Make this pass @code_warntype +# e..g +# +# d = For(eachrow(rand(4, 2))) do x +# Dirac(x[1]) ⊗ Dirac(x[2]) +# end +@inline function basemeasure(d::For{T,F,I}) where {N,T,F,I<:NTuple{N,<:Base.Generator}} + B = tbasemeasure_type(T) + if static_hasmethod(tbasemeasure_type, Tuple{Type{T}}) && Base.issingletontype(B) + return instance(B) ^ minimum(length, d.inds) + end + + return For(basekleisli(d.f), d.inds) end -function tproxy(::Type{For{T,F,I}}) where {M,Ta,N,T,F,I<:NTuple{M,<:AbstractArray{Ta,N}}} - ProductMeasure{MappedArrays.ReadonlyMultiMappedArray{T, N, I, F}} +function tbasemeasure_type(::Type{For{T, F, I}}) where {T,F,I} + B = tbasemeasure_type(T) + return tbasemeasure_type(For{T, F, I}, B) end -# function tproxy(::Type{For{ProductMeasure{T}, F, I}}) where {N,T<:NTuple{N,<:AbstractMeasure},F,I} +function tbasemeasure_type(::Type{For{T, F, I}}, ::Type{B}) where {B,T,F,I} + if Base.issingletontype(B) + return PowerMeasure{B, I} + end -# end + return For{B, typeof(basekleisli(instance(F))), I} +end -tbasemeasure_type(::Type{For{T,F,I}}) where {T,F,I} = tbasemeasure_type(tproxy(For{T,F,I})) +@inline function basemeasure_depth(d::For{T,F,I}) where {N,T,F,I<:NTuple{N,<:Base.Generator}} + MeasureBase.basemeasure_depth(proxy(d)) +end function Pretty.tile(d::For{T}) where {T} result = Pretty.literal("For{") result *= Pretty.tile(T) result *= Pretty.literal("}(") - result *= Pretty.literal(func_string(d.f, Tuple{eltype.(d.inds)...})) + result *= Pretty.literal(func_string(d.f, Tuple{_eltype.(d.inds)...})) for ind in d.inds result *= Pretty.literal(", ") result *= Pretty.tile(ind) @@ -131,3 +149,5 @@ julia> For(eachrow(rand(4,2))) do x Normal(x[1], x[2]) end |> marginals |> colle For(f, inds...) = For(f, inds) For(f, n::Integer) = For(f, Base.OneTo(n)) For(f, inds::Integer...) = For(i -> f(Tuple(i)...), Base.CartesianIndices(inds)) +# For(f, inds::Base.Generator) = productmeasure(mymap(f, inds)) + diff --git a/src/combinators/product.jl b/src/combinators/product.jl index be451e11..e411b76f 100644 --- a/src/combinators/product.jl +++ b/src/combinators/product.jl @@ -47,12 +47,27 @@ end sum(ℓs) end + +function basemeasure(μ::ProductMeasure{Base.Generator{I,F}}) where {I,F} + mar = marginals(μ) + T = Core.Compiler.return_type(mar.f, Tuple{_eltype(mar.iter)}) + if static_hasmethod(tbasemeasure_type, Tuple{Type{T}}) + B = tbasemeasure_type(T) + if Base.issingletontype(B) + b = instance(B)::B + return b ^ size(mar) + end + end + + return productmeasure(Base.Generator(basekleisli(mar.f), mar.iter)) +end + function basemeasure(μ::ProductMeasure{A}) where {T,A<:AbstractMappedArray{T}} mar = marginals(μ) if static_hasmethod(tbasemeasure_type, Tuple{Type{T}}) B = tbasemeasure_type(T) if Base.issingletontype(B) - return B.instance ^ size(mar) + return instance(B) ^ size(mar) end end @@ -61,14 +76,14 @@ end marginals(μ::ProductMeasure) = μ.marginals -@inline function tbasemeasure_type(::Type{P}) where {T,N,A,F,M<:ReadonlyMultiMappedArray{T,N,A,F},P<:ProductMeasure{M}} +@inline function tbasemeasure_type(::Type{ProductMeasure{M}}) where {T,N,A,F,M<:ReadonlyMultiMappedArray{T,N,A,F}} if static_hasmethod(tbasemeasure_type, Tuple{Type{T}}) B = tbasemeasure_type(T) if Base.issingletontype(B) return PowerMeasure{B, A} end end - tmap(tbasemeasure_type, P) + tmap(tbasemeasure_type, ProductMeasure{M}) end @inline function tbasemeasure_type(::Type{P}) where {T,N,A,F,M<:ReadonlyMappedArray{T,N,A,F},P<:ProductMeasure{M}} diff --git a/src/proxies.jl b/src/proxies.jl index 0cef6d38..89c60489 100644 --- a/src/proxies.jl +++ b/src/proxies.jl @@ -16,8 +16,6 @@ macro useproxy(M) quote @inline $__module__.logdensity_def(μ::$M, x) = logdensity_def(proxy(μ), x) @inline $__module__.basemeasure(μ::$M) = basemeasure(proxy(μ)) - @inline $__module__.basemeasure(μ::$M, x) = basemeasure(proxy(μ), x) - @inline $__module__.basemeasure_type(μ::$M) = basemeasure_type(proxy(μ)) @inline $__module__.basemeasure_depth(μ::$M) = basemeasure_depth(proxy(μ)) end end diff --git a/src/tmap.jl b/src/tmap.jl index 823a9580..18b0560e 100644 --- a/src/tmap.jl +++ b/src/tmap.jl @@ -1,12 +1,10 @@ # A type-level map -@generated function tmap(f::F, ::Type{T}) where {F,T<:Tuple} - f = functioninstance(F) +function tmap(f::F, ::Type{T}) where {F,T<:Tuple} Tuple{map(f, T.types)...} end function tmap(f::F, ::Type{A}) where {F,T,A<:AbstractArray{T}} - f = functioninstance(F) p = Tuple(A.parameters) C = constructorof(A) C{(f(T), Base.tail(p)...)...} @@ -16,7 +14,6 @@ function tmap(f::F, ::Type{Base.Generator{G,I}}) where {F,G,I} Base.Generator{ComposedFunction{F,G}, I} end -function tmap(f::F, ::Type{ProductMeasure{T}}) where {F,T} - f = functioninstance(F) +function tmap(f, ::Type{ProductMeasure{T}}) where {T} ProductMeasure{tmap(f, T)} end diff --git a/src/utils.jl b/src/utils.jl index 68e6593c..64737cb7 100644 --- a/src/utils.jl +++ b/src/utils.jl @@ -44,7 +44,10 @@ struct NonIterable end isiterable(::Type{T}) where {T} = static_hasmethod(iterate, Tuple{T}) ? Iterable() : NonIterable() -functioninstance(::Type{F}) where {F<:Function} = F.instance +@inline function instance(@nospecialize(T)) + Base.@_pure_meta + return getfield(T, :instance)::T +end # See https://github.com/cscherrer/KeywordCalls.jl/issues/22 @inline instance_type(f::F) where {F<:Function} = F @@ -52,21 +55,19 @@ functioninstance(::Type{F}) where {F<:Function} = F.instance export basemeasure_depth -@inline function basemeasure_type(μ::M) where {M<:AbstractMeasure} - return tbasemeasure_type(M) -end - -@inline function basemeasure_depth(μ::M) where {M<:AbstractMeasure} +@generated function basemeasure_depth(μ::M) where {M<:AbstractMeasure} return tbasemeasure_depth(M) end @inline tbasemeasure_depth(::Type{M}) where M = tbasemeasure_depth(M, tbasemeasure_type(M), static(0)) -@generated function tbasemeasure_depth(::Type{M}, ::Type{B}, S::StaticInt{N}) where {M,B,N} +function tbasemeasure_depth(::Type{M}, ::Type{B}, S::StaticInt{N}) where {M,B,N} M === B && return static(N) return tbasemeasure_depth(B, tbasemeasure_type(B), static(N+1)) end +@generated basemeasure_type(μ::M) where M = tbasemeasure_type(M) + # Adapted from https://github.com/JuliaArrays/MappedArrays.jl/blob/46bf47f3388d011419fe43404214c1b7a44a49cc/src/MappedArrays.jl#L229 function func_string(f, types) ft = typeof(f) @@ -104,3 +105,26 @@ function func_string(f, types) return string(f) end end + +_eltype(T) = eltype(T) + +function _eltype(g::Base.Generator{I}) where {I} + Core.Compiler.return_type(g.f, Tuple{_eltype(I)}) +end + +function _eltype(::Type{Base.Generator{I,ComposedFunction{Outer,Inner}}}) where {Outer,Inner,I} + _eltype(Base.Generator{_eltype(Base.Generator{I,Inner}), Outer}) +end + +function _eltype(::Type{Base.Generator{I,F}}) where {F<:Function,I} + f = instance(F) + Core.Compiler.return_type(f, Tuple{_eltype(I)}) +end + +function _eltype(::Type{Z}) where {Z<:Iterators.Zip} + map(_eltype, Z.types[1].types) +end + +mymap(f, gen::Base.Generator) = mymap(f ∘ gen.f, gen.iter) +mymap(f, inds...) = Iterators.map(f, inds...) + diff --git a/test/runtests.jl b/test/runtests.jl index 604ff263..8e61a905 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -98,8 +98,7 @@ end end ] - for (n,d) in enumerate(FORDISTS) - # @show n,d + for d in FORDISTS test_interface(d) end end From 73eb70a08dc805d3a47c0b21cf7e0459459d57a2 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 22 Dec 2021 13:08:20 -0800 Subject: [PATCH 119/368] almost there! --- src/combinators/product.jl | 15 +- src/density.jl | 10 +- stderr.log | 66404 +++++++++++++++++++++++++++++++++++ 3 files changed, 66421 insertions(+), 8 deletions(-) create mode 100644 stderr.log diff --git a/src/combinators/product.jl b/src/combinators/product.jl index e411b76f..46850a2f 100644 --- a/src/combinators/product.jl +++ b/src/combinators/product.jl @@ -62,16 +62,21 @@ function basemeasure(μ::ProductMeasure{Base.Generator{I,F}}) where {I,F} return productmeasure(Base.Generator(basekleisli(mar.f), mar.iter)) end -function basemeasure(μ::ProductMeasure{A}) where {T,A<:AbstractMappedArray{T}} - mar = marginals(μ) +@generated function basemeasure(μ::ProductMeasure{A}) where {T,A<:AbstractMappedArray{T}} if static_hasmethod(tbasemeasure_type, Tuple{Type{T}}) B = tbasemeasure_type(T) if Base.issingletontype(B) - return instance(B) ^ size(mar) + b = instance(B) + return quote + mar = marginals(μ) + $b ^ size(mar) + end end end - - return productmeasure(mappedarray(basekleisli(mar.f), mar.data)) + return quote + mar = marginals(μ) + productmeasure(mappedarray(basekleisli(mar.f), mar.data)) + end end marginals(μ::ProductMeasure) = μ.marginals diff --git a/src/density.jl b/src/density.jl index 5c3f0288..3322a5eb 100644 --- a/src/density.jl +++ b/src/density.jl @@ -141,9 +141,13 @@ end @inline logdensityof(μ, x) = _logdensityof(μ, basemeasure(μ, x), x, logdensity_def(μ, x)) -# Because it's sometimes useful, this returns a pair (ℓ,r) where -# • ℓ is the log-density -# • r is the rootmeasure of μ +@inline function _logdensityof(μ::M, β::M, x, ℓ::T) where {M,T} + if μ === β + return ℓ + end + invoke(_logdensity, Tuple{Any, Any, Any, T}, μ, β, x, ℓ)::T +end + @inline function _logdensityof(μ, β, x, ℓ) n = basemeasure_depth(μ) - static(1) iszero(n) && return ℓ diff --git a/stderr.log b/stderr.log new file mode 100644 index 00000000..6113f8a9 --- /dev/null +++ b/stderr.log @@ -0,0 +1,66404 @@ + Activating project at `~/git/MeasureBase.jl` + Testing MeasureBase + Status `/tmp/jl_WiZTr1/Project.toml` + [4c88cf16] Aqua v0.5.2 + [34da2185] Compat v3.40.0 + [187b0558] ConstructionBase v1.3.0 + [b429d917] DensityInterface v0.4.0 + [1a297f60] FillArrays v0.12.7 + [2ab3a3ac] LogExpFunctions v0.3.5 + [dbb5928d] MappedArrays v0.4.1 + [fa1605e6] MeasureBase v0.5.1 `~/git/MeasureBase.jl` + [54e16d92] PrettyPrinting v0.3.2 + [aedffcd0] Static v0.4.1 `~/git/Static.jl` + [410a4b4d] Tricks v0.1.6 + [37e2e46d] LinearAlgebra `@stdlib/LinearAlgebra` + [9a3f8284] Random `@stdlib/Random` + [10745b16] Statistics `@stdlib/Statistics` + [8dfed614] Test `@stdlib/Test` + Status `/tmp/jl_WiZTr1/Manifest.toml` + [4c88cf16] Aqua v0.5.2 + [d360d2e6] ChainRulesCore v1.11.1 + [9e997f8a] ChangesOfVariables v0.1.1 + [34da2185] Compat v3.40.0 + [187b0558] ConstructionBase v1.3.0 + [b429d917] DensityInterface v0.4.0 + [ffbed154] DocStringExtensions v0.8.6 + [1a297f60] FillArrays v0.12.7 + [615f187c] IfElse v0.1.1 + [3587e190] InverseFunctions v0.1.2 + [92d709cd] IrrationalConstants v0.1.1 + [2ab3a3ac] LogExpFunctions v0.3.5 + [dbb5928d] MappedArrays v0.4.1 + [fa1605e6] MeasureBase v0.5.1 `~/git/MeasureBase.jl` + [54e16d92] PrettyPrinting v0.3.2 + [aedffcd0] Static v0.4.1 `~/git/Static.jl` + [410a4b4d] Tricks v0.1.6 + [0dad84c5] ArgTools `@stdlib/ArgTools` + [56f22d72] Artifacts `@stdlib/Artifacts` + [2a0f44e3] Base64 `@stdlib/Base64` + [ade2ca70] Dates `@stdlib/Dates` + [8bb1440f] DelimitedFiles `@stdlib/DelimitedFiles` + [8ba89e20] Distributed `@stdlib/Distributed` + [f43a241f] Downloads `@stdlib/Downloads` + [b77e0a4c] InteractiveUtils `@stdlib/InteractiveUtils` + [b27032c2] LibCURL `@stdlib/LibCURL` + [76f85450] LibGit2 `@stdlib/LibGit2` + [8f399da3] Libdl `@stdlib/Libdl` + [37e2e46d] LinearAlgebra `@stdlib/LinearAlgebra` + [56ddb016] Logging `@stdlib/Logging` + [d6f4376e] Markdown `@stdlib/Markdown` + [a63ad114] Mmap `@stdlib/Mmap` + [ca575930] NetworkOptions `@stdlib/NetworkOptions` + [44cfe95a] Pkg `@stdlib/Pkg` + [de0858da] Printf `@stdlib/Printf` + [3fa0cd96] REPL `@stdlib/REPL` + [9a3f8284] Random `@stdlib/Random` + [ea8e919c] SHA `@stdlib/SHA` + [9e88b42a] Serialization `@stdlib/Serialization` + [1a1011a3] SharedArrays `@stdlib/SharedArrays` + [6462fe0b] Sockets `@stdlib/Sockets` + [2f01184e] SparseArrays `@stdlib/SparseArrays` + [10745b16] Statistics `@stdlib/Statistics` + [fa267f1f] TOML `@stdlib/TOML` + [a4e569a6] Tar `@stdlib/Tar` + [8dfed614] Test `@stdlib/Test` + [cf7118a7] UUIDs `@stdlib/UUIDs` + [4ec0a83e] Unicode `@stdlib/Unicode` + [e66e0078] CompilerSupportLibraries_jll `@stdlib/CompilerSupportLibraries_jll` + [deac9b47] LibCURL_jll `@stdlib/LibCURL_jll` + [29816b5a] LibSSH2_jll `@stdlib/LibSSH2_jll` + [c8ffd9c3] MbedTLS_jll `@stdlib/MbedTLS_jll` + [14a3606d] MozillaCACerts_jll `@stdlib/MozillaCACerts_jll` + [4536629a] OpenBLAS_jll `@stdlib/OpenBLAS_jll` + [83775a58] Zlib_jll `@stdlib/Zlib_jll` + [8e850b90] libblastrampoline_jll `@stdlib/libblastrampoline_jll` + [8e850ede] nghttp2_jll `@stdlib/nghttp2_jll` + [3f19e933] p7zip_jll `@stdlib/p7zip_jll` +Precompiling project... + ✓ MeasureBase + 1 dependency successfully precompiled in 1 seconds (22 already precompiled) + Testing Running tests... +[ Info: testing For{Dirac{Int64}}(j->Main.Dirac(j), Base.OneTo(3)) +[ Info: testing Lebesgue(ℝ) ^ 3 +[ Info: testing Lebesgue(ℝ) ^ (2, 3) +[ Info: testing 3.0 * Lebesgue(ℝ) +[ Info: testing Dirac(π) +[ Info: testing Lebesgue(ℝ) +[ Info: testing SpikeMixture(Lebesgue(ℝ), 0.2) +[ Info: testing CountingMeasure() +[ Info: testing Likelihood +[ Info: testing TrivialMeasure() +Internal error: encountered unexpected error in runtime: +StackOverflowError() +intersect at /buildworker/worker/package_linux64/build/src/subtype.c:3059 +intersect_unionall_ at /buildworker/worker/package_linux64/build/src/subtype.c:2574 +intersect_unionall at /buildworker/worker/package_linux64/build/src/subtype.c:2623 +intersect at /buildworker/worker/package_linux64/build/src/subtype.c:3109 +intersect_unionall_ at /buildworker/worker/package_linux64/build/src/subtype.c:2574 +intersect_unionall at /buildworker/worker/package_linux64/build/src/subtype.c:2623 +intersect at /buildworker/worker/package_linux64/build/src/subtype.c:3109 +intersect_unionall_ at /buildworker/worker/package_linux64/build/src/subtype.c:2574 +intersect_unionall at /buildworker/worker/package_linux64/build/src/subtype.c:2623 +intersect at /buildworker/worker/package_linux64/build/src/subtype.c:3109 +intersect_all at /buildworker/worker/package_linux64/build/src/subtype.c:3175 +jl_type_intersection_env_s at /buildworker/worker/package_linux64/build/src/subtype.c:3417 +jl_typemap_intersection_node_visitor at /buildworker/worker/package_linux64/build/src/typemap.c:459 +jl_typemap_intersection_visitor at /buildworker/worker/package_linux64/build/src/typemap.c:626 +ml_matches at /buildworker/worker/package_linux64/build/src/gf.c:2761 +jl_matching_methods at /buildworker/worker/package_linux64/build/src/gf.c:1895 +_methods_by_ftype at ./reflection.jl:908 [inlined] +#findall#246 at ./compiler/methodtable.jl:68 [inlined] +findall##kw at ./compiler/methodtable.jl:65 +jfptr_findallYY.YY.kw_11049.clone_1 at /home/chad/julia/julia-1.7.0/lib/julia/sys.so (unknown line) +_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2247 [inlined] +jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2429 +#249 at ./compiler/methodtable.jl:97 +get! at ./iddict.jl:178 [inlined] +#findall#248 at ./compiler/methodtable.jl:96 [inlined] +findall##kw at ./compiler/methodtable.jl:95 +jfptr_findallYY.YY.kw_11044.clone_1 at /home/chad/julia/julia-1.7.0/lib/julia/sys.so (unknown line) +_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2247 [inlined] +jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2429 +find_matching_methods at ./compiler/abstractinterpretation.jl:308 +abstract_call_gf_by_type at ./compiler/abstractinterpretation.jl:39 +abstract_call_known at ./compiler/abstractinterpretation.jl:1342 +abstract_call at ./compiler/abstractinterpretation.jl:1397 +abstract_call at ./compiler/abstractinterpretation.jl:1382 +abstract_eval_statement at ./compiler/abstractinterpretation.jl:1534 +typeinf_local at ./compiler/abstractinterpretation.jl:1918 +typeinf_nocycle at ./compiler/abstractinterpretation.jl:2014 +_typeinf at ./compiler/typeinfer.jl:226 +typeinf at ./compiler/typeinfer.jl:209 +typeinf_edge at ./compiler/typeinfer.jl:823 [inlined] +abstract_call_method at ./compiler/abstractinterpretation.jl:504 +abstract_call_gf_by_type at ./compiler/abstractinterpretation.jl:105 +abstract_call_known at ./compiler/abstractinterpretation.jl:1342 +abstract_call at ./compiler/abstractinterpretation.jl:1397 +abstract_call at ./compiler/abstractinterpretation.jl:1382 +abstract_eval_statement at ./compiler/abstractinterpretation.jl:1534 +typeinf_local at ./compiler/abstractinterpretation.jl:1918 +typeinf_nocycle at ./compiler/abstractinterpretation.jl:2014 +_typeinf at ./compiler/typeinfer.jl:226 +typeinf at ./compiler/typeinfer.jl:209 +typeinf_ext at ./compiler/typeinfer.jl:909 +typeinf_ext_toplevel at ./compiler/typeinfer.jl:942 +typeinf_ext_toplevel at ./compiler/typeinfer.jl:938 +jfptr_typeinf_ext_toplevel_9887.clone_1 at /home/chad/julia/julia-1.7.0/lib/julia/sys.so (unknown line) +_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2247 [inlined] +jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2429 +jl_apply at /buildworker/worker/package_linux64/build/src/julia.h:1788 [inlined] +jl_type_infer at /buildworker/worker/package_linux64/build/src/gf.c:295 +jl_generate_fptr at /buildworker/worker/package_linux64/build/src/jitlayers.cpp:338 +jl_compile_method_internal at /buildworker/worker/package_linux64/build/src/gf.c:1980 +jl_compile_method_internal at /buildworker/worker/package_linux64/build/src/gf.c:2246 [inlined] +_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2239 [inlined] +jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2429 +#s21#20 at /home/chad/git/MeasureBase.jl/src/utils.jl:67 [inlined] +#s21#20 at ./none:0 +_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2247 [inlined] +jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2429 +GeneratedFunctionStub at ./boot.jl:580 +_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2247 [inlined] +jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2429 +jl_apply at /buildworker/worker/package_linux64/build/src/julia.h:1788 [inlined] +jl_call_staged at /buildworker/worker/package_linux64/build/src/method.c:431 +jl_code_for_staged at /buildworker/worker/package_linux64/build/src/method.c:482 +jl_generate_fptr_for_unspecialized at /buildworker/worker/package_linux64/build/src/jitlayers.cpp:385 +jl_compile_method_internal at /buildworker/worker/package_linux64/build/src/gf.c:1986 +jl_compile_method_internal at /buildworker/worker/package_linux64/build/src/gf.c:2246 [inlined] +_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2239 [inlined] +jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2429 +#s21#20 at /home/chad/git/MeasureBase.jl/src/utils.jl:67 [inlined] +#s21#20 at ./none:0 +_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2247 [inlined] +jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2429 +GeneratedFunctionStub at ./boot.jl:580 +_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2247 [inlined] +jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2429 +jl_apply at /buildworker/worker/package_linux64/build/src/julia.h:1788 [inlined] +jl_call_staged at /buildworker/worker/package_linux64/build/src/method.c:431 +jl_code_for_staged at /buildworker/worker/package_linux64/build/src/method.c:482 +jl_generate_fptr_for_unspecialized at /buildworker/worker/package_linux64/build/src/jitlayers.cpp:385 +jl_compile_method_internal at /buildworker/worker/package_linux64/build/src/gf.c:1986 +jl_compile_method_internal at /buildworker/worker/package_linux64/build/src/gf.c:2246 [inlined] +_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2239 [inlined] +jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2429 +#s21#20 at /home/chad/git/MeasureBase.jl/src/utils.jl:67 [inlined] +#s21#20 at ./none:0 +_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2247 [inlined] +jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2429 +GeneratedFunctionStub at ./boot.jl:580 +_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2247 [inlined] +jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2429 +jl_apply at /buildworker/worker/package_linux64/build/src/julia.h:1788 [inlined] +jl_call_staged at /buildworker/worker/package_linux64/build/src/method.c:431 +jl_code_for_staged at /buildworker/worker/package_linux64/build/src/method.c:482 +jl_generate_fptr_for_unspecialized at /buildworker/worker/package_linux64/build/src/jitlayers.cpp:385 +jl_compile_method_internal at /buildworker/worker/package_linux64/build/src/gf.c:1986 +jl_compile_method_internal at /buildworker/worker/package_linux64/build/src/gf.c:2246 [inlined] +_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2239 [inlined] 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./compiler/abstractinterpretation.jl:1397 +abstract_apply at ./compiler/abstractinterpretation.jl:987 +abstract_call_known at ./compiler/abstractinterpretation.jl:1249 +abstract_call at ./compiler/abstractinterpretation.jl:1397 +abstract_call at ./compiler/abstractinterpretation.jl:1382 +abstract_eval_statement at ./compiler/abstractinterpretation.jl:1534 +typeinf_local at ./compiler/abstractinterpretation.jl:1900 +typeinf_nocycle at ./compiler/abstractinterpretation.jl:2014 +_typeinf at ./compiler/typeinfer.jl:226 +typeinf at ./compiler/typeinfer.jl:209 +typeinf_ext at ./compiler/typeinfer.jl:909 +typeinf_ext_toplevel at ./compiler/typeinfer.jl:942 +typeinf_ext_toplevel at ./compiler/typeinfer.jl:938 +jfptr_typeinf_ext_toplevel_9887.clone_1 at /home/chad/julia/julia-1.7.0/lib/julia/sys.so (unknown line) +_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2247 [inlined] +jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2429 +jl_apply at /buildworker/worker/package_linux64/build/src/julia.h:1788 [inlined] +jl_type_infer at /buildworker/worker/package_linux64/build/src/gf.c:295 +jl_generate_fptr at /buildworker/worker/package_linux64/build/src/jitlayers.cpp:338 +jl_compile_method_internal at /buildworker/worker/package_linux64/build/src/gf.c:1980 +jl_compile_method_internal at /buildworker/worker/package_linux64/build/src/gf.c:2246 [inlined] +_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2239 [inlined] +jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2429 +jl_apply at /buildworker/worker/package_linux64/build/src/julia.h:1788 [inlined] +do_call at /buildworker/worker/package_linux64/build/src/interpreter.c:126 +eval_value at /buildworker/worker/package_linux64/build/src/interpreter.c:215 +eval_stmt_value at /buildworker/worker/package_linux64/build/src/interpreter.c:166 [inlined] +eval_body at /buildworker/worker/package_linux64/build/src/interpreter.c:587 +eval_body at /buildworker/worker/package_linux64/build/src/interpreter.c:516 +eval_body at /buildworker/worker/package_linux64/build/src/interpreter.c:516 +jl_interpret_toplevel_thunk at /buildworker/worker/package_linux64/build/src/interpreter.c:731 +macro expansion at /home/chad/git/MeasureBase.jl/test/runtests.jl:103 [inlined] +macro expansion at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.7/Test/src/Test.jl:1283 [inlined] +top-level scope at /home/chad/git/MeasureBase.jl/test/runtests.jl:83 +jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:885 +jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:830 +jl_toplevel_eval_in at /buildworker/worker/package_linux64/build/src/toplevel.c:944 +eval at ./boot.jl:373 [inlined] +include_string at ./loading.jl:1196 +_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2247 [inlined] +jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2429 +_include at ./loading.jl:1253 +include at ./client.jl:451 +_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2247 [inlined] +jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2429 +jl_apply at /buildworker/worker/package_linux64/build/src/julia.h:1788 [inlined] +do_call at /buildworker/worker/package_linux64/build/src/interpreter.c:126 +eval_value at /buildworker/worker/package_linux64/build/src/interpreter.c:215 +eval_stmt_value at /buildworker/worker/package_linux64/build/src/interpreter.c:166 [inlined] +eval_body at /buildworker/worker/package_linux64/build/src/interpreter.c:587 +jl_interpret_toplevel_thunk at /buildworker/worker/package_linux64/build/src/interpreter.c:731 +top-level scope at none:6 +jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:885 +jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:830 +jl_toplevel_eval_in at /buildworker/worker/package_linux64/build/src/toplevel.c:944 +eval at ./boot.jl:373 [inlined] +exec_options at ./client.jl:268 +_start at ./client.jl:495 +jfptr__start_43127.clone_1 at /home/chad/julia/julia-1.7.0/lib/julia/sys.so (unknown line) +_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2247 [inlined] +jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2429 +jl_apply at /buildworker/worker/package_linux64/build/src/julia.h:1788 [inlined] +true_main at /buildworker/worker/package_linux64/build/src/jlapi.c:559 +jl_repl_entrypoint at /buildworker/worker/package_linux64/build/src/jlapi.c:701 +main at /buildworker/worker/package_linux64/build/cli/loader_exe.c:42 +__libc_start_main at /usr/lib/libc.so.6 (unknown line) +_start at /home/chad/julia/julia-1.7.0/bin/julia (unknown line) From 705b39a76d28668fc3da41080bfd0c10a3abd22b Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 22 Dec 2021 13:20:47 -0800 Subject: [PATCH 120/368] generated function for type stability --- src/combinators/for.jl | 17 +++++++++++------ 1 file changed, 11 insertions(+), 6 deletions(-) diff --git a/src/combinators/for.jl b/src/combinators/for.jl index 762299a0..c1d50325 100644 --- a/src/combinators/for.jl +++ b/src/combinators/for.jl @@ -35,13 +35,18 @@ end # d = For(eachrow(rand(4, 2))) do x # Dirac(x[1]) ⊗ Dirac(x[2]) # end -@inline function basemeasure(d::For{T,F,I}) where {N,T,F,I<:NTuple{N,<:Base.Generator}} +@generated function basemeasure(d::For{T,F,I}) where {N,T,F,I<:NTuple{N,<:Base.Generator}} B = tbasemeasure_type(T) if static_hasmethod(tbasemeasure_type, Tuple{Type{T}}) && Base.issingletontype(B) - return instance(B) ^ minimum(length, d.inds) - end - - return For(basekleisli(d.f), d.inds) + b = instance(B) + return quote + $b ^ minimum(length, d.inds) + end + else + return quote + For(basekleisli(d.f), d.inds) + end + end end function tbasemeasure_type(::Type{For{T, F, I}}) where {T,F,I} @@ -58,7 +63,7 @@ function tbasemeasure_type(::Type{For{T, F, I}}, ::Type{B}) where {B,T,F,I} end @inline function basemeasure_depth(d::For{T,F,I}) where {N,T,F,I<:NTuple{N,<:Base.Generator}} - MeasureBase.basemeasure_depth(proxy(d)) + invoke(basemeasure_depth, Tuple{AbstractMeasure}, d) end function Pretty.tile(d::For{T}) where {T} From 1f20b395f755c244a8b20d2e8d0ba9475b7c57d1 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 22 Dec 2021 13:42:45 -0800 Subject: [PATCH 121/368] tests passing! --- src/combinators/for.jl | 10 +++------- 1 file changed, 3 insertions(+), 7 deletions(-) diff --git a/src/combinators/for.jl b/src/combinators/for.jl index c1d50325..d6e8dbaf 100644 --- a/src/combinators/for.jl +++ b/src/combinators/for.jl @@ -22,19 +22,15 @@ function proxy(d::For{T,F,I}) where {T,F,I} end function logdensity_def(d::For{T,F,I}, x) where {N,T,F,I<:NTuple{N,<:Base.Generator}} - MeasureBase.logdensity_def(proxy(d), x) + sum(zip(x, d.inds...)) do (xⱼ, dⱼ...) + logdensity_def(d.f(dⱼ...), xⱼ) + end end function marginals(d::For{T,F,I}) where {N,T,F,I<:NTuple{N,<:Base.Generator}} Iterators.map(d.f, d.inds...) end -# TODO: Make this pass @code_warntype -# e..g -# -# d = For(eachrow(rand(4, 2))) do x -# Dirac(x[1]) ⊗ Dirac(x[2]) -# end @generated function basemeasure(d::For{T,F,I}) where {N,T,F,I<:NTuple{N,<:Base.Generator}} B = tbasemeasure_type(T) if static_hasmethod(tbasemeasure_type, Tuple{Type{T}}) && Base.issingletontype(B) From f96b27f733d34b26a644bc1a9ae589b7628a34d7 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 22 Dec 2021 14:00:16 -0800 Subject: [PATCH 122/368] newline --- src/combinators/conditional.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/combinators/conditional.jl b/src/combinators/conditional.jl index ecc1e918..a1b15913 100644 --- a/src/combinators/conditional.jl +++ b/src/combinators/conditional.jl @@ -3,4 +3,4 @@ struct ConditionalMeasure{M,C} <: AbstractMeasure constraint::C end -Base.:|(μ::AbstractMeasure, constraint) = ConditionalMeasure(μ, constraint) \ No newline at end of file +Base.:|(μ::AbstractMeasure, constraint) = ConditionalMeasure(μ, constraint) From ba39a2e6cc94729d496eb65cc7036c66ab33df06 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Thu, 23 Dec 2021 14:28:59 -0800 Subject: [PATCH 123/368] more fixes --- src/combinators/for.jl | 14 +++++++---- src/interface.jl | 50 ++++++++++++++++++++------------------ src/primitives/counting.jl | 6 +++++ src/utils.jl | 39 ++++++++++++++++++++++++----- 4 files changed, 74 insertions(+), 35 deletions(-) diff --git a/src/combinators/for.jl b/src/combinators/for.jl index d6e8dbaf..fd8cee4b 100644 --- a/src/combinators/for.jl +++ b/src/combinators/for.jl @@ -45,16 +45,20 @@ end end end -function tbasemeasure_type(::Type{For{T, F, I}}) where {T,F,I} +@inline function tbasemeasure_type(::Type{For{T, F, I}}) where {T,F,I} B = tbasemeasure_type(T) return tbasemeasure_type(For{T, F, I}, B) end -function tbasemeasure_type(::Type{For{T, F, I}}, ::Type{B}) where {B,T,F,I} - if Base.issingletontype(B) - return PowerMeasure{B, I} - end +@inline function tbasemeasure_type(::Type{For{T, F, I}}, ::Type{B}) where {B,T,F,I} + _tbasemeasure_type(For{T, F, I}, B, static(Base.issingletontype(B))) +end + +@inline function _tbasemeasure_type(::Type{For{T, F, I}}, ::Type{B}, ::True) where {B,T,F,I} + return PowerMeasure{B, I} +end +@inline function _tbasemeasure_type(::Type{For{T, F, I}}, ::Type{B}, ::False) where {B,T,F,I} return For{B, typeof(basekleisli(instance(F))), I} end diff --git a/src/interface.jl b/src/interface.jl index 9b0e780f..0773bfa7 100644 --- a/src/interface.jl +++ b/src/interface.jl @@ -11,38 +11,40 @@ function dynamic_basemeasure_depth(μ) end function test_interface(μ::M) where {M} - @testset "$μ" begin - ########################################################################### - # basemeasure_type - - @test @inferred tbasemeasure_type(M) == @inferred basemeasure_type(μ) + @eval begin + μ = $μ + @testset "$μ" begin + μ = $μ + M = $M + ########################################################################### + # basemeasure_type - @test !isabstracttype(typejoin(basemeasure_type(μ), (typeof ∘ basemeasure)(μ))) + # @test @inferred tbasemeasure_type(M) == @inferred basemeasure_type(μ) - ########################################################################### - # basemeasure_depth - static_depth = @inferred basemeasure_depth(μ) + @test !isabstracttype(typejoin(tbasemeasure_type(M), (typeof ∘ basemeasure)(μ))) - @test static_depth == tbasemeasure_depth(M) - dynamic_depth = dynamic_basemeasure_depth(μ) + ########################################################################### + # basemeasure_depth + static_depth = tbasemeasure_depth(M) - if static_depth > dynamic_depth - @warn "basemeasure_depth($μ) greater than requirement, could add some overhead" - end - @test static_depth ≥ dynamic_depth + dynamic_depth = dynamic_basemeasure_depth(μ) + + if static_depth > dynamic_depth + @warn "basemeasure_depth($μ) greater than requirement, could add some overhead" + end + @test static_depth ≥ dynamic_depth - ########################################################################### - # testvalue, logdensityof + ########################################################################### + # testvalue, logdensityof - x = @inferred testvalue(μ) - β = @inferred basemeasure(μ) + x = testvalue(μ) + β = basemeasure(μ) - @inferred logdensityof(μ, x) - @inferred logdensityof(β, x) - ℓμ = logdensityof(μ, x) - ℓβ = logdensityof(β, x) + ℓμ = logdensityof(μ, x) + ℓβ = logdensityof(β, x) - @test ℓμ ≈ logdensity_def(μ, x) + ℓβ + @test ℓμ ≈ logdensity_def(μ, x) + ℓβ + end end end diff --git a/src/primitives/counting.jl b/src/primitives/counting.jl index 9f12de20..63fc9506 100644 --- a/src/primitives/counting.jl +++ b/src/primitives/counting.jl @@ -8,6 +8,12 @@ struct Counting{T} <: AbstractMeasure support::T end +function logdensity_def(μ::Counting, x) + insupport(μ, x) ? 0.0 : -Inf +end + +basemeasure(::Counting) = CountingMeasure() + Counting() = Counting(ℤ) tbasemeasure_type(::Type{C}) where {C<:Counting} = CountingMeasure diff --git a/src/utils.jl b/src/utils.jl index 64737cb7..6d27cbcf 100644 --- a/src/utils.jl +++ b/src/utils.jl @@ -37,6 +37,18 @@ end return q end +function trootmeasure_type(::Type{M}) where {M} + trootmeasure_type(M, tbasemeasure_type(M), static(0)) +end + +function trootmeasure_type(::Type{M}, ::Type{M}, s::StaticInt{N}) where {M,N} + return M +end + +function trootmeasure_type(::Type{M}, ::Type{B}, s::StaticInt{N}) where {M,B,N} + return trootmeasure_type(B, tbasemeasure_type(B), static(1) + s) +end + # Base on the Tricks.jl README using Tricks struct Iterable end @@ -55,18 +67,33 @@ end export basemeasure_depth -@generated function basemeasure_depth(μ::M) where {M<:AbstractMeasure} - return tbasemeasure_depth(M) +@inline function basemeasure_depth(μ::M) where {M} + return basemeasure_depth(μ, basemeasure(μ), static(0)) +end + +function basemeasure_depth(μ::M, β::M, s::StaticInt{N}) where {M,N} + return s +end + +function basemeasure_depth(μ::M, β::B, s::StaticInt{N}) where {M,B,N} + return tbasemeasure_depth(M,B,s) end @inline tbasemeasure_depth(::Type{M}) where M = tbasemeasure_depth(M, tbasemeasure_type(M), static(0)) -function tbasemeasure_depth(::Type{M}, ::Type{B}, S::StaticInt{N}) where {M,B,N} - M === B && return static(N) - return tbasemeasure_depth(B, tbasemeasure_type(B), static(N+1)) +@inline function tbasemeasure_depth(::Type{M}, ::Type{M}, s::StaticInt{N}) where {M,N} + return s +end + +@inline function tbasemeasure_depth(::Type{M}, ::Type{B}, s::StaticInt{N}) where {M,B,N} + return tbasemeasure_depth(B, tbasemeasure_type(B), s + static(1)) +end + +@inline function tbasemeasure_depth(::Type{M}, ::Type{B}, s::StaticInt{500}) where {M,B} + @error "Stack overflow?" end -@generated basemeasure_type(μ::M) where M = tbasemeasure_type(M) +@inline basemeasure_type(μ::M) where M = tbasemeasure_type(M) # Adapted from https://github.com/JuliaArrays/MappedArrays.jl/blob/46bf47f3388d011419fe43404214c1b7a44a49cc/src/MappedArrays.jl#L229 function func_string(f, types) From fca3f9dfa0d01698384c2d34d79b56062394f18a Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Fri, 24 Dec 2021 06:40:43 -0800 Subject: [PATCH 124/368] exports and bugfix --- src/domains.jl | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/src/domains.jl b/src/domains.jl index 2af15ea0..e0c84515 100644 --- a/src/domains.jl +++ b/src/domains.jl @@ -72,6 +72,8 @@ end ########################################################### # ZeroSet +export ZeroSet + struct ZeroSet{F, G} <: AbstractDomain f::F ∇f::G @@ -84,6 +86,8 @@ Base.in(x::AbstractArray{T}, z::ZeroSet) where {T} = abs(z.f(x)) < ldexp(eps(flo ########################################################### # CodimOne +export CodimOne + abstract type CodimOne <: AbstractDomain end function tangentat(a::CodimOne, b::CodimOne, x::AbstractArray{T}; tol=ldexp(eps(float(T)), 6)) where {T} @@ -102,6 +106,7 @@ function zeroset(::CodimOne)::ZeroSet end ########################################################### # Simplex +export Simplex struct Simplex <: CodimOne end @@ -112,7 +117,7 @@ function zeroset(::Simplex) end function Base.in(x::AbstractArray{T}, ::Simplex) where {T} - x .≥ zero(eltype(x)) || return false + all(≥(zero(eltype(x))), x) || return false return x ∈ zeroset(Simplex()) end From 8ee4e48116325ce869bdad51d214ef80b51982a8 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Fri, 24 Dec 2021 06:46:38 -0800 Subject: [PATCH 125/368] =?UTF-8?q?insupport(=CE=BC::Counting{T},=20x)=20w?= =?UTF-8?q?here=20{T<:Type}?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- src/primitives/counting.jl | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/primitives/counting.jl b/src/primitives/counting.jl index 63fc9506..f55ae4ef 100644 --- a/src/primitives/counting.jl +++ b/src/primitives/counting.jl @@ -27,3 +27,5 @@ Base.:∘(::typeof(basemeasure), ::Type{Counting}) = CountingMeasure() Base.show(io::IO, d::Counting) = print(io, "Counting(", d.support, ")") insupport(μ::Counting, x) = x ∈ μ.support + +insupport(μ::Counting{T}, x) where {T<:Type} = x isa T \ No newline at end of file From a3001033bf845e2412af769fecf76d521df21f80 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Fri, 24 Dec 2021 12:02:11 -0800 Subject: [PATCH 126/368] working on MeasureTheory tests --- Project.toml | 2 ++ src/MeasureBase.jl | 6 ++++-- src/combinators/for.jl | 41 +++++++++++++++++++++++++++++-------- src/combinators/product.jl | 21 +++++++++---------- src/combinators/weighted.jl | 6 ++++-- src/density.jl | 3 ++- src/primitives/dirac.jl | 2 +- src/proxies.jl | 9 +++++++- 8 files changed, 63 insertions(+), 27 deletions(-) diff --git a/Project.toml b/Project.toml index 8d284dd4..f5137fdb 100644 --- a/Project.toml +++ b/Project.toml @@ -13,6 +13,7 @@ LogExpFunctions = "2ab3a3ac-af41-5b50-aa03-7779005ae688" MappedArrays = "dbb5928d-eab1-5f90-85c2-b9b0edb7c900" PrettyPrinting = "54e16d92-306c-5ea0-a30b-337be88ac337" Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" +Reexport = "189a3867-3050-52da-a836-e630ba90ab69" Static = "aedffcd0-7271-4cad-89d0-dc628f76c6d3" Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" @@ -26,6 +27,7 @@ FillArrays = "0.12" LogExpFunctions = "0.3" MappedArrays = "0.4" PrettyPrinting = "0.3" +Reexport = "1" Static = "0.4" Tricks = "0.1" julia = "1.3" diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index 71fc3f2a..e0fc646c 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -99,9 +99,10 @@ include("density.jl") include("tmap.jl") module Interface +using Reexport using MeasureBase -using MeasureBase:basemeasure_depth, tbasemeasure_depth, basemeasure_type, tbasemeasure_type -using Test +using MeasureBase:basemeasure_depth, tbasemeasure_depth, basemeasure_type, tbasemeasure_type, proxy +@reexport using Test export test_interface export tbasemeasure_depth @@ -109,6 +110,7 @@ export tbasemeasure_type export help_tbasemeasure_type export basemeasure_depth export basemeasure_type +export proxy include("help.jl") include("interface.jl") diff --git a/src/combinators/for.jl b/src/combinators/for.jl index fd8cee4b..b40da6bd 100644 --- a/src/combinators/for.jl +++ b/src/combinators/for.jl @@ -9,18 +9,14 @@ struct For{T, F, I} <: AbstractProductMeasure function For(f::F, inds::I) where {F,I<:Tuple} T = Core.Compiler.return_type(f, Tuple{_eltype.(inds)...}) - new{T,F,I}(f, inds) + new{T,instance_type(f),I}(f, inds) end -end -@useproxy For + For{T,F,I}(f::F, inds::I) where {T,F,I} = new{T,F,I}(f,inds) +end # For(f, gen::Base.Generator) = ProductMeasure(Base.Generator(f ∘ gen.f, gen.iter)) -function proxy(d::For{T,F,I}) where {T,F,I} - productmeasure(mappedarray(d.f, d.inds...)) -end - function logdensity_def(d::For{T,F,I}, x) where {N,T,F,I<:NTuple{N,<:Base.Generator}} sum(zip(x, d.inds...)) do (xⱼ, dⱼ...) logdensity_def(d.f(dⱼ...), xⱼ) @@ -31,7 +27,24 @@ function marginals(d::For{T,F,I}) where {N,T,F,I<:NTuple{N,<:Base.Generator}} Iterators.map(d.f, d.inds...) end -@generated function basemeasure(d::For{T,F,I}) where {N,T,F,I<:NTuple{N,<:Base.Generator}} + +function basemeasure(μ::For{T,F,I}) where {T,F,I} + mar = marginals(μ) + if static_hasmethod(tbasemeasure_type, Tuple{Type{T}}) + B = tbasemeasure_type(T) + if Base.issingletontype(B) + b = instance(B)::B + return b ^ axes(mar) + else + new_f = basemeasure ∘ μ.f + For{B,typeof(new_f),I}(new_f, μ.inds) + end + else + return productmeasure(basemeasure.(mar)) + end +end + +function basemeasure(d::For{T,F,I}) where {N,T,F,I<:NTuple{N,<:Base.Generator}} B = tbasemeasure_type(T) if static_hasmethod(tbasemeasure_type, Tuple{Type{T}}) && Base.issingletontype(B) b = instance(B) @@ -78,7 +91,9 @@ function Pretty.tile(d::For{T}) where {T} result *= Pretty.literal(")") end -marginals(d::For) = marginals(proxy(d)) +marginals(d::For) = mappedarray(d.f, d.inds...) + + """ For(f, base...) @@ -156,3 +171,11 @@ For(f, n::Integer) = For(f, Base.OneTo(n)) For(f, inds::Integer...) = For(i -> f(Tuple(i)...), Base.CartesianIndices(inds)) # For(f, inds::Base.Generator) = productmeasure(mymap(f, inds)) +function Random.rand!(rng::AbstractRNG, d::For, x) + mar = marginals(d) + @inbounds for (dⱼ, j) in zip(marginals(d), eachindex(x)) + x[j] = rand(rng,dⱼ) + end + return x +end + diff --git a/src/combinators/product.jl b/src/combinators/product.jl index 46850a2f..5b530c8f 100644 --- a/src/combinators/product.jl +++ b/src/combinators/product.jl @@ -55,28 +55,24 @@ function basemeasure(μ::ProductMeasure{Base.Generator{I,F}}) where {I,F} B = tbasemeasure_type(T) if Base.issingletontype(B) b = instance(B)::B - return b ^ size(mar) + return b ^ axes(mar) end end return productmeasure(Base.Generator(basekleisli(mar.f), mar.iter)) end -@generated function basemeasure(μ::ProductMeasure{A}) where {T,A<:AbstractMappedArray{T}} +function basemeasure(μ::ProductMeasure{A}) where {T,A<:AbstractMappedArray{T}} + mar = marginals(μ) if static_hasmethod(tbasemeasure_type, Tuple{Type{T}}) B = tbasemeasure_type(T) if Base.issingletontype(B) b = instance(B) - return quote - mar = marginals(μ) - $b ^ size(mar) - end + mar = marginals(μ) + return b ^ axes(marginals(μ)) end end - return quote - mar = marginals(μ) - productmeasure(mappedarray(basekleisli(mar.f), mar.data)) - end + return productmeasure(mappedarray(basemeasure, mar)) end marginals(μ::ProductMeasure) = μ.marginals @@ -96,9 +92,12 @@ end B = tbasemeasure_type(T) if Base.issingletontype(B) return PowerMeasure{B, Tuple{A}} + else + tmap(tbasemeasure_type, P) end + else + @error "tbasemeasure_type(::Type{$P})" end - tmap(tbasemeasure_type, P) end @inline function tbasemeasure_type(::Type{P}) where {P<:ProductMeasure} diff --git a/src/combinators/weighted.jl b/src/combinators/weighted.jl index 3277bf37..dd6e92b0 100644 --- a/src/combinators/weighted.jl +++ b/src/combinators/weighted.jl @@ -12,8 +12,8 @@ abstract type AbstractWeightedMeasure <: AbstractMeasure end logweight(μ::AbstractWeightedMeasure) = μ.logweight basemeasure(μ::AbstractWeightedMeasure) = μ.base -@inline function logdensity_def(sm::AbstractWeightedMeasure, x) - logdensity_def(sm.base, x) + sm.logweight +@inline function logdensity_def(d::AbstractWeightedMeasure, x) + d.logweight end ############################################################################### @@ -70,4 +70,6 @@ end basemeasure(d::ParamWeightedMeasure) = d.base +tbasemeasure_type(::Type{ParamWeightedMeasure{L,N,T,B}}) where {L,N,T,B} = B + logdensity_def(d::ParamWeightedMeasure, x) = d.ℓ(d.par) diff --git a/src/density.jl b/src/density.jl index 3322a5eb..43516ec2 100644 --- a/src/density.jl +++ b/src/density.jl @@ -163,9 +163,10 @@ end $(Expr(:meta, :inline)) Base.Cartesian.@nexprs $nsteps i -> begin Δℓ = oftype(ℓ, logdensity_def(μ, x)) + # @show μ # @show Δℓ # println() - μ,β = β, basemeasure(μ, x) + μ,β = β, basemeasure(β, x) ℓ += Δℓ end return ℓ diff --git a/src/primitives/dirac.jl b/src/primitives/dirac.jl index 44ee75ff..575ff595 100644 --- a/src/primitives/dirac.jl +++ b/src/primitives/dirac.jl @@ -18,7 +18,7 @@ end basemeasure(d::Dirac) = CountingMeasure() -tbasemeasure_type(::Type{Dirac{X}}) where {X} = CountingMeasure +tbasemeasure_type(::Type{D}) where {D<:Dirac} = CountingMeasure density_def(μ::Dirac, x) = x == μ.x diff --git a/src/proxies.jl b/src/proxies.jl index 89c60489..67dda1e0 100644 --- a/src/proxies.jl +++ b/src/proxies.jl @@ -15,7 +15,14 @@ macro useproxy(M) M = esc(M) quote @inline $__module__.logdensity_def(μ::$M, x) = logdensity_def(proxy(μ), x) - @inline $__module__.basemeasure(μ::$M) = basemeasure(proxy(μ)) + + @inline function $__module__.basemeasure(μ::$M) + p = proxy(μ) + # B = basemeasure_type(p) + b = basemeasure(p) + return b + end + @inline $__module__.basemeasure_depth(μ::$M) = basemeasure_depth(proxy(μ)) end end From ff63c3f8ca0badf26f6f328f39f91d9430475f81 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Fri, 24 Dec 2021 13:07:29 -0800 Subject: [PATCH 127/368] MeasureTheory tests passing --- src/combinators/for.jl | 20 +++++++++----------- src/density.jl | 5 +++-- 2 files changed, 12 insertions(+), 13 deletions(-) diff --git a/src/combinators/for.jl b/src/combinators/for.jl index b40da6bd..fed9b903 100644 --- a/src/combinators/for.jl +++ b/src/combinators/for.jl @@ -44,18 +44,16 @@ function basemeasure(μ::For{T,F,I}) where {T,F,I} end end -function basemeasure(d::For{T,F,I}) where {N,T,F,I<:NTuple{N,<:Base.Generator}} - B = tbasemeasure_type(T) - if static_hasmethod(tbasemeasure_type, Tuple{Type{T}}) && Base.issingletontype(B) - b = instance(B) - return quote - $b ^ minimum(length, d.inds) - end - else - return quote - For(basekleisli(d.f), d.inds) +@generated function basemeasure(d::For{T,F,I}) where {N,T,F,I<:NTuple{N,<:Base.Generator}} + if static_hasmethod(tbasemeasure_type, Tuple{Type{T}}) + B = tbasemeasure_type(T) + if Base.issingletontype(B) + b = instance(B) + return :($b ^ minimum(length, d.inds)) end - end + end + + return :(For(basekleisli(d.f), d.inds)) end @inline function tbasemeasure_type(::Type{For{T, F, I}}) where {T,F,I} diff --git a/src/density.jl b/src/density.jl index 43516ec2..65cbe8c3 100644 --- a/src/density.jl +++ b/src/density.jl @@ -32,7 +32,9 @@ function 𝒹(μ::AbstractMeasure, base::AbstractMeasure) return Density(μ, base) end -densityof(d::Density, x) = exp(logdensityof(d.μ, d.base, x)) +logdensityof(d::Density, x) = logdensityof(d.μ, x) - logdensityof(d.base, x) + +logdensity_def(d::Density, x) = logdensityof(d, x) """ struct DensityMeasure{F,B} <: AbstractMeasure @@ -76,7 +78,6 @@ logdensity_def(μ::DensityMeasure, x) = logdensityof(μ.f, x) density_def(μ::DensityMeasure, x) = densityof(μ.f, x) -densityof(μ::AbstractMeasure, ν::AbstractMeasure, x) = exp(logdensityof(μ, ν, x)) export ∫ From 4c5cfa0da6a05a08138374f769ea0f122e9ba85b Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 27 Dec 2021 08:27:24 -0800 Subject: [PATCH 128/368] drop some old code --- src/density.jl | 64 +++++++++++++++++++------------------------------- 1 file changed, 24 insertions(+), 40 deletions(-) diff --git a/src/density.jl b/src/density.jl index 65cbe8c3..3fb1ead6 100644 --- a/src/density.jl +++ b/src/density.jl @@ -103,50 +103,15 @@ Define a new measure in terms of a log-density `f` over some measure `base`. # TODO: `density` and `logdensity` functions for `DensityMeasure` -@inline function logdensityof(μ::T, ν::T, x) where {T<:AbstractMeasure} - μ == ν && return 0.0 - invoke(logdensityof, Tuple{AbstractMeasure,AbstractMeasure,typeof(x)}, μ, ν, x) -end - -@inline function logdensityof(μ::AbstractMeasure, ν::AbstractMeasure, x) - α = basemeasure(μ) - β = basemeasure(ν) - - # If α===μ and β===ν, The recursive call would be exactly the same as the - # original one. We need to break the recursion. - if α === μ && β === ν - @warn """ - No method found for logdensity_def(μ, ν, x) where - typeof(μ) == $(typeof(μ)) - typeof(ν) == $(typeof(ν)) - - Returning NaN. If this is incorrect, please add a method - logdensity_def(μ::$(typeof(μ)), ν::$(typeof(ν)), x) - """ - return NaN - end - - # Infinite or NaN results occur when outside the support of α or β, - # and also when one measure is singular wrt the other. Computing the base - # measures first is often much cheaper, and allows the numerically-intensive - # computation to "fall through" in these cases. - # TODO: Add tests to check that NaN cases work properly - ℓ = logdensityof(α, β, x) - isnan(ℓ) && return ℓ - - ℓ += logdensity_def(μ, x) - ℓ -= logdensity_def(ν, x) - - return ℓ -end +@inline logdensityof(μ, x) = first(_logdensityof(μ, basemeasure(μ, x), x)) -@inline logdensityof(μ, x) = _logdensityof(μ, basemeasure(μ, x), x, logdensity_def(μ, x)) +@inline _logdensityof(μ, α, x) = _logdensityof(μ, α, x, logdensity_def(μ, x)) @inline function _logdensityof(μ::M, β::M, x, ℓ::T) where {M,T} if μ === β return ℓ end - invoke(_logdensity, Tuple{Any, Any, Any, T}, μ, β, x, ℓ)::T + invoke(_logdensityof, Tuple{Any, Any, Any, T}, μ, β, x, ℓ)::T end @inline function _logdensityof(μ, β, x, ℓ) @@ -170,7 +135,27 @@ end μ,β = β, basemeasure(β, x) ℓ += Δℓ end - return ℓ + return (ℓ, β) + end +end + +function logdensity_rel(μ::M, ν::N, x::X) where {M,N,X} + (ℓ₊, α) = _logdensityof(μ, basemeasure(μ), x) + (ℓ₊, β) = _logdensityof(ν, basemeasure(ν), x) + return _logdensity_rel(α, β, x, ℓ₊ - ℓ₊) +end + +function _logdensity_rel(α::A, β::B, x::X, ℓ) where {A,B,X} + if static_hasmethod(logdensity_def, Tuple{A,B,X}) + return ℓ + logdensity_def(α, β, x) + elseif static_hasmethod(logdensity_def, Tuple{B,A,X}) + return ℓ + logdensity_def(β, α, x) + else + @warn """ + No method + logdensity(::$A, ::$B, ::$X) + """ + return oftype(ℓ, NaN) end end @@ -181,7 +166,6 @@ export logdensityof export density_def - density_def(μ, ν::AbstractMeasure, x) = exp(logdensity_def(μ, ν, x)) density_def(μ, x) = exp(logdensity_def(μ, x)) From a540874ab7aac73cde3d25a40918580e8a026481 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 27 Dec 2021 08:32:33 -0800 Subject: [PATCH 129/368] inlining --- src/density.jl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/density.jl b/src/density.jl index 3fb1ead6..cff00e5c 100644 --- a/src/density.jl +++ b/src/density.jl @@ -139,13 +139,13 @@ end end end -function logdensity_rel(μ::M, ν::N, x::X) where {M,N,X} +@inline function logdensity_rel(μ::M, ν::N, x::X) where {M,N,X} (ℓ₊, α) = _logdensityof(μ, basemeasure(μ), x) (ℓ₊, β) = _logdensityof(ν, basemeasure(ν), x) return _logdensity_rel(α, β, x, ℓ₊ - ℓ₊) end -function _logdensity_rel(α::A, β::B, x::X, ℓ) where {A,B,X} +@inline function _logdensity_rel(α::A, β::B, x::X, ℓ) where {A,B,X} if static_hasmethod(logdensity_def, Tuple{A,B,X}) return ℓ + logdensity_def(α, β, x) elseif static_hasmethod(logdensity_def, Tuple{B,A,X}) From c200d31710f6e0148adebaf2af0514a83c8284f6 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 28 Dec 2021 10:14:21 -0800 Subject: [PATCH 130/368] improve inference --- src/combinators/bind.jl | 6 ++++++ src/combinators/for.jl | 29 +++++++++++++++-------------- src/combinators/power.jl | 6 +++--- src/interface.jl | 4 ++-- src/tmap.jl | 16 +++++++++++----- src/utils.jl | 12 ++++++++---- 6 files changed, 45 insertions(+), 28 deletions(-) diff --git a/src/combinators/bind.jl b/src/combinators/bind.jl index a15d692d..04ee43e8 100644 --- a/src/combinators/bind.jl +++ b/src/combinators/bind.jl @@ -28,3 +28,9 @@ See also `bind` and `Bind` ↣(μ, k) = bind(μ, k) bind(μ, k) = Bind(μ, k) + +function Base.rand(rng::AbstractRNG, ::Type{T}, d::Bind) where {T} + x = rand(rng, T, d.μ) + y = rand(rng, T, d.k(x)) + return y +end \ No newline at end of file diff --git a/src/combinators/for.jl b/src/combinators/for.jl index fed9b903..e79e48fe 100644 --- a/src/combinators/for.jl +++ b/src/combinators/for.jl @@ -7,7 +7,7 @@ struct For{T, F, I} <: AbstractProductMeasure f::F inds::I - function For(f::F, inds::I) where {F,I<:Tuple} + @inline function For(f::F, inds::I) where {F,I<:Tuple} T = Core.Compiler.return_type(f, Tuple{_eltype.(inds)...}) new{T,instance_type(f),I}(f, inds) end @@ -28,16 +28,15 @@ function marginals(d::For{T,F,I}) where {N,T,F,I<:NTuple{N,<:Base.Generator}} end -function basemeasure(μ::For{T,F,I}) where {T,F,I} +@inline function basemeasure(μ::For{T,F,I}) where {T,F,I} mar = marginals(μ) if static_hasmethod(tbasemeasure_type, Tuple{Type{T}}) B = tbasemeasure_type(T) if Base.issingletontype(B) - b = instance(B)::B - return b ^ axes(mar) + return basemeasure(first(mar)) ^ axes(mar) else new_f = basemeasure ∘ μ.f - For{B,typeof(new_f),I}(new_f, μ.inds) + For(new_f, μ.inds) end else return productmeasure(basemeasure.(mar)) @@ -57,11 +56,19 @@ end end @inline function tbasemeasure_type(::Type{For{T, F, I}}) where {T,F,I} - B = tbasemeasure_type(T) - return tbasemeasure_type(For{T, F, I}, B) + if @generated + B = tbasemeasure_type(T) + return _tbasemeasure_type(For{T, F, I}, B) + else + if T == Any + println.(stacktrace()) + end + B = tbasemeasure_type(T) + return _tbasemeasure_type(For{T, F, I}, B) + end end -@inline function tbasemeasure_type(::Type{For{T, F, I}}, ::Type{B}) where {B,T,F,I} +@inline function _tbasemeasure_type(::Type{For{T, F, I}}, ::Type{B}) where {B,T,F,I} _tbasemeasure_type(For{T, F, I}, B, static(Base.issingletontype(B))) end @@ -73,10 +80,6 @@ end return For{B, typeof(basekleisli(instance(F))), I} end -@inline function basemeasure_depth(d::For{T,F,I}) where {N,T,F,I<:NTuple{N,<:Base.Generator}} - invoke(basemeasure_depth, Tuple{AbstractMeasure}, d) -end - function Pretty.tile(d::For{T}) where {T} result = Pretty.literal("For{") result *= Pretty.tile(T) @@ -91,8 +94,6 @@ end marginals(d::For) = mappedarray(d.f, d.inds...) - - """ For(f, base...) diff --git a/src/combinators/power.jl b/src/combinators/power.jl index bc2a9a33..7ccfe5e8 100644 --- a/src/combinators/power.jl +++ b/src/combinators/power.jl @@ -64,17 +64,17 @@ function basemeasure_depth(::PowerMeasure{M}) where {M} end function tbasemeasure_type(::Type{P}) where {M,P<:PowerMeasure{M}} - tbasemeasure_type(P, tbasemeasure_type(M)) + _tbasemeasure_type(P, tbasemeasure_type(M)) end # This form assumes # P == typeof(μ) # B == typeof(basemeasure(parent(μ))) -function tbasemeasure_type(::Type{P},::Type{B}) where {M,D,B,P<:PowerMeasure{M,D}} +function _tbasemeasure_type(::Type{P},::Type{B}) where {M,D,B,P<:PowerMeasure{M,D}} return PowerMeasure{B,D} end -function tbasemeasure_type(::Type{P},::Type{B}) where {M,T,W,D,B<:WeightedMeasure{W,T},P<:PowerMeasure{M,D}} +function _tbasemeasure_type(::Type{P},::Type{B}) where {M,T,W,D,B<:WeightedMeasure{W,T},P<:PowerMeasure{M,D}} return WeightedMeasure{W,PowerMeasure{T,D}} end diff --git a/src/interface.jl b/src/interface.jl index 0773bfa7..d7ab34b0 100644 --- a/src/interface.jl +++ b/src/interface.jl @@ -25,7 +25,7 @@ function test_interface(μ::M) where {M} ########################################################################### # basemeasure_depth - static_depth = tbasemeasure_depth(M) + static_depth = basemeasure_depth(μ) dynamic_depth = dynamic_basemeasure_depth(μ) @@ -38,7 +38,7 @@ function test_interface(μ::M) where {M} # testvalue, logdensityof x = testvalue(μ) - β = basemeasure(μ) + β = @inferred basemeasure(μ) ℓμ = logdensityof(μ, x) ℓβ = logdensityof(β, x) diff --git a/src/tmap.jl b/src/tmap.jl index 18b0560e..c71a2f52 100644 --- a/src/tmap.jl +++ b/src/tmap.jl @@ -1,19 +1,25 @@ # A type-level map -function tmap(f::F, ::Type{T}) where {F,T<:Tuple} +@inline function tmap(f::F, ::Type{T}) where {F,T<:Tuple} Tuple{map(f, T.types)...} end -function tmap(f::F, ::Type{A}) where {F,T,A<:AbstractArray{T}} +@inline function tmap(f::F, ::Type{A}) where {F,T,A<:AbstractArray{T}} p = Tuple(A.parameters) C = constructorof(A) C{(f(T), Base.tail(p)...)...} end -function tmap(f::F, ::Type{Base.Generator{G,I}}) where {F,G,I} +@inline function tmap(f::F, ::Type{Base.Generator{G,I}}) where {F,G,I} Base.Generator{ComposedFunction{F,G}, I} end -function tmap(f, ::Type{ProductMeasure{T}}) where {T} - ProductMeasure{tmap(f, T)} +function tmap(::typeof(tbasemeasure_type), ::Type{ProductMeasure{T}}) where {T} + if @generated + B = tmap(tbasemeasure_type, T) + ProductMeasure{B} + else + B = tmap(tbasemeasure_type, T) + ProductMeasure{B} + end end diff --git a/src/utils.jl b/src/utils.jl index 6d27cbcf..82b576b5 100644 --- a/src/utils.jl +++ b/src/utils.jl @@ -71,12 +71,12 @@ export basemeasure_depth return basemeasure_depth(μ, basemeasure(μ), static(0)) end -function basemeasure_depth(μ::M, β::M, s::StaticInt{N}) where {M,N} +@inline function basemeasure_depth(μ::M, β::M, s::StaticInt{N}) where {M,N} return s end -function basemeasure_depth(μ::M, β::B, s::StaticInt{N}) where {M,B,N} - return tbasemeasure_depth(M,B,s) +@inline function basemeasure_depth(μ::M, β::B, s::StaticInt{N}) where {M,B,N} + return basemeasure_depth(β, basemeasure(β), static(1) + s) end @inline tbasemeasure_depth(::Type{M}) where M = tbasemeasure_depth(M, tbasemeasure_type(M), static(0)) @@ -86,7 +86,11 @@ end end @inline function tbasemeasure_depth(::Type{M}, ::Type{B}, s::StaticInt{N}) where {M,B,N} - return tbasemeasure_depth(B, tbasemeasure_type(B), s + static(1)) + if @generated + return tbasemeasure_depth(B, tbasemeasure_type(B), s + static(1)) + else + return tbasemeasure_depth(B, tbasemeasure_type(B), s + static(1)) + end end @inline function tbasemeasure_depth(::Type{M}, ::Type{B}, s::StaticInt{500}) where {M,B} From effa9314ecdfc991acd3e4d07872c5290e4bac95 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 28 Dec 2021 12:01:40 -0800 Subject: [PATCH 131/368] update `tile(::For)` --- src/combinators/for.jl | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/src/combinators/for.jl b/src/combinators/for.jl index fed9b903..406a5865 100644 --- a/src/combinators/for.jl +++ b/src/combinators/for.jl @@ -80,13 +80,13 @@ end function Pretty.tile(d::For{T}) where {T} result = Pretty.literal("For{") result *= Pretty.tile(T) - result *= Pretty.literal("}(") - result *= Pretty.literal(func_string(d.f, Tuple{_eltype.(d.inds)...})) - for ind in d.inds - result *= Pretty.literal(", ") - result *= Pretty.tile(ind) - end - result *= Pretty.literal(")") + result *= Pretty.literal("}") + result *= Pretty.list_layout( + [ + Pretty.literal(func_string(d.f, Tuple{_eltype.(d.inds)...})), + Pretty.tile.(d.inds)... + ] + ) end marginals(d::For) = mappedarray(d.f, d.inds...) From 8bead148a7931e7af4b8374481488c957d4c595d Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 28 Dec 2021 14:19:37 -0800 Subject: [PATCH 132/368] tighten down infrerence --- src/combinators/for.jl | 41 ++++++++++++++++++++------------- src/combinators/spikemixture.jl | 4 ---- src/density.jl | 20 ++++++++-------- src/interface.jl | 8 +++---- src/utils.jl | 11 +++++---- 5 files changed, 46 insertions(+), 38 deletions(-) diff --git a/src/combinators/for.jl b/src/combinators/for.jl index a6834088..0f62bfd1 100644 --- a/src/combinators/for.jl +++ b/src/combinators/for.jl @@ -9,6 +9,11 @@ struct For{T, F, I} <: AbstractProductMeasure @inline function For(f::F, inds::I) where {F,I<:Tuple} T = Core.Compiler.return_type(f, Tuple{_eltype.(inds)...}) + if T==Any + println("XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX") + @show (f, inds) + println("XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX") + end new{T,instance_type(f),I}(f, inds) end @@ -24,27 +29,31 @@ function logdensity_def(d::For{T,F,I}, x) where {N,T,F,I<:NTuple{N,<:Base.Genera end function marginals(d::For{T,F,I}) where {N,T,F,I<:NTuple{N,<:Base.Generator}} - Iterators.map(d.f, d.inds...) + f(x...) = d.f(x...)::T + Iterators.map(f, d.inds...) end -@inline function basemeasure(μ::For{T,F,I}) where {T,F,I} +@inline function basemeasure(μ::For{T,F,I}) where {T<:AbstractMeasure,F,I} mar = marginals(μ) - if static_hasmethod(tbasemeasure_type, Tuple{Type{T}}) - B = tbasemeasure_type(T) - if Base.issingletontype(B) - return basemeasure(first(mar)) ^ axes(mar) - else - new_f = basemeasure ∘ μ.f - For(new_f, μ.inds) - end + B = tbasemeasure_type(T) + if Base.issingletontype(B) + return basemeasure(first(mar)) ^ axes(mar) + elseif B <: AbstractMeasure + new_f = basekleisli(μ.f) + new_F = typeof(new_f) + return For{B,new_F, I}(new_f, μ.inds) else - return productmeasure(basemeasure.(mar)) + return productmeasure(basemeasure.(marginals(μ))) end end +@inline function basemeasure(μ::For{T,F,I}) where {T,F,I} + return productmeasure(basemeasure.(marginals(μ))) +end + @generated function basemeasure(d::For{T,F,I}) where {N,T,F,I<:NTuple{N,<:Base.Generator}} - if static_hasmethod(tbasemeasure_type, Tuple{Type{T}}) + if static_hasmethod(tbasemeasure_type, Tuple{T}) B = tbasemeasure_type(T) if Base.issingletontype(B) b = instance(B) @@ -60,9 +69,6 @@ end B = tbasemeasure_type(T) return _tbasemeasure_type(For{T, F, I}, B) else - if T == Any - println.(stacktrace()) - end B = tbasemeasure_type(T) return _tbasemeasure_type(For{T, F, I}, B) end @@ -92,7 +98,10 @@ function Pretty.tile(d::For{T}) where {T} ) end -marginals(d::For) = mappedarray(d.f, d.inds...) +function marginals(d::For{T,F,I}) where {T,F,I} + f(x...) = d.f(x...)::T + mappedarray(f, d.inds...) +end """ For(f, base...) diff --git a/src/combinators/spikemixture.jl b/src/combinators/spikemixture.jl index 606d1c94..1891b7d5 100644 --- a/src/combinators/spikemixture.jl +++ b/src/combinators/spikemixture.jl @@ -21,10 +21,6 @@ end SpikeMixture(basemeasure(μ.m), static(1.0), static(1.0)) end -# tbasemeasure_depth(::Type{SpikeMixture{M,W}}) where {M,W} = static(1) + tbasemeasure_depth(M) - -# basemeasure_type(::Type{SpikeMixture{T,S}}) where {T,S} = SpikeMixture{} - function tbasemeasure_type(::Type{SpikeMixture{M,W,S}}) where {M,W,S} B = tbasemeasure_type(M) SpikeMixture{B,StaticFloat64{1.0},StaticFloat64{1.0}} diff --git a/src/density.jl b/src/density.jl index cff00e5c..7e5b2054 100644 --- a/src/density.jl +++ b/src/density.jl @@ -105,18 +105,20 @@ Define a new measure in terms of a log-density `f` over some measure `base`. @inline logdensityof(μ, x) = first(_logdensityof(μ, basemeasure(μ, x), x)) -@inline _logdensityof(μ, α, x) = _logdensityof(μ, α, x, logdensity_def(μ, x)) +@inline function _logdensityof(μ, α, x) + ℓ = dynamic(logdensity_def(μ, x)) + L = typeof(ℓ) + (ℓ,r) = _logdensityof(μ, α, x, ℓ)::Tuple{L,Any} + + return (ℓ, r) +end @inline function _logdensityof(μ::M, β::M, x, ℓ::T) where {M,T} - if μ === β - return ℓ - end - invoke(_logdensityof, Tuple{Any, Any, Any, T}, μ, β, x, ℓ)::T + return (ℓ, μ) end -@inline function _logdensityof(μ, β, x, ℓ) +@inline function _logdensityof(μ::M, β, x, ℓ) where {M} n = basemeasure_depth(μ) - static(1) - iszero(n) && return ℓ # @show μ # @show ℓ # println() @@ -141,8 +143,8 @@ end @inline function logdensity_rel(μ::M, ν::N, x::X) where {M,N,X} (ℓ₊, α) = _logdensityof(μ, basemeasure(μ), x) - (ℓ₊, β) = _logdensityof(ν, basemeasure(ν), x) - return _logdensity_rel(α, β, x, ℓ₊ - ℓ₊) + (ℓ₋, β) = _logdensityof(ν, basemeasure(ν), x) + return _logdensity_rel(α, β, x, ℓ₊ - ℓ₋) end @inline function _logdensity_rel(α::A, β::B, x::X, ℓ) where {A,B,X} diff --git a/src/interface.jl b/src/interface.jl index d7ab34b0..879f8119 100644 --- a/src/interface.jl +++ b/src/interface.jl @@ -21,7 +21,7 @@ function test_interface(μ::M) where {M} # @test @inferred tbasemeasure_type(M) == @inferred basemeasure_type(μ) - @test !isabstracttype(typejoin(tbasemeasure_type(M), (typeof ∘ basemeasure)(μ))) + # @test !isabstracttype(typejoin(basemeasure_type(μ ), (typeof ∘ basemeasure)(μ))) ########################################################################### # basemeasure_depth @@ -38,10 +38,10 @@ function test_interface(μ::M) where {M} # testvalue, logdensityof x = testvalue(μ) - β = @inferred basemeasure(μ) + β = @inferred basemeasure(μ, x) - ℓμ = logdensityof(μ, x) - ℓβ = logdensityof(β, x) + ℓμ = @inferred logdensityof(μ, x) + ℓβ = @inferred logdensityof(β, x) @test ℓμ ≈ logdensity_def(μ, x) + ℓβ diff --git a/src/utils.jl b/src/utils.jl index 82b576b5..38945214 100644 --- a/src/utils.jl +++ b/src/utils.jl @@ -75,8 +75,12 @@ end return s end -@inline function basemeasure_depth(μ::M, β::B, s::StaticInt{N}) where {M,B,N} - return basemeasure_depth(β, basemeasure(β), static(1) + s) +@inline function basemeasure_depth(μ::M, β::B, s) where {M,B,N} + if @generated + return tbasemeasure_depth(M, B, s) + else + return basemeasure_depth(β, basemeasure(β) , s + static(1)) + end end @inline tbasemeasure_depth(::Type{M}) where M = tbasemeasure_depth(M, tbasemeasure_type(M), static(0)) @@ -93,9 +97,6 @@ end end end -@inline function tbasemeasure_depth(::Type{M}, ::Type{B}, s::StaticInt{500}) where {M,B} - @error "Stack overflow?" -end @inline basemeasure_type(μ::M) where M = tbasemeasure_type(M) From 08ca84bec9bcc19d716b868ea2718facb1b79745 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 28 Dec 2021 14:39:20 -0800 Subject: [PATCH 133/368] update basemeasure(::For) for generators --- src/combinators/for.jl | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/src/combinators/for.jl b/src/combinators/for.jl index 0f62bfd1..f4d95480 100644 --- a/src/combinators/for.jl +++ b/src/combinators/for.jl @@ -52,6 +52,20 @@ end return productmeasure(basemeasure.(marginals(μ))) end +@generated function basemeasure(d::For{T,F,I}) where {N,T<:AbstractMeasure,F,I<:NTuple{N,<:Base.Generator}} + B = tbasemeasure_type(T) + if Base.issingletontype(B) + b = instance(B) + return :($b ^ minimum(length, d.inds)) + end + + return quote + f = basekleisli(d.f) + newF = typeof(f) + For{B,newF,I}(f, d.inds) + end +end + @generated function basemeasure(d::For{T,F,I}) where {N,T,F,I<:NTuple{N,<:Base.Generator}} if static_hasmethod(tbasemeasure_type, Tuple{T}) B = tbasemeasure_type(T) From 953041e5f4f3a4a6263f1dff55bf5f96df117e5f Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 29 Dec 2021 06:21:05 -0800 Subject: [PATCH 134/368] loosen type bound on instance_type --- src/utils.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/utils.jl b/src/utils.jl index 38945214..32d4dc5f 100644 --- a/src/utils.jl +++ b/src/utils.jl @@ -62,7 +62,7 @@ isiterable(::Type{T}) where {T} = end # See https://github.com/cscherrer/KeywordCalls.jl/issues/22 -@inline instance_type(f::F) where {F<:Function} = F +@inline instance_type(f::F) where {F} = F @inline instance_type(f::UnionAll) = Type{f} export basemeasure_depth From 1d2b66cbff9efd482b04dd39e4cf260a9846a7ef Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Thu, 30 Dec 2021 06:03:31 -0800 Subject: [PATCH 135/368] drop debugging code --- src/combinators/for.jl | 5 ----- 1 file changed, 5 deletions(-) diff --git a/src/combinators/for.jl b/src/combinators/for.jl index f4d95480..0f0a1ab9 100644 --- a/src/combinators/for.jl +++ b/src/combinators/for.jl @@ -9,11 +9,6 @@ struct For{T, F, I} <: AbstractProductMeasure @inline function For(f::F, inds::I) where {F,I<:Tuple} T = Core.Compiler.return_type(f, Tuple{_eltype.(inds)...}) - if T==Any - println("XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX") - @show (f, inds) - println("XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX") - end new{T,instance_type(f),I}(f, inds) end From b5891c5194ec148373137df7f4abf75d602c02ca Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Thu, 30 Dec 2021 06:31:31 -0800 Subject: [PATCH 136/368] small update for Likelihood, and a test --- src/combinators/likelihood.jl | 5 +++++ test/runtests.jl | 10 ++++++++++ 2 files changed, 15 insertions(+) diff --git a/src/combinators/likelihood.jl b/src/combinators/likelihood.jl index 3047a5bc..fec3aac1 100644 --- a/src/combinators/likelihood.jl +++ b/src/combinators/likelihood.jl @@ -110,6 +110,7 @@ end @inline DensityKind(::Likelihood) = IsDensity() Likelihood(k::K, x::X) where {K<:AbstractKleisli,X} = Likelihood{K,X}(k,x) +Likelihood(k::K, x::X) where {K<:Function,X} = Likelihood{K,X}(k,x) Likelihood(μ::AbstractMeasure, x) = Likelihood(kleisli(μ), x) @@ -129,3 +130,7 @@ end @inline function logdensity_def(ℓ::Likelihood, p) return logdensity_def(ℓ.k(p), ℓ.x) end + +@inline function logdensityof(ℓ::Likelihood, p) + return logdensityof(ℓ.k(p), ℓ.x) +end diff --git a/test/runtests.jl b/test/runtests.jl index 8e61a905..5ac2d96d 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -111,6 +111,16 @@ end @test densityof(HalfNormal(), 0.2) ≈ 2 * densityof(Normal(), 0.2) end +@testset "Likelihood" begin + ℓ = Likelihood(3) do μ + ∫exp(Lebesgue(ℝ)) do x + -(x - μ)^2 + end + end + + @inferred logdensityof(ℓ, 2.0) +end + # @testset "Likelihood" begin # dps = [ # (Normal() , 2.0 ) From 21e2c193c67b9e911183a01a5e3ee4355c55e7ba Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Thu, 30 Dec 2021 07:00:14 -0800 Subject: [PATCH 137/368] fixing up likelihoods --- src/combinators/likelihood.jl | 11 ++++------- src/combinators/smart-constructors.jl | 2 +- src/interface.jl | 2 +- src/parameterized.jl | 3 ++- 4 files changed, 8 insertions(+), 10 deletions(-) diff --git a/src/combinators/likelihood.jl b/src/combinators/likelihood.jl index fec3aac1..7e1f1c04 100644 --- a/src/combinators/likelihood.jl +++ b/src/combinators/likelihood.jl @@ -104,18 +104,15 @@ and we observe `x=3`. We can compute the posterior measure on `μ` as struct Likelihood{K,X} k::K x::X + + Likelihood(k::K, x::X) where {K<:AbstractKleisli,X} = new{K,X}(k,x) + Likelihood(k::K, x::X) where {K<:Function,X} = new{K,X}(k,x) + Likelihood(μ, x) = Likelihood(kleisli(μ), x) end # Not really a density, but this makes the code work @inline DensityKind(::Likelihood) = IsDensity() -Likelihood(k::K, x::X) where {K<:AbstractKleisli,X} = Likelihood{K,X}(k,x) -Likelihood(k::K, x::X) where {K<:Function,X} = Likelihood{K,X}(k,x) - -Likelihood(μ::AbstractMeasure, x) = Likelihood(kleisli(μ), x) - -Likelihood(::Type{M}, x) where {M<:AbstractMeasure} = Likelihood(kleisli(M), x) - function Pretty.quoteof(ℓ::Likelihood) k = Pretty.quoteof(ℓ.k) x = Pretty.quoteof(ℓ.x) diff --git a/src/combinators/smart-constructors.jl b/src/combinators/smart-constructors.jl index d1029b26..426ed9cc 100644 --- a/src/combinators/smart-constructors.jl +++ b/src/combinators/smart-constructors.jl @@ -95,7 +95,7 @@ kleisli(μ, op1, op2, param_maps...) = ParameterizedKleisli(μ, op1, op2, param_ # kleisli(Normal(μ=2)) function kleisli(μ::M) where {M<:AbstractMeasure} - constructorof(M) + kleisli(M) end # kleisli(Normal{(:μ,), Tuple{Int64}}) diff --git a/src/interface.jl b/src/interface.jl index 879f8119..fb307b1f 100644 --- a/src/interface.jl +++ b/src/interface.jl @@ -25,7 +25,7 @@ function test_interface(μ::M) where {M} ########################################################################### # basemeasure_depth - static_depth = basemeasure_depth(μ) + static_depth = @inferred basemeasure_depth(μ) dynamic_depth = dynamic_basemeasure_depth(μ) diff --git a/src/parameterized.jl b/src/parameterized.jl index d7ff7362..13ef5955 100644 --- a/src/parameterized.jl +++ b/src/parameterized.jl @@ -29,7 +29,8 @@ end export kleisli function kleisli(::Type{P}) where {N,P<:ParameterizedMeasure{N}} - function(args...) P(args...) end + C = constructorof(P) + function(args...) C(NamedTuple{N}(args...)) end end function (::Type{P})(args...) where {N,P<:ParameterizedMeasure{N}} From 622fa3262bd60b8c909aed13b2fb2f624bcb0e97 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Thu, 30 Dec 2021 13:17:29 -0800 Subject: [PATCH 138/368] improve `basemeasure_depth` dispatch --- src/utils.jl | 32 +++++++++++++------------------- 1 file changed, 13 insertions(+), 19 deletions(-) diff --git a/src/utils.jl b/src/utils.jl index 32d4dc5f..ec5ae1e5 100644 --- a/src/utils.jl +++ b/src/utils.jl @@ -67,34 +67,28 @@ end export basemeasure_depth -@inline function basemeasure_depth(μ::M) where {M} - return basemeasure_depth(μ, basemeasure(μ), static(0)) +@constprop :aggressive function basemeasure_depth(μ::M) where {M} + return static(tbasemeasure_depth(M, typeof(basemeasure(μ)), 0)) end -@inline function basemeasure_depth(μ::M, β::M, s::StaticInt{N}) where {M,N} - return s +@inline function basemeasure_depth(μ::M, β::M, n) where {M} + return n end -@inline function basemeasure_depth(μ::M, β::B, s) where {M,B,N} - if @generated - return tbasemeasure_depth(M, B, s) - else - return basemeasure_depth(β, basemeasure(β) , s + static(1)) - end +@inline function basemeasure_depth(μ::M, β::B, n) where {M,B} + return tbasemeasure_depth(M, B, n) end -@inline tbasemeasure_depth(::Type{M}) where M = tbasemeasure_depth(M, tbasemeasure_type(M), static(0)) +@constprop :aggressive function tbasemeasure_depth(::Type{M}) where {M} + static(tbasemeasure_depth(M, tbasemeasure_type(M), 0)) +end -@inline function tbasemeasure_depth(::Type{M}, ::Type{M}, s::StaticInt{N}) where {M,N} - return s +@inline function tbasemeasure_depth(::Type{M}, ::Type{M}, n) where {M} + return n end -@inline function tbasemeasure_depth(::Type{M}, ::Type{B}, s::StaticInt{N}) where {M,B,N} - if @generated - return tbasemeasure_depth(B, tbasemeasure_type(B), s + static(1)) - else - return tbasemeasure_depth(B, tbasemeasure_type(B), s + static(1)) - end +@inline function tbasemeasure_depth(::Type{M}, ::Type{B}, n) where {M,B} + return tbasemeasure_depth(B, tbasemeasure_type(B), n + 1) end From 630067b6b6a707baaa6a0ec678b9bf1f5c699ee9 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Thu, 30 Dec 2021 13:19:39 -0800 Subject: [PATCH 139/368] still some trouble with inferred basemeasure_depth --- src/interface.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/interface.jl b/src/interface.jl index fb307b1f..879f8119 100644 --- a/src/interface.jl +++ b/src/interface.jl @@ -25,7 +25,7 @@ function test_interface(μ::M) where {M} ########################################################################### # basemeasure_depth - static_depth = @inferred basemeasure_depth(μ) + static_depth = basemeasure_depth(μ) dynamic_depth = dynamic_basemeasure_depth(μ) From b0a0f66c98680ba6c5b68c354500f808267256fd Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Thu, 30 Dec 2021 13:20:32 -0800 Subject: [PATCH 140/368] clean up `For` dispatch --- src/combinators/for.jl | 54 +++++++++++++++--------------------------- 1 file changed, 19 insertions(+), 35 deletions(-) diff --git a/src/combinators/for.jl b/src/combinators/for.jl index 0f0a1ab9..116985ac 100644 --- a/src/combinators/for.jl +++ b/src/combinators/for.jl @@ -28,49 +28,33 @@ function marginals(d::For{T,F,I}) where {N,T,F,I<:NTuple{N,<:Base.Generator}} Iterators.map(f, d.inds...) end - -@inline function basemeasure(μ::For{T,F,I}) where {T<:AbstractMeasure,F,I} - mar = marginals(μ) +@inline function basemeasure(d::For{T,F,I}) where {T,F,I} B = tbasemeasure_type(T) - if Base.issingletontype(B) - return basemeasure(first(mar)) ^ axes(mar) - elseif B <: AbstractMeasure - new_f = basekleisli(μ.f) - new_F = typeof(new_f) - return For{B,new_F, I}(new_f, μ.inds) - else - return productmeasure(basemeasure.(marginals(μ))) - end + _basemeasure(d, B, static(Base.issingletontype(B))) end -@inline function basemeasure(μ::For{T,F,I}) where {T,F,I} - return productmeasure(basemeasure.(marginals(μ))) +@inline function _basemeasure(d::For{T,F,I}, ::Type{B}, ::True) where {T,F,I,B} + instance(B) ^ axes(d.inds) end -@generated function basemeasure(d::For{T,F,I}) where {N,T<:AbstractMeasure,F,I<:NTuple{N,<:Base.Generator}} - B = tbasemeasure_type(T) - if Base.issingletontype(B) - b = instance(B) - return :($b ^ minimum(length, d.inds)) - end +@inline function _basemeasure(d::For{T,F,I}, ::Type{B}, ::False) where {T,F,I,B<:AbstractMeasure} + new_f = basekleisli(d.f) + new_F = typeof(new_f) + For{B,new_F, I}(new_f, d.inds) +end - return quote - f = basekleisli(d.f) - newF = typeof(f) - For{B,newF,I}(f, d.inds) - end +@inline function _basemeasure(d::For{T,F,I}, ::Type{B}, ::False) where {T,F,I,B} + productmeasure(basemeasure.(marginals(d))) end -@generated function basemeasure(d::For{T,F,I}) where {N,T,F,I<:NTuple{N,<:Base.Generator}} - if static_hasmethod(tbasemeasure_type, Tuple{T}) - B = tbasemeasure_type(T) - if Base.issingletontype(B) - b = instance(B) - return :($b ^ minimum(length, d.inds)) - end - end - - return :(For(basekleisli(d.f), d.inds)) +function _basemeasure(d::For{T,F,I}, ::Type{B}, ::True) where {N,T<:AbstractMeasure,F,I<:NTuple{N,<:Base.Generator},B} + return instance(B) ^ minimum(length, d.inds) +end + +function _basemeasure(d::For{T,F,I}, ::Type{B}, ::False) where {N,T<:AbstractMeasure,F,I<:NTuple{N,<:Base.Generator},B} + f = basekleisli(d.f) + newF = typeof(f) + For{B,newF,I}(f, d.inds) end @inline function tbasemeasure_type(::Type{For{T, F, I}}) where {T,F,I} From 8f28472049aed570e0d247d6e03ff97d5fab5aa9 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Thu, 30 Dec 2021 13:24:00 -0800 Subject: [PATCH 141/368] simplify _logdensityof --- src/density.jl | 19 ++++++++----------- 1 file changed, 8 insertions(+), 11 deletions(-) diff --git a/src/density.jl b/src/density.jl index 7e5b2054..bc6755e9 100644 --- a/src/density.jl +++ b/src/density.jl @@ -103,26 +103,23 @@ Define a new measure in terms of a log-density `f` over some measure `base`. # TODO: `density` and `logdensity` functions for `DensityMeasure` -@inline logdensityof(μ, x) = first(_logdensityof(μ, basemeasure(μ, x), x)) +@inline logdensityof(μ, x) = _logdensityof(μ, x) + +@inline _logdensityof(μ, x) = _logdensityof(μ, basemeasure(μ, x), x) @inline function _logdensityof(μ, α, x) ℓ = dynamic(logdensity_def(μ, x)) L = typeof(ℓ) - (ℓ,r) = _logdensityof(μ, α, x, ℓ)::Tuple{L,Any} - - return (ℓ, r) + _logdensityof(μ, α, x, ℓ)::L end -@inline function _logdensityof(μ::M, β::M, x, ℓ::T) where {M,T} - return (ℓ, μ) +@inline function _logdensityof(μ::M, β::M, x, ℓ) where {M} + return ℓ end @inline function _logdensityof(μ::M, β, x, ℓ) where {M} n = basemeasure_depth(μ) - static(1) - # @show μ - # @show ℓ - # println() - return _logdensityof(β, basemeasure(β,x), x, ℓ, n) + _logdensityof(β, basemeasure(β,x), x, ℓ, n) end @generated function _logdensityof(μ, β, x, ℓ::T, ::StaticInt{n}) where {n,T} @@ -137,7 +134,7 @@ end μ,β = β, basemeasure(β, x) ℓ += Δℓ end - return (ℓ, β) + return ℓ end end From 80be728d738dc3681b1c8a11c59eccb3ac51222a Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Fri, 31 Dec 2021 05:58:39 -0800 Subject: [PATCH 142/368] optimize for Returns{True} case --- src/combinators/factoredbase.jl | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/src/combinators/factoredbase.jl b/src/combinators/factoredbase.jl index 6ed94d3e..059266c3 100644 --- a/src/combinators/factoredbase.jl +++ b/src/combinators/factoredbase.jl @@ -7,6 +7,10 @@ struct FactoredBase{R,C,V,B} <: AbstractMeasure base::B end +@inline function logdensity_def(d::FactoredBase{Returns{True}}, x) + d.constℓ + d.varℓ() +end + @inline function logdensity_def(d::FactoredBase, x) d.inbounds(x) || return -Inf d.constℓ + d.varℓ() From 1b65a576f36bcb937fc4de34ac4b2a67dfe8fbc5 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Fri, 31 Dec 2021 06:14:55 -0800 Subject: [PATCH 143/368] rework basemeasure_depth --- src/utils.jl | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/src/utils.jl b/src/utils.jl index ec5ae1e5..3fee1d32 100644 --- a/src/utils.jl +++ b/src/utils.jl @@ -67,28 +67,28 @@ end export basemeasure_depth -@constprop :aggressive function basemeasure_depth(μ::M) where {M} - return static(tbasemeasure_depth(M, typeof(basemeasure(μ)), 0)) +@inline function basemeasure_depth(μ::M) where {M} + return static(tbasemeasure_depth(M, typeof(basemeasure(μ)))) end -@inline function basemeasure_depth(μ::M, β::M, n) where {M} - return n +@inline function basemeasure_depth(μ::M, β::M) where {M} + return 0 end -@inline function basemeasure_depth(μ::M, β::B, n) where {M,B} - return tbasemeasure_depth(M, B, n) +@inline function basemeasure_depth(μ::M, β::B) where {M,B} + return tbasemeasure_depth(M, B) end -@constprop :aggressive function tbasemeasure_depth(::Type{M}) where {M} - static(tbasemeasure_depth(M, tbasemeasure_type(M), 0)) +@inline function tbasemeasure_depth(::Type{M}) where {M} + static(tbasemeasure_depth(M, tbasemeasure_type(M))) end -@inline function tbasemeasure_depth(::Type{M}, ::Type{M}, n) where {M} - return n +@inline function tbasemeasure_depth(::Type{M}, ::Type{M}) where {M} + return 0 end -@inline function tbasemeasure_depth(::Type{M}, ::Type{B}, n) where {M,B} - return tbasemeasure_depth(B, tbasemeasure_type(B), n + 1) +@inline function tbasemeasure_depth(::Type{M}, ::Type{B}) where {M,B} + return 1 + tbasemeasure_depth(B, tbasemeasure_type(B)) end From 18e5605edd5fccc311bfb76c8761f73821397ba7 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Fri, 31 Dec 2021 06:52:57 -0800 Subject: [PATCH 144/368] aggressive tests passing!! --- src/interface.jl | 2 +- src/utils.jl | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/interface.jl b/src/interface.jl index 879f8119..fb307b1f 100644 --- a/src/interface.jl +++ b/src/interface.jl @@ -25,7 +25,7 @@ function test_interface(μ::M) where {M} ########################################################################### # basemeasure_depth - static_depth = basemeasure_depth(μ) + static_depth = @inferred basemeasure_depth(μ) dynamic_depth = dynamic_basemeasure_depth(μ) diff --git a/src/utils.jl b/src/utils.jl index 3fee1d32..5e785581 100644 --- a/src/utils.jl +++ b/src/utils.jl @@ -68,7 +68,7 @@ end export basemeasure_depth @inline function basemeasure_depth(μ::M) where {M} - return static(tbasemeasure_depth(M, typeof(basemeasure(μ)))) + return static(basemeasure_depth(μ, basemeasure(μ))) end @inline function basemeasure_depth(μ::M, β::M) where {M} @@ -76,7 +76,7 @@ end end @inline function basemeasure_depth(μ::M, β::B) where {M,B} - return tbasemeasure_depth(M, B) + return 1 + basemeasure_depth(β, basemeasure(β)) end @inline function tbasemeasure_depth(::Type{M}) where {M} From 9b7e8aaef2420d1cd5b4705ad6cf4cf4008e2c92 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Fri, 31 Dec 2021 07:37:10 -0800 Subject: [PATCH 145/368] drop type-level stuff --- src/MeasureBase.jl | 7 +--- src/combinators/factoredbase.jl | 2 -- src/combinators/for.jl | 33 ++++-------------- src/combinators/half.jl | 5 --- src/combinators/power.jl | 24 ------------- src/combinators/product.jl | 60 +++++++++------------------------ src/combinators/restricted.jl | 2 -- src/combinators/spikemixture.jl | 4 --- src/combinators/superpose.jl | 4 --- src/combinators/weighted.jl | 4 --- src/density.jl | 2 -- src/help.jl | 13 ------- src/interface.jl | 8 +---- src/primitive.jl | 3 -- src/primitives/counting.jl | 2 -- src/primitives/dirac.jl | 2 -- src/primitives/lebesgue.jl | 2 -- src/tmap.jl | 25 -------------- src/utils.jl | 27 --------------- 19 files changed, 24 insertions(+), 205 deletions(-) delete mode 100644 src/tmap.jl diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index e0fc646c..4fc7fa13 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -96,20 +96,15 @@ include("combinators/conditional.jl") include("rand.jl") include("density.jl") -include("tmap.jl") module Interface using Reexport using MeasureBase -using MeasureBase:basemeasure_depth, tbasemeasure_depth, basemeasure_type, tbasemeasure_type, proxy +using MeasureBase:basemeasure_depth, proxy @reexport using Test export test_interface -export tbasemeasure_depth -export tbasemeasure_type -export help_tbasemeasure_type export basemeasure_depth -export basemeasure_type export proxy include("help.jl") diff --git a/src/combinators/factoredbase.jl b/src/combinators/factoredbase.jl index 059266c3..32aed8ca 100644 --- a/src/combinators/factoredbase.jl +++ b/src/combinators/factoredbase.jl @@ -23,5 +23,3 @@ function Pretty.tile(fb::FactoredBase) end basemeasure(d::FactoredBase) = d.base - -tbasemeasure_type(::Type{FactoredBase{R,C,V,B}}) where {R,C,V,B} = B diff --git a/src/combinators/for.jl b/src/combinators/for.jl index 116985ac..d8c1c14b 100644 --- a/src/combinators/for.jl +++ b/src/combinators/for.jl @@ -23,13 +23,18 @@ function logdensity_def(d::For{T,F,I}, x) where {N,T,F,I<:NTuple{N,<:Base.Genera end end +function marginals(d::For{T,F,I}) where {T,F,I} + f(x...) = d.f(x...)::T + mappedarray(f, d.inds...) +end + function marginals(d::For{T,F,I}) where {N,T,F,I<:NTuple{N,<:Base.Generator}} f(x...) = d.f(x...)::T Iterators.map(f, d.inds...) end @inline function basemeasure(d::For{T,F,I}) where {T,F,I} - B = tbasemeasure_type(T) + B = Core.Compiler.return_type(basemeasure, Tuple{T}) _basemeasure(d, B, static(Base.issingletontype(B))) end @@ -57,28 +62,6 @@ function _basemeasure(d::For{T,F,I}, ::Type{B}, ::False) where {N,T<:AbstractMea For{B,newF,I}(f, d.inds) end -@inline function tbasemeasure_type(::Type{For{T, F, I}}) where {T,F,I} - if @generated - B = tbasemeasure_type(T) - return _tbasemeasure_type(For{T, F, I}, B) - else - B = tbasemeasure_type(T) - return _tbasemeasure_type(For{T, F, I}, B) - end -end - -@inline function _tbasemeasure_type(::Type{For{T, F, I}}, ::Type{B}) where {B,T,F,I} - _tbasemeasure_type(For{T, F, I}, B, static(Base.issingletontype(B))) -end - -@inline function _tbasemeasure_type(::Type{For{T, F, I}}, ::Type{B}, ::True) where {B,T,F,I} - return PowerMeasure{B, I} -end - -@inline function _tbasemeasure_type(::Type{For{T, F, I}}, ::Type{B}, ::False) where {B,T,F,I} - return For{B, typeof(basekleisli(instance(F))), I} -end - function Pretty.tile(d::For{T}) where {T} result = Pretty.literal("For{") result *= Pretty.tile(T) @@ -91,10 +74,6 @@ function Pretty.tile(d::For{T}) where {T} ) end -function marginals(d::For{T,F,I}) where {T,F,I} - f(x...) = d.f(x...)::T - mappedarray(f, d.inds...) -end """ For(f, base...) diff --git a/src/combinators/half.jl b/src/combinators/half.jl index 9f9ebbd3..1c9bf4dd 100644 --- a/src/combinators/half.jl +++ b/src/combinators/half.jl @@ -21,11 +21,6 @@ isnonnegative(x) = x ≥ 0.0 FactoredBase(inbounds, constℓ, varℓ, base) end -function tbasemeasure_type(::Type{Half{M}}) where {M} - B = tbasemeasure_type(M) - FactoredBase{typeof(isnonnegative),StaticFloat64{logtwo},Returns{StaticFloat64{0.0}},B} -end - function Base.rand(rng::AbstractRNG, T::Type, μ::Half) return abs(rand(rng, T, unhalf(μ))) end diff --git a/src/combinators/power.jl b/src/combinators/power.jl index 7ccfe5e8..10f1088f 100644 --- a/src/combinators/power.jl +++ b/src/combinators/power.jl @@ -59,30 +59,6 @@ params(d::PowerMeasure) = params(first(marginals(d))) basemeasure(d.parent) ^ d.axes end -function basemeasure_depth(::PowerMeasure{M}) where {M} - return tbasemeasure_depth(M) -end - -function tbasemeasure_type(::Type{P}) where {M,P<:PowerMeasure{M}} - _tbasemeasure_type(P, tbasemeasure_type(M)) -end - -# This form assumes -# P == typeof(μ) -# B == typeof(basemeasure(parent(μ))) -function _tbasemeasure_type(::Type{P},::Type{B}) where {M,D,B,P<:PowerMeasure{M,D}} - return PowerMeasure{B,D} -end - -function _tbasemeasure_type(::Type{P},::Type{B}) where {M,T,W,D,B<:WeightedMeasure{W,T},P<:PowerMeasure{M,D}} - return WeightedMeasure{W,PowerMeasure{T,D}} -end - - -function tbasemeasure_depth(::Type{PowerMeasure{M,D}}) where {M<:PrimitiveMeasure,D} - return static(0) -end - @inline function logdensity_def(d::PowerMeasure, x) sum(x) do xj logdensity_def(d.parent, xj) diff --git a/src/combinators/product.jl b/src/combinators/product.jl index 5b530c8f..542c35e4 100644 --- a/src/combinators/product.jl +++ b/src/combinators/product.jl @@ -47,63 +47,35 @@ end sum(ℓs) end - function basemeasure(μ::ProductMeasure{Base.Generator{I,F}}) where {I,F} - mar = marginals(μ) T = Core.Compiler.return_type(mar.f, Tuple{_eltype(mar.iter)}) - if static_hasmethod(tbasemeasure_type, Tuple{Type{T}}) - B = tbasemeasure_type(T) - if Base.issingletontype(B) - b = instance(B)::B - return b ^ axes(mar) - end - end - - return productmeasure(Base.Generator(basekleisli(mar.f), mar.iter)) + B = Core.Compiler.return_type(basemeasure, Tuple{T}) + _basemeasure(μ, B, static(Base.issingulartype(B))) end + + function basemeasure(μ::ProductMeasure{A}) where {T,A<:AbstractMappedArray{T}} - mar = marginals(μ) - if static_hasmethod(tbasemeasure_type, Tuple{Type{T}}) - B = tbasemeasure_type(T) - if Base.issingletontype(B) - b = instance(B) - mar = marginals(μ) - return b ^ axes(marginals(μ)) - end - end - return productmeasure(mappedarray(basemeasure, mar)) + B = Core.Compiler.return_type(basemeasure, Tuple{T}) + _basemeasure(μ, B, static(Base.issingulartype(B))) end -marginals(μ::ProductMeasure) = μ.marginals - -@inline function tbasemeasure_type(::Type{ProductMeasure{M}}) where {T,N,A,F,M<:ReadonlyMultiMappedArray{T,N,A,F}} - if static_hasmethod(tbasemeasure_type, Tuple{Type{T}}) - B = tbasemeasure_type(T) - if Base.issingletontype(B) - return PowerMeasure{B, A} - end - end - tmap(tbasemeasure_type, ProductMeasure{M}) +function _basemeasure(μ::ProductMeasure, ::Type{B}, ::True) where {T,B} + return instance(B) ^ axes(marginals(μ)) end -@inline function tbasemeasure_type(::Type{P}) where {T,N,A,F,M<:ReadonlyMappedArray{T,N,A,F},P<:ProductMeasure{M}} - if static_hasmethod(tbasemeasure_type, Tuple{Type{T}}) - B = tbasemeasure_type(T) - if Base.issingletontype(B) - return PowerMeasure{B, Tuple{A}} - else - tmap(tbasemeasure_type, P) - end - else - @error "tbasemeasure_type(::Type{$P})" - end +function _basemeasure(μ::ProductMeasure{A}, ::Type{B}, ::False) where {T,A<:AbstractMappedArray{T},B} + productmeasure(mappedarray(basemeasure, mar)) end -@inline function tbasemeasure_type(::Type{P}) where {P<:ProductMeasure} - tmap(tbasemeasure_type, P) +function _basemeasure(μ::ProductMeasure{Base.Generator{I,F}}, ::Type{B}, ::False) where {I,F,B} + mar = marginals(μ) + productmeasure(Base.Generator(basekleisli(mar.f), mar.iter)) end +marginals(μ::ProductMeasure) = μ.marginals + + testvalue(d::AbstractProductMeasure) = map(testvalue, marginals(d)) export ⊗ diff --git a/src/combinators/restricted.jl b/src/combinators/restricted.jl index 9b654734..c0711efd 100644 --- a/src/combinators/restricted.jl +++ b/src/combinators/restricted.jl @@ -15,6 +15,4 @@ end basemeasure(μ::RestrictedMeasure) = μ.base -tbasemeasure_type(::Type{RestrictedMeasure{F,M}}) where {F,M} = M - insupport(μ::RestrictedMeasure, x) = μ.f(x) && insupport(μ.base, x) diff --git a/src/combinators/spikemixture.jl b/src/combinators/spikemixture.jl index 1891b7d5..04b37a28 100644 --- a/src/combinators/spikemixture.jl +++ b/src/combinators/spikemixture.jl @@ -21,10 +21,6 @@ end SpikeMixture(basemeasure(μ.m), static(1.0), static(1.0)) end -function tbasemeasure_type(::Type{SpikeMixture{M,W,S}}) where {M,W,S} - B = tbasemeasure_type(M) - SpikeMixture{B,StaticFloat64{1.0},StaticFloat64{1.0}} -end @inline function logdensity_def(μ::SpikeMixture, x) if iszero(x) diff --git a/src/combinators/superpose.jl b/src/combinators/superpose.jl index ed49bbda..2c06618b 100644 --- a/src/combinators/superpose.jl +++ b/src/combinators/superpose.jl @@ -64,10 +64,6 @@ end basemeasure(μ::SuperpositionMeasure) = superpose(map(basemeasure, μ.components)) -function tbasemeasure_type(::Type{S}) where {C,S<:SuperpositionMeasure{C}} - SuperpositionMeasure{tmap(tbasemeasure_type, C)} -end - # TODO: Fix `rand` method (this one is wrong) # function Base.rand(μ::SuperpositionMeasure{X,N}) where {X,N} # return rand(rand(μ.components)) diff --git a/src/combinators/weighted.jl b/src/combinators/weighted.jl index dd6e92b0..7018de2a 100644 --- a/src/combinators/weighted.jl +++ b/src/combinators/weighted.jl @@ -23,8 +23,6 @@ struct WeightedMeasure{R,M} <: AbstractWeightedMeasure base::M end -tbasemeasure_type(::Type{WeightedMeasure{R,M}}) where {R,M} = M - function Base.show(io::IO, μ::WeightedMeasure) io = IOContext(io, :compact => true) print(io, exp(μ.logweight), " * ", μ.base) @@ -70,6 +68,4 @@ end basemeasure(d::ParamWeightedMeasure) = d.base -tbasemeasure_type(::Type{ParamWeightedMeasure{L,N,T,B}}) where {L,N,T,B} = B - logdensity_def(d::ParamWeightedMeasure, x) = d.ℓ(d.par) diff --git a/src/density.jl b/src/density.jl index bc6755e9..fccd1ca8 100644 --- a/src/density.jl +++ b/src/density.jl @@ -72,8 +72,6 @@ end basemeasure(μ::DensityMeasure) = μ.base -tbasemeasure_type(::Type{DensityMeasure{F,B}}) where {F,B} = B - logdensity_def(μ::DensityMeasure, x) = logdensityof(μ.f, x) density_def(μ::DensityMeasure, x) = densityof(μ.f, x) diff --git a/src/help.jl b/src/help.jl index 77d37476..e69de29b 100644 --- a/src/help.jl +++ b/src/help.jl @@ -1,13 +0,0 @@ -export help_tbasemeasure_type - -function help_tbasemeasure_type(μ::M) where M - b = basemeasure(μ) - B = typeof(b) - println(""" - function tbasemeasure_type(::Type{$M}) - $B - end - """ - ) - return nothing -end diff --git a/src/interface.jl b/src/interface.jl index fb307b1f..c9a4d625 100644 --- a/src/interface.jl +++ b/src/interface.jl @@ -16,13 +16,7 @@ function test_interface(μ::M) where {M} @testset "$μ" begin μ = $μ M = $M - ########################################################################### - # basemeasure_type - - # @test @inferred tbasemeasure_type(M) == @inferred basemeasure_type(μ) - - # @test !isabstracttype(typejoin(basemeasure_type(μ ), (typeof ∘ basemeasure)(μ))) - + ########################################################################### # basemeasure_depth static_depth = @inferred basemeasure_depth(μ) diff --git a/src/primitive.jl b/src/primitive.jl index fd928cf0..8d2c13d0 100644 --- a/src/primitive.jl +++ b/src/primitive.jl @@ -17,10 +17,7 @@ abstract type PrimitiveMeasure <: AbstractMeasure end basemeasure(μ::PrimitiveMeasure) = μ -tbasemeasure_type(::Type{M}) where {M<:PrimitiveMeasure} = M - @inline basemeasure_depth(::PrimitiveMeasure) = static(0) -@inline tbasemeasure_depth(::Type{M}) where {M<:PrimitiveMeasure} = static(0) logdensity_def(μ::PrimitiveMeasure, x) = static(0.0) diff --git a/src/primitives/counting.jl b/src/primitives/counting.jl index f55ae4ef..d96c748c 100644 --- a/src/primitives/counting.jl +++ b/src/primitives/counting.jl @@ -16,8 +16,6 @@ basemeasure(::Counting) = CountingMeasure() Counting() = Counting(ℤ) -tbasemeasure_type(::Type{C}) where {C<:Counting} = CountingMeasure - testvalue(d::Counting) = testvalue(d.support) proxy(d::Counting) = restrict(in(d.support), CountingMeasure()) diff --git a/src/primitives/dirac.jl b/src/primitives/dirac.jl index 575ff595..2d137d55 100644 --- a/src/primitives/dirac.jl +++ b/src/primitives/dirac.jl @@ -18,8 +18,6 @@ end basemeasure(d::Dirac) = CountingMeasure() -tbasemeasure_type(::Type{D}) where {D<:Dirac} = CountingMeasure - density_def(μ::Dirac, x) = x == μ.x logdensity_def(μ::Dirac, x) = (x == μ.x) ? 0.0 : -Inf diff --git a/src/primitives/lebesgue.jl b/src/primitives/lebesgue.jl index 9db9e51f..d218064f 100644 --- a/src/primitives/lebesgue.jl +++ b/src/primitives/lebesgue.jl @@ -20,8 +20,6 @@ Lebesgue() = Lebesgue(ℝ) # basemeasure(::Lebesgue) = LebesgueMeasure() -tbasemeasure_type(::Type{<:Lebesgue}) = LebesgueMeasure - testvalue(d::Lebesgue) = testvalue(d.support) proxy(d::Lebesgue) = restrict(in(d.support), LebesgueMeasure()) diff --git a/src/tmap.jl b/src/tmap.jl deleted file mode 100644 index c71a2f52..00000000 --- a/src/tmap.jl +++ /dev/null @@ -1,25 +0,0 @@ -# A type-level map - -@inline function tmap(f::F, ::Type{T}) where {F,T<:Tuple} - Tuple{map(f, T.types)...} -end - -@inline function tmap(f::F, ::Type{A}) where {F,T,A<:AbstractArray{T}} - p = Tuple(A.parameters) - C = constructorof(A) - C{(f(T), Base.tail(p)...)...} -end - -@inline function tmap(f::F, ::Type{Base.Generator{G,I}}) where {F,G,I} - Base.Generator{ComposedFunction{F,G}, I} -end - -function tmap(::typeof(tbasemeasure_type), ::Type{ProductMeasure{T}}) where {T} - if @generated - B = tmap(tbasemeasure_type, T) - ProductMeasure{B} - else - B = tmap(tbasemeasure_type, T) - ProductMeasure{B} - end -end diff --git a/src/utils.jl b/src/utils.jl index 5e785581..f9ecaa21 100644 --- a/src/utils.jl +++ b/src/utils.jl @@ -37,18 +37,6 @@ end return q end -function trootmeasure_type(::Type{M}) where {M} - trootmeasure_type(M, tbasemeasure_type(M), static(0)) -end - -function trootmeasure_type(::Type{M}, ::Type{M}, s::StaticInt{N}) where {M,N} - return M -end - -function trootmeasure_type(::Type{M}, ::Type{B}, s::StaticInt{N}) where {M,B,N} - return trootmeasure_type(B, tbasemeasure_type(B), static(1) + s) -end - # Base on the Tricks.jl README using Tricks struct Iterable end @@ -79,21 +67,6 @@ end return 1 + basemeasure_depth(β, basemeasure(β)) end -@inline function tbasemeasure_depth(::Type{M}) where {M} - static(tbasemeasure_depth(M, tbasemeasure_type(M))) -end - -@inline function tbasemeasure_depth(::Type{M}, ::Type{M}) where {M} - return 0 -end - -@inline function tbasemeasure_depth(::Type{M}, ::Type{B}) where {M,B} - return 1 + tbasemeasure_depth(B, tbasemeasure_type(B)) -end - - -@inline basemeasure_type(μ::M) where M = tbasemeasure_type(M) - # Adapted from https://github.com/JuliaArrays/MappedArrays.jl/blob/46bf47f3388d011419fe43404214c1b7a44a49cc/src/MappedArrays.jl#L229 function func_string(f, types) ft = typeof(f) From f907b8f296c10a96c126751c2412bb6cddbefae1 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Fri, 31 Dec 2021 07:38:44 -0800 Subject: [PATCH 146/368] drop help --- src/MeasureBase.jl | 1 - src/help.jl | 0 2 files changed, 1 deletion(-) delete mode 100644 src/help.jl diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index 4fc7fa13..55409c14 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -107,7 +107,6 @@ export test_interface export basemeasure_depth export proxy -include("help.jl") include("interface.jl") end # module Interface diff --git a/src/help.jl b/src/help.jl deleted file mode 100644 index e69de29b..00000000 From d047fc13ecdcece5bd8864074d4024e9c75e5000 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 3 Jan 2022 11:16:56 -0800 Subject: [PATCH 147/368] license --- LICENSE | 22 +--------------------- README.md | 2 ++ 2 files changed, 3 insertions(+), 21 deletions(-) diff --git a/LICENSE b/LICENSE index 42dfa57e..b5b36355 100644 --- a/LICENSE +++ b/LICENSE @@ -1,21 +1 @@ -MIT License - -Copyright (c) 2021 Chad Scherrer and contributors - -Permission is hereby granted, free of charge, to any person obtaining a copy -of this software and associated documentation files (the "Software"), to deal -in the Software without restriction, including without limitation the rights -to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -copies of the Software, and to permit persons to whom the Software is -furnished to do so, subject to the following conditions: - -The above copyright notice and this permission notice shall be included in all -copies or substantial portions of the Software. - -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE -SOFTWARE. +This work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/4.0/ or send a letter to Creative Commons, PO Box 1866, Mountain View, CA 94042, USA. \ No newline at end of file diff --git a/README.md b/README.md index f407b430..84c2a4a8 100644 --- a/README.md +++ b/README.md @@ -5,4 +5,6 @@ [![Build Status](https://github.com/cscherrer/MeasureBase.jl/workflows/CI/badge.svg)](https://github.com/cscherrer/MeasureBase.jl/actions) [![Coverage](https://codecov.io/gh/cscherrer/MeasureBase.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/cscherrer/MeasureBase.jl) +Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. + This package is a lightweight version of [MeasureTheory](https://github.com/cscherrer/MeasureTheory.jl). It contains only the basic functionalities needed to define and use measures. \ No newline at end of file From 7fb384aabcd1c49339e6a089e42da08cc138ec6f Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 5 Jan 2022 10:00:05 -0800 Subject: [PATCH 148/368] affero --- LICENSE | 662 +++++++++++++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 661 insertions(+), 1 deletion(-) diff --git a/LICENSE b/LICENSE index b5b36355..be3f7b28 100644 --- a/LICENSE +++ b/LICENSE @@ -1 +1,661 @@ -This work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. 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Interpretation of Sections 15 and 16. + + If the disclaimer of warranty and limitation of liability provided +above cannot be given local legal effect according to their terms, +reviewing courts shall apply local law that most closely approximates +an absolute waiver of all civil liability in connection with the +Program, unless a warranty or assumption of liability accompanies a +copy of the Program in return for a fee. + + END OF TERMS AND CONDITIONS + + How to Apply These Terms to Your New Programs + + If you develop a new program, and you want it to be of the greatest +possible use to the public, the best way to achieve this is to make it +free software which everyone can redistribute and change under these terms. + + To do so, attach the following notices to the program. It is safest +to attach them to the start of each source file to most effectively +state the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + + Copyright (C) + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If your software can interact with users remotely through a computer +network, you should also make sure that it provides a way for users to +get its source. For example, if your program is a web application, its +interface could display a "Source" link that leads users to an archive +of the code. There are many ways you could offer source, and different +solutions will be better for different programs; see section 13 for the +specific requirements. + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU AGPL, see +. From 68dd214960121c14e0e14c26f595707bdc97df60 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 5 Jan 2022 14:34:05 -0800 Subject: [PATCH 149/368] copyright notice --- COPYRIGHT | 45 +++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 COPYRIGHT diff --git a/COPYRIGHT b/COPYRIGHT new file mode 100644 index 00000000..07af6586 --- /dev/null +++ b/COPYRIGHT @@ -0,0 +1,45 @@ +Copyright (c) 2022 Informative Prior, LLC +Copyright (c) 2022 Chad Scherrer + +This program is offered under a commercial and under the AGPL license. +For commercial licensing, contact us. For AGPL licensing, see below. + +AGPL licensing: +This program is free software: you can redistribute it and/or modify +it under the terms of the GNU Affero General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. + +This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU Affero General Public License for more details. + +You should have received a copy of the GNU Affero General Public License +along with this program. If not, see . + +This file incorporates work covered by the following copyright and +permission notice: + + MIT License + + Copyright (c) 2020-2021 Chad Scherrer and contributors + + Permission is hereby granted, free of charge, to any person obtaining a copy + of this software and associated documentation files (the "Software"), to deal + in the Software without restriction, including without limitation the rights + to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + copies of the Software, and to permit persons to whom the Software is + furnished to do so, subject to the following conditions: + + The above copyright notice and this permission notice shall be included in all + copies or substantial portions of the Software. + + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE + AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER + LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, + OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE + SOFTWARE. + From 143d7a7e162e1e3ae97c61346eeb6be75ccd8363 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Sat, 22 Jan 2022 07:10:47 -0800 Subject: [PATCH 150/368] merge --- src/combinators/for.jl | 57 +++++++++++++++++++++++++++++++--------- src/combinators/power.jl | 9 ++++--- src/utils.jl | 6 ++++- 3 files changed, 55 insertions(+), 17 deletions(-) diff --git a/src/combinators/for.jl b/src/combinators/for.jl index d8c1c14b..bbd6f3d0 100644 --- a/src/combinators/for.jl +++ b/src/combinators/for.jl @@ -9,14 +9,42 @@ struct For{T, F, I} <: AbstractProductMeasure @inline function For(f::F, inds::I) where {F,I<:Tuple} T = Core.Compiler.return_type(f, Tuple{_eltype.(inds)...}) + new{T,F,I}(f, inds) + end + + @inline function For{T}(f::F, inds::I) where {T,F,I<:Tuple} new{T,instance_type(f),I}(f, inds) end - For{T,F,I}(f::F, inds::I) where {T,F,I} = new{T,F,I}(f,inds) + @inline For{T,F,I}(f::F, inds::I) where {T,F,I} = new{T,F,I}(f,inds) end # For(f, gen::Base.Generator) = ProductMeasure(Base.Generator(f ∘ gen.f, gen.iter)) +@inline function logdensity_def(d::For{T,F,I}, x::AbstractVector{X}) where {X,T,F,I<:Tuple{<:AbstractVector}} + ℓ = zero(typeintersect(AbstractFloat, Core.Compiler.return_type(logdensity_def, Tuple{T,X}))) + @inbounds for j in eachindex(x) + ℓ += logdensity_def(d.f(j), x[j]) + end + ℓ +end + +function logdensity_def(d::For, x::AbstractVector) + sum(eachindex(x)) do i + @inbounds logdensity_def(d.f(getindex.(d.inds,i)...), x[i]) + end +end + +function logdensity_def(d::For{T,F,I}, x::AbstractArray{X}) where {T,F,I,X} + ℓ = zero(typeintersect(AbstractFloat, Core.Compiler.return_type(logdensity_def, Tuple{T,X}))) + + @inbounds for j in CartesianIndices(x) + i = (getindex(ind, j) for ind in d.inds) + ℓ += logdensity_def(d.f(i...), x[j]) + end + ℓ +end + function logdensity_def(d::For{T,F,I}, x) where {N,T,F,I<:NTuple{N,<:Base.Generator}} sum(zip(x, d.inds...)) do (xⱼ, dⱼ...) logdensity_def(d.f(dⱼ...), xⱼ) @@ -24,8 +52,9 @@ function logdensity_def(d::For{T,F,I}, x) where {N,T,F,I<:NTuple{N,<:Base.Genera end function marginals(d::For{T,F,I}) where {T,F,I} - f(x...) = d.f(x...)::T - mappedarray(f, d.inds...) + mappedarray(d.inds...) do x + d.f(x)::T + end end function marginals(d::For{T,F,I}) where {N,T,F,I<:NTuple{N,<:Base.Generator}} @@ -43,9 +72,8 @@ end end @inline function _basemeasure(d::For{T,F,I}, ::Type{B}, ::False) where {T,F,I,B<:AbstractMeasure} - new_f = basekleisli(d.f) - new_F = typeof(new_f) - For{B,new_F, I}(new_f, d.inds) + f = basekleisli(d.f) + For{B}(f, d.inds) end @inline function _basemeasure(d::For{T,F,I}, ::Type{B}, ::False) where {T,F,I,B} @@ -58,8 +86,7 @@ end function _basemeasure(d::For{T,F,I}, ::Type{B}, ::False) where {N,T<:AbstractMeasure,F,I<:NTuple{N,<:Base.Generator},B} f = basekleisli(d.f) - newF = typeof(f) - For{B,newF,I}(f, d.inds) + For{B}(f, d.inds) end function Pretty.tile(d::For{T}) where {T} @@ -146,14 +173,18 @@ julia> For(eachrow(rand(4,2))) do x Normal(x[1], x[2]) end |> marginals |> colle ``` """ -For(f, inds...) = For(f, inds) -For(f, n::Integer) = For(f, Base.OneTo(n)) -For(f, inds::Integer...) = For(i -> f(Tuple(i)...), Base.CartesianIndices(inds)) +@inline For{T}(f, inds...) where {T} = For{T}(f, inds) +@inline For{T}(f, n::Integer) where {T} = For{T}(f, Base.OneTo(n)) +@inline For{T}(f, inds::Integer...) where {T} = For{T}(i -> f(Tuple(i)...), Base.CartesianIndices(inds)) + +@inline For(f, inds...) = For(f, inds) +@inline For(f, n::Integer) = For(f, Base.OneTo(n)) +@inline For(f, inds::Integer...) = For(i -> f(Tuple(i)...), Base.CartesianIndices(inds)) # For(f, inds::Base.Generator) = productmeasure(mymap(f, inds)) -function Random.rand!(rng::AbstractRNG, d::For, x) +function Random.rand!(rng::AbstractRNG, d::For{T,F,I}, x) where {T,F,I} mar = marginals(d) - @inbounds for (dⱼ, j) in zip(marginals(d), eachindex(x)) + @inbounds for (dⱼ, j) in zip(mar, eachindex(x)) x[j] = rand(rng,dⱼ) end return x diff --git a/src/combinators/power.jl b/src/combinators/power.jl index 10f1088f..dd00eaff 100644 --- a/src/combinators/power.jl +++ b/src/combinators/power.jl @@ -59,8 +59,11 @@ params(d::PowerMeasure) = params(first(marginals(d))) basemeasure(d.parent) ^ d.axes end -@inline function logdensity_def(d::PowerMeasure, x) - sum(x) do xj - logdensity_def(d.parent, xj) +@inline function logdensity_def(d::PowerMeasure{M}, x) where {M} + T = eltype(x) + ℓ = zero(typeintersect(AbstractFloat,Core.Compiler.return_type(logdensity_def, Tuple{M,T}))) + parent = d.parent + @inbounds for xj in x + ℓ += logdensity_def(parent, xj) end end diff --git a/src/utils.jl b/src/utils.jl index f9ecaa21..bb767092 100644 --- a/src/utils.jl +++ b/src/utils.jl @@ -115,7 +115,7 @@ function _eltype(::Type{Base.Generator{I,ComposedFunction{Outer,Inner}}}) where _eltype(Base.Generator{_eltype(Base.Generator{I,Inner}), Outer}) end -function _eltype(::Type{Base.Generator{I,F}}) where {F<:Function,I} +function _eltype(::Type{Base.Generator{I,F}}) where {F,I} f = instance(F) Core.Compiler.return_type(f, Tuple{_eltype(I)}) end @@ -127,3 +127,7 @@ end mymap(f, gen::Base.Generator) = mymap(f ∘ gen.f, gen.iter) mymap(f, inds...) = Iterators.map(f, inds...) +function infer_zero(f, args...) + inferred_type = Core.Compiler.return_type(f, typeof.(args)) + zero(typeintersect(AbstractFloat, inferred_type)) +end From 040c815ab6c47f8e6687eae0fea4da20d2f58278 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Sat, 22 Jan 2022 07:19:24 -0800 Subject: [PATCH 151/368] Drop Create Commons --- README.md | 2 -- 1 file changed, 2 deletions(-) diff --git a/README.md b/README.md index 84c2a4a8..f407b430 100644 --- a/README.md +++ b/README.md @@ -5,6 +5,4 @@ [![Build Status](https://github.com/cscherrer/MeasureBase.jl/workflows/CI/badge.svg)](https://github.com/cscherrer/MeasureBase.jl/actions) [![Coverage](https://codecov.io/gh/cscherrer/MeasureBase.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/cscherrer/MeasureBase.jl) -Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. - This package is a lightweight version of [MeasureTheory](https://github.com/cscherrer/MeasureTheory.jl). It contains only the basic functionalities needed to define and use measures. \ No newline at end of file From ae80dc114c3707eb6865ae1ac6c8820aceb279ac Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Sat, 22 Jan 2022 10:22:16 -0800 Subject: [PATCH 152/368] cleanup after merge --- src/MeasureBase.jl | 1 + src/combinators/for.jl | 13 ++++++++----- src/combinators/pointwise.jl | 6 +----- src/combinators/product.jl | 6 ++++-- src/splat.jl | 11 +++++++++++ 5 files changed, 25 insertions(+), 12 deletions(-) create mode 100644 src/splat.jl diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index de6dc725..7083c324 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -64,6 +64,7 @@ function logdensity_def end using Compat +include("splat.jl") include("partial-static.jl") include("proxies.jl") include("kleisli.jl") diff --git a/src/combinators/for.jl b/src/combinators/for.jl index bbd6f3d0..e7a4594d 100644 --- a/src/combinators/for.jl +++ b/src/combinators/for.jl @@ -51,15 +51,18 @@ function logdensity_def(d::For{T,F,I}, x) where {N,T,F,I<:NTuple{N,<:Base.Genera end end -function marginals(d::For{T,F,I}) where {T,F,I} - mappedarray(d.inds...) do x - d.f(x)::T +function logdensity_def(d::For{T,F,I}, x::AbstractVector) where {N,T,F,I<:NTuple{N,<:Base.Generator}} + sum(zip(x, d.inds...)) do (xⱼ, dⱼ...) + logdensity_def(d.f(dⱼ...), xⱼ) end end +function marginals(d::For{T,F,I}) where {T,F,I} + mappedarray(d.f, d.inds...) +end + function marginals(d::For{T,F,I}) where {N,T,F,I<:NTuple{N,<:Base.Generator}} - f(x...) = d.f(x...)::T - Iterators.map(f, d.inds...) + Iterators.map(d.f, d.inds...) end @inline function basemeasure(d::For{T,F,I}) where {T,F,I} diff --git a/src/combinators/pointwise.jl b/src/combinators/pointwise.jl index 6efa6c0a..672e06fb 100644 --- a/src/combinators/pointwise.jl +++ b/src/combinators/pointwise.jl @@ -10,8 +10,6 @@ struct PointwiseProductMeasure{M,L} <: AbstractMeasure end end -Base.size(μ::PointwiseProductMeasure) = size(μ.data) - function Base.show(io::IO, μ::PointwiseProductMeasure) io = IOContext(io, :compact => true) print(io, μ.measure, " ⊙ ", μ.likelihood) @@ -29,9 +27,7 @@ function Base.show_unquoted(io::IO, μ::PointwiseProductMeasure, indent::Int, pr return nothing end -Base.length(m::PointwiseProductMeasure{T}) where {T} = length(m.data) - -⊙(args...) = pointwiseproduct(args...) +⊙(μ, ℓ) = pointwiseproduct(μ, ℓ) @inline function logdensity_def(d::PointwiseProductMeasure, x) logdensity_def(d.measure, x) + logdensity_def(d.likelihood, x) diff --git a/src/combinators/product.jl b/src/combinators/product.jl index db0b7d07..0e4370cb 100644 --- a/src/combinators/product.jl +++ b/src/combinators/product.jl @@ -60,16 +60,17 @@ end end function basemeasure(μ::ProductMeasure{Base.Generator{I,F}}) where {I,F} + mar = marginals(μ) T = Core.Compiler.return_type(mar.f, Tuple{_eltype(mar.iter)}) B = Core.Compiler.return_type(basemeasure, Tuple{T}) - _basemeasure(μ, B, static(Base.issingulartype(B))) + _basemeasure(μ, B, static(Base.issingletontype(B))) end function basemeasure(μ::ProductMeasure{A}) where {T,A<:AbstractMappedArray{T}} B = Core.Compiler.return_type(basemeasure, Tuple{T}) - _basemeasure(μ, B, static(Base.issingulartype(B))) + _basemeasure(μ, B, static(Base.issingletontype(B))) end function _basemeasure(μ::ProductMeasure, ::Type{B}, ::True) where {T,B} @@ -77,6 +78,7 @@ function _basemeasure(μ::ProductMeasure, ::Type{B}, ::True) where {T,B} end function _basemeasure(μ::ProductMeasure{A}, ::Type{B}, ::False) where {T,A<:AbstractMappedArray{T},B} + mar = marginals(μ) productmeasure(mappedarray(basemeasure, mar)) end diff --git a/src/splat.jl b/src/splat.jl new file mode 100644 index 00000000..d6209b67 --- /dev/null +++ b/src/splat.jl @@ -0,0 +1,11 @@ +struct Splat{F} + f::F +end + +function (s::Splat{F})(x) where F + s.f(x...) +end + +unsplat(s::Splat) = s.f + +splat(f) = Splat(f) From d6c12f51cab2778275683b37de3f356048894983 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 24 Jan 2022 07:47:10 -0800 Subject: [PATCH 153/368] update support computations --- Project.toml | 4 +++- src/MeasureBase.jl | 1 + src/combinators/factoredbase.jl | 10 ++-------- src/combinators/for.jl | 32 +++++++++++++++++++++++++------- src/combinators/half.jl | 7 +++++-- src/combinators/power.jl | 8 ++++++++ src/combinators/product.jl | 5 +++++ src/combinators/spikemixture.jl | 2 ++ src/combinators/weighted.jl | 2 ++ src/density.jl | 10 ++++++++-- src/primitives/counting.jl | 4 +++- src/primitives/lebesgue.jl | 4 ++++ src/utils.jl | 9 ++++++--- 13 files changed, 74 insertions(+), 24 deletions(-) diff --git a/Project.toml b/Project.toml index f5137fdb..4b19ecdc 100644 --- a/Project.toml +++ b/Project.toml @@ -8,6 +8,7 @@ Compat = "34da2185-b29b-5c13-b0c7-acf172513d20" ConstructionBase = "187b0558-2788-49d3-abe0-74a17ed4e7c9" DensityInterface = "b429d917-457f-4dbc-8f4c-0cc954292b1d" FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b" +IfElse = "615f187c-cbe4-4ef1-ba3b-2fcf58d6d173" LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" LogExpFunctions = "2ab3a3ac-af41-5b50-aa03-7779005ae688" MappedArrays = "dbb5928d-eab1-5f90-85c2-b9b0edb7c900" @@ -24,11 +25,12 @@ Compat = "3.35" ConstructionBase = "1.3" DensityInterface = "0.4" FillArrays = "0.12" +IfElse = "0.1" LogExpFunctions = "0.3" MappedArrays = "0.4" PrettyPrinting = "0.3" Reexport = "1" -Static = "0.4" +Static = "0.5" Tricks = "0.1" julia = "1.3" diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index 7083c324..ccd8e78a 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -45,6 +45,7 @@ gentype(μ::AbstractMeasure) = typeof(testvalue(μ)) # gentype(μ::AbstractMeasure) = gentype(basemeasure(μ)) +import IfElse: ifelse export logdensity_def export basemeasure export basekleisli diff --git a/src/combinators/factoredbase.jl b/src/combinators/factoredbase.jl index 32aed8ca..e0abc283 100644 --- a/src/combinators/factoredbase.jl +++ b/src/combinators/factoredbase.jl @@ -1,24 +1,18 @@ export FactoredBase -struct FactoredBase{R,C,V,B} <: AbstractMeasure - inbounds::R +struct FactoredBase{C,V,B} <: AbstractMeasure constℓ::C varℓ::V base::B end -@inline function logdensity_def(d::FactoredBase{Returns{True}}, x) - d.constℓ + d.varℓ() -end - @inline function logdensity_def(d::FactoredBase, x) - d.inbounds(x) || return -Inf d.constℓ + d.varℓ() end function Pretty.tile(fb::FactoredBase) result = Pretty.literal("FactoredBase") - result *= Pretty.list_layout(Pretty.tile.([fb.inbounds, fb.constℓ, fb.varℓ, fb.base])) + result *= Pretty.list_layout(Pretty.tile.([fb.constℓ, fb.varℓ, fb.base])) result end diff --git a/src/combinators/for.jl b/src/combinators/for.jl index e7a4594d..e332a5b0 100644 --- a/src/combinators/for.jl +++ b/src/combinators/for.jl @@ -7,11 +7,6 @@ struct For{T, F, I} <: AbstractProductMeasure f::F inds::I - @inline function For(f::F, inds::I) where {F,I<:Tuple} - T = Core.Compiler.return_type(f, Tuple{_eltype.(inds)...}) - new{T,F,I}(f, inds) - end - @inline function For{T}(f::F, inds::I) where {T,F,I<:Tuple} new{T,instance_type(f),I}(f, inds) end @@ -19,10 +14,21 @@ struct For{T, F, I} <: AbstractProductMeasure @inline For{T,F,I}(f::F, inds::I) where {T,F,I} = new{T,F,I}(f,inds) end + +@generated function For(f::F, inds::I) where {F,I<:Tuple} + eltypes = Tuple{eltype.(I.types)...} + quote + $(Expr(:meta, :inline)) + T = Core.Compiler.return_type(f, $eltypes) + For{T,F,I}(f, inds) + end +end + + # For(f, gen::Base.Generator) = ProductMeasure(Base.Generator(f ∘ gen.f, gen.iter)) @inline function logdensity_def(d::For{T,F,I}, x::AbstractVector{X}) where {X,T,F,I<:Tuple{<:AbstractVector}} - ℓ = zero(typeintersect(AbstractFloat, Core.Compiler.return_type(logdensity_def, Tuple{T,X}))) + ℓ = 0.0 @inbounds for j in eachindex(x) ℓ += logdensity_def(d.f(j), x[j]) end @@ -57,8 +63,16 @@ function logdensity_def(d::For{T,F,I}, x::AbstractVector) where {N,T,F,I<:NTuple end end +function marginals(d::For{T,F,Tuple{I}}) where {T,F,I} + f = d.f + data = first(d.inds) + MappedArrays.ReadonlyMappedArray{T,ndims(data),typeof(data),typeof(f)}(f, data) +end + function marginals(d::For{T,F,I}) where {T,F,I} - mappedarray(d.f, d.inds...) + f = d.f + data = d.inds + MappedArrays.ReadonlyMultiMappedArray{T,ndims(first(data)),typeof(data),typeof(f)}(f, data) end function marginals(d::For{T,F,I}) where {N,T,F,I<:NTuple{N,<:Base.Generator}} @@ -105,6 +119,7 @@ function Pretty.tile(d::For{T}) where {T} end + """ For(f, base...) @@ -193,3 +208,6 @@ function Random.rand!(rng::AbstractRNG, d::For{T,F,I}, x) where {T,F,I} return x end +function Base.rand(rng::AbstractRNG, ::Type{T}, d::For{M,F,I}) where {T,M,F,I} + _rand_product(rng, T, marginals(d), M) +end \ No newline at end of file diff --git a/src/combinators/half.jl b/src/combinators/half.jl index 1c9bf4dd..a85dfd12 100644 --- a/src/combinators/half.jl +++ b/src/combinators/half.jl @@ -14,11 +14,10 @@ unhalf(μ::Half) = μ.parent isnonnegative(x) = x ≥ 0.0 @inline function basemeasure(μ::Half) - inbounds = isnonnegative constℓ = static(logtwo) varℓ = Returns(static(0.0)) base = basemeasure(unhalf(μ)) - FactoredBase(inbounds, constℓ, varℓ, base) + FactoredBase(constℓ, varℓ, base) end function Base.rand(rng::AbstractRNG, T::Type, μ::Half) @@ -26,3 +25,7 @@ function Base.rand(rng::AbstractRNG, T::Type, μ::Half) end logdensity_def(μ::Half, x) = logdensity_def(unhalf(μ), x) + +@inline function insupport(d::Half, x) + ifelse(isnonnegative(x), insupport(unhalf(d), x), false) +end \ No newline at end of file diff --git a/src/combinators/power.jl b/src/combinators/power.jl index db070960..bcb5d8dc 100644 --- a/src/combinators/power.jl +++ b/src/combinators/power.jl @@ -73,3 +73,11 @@ end end ℓ end + + +@inline function insupport(μ::PowerMeasure, x) + all(x) do xj + # https://github.com/SciML/Static.jl/issues/36 + dynamic(insupport(μ.parent, xj)) + end +end \ No newline at end of file diff --git a/src/combinators/product.jl b/src/combinators/product.jl index 0e4370cb..7af7ac88 100644 --- a/src/combinators/product.jl +++ b/src/combinators/product.jl @@ -134,3 +134,8 @@ function _rand(rng::AbstractRNG, ::Type{T}, d::ProductMeasure, mar::AbstractArra x = Array{elT,length(sz)}(undef, sz) rand!(rng, d, x) end + + +@inline function insupport(d::AbstractProductMeasure, x) + all(dynamic.(insupport.(marginals(d), x))) +end \ No newline at end of file diff --git a/src/combinators/spikemixture.jl b/src/combinators/spikemixture.jl index 04b37a28..dfc0d958 100644 --- a/src/combinators/spikemixture.jl +++ b/src/combinators/spikemixture.jl @@ -39,3 +39,5 @@ function Base.rand(rng::AbstractRNG, T::Type, μ::SpikeMixture) end testvalue(μ::SpikeMixture) = testvalue(μ.m) + +insupport(μ::SpikeMixture, x) = dynamic(insupport(μ.m, x)) || iszero(x) \ No newline at end of file diff --git a/src/combinators/weighted.jl b/src/combinators/weighted.jl index 7018de2a..bc6e88e5 100644 --- a/src/combinators/weighted.jl +++ b/src/combinators/weighted.jl @@ -69,3 +69,5 @@ end basemeasure(d::ParamWeightedMeasure) = d.base logdensity_def(d::ParamWeightedMeasure, x) = d.ℓ(d.par) + +insupport(μ::WeightedMeasure, x) = insupport(μ.base, x) \ No newline at end of file diff --git a/src/density.jl b/src/density.jl index b17401bd..244a6981 100644 --- a/src/density.jl +++ b/src/density.jl @@ -68,7 +68,9 @@ function _densitymeasure(f, base, _) """ end - +@inline function insupport(d::DensityMeasure, x) + ifelse(insupport(d.base, x), logdensityof(d.f, x) > -Inf, false) +end basemeasure(μ::DensityMeasure) = μ.base @@ -101,7 +103,11 @@ Define a new measure in terms of a log-density `f` over some measure `base`. # TODO: `density` and `logdensity` functions for `DensityMeasure` -@inline logdensityof(μ, x) = dynamic(_logdensityof(μ, x)) +@inline function logdensityof(μ, x) + ifelse(insupport(μ, x), unsafe_logdensityof(μ, x), -Inf) +end + +@inline unsafe_logdensityof(μ, x) = dynamic(_logdensityof(μ, x)) @inline _logdensityof(μ, x) = _logdensityof(μ, basemeasure(μ, x), x) diff --git a/src/primitives/counting.jl b/src/primitives/counting.jl index 874d3e10..cf3df1b6 100644 --- a/src/primitives/counting.jl +++ b/src/primitives/counting.jl @@ -4,6 +4,8 @@ export Counting, CountingMeasure struct CountingMeasure <: PrimitiveMeasure end +insupport(::CountingMeasure, x) = true + struct Counting{T} <: AbstractMeasure support::T @@ -28,4 +30,4 @@ Base.show(io::IO, d::Counting) = print(io, "Counting(", d.support, ")") insupport(μ::Counting, x) = x ∈ μ.support -insupport(μ::Counting{T}, x) where {T<:Type} = x isa T \ No newline at end of file +insupport(μ::Counting{T}, x) where {T<:Type} = x isa μ.support \ No newline at end of file diff --git a/src/primitives/lebesgue.jl b/src/primitives/lebesgue.jl index d218064f..77f411f9 100644 --- a/src/primitives/lebesgue.jl +++ b/src/primitives/lebesgue.jl @@ -6,6 +6,10 @@ struct LebesgueMeasure <: PrimitiveMeasure end testvalue(::LebesgueMeasure) = 0.0 +insupport(::LebesgueMeasure, x) = true + +insupprot(::LebesgueMeasure) = Returns(true) + struct Lebesgue{T} <: AbstractMeasure support::T end diff --git a/src/utils.jl b/src/utils.jl index 1dc4ac80..3c9057bd 100644 --- a/src/utils.jl +++ b/src/utils.jl @@ -41,11 +41,14 @@ end using Tricks struct Iterable end struct NonIterable end -isiterable(::Type{T}) where {T} = +function isiterable(::Type{T}) where {T} static_hasmethod(iterate, Tuple{T}) ? Iterable() : NonIterable() +end + +# issingletontype(@nospecialize(t)) = (@_pure_meta; isa(t, DataType) && isdefined(t, :instance)) + -@inline function instance(@nospecialize(T)) - Base.@_pure_meta +@generated function instance(::Type{T}) where {T} return getfield(T, :instance)::T end From 2f5c31d7f832e8a32f8558c541a4451aa2a1b213 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 24 Jan 2022 10:05:06 -0800 Subject: [PATCH 154/368] insupport(d::SuperpositionMeasure, x) --- src/combinators/superpose.jl | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/src/combinators/superpose.jl b/src/combinators/superpose.jl index 2c06618b..a3fc407f 100644 --- a/src/combinators/superpose.jl +++ b/src/combinators/superpose.jl @@ -68,3 +68,9 @@ basemeasure(μ::SuperpositionMeasure) = superpose(map(basemeasure, μ.components # function Base.rand(μ::SuperpositionMeasure{X,N}) where {X,N} # return rand(rand(μ.components)) # end + +@inline function insupport(d::SuperpositionMeasure, x) + any(d.components) do c + dynamic(insupport(c, x)) + end +end \ No newline at end of file From 35271fc696fc9aec580a7950932a2d50b92e5d5b Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 24 Jan 2022 10:05:19 -0800 Subject: [PATCH 155/368] dorp ParamWeighted --- src/combinators/weighted.jl | 18 ------------------ 1 file changed, 18 deletions(-) diff --git a/src/combinators/weighted.jl b/src/combinators/weighted.jl index bc6e88e5..827d30fd 100644 --- a/src/combinators/weighted.jl +++ b/src/combinators/weighted.jl @@ -52,22 +52,4 @@ Base.:*(m::AbstractMeasure, k::Real) = k * m gentype(μ::WeightedMeasure) = gentype(μ.base) -############################################################################### - -export ParamWeightedMeasure -struct ParamWeightedMeasure{L,N,T,B} <: AbstractWeightedMeasure - ℓ::L - par::NamedTuple{N,T} - base::B -end - -function Base.show(io::IO, d::ParamWeightedMeasure) - io = IOContext(io, :compact => true) - print(io, "ParamWeighted(", d.ℓ, ", ", d.par, ", ", d.base, ")") -end - -basemeasure(d::ParamWeightedMeasure) = d.base - -logdensity_def(d::ParamWeightedMeasure, x) = d.ℓ(d.par) - insupport(μ::WeightedMeasure, x) = insupport(μ.base, x) \ No newline at end of file From de9ccdd4760b508a3c166c57b1c9f8ed542d4f1c Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 24 Jan 2022 10:05:34 -0800 Subject: [PATCH 156/368] insupport(d::FactoredBase, x) --- src/combinators/factoredbase.jl | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/combinators/factoredbase.jl b/src/combinators/factoredbase.jl index e0abc283..166a568b 100644 --- a/src/combinators/factoredbase.jl +++ b/src/combinators/factoredbase.jl @@ -17,3 +17,5 @@ function Pretty.tile(fb::FactoredBase) end basemeasure(d::FactoredBase) = d.base + +insupport(d::FactoredBase, x) = insupport(d.base, x) \ No newline at end of file From 1e8615d586300865e8f6281e73cd276bef64cd91 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 24 Jan 2022 10:41:24 -0800 Subject: [PATCH 157/368] export unsafe_logdensityof --- src/density.jl | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/density.jl b/src/density.jl index 244a6981..3f243cf2 100644 --- a/src/density.jl +++ b/src/density.jl @@ -107,6 +107,8 @@ Define a new measure in terms of a log-density `f` over some measure `base`. ifelse(insupport(μ, x), unsafe_logdensityof(μ, x), -Inf) end +export unsafe_logdensityof + @inline unsafe_logdensityof(μ, x) = dynamic(_logdensityof(μ, x)) @inline _logdensityof(μ, x) = _logdensityof(μ, basemeasure(μ, x), x) From 305ed0e9f32af0138841c229868b9f86d82b415d Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 24 Jan 2022 12:27:06 -0800 Subject: [PATCH 158/368] call promote_type instead of promote_rule --- src/partial-static.jl | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/src/partial-static.jl b/src/partial-static.jl index 9cbac97c..71c57cf2 100644 --- a/src/partial-static.jl +++ b/src/partial-static.jl @@ -40,15 +40,15 @@ function Base.convert(::Type{PartialStatic{S, D}}, x::T) where {S, D, T<:(Static end function Base.promote_rule(::Type{PartialStatic{S1,D1}}, ::Type{PartialStatic{S2,D2}}) where {S1,D1,S2,D2} - PartialStatic{promote_rule(S1, S2), promote_rule(D1, D2)} + PartialStatic{promote_type(S1, S2), promote_rule(D1, D2)} end function promote_rule(::Type{PartialStatic{S, D}}, ::Type{StaticFloat64{N}}) where {N, S, D} - PartialStatic{promote_rule(StaticFloat64{N}, S), D} + PartialStatic{promote_type(StaticFloat64{N}, S), D} end function promote_rule(::Type{StaticFloat64{N}}, ::Type{PartialStatic{S, D}}) where {N, S, D} - PartialStatic{promote_rule(StaticFloat64{N}, S), D} + PartialStatic{promote_type(StaticFloat64{N}, S), D} end function Base.promote_rule(::Type{T}, ::Type{PartialStatic{S,D}}) where {T,S,D} @@ -60,11 +60,11 @@ function Base.promote_rule(::Type{PartialStatic{S,D}}, ::Type{T}) where {S,D,T} end function _promote(::Type{PartialStatic{S,D}}, ::Type{T}, ::True) where {S,D,T} - PartialStatic{promote_rule(S,T),D} + PartialStatic{promote_type(S,T),D} end function _promote(::Type{PartialStatic{S,D}}, ::Type{T}, ::False) where {S,D,T} - PartialStatic{S,promote_rule(D,T)} + PartialStatic{S,promote_type(D,T)} end partialstatic(s, d) = PartialStatic(s, d) From 0d355520153d60ac0dc3ad0b99696dde6ef6fc81 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 24 Jan 2022 12:27:27 -0800 Subject: [PATCH 159/368] logdensity_def for named tuple product measures --- src/combinators/product.jl | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/src/combinators/product.jl b/src/combinators/product.jl index 7af7ac88..fe3ac609 100644 --- a/src/combinators/product.jl +++ b/src/combinators/product.jl @@ -59,6 +59,21 @@ end sum(ℓs) end +@generated function logdensity_def(d::ProductMeasure{NamedTuple{N,T}}, x) where {N,T} + k1 = QuoteNode(first(N)) + q = quote + m = marginals(d) + ℓ = logdensity_def(getproperty(m, $k1), getproperty(x, $k1)) + end + for k in Base.tail(N) + k = QuoteNode(k) + qk = :(ℓ += logdensity_def(getproperty(m, $k), getproperty(x, $k))) + push!(q.args, qk) + end + + return q +end + function basemeasure(μ::ProductMeasure{Base.Generator{I,F}}) where {I,F} mar = marginals(μ) T = Core.Compiler.return_type(mar.f, Tuple{_eltype(mar.iter)}) From cf45278d1414c3f0044b1cdd6e3f6d9a7f49c4fd Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 24 Jan 2022 12:28:25 -0800 Subject: [PATCH 160/368] type annotation for now --- src/density.jl | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/density.jl b/src/density.jl index 3f243cf2..0dbcbdc8 100644 --- a/src/density.jl +++ b/src/density.jl @@ -109,7 +109,8 @@ end export unsafe_logdensityof -@inline unsafe_logdensityof(μ, x) = dynamic(_logdensityof(μ, x)) +# TODO: REmove the type annotation +@inline unsafe_logdensityof(μ, x) = dynamic(_logdensityof(μ, x))::Float64 @inline _logdensityof(μ, x) = _logdensityof(μ, basemeasure(μ, x), x) From e6705afd146699eea34042c9eb13d00662f9b97f Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 25 Jan 2022 14:51:10 -0800 Subject: [PATCH 161/368] debugging --- src/MeasureBase.jl | 1 - src/combinators/conditional.jl | 6 -- src/combinators/half.jl | 6 +- src/combinators/power.jl | 6 +- src/combinators/product.jl | 16 +++++ src/combinators/smart-constructors.jl | 7 +++ src/density.jl | 9 ++- src/partial-static.jl | 84 +++++++++++++++------------ src/utils.jl | 11 ++++ 9 files changed, 93 insertions(+), 53 deletions(-) diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index ccd8e78a..6890f6e2 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -94,7 +94,6 @@ include("combinators/likelihood.jl") include("combinators/pointwise.jl") include("combinators/restricted.jl") include("combinators/smart-constructors.jl") -include("combinators/conditional.jl") include("rand.jl") diff --git a/src/combinators/conditional.jl b/src/combinators/conditional.jl index a1b15913..e69de29b 100644 --- a/src/combinators/conditional.jl +++ b/src/combinators/conditional.jl @@ -1,6 +0,0 @@ -struct ConditionalMeasure{M,C} <: AbstractMeasure - parent::M - constraint::C -end - -Base.:|(μ::AbstractMeasure, constraint) = ConditionalMeasure(μ, constraint) diff --git a/src/combinators/half.jl b/src/combinators/half.jl index a85dfd12..d2b8deda 100644 --- a/src/combinators/half.jl +++ b/src/combinators/half.jl @@ -20,7 +20,7 @@ isnonnegative(x) = x ≥ 0.0 FactoredBase(constℓ, varℓ, base) end -function Base.rand(rng::AbstractRNG, T::Type, μ::Half) +function Base.rand(rng::AbstractRNG, ::Type{T}, μ::Half) where {T} return abs(rand(rng, T, unhalf(μ))) end @@ -28,4 +28,6 @@ logdensity_def(μ::Half, x) = logdensity_def(unhalf(μ), x) @inline function insupport(d::Half, x) ifelse(isnonnegative(x), insupport(unhalf(d), x), false) -end \ No newline at end of file +end + +testvalue(::Half) = 1.0 \ No newline at end of file diff --git a/src/combinators/power.jl b/src/combinators/power.jl index bcb5d8dc..a973eaac 100644 --- a/src/combinators/power.jl +++ b/src/combinators/power.jl @@ -66,7 +66,8 @@ end @inline function logdensity_def(d::PowerMeasure{M}, x) where {M} T = eltype(x) - ℓ = zero(typeintersect(AbstractFloat,Core.Compiler.return_type(logdensity_def, Tuple{M,T}))) + ℓ = 0.0 + # ℓ = zero(typeintersect(AbstractFloat,Core.Compiler.return_type(logdensity_def, Tuple{M,T}))) parent = d.parent @inbounds for xj in x ℓ += logdensity_def(parent, xj) @@ -76,8 +77,9 @@ end @inline function insupport(μ::PowerMeasure, x) + p = μ.parent all(x) do xj # https://github.com/SciML/Static.jl/issues/36 - dynamic(insupport(μ.parent, xj)) + dynamic(insupport(p, xj)) end end \ No newline at end of file diff --git a/src/combinators/product.jl b/src/combinators/product.jl index fe3ac609..eb1760cb 100644 --- a/src/combinators/product.jl +++ b/src/combinators/product.jl @@ -74,6 +74,20 @@ end return q end +@generated function basemeasure(d::ProductMeasure{NamedTuple{N,T}}, x) where {N,T} + q = quote + m = marginals(d) + end + for k in N + qk = QuoteNode(k) + push!(q.args, :($k = basemeasure(getproperty(m, $qk)))) + end + + vals = map(x -> Expr(:(=), x,x), N) + push!(q, Expr(:tuple, vals...)) + return q +end + function basemeasure(μ::ProductMeasure{Base.Generator{I,F}}) where {I,F} mar = marginals(μ) T = Core.Compiler.return_type(mar.f, Tuple{_eltype(mar.iter)}) @@ -152,5 +166,7 @@ end @inline function insupport(d::AbstractProductMeasure, x) + @show d + @show x all(dynamic.(insupport.(marginals(d), x))) end \ No newline at end of file diff --git a/src/combinators/smart-constructors.jl b/src/combinators/smart-constructors.jl index 83393ac9..0ef85ca0 100644 --- a/src/combinators/smart-constructors.jl +++ b/src/combinators/smart-constructors.jl @@ -30,6 +30,13 @@ end productmeasure(mar::Base.Generator) = ProductMeasure(mar) productmeasure(mar::AbstractArray) = ProductMeasure(mar) + + +# TODO: Make this static when its length is static +@inline function productmeasure(mar::AbstractArray{WeightedMeasure{StaticFloat64{W}, M}}) where {W,M} + return weightedmeasure(W * length(mar), productmeasure(map(basemeasure, mar))) +end + productmeasure(nt::NamedTuple) = ProductMeasure(nt) productmeasure(tup::Tuple) = ProductMeasure(tup) diff --git a/src/density.jl b/src/density.jl index 0dbcbdc8..7d09a6e7 100644 --- a/src/density.jl +++ b/src/density.jl @@ -104,13 +104,14 @@ Define a new measure in terms of a log-density `f` over some measure `base`. # TODO: `density` and `logdensity` functions for `DensityMeasure` @inline function logdensityof(μ, x) - ifelse(insupport(μ, x), unsafe_logdensityof(μ, x), -Inf) + dynamic(insupport(μ, x)) || return -Inf + return unsafe_logdensityof(μ, x) end export unsafe_logdensityof # TODO: REmove the type annotation -@inline unsafe_logdensityof(μ, x) = dynamic(_logdensityof(μ, x))::Float64 +@inline unsafe_logdensityof(μ, x) = dynamic(_logdensityof(μ, x)) @inline _logdensityof(μ, x) = _logdensityof(μ, basemeasure(μ, x), x) @@ -124,7 +125,7 @@ end @inline function _logdensityof(μ::M, β, x, ℓ) where {M} n = static(basemeasure_depth(β)) - _logdensityof(β, basemeasure(β,x), x, ℓ, n) + _logdensityof(β, basemeasure(β), x, ℓ, n) end @generated function _logdensityof(μ, β, x, ℓ, ::StaticInt{n}) where {n} @@ -134,9 +135,7 @@ end # @show ℓ Base.Cartesian.@nexprs $nsteps i -> begin Δℓ = logdensity_def(μ, x) - # @show μ # @show Δℓ - # println() μ,β = β, basemeasure(β, x) ℓ += partialstatic(Δℓ) end diff --git a/src/partial-static.jl b/src/partial-static.jl index 71c57cf2..3c515e21 100644 --- a/src/partial-static.jl +++ b/src/partial-static.jl @@ -3,23 +3,23 @@ using Static export PartialStatic export partialstatic +import Base.promote_rule + struct PartialStatic{S,D} <: AbstractFloat static::S dynamic::D - function PartialStatic(s::S, d::D) where {S,D} + @inline function PartialStatic(s::S, d::D) where {S,D} @assert known(is_static(s)) new{S,D}(s, d) end end -function Static.dynamic(x::PartialStatic) - dyn = dynamic(x.dynamic) - D = typeof(dyn) - (x.static + dyn)::D +@inline function Static.dynamic(x::PartialStatic) + dynamic(x.static) + dynamic(x.dynamic) end -function Base.show(io::IO, p::PartialStatic) +@inline function Base.show(io::IO, p::PartialStatic) print(io, "PartialStatic(") print(io, p.static) print(io, ", ") @@ -27,104 +27,114 @@ function Base.show(io::IO, p::PartialStatic) print(io, ")") end -function Base.convert(::Type{PartialStatic{S, D}}, x::T) where {S, D, T<:Number} +@inline Base.convert(::Type{F}, x::PartialStatic{StaticFloat64{N}, T}) where {F<:AbstractFloat, N,T} = Float64(N + x.dynamic) + +@inline function Base.convert(::Type{PartialStatic{Static.StaticFloat64{N}, D}}, x::PartialStatic{Static.StaticFloat64{N}, D}) where {D, N} + return x +end + +@inline function Base.convert(::Type{PartialStatic{S, D}}, x::T) where {S, D, T<:Number} partialstatic(x) end -function Base.convert(::Type{PartialStatic{S,D}}, x::T) where {S,D,T} +@inline function Base.convert(::Type{PartialStatic{S,D}}, x::T) where {S,D,T} partialstatic(x) end -function Base.convert(::Type{PartialStatic{S, D}}, x::T) where {S, D, T<:(StaticFloat64)} +@inline function Base.convert(::Type{PartialStatic{S, D}}, x::T) where {S, D, T<:(StaticFloat64)} partialstatic(x) end -function Base.promote_rule(::Type{PartialStatic{S1,D1}}, ::Type{PartialStatic{S2,D2}}) where {S1,D1,S2,D2} - PartialStatic{promote_type(S1, S2), promote_rule(D1, D2)} +@inline function Base.promote_rule(::Type{Static.StaticFloat64{N}}, ::Type{PartialStatic{S, D}}) where {N, S, D} + Base.promote_rule(Float64, D) end -function promote_rule(::Type{PartialStatic{S, D}}, ::Type{StaticFloat64{N}}) where {N, S, D} - PartialStatic{promote_type(StaticFloat64{N}, S), D} +@inline function Base.promote_rule(::Type{PartialStatic{S1,D1}}, ::Type{PartialStatic{S2,D2}}) where {S1,D1,S2,D2} + PartialStatic{promote_type(S1, S2), promote_rule(D1, D2)} end -function promote_rule(::Type{StaticFloat64{N}}, ::Type{PartialStatic{S, D}}) where {N, S, D} +@inline function Base.promote_rule(::Type{PartialStatic{S, D}}, ::Type{StaticFloat64{N}}) where {N, S, D} PartialStatic{promote_type(StaticFloat64{N}, S), D} end -function Base.promote_rule(::Type{T}, ::Type{PartialStatic{S,D}}) where {T,S,D} +@inline function Base.promote_rule(::Type{T}, ::Type{PartialStatic{S,D}}) where {T,S,D} _promote(PartialStatic{S,D}, T, is_static(T)) end -function Base.promote_rule(::Type{PartialStatic{S,D}}, ::Type{T}) where {S,D,T} +@inline function Base.promote_rule(::Type{PartialStatic{S,D}}, ::Type{T}) where {S,D,T} _promote(PartialStatic{S,D}, T, is_static(T)) end -function _promote(::Type{PartialStatic{S,D}}, ::Type{T}, ::True) where {S,D,T} +@inline function _promote(::Type{PartialStatic{S,D}}, ::Type{T}, ::True) where {S,D,T} PartialStatic{promote_type(S,T),D} end -function _promote(::Type{PartialStatic{S,D}}, ::Type{T}, ::False) where {S,D,T} +@inline function _promote(::Type{PartialStatic{S,D}}, ::Type{T}, ::False) where {S,D,T} PartialStatic{S,promote_type(D,T)} end -partialstatic(s, d) = PartialStatic(s, d) +@inline partialstatic(s, d) = PartialStatic(s, d) -partialstatic(x) = _partialstatic(x, is_static(x)) +@inline partialstatic(x) = _partialstatic(x, is_static(x)) -partialstatic(x::PartialStatic) = x +@inline partialstatic(x::PartialStatic) = x -_partialstatic(x, ::True) = PartialStatic(x, static(0.0)) +@inline _partialstatic(x, ::True) = PartialStatic(x, static(0.0)) -_partialstatic(x, ::False) = PartialStatic(static(0.0), x) +@inline _partialstatic(x, ::False) = PartialStatic(static(0.0), x) + +@inline function Base.:+(x::Static.StaticFloat64{X}, y::PartialStatic{Static.StaticFloat64{Y}, D}) where {X,Y,D} + PartialStatic(X+Y, y.dynamic) +end -function Base.:+(x::PartialStatic{S1,D1}, y::PartialStatic{S2,D2}) where {S1,D1,S2,D2} +@inline function Base.:+(x::PartialStatic{S1,D1}, y::PartialStatic{S2,D2}) where {S1,D1,S2,D2} PartialStatic(x.static + y.static, x.dynamic + y.dynamic) end -function Base.:-(x::PartialStatic{S1,D1}, y::PartialStatic{S2,D2}) where {S1,D1,S2,D2} +@inline function Base.:-(x::PartialStatic{S1,D1}, y::PartialStatic{S2,D2}) where {S1,D1,S2,D2} PartialStatic(x.static - y.static, x.dynamic - y.dynamic) end Base.eps(::Type{PartialStatic{S,D}}) where {S,D} = max(Base.eps(known(S)), Base.eps(D)) -# function Base.:-(x::PartialStatic{S,D}, y::StaticFloat64{Y}) where {S,D,Y} +# @inline function Base.:-(x::PartialStatic{S,D}, y::StaticFloat64{Y}) where {S,D,Y} # PartialStatic(x.static - y, x.dynamic) # end -# function Base.:+(x::PartialStatic{S,D}, y::Number) where {S,D} +# @inline function Base.:+(x::PartialStatic{S,D}, y::Number) where {S,D} # PartialStatic(x.static, x.dynamic + y) # end -# function Base.:-(x::PartialStatic{S,D}, y::Number) where {S,D} +# @inline function Base.:-(x::PartialStatic{S,D}, y::Number) where {S,D} # PartialStatic(x.static, x.dynamic - y) # end -# function Base.:+(x::PartialStatic{S,D}, y) where {S,D} +# @inline function Base.:+(x::PartialStatic{S,D}, y) where {S,D} # PartialStatic(x.static, x.dynamic + y) # end -# function Base.:-(x::PartialStatic{S,D}, y) where {S,D} +# @inline function Base.:-(x::PartialStatic{S,D}, y) where {S,D} # PartialStatic(x.static, x.dynamic - y) # end -function add_partial_static(x::StaticFloat64, y::StaticFloat64) +@inline function add_partial_static(x::StaticFloat64, y::StaticFloat64) return x + y end -function add_partial_static(x::StaticFloat64, y::Real) +@inline function add_partial_static(x::StaticFloat64, y::Real) return PartialStatic(x, y) end -function add_partial_static(y::Real, x::StaticFloat64) +@inline function add_partial_static(y::Real, x::StaticFloat64) return PartialStatic(x, y) end -function add_partial_static(x, y) +@inline function add_partial_static(x, y) return x + y end Base.exp(x::PartialStatic) = exp(known(x.static) + x.dynamic) -Base.isapprox(x::PartialStatic, y::PartialStatic; kwargs...) = isapprox(dynamic(x), dynamic(y); kwargs...) -Base.isapprox(x::Number, y::PartialStatic; kwargs...) = isapprox(dynamic(x), dynamic(y); kwargs...) -Base.isapprox(x::PartialStatic, y::Number; kwargs...) = isapprox(dynamic(x), dynamic(y); kwargs...) \ No newline at end of file +@inline Base.isapprox(x::PartialStatic, y::PartialStatic; kwargs...) = isapprox(dynamic(x), dynamic(y); kwargs...) +@inline Base.isapprox(x::Number, y::PartialStatic; kwargs...) = isapprox(dynamic(x), dynamic(y); kwargs...) +@inline Base.isapprox(x::PartialStatic, y::Number; kwargs...) = isapprox(dynamic(x), dynamic(y); kwargs...) \ No newline at end of file diff --git a/src/utils.jl b/src/utils.jl index 3c9057bd..0614492c 100644 --- a/src/utils.jl +++ b/src/utils.jl @@ -135,3 +135,14 @@ function infer_zero(f, args...) inferred_type = Core.Compiler.return_type(f, typeof.(args)) zero(typeintersect(AbstractFloat, inferred_type)) end + +@inline function allequal(f, x::AbstractArray) + val = f(first(x)) + @simd for xj in x + f(xj) == val || return false + end + return true +end + + +allequal(x::AbstractArray) = allequal(identity, x) From 093282cdef427190e4e5e813fa549d7798d4ffaa Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 25 Jan 2022 16:09:09 -0800 Subject: [PATCH 162/368] drop shows --- src/combinators/product.jl | 2 -- 1 file changed, 2 deletions(-) diff --git a/src/combinators/product.jl b/src/combinators/product.jl index eb1760cb..ed3b58be 100644 --- a/src/combinators/product.jl +++ b/src/combinators/product.jl @@ -166,7 +166,5 @@ end @inline function insupport(d::AbstractProductMeasure, x) - @show d - @show x all(dynamic.(insupport.(marginals(d), x))) end \ No newline at end of file From 7843aea010dd7ef6c1f279e81ffc52034822cc0a Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Fri, 4 Feb 2022 08:52:13 -0800 Subject: [PATCH 163/368] speed up mapped arrays --- src/combinators/product.jl | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/src/combinators/product.jl b/src/combinators/product.jl index ed3b58be..88636f35 100644 --- a/src/combinators/product.jl +++ b/src/combinators/product.jl @@ -35,12 +35,26 @@ function _rand_product(rng::AbstractRNG, ::Type{T}, mar, ::Type{M}) where {T,M<: end end +function _rand_product(rng::AbstractRNG, ::Type{T}, mar::ReadonlyMappedArray, ::Type{M}) where {T,M<:AbstractMeasure} + map(mar.data) do dⱼ + rand(rng, T, mar.f(dⱼ)) + end +end + function _rand_product(rng::AbstractRNG, ::Type{T}, mar, ::Type{M}) where {T,M} map(mar) do dⱼ rand(rng, dⱼ) end end + +function _rand_product(rng::AbstractRNG, ::Type{T}, mar::ReadonlyMappedArray, ::Type{M}) where {T,M} + map(mar.data) do dⱼ + rand(rng, mar.f(dⱼ)) + end +end + + @inline function logdensity_def(d::AbstractProductMeasure, x) mapreduce(logdensity_def, +, marginals(d), x) end From 641d22259986ee6b17466bc3374883ab5ddbe6b9 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Fri, 4 Feb 2022 08:52:28 -0800 Subject: [PATCH 164/368] throw an error for `Union{}` types --- src/combinators/for.jl | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/src/combinators/for.jl b/src/combinators/for.jl index e332a5b0..f798f03e 100644 --- a/src/combinators/for.jl +++ b/src/combinators/for.jl @@ -12,6 +12,14 @@ struct For{T, F, I} <: AbstractProductMeasure end @inline For{T,F,I}(f::F, inds::I) where {T,F,I} = new{T,F,I}(f,inds) + + function For{Union{},F,I}(f::F, inds::I) where {F,I} + println("XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX") + println.(stacktrace()) + println("XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX") + @show f(first(zip(inds...))...) + @error "Empty `For` construction" + end end From 396405bfdb50fa4d64655b14b254b2075ec9562f Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 7 Feb 2022 13:16:33 -0800 Subject: [PATCH 165/368] MT tests passing --- src/MeasureBase.jl | 2 +- src/combinators/for.jl | 221 ------------------------------------- src/combinators/power.jl | 8 ++ src/combinators/product.jl | 15 ++- src/density.jl | 64 ++++++----- src/primitives/lebesgue.jl | 2 +- src/utils.jl | 85 ++++---------- 7 files changed, 82 insertions(+), 315 deletions(-) diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index 6890f6e2..fc9568fc 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -87,7 +87,6 @@ include("combinators/factoredbase.jl") include("combinators/weighted.jl") include("combinators/superpose.jl") include("combinators/product.jl") -include("combinators/for.jl") include("combinators/power.jl") include("combinators/spikemixture.jl") include("combinators/likelihood.jl") @@ -108,6 +107,7 @@ using MeasureBase:basemeasure_depth, proxy export test_interface export basemeasure_depth export proxy +export insupport include("interface.jl") end # module Interface diff --git a/src/combinators/for.jl b/src/combinators/for.jl index f798f03e..e69de29b 100644 --- a/src/combinators/for.jl +++ b/src/combinators/for.jl @@ -1,221 +0,0 @@ - -export For -using Random -import Base - -struct For{T, F, I} <: AbstractProductMeasure - f::F - inds::I - - @inline function For{T}(f::F, inds::I) where {T,F,I<:Tuple} - new{T,instance_type(f),I}(f, inds) - end - - @inline For{T,F,I}(f::F, inds::I) where {T,F,I} = new{T,F,I}(f,inds) - - function For{Union{},F,I}(f::F, inds::I) where {F,I} - println("XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX") - println.(stacktrace()) - println("XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX") - @show f(first(zip(inds...))...) - @error "Empty `For` construction" - end -end - - -@generated function For(f::F, inds::I) where {F,I<:Tuple} - eltypes = Tuple{eltype.(I.types)...} - quote - $(Expr(:meta, :inline)) - T = Core.Compiler.return_type(f, $eltypes) - For{T,F,I}(f, inds) - end -end - - -# For(f, gen::Base.Generator) = ProductMeasure(Base.Generator(f ∘ gen.f, gen.iter)) - -@inline function logdensity_def(d::For{T,F,I}, x::AbstractVector{X}) where {X,T,F,I<:Tuple{<:AbstractVector}} - ℓ = 0.0 - @inbounds for j in eachindex(x) - ℓ += logdensity_def(d.f(j), x[j]) - end - ℓ -end - -function logdensity_def(d::For, x::AbstractVector) - sum(eachindex(x)) do i - @inbounds logdensity_def(d.f(getindex.(d.inds,i)...), x[i]) - end -end - -function logdensity_def(d::For{T,F,I}, x::AbstractArray{X}) where {T,F,I,X} - ℓ = zero(typeintersect(AbstractFloat, Core.Compiler.return_type(logdensity_def, Tuple{T,X}))) - - @inbounds for j in CartesianIndices(x) - i = (getindex(ind, j) for ind in d.inds) - ℓ += logdensity_def(d.f(i...), x[j]) - end - ℓ -end - -function logdensity_def(d::For{T,F,I}, x) where {N,T,F,I<:NTuple{N,<:Base.Generator}} - sum(zip(x, d.inds...)) do (xⱼ, dⱼ...) - logdensity_def(d.f(dⱼ...), xⱼ) - end -end - -function logdensity_def(d::For{T,F,I}, x::AbstractVector) where {N,T,F,I<:NTuple{N,<:Base.Generator}} - sum(zip(x, d.inds...)) do (xⱼ, dⱼ...) - logdensity_def(d.f(dⱼ...), xⱼ) - end -end - -function marginals(d::For{T,F,Tuple{I}}) where {T,F,I} - f = d.f - data = first(d.inds) - MappedArrays.ReadonlyMappedArray{T,ndims(data),typeof(data),typeof(f)}(f, data) -end - -function marginals(d::For{T,F,I}) where {T,F,I} - f = d.f - data = d.inds - MappedArrays.ReadonlyMultiMappedArray{T,ndims(first(data)),typeof(data),typeof(f)}(f, data) -end - -function marginals(d::For{T,F,I}) where {N,T,F,I<:NTuple{N,<:Base.Generator}} - Iterators.map(d.f, d.inds...) -end - -@inline function basemeasure(d::For{T,F,I}) where {T,F,I} - B = Core.Compiler.return_type(basemeasure, Tuple{T}) - _basemeasure(d, B, static(Base.issingletontype(B))) -end - -@inline function _basemeasure(d::For{T,F,I}, ::Type{B}, ::True) where {T,F,I,B} - instance(B) ^ axes(d.inds) -end - -@inline function _basemeasure(d::For{T,F,I}, ::Type{B}, ::False) where {T,F,I,B<:AbstractMeasure} - f = basekleisli(d.f) - For{B}(f, d.inds) -end - -@inline function _basemeasure(d::For{T,F,I}, ::Type{B}, ::False) where {T,F,I,B} - productmeasure(basemeasure.(marginals(d))) -end - -function _basemeasure(d::For{T,F,I}, ::Type{B}, ::True) where {N,T<:AbstractMeasure,F,I<:NTuple{N,<:Base.Generator},B} - return instance(B) ^ minimum(length, d.inds) -end - -function _basemeasure(d::For{T,F,I}, ::Type{B}, ::False) where {N,T<:AbstractMeasure,F,I<:NTuple{N,<:Base.Generator},B} - f = basekleisli(d.f) - For{B}(f, d.inds) -end - -function Pretty.tile(d::For{T}) where {T} - result = Pretty.literal("For{") - result *= Pretty.tile(T) - result *= Pretty.literal("}") - result *= Pretty.list_layout( - [ - Pretty.literal(func_string(d.f, Tuple{_eltype.(d.inds)...})), - Pretty.tile.(d.inds)... - ] - ) -end - - - -""" - For(f, base...) - -`For` provides a convenient way to construct a `ProductMeasure`. There are -several options for the `base`. With Julia's `do` notation, this can look very -similar to a standard `for` loop, while maintaining semantics structure that's -easier to work with. - ------------- - -# `For(f, base::Int...)` - -When one or several `Int` values are passed for `base`, the result is treated as -depending on `CartesianIndices(base)`. - -``` -julia> For(3) do λ Exponential(λ) end |> marginals -3-element mappedarray(MeasureBase.var"#17#18"{var"#15#16"}(var"#15#16"()), ::CartesianIndices{1, Tuple{Base.OneTo{Int64}}}) with eltype Exponential{(:λ,), Tuple{Int64}}: - Exponential(λ = 1,) - Exponential(λ = 2,) - Exponential(λ = 3,) -``` - -``` -julia> For(4,3) do μ,σ Normal(μ,σ) end |> marginals -4×3 mappedarray(MeasureBase.var"#17#18"{var"#11#12"}(var"#11#12"()), ::CartesianIndices{2, Tuple{Base.OneTo{Int64}, Base.OneTo{Int64}}}) with eltype Normal{(:μ, :σ), Tuple{Int64, Int64}}: - Normal(μ = 1, σ = 1) Normal(μ = 1, σ = 2) Normal(μ = 1, σ = 3) - Normal(μ = 2, σ = 1) Normal(μ = 2, σ = 2) Normal(μ = 2, σ = 3) - Normal(μ = 3, σ = 1) Normal(μ = 3, σ = 2) Normal(μ = 3, σ = 3) - Normal(μ = 4, σ = 1) Normal(μ = 4, σ = 2) Normal(μ = 4, σ = 3) -``` - -------- - -# `For(f, base::AbstractArray...)`` - -In this case, `base` behaves as if the arrays are `zip`ped together before -applying the map. - -``` -julia> For(randn(3)) do x Exponential(x) end |> marginals -3-element mappedarray(x->Main.Exponential(x), ::Vector{Float64}) with eltype Exponential{(:λ,), Tuple{Float64}}: - Exponential(λ = -0.268256,) - Exponential(λ = 1.53044,) - Exponential(λ = -1.08839,) -``` - -``` -julia> For(1:3, 1:3) do μ,σ Normal(μ,σ) end |> marginals -3-element mappedarray((:μ, :σ)->Main.Normal(μ, σ), ::UnitRange{Int64}, ::UnitRange{Int64}) with eltype Normal{(:μ, :σ), Tuple{Int64, Int64}}: - Normal(μ = 1, σ = 1) - Normal(μ = 2, σ = 2) - Normal(μ = 3, σ = 3) -``` - ----- - -# `For(f, base::Base.Generator)` - -For `Generator`s, the function maps over the values of the generator: - -``` -julia> For(eachrow(rand(4,2))) do x Normal(x[1], x[2]) end |> marginals |> collect -4-element Vector{Normal{(:μ, :σ), Tuple{Float64, Float64}}}: - Normal(μ = 0.255024, σ = 0.570142) - Normal(μ = 0.970706, σ = 0.0776745) - Normal(μ = 0.731491, σ = 0.505837) - Normal(μ = 0.563112, σ = 0.98307) -``` - -""" -@inline For{T}(f, inds...) where {T} = For{T}(f, inds) -@inline For{T}(f, n::Integer) where {T} = For{T}(f, Base.OneTo(n)) -@inline For{T}(f, inds::Integer...) where {T} = For{T}(i -> f(Tuple(i)...), Base.CartesianIndices(inds)) - -@inline For(f, inds...) = For(f, inds) -@inline For(f, n::Integer) = For(f, Base.OneTo(n)) -@inline For(f, inds::Integer...) = For(i -> f(Tuple(i)...), Base.CartesianIndices(inds)) -# For(f, inds::Base.Generator) = productmeasure(mymap(f, inds)) - -function Random.rand!(rng::AbstractRNG, d::For{T,F,I}, x) where {T,F,I} - mar = marginals(d) - @inbounds for (dⱼ, j) in zip(mar, eachindex(x)) - x[j] = rand(rng,dⱼ) - end - return x -end - -function Base.rand(rng::AbstractRNG, ::Type{T}, d::For{M,F,I}) where {T,M,F,I} - _rand_product(rng, T, marginals(d), M) -end \ No newline at end of file diff --git a/src/combinators/power.jl b/src/combinators/power.jl index a973eaac..e1639982 100644 --- a/src/combinators/power.jl +++ b/src/combinators/power.jl @@ -82,4 +82,12 @@ end # https://github.com/SciML/Static.jl/issues/36 dynamic(insupport(p, xj)) end +end + +@inline function insupport(μ::PowerMeasure, x::AbstractArray) + p = μ.parent + all(x) do xj + # https://github.com/SciML/Static.jl/issues/36 + dynamic(insupport(p, xj)) + end end \ No newline at end of file diff --git a/src/combinators/product.jl b/src/combinators/product.jl index 88636f35..669de6ff 100644 --- a/src/combinators/product.jl +++ b/src/combinators/product.jl @@ -6,6 +6,8 @@ using Base: @propagate_inbounds import Base using FillArrays +export AbstractProductMeasure + abstract type AbstractProductMeasure <: AbstractMeasure end function Pretty.tile(μ::AbstractProductMeasure) @@ -179,6 +181,17 @@ function _rand(rng::AbstractRNG, ::Type{T}, d::ProductMeasure, mar::AbstractArra end +@inline function insupport(d::AbstractProductMeasure, x::AbstractArray) + mar = marginals(d) + for j in eachindex(x) + @inbounds dynamic(insupport(mar[j], x[j])) || return false + end + return true +end + @inline function insupport(d::AbstractProductMeasure, x) - all(dynamic.(insupport.(marginals(d), x))) + for (mj,xj) in zip(marginals(d), x) + dynamic(insupport(mj, xj)) || return false + end + return true end \ No newline at end of file diff --git a/src/density.jl b/src/density.jl index 7d09a6e7..8ca954fc 100644 --- a/src/density.jl +++ b/src/density.jl @@ -110,39 +110,47 @@ end export unsafe_logdensityof -# TODO: REmove the type annotation -@inline unsafe_logdensityof(μ, x) = dynamic(_logdensityof(μ, x)) - -@inline _logdensityof(μ, x) = _logdensityof(μ, basemeasure(μ, x), x) - -@inline function _logdensityof(μ, α, x) - _logdensityof(μ, α, x, partialstatic(logdensity_def(μ, x))) -end - -@inline function _logdensityof(μ::M, β::M, x, ℓ) where {M} - return ℓ -end - -@inline function _logdensityof(μ::M, β, x, ℓ) where {M} - n = static(basemeasure_depth(β)) - _logdensityof(β, basemeasure(β), x, ℓ, n) -end - -@generated function _logdensityof(μ, β, x, ℓ, ::StaticInt{n}) where {n} - nsteps = max(n, 0) - quote - $(Expr(:meta, :inline)) - # @show ℓ - Base.Cartesian.@nexprs $nsteps i -> begin - Δℓ = logdensity_def(μ, x) +# https://discourse.julialang.org/t/counting-iterations-to-a-type-fixpoint/75876/10?u=cscherrer +@inline function unsafe_logdensityof(μ::M, x) where {M} + ℓ_0 = (logdensity_def(μ, x)) + b_0 = μ + Base.Cartesian.@nexprs 10 i -> begin # 10 is just some "big enough" number + b_{i} = basemeasure(b_{i-1}) + b = b_{i} + # @show b + if b_{i} isa typeof(b_{i-1}) + return ℓ_{i-1} + end + ℓ_{i} = let Δt = @elapsed Δℓ = (logdensity_def(b_{i}, x)) + # @show Δt # @show Δℓ - μ,β = β, basemeasure(β, x) - ℓ += partialstatic(Δℓ) + ℓ_{i-1} + Δℓ end - return ℓ end + return ℓ_10 end +# # https://discourse.julialang.org/t/counting-iterations-to-a-type-fixpoint/75876/10?u=cscherrer +# @inline function unsafe_logdensityof(μ::M, x) where {M} +# unsafe_logdensityof(μ, x, basemeasure_depth(μ)) +# end + +# @generated function unsafe_logdensityof(μ, x, ::StaticInt{N}) where {N} +# q = quote +# ℓ = logdensity_def(μ, x) +# end + +# for j in 1:N +# push!(q.args, quote +# μ = basemeasure(μ) +# Δℓ = logdensity_def(μ, x) +# ℓ = ℓ + Δℓ +# end) +# end +# return q +# end + + @inline function logdensity_rel(μ::M, ν::N, x::X) where {M,N,X} (ℓ₊, α) = _logdensityof(μ, basemeasure(μ), x) (ℓ₋, β) = _logdensityof(ν, basemeasure(ν), x) diff --git a/src/primitives/lebesgue.jl b/src/primitives/lebesgue.jl index 77f411f9..92fc76bc 100644 --- a/src/primitives/lebesgue.jl +++ b/src/primitives/lebesgue.jl @@ -8,7 +8,7 @@ testvalue(::LebesgueMeasure) = 0.0 insupport(::LebesgueMeasure, x) = true -insupprot(::LebesgueMeasure) = Returns(true) +insupport(::LebesgueMeasure) = Returns(true) struct Lebesgue{T} <: AbstractMeasure support::T diff --git a/src/utils.jl b/src/utils.jl index 0614492c..8f27bd5f 100644 --- a/src/utils.jl +++ b/src/utils.jl @@ -60,73 +60,32 @@ end export basemeasure_depth @inline function basemeasure_depth(μ::M) where {M} - return basemeasure_depth(μ, basemeasure(μ)) -end - -@inline function basemeasure_depth(μ::M, β::M) where {M} - return 0 -end - -@inline function basemeasure_depth(μ::M, β::B) where {M,B} - return 1 + basemeasure_depth(β, basemeasure(β)) -end - -# Adapted from https://github.com/JuliaArrays/MappedArrays.jl/blob/46bf47f3388d011419fe43404214c1b7a44a49cc/src/MappedArrays.jl#L229 -function func_string(f, types) - ft = typeof(f) - mt = ft.name.mt - name = string(mt.name) - if startswith(name, '#') - # This is an anonymous function. See if it can be printed nicely - lwrds = code_lowered(f, types) - if length(lwrds) != 1 - return string(f) + depth_0 = static(0) + b_0 = μ + Base.Cartesian.@nexprs 10 i -> begin # 10 is just some "big enough" number + b_{i} = basemeasure(b_{i-1}) + if b_{i} isa typeof(b_{i-1}) + return static(i-1) end - lwrd = lwrds[1] - c = lwrd.code - if length(c) == 2 && ((isa(c[2], Expr) && c[2].head === :return) || (isdefined(Core, :ReturnNode) && isa(c[2], Core.ReturnNode))) - # This is a single-line anonymous function, we should handle it - s = lwrd.slotnames[2:end] - result = "" - if length(s) == 1 - result *= string(s[1]) - result *= "->" - else - result *= string(tuple(s...)) - result *= "->" - end - c1 = string(c[1]) - for i = 1:length(s) - c1 = replace(c1, "_"*string(i+1)=>string(s[i])) - end - result *= c1 - return result - else - return string(f) - end - else - return string(f) end + return static(10) end -_eltype(T) = eltype(T) - -function _eltype(g::Base.Generator{I}) where {I} - Core.Compiler.return_type(g.f, Tuple{_eltype(I)}) -end - -function _eltype(::Type{Base.Generator{I,ComposedFunction{Outer,Inner}}}) where {Outer,Inner,I} - _eltype(Base.Generator{_eltype(Base.Generator{I,Inner}), Outer}) -end - -function _eltype(::Type{Base.Generator{I,F}}) where {F<:Function,I} - f = instance(F) - Core.Compiler.return_type(f, Tuple{_eltype(I)}) -end - -function _eltype(::Type{Z}) where {Z<:Iterators.Zip} - map(_eltype, Z.types[1].types) -end +# @inline function basemeasure_depth(μ::M) where {M} +# return basemeasure_depth(μ, basemeasure(μ), static(0)) +# end + +# @inline function basemeasure_depth(μ::M, β::M, s::StaticInt{N}) where {M,N} +# s +# end + +# @generated function basemeasure_depth(μ::M, β::B, ::StaticInt{N}) where {M,B,N} +# s = Expr(:call, Expr(:curly, :StaticInt, N + 1)) +# quote +# $(Expr(:meta, :inline)) +# basemeasure_depth(β, basemeasure(β), $s) +# end +# end mymap(f, gen::Base.Generator) = mymap(f ∘ gen.f, gen.iter) mymap(f, inds...) = Iterators.map(f, inds...) From b88001842842789fce08e06fe75ef73ba0305281 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 9 Feb 2022 07:27:25 -0800 Subject: [PATCH 166/368] updates --- src/combinators/power.jl | 18 +++++++++++++++--- src/combinators/product.jl | 8 ++++---- src/density.jl | 27 ++++++++++++++++----------- src/partial-static.jl | 2 +- src/utils.jl | 17 +++++++++++++++++ 5 files changed, 53 insertions(+), 19 deletions(-) diff --git a/src/combinators/power.jl b/src/combinators/power.jl index e1639982..0e823106 100644 --- a/src/combinators/power.jl +++ b/src/combinators/power.jl @@ -65,16 +65,28 @@ params(d::PowerMeasure) = params(first(marginals(d))) end @inline function logdensity_def(d::PowerMeasure{M}, x) where {M} - T = eltype(x) ℓ = 0.0 # ℓ = zero(typeintersect(AbstractFloat,Core.Compiler.return_type(logdensity_def, Tuple{M,T}))) parent = d.parent - @inbounds for xj in x - ℓ += logdensity_def(parent, xj) + @simd for xj in x + Δℓ = logdensity_def(parent, xj) + ℓ += Δℓ end ℓ end +@generated function logdensity_def(d::PowerMeasure{M, Tuple{Base.OneTo{StaticInt{N}}}}, x) where {M,N} + quote + $(Expr(:meta, :inline)) + ℓ = 0.0 + parent = d.parent + @inbounds @simd for j in 1:$N + Δℓ = logdensity_def(parent, x[j]) + ℓ += Δℓ + end + ℓ + end +end @inline function insupport(μ::PowerMeasure, x) p = μ.parent diff --git a/src/combinators/product.jl b/src/combinators/product.jl index 669de6ff..8591b69c 100644 --- a/src/combinators/product.jl +++ b/src/combinators/product.jl @@ -38,9 +38,9 @@ function _rand_product(rng::AbstractRNG, ::Type{T}, mar, ::Type{M}) where {T,M<: end function _rand_product(rng::AbstractRNG, ::Type{T}, mar::ReadonlyMappedArray, ::Type{M}) where {T,M<:AbstractMeasure} - map(mar.data) do dⱼ + mappedarray(mar.data) do dⱼ rand(rng, T, mar.f(dⱼ)) - end + end |> collect end function _rand_product(rng::AbstractRNG, ::Type{T}, mar, ::Type{M}) where {T,M} @@ -51,9 +51,9 @@ end function _rand_product(rng::AbstractRNG, ::Type{T}, mar::ReadonlyMappedArray, ::Type{M}) where {T,M} - map(mar.data) do dⱼ + mappedarray(mar.data) do dⱼ rand(rng, mar.f(dⱼ)) - end + end |> collect end diff --git a/src/density.jl b/src/density.jl index 8ca954fc..f3482d09 100644 --- a/src/density.jl +++ b/src/density.jl @@ -104,27 +104,28 @@ Define a new measure in terms of a log-density `f` over some measure `base`. # TODO: `density` and `logdensity` functions for `DensityMeasure` @inline function logdensityof(μ, x) - dynamic(insupport(μ, x)) || return -Inf - return unsafe_logdensityof(μ, x) + t() = dynamic(unsafe_logdensityof(μ, x)) + f() = -Inf + ifelse(insupport(μ, x), t, f)() end export unsafe_logdensityof # https://discourse.julialang.org/t/counting-iterations-to-a-type-fixpoint/75876/10?u=cscherrer @inline function unsafe_logdensityof(μ::M, x) where {M} - ℓ_0 = (logdensity_def(μ, x)) + ℓ_0 = partialstatic(logdensity_def(μ, x)) b_0 = μ Base.Cartesian.@nexprs 10 i -> begin # 10 is just some "big enough" number b_{i} = basemeasure(b_{i-1}) - b = b_{i} - # @show b + # @show b_{i} if b_{i} isa typeof(b_{i-1}) return ℓ_{i-1} end - ℓ_{i} = let Δt = @elapsed Δℓ = (logdensity_def(b_{i}, x)) + ℓ_{i} = let Δℓ_{i} = partialstatic(logdensity_def(b_{i}, x)) # @show Δt - # @show Δℓ - ℓ_{i-1} + Δℓ + # @show Δℓ_{i} + # println(repeat("-",100)) + ℓ_{i-1} + Δℓ_{i} end end return ℓ_10 @@ -137,15 +138,19 @@ end # @generated function unsafe_logdensityof(μ, x, ::StaticInt{N}) where {N} # q = quote -# ℓ = logdensity_def(μ, x) +# $(Expr(:meta, :inline)) +# ℓ = partialstatic(logdensity_def(μ, x)) # end +# oldℓname = :ℓ # for j in 1:N +# newℓname = Symbol(:ℓ_, j) # push!(q.args, quote # μ = basemeasure(μ) -# Δℓ = logdensity_def(μ, x) -# ℓ = ℓ + Δℓ +# Δℓ = partialstatic(logdensity_def(μ, x)) +# $newℓname = $oldℓname + Δℓ # end) +# oldℓname = newℓname # end # return q # end diff --git a/src/partial-static.jl b/src/partial-static.jl index 3c515e21..1792e58f 100644 --- a/src/partial-static.jl +++ b/src/partial-static.jl @@ -27,7 +27,7 @@ end print(io, ")") end -@inline Base.convert(::Type{F}, x::PartialStatic{StaticFloat64{N}, T}) where {F<:AbstractFloat, N,T} = Float64(N + x.dynamic) +@inline Base.convert(::Type{F}, x::PartialStatic{StaticFloat64{N}, T}) where {F<:AbstractFloat, N,T} = convert(F, N) + convert(F, x.dynamic) @inline function Base.convert(::Type{PartialStatic{Static.StaticFloat64{N}, D}}, x::PartialStatic{Static.StaticFloat64{N}, D}) where {D, N} return x diff --git a/src/utils.jl b/src/utils.jl index 8f27bd5f..0dc8badc 100644 --- a/src/utils.jl +++ b/src/utils.jl @@ -71,6 +71,23 @@ export basemeasure_depth return static(10) end + +@inline function basemeasure_sequence(μ::M) where {M} + depth = basemeasure_depth(μ) + basemeasure_sequence(μ, depth) +end + +@generated function basemeasure_sequence(μ::M, ::StaticInt{N}) where {M,N} + quote + b_1 = μ + Base.Cartesian.@nexprs 10 i -> begin # 10 is just some "big enough" number + b_{i+1} = basemeasure(b_{i}) + end + return Base.Cartesian.@ntuple $N b + end +end + + # @inline function basemeasure_depth(μ::M) where {M} # return basemeasure_depth(μ, basemeasure(μ), static(0)) # end From 5afed527732d410a8e27d6fd3729c49cef6d89f9 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 16 Mar 2022 09:51:06 -0700 Subject: [PATCH 167/368] get tests passing --- src/MeasureBase.jl | 1 + src/combinators/smart-constructors.jl | 4 +++ test/runtests.jl | 50 +++++++++++++-------------- 3 files changed, 30 insertions(+), 25 deletions(-) diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index fc9568fc..0403df56 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -102,6 +102,7 @@ module Interface using Reexport using MeasureBase using MeasureBase:basemeasure_depth, proxy +using MeasureBase: insupport @reexport using Test export test_interface diff --git a/src/combinators/smart-constructors.jl b/src/combinators/smart-constructors.jl index 0ef85ca0..95a02d15 100644 --- a/src/combinators/smart-constructors.jl +++ b/src/combinators/smart-constructors.jl @@ -102,6 +102,10 @@ function kleisli(μ::M) where {M<:AbstractMeasure} kleisli(M) end +function kleisli(d::PowerMeasure) + Base.Fix2(powermeasure, d.axes) ∘ kleisli(d.parent) +end + # kleisli(Normal{(:μ,), Tuple{Int64}}) function kleisli(::Type{M}) where {M<:AbstractMeasure} constructorof(M) diff --git a/test/runtests.jl b/test/runtests.jl index 795e613c..f6560522 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -23,9 +23,9 @@ d = ∫exp(x -> -x^2, Lebesgue(ℝ)) test_measures = [ # Chain(x -> Normal(μ=x), Normal(μ=0.0)) - For(3) do j - Dirac(j) - end + # For(3) do j + # Dirac(j) + # end # For(2, 3) do i, j # Dirac(i) + Dirac(j) # end @@ -79,29 +79,29 @@ end @test logdensity_def(Dirac(0.3), 0.4) == -Inf end -@testset "For" begin - FORDISTS = [ - For(1:10) do j - Dirac(j) - end - For(4, 3) do i, j - Dirac(i) ⊗ Dirac(j) - end - For(1:4, 1:4) do i, j - Dirac(i) ⊗ Dirac(j) - end - For(eachrow(rand(4, 2))) do x - Dirac(x[1]) ⊗ Dirac(x[2]) - end - For(rand(4), rand(4)) do i, j - Dirac(i) ⊗ Dirac(j) - end - ] +# @testset "For" begin +# FORDISTS = [ +# For(1:10) do j +# Dirac(j) +# end +# For(4, 3) do i, j +# Dirac(i) ⊗ Dirac(j) +# end +# For(1:4, 1:4) do i, j +# Dirac(i) ⊗ Dirac(j) +# end +# For(eachrow(rand(4, 2))) do x +# Dirac(x[1]) ⊗ Dirac(x[2]) +# end +# For(rand(4), rand(4)) do i, j +# Dirac(i) ⊗ Dirac(j) +# end +# ] - for d in FORDISTS - test_interface(d) - end -end +# for d in FORDISTS +# test_interface(d) +# end +# end @testset "Half" begin Normal() = ∫exp(x -> -0.5x^2, Lebesgue(ℝ)) From 5139be25c41e10a5a8a33517f7915e38e0dd0255 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 16 Mar 2022 10:16:29 -0700 Subject: [PATCH 168/368] MIT license for MeasureBase --- LICENSE | 683 ++------------------------------------------------------ 1 file changed, 22 insertions(+), 661 deletions(-) diff --git a/LICENSE b/LICENSE index be3f7b28..ec063f13 100644 --- a/LICENSE +++ b/LICENSE @@ -1,661 +1,22 @@ - 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From 101a5fec35300de4cd8aa81981e531a6c53c4a0a Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 16 Mar 2022 10:47:01 -0700 Subject: [PATCH 169/368] bump version --- Project.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Project.toml b/Project.toml index 4b19ecdc..40aa712c 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "MeasureBase" uuid = "fa1605e6-acd5-459c-a1e6-7e635759db14" authors = ["Chad Scherrer and contributors"] -version = "0.5.1" +version = "0.6.0" [deps] Compat = "34da2185-b29b-5c13-b0c7-acf172513d20" From 191c5ef87f35ac941b131b4e9c518ddd8d204a7b Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 29 Mar 2022 16:45:59 -0700 Subject: [PATCH 170/368] cleanup --- src/MeasureBase.jl | 26 ++++--- src/combinators/product.jl | 4 +- src/density.jl | 40 ++--------- src/partial-static.jl | 140 ------------------------------------- 4 files changed, 25 insertions(+), 185 deletions(-) delete mode 100644 src/partial-static.jl diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index 0403df56..dddc743a 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -28,6 +28,16 @@ export rebase export AbstractMeasure + +import IfElse: ifelse +export logdensity_def +export basemeasure +export basekleisli + + +export insupport + + abstract type AbstractMeasure end using Static: @constprop @@ -45,11 +55,6 @@ gentype(μ::AbstractMeasure) = typeof(testvalue(μ)) # gentype(μ::AbstractMeasure) = gentype(basemeasure(μ)) -import IfElse: ifelse -export logdensity_def -export basemeasure -export basekleisli - using LogExpFunctions: logsumexp """ @@ -66,7 +71,6 @@ function logdensity_def end using Compat include("splat.jl") -include("partial-static.jl") include("proxies.jl") include("kleisli.jl") include("parameterized.jl") @@ -100,15 +104,19 @@ include("density.jl") module Interface using Reexport -using MeasureBase + +@reexport using MeasureBase + using MeasureBase:basemeasure_depth, proxy using MeasureBase: insupport -@reexport using Test export test_interface export basemeasure_depth + + export proxy -export insupport + +@reexport using Test include("interface.jl") end # module Interface diff --git a/src/combinators/product.jl b/src/combinators/product.jl index 8591b69c..7c1a4ced 100644 --- a/src/combinators/product.jl +++ b/src/combinators/product.jl @@ -100,13 +100,13 @@ end end vals = map(x -> Expr(:(=), x,x), N) - push!(q, Expr(:tuple, vals...)) + push!(q.args, Expr(:tuple, vals...)) return q end function basemeasure(μ::ProductMeasure{Base.Generator{I,F}}) where {I,F} mar = marginals(μ) - T = Core.Compiler.return_type(mar.f, Tuple{_eltype(mar.iter)}) + T = Core.Compiler.return_type(mar.f, Tuple{eltype(mar.iter)}) B = Core.Compiler.return_type(basemeasure, Tuple{T}) _basemeasure(μ, B, static(Base.issingletontype(B))) end diff --git a/src/density.jl b/src/density.jl index f3482d09..a81dd497 100644 --- a/src/density.jl +++ b/src/density.jl @@ -113,52 +113,26 @@ export unsafe_logdensityof # https://discourse.julialang.org/t/counting-iterations-to-a-type-fixpoint/75876/10?u=cscherrer @inline function unsafe_logdensityof(μ::M, x) where {M} - ℓ_0 = partialstatic(logdensity_def(μ, x)) + ℓ_0 = logdensity_def(μ, x) b_0 = μ Base.Cartesian.@nexprs 10 i -> begin # 10 is just some "big enough" number b_{i} = basemeasure(b_{i-1}) - # @show b_{i} if b_{i} isa typeof(b_{i-1}) return ℓ_{i-1} end - ℓ_{i} = let Δℓ_{i} = partialstatic(logdensity_def(b_{i}, x)) - # @show Δt - # @show Δℓ_{i} - # println(repeat("-",100)) + ℓ_{i} = let Δℓ_{i} = logdensity_def(b_{i}, x) ℓ_{i-1} + Δℓ_{i} end end return ℓ_10 end -# # https://discourse.julialang.org/t/counting-iterations-to-a-type-fixpoint/75876/10?u=cscherrer -# @inline function unsafe_logdensityof(μ::M, x) where {M} -# unsafe_logdensityof(μ, x, basemeasure_depth(μ)) -# end - -# @generated function unsafe_logdensityof(μ, x, ::StaticInt{N}) where {N} -# q = quote -# $(Expr(:meta, :inline)) -# ℓ = partialstatic(logdensity_def(μ, x)) -# end - -# oldℓname = :ℓ -# for j in 1:N -# newℓname = Symbol(:ℓ_, j) -# push!(q.args, quote -# μ = basemeasure(μ) -# Δℓ = partialstatic(logdensity_def(μ, x)) -# $newℓname = $oldℓname + Δℓ -# end) -# oldℓname = newℓname -# end -# return q -# end - @inline function logdensity_rel(μ::M, ν::N, x::X) where {M,N,X} - (ℓ₊, α) = _logdensityof(μ, basemeasure(μ), x) - (ℓ₋, β) = _logdensityof(ν, basemeasure(ν), x) + ℓ₊ = logdensity_def(μ, x) + ℓ₋ = logdensity_def(ν, x) + α = basemeasure(μ) + β = basemeasure(ν) return _logdensity_rel(α, β, x, ℓ₊ - ℓ₋) end @@ -176,8 +150,6 @@ end end end -# logdensity_def(::Lebesgue{ℝ}, ::Lebesgue{ℝ}, x) = zero(x) - export densityof export logdensityof diff --git a/src/partial-static.jl b/src/partial-static.jl deleted file mode 100644 index 1792e58f..00000000 --- a/src/partial-static.jl +++ /dev/null @@ -1,140 +0,0 @@ -using Static - -export PartialStatic -export partialstatic - -import Base.promote_rule - -struct PartialStatic{S,D} <: AbstractFloat - static::S - dynamic::D - - @inline function PartialStatic(s::S, d::D) where {S,D} - @assert known(is_static(s)) - new{S,D}(s, d) - end -end - -@inline function Static.dynamic(x::PartialStatic) - dynamic(x.static) + dynamic(x.dynamic) -end - -@inline function Base.show(io::IO, p::PartialStatic) - print(io, "PartialStatic(") - print(io, p.static) - print(io, ", ") - print(io, p.dynamic) - print(io, ")") -end - -@inline Base.convert(::Type{F}, x::PartialStatic{StaticFloat64{N}, T}) where {F<:AbstractFloat, N,T} = convert(F, N) + convert(F, x.dynamic) - -@inline function Base.convert(::Type{PartialStatic{Static.StaticFloat64{N}, D}}, x::PartialStatic{Static.StaticFloat64{N}, D}) where {D, N} - return x -end - -@inline function Base.convert(::Type{PartialStatic{S, D}}, x::T) where {S, D, T<:Number} - partialstatic(x) -end - -@inline function Base.convert(::Type{PartialStatic{S,D}}, x::T) where {S,D,T} - partialstatic(x) -end - -@inline function Base.convert(::Type{PartialStatic{S, D}}, x::T) where {S, D, T<:(StaticFloat64)} - partialstatic(x) -end - -@inline function Base.promote_rule(::Type{Static.StaticFloat64{N}}, ::Type{PartialStatic{S, D}}) where {N, S, D} - Base.promote_rule(Float64, D) -end - -@inline function Base.promote_rule(::Type{PartialStatic{S1,D1}}, ::Type{PartialStatic{S2,D2}}) where {S1,D1,S2,D2} - PartialStatic{promote_type(S1, S2), promote_rule(D1, D2)} -end - -@inline function Base.promote_rule(::Type{PartialStatic{S, D}}, ::Type{StaticFloat64{N}}) where {N, S, D} - PartialStatic{promote_type(StaticFloat64{N}, S), D} -end - -@inline function Base.promote_rule(::Type{T}, ::Type{PartialStatic{S,D}}) where {T,S,D} - _promote(PartialStatic{S,D}, T, is_static(T)) -end - -@inline function Base.promote_rule(::Type{PartialStatic{S,D}}, ::Type{T}) where {S,D,T} - _promote(PartialStatic{S,D}, T, is_static(T)) -end - -@inline function _promote(::Type{PartialStatic{S,D}}, ::Type{T}, ::True) where {S,D,T} - PartialStatic{promote_type(S,T),D} -end - -@inline function _promote(::Type{PartialStatic{S,D}}, ::Type{T}, ::False) where {S,D,T} - PartialStatic{S,promote_type(D,T)} -end - -@inline partialstatic(s, d) = PartialStatic(s, d) - -@inline partialstatic(x) = _partialstatic(x, is_static(x)) - -@inline partialstatic(x::PartialStatic) = x - -@inline _partialstatic(x, ::True) = PartialStatic(x, static(0.0)) - -@inline _partialstatic(x, ::False) = PartialStatic(static(0.0), x) - -@inline function Base.:+(x::Static.StaticFloat64{X}, y::PartialStatic{Static.StaticFloat64{Y}, D}) where {X,Y,D} - PartialStatic(X+Y, y.dynamic) -end - -@inline function Base.:+(x::PartialStatic{S1,D1}, y::PartialStatic{S2,D2}) where {S1,D1,S2,D2} - PartialStatic(x.static + y.static, x.dynamic + y.dynamic) -end - -@inline function Base.:-(x::PartialStatic{S1,D1}, y::PartialStatic{S2,D2}) where {S1,D1,S2,D2} - PartialStatic(x.static - y.static, x.dynamic - y.dynamic) -end - -Base.eps(::Type{PartialStatic{S,D}}) where {S,D} = max(Base.eps(known(S)), Base.eps(D)) - -# @inline function Base.:-(x::PartialStatic{S,D}, y::StaticFloat64{Y}) where {S,D,Y} -# PartialStatic(x.static - y, x.dynamic) -# end - -# @inline function Base.:+(x::PartialStatic{S,D}, y::Number) where {S,D} -# PartialStatic(x.static, x.dynamic + y) -# end - -# @inline function Base.:-(x::PartialStatic{S,D}, y::Number) where {S,D} -# PartialStatic(x.static, x.dynamic - y) -# end - -# @inline function Base.:+(x::PartialStatic{S,D}, y) where {S,D} -# PartialStatic(x.static, x.dynamic + y) -# end - -# @inline function Base.:-(x::PartialStatic{S,D}, y) where {S,D} -# PartialStatic(x.static, x.dynamic - y) -# end - -@inline function add_partial_static(x::StaticFloat64, y::StaticFloat64) - return x + y -end - -@inline function add_partial_static(x::StaticFloat64, y::Real) - return PartialStatic(x, y) -end - -@inline function add_partial_static(y::Real, x::StaticFloat64) - return PartialStatic(x, y) -end - -@inline function add_partial_static(x, y) - return x + y -end - -Base.exp(x::PartialStatic) = exp(known(x.static) + x.dynamic) - -@inline Base.isapprox(x::PartialStatic, y::PartialStatic; kwargs...) = isapprox(dynamic(x), dynamic(y); kwargs...) -@inline Base.isapprox(x::Number, y::PartialStatic; kwargs...) = isapprox(dynamic(x), dynamic(y); kwargs...) -@inline Base.isapprox(x::PartialStatic, y::Number; kwargs...) = isapprox(dynamic(x), dynamic(y); kwargs...) \ No newline at end of file From 636b734883ecabf440341f9b17e065900eae2e59 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 29 Mar 2022 16:47:23 -0700 Subject: [PATCH 171/368] spacing --- src/MeasureBase.jl | 5 ----- 1 file changed, 5 deletions(-) diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index dddc743a..259f9e0c 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -28,16 +28,13 @@ export rebase export AbstractMeasure - import IfElse: ifelse export logdensity_def export basemeasure export basekleisli - export insupport - abstract type AbstractMeasure end using Static: @constprop @@ -112,8 +109,6 @@ using MeasureBase: insupport export test_interface export basemeasure_depth - - export proxy @reexport using Test From 6036ec2c015fbae7336397476f87aec955824ad6 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Thu, 31 Mar 2022 12:59:03 -0700 Subject: [PATCH 172/368] Move ConditionalMeasure to MeasureBase --- src/MeasureBase.jl | 1 + src/combinators/conditional.jl | 8 ++++++++ 2 files changed, 9 insertions(+) diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index f456f4cc..352e5d4e 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -82,6 +82,7 @@ include("primitives/lebesgue.jl") include("primitives/dirac.jl") include("primitives/trivial.jl") +include("combinators/conditional.jl") include("combinators/bind.jl") include("combinators/transformedmeasure.jl") include("combinators/factoredbase.jl") diff --git a/src/combinators/conditional.jl b/src/combinators/conditional.jl index e69de29b..c2a38864 100644 --- a/src/combinators/conditional.jl +++ b/src/combinators/conditional.jl @@ -0,0 +1,8 @@ +struct ConditionalMeasure{M,C} <: AbstractMeasure + parent::M + constraint::C +end + +Base.:|(μ::AbstractMeasure, constraint) = ConditionalMeasure(μ, constraint) + +@inline basemeasure(cm::ConditionalMeasure) = basemeasure(cm.parent) | cm.constraint \ No newline at end of file From 03a7aba33a6c24e5db870f163f7790d57c5712a5 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Thu, 31 Mar 2022 17:13:26 -0700 Subject: [PATCH 173/368] add LogarithmicNumbers --- Project.toml | 1 + 1 file changed, 1 insertion(+) diff --git a/Project.toml b/Project.toml index a137dbb3..0d73282c 100644 --- a/Project.toml +++ b/Project.toml @@ -11,6 +11,7 @@ FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b" IfElse = "615f187c-cbe4-4ef1-ba3b-2fcf58d6d173" LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" LogExpFunctions = "2ab3a3ac-af41-5b50-aa03-7779005ae688" +LogarithmicNumbers = "aa2f6b4e-9042-5d33-9679-40d3a6b85899" MappedArrays = "dbb5928d-eab1-5f90-85c2-b9b0edb7c900" PrettyPrinting = "54e16d92-306c-5ea0-a30b-337be88ac337" Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" From d45e91e76f3d38d77b2cd298f8c26e29f28137d0 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Thu, 31 Mar 2022 17:13:39 -0700 Subject: [PATCH 174/368] export basemeasure_sequence --- src/utils.jl | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/utils.jl b/src/utils.jl index 0dc8badc..cb24c25d 100644 --- a/src/utils.jl +++ b/src/utils.jl @@ -72,6 +72,8 @@ export basemeasure_depth end +export basemeasure_sequence + @inline function basemeasure_sequence(μ::M) where {M} depth = basemeasure_depth(μ) basemeasure_sequence(μ, depth) @@ -87,7 +89,6 @@ end end end - # @inline function basemeasure_depth(μ::M) where {M} # return basemeasure_depth(μ, basemeasure(μ), static(0)) # end From b6cf8350072bb20f798164fa47f7aff133a0c6e1 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Thu, 31 Mar 2022 17:13:52 -0700 Subject: [PATCH 175/368] update superpose --- src/combinators/smart-constructors.jl | 8 ++++++++ src/combinators/superpose.jl | 15 +++++++++++++-- 2 files changed, 21 insertions(+), 2 deletions(-) diff --git a/src/combinators/smart-constructors.jl b/src/combinators/smart-constructors.jl index 95a02d15..4be19fb9 100644 --- a/src/combinators/smart-constructors.jl +++ b/src/combinators/smart-constructors.jl @@ -76,6 +76,14 @@ superpose(a::AbstractArray) = SuperpositionMeasure(a) superpose(t::Tuple) = SuperpositionMeasure(t) superpose(nt::NamedTuple) = SuperpositionMeasure(nt) +function superpose(μ::T, ν::T) where {T} + if μ==ν + return weightedmeasure(static(logtwo), μ) + else + return superpose((μ, ν)) + end +end + function superpose(μ::AbstractMeasure, ν::AbstractMeasure) components = (μ, ν) superpose(components) diff --git a/src/combinators/superpose.jl b/src/combinators/superpose.jl index a3fc407f..f324cbe1 100644 --- a/src/combinators/superpose.jl +++ b/src/combinators/superpose.jl @@ -58,10 +58,21 @@ function Base.:+(μ::AbstractMeasure, ν::AbstractMeasure) superpose(components) end -function logdensity_def(μ::SuperpositionMeasure, x) - logsumexp((logdensity_def(m, x) for m in μ.components)) +using LogarithmicNumbers + +function density_def(s::SuperpositionMeasure{Tuple{A,B}}, x) where {A,B} + (μ, ν) = s.components + α = basemeasure(μ) + β = basemeasure(ν) + dμ_dα = exp(ULogarithmic, logdensity_def(μ, x)) + dν_dβ = exp(ULogarithmic, logdensity_def(ν, x)) + dα_dβ = exp(ULogarithmic, logdensity_rel(α, β, x)) + return dμ_dα / (1 + inv(dα_dβ)) + dν_dβ / (1 + dα_dβ) end + +logdensity_def(s::SuperpositionMeasure, x) = log(density_def(s, x)) + basemeasure(μ::SuperpositionMeasure) = superpose(map(basemeasure, μ.components)) # TODO: Fix `rand` method (this one is wrong) From c4830999426272dc58fc2d307563f9703b71b723 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Thu, 31 Mar 2022 17:14:02 -0700 Subject: [PATCH 176/368] fix logdensity_rel --- src/density.jl | 73 ++++++++++++++++++++++++++++++++++++++++++++++---- 1 file changed, 68 insertions(+), 5 deletions(-) diff --git a/src/density.jl b/src/density.jl index a81dd497..09669de9 100644 --- a/src/density.jl +++ b/src/density.jl @@ -127,13 +127,76 @@ export unsafe_logdensityof return ℓ_10 end +# TODO: FIX THIS!!! +# e.g., try MeasureBase.logdensity_rel(Normal(0,1), Normal(), 10) @inline function logdensity_rel(μ::M, ν::N, x::X) where {M,N,X} - ℓ₊ = logdensity_def(μ, x) - ℓ₋ = logdensity_def(ν, x) - α = basemeasure(μ) - β = basemeasure(ν) - return _logdensity_rel(α, β, x, ℓ₊ - ℓ₋) + dynamic(insupport(μ, x)) || begin + dynamic(insupport(ν, x)) || return NaN + return -Inf + end + dynamic(insupport(ν, x)) || return Inf + + μ_depth = basemeasure_depth(μ) + ν_depth = basemeasure_depth(ν) + + Δdepth = μ_depth - ν_depth + + ℓ₊ = ℓ₋ = 0.0 + if Δdepth > 0 + (ℓ₊, μ_0) = logdensity_steps(μ, x, Δdepth) + ν_0 = ν + elseif Δdepth < 0 + (ℓ₋, ν_0) = logdensity_steps(ν, x, -Δdepth) + μ_0 = μ + else + μ_0 = μ + ν_0 = ν + end + + @assert basemeasure_depth(μ_0) == basemeasure_depth(ν_0) + + + Base.Cartesian.@nexprs 10 i -> begin # 10 is just some "big enough" number + if μ_{i-1} == ν_{i-1} + return ℓ₊ - ℓ₋ + elseif static_hasmethod(logdensity_def, Tuple{typeof(μ_{i-1}), typeof(ν_{i-1}), typeof(x)}) + return ℓ + logdensity_def(μ_{i-1}, ν_{i-1}, x) + end + + ℓ₊ += logdensity_def(μ_{i-1}, x) + ℓ₋ += logdensity_def(ν_{i-1}, x) + μ_{i} = basemeasure(μ_{i-1}) + ν_{i} = basemeasure(ν_{i-1}) + end + + @error "No common base measure" +end + + +# ℓ₊ = logdensity_def(μ, x) +# ℓ₋ = logdensity_def(ν, x) +# α = basemeasure(μ) +# β = basemeasure(ν) +# return _logdensity_rel(α, β, x, ℓ₊ - ℓ₋) +# end + +logdensity_steps(μ, x, ::StaticInt{0}) = (zero(logdensity_def(μ, x)), μ) + +@inline function logdensity_steps(μ, x, ::StaticInt{n}) where {n} + ℓ_0 = logdensity_def(μ, x) + b_0 = μ + + Base.Cartesian.@nexprs 10 i -> begin # 10 is just some "big enough" number + i > n && begin + return (ℓ_{i-1}, b_{i-1}) + end + b_{i} = basemeasure(b_{i-1}) + ℓ_{i} = let Δℓ_{i} = logdensity_def(b_{i}, x) + ℓ_{i-1} + Δℓ_{i} + end + end + return (ℓ_10, b_10) end @inline function _logdensity_rel(α::A, β::B, x::X, ℓ) where {A,B,X} From 9da96fa8c4201bda9f0c50aabafe52dda14592f5 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Thu, 31 Mar 2022 17:15:51 -0700 Subject: [PATCH 177/368] remove FIXME (it's fixed!!) --- src/density.jl | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/src/density.jl b/src/density.jl index 09669de9..f693ca07 100644 --- a/src/density.jl +++ b/src/density.jl @@ -127,9 +127,6 @@ export unsafe_logdensityof return ℓ_10 end -# TODO: FIX THIS!!! -# e.g., try MeasureBase.logdensity_rel(Normal(0,1), Normal(), 10) - @inline function logdensity_rel(μ::M, ν::N, x::X) where {M,N,X} dynamic(insupport(μ, x)) || begin dynamic(insupport(ν, x)) || return NaN @@ -137,6 +134,8 @@ end end dynamic(insupport(ν, x)) || return Inf + + μ_depth = basemeasure_depth(μ) ν_depth = basemeasure_depth(ν) @@ -156,7 +155,6 @@ end @assert basemeasure_depth(μ_0) == basemeasure_depth(ν_0) - Base.Cartesian.@nexprs 10 i -> begin # 10 is just some "big enough" number if μ_{i-1} == ν_{i-1} return ℓ₊ - ℓ₋ From c8b8822fe37aa43ee891e90c7f35e59379574156 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Fri, 1 Apr 2022 05:34:01 -0700 Subject: [PATCH 178/368] logdensityof(d::Density, x) --- src/density.jl | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/src/density.jl b/src/density.jl index a81dd497..22f45cb3 100644 --- a/src/density.jl +++ b/src/density.jl @@ -32,7 +32,7 @@ function 𝒹(μ::AbstractMeasure, base::AbstractMeasure) return Density(μ, base) end -logdensityof(d::Density, x) = logdensityof(d.μ, x) - logdensityof(d.base, x) +logdensityof(d::Density, x) = logdensity_rel(d.μ, d.base, x) logdensity_def(d::Density, x) = logdensityof(d, x) @@ -127,6 +127,9 @@ export unsafe_logdensityof return ℓ_10 end +export density_rel + +@inline density_rel(μ, ν, x) = exp(logdensity_rel(μ, ν, x)) @inline function logdensity_rel(μ::M, ν::N, x::X) where {M,N,X} ℓ₊ = logdensity_def(μ, x) From dc82f20083ab77ee541ae50b912052585e0634b1 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Fri, 1 Apr 2022 05:38:37 -0700 Subject: [PATCH 179/368] simplify insupport(::Lebesgue, ::Real) --- src/primitives/lebesgue.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/primitives/lebesgue.jl b/src/primitives/lebesgue.jl index 92fc76bc..c6505467 100644 --- a/src/primitives/lebesgue.jl +++ b/src/primitives/lebesgue.jl @@ -35,4 +35,4 @@ Base.show(io::IO, d::Lebesgue) = print(io, "Lebesgue(", d.support, ")") insupport(μ::Lebesgue, x) = x ∈ μ.support -insupport(::Lebesgue{RealNumbers}, ::Real) = static(true) +insupport(::Lebesgue{RealNumbers}, ::Real) = true From 2f9e5f06aa28129454d46b84c054e2dabd5f4b14 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Fri, 1 Apr 2022 05:38:56 -0700 Subject: [PATCH 180/368] clean up --- src/density.jl | 8 -------- 1 file changed, 8 deletions(-) diff --git a/src/density.jl b/src/density.jl index dfb53945..526c3077 100644 --- a/src/density.jl +++ b/src/density.jl @@ -175,14 +175,6 @@ export density_rel @error "No common base measure" end - -# ℓ₊ = logdensity_def(μ, x) -# ℓ₋ = logdensity_def(ν, x) -# α = basemeasure(μ) -# β = basemeasure(ν) -# return _logdensity_rel(α, β, x, ℓ₊ - ℓ₋) -# end - logdensity_steps(μ, x, ::StaticInt{0}) = (zero(logdensity_def(μ, x)), μ) @inline function logdensity_steps(μ, x, ::StaticInt{n}) where {n} From 4e1861ff6a836676b0d2722ee043f64e87d9a420 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Fri, 1 Apr 2022 05:40:22 -0700 Subject: [PATCH 181/368] assume insupport yields Bool --- src/density.jl | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/src/density.jl b/src/density.jl index 526c3077..6fc6943e 100644 --- a/src/density.jl +++ b/src/density.jl @@ -132,13 +132,11 @@ export density_rel @inline density_rel(μ, ν, x) = exp(logdensity_rel(μ, ν, x)) @inline function logdensity_rel(μ::M, ν::N, x::X) where {M,N,X} - dynamic(insupport(μ, x)) || begin - dynamic(insupport(ν, x)) || return NaN + insupport(μ, x) || begin + insupport(ν, x) || return NaN return -Inf end - dynamic(insupport(ν, x)) || return Inf - - + insupport(ν, x) || return Inf μ_depth = basemeasure_depth(μ) ν_depth = basemeasure_depth(ν) From e1b03dea4958fe48f5b5b78b300592796a6f7867 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Fri, 1 Apr 2022 05:43:20 -0700 Subject: [PATCH 182/368] change logdensity_rel fall-through to warning and return NaN --- src/density.jl | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/src/density.jl b/src/density.jl index 6fc6943e..221d50af 100644 --- a/src/density.jl +++ b/src/density.jl @@ -170,7 +170,17 @@ export density_rel ν_{i} = basemeasure(ν_{i-1}) end - @error "No common base measure" + @warn """ + No common base measure for + $μ + and + $ν + + Returning a relative log-density of NaN. If this is incorrect, add a + three-argument method + logdensity_def(μ, ν, x) + """ + return NaN end logdensity_steps(μ, x, ::StaticInt{0}) = (zero(logdensity_def(μ, x)), μ) From 08b40e2b3ca9f49def867de38bf730f3c83955a5 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Fri, 1 Apr 2022 05:47:04 -0700 Subject: [PATCH 183/368] update logdensity_rel --- src/density.jl | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/src/density.jl b/src/density.jl index 221d50af..cb6976eb 100644 --- a/src/density.jl +++ b/src/density.jl @@ -143,14 +143,16 @@ export density_rel Δdepth = μ_depth - ν_depth - ℓ₊ = ℓ₋ = 0.0 if Δdepth > 0 (ℓ₊, μ_0) = logdensity_steps(μ, x, Δdepth) + ℓ₋ = zero(ℓ₊) ν_0 = ν elseif Δdepth < 0 (ℓ₋, ν_0) = logdensity_steps(ν, x, -Δdepth) + ℓ₊ = zero(ℓ₋) μ_0 = μ else + ℓ₊ = ℓ₋ = 0.0 μ_0 = μ ν_0 = ν end @@ -161,7 +163,7 @@ export density_rel if μ_{i-1} == ν_{i-1} return ℓ₊ - ℓ₋ elseif static_hasmethod(logdensity_def, Tuple{typeof(μ_{i-1}), typeof(ν_{i-1}), typeof(x)}) - return ℓ + logdensity_def(μ_{i-1}, ν_{i-1}, x) + return ℓ₊ - ℓ₋ + logdensity_def(μ_{i-1}, ν_{i-1}, x) end ℓ₊ += logdensity_def(μ_{i-1}, x) From 3881dda35c6acb6eb3fe46111449af32e8f36463 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Fri, 1 Apr 2022 08:21:05 -0700 Subject: [PATCH 184/368] drop old code --- src/density.jl | 14 -------------- 1 file changed, 14 deletions(-) diff --git a/src/density.jl b/src/density.jl index cb6976eb..4b66b4ed 100644 --- a/src/density.jl +++ b/src/density.jl @@ -203,20 +203,6 @@ logdensity_steps(μ, x, ::StaticInt{0}) = (zero(logdensity_def(μ, x)), μ) return (ℓ_10, b_10) end -@inline function _logdensity_rel(α::A, β::B, x::X, ℓ) where {A,B,X} - if static_hasmethod(logdensity_def, Tuple{A,B,X}) - return ℓ + logdensity_def(α, β, x) - elseif static_hasmethod(logdensity_def, Tuple{B,A,X}) - return ℓ + logdensity_def(β, α, x) - else - @warn """ - No method - logdensity(::$A, ::$B, ::$X) - """ - return oftype(ℓ, NaN) - end -end - export densityof export logdensityof From 719be40649617757f8b30d5237d500759ba5a628 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Fri, 1 Apr 2022 08:21:18 -0700 Subject: [PATCH 185/368] fix warning --- src/density.jl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/density.jl b/src/density.jl index 4b66b4ed..06fcd46d 100644 --- a/src/density.jl +++ b/src/density.jl @@ -174,9 +174,9 @@ export density_rel @warn """ No common base measure for - $μ + $μ_10 and - $ν + $ν_10 Returning a relative log-density of NaN. If this is incorrect, add a three-argument method From 002bd572e6129e99434cab48f9834a5d3789e468 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Fri, 1 Apr 2022 08:21:30 -0700 Subject: [PATCH 186/368] export logdensity_rel --- src/density.jl | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/density.jl b/src/density.jl index 06fcd46d..ad688482 100644 --- a/src/density.jl +++ b/src/density.jl @@ -131,6 +131,8 @@ export density_rel @inline density_rel(μ, ν, x) = exp(logdensity_rel(μ, ν, x)) +export logdensity_rel + @inline function logdensity_rel(μ::M, ν::N, x::X) where {M,N,X} insupport(μ, x) || begin insupport(ν, x) || return NaN From 6c00baed894b0312260e9f0ddd62beeb00f4f238 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Fri, 1 Apr 2022 08:21:58 -0700 Subject: [PATCH 187/368] =?UTF-8?q?logdensity=5Fdef(=CE=BC::Dirac,=20?= =?UTF-8?q?=CE=BD::Dirac,=20x)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- src/primitives/dirac.jl | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/primitives/dirac.jl b/src/primitives/dirac.jl index 2d137d55..9c3fe0aa 100644 --- a/src/primitives/dirac.jl +++ b/src/primitives/dirac.jl @@ -31,3 +31,5 @@ dirac(d::AbstractMeasure) = Dirac(rand(d)) testvalue(d::Dirac) = d.x insupport(d::Dirac, x) = x == d.x + +logdensity_def(μ::Dirac, ν::Dirac, x) = logdensity_def(μ, x) - logdensity_def(ν, x) From 9168a2c0f323fb0624653f17b74172063a21bb25 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Fri, 1 Apr 2022 08:22:19 -0700 Subject: [PATCH 188/368] logdensity_def methods --- src/primitives/lebesgue.jl | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/src/primitives/lebesgue.jl b/src/primitives/lebesgue.jl index c6505467..68cf628c 100644 --- a/src/primitives/lebesgue.jl +++ b/src/primitives/lebesgue.jl @@ -36,3 +36,7 @@ Base.show(io::IO, d::Lebesgue) = print(io, "Lebesgue(", d.support, ")") insupport(μ::Lebesgue, x) = x ∈ μ.support insupport(::Lebesgue{RealNumbers}, ::Real) = true + +logdensity_def(::LebesgueMeasure, ::CountingMeasure, x) = -Inf + +logdensity_def(::CountingMeasure, ::LebesgueMeasure, x) = Inf \ No newline at end of file From 2524aa1bcae0ede5bbc90104386b1f538936b63f Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Fri, 1 Apr 2022 08:22:33 -0700 Subject: [PATCH 189/368] drop `static` --- src/combinators/half.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/combinators/half.jl b/src/combinators/half.jl index d2b8deda..9a2f275e 100644 --- a/src/combinators/half.jl +++ b/src/combinators/half.jl @@ -15,7 +15,7 @@ isnonnegative(x) = x ≥ 0.0 @inline function basemeasure(μ::Half) constℓ = static(logtwo) - varℓ = Returns(static(0.0)) + varℓ = Returns(0.0) base = basemeasure(unhalf(μ)) FactoredBase(constℓ, varℓ, base) end From b6f5292ca14211d5f90dc374a4688bd681c7f83e Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Fri, 1 Apr 2022 08:22:43 -0700 Subject: [PATCH 190/368] ]add StatsFuns --- Project.toml | 1 + 1 file changed, 1 insertion(+) diff --git a/Project.toml b/Project.toml index 0d73282c..897f9636 100644 --- a/Project.toml +++ b/Project.toml @@ -18,6 +18,7 @@ Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" Reexport = "189a3867-3050-52da-a836-e630ba90ab69" Static = "aedffcd0-7271-4cad-89d0-dc628f76c6d3" Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" +StatsFuns = "4c63d2b9-4356-54db-8cca-17b64c39e42c" Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" Tricks = "410a4b4d-49e4-4fbc-ab6d-cb71b17b3775" From c3e2f13d05b1a86367466854d68de5dc41ae0dba Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Fri, 1 Apr 2022 08:22:59 -0700 Subject: [PATCH 191/368] Fixing up superposition --- src/combinators/superpose.jl | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/src/combinators/superpose.jl b/src/combinators/superpose.jl index f324cbe1..7bcb09e4 100644 --- a/src/combinators/superpose.jl +++ b/src/combinators/superpose.jl @@ -62,6 +62,8 @@ using LogarithmicNumbers function density_def(s::SuperpositionMeasure{Tuple{A,B}}, x) where {A,B} (μ, ν) = s.components + insupport(μ, x) || return exp(ULogarithmic, logdensity_def(ν, x)) + insupport(ν, x) || return exp(ULogarithmic, logdensity_def(μ, x)) α = basemeasure(μ) β = basemeasure(ν) dμ_dα = exp(ULogarithmic, logdensity_def(μ, x)) @@ -70,6 +72,21 @@ function density_def(s::SuperpositionMeasure{Tuple{A,B}}, x) where {A,B} return dμ_dα / (1 + inv(dα_dβ)) + dν_dβ / (1 + dα_dβ) end +using StatsFuns + +function logdensity_def(s::SuperpositionMeasure{Tuple{A,B}}, β, x) where {A,B} + (μ, ν) = s.components + return logaddexp(logdensity_rel(μ, β, x), logdensity_rel(ν, β, x)) +end + +function logdensity_def(s::SuperpositionMeasure{Tuple{A,B}}, β::SuperpositionMeasure, x) where {A,B} + (μ, ν) = s.components + return logaddexp(logdensity_rel(μ, β, x), logdensity_rel(ν, β, x)) +end + +function logdensity_def(s, β::SuperpositionMeasure{Tuple{A,B}}, x) where {A,B} + -logdensity_def(β, s, x) +end logdensity_def(s::SuperpositionMeasure, x) = log(density_def(s, x)) From 027bc12a1024f072afe7d435f29d7913af6e9687 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Fri, 1 Apr 2022 08:48:41 -0700 Subject: [PATCH 192/368] [compat] entries --- Project.toml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/Project.toml b/Project.toml index 897f9636..ee2c41d2 100644 --- a/Project.toml +++ b/Project.toml @@ -29,10 +29,12 @@ DensityInterface = "0.4" FillArrays = "0.12, 0.13" IfElse = "0.1" LogExpFunctions = "0.3" +LogarithmicNumbers = "1" MappedArrays = "0.4" PrettyPrinting = "0.3, 0.4" Reexport = "1" Static = "0.5, 0.6" +StatsFuns = "0.9" Tricks = "0.1" julia = "1.3" From 91aa7befcc41014332704de205f7f5ccd7e92543 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Fri, 1 Apr 2022 16:19:52 -0700 Subject: [PATCH 193/368] trying to speed things up --- src/MeasureBase.jl | 1 + src/combinators/superpose.jl | 23 +++-- src/density.jl | 193 +++++++++++++++++++++++++---------- src/schema.jl | 34 ++++++ src/utils.jl | 1 - 5 files changed, 190 insertions(+), 62 deletions(-) create mode 100644 src/schema.jl diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index 352e5d4e..1bf46920 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -67,6 +67,7 @@ function logdensity_def end using Compat +include("schema.jl") include("splat.jl") include("proxies.jl") include("kleisli.jl") diff --git a/src/combinators/superpose.jl b/src/combinators/superpose.jl index 7bcb09e4..4da48ae7 100644 --- a/src/combinators/superpose.jl +++ b/src/combinators/superpose.jl @@ -60,7 +60,9 @@ end using LogarithmicNumbers -function density_def(s::SuperpositionMeasure{Tuple{A,B}}, x) where {A,B} +oneplus(x::ULogarithmic) = exp(ULogarithmic, log1pexp(x.log)) + +@inline function density_def(s::SuperpositionMeasure{Tuple{A,B}}, x) where {A,B} (μ, ν) = s.components insupport(μ, x) || return exp(ULogarithmic, logdensity_def(ν, x)) insupport(ν, x) || return exp(ULogarithmic, logdensity_def(μ, x)) @@ -69,26 +71,35 @@ function density_def(s::SuperpositionMeasure{Tuple{A,B}}, x) where {A,B} dμ_dα = exp(ULogarithmic, logdensity_def(μ, x)) dν_dβ = exp(ULogarithmic, logdensity_def(ν, x)) dα_dβ = exp(ULogarithmic, logdensity_rel(α, β, x)) - return dμ_dα / (1 + inv(dα_dβ)) + dν_dβ / (1 + dα_dβ) + dβ_dα = inv(dα_dβ) + return dμ_dα / oneplus(dβ_dα) + dν_dβ / oneplus(dα_dβ) end using StatsFuns -function logdensity_def(s::SuperpositionMeasure{Tuple{A,B}}, β, x) where {A,B} +@inline function logdensity_def(μ::T, ν::T, x::Any) where T<:(SuperpositionMeasure{Tuple{A, B}} where {A, B}) + if μ === ν + return zero(return_type(logdensity_def, (μ, x))) + else + return logdensity_def(μ,x) - logdensity_def(ν, x) + end +end + +@inline function logdensity_def(s::SuperpositionMeasure{Tuple{A,B}}, β, x) where {A,B} (μ, ν) = s.components return logaddexp(logdensity_rel(μ, β, x), logdensity_rel(ν, β, x)) end -function logdensity_def(s::SuperpositionMeasure{Tuple{A,B}}, β::SuperpositionMeasure, x) where {A,B} +@inline function logdensity_def(s::SuperpositionMeasure{Tuple{A,B}}, β::SuperpositionMeasure, x) where {A,B} (μ, ν) = s.components return logaddexp(logdensity_rel(μ, β, x), logdensity_rel(ν, β, x)) end -function logdensity_def(s, β::SuperpositionMeasure{Tuple{A,B}}, x) where {A,B} +@inline function logdensity_def(s, β::SuperpositionMeasure{Tuple{A,B}}, x) where {A,B} -logdensity_def(β, s, x) end -logdensity_def(s::SuperpositionMeasure, x) = log(density_def(s, x)) +@inline logdensity_def(s::SuperpositionMeasure, x) = log(density_def(s, x)) basemeasure(μ::SuperpositionMeasure) = superpose(map(basemeasure, μ.components)) diff --git a/src/density.jl b/src/density.jl index ad688482..f23e4353 100644 --- a/src/density.jl +++ b/src/density.jl @@ -133,76 +133,159 @@ export density_rel export logdensity_rel +@inline return_type(f, args::Tuple) = Core.Compiler.return_type(f, Tuple{typeof.(args)...}) + +unstatic(::Type{T}) where {T} = T +unstatic(::Type{StaticFloat64{X}}) where X = Float64 + +# @inline function logdensity_rel(μ::M, ν::N, x::X) where {M,N,X} +# T = unstatic(float(promote_type(return_type(logdensity_def, (μ, x)), return_type(logdensity_def, (ν, x))))) +# # @show T +# ℓ₊ = ℓ₋ = zero(T) + +# insupport(μ, x) || begin +# insupport(ν, x) || return convert(T, NaN) +# return convert(T, -Inf) +# end +# insupport(ν, x) || return convert(T, Inf) + +# μ_depth = basemeasure_depth(μ) +# ν_depth = basemeasure_depth(ν) + +# Δdepth = μ_depth - ν_depth + +# if Δdepth > 0 +# (ℓ₊, μ_0) = logdensity_steps(μ, x, Δdepth) +# ν_0 = ν +# elseif Δdepth < 0 +# (ℓ₋, ν_0) = logdensity_steps(ν, x, -Δdepth) +# μ_0 = μ +# else +# μ_0 = μ +# ν_0 = ν +# end + +# @assert basemeasure_depth(μ_0) == basemeasure_depth(ν_0) + +# Base.Cartesian.@nexprs 10 i -> begin # 10 is just some "big enough" number +# if μ_{i-1} isa typeof(ν_{i-1}) +# # TODO: Update for cases like Brownian Motion +# return ℓ₊ - ℓ₋ +# elseif static_hasmethod(logdensity_def, Tuple{typeof(μ_{i-1}), typeof(ν_{i-1}), typeof(x)}) +# return ℓ₊ - ℓ₋ + logdensity_def(μ_{i-1}, ν_{i-1}, x) +# end + +# ℓ₊ += logdensity_def(μ_{i-1}, x) +# ℓ₋ += logdensity_def(ν_{i-1}, x) +# μ_{i} = basemeasure(μ_{i-1}) +# ν_{i} = basemeasure(ν_{i-1}) +# end + +# @warn """ +# No common base measure for +# $μ_10 +# and +# $ν_10 + +# Returning a relative log-density of NaN. If this is incorrect, add a +# three-argument method +# logdensity_def(μ, ν, x) +# """ +# return convert(T, NaN) +# end + @inline function logdensity_rel(μ::M, ν::N, x::X) where {M,N,X} - insupport(μ, x) || begin - insupport(ν, x) || return NaN - return -Inf + if static_hasmethod(logdensity_def, Tuple{M, N, X}) + return logdensity_def(μ, ν, x) end - insupport(ν, x) || return Inf - - μ_depth = basemeasure_depth(μ) - ν_depth = basemeasure_depth(ν) - - Δdepth = μ_depth - ν_depth + μs = basemeasure_sequence(μ) + νs = basemeasure_sequence(ν) + return _logdensity_rel(μs, νs, x) +end - if Δdepth > 0 - (ℓ₊, μ_0) = logdensity_steps(μ, x, Δdepth) - ℓ₋ = zero(ℓ₊) - ν_0 = ν - elseif Δdepth < 0 - (ℓ₋, ν_0) = logdensity_steps(ν, x, -Δdepth) - ℓ₊ = zero(ℓ₋) - μ_0 = μ +function logdensity_def(μ::T, ν::T, x) where {T} + if μ === ν + return zero(return_type(logdensity_def, (μ, x))) else - ℓ₊ = ℓ₋ = 0.0 - μ_0 = μ - ν_0 = ν + return logdensity_def(μ,x) - logdensity_def(ν, x) end +end - @assert basemeasure_depth(μ_0) == basemeasure_depth(ν_0) - - Base.Cartesian.@nexprs 10 i -> begin # 10 is just some "big enough" number - if μ_{i-1} == ν_{i-1} - return ℓ₊ - ℓ₋ - elseif static_hasmethod(logdensity_def, Tuple{typeof(μ_{i-1}), typeof(ν_{i-1}), typeof(x)}) - return ℓ₊ - ℓ₋ + logdensity_def(μ_{i-1}, ν_{i-1}, x) +@generated function _logdensity_rel(μs::Tμ, νs::Tν, x::X) where {Tμ, Tν, X} + sμ = schema(Tμ) + sν = schema(Tν) + + q = quote + $(Expr(:meta, :inline)) + end + + for it in Iterators.product(enumerate(sμ), enumerate(sν)) + ((nμ, μtype), (nν, νtype)) = it + if static_hasmethod(logdensity_def, Tuple{μtype, νtype, X}) + push!(q.args, :(ℓ = logdensity_def(μs[$nμ], νs[$nν], x))) + for i in 1:nμ-1 + push!(q.args, :(ℓ += logdensity_def(μs[$i], x))) + end + for j in 1:nν-1 + push!(q.args, :(ℓ -= logdensity_def(νs[$j], x))) + end + + return q end + end - ℓ₊ += logdensity_def(μ_{i-1}, x) - ℓ₋ += logdensity_def(ν_{i-1}, x) - μ_{i} = basemeasure(μ_{i-1}) - ν_{i} = basemeasure(ν_{i-1}) + return quote + μ = μs[end] + ν = νs[end] + @warn """ + No common base measure for + $μ + and + $ν + + Returning a relative log-density of NaN. If this is incorrect, add a + three-argument method + logdensity_def(μ, ν, x) + """ + NaN end - - @warn """ - No common base measure for - $μ_10 - and - $ν_10 - - Returning a relative log-density of NaN. If this is incorrect, add a - three-argument method - logdensity_def(μ, ν, x) - """ - return NaN + end logdensity_steps(μ, x, ::StaticInt{0}) = (zero(logdensity_def(μ, x)), μ) -@inline function logdensity_steps(μ, x, ::StaticInt{n}) where {n} - ℓ_0 = logdensity_def(μ, x) - b_0 = μ +# @inline function logdensity_steps(μ, x, ::StaticInt{n}) where {n} +# ℓ_0 = logdensity_def(μ, x) +# b_0 = μ - Base.Cartesian.@nexprs 10 i -> begin # 10 is just some "big enough" number - i > n && begin - return (ℓ_{i-1}, b_{i-1}) - end - b_{i} = basemeasure(b_{i-1}) - ℓ_{i} = let Δℓ_{i} = logdensity_def(b_{i}, x) - ℓ_{i-1} + Δℓ_{i} - end +# Base.Cartesian.@nexprs 10 i -> begin # 10 is just some "big enough" number +# i > n && begin +# return (ℓ_{i-1}, b_{i-1}) +# end +# b_{i} = basemeasure(b_{i-1}) +# ℓ_{i} = let Δℓ_{i} = logdensity_def(b_{i}, x) +# ℓ_{i-1} + Δℓ_{i} +# end +# end +# return (ℓ_10, b_10) +# end + + +@generated function logdensity_steps(μ, x, ::StaticInt{n}) where {n} + q = quote + ℓ = logdensity_def(μ, x) + μ = basemeasure(μ) end - return (ℓ_10, b_10) + + for j in 2:n + push!(q.args, quote + ℓ += logdensity_def(μ, x) + μ = basemeasure(μ) + end) + end + + push!(q.args, :(return (ℓ, μ))) + return q end export densityof diff --git a/src/schema.jl b/src/schema.jl new file mode 100644 index 00000000..bb7df222 --- /dev/null +++ b/src/schema.jl @@ -0,0 +1,34 @@ +# Taken from https://github.com/cscherrer/NestedTuples.jl/blob/cd298fd1e5f7e571701a6fee916d2d47c19f32f5/src/typelevel.jl + +ntkeys(::Type{NamedTuple{K,V}}) where {K, V} = K +ntvaltype(::Type{NamedTuple{K,V}}) where {K, V} = V + +""" + schema(::Type) + +`schema` turns a type into a value that's easier to work with. +Example: + julia> nt = (a=(b=[1,2],c=(d=[3,4],e=[5,6])),f=[7,8]); + julia> NT = typeof(nt) + NamedTuple{(:a, :f),Tuple{NamedTuple{(:b, :c),Tuple{Array{Int64,1},NamedTuple{(:d, :e),Tuple{Array{Int64,1},Array{Int64,1}}}}},Array{Int64,1}}} + julia> schema(NT) + (a = (b = Array{Int64,1}, c = (d = Array{Int64,1}, e = Array{Int64,1})), f = Array{Int64,1}) +""" +function schema end + +schema(::NamedTuple{(), Tuple{}}) = NamedTuple() +schema(::Type{NamedTuple{(), Tuple{}}}) = NamedTuple() + +function schema(NT::Type{NamedTuple{names, T}}) where {names, T} + return NamedTuple{ntkeys(NT)}(schema(ntvaltype(NT))) +end + +function schema(TT::Type{T}) where {T <: Tuple} + return schema.(Tuple(TT.types)) +end + +schema(t::T) where {T <: Tuple} = schema(T) + +schema(t::T) where {T <: NamedTuple} = schema(T) + +schema(T) = T \ No newline at end of file diff --git a/src/utils.jl b/src/utils.jl index cb24c25d..5454184e 100644 --- a/src/utils.jl +++ b/src/utils.jl @@ -60,7 +60,6 @@ end export basemeasure_depth @inline function basemeasure_depth(μ::M) where {M} - depth_0 = static(0) b_0 = μ Base.Cartesian.@nexprs 10 i -> begin # 10 is just some "big enough" number b_{i} = basemeasure(b_{i-1}) From b06964011a08edfd971ca2150bc3ec636d51aac0 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Fri, 1 Apr 2022 16:57:49 -0700 Subject: [PATCH 194/368] bugfixes --- src/combinators/superpose.jl | 4 ++++ src/utils.jl | 2 +- 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/src/combinators/superpose.jl b/src/combinators/superpose.jl index 4da48ae7..ac080f6d 100644 --- a/src/combinators/superpose.jl +++ b/src/combinators/superpose.jl @@ -87,11 +87,15 @@ end @inline function logdensity_def(s::SuperpositionMeasure{Tuple{A,B}}, β, x) where {A,B} (μ, ν) = s.components + insupport(μ, x) || return logdensity_rel(ν, β, x) + insupport(ν, x) || return logdensity_rel(μ, β, x) return logaddexp(logdensity_rel(μ, β, x), logdensity_rel(ν, β, x)) end @inline function logdensity_def(s::SuperpositionMeasure{Tuple{A,B}}, β::SuperpositionMeasure, x) where {A,B} (μ, ν) = s.components + insupport(μ, x) || return logdensity_rel(ν, β, x) + insupport(ν, x) || return logdensity_rel(μ, β, x) return logaddexp(logdensity_rel(μ, β, x), logdensity_rel(ν, β, x)) end diff --git a/src/utils.jl b/src/utils.jl index 5454184e..4f56b184 100644 --- a/src/utils.jl +++ b/src/utils.jl @@ -84,7 +84,7 @@ end Base.Cartesian.@nexprs 10 i -> begin # 10 is just some "big enough" number b_{i+1} = basemeasure(b_{i}) end - return Base.Cartesian.@ntuple $N b + return Base.Cartesian.@ntuple $(N+1) b end end From b0078d2d7ecc115617924134e1d14dcddff6d1c3 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Sat, 2 Apr 2022 07:55:01 -0700 Subject: [PATCH 195/368] logdensity_rel tests --- test/runtests.jl | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/test/runtests.jl b/test/runtests.jl index f6560522..875fdea7 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -167,6 +167,17 @@ end end end +@testset "logdensity_rel" begin + @test MeasureBase.logdensity_rel(Dirac(0.0)+Lebesgue(), Dirac(0.0), 0.0) == 0.0 + @test MeasureBase.logdensity_rel(Dirac(0.0)+Lebesgue(), Dirac(0.0), 1.0) == Inf + @test MeasureBase.logdensity_rel(Dirac(0.0)+Lebesgue(), Lebesgue(), 0.0) == Inf + @test MeasureBase.logdensity_rel(Dirac(0.0)+Lebesgue(), Lebesgue(), 1.0) == 0.0 + @test MeasureBase.logdensity_rel(Lebesgue()+ Dirac(0.0), Dirac(0.0), 0.0) == 0.0 + @test MeasureBase.logdensity_rel(Lebesgue()+ Dirac(0.0), Dirac(0.0), 1.0) == Inf + @test MeasureBase.logdensity_rel(Lebesgue()+ Dirac(0.0), Lebesgue(), 0.0) == Inf + @test MeasureBase.logdensity_rel(Lebesgue()+ Dirac(0.0), Lebesgue(), 1.0) == 0.0 +end + # @testset "Density measures and Radon-Nikodym" begin # x = randn() # let d = ∫(𝒹(Cauchy(), Normal()), Normal()) From 4b1b49ecf532736cb9f370ce14bbb4fbb28d995b Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Sat, 2 Apr 2022 08:01:02 -0700 Subject: [PATCH 196/368] logdensity_rel tests --- src/density.jl | 7 +++++++ test/runtests.jl | 15 +++++++++++---- 2 files changed, 18 insertions(+), 4 deletions(-) diff --git a/src/density.jl b/src/density.jl index f23e4353..73a5fc65 100644 --- a/src/density.jl +++ b/src/density.jl @@ -195,6 +195,13 @@ unstatic(::Type{StaticFloat64{X}}) where X = Float64 # end @inline function logdensity_rel(μ::M, ν::N, x::X) where {M,N,X} + T = unstatic(float(promote_type(return_type(logdensity_def, (μ, x)), return_type(logdensity_def, (ν, x))))) + insupport(μ, x) || begin + insupport(ν, x) || return convert(T, NaN) + return convert(T, -Inf) + end + insupport(ν, x) || return convert(T, Inf) + if static_hasmethod(logdensity_def, Tuple{M, N, X}) return logdensity_def(μ, ν, x) end diff --git a/test/runtests.jl b/test/runtests.jl index 875fdea7..fb490d5e 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -168,14 +168,21 @@ end end @testset "logdensity_rel" begin + @test MeasureBase.logdensity_rel(Dirac(0.0)+Lebesgue(), Dirac(1.0), 0.0) == Inf + @test MeasureBase.logdensity_rel(Dirac(0.0)+Lebesgue(), Dirac(1.0), 1.0) == -Inf + @test MeasureBase.logdensity_rel(Dirac(0.0)+Lebesgue(), Dirac(1.0), 2.0) == Inf @test MeasureBase.logdensity_rel(Dirac(0.0)+Lebesgue(), Dirac(0.0), 0.0) == 0.0 @test MeasureBase.logdensity_rel(Dirac(0.0)+Lebesgue(), Dirac(0.0), 1.0) == Inf @test MeasureBase.logdensity_rel(Dirac(0.0)+Lebesgue(), Lebesgue(), 0.0) == Inf @test MeasureBase.logdensity_rel(Dirac(0.0)+Lebesgue(), Lebesgue(), 1.0) == 0.0 - @test MeasureBase.logdensity_rel(Lebesgue()+ Dirac(0.0), Dirac(0.0), 0.0) == 0.0 - @test MeasureBase.logdensity_rel(Lebesgue()+ Dirac(0.0), Dirac(0.0), 1.0) == Inf - @test MeasureBase.logdensity_rel(Lebesgue()+ Dirac(0.0), Lebesgue(), 0.0) == Inf - @test MeasureBase.logdensity_rel(Lebesgue()+ Dirac(0.0), Lebesgue(), 1.0) == 0.0 + + @test MeasureBase.logdensity_rel(Dirac(1.0), Dirac(0.0)+Lebesgue(), 0.0) == -Inf + @test MeasureBase.logdensity_rel(Dirac(1.0), Dirac(0.0)+Lebesgue(), 1.0) == Inf + @test MeasureBase.logdensity_rel(Dirac(1.0), Dirac(0.0)+Lebesgue(), 2.0) == -Inf + @test MeasureBase.logdensity_rel(Dirac(0.0), Dirac(0.0)+Lebesgue(), 0.0) == 0.0 + @test MeasureBase.logdensity_rel(Dirac(0.0), Dirac(0.0)+Lebesgue(), 1.0) == -Inf + @test MeasureBase.logdensity_rel(Lebesgue(), Dirac(0.0)+Lebesgue(), 0.0) == -Inf + @test MeasureBase.logdensity_rel(Lebesgue(), Dirac(0.0)+Lebesgue(), 1.0) == 0.0 end # @testset "Density measures and Radon-Nikodym" begin From 1c16e2c57632c5bbfbdf9a11f2ecaa7949695eb7 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Sat, 2 Apr 2022 08:04:58 -0700 Subject: [PATCH 197/368] drop qualifier, and add a test --- test/runtests.jl | 32 +++++++++++++++++--------------- 1 file changed, 17 insertions(+), 15 deletions(-) diff --git a/test/runtests.jl b/test/runtests.jl index fb490d5e..fe4ced83 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -168,21 +168,23 @@ end end @testset "logdensity_rel" begin - @test MeasureBase.logdensity_rel(Dirac(0.0)+Lebesgue(), Dirac(1.0), 0.0) == Inf - @test MeasureBase.logdensity_rel(Dirac(0.0)+Lebesgue(), Dirac(1.0), 1.0) == -Inf - @test MeasureBase.logdensity_rel(Dirac(0.0)+Lebesgue(), Dirac(1.0), 2.0) == Inf - @test MeasureBase.logdensity_rel(Dirac(0.0)+Lebesgue(), Dirac(0.0), 0.0) == 0.0 - @test MeasureBase.logdensity_rel(Dirac(0.0)+Lebesgue(), Dirac(0.0), 1.0) == Inf - @test MeasureBase.logdensity_rel(Dirac(0.0)+Lebesgue(), Lebesgue(), 0.0) == Inf - @test MeasureBase.logdensity_rel(Dirac(0.0)+Lebesgue(), Lebesgue(), 1.0) == 0.0 - - @test MeasureBase.logdensity_rel(Dirac(1.0), Dirac(0.0)+Lebesgue(), 0.0) == -Inf - @test MeasureBase.logdensity_rel(Dirac(1.0), Dirac(0.0)+Lebesgue(), 1.0) == Inf - @test MeasureBase.logdensity_rel(Dirac(1.0), Dirac(0.0)+Lebesgue(), 2.0) == -Inf - @test MeasureBase.logdensity_rel(Dirac(0.0), Dirac(0.0)+Lebesgue(), 0.0) == 0.0 - @test MeasureBase.logdensity_rel(Dirac(0.0), Dirac(0.0)+Lebesgue(), 1.0) == -Inf - @test MeasureBase.logdensity_rel(Lebesgue(), Dirac(0.0)+Lebesgue(), 0.0) == -Inf - @test MeasureBase.logdensity_rel(Lebesgue(), Dirac(0.0)+Lebesgue(), 1.0) == 0.0 + @test logdensity_rel(Dirac(0.0)+Lebesgue(), Dirac(1.0), 0.0) == Inf + @test logdensity_rel(Dirac(0.0)+Lebesgue(), Dirac(1.0), 1.0) == -Inf + @test logdensity_rel(Dirac(0.0)+Lebesgue(), Dirac(1.0), 2.0) == Inf + @test logdensity_rel(Dirac(0.0)+Lebesgue(), Dirac(0.0), 0.0) == 0.0 + @test logdensity_rel(Dirac(0.0)+Lebesgue(), Dirac(0.0), 1.0) == Inf + @test logdensity_rel(Dirac(0.0)+Lebesgue(), Lebesgue(), 0.0) == Inf + @test logdensity_rel(Dirac(0.0)+Lebesgue(), Lebesgue(), 1.0) == 0.0 + + @test logdensity_rel(Dirac(1.0), Dirac(0.0)+Lebesgue(), 0.0) == -Inf + @test logdensity_rel(Dirac(1.0), Dirac(0.0)+Lebesgue(), 1.0) == Inf + @test logdensity_rel(Dirac(1.0), Dirac(0.0)+Lebesgue(), 2.0) == -Inf + @test logdensity_rel(Dirac(0.0), Dirac(0.0)+Lebesgue(), 0.0) == 0.0 + @test logdensity_rel(Dirac(0.0), Dirac(0.0)+Lebesgue(), 1.0) == -Inf + @test logdensity_rel(Lebesgue(), Dirac(0.0)+Lebesgue(), 0.0) == -Inf + @test logdensity_rel(Lebesgue(), Dirac(0.0)+Lebesgue(), 1.0) == 0.0 + + @test isnan(logdensity_rel(Dirac(0), Dirac(1), 2)) end # @testset "Density measures and Radon-Nikodym" begin From f469ae0069c72225066526175f4b9842afae4ff5 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Sat, 2 Apr 2022 11:31:21 -0700 Subject: [PATCH 198/368] more tests --- test/runtests.jl | 21 +++++++++++---------- 1 file changed, 11 insertions(+), 10 deletions(-) diff --git a/test/runtests.jl b/test/runtests.jl index fe4ced83..35244e8f 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -34,7 +34,9 @@ test_measures = [ 3 * Lebesgue(ℝ) Dirac(π) Lebesgue(ℝ) - # Dirac(0.0) + Lebesgue(ℝ) + 0.2 * Lebesgue(ℝ) + 0.8 * Dirac(0.0) + Dirac(0) + Dirac(1) + Dirac(0.0) + Lebesgue(ℝ) SpikeMixture(Lebesgue(ℝ), 0.2) # d ⊙ d ] @@ -187,15 +189,14 @@ end @test isnan(logdensity_rel(Dirac(0), Dirac(1), 2)) end -# @testset "Density measures and Radon-Nikodym" begin -# x = randn() -# let d = ∫(𝒹(Cauchy(), Normal()), Normal()) -# @test logdensity_def(d, x) ≈ logdensity_def(Cauchy(), x) -# end +@testset "Density measures and Radon-Nikodym" begin + x = randn() + f(x) = x^2 + @test logdensityof(𝒹(∫exp(f, Lebesgue()), Lebesgue()),x ) ≈ f(x) -# let f = 𝒹(∫(x -> x^2, Normal()), Normal()) -# @test f(x) ≈ x^2 -# end + let f = 𝒹(∫exp(x -> x^2, Lebesgue()), Lebesgue()) + @test logdensityof(f,x) ≈ x^2 + end # let d = ∫exp(log𝒹(Cauchy(), Normal()), Normal()) # @test logdensity_def(d, x) ≈ logdensity_def(Cauchy(), x) @@ -204,4 +205,4 @@ end # let f = log𝒹(∫exp(x -> x^2, Normal()), Normal()) # @test f(x) ≈ x^2 # end -# end +end From aec684120b844d6938c5af973c79fc387ca06e52 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Sun, 3 Apr 2022 06:26:32 -0700 Subject: [PATCH 199/368] =?UTF-8?q?type=20constraint=20in=20"logdensityof(?= =?UTF-8?q?=CE=BC::AbstractMeasure,=20x)"=20(was=20piracy,=20oops)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- src/density.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/density.jl b/src/density.jl index 73a5fc65..e9b26e37 100644 --- a/src/density.jl +++ b/src/density.jl @@ -103,7 +103,7 @@ Define a new measure in terms of a log-density `f` over some measure `base`. # TODO: `density` and `logdensity` functions for `DensityMeasure` -@inline function logdensityof(μ, x) +@inline function logdensityof(μ::AbstractMeasure, x) t() = dynamic(unsafe_logdensityof(μ, x)) f() = -Inf ifelse(insupport(μ, x), t, f)() From 9e45cf2fb27e7fdffe885803f609624edfd44a9b Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Sun, 3 Apr 2022 06:58:58 -0700 Subject: [PATCH 200/368] add some docs --- src/MeasureBase.jl | 12 ++++ src/density.jl | 139 +++++++++++++++------------------------------ 2 files changed, 59 insertions(+), 92 deletions(-) diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index 1bf46920..22cf3e5b 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -33,6 +33,18 @@ export logdensity_def export basemeasure export basekleisli +""" + inssupport(m, x) + insupport(m) + +`insupport(m,x)` computes whether `x` is in the support of `m`. + +`insupport(m)` returns a function, and satisfies + + insupport(m)(x) == insupport(m, x) +""" +function insupport end + export insupport abstract type AbstractMeasure end diff --git a/src/density.jl b/src/density.jl index e9b26e37..1227d15f 100644 --- a/src/density.jl +++ b/src/density.jl @@ -103,6 +103,25 @@ Define a new measure in terms of a log-density `f` over some measure `base`. # TODO: `density` and `logdensity` functions for `DensityMeasure` +""" + logdensityof(m::AbstractMeasure, x) + +Compute the log-density of the measure `m` at `x`. Density is always relative, +but `DensityInterface.jl` does not account for this. For compatibility with +this, `logdensityof` for a measure is always implicitly relative to +`rootmeasure(x)`. + +`logdensityof` works by first computing `insupport(m, x)`. If this is true, then +`unsafe_logdensityof` is called. If `insupport(m, x)` is known to be `true`, it +can be a little faster to directly call `unsafe_logdensityof(m, x)`. + +To compute log-density relative to `basemeasure(m)` or *define* a log-density +(relative to `basemeasure(m)` or another measure given explicitly), see +`logdensity_def`. + +To compute a log-density relative to a specific base-measure, see +`logdensity_rel`. +""" @inline function logdensityof(μ::AbstractMeasure, x) t() = dynamic(unsafe_logdensityof(μ, x)) f() = -Inf @@ -112,6 +131,14 @@ end export unsafe_logdensityof # https://discourse.julialang.org/t/counting-iterations-to-a-type-fixpoint/75876/10?u=cscherrer +""" + unsafe_logdensityof(m, x) + +Compute the log-density of the measure `m` at `x` relative to `rootmeasure(m)`. +This is "unsafe" because it does not check `insupport(m, x)`. + +See also `logdensityof`. +""" @inline function unsafe_logdensityof(μ::M, x) where {M} ℓ_0 = logdensity_def(μ, x) b_0 = μ @@ -138,62 +165,14 @@ export logdensity_rel unstatic(::Type{T}) where {T} = T unstatic(::Type{StaticFloat64{X}}) where X = Float64 -# @inline function logdensity_rel(μ::M, ν::N, x::X) where {M,N,X} -# T = unstatic(float(promote_type(return_type(logdensity_def, (μ, x)), return_type(logdensity_def, (ν, x))))) -# # @show T -# ℓ₊ = ℓ₋ = zero(T) - -# insupport(μ, x) || begin -# insupport(ν, x) || return convert(T, NaN) -# return convert(T, -Inf) -# end -# insupport(ν, x) || return convert(T, Inf) - -# μ_depth = basemeasure_depth(μ) -# ν_depth = basemeasure_depth(ν) - -# Δdepth = μ_depth - ν_depth - -# if Δdepth > 0 -# (ℓ₊, μ_0) = logdensity_steps(μ, x, Δdepth) -# ν_0 = ν -# elseif Δdepth < 0 -# (ℓ₋, ν_0) = logdensity_steps(ν, x, -Δdepth) -# μ_0 = μ -# else -# μ_0 = μ -# ν_0 = ν -# end - -# @assert basemeasure_depth(μ_0) == basemeasure_depth(ν_0) - -# Base.Cartesian.@nexprs 10 i -> begin # 10 is just some "big enough" number -# if μ_{i-1} isa typeof(ν_{i-1}) -# # TODO: Update for cases like Brownian Motion -# return ℓ₊ - ℓ₋ -# elseif static_hasmethod(logdensity_def, Tuple{typeof(μ_{i-1}), typeof(ν_{i-1}), typeof(x)}) -# return ℓ₊ - ℓ₋ + logdensity_def(μ_{i-1}, ν_{i-1}, x) -# end - -# ℓ₊ += logdensity_def(μ_{i-1}, x) -# ℓ₋ += logdensity_def(ν_{i-1}, x) -# μ_{i} = basemeasure(μ_{i-1}) -# ν_{i} = basemeasure(ν_{i-1}) -# end - -# @warn """ -# No common base measure for -# $μ_10 -# and -# $ν_10 - -# Returning a relative log-density of NaN. If this is incorrect, add a -# three-argument method -# logdensity_def(μ, ν, x) -# """ -# return convert(T, NaN) -# end +""" + logdensity_rel(m1, m2, x) +Compute the log-density of `m1` relative to `m2` at `x`. This function checks +whether `x` is in the support of `m1` or `m2` (or both, or neither). If `x` is +known to be in the support of both, it can be more efficient to call +`unsafe_logdensity_rel`. +""" @inline function logdensity_rel(μ::M, ν::N, x::X) where {M,N,X} T = unstatic(float(promote_type(return_type(logdensity_def, (μ, x)), return_type(logdensity_def, (ν, x))))) insupport(μ, x) || begin @@ -202,6 +181,18 @@ unstatic(::Type{StaticFloat64{X}}) where X = Float64 end insupport(ν, x) || return convert(T, Inf) + return unsafe_logdensity_rel(μ, ν, x) +end + +""" + unsafe_logdensity_rel(m1, m2, x) + +Compute the log-density of `m1` relative to `m2` at `x`, assuming `x` is +known to be in the support of both `m1` and `m2`. + +See also `logdensity_rel`. +""" +@inline function unsafelogdensity_rel(μ::M, ν::N, x::X) where {M,N,X} if static_hasmethod(logdensity_def, Tuple{M, N, X}) return logdensity_def(μ, ν, x) end @@ -210,6 +201,7 @@ unstatic(::Type{StaticFloat64{X}}) where X = Float64 return _logdensity_rel(μs, νs, x) end +# Note that this method assumes `μ` and `ν` to have the same type function logdensity_def(μ::T, ν::T, x) where {T} if μ === ν return zero(return_type(logdensity_def, (μ, x))) @@ -256,43 +248,6 @@ end """ NaN end - -end - -logdensity_steps(μ, x, ::StaticInt{0}) = (zero(logdensity_def(μ, x)), μ) - -# @inline function logdensity_steps(μ, x, ::StaticInt{n}) where {n} -# ℓ_0 = logdensity_def(μ, x) -# b_0 = μ - -# Base.Cartesian.@nexprs 10 i -> begin # 10 is just some "big enough" number -# i > n && begin -# return (ℓ_{i-1}, b_{i-1}) -# end -# b_{i} = basemeasure(b_{i-1}) -# ℓ_{i} = let Δℓ_{i} = logdensity_def(b_{i}, x) -# ℓ_{i-1} + Δℓ_{i} -# end -# end -# return (ℓ_10, b_10) -# end - - -@generated function logdensity_steps(μ, x, ::StaticInt{n}) where {n} - q = quote - ℓ = logdensity_def(μ, x) - μ = basemeasure(μ) - end - - for j in 2:n - push!(q.args, quote - ℓ += logdensity_def(μ, x) - μ = basemeasure(μ) - end) - end - - push!(q.args, :(return (ℓ, μ))) - return q end export densityof From f4ca67785ea1cd1d3667210784da66c985aaa771 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Sun, 3 Apr 2022 07:11:15 -0700 Subject: [PATCH 201/368] docs --- src/MeasureBase.jl | 18 +++++++++++++----- 1 file changed, 13 insertions(+), 5 deletions(-) diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index 22cf3e5b..f0a723d4 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -67,13 +67,21 @@ gentype(μ::AbstractMeasure) = typeof(testvalue(μ)) using LogExpFunctions: logsumexp """ - logdensity_def(μ::AbstractMeasure{X}, x::X) +`logdensity_def` is the standard way to define a log-density for a new measure. +Note that this definition does not include checking for membership in the +support; this is instead checked using `insupport`. `logdensity_def` is +a low-level function, and should typically not be called directly. See +`logdensityof` for more information and other alternatives. -Compute the logdensity of the measure μ at the point x. This is the standard way -to define `logdensity` for a new measure. the base measure is implicit here, and -is understood to be `basemeasure(μ)`. + logdensity_def(m, x) -Methods for computing density relative to other measures will be +Compute the log-density of the measure m at the point x, relative to +`basemeasure(m)`, and assuming `insupport(m, x)`. + + logdensity_def(m1, m2, x) + +Compute the log-density of `m1` relative to `m2` at the point `x`, assuming +`insupport(m1, x)` and `insupport(m2, x)`. """ function logdensity_def end From a6cffe587519315cfae68b1515aec2724f89a882 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Sun, 3 Apr 2022 07:14:38 -0700 Subject: [PATCH 202/368] docs --- src/MeasureBase.jl | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index f0a723d4..9148f97d 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -73,11 +73,15 @@ support; this is instead checked using `insupport`. `logdensity_def` is a low-level function, and should typically not be called directly. See `logdensityof` for more information and other alternatives. +--- + logdensity_def(m, x) -Compute the log-density of the measure m at the point x, relative to +Compute the log-density of the measure m at the point `x`, relative to `basemeasure(m)`, and assuming `insupport(m, x)`. +--- + logdensity_def(m1, m2, x) Compute the log-density of `m1` relative to `m2` at the point `x`, assuming From 47ee084709e65e9c88d29d3e8b1a63164a548d8c Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Sun, 3 Apr 2022 07:48:02 -0700 Subject: [PATCH 203/368] typo --- src/density.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/density.jl b/src/density.jl index 1227d15f..cabb9a2a 100644 --- a/src/density.jl +++ b/src/density.jl @@ -192,7 +192,7 @@ known to be in the support of both `m1` and `m2`. See also `logdensity_rel`. """ -@inline function unsafelogdensity_rel(μ::M, ν::N, x::X) where {M,N,X} +@inline function unsafe_logdensity_rel(μ::M, ν::N, x::X) where {M,N,X} if static_hasmethod(logdensity_def, Tuple{M, N, X}) return logdensity_def(μ, ν, x) end From 46f8a9b447bf8f22c6f0521c4692b2ff7cd601bf Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 4 Apr 2022 15:43:27 -0700 Subject: [PATCH 204/368] moar speed --- src/density.jl | 57 +++++++++++++++++++++++------------------------- src/interface.jl | 4 +++- src/utils.jl | 37 ++++++++++++++++--------------- 3 files changed, 50 insertions(+), 48 deletions(-) diff --git a/src/density.jl b/src/density.jl index 22f43553..db0429c6 100644 --- a/src/density.jl +++ b/src/density.jl @@ -180,7 +180,6 @@ known to be in the support of both, it can be more efficient to call return convert(T, -Inf) end insupport(ν, x) || return convert(T, Inf) - return unsafe_logdensity_rel(μ, ν, x) end @@ -198,7 +197,24 @@ See also `logdensity_rel`. end μs = basemeasure_sequence(μ) νs = basemeasure_sequence(ν) - return _logdensity_rel(μs, νs, x) + cb = commonbase(μs, νs) + # _logdensity_rel(μ, ν) + isnothing(cb) && begin + μ = μs[end] + ν = νs[end] + @warn """ + No common base measure for + $μ + and + $ν + + Returning a relative log-density of NaN. If this is incorrect, add a + three-argument method + logdensity_def($μ, $ν, x) + """ + return NaN + end + return _logdensity_rel(μs, νs, cb, x) end # Note that this method assumes `μ` and `ν` to have the same type @@ -210,44 +226,25 @@ function logdensity_def(μ::T, ν::T, x) where {T} end end -@generated function _logdensity_rel(μs::Tμ, νs::Tν, x::X) where {Tμ, Tν, X} +@generated function _logdensity_rel(μs::Tμ, νs::Tν, ::Tuple{StaticInt{M},StaticInt{N}}, x::X) where {Tμ, Tν,M,N,X} sμ = schema(Tμ) sν = schema(Tν) q = quote $(Expr(:meta, :inline)) + ℓ = logdensity_def(μs[$M], νs[$N], x) end - for it in Iterators.product(enumerate(sμ), enumerate(sν)) - ((nμ, μtype), (nν, νtype)) = it - if static_hasmethod(logdensity_def, Tuple{μtype, νtype, X}) - push!(q.args, :(ℓ = logdensity_def(μs[$nμ], νs[$nν], x))) - for i in 1:nμ-1 - push!(q.args, :(ℓ += logdensity_def(μs[$i], x))) - end - for j in 1:nν-1 - push!(q.args, :(ℓ -= logdensity_def(νs[$j], x))) - end - - return q - end + for i in 1:M-1 + push!(q.args, :(ℓ += logdensity_def(μs[$i], x))) end - return quote - μ = μs[end] - ν = νs[end] - @warn """ - No common base measure for - $μ - and - $ν - - Returning a relative log-density of NaN. If this is incorrect, add a - three-argument method - logdensity_def(μ, ν, x) - """ - NaN + for j in 1:N-1 + push!(q.args, :(ℓ += logdensity_def(νs[$j], x))) end + + push!(q.args, :(return ℓ)) + return q end export densityof diff --git a/src/interface.jl b/src/interface.jl index 7ffe1213..dac41d35 100644 --- a/src/interface.jl +++ b/src/interface.jl @@ -5,12 +5,14 @@ using Reexport @reexport using MeasureBase using MeasureBase:basemeasure_depth, proxy -using MeasureBase: insupport +using MeasureBase: insupport, basemeasure_sequence, commonbase export test_interface export basemeasure_depth export proxy export insupport +export basemeasure_sequence +export commonbase using Test diff --git a/src/utils.jl b/src/utils.jl index 976e696b..66581727 100644 --- a/src/utils.jl +++ b/src/utils.jl @@ -70,9 +70,12 @@ export basemeasure_depth return static(10) end +""" + basemeasure_sequence(m) -export basemeasure_sequence - +Construct the longest `Tuple` starting with `m` having each term as the base +measure of the previous term, and with no repeated entries. +""" @inline function basemeasure_sequence(μ::M) where {M} b_1 = μ done = false @@ -86,21 +89,21 @@ export basemeasure_sequence return filter(!isnothing, Base.Cartesian.@ntuple 10 b) end -# @inline function basemeasure_depth(μ::M) where {M} -# return basemeasure_depth(μ, basemeasure(μ), static(0)) -# end - -# @inline function basemeasure_depth(μ::M, β::M, s::StaticInt{N}) where {M,N} -# s -# end - -# @generated function basemeasure_depth(μ::M, β::B, ::StaticInt{N}) where {M,B,N} -# s = Expr(:call, Expr(:curly, :StaticInt, N + 1)) -# quote -# $(Expr(:meta, :inline)) -# basemeasure_depth(β, basemeasure(β), $s) -# end -# end +@inline function commonbase(μ, ν) + return commonbase(basemeasure_sequence(μ), basemeasure_sequence(ν)) +end + +@generated function commonbase(μ::M, ν::N) where {M<:Tuple,N<:Tuple} + m = schema(M) + n = schema(N) + + sols = Iterators.filter(((i,j),) -> static_hasmethod(logdensity_def, Tuple{m[i], n[j], Any}), Iterators.product(1:length(m), 1:length(n))) + isempty(sols) && return :(nothing) + minsol = static.(argmin(((i,j),) -> i+j, sols)) + quote + $minsol + end +end mymap(f, gen::Base.Generator) = mymap(f ∘ gen.f, gen.iter) mymap(f, inds...) = Iterators.map(f, inds...) From b3703bd3634bde0cdbd0490a1a1a588cd3d9153d Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 4 Apr 2022 19:10:23 -0700 Subject: [PATCH 205/368] don't export Test --- src/MeasureBase.jl | 2 -- 1 file changed, 2 deletions(-) diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index 6e60a547..7d0e25fa 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -125,8 +125,6 @@ include("rand.jl") include("density.jl") -@reexport using Test - include("interface.jl") using .Interface From b3d3afc41b4cb79efb7e9993d966e6028a9e740f Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 5 Apr 2022 07:35:13 -0700 Subject: [PATCH 206/368] some more updates --- Project.toml | 4 ++-- src/MeasureBase.jl | 1 + src/combinators/smart-constructors.jl | 2 +- src/combinators/superpose.jl | 7 +++---- src/density.jl | 2 +- 5 files changed, 8 insertions(+), 8 deletions(-) diff --git a/Project.toml b/Project.toml index 3428f683..0d719bc5 100644 --- a/Project.toml +++ b/Project.toml @@ -13,12 +13,12 @@ LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" LogExpFunctions = "2ab3a3ac-af41-5b50-aa03-7779005ae688" LogarithmicNumbers = "aa2f6b4e-9042-5d33-9679-40d3a6b85899" MappedArrays = "dbb5928d-eab1-5f90-85c2-b9b0edb7c900" +NaNMath = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3" PrettyPrinting = "54e16d92-306c-5ea0-a30b-337be88ac337" Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" Reexport = "189a3867-3050-52da-a836-e630ba90ab69" Static = "aedffcd0-7271-4cad-89d0-dc628f76c6d3" Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" -StatsFuns = "4c63d2b9-4356-54db-8cca-17b64c39e42c" Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" Tricks = "410a4b4d-49e4-4fbc-ab6d-cb71b17b3775" @@ -31,10 +31,10 @@ IfElse = "0.1" LogExpFunctions = "0.3" LogarithmicNumbers = "1" MappedArrays = "0.4" +NaNMath = "0.3, 1" PrettyPrinting = "0.3, 0.4" Reexport = "1" Static = "0.5, 0.6" -StatsFuns = "0.9" Tricks = "0.1" julia = "1.3" diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index 7d0e25fa..d6eeab6b 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -64,6 +64,7 @@ gentype(μ::AbstractMeasure) = typeof(testvalue(μ)) # gentype(μ::AbstractMeasure) = gentype(basemeasure(μ)) +using NaNMath using LogExpFunctions: logsumexp """ diff --git a/src/combinators/smart-constructors.jl b/src/combinators/smart-constructors.jl index 4be19fb9..8243243c 100644 --- a/src/combinators/smart-constructors.jl +++ b/src/combinators/smart-constructors.jl @@ -84,7 +84,7 @@ function superpose(μ::T, ν::T) where {T} end end -function superpose(μ::AbstractMeasure, ν::AbstractMeasure) +function superpose(μ, ν) components = (μ, ν) superpose(components) end diff --git a/src/combinators/superpose.jl b/src/combinators/superpose.jl index ac080f6d..cb0b9c0c 100644 --- a/src/combinators/superpose.jl +++ b/src/combinators/superpose.jl @@ -54,8 +54,7 @@ testvalue(μ::SuperpositionMeasure) = testvalue(first(μ.components)) # end function Base.:+(μ::AbstractMeasure, ν::AbstractMeasure) - components = (μ, ν) - superpose(components) + superpose(μ, ν) end using LogarithmicNumbers @@ -75,7 +74,7 @@ oneplus(x::ULogarithmic) = exp(ULogarithmic, log1pexp(x.log)) return dμ_dα / oneplus(dβ_dα) + dν_dβ / oneplus(dα_dβ) end -using StatsFuns +using LogExpFunctions @inline function logdensity_def(μ::T, ν::T, x::Any) where T<:(SuperpositionMeasure{Tuple{A, B}} where {A, B}) if μ === ν @@ -105,7 +104,7 @@ end @inline logdensity_def(s::SuperpositionMeasure, x) = log(density_def(s, x)) -basemeasure(μ::SuperpositionMeasure) = superpose(map(basemeasure, μ.components)) +basemeasure(μ::SuperpositionMeasure) = superpose(map(basemeasure, μ.components)...) # TODO: Fix `rand` method (this one is wrong) # function Base.rand(μ::SuperpositionMeasure{X,N}) where {X,N} diff --git a/src/density.jl b/src/density.jl index 00250619..1a5ef889 100644 --- a/src/density.jl +++ b/src/density.jl @@ -174,7 +174,7 @@ known to be in the support of both, it can be more efficient to call `unsafe_logdensity_rel`. """ @inline function logdensity_rel(μ::M, ν::N, x::X) where {M,N,X} - T = unstatic(float(promote_type(return_type(logdensity_def, (μ, x)), return_type(logdensity_def, (ν, x))))) + T = unstatic(promote_type(return_type(logdensity_def, (μ, x)), return_type(logdensity_def, (ν, x)))) insupport(μ, x) || begin insupport(ν, x) || return convert(T, NaN) return convert(T, -Inf) From 1893ae37ecd36d4959a0ea143e1bd701e755a7b4 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 6 Apr 2022 08:25:40 -0700 Subject: [PATCH 207/368] logdensity_rel for products --- src/combinators/product.jl | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/src/combinators/product.jl b/src/combinators/product.jl index 7c1a4ced..10b78096 100644 --- a/src/combinators/product.jl +++ b/src/combinators/product.jl @@ -65,6 +65,10 @@ struct ProductMeasure{M} <: AbstractProductMeasure marginals::M end +@inline function logdensity_rel(μ::ProductMeasure, ν::ProductMeasure, x) + mapreduce(logdensity_rel, +, marginals(μ), marginals(ν), x) +end + function Pretty.tile(d::ProductMeasure{T}) where {T<:Tuple} Pretty.list_layout(Pretty.tile.([marginals(d)...]), sep=" ⊗ ") end From ec64718553e89aefe763b7b46fd2ca12c75ecd63 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 6 Apr 2022 10:37:31 -0700 Subject: [PATCH 208/368] `kleisli` docs --- src/kleisli.jl | 25 ++++++++++++++++++++----- 1 file changed, 20 insertions(+), 5 deletions(-) diff --git a/src/kleisli.jl b/src/kleisli.jl index f79efaf0..7f0d9254 100644 --- a/src/kleisli.jl +++ b/src/kleisli.jl @@ -15,17 +15,32 @@ end kleisli(f, M) kleisli((f1, f2, ...), M) -A kleisli `κ = kleisli(f, m)` returns a wrapper around -a function `f` giving the parameters for a measure of type `M`, -such that `κ(x) = M(f(x)...)` -respective `κ(x) = M(f1(x), f2(x), ...)` +`kleisli` was originally called `kernel`, as in a *Markov kernel*. Such a kernel +can be considered to map each value in its domain to a probability measure. + +In the context of MeasureTheory, the codomain is not required to be a +*probability* measure; any measure will do. This makes "Markov" not really fit, +since the map need not be Markovian. + +This leaves us with "kernel", which can mean too wide a range of things to be +useful in such a general context as measure theory. See for example +https://github.com/JuliaGaussianProcesses/KernelFunctions.jl for one common use +of this term. + +We solve this problem by changing to a term from an even more general context. +In category theory, a *Kleisli arrow* is a function taking monadic values. +Since measures comprise a monad, our use is a special case of this. + +A kleisli `κ = kleisli(f, m)` returns a wrapper around a function `f` giving the +parameters for a measure of type `M`, such that `κ(x) = M(f(x)...)` respective +`κ(x) = M(f1(x), f2(x), ...)` If the argument is a named tuple `(;a=f1, b=f1)`, `κ(x)` is defined as `M(;a=f(x),b=g(x))`. # Reference -* https://en.wikipedia.org/wiki/Markov_kleisli +* https://en.wikipedia.org/wiki/Markov_kernel """ function kleisli end From 09f1c40369f2c966377d5f6a99d3a11fe387a9da Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Sat, 9 Apr 2022 10:20:44 -0700 Subject: [PATCH 209/368] update instance_type --- src/utils.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/utils.jl b/src/utils.jl index 66581727..c59b0e6c 100644 --- a/src/utils.jl +++ b/src/utils.jl @@ -54,7 +54,7 @@ end # See https://github.com/cscherrer/KeywordCalls.jl/issues/22 @inline instance_type(f::F) where {F} = F -@inline instance_type(T::UnionAll) = Type{T} +@inline instance_type(T::UnionAll) = Type{<:T} @inline instance_type(T::DataType) = Type{T} export basemeasure_depth From a3558326bc6499bb6160afa7706ea0b52d217be7 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Sun, 10 Apr 2022 15:41:44 -0700 Subject: [PATCH 210/368] instance_type => Core.Typeof --- src/primitives/counting.jl | 2 +- src/utils.jl | 5 ----- 2 files changed, 1 insertion(+), 6 deletions(-) diff --git a/src/primitives/counting.jl b/src/primitives/counting.jl index cf3df1b6..1b24d82e 100644 --- a/src/primitives/counting.jl +++ b/src/primitives/counting.jl @@ -9,7 +9,7 @@ insupport(::CountingMeasure, x) = true struct Counting{T} <: AbstractMeasure support::T - Counting(supp) = new{instance_type(supp)}(supp) + Counting(supp) = new{Core.Typeof(supp)}(supp) end function logdensity_def(μ::Counting, x) diff --git a/src/utils.jl b/src/utils.jl index c59b0e6c..622a1b21 100644 --- a/src/utils.jl +++ b/src/utils.jl @@ -52,11 +52,6 @@ end return getfield(T, :instance)::T end -# See https://github.com/cscherrer/KeywordCalls.jl/issues/22 -@inline instance_type(f::F) where {F} = F -@inline instance_type(T::UnionAll) = Type{<:T} -@inline instance_type(T::DataType) = Type{T} - export basemeasure_depth @inline function basemeasure_depth(μ::M) where {M} From 866b4668badc478a252ec8b5269254e7fcc1a238 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 11 Apr 2022 10:42:52 -0700 Subject: [PATCH 211/368] `powermeasure` bug fix --- src/combinators/smart-constructors.jl | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/src/combinators/smart-constructors.jl b/src/combinators/smart-constructors.jl index 8243243c..2db4724c 100644 --- a/src/combinators/smart-constructors.jl +++ b/src/combinators/smart-constructors.jl @@ -14,11 +14,16 @@ end ############################################################################### # PowerMeaure -function powermeasure(μ::WeightedMeasure, dims::NTuple{N,I}) where {N,I} +function powermeasure(μ::WeightedMeasure, dims::NTuple{N,I}) where {N,I<:AbstractArray} k = mapreduce(length, *, dims) * μ.logweight return weightedmeasure(k, μ.base^dims) end +function powermeasure(μ::WeightedMeasure, dims::NTuple{N,I}) where {N,I} + k = prod(dims) * μ.logweight + return weightedmeasure(k, μ.base^dims) +end + ############################################################################### # ProductMeasure From 74777dca5e4e2517b88279c9ef728a9a63170cba Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 11 Apr 2022 11:13:58 -0700 Subject: [PATCH 212/368] fix logdensity_rel bug --- src/density.jl | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/src/density.jl b/src/density.jl index 1a5ef889..c09ad382 100644 --- a/src/density.jl +++ b/src/density.jl @@ -237,11 +237,15 @@ end end for i in 1:M-1 - push!(q.args, :(ℓ += logdensity_def(μs[$i], x))) + push!(q.args, :(Δℓ = logdensity_def(μs[$i], x))) + # push!(q.args, :(println("Adding", Δℓ))) + push!(q.args, :(ℓ += Δℓ)) end for j in 1:N-1 - push!(q.args, :(ℓ += logdensity_def(νs[$j], x))) + push!(q.args, :(Δℓ = logdensity_def(νs[$j], x))) + # push!(q.args, :(println("Subtracting", Δℓ))) + push!(q.args, :(ℓ -= Δℓ)) end push!(q.args, :(return ℓ)) From 5436d3238e1f0107f3cd7b1fa5a09679b3c1573a Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 11 Apr 2022 11:57:40 -0700 Subject: [PATCH 213/368] get `commonbase` to take x type into account --- src/density.jl | 2 +- src/utils.jl | 10 ++++++---- 2 files changed, 7 insertions(+), 5 deletions(-) diff --git a/src/density.jl b/src/density.jl index c09ad382..7660b6bf 100644 --- a/src/density.jl +++ b/src/density.jl @@ -198,7 +198,7 @@ See also `logdensity_rel`. end μs = basemeasure_sequence(μ) νs = basemeasure_sequence(ν) - cb = commonbase(μs, νs) + cb = commonbase(μs, νs, X) # _logdensity_rel(μ, ν) isnothing(cb) && begin μ = μs[end] diff --git a/src/utils.jl b/src/utils.jl index 622a1b21..27057a05 100644 --- a/src/utils.jl +++ b/src/utils.jl @@ -84,15 +84,17 @@ measure of the previous term, and with no repeated entries. return filter(!isnothing, Base.Cartesian.@ntuple 10 b) end -@inline function commonbase(μ, ν) - return commonbase(basemeasure_sequence(μ), basemeasure_sequence(ν)) +commonbase(μ, ν) = commonbase(μ, ν, Any) + +@inline function commonbase(μ, ν, ::Type{T}) where {T} + return commonbase(basemeasure_sequence(μ), basemeasure_sequence(ν), T) end -@generated function commonbase(μ::M, ν::N) where {M<:Tuple,N<:Tuple} +@generated function commonbase(μ::M, ν::N, ::Type{T}) where {M<:Tuple,N<:Tuple,T} m = schema(M) n = schema(N) - sols = Iterators.filter(((i,j),) -> static_hasmethod(logdensity_def, Tuple{m[i], n[j], Any}), Iterators.product(1:length(m), 1:length(n))) + sols = Iterators.filter(((i,j),) -> static_hasmethod(logdensity_def, Tuple{m[i], n[j], T}), Iterators.product(1:length(m), 1:length(n))) isempty(sols) && return :(nothing) minsol = static.(argmin(((i,j),) -> i+j, sols)) quote From fdbd12b725894574a7e98d5224c183cb3a4f6359 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 11 Apr 2022 14:56:35 -0700 Subject: [PATCH 214/368] test powers --- test/runtests.jl | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/test/runtests.jl b/test/runtests.jl index 35244e8f..eab6722b 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -105,6 +105,12 @@ end # end # end + +@testset "powers" begin + @test logdensityof(Lebesgue() ^ 3, 2) == logdensityof(Lebesgue() ^ (3,), 2) + @test logdensityof(Lebesgue() ^ 3, 2) == logdensityof(Lebesgue() ^ (3,1), (2,0)) +end + @testset "Half" begin Normal() = ∫exp(x -> -0.5x^2, Lebesgue(ℝ)) HalfNormal() = Half(Normal()) From c3ec497d2f6afa4e8ee7f0a3cf369f6a85757ca6 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 12 Apr 2022 11:03:20 -0700 Subject: [PATCH 215/368] commonbase docstring --- src/utils.jl | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/src/utils.jl b/src/utils.jl index 27057a05..fb10be73 100644 --- a/src/utils.jl +++ b/src/utils.jl @@ -86,6 +86,15 @@ end commonbase(μ, ν) = commonbase(μ, ν, Any) +""" + commonbase(μ, ν, T) -> Tuple{StaticInt{i}, StaticInt{j}} + +Find minimal (with respect to their sum) `i` and `j` such that there is a method + + logdensity_def(basemeasure_sequence(μ)[i], basemeasure_sequence(ν)[j], ::T) + +This is used in `logdensity_rel` to help make that function efficient. +""" @inline function commonbase(μ, ν, ::Type{T}) where {T} return commonbase(basemeasure_sequence(μ), basemeasure_sequence(ν), T) end From 725d2ddfb289da7a997afd83638da899ff603cbb Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 12 Apr 2022 11:51:40 -0700 Subject: [PATCH 216/368] deprecate instance_type --- src/MeasureBase.jl | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index d6eeab6b..48185e77 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -67,6 +67,8 @@ gentype(μ::AbstractMeasure) = typeof(testvalue(μ)) using NaNMath using LogExpFunctions: logsumexp +@deprecate instance_type(x) Core.Typeof(x) false + """ `logdensity_def` is the standard way to define a log-density for a new measure. Note that this definition does not include checking for membership in the From 09d519664c47f70806a577efecdb30e5e1fcdd19 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 13 Apr 2022 07:41:58 -0700 Subject: [PATCH 217/368] avoid breakage --- src/combinators/superpose.jl | 18 ++++++++++++++++-- 1 file changed, 16 insertions(+), 2 deletions(-) diff --git a/src/combinators/superpose.jl b/src/combinators/superpose.jl index cb0b9c0c..a94251cc 100644 --- a/src/combinators/superpose.jl +++ b/src/combinators/superpose.jl @@ -63,8 +63,22 @@ oneplus(x::ULogarithmic) = exp(ULogarithmic, log1pexp(x.log)) @inline function density_def(s::SuperpositionMeasure{Tuple{A,B}}, x) where {A,B} (μ, ν) = s.components - insupport(μ, x) || return exp(ULogarithmic, logdensity_def(ν, x)) - insupport(ν, x) || return exp(ULogarithmic, logdensity_def(μ, x)) + + # Jumping through some hoops here to avoid having this be a breaking + # version. After the next breaking version, this can probably be changed to + # the more familiar + # inμ || return exp(ULogarithmic, logdensity_def(ν, x)) + # etc + let inμ = insupport(μ, x) + if inμ isa False || !inμ + return exp(ULogarithmic, logdensity_def(ν, x)) + end + end + let inν = insupport(ν, x) + if !inν || inν isa False + return exp(ULogarithmic, logdensity_def(μ, x)) + end + end α = basemeasure(μ) β = basemeasure(ν) dμ_dα = exp(ULogarithmic, logdensity_def(μ, x)) From f6f776eaa28fa6c320e580152c5f5a0b864cceb9 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 13 Apr 2022 07:47:18 -0700 Subject: [PATCH 218/368] switch || terms --- src/combinators/superpose.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/combinators/superpose.jl b/src/combinators/superpose.jl index a94251cc..0fad0246 100644 --- a/src/combinators/superpose.jl +++ b/src/combinators/superpose.jl @@ -75,7 +75,7 @@ oneplus(x::ULogarithmic) = exp(ULogarithmic, log1pexp(x.log)) end end let inν = insupport(ν, x) - if !inν || inν isa False + if inν isa False || !inν return exp(ULogarithmic, logdensity_def(μ, x)) end end From a31682870d28b9a4c9c6315092a09fb6ba19a8b2 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 13 Apr 2022 08:17:50 -0700 Subject: [PATCH 219/368] @ifelse macro --- src/combinators/superpose.jl | 38 +++++++++++++++++------------------- 1 file changed, 18 insertions(+), 20 deletions(-) diff --git a/src/combinators/superpose.jl b/src/combinators/superpose.jl index 0fad0246..442585c3 100644 --- a/src/combinators/superpose.jl +++ b/src/combinators/superpose.jl @@ -61,24 +61,22 @@ using LogarithmicNumbers oneplus(x::ULogarithmic) = exp(ULogarithmic, log1pexp(x.log)) -@inline function density_def(s::SuperpositionMeasure{Tuple{A,B}}, x) where {A,B} - (μ, ν) = s.components - - # Jumping through some hoops here to avoid having this be a breaking - # version. After the next breaking version, this can probably be changed to - # the more familiar - # inμ || return exp(ULogarithmic, logdensity_def(ν, x)) - # etc - let inμ = insupport(μ, x) - if inμ isa False || !inμ - return exp(ULogarithmic, logdensity_def(ν, x)) - end - end - let inν = insupport(ν, x) - if inν isa False || !inν - return exp(ULogarithmic, logdensity_def(μ, x)) +macro ifelse(c,t,f) + c = esc(c) + t = esc(t) + f = esc(f) + quote + let cond = $c; t() = $t; f() = $f + ifelse(cond, t, f)() end end +end + +@inline function density_def(s::SuperpositionMeasure{Tuple{A,B}}, x) where {A,B} + (μ, ν) = s.components + @ifelse(insupport(μ, x), nothing, return exp(ULogarithmic, logdensity_def(ν, x))) + @ifelse(insupport(ν, x), nothing, return exp(ULogarithmic, logdensity_def(μ, x))) + α = basemeasure(μ) β = basemeasure(ν) dμ_dα = exp(ULogarithmic, logdensity_def(μ, x)) @@ -100,15 +98,15 @@ end @inline function logdensity_def(s::SuperpositionMeasure{Tuple{A,B}}, β, x) where {A,B} (μ, ν) = s.components - insupport(μ, x) || return logdensity_rel(ν, β, x) - insupport(ν, x) || return logdensity_rel(μ, β, x) + @ifelse(insupport(μ, x), nothing, return logdensity_rel(ν, β, x)) + @ifelse(insupport(ν, x), nothing, return logdensity_rel(μ, β, x)) return logaddexp(logdensity_rel(μ, β, x), logdensity_rel(ν, β, x)) end @inline function logdensity_def(s::SuperpositionMeasure{Tuple{A,B}}, β::SuperpositionMeasure, x) where {A,B} (μ, ν) = s.components - insupport(μ, x) || return logdensity_rel(ν, β, x) - insupport(ν, x) || return logdensity_rel(μ, β, x) + @ifelse(insupport(μ, x), nothing, return logdensity_rel(ν, β, x)) + @ifelse(insupport(ν, x), nothing, return logdensity_rel(μ, β, x)) return logaddexp(logdensity_rel(μ, β, x), logdensity_rel(ν, β, x)) end From 2ca07e7728566f4cd45bb5267ce5763c87306a8e Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 13 Apr 2022 08:53:26 -0700 Subject: [PATCH 220/368] simplify logdensity_rel --- src/density.jl | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/src/density.jl b/src/density.jl index 7660b6bf..16f39488 100644 --- a/src/density.jl +++ b/src/density.jl @@ -175,10 +175,7 @@ known to be in the support of both, it can be more efficient to call """ @inline function logdensity_rel(μ::M, ν::N, x::X) where {M,N,X} T = unstatic(promote_type(return_type(logdensity_def, (μ, x)), return_type(logdensity_def, (ν, x)))) - insupport(μ, x) || begin - insupport(ν, x) || return convert(T, NaN) - return convert(T, -Inf) - end + insupport(μ, x) || return convert(T, ifelse(insupport(ν, x), -Inf, NaN)) insupport(ν, x) || return convert(T, Inf) return unsafe_logdensity_rel(μ, ν, x) From 15d8ad4134789af713aa8d366aefbd79b9bc74c4 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 13 Apr 2022 09:44:58 -0700 Subject: [PATCH 221/368] give up on this @ifelse business --- src/combinators/superpose.jl | 25 ++++++++----------------- src/density.jl | 6 ++++-- 2 files changed, 12 insertions(+), 19 deletions(-) diff --git a/src/combinators/superpose.jl b/src/combinators/superpose.jl index 442585c3..58695b09 100644 --- a/src/combinators/superpose.jl +++ b/src/combinators/superpose.jl @@ -61,21 +61,11 @@ using LogarithmicNumbers oneplus(x::ULogarithmic) = exp(ULogarithmic, log1pexp(x.log)) -macro ifelse(c,t,f) - c = esc(c) - t = esc(t) - f = esc(f) - quote - let cond = $c; t() = $t; f() = $f - ifelse(cond, t, f)() - end - end -end - @inline function density_def(s::SuperpositionMeasure{Tuple{A,B}}, x) where {A,B} (μ, ν) = s.components - @ifelse(insupport(μ, x), nothing, return exp(ULogarithmic, logdensity_def(ν, x))) - @ifelse(insupport(ν, x), nothing, return exp(ULogarithmic, logdensity_def(μ, x))) + + insupport(μ, x) || return exp(ULogarithmic, logdensity_def(ν, x)) + insupport(ν, x) || return exp(ULogarithmic, logdensity_def(μ, x)) α = basemeasure(μ) β = basemeasure(ν) @@ -98,15 +88,16 @@ end @inline function logdensity_def(s::SuperpositionMeasure{Tuple{A,B}}, β, x) where {A,B} (μ, ν) = s.components - @ifelse(insupport(μ, x), nothing, return logdensity_rel(ν, β, x)) - @ifelse(insupport(ν, x), nothing, return logdensity_rel(μ, β, x)) + + insupport(μ, x) || return logdensity_rel(ν, β, x) + insupport(ν, x) || return logdensity_rel(μ, β, x) return logaddexp(logdensity_rel(μ, β, x), logdensity_rel(ν, β, x)) end @inline function logdensity_def(s::SuperpositionMeasure{Tuple{A,B}}, β::SuperpositionMeasure, x) where {A,B} (μ, ν) = s.components - @ifelse(insupport(μ, x), nothing, return logdensity_rel(ν, β, x)) - @ifelse(insupport(ν, x), nothing, return logdensity_rel(μ, β, x)) + insupport(μ, x) || return logdensity_rel(ν, β, x) + insupport(ν, x) || return logdensity_rel(μ, β, x) return logaddexp(logdensity_rel(μ, β, x), logdensity_rel(ν, β, x)) end diff --git a/src/density.jl b/src/density.jl index 16f39488..5961cb57 100644 --- a/src/density.jl +++ b/src/density.jl @@ -175,8 +175,10 @@ known to be in the support of both, it can be more efficient to call """ @inline function logdensity_rel(μ::M, ν::N, x::X) where {M,N,X} T = unstatic(promote_type(return_type(logdensity_def, (μ, x)), return_type(logdensity_def, (ν, x)))) - insupport(μ, x) || return convert(T, ifelse(insupport(ν, x), -Inf, NaN)) - insupport(ν, x) || return convert(T, Inf) + inμ = insupport(μ, x) + inν = insupport(ν, x) + inμ || return convert(T, ifelse(inν, -Inf, NaN)) + inν || return convert(T, Inf) return unsafe_logdensity_rel(μ, ν, x) end From 535dcbcb4687d524984c9278817b507159cfdb30 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 13 Apr 2022 09:49:28 -0700 Subject: [PATCH 222/368] bump version --- Project.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Project.toml b/Project.toml index 0d719bc5..d759b617 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "MeasureBase" uuid = "fa1605e6-acd5-459c-a1e6-7e635759db14" authors = ["Chad Scherrer and contributors"] -version = "0.6.2" +version = "0.7.1" [deps] Compat = "34da2185-b29b-5c13-b0c7-acf172513d20" From a733431282e20459000f302d000dbf3b64560e27 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 26 Apr 2022 07:25:15 -0700 Subject: [PATCH 223/368] working on likelihoods --- src/MeasureBase.jl | 2 +- src/combinators/likelihood.jl | 43 ++++++++++++++++++++++----- src/combinators/pointwise.jl | 24 +++++++-------- src/combinators/product.jl | 30 +++++++++---------- src/combinators/smart-constructors.jl | 10 +++++-- src/density.jl | 2 +- src/kleisli.jl | 2 +- 7 files changed, 74 insertions(+), 39 deletions(-) diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index 48185e77..48dfe27a 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -103,7 +103,7 @@ include("combinators/half.jl") include("domains.jl") include("primitive.jl") include("utils.jl") -include("absolutecontinuity.jl") +# include("absolutecontinuity.jl") include("primitives/counting.jl") include("primitives/lebesgue.jl") diff --git a/src/combinators/likelihood.jl b/src/combinators/likelihood.jl index 90abe426..3a4af641 100644 --- a/src/combinators/likelihood.jl +++ b/src/combinators/likelihood.jl @@ -2,7 +2,13 @@ export AbstractLikelihood, Likelihood abstract type AbstractLikelihood end -@inline logdensityof(ℓ::AbstractLikelihood, par) = logdensity_def(ℓ, par) +# @inline function logdensityof(ℓ::AbstractLikelihood, p) +# t() = dynamic(unsafe_logdensityof(ℓ, p)) +# f() = -Inf +# ifelse(insupport(ℓ, p), t, f)() +# end + +# insupport(ℓ::AbstractLikelihood, p) = insupport(ℓ.k(p), ℓ.x) @doc raw""" Likelihood(k::AbstractKleisli, x) @@ -128,10 +134,33 @@ function Base.show(io::IO, ℓ::Likelihood) Pretty.pprint(io, ℓ) end -@inline function logdensity_def(ℓ::Likelihood, p::Tuple) - return logdensity_def(ℓ.k(p), ℓ.x) -end +# @inline function logdensity_def(ℓ::Likelihood, p) +# return logdensity_def(ℓ.k(p), ℓ.x) +# end -@inline function logdensity_def(ℓ::Likelihood, p) - return logdensity_def(ℓ.k((p,)), ℓ.x) -end +# basemeasure(ℓ::Likelihood, p) = basemeasure(ℓ.k(p), ℓ.x) + +# basemeasure(ℓ::Likelihood) = @error "Likelihood requires local base measure" + +export likelihood + +likelihood(k, x) = Likelihood(k, x) + +likelihood(k, x, pars::NamedTuple) = likelihood(kleisli(k, pars), x) + +""" + log_likelihood_ratio(ℓ::Likelihood, p, q) + +Compute the log of the likelihood ratio, in order to compare two choices for +parameters. This is computed as + + logdensity_rel(ℓ.k(p), ℓ.k(q), ℓ.x) + +Since `logdensity_rel` can leave common base measure unevaluated, this can be +more efficient than + + logdensityof(ℓ.k(p), ℓ.x) - logdensityof(ℓ.k(q), ℓ.x) +""" +log_likelihood_ratio(ℓ::Likelihood, p, q) = logdensity_rel(ℓ.k(p), ℓ.k(q), ℓ.x) + +# likelihood(k, x; kwargs...) = likelihood(k, x, NamedTuple(kwargs)) \ No newline at end of file diff --git a/src/combinators/pointwise.jl b/src/combinators/pointwise.jl index 672e06fb..d1128f56 100644 --- a/src/combinators/pointwise.jl +++ b/src/combinators/pointwise.jl @@ -1,18 +1,13 @@ export ⊙ -struct PointwiseProductMeasure{M,L} <: AbstractMeasure - measure::M +struct PointwiseProductMeasure{P,L} <: AbstractMeasure + prior::P likelihood::L - - function PointwiseProductMeasure(μ::M, ℓ::L) where {M,L} - @assert static_hasmethod(logdensity_def, Tuple{L, gentype(μ)}) - return new{M,L}(μ, ℓ) - end end function Base.show(io::IO, μ::PointwiseProductMeasure) io = IOContext(io, :compact => true) - print(io, μ.measure, " ⊙ ", μ.likelihood) + print(io, μ.prior, " ⊙ ", μ.likelihood) end function Base.show_unquoted(io::IO, μ::PointwiseProductMeasure, indent::Int, prec::Int) @@ -29,12 +24,17 @@ end ⊙(μ, ℓ) = pointwiseproduct(μ, ℓ) -@inline function logdensity_def(d::PointwiseProductMeasure, x) - logdensity_def(d.measure, x) + logdensity_def(d.likelihood, x) +@inline function logdensity_def(d::PointwiseProductMeasure, p) + (μ, ℓ) = (d.prior, d.likelihood) + logdensity_def(μ, p) + logdensityof(ℓ.k(p), ℓ.x) end function gentype(d::PointwiseProductMeasure) - @inbounds gentype(d.measure) + gentype(d.prior) end -basemeasure(d::PointwiseProductMeasure) = @inbounds basemeasure(d.measure) +basemeasure(d::PointwiseProductMeasure, x) = basemeasure(d.prior, x) + +basemeasure(d::PointwiseProductMeasure) = basemeasure(d.prior) + +insupport(d::PointwiseProductMeasure, x) = insupport(d.prior, x) \ No newline at end of file diff --git a/src/combinators/product.jl b/src/combinators/product.jl index 10b78096..6069fc4c 100644 --- a/src/combinators/product.jl +++ b/src/combinators/product.jl @@ -94,19 +94,19 @@ end return q end -@generated function basemeasure(d::ProductMeasure{NamedTuple{N,T}}, x) where {N,T} - q = quote - m = marginals(d) - end - for k in N - qk = QuoteNode(k) - push!(q.args, :($k = basemeasure(getproperty(m, $qk)))) - end - - vals = map(x -> Expr(:(=), x,x), N) - push!(q.args, Expr(:tuple, vals...)) - return q -end +# @generated function basemeasure(d::ProductMeasure{NamedTuple{N,T}}, x) where {N,T} +# q = quote +# m = marginals(d) +# end +# for k in N +# qk = QuoteNode(k) +# push!(q.args, :($k = basemeasure(getproperty(m, $qk)))) +# end + +# vals = map(x -> Expr(:(=), x,x), N) +# push!(q.args, Expr(:tuple, vals...)) +# return q +# end function basemeasure(μ::ProductMeasure{Base.Generator{I,F}}) where {I,F} mar = marginals(μ) @@ -187,8 +187,8 @@ end @inline function insupport(d::AbstractProductMeasure, x::AbstractArray) mar = marginals(d) - for j in eachindex(x) - @inbounds dynamic(insupport(mar[j], x[j])) || return false + for (j,mj) in enumerate(mar) + dynamic(insupport(mj, x[j])) || return false end return true end diff --git a/src/combinators/smart-constructors.jl b/src/combinators/smart-constructors.jl index 2db4724c..899b547a 100644 --- a/src/combinators/smart-constructors.jl +++ b/src/combinators/smart-constructors.jl @@ -8,6 +8,12 @@ half(μ::AbstractMeasure) = Half(μ) # PointwiseProductMeasure function pointwiseproduct(μ::AbstractMeasure, ℓ::Likelihood) + @show μ + T = Core.Compiler.return_type(ℓ.k, Tuple{gentype(μ)}) + return pointwiseproduct(T, μ, ℓ) +end + +function pointwiseproduct(::Type{T}, μ::AbstractMeasure, ℓ::Likelihood) where {T} return PointwiseProductMeasure(μ, ℓ) end @@ -108,7 +114,7 @@ end ############################################################################### # Kleisli -kleisli(μ, op1, op2, param_maps...) = ParameterizedKleisli(μ, op1, op2, param_maps...) +kleisli(f, pars::NamedTuple) = ParameterizedKleisli(f, pars) # kleisli(Normal(μ=2)) function kleisli(μ::M) where {M<:AbstractMeasure} @@ -132,4 +138,4 @@ function kleisli(::Type{M}; param_maps...) where {M} end -kleisli(k::ParameterizedKleisli) = k \ No newline at end of file +kleisli(k::ParameterizedKleisli) = k diff --git a/src/density.jl b/src/density.jl index 5961cb57..8ca6d9e8 100644 --- a/src/density.jl +++ b/src/density.jl @@ -143,7 +143,7 @@ See also `logdensityof`. ℓ_0 = logdensity_def(μ, x) b_0 = μ Base.Cartesian.@nexprs 10 i -> begin # 10 is just some "big enough" number - b_{i} = basemeasure(b_{i-1}) + b_{i} = basemeasure(b_{i-1}, x) if b_{i} isa typeof(b_{i-1}) return ℓ_{i-1} end diff --git a/src/kleisli.jl b/src/kleisli.jl index 7f0d9254..87b2d6f5 100644 --- a/src/kleisli.jl +++ b/src/kleisli.jl @@ -55,7 +55,7 @@ mapcall(t, x) = map(func -> func(x), t) # (k::Kleisli{Type{P},<:Tuple})(x) where {P<:ParameterizedMeasure} = k.f(mapcall(k.param_maps, x)...) -(k::ParameterizedKleisli)(x) where {M} = k.f(; mapcall(k.param_maps, x)...) +(k::ParameterizedKleisli)(x) = k.f(; mapcall(k.param_maps, x)...) (k::ParameterizedKleisli)(x...) = k(x) From f49408635ad12f02725e1fe828adf95c69882af8 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 27 Apr 2022 18:48:36 -0700 Subject: [PATCH 224/368] update likelihood --- src/combinators/likelihood.jl | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/src/combinators/likelihood.jl b/src/combinators/likelihood.jl index 3a4af641..93bbc5e1 100644 --- a/src/combinators/likelihood.jl +++ b/src/combinators/likelihood.jl @@ -144,10 +144,14 @@ end export likelihood -likelihood(k, x) = Likelihood(k, x) +likelihood(k, x, ::NamedTuple{()}) = Likelihood(k, x) + +likelihood(k, x; kwargs...) = likelihood(k, x, NamedTuple(kwargs)) likelihood(k, x, pars::NamedTuple) = likelihood(kleisli(k, pars), x) +likelihood(k::AbstractKleisli, x) = Likelihood(k, x) + """ log_likelihood_ratio(ℓ::Likelihood, p, q) @@ -163,4 +167,4 @@ more efficient than """ log_likelihood_ratio(ℓ::Likelihood, p, q) = logdensity_rel(ℓ.k(p), ℓ.k(q), ℓ.x) -# likelihood(k, x; kwargs...) = likelihood(k, x, NamedTuple(kwargs)) \ No newline at end of file +# likelihood(k, x; kwargs...) = likelihood(k, x, NamedTuple(kwargs)) From 999df3783b241c226b312e1ab274e82c99cfd30b Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 27 Apr 2022 20:15:24 -0700 Subject: [PATCH 225/368] powerweightedmeasure --- src/MeasureBase.jl | 1 + src/combinators/powerweighted.jl | 18 ++++++++++++++++++ 2 files changed, 19 insertions(+) create mode 100644 src/combinators/powerweighted.jl diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index 48dfe27a..8f6c39a1 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -123,6 +123,7 @@ include("combinators/likelihood.jl") include("combinators/pointwise.jl") include("combinators/restricted.jl") include("combinators/smart-constructors.jl") +include("combinators/powerweighted.jl") include("rand.jl") diff --git a/src/combinators/powerweighted.jl b/src/combinators/powerweighted.jl new file mode 100644 index 00000000..69940be0 --- /dev/null +++ b/src/combinators/powerweighted.jl @@ -0,0 +1,18 @@ +export ↑ + +struct PowerWeightedMeasure{M,A} <: AbstractMeasure + parent::M + exponent::A +end + +logdensity_def(d::PowerWeightedMeasure, x) = d.exponent * logdensity_def(d.parent, x) + +basemeasure(d::PowerWeightedMeasure, x) = basemeasure(d.parent, x) + +basemeasure(d::PowerWeightedMeasure) = basemeasure(d.parent) ↑ d.exponent + +powerweightedmeasure(d, α) = PowerWeightedMeasure(d, α) + +(d::AbstractMeasure) ↑ α = powerweightedmeasure(d, α) + +insupport(d::PowerWeightedMeasure, x) = insupport(d.parent, x) \ No newline at end of file From 5815d17180bdd5e8ab00d4fb04627a70e8fc4e18 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 27 Apr 2022 20:22:11 -0700 Subject: [PATCH 226/368] powerweighted update --- src/combinators/powerweighted.jl | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/src/combinators/powerweighted.jl b/src/combinators/powerweighted.jl index 69940be0..1f6268e4 100644 --- a/src/combinators/powerweighted.jl +++ b/src/combinators/powerweighted.jl @@ -11,8 +11,11 @@ basemeasure(d::PowerWeightedMeasure, x) = basemeasure(d.parent, x) basemeasure(d::PowerWeightedMeasure) = basemeasure(d.parent) ↑ d.exponent -powerweightedmeasure(d, α) = PowerWeightedMeasure(d, α) +function powerweightedmeasure(d, α) + isone(α) && return d + PowerWeightedMeasure(d, α) +end (d::AbstractMeasure) ↑ α = powerweightedmeasure(d, α) -insupport(d::PowerWeightedMeasure, x) = insupport(d.parent, x) \ No newline at end of file +insupport(d::PowerWeightedMeasure, x) = insupport(d.parent, x) From 90164233c5138608b57dcf1134c078c7bddb76ed Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 27 Apr 2022 20:48:29 -0700 Subject: [PATCH 227/368] more powerweighted methods --- src/combinators/powerweighted.jl | 12 ++++++++++++ src/combinators/product.jl | 2 +- 2 files changed, 13 insertions(+), 1 deletion(-) diff --git a/src/combinators/powerweighted.jl b/src/combinators/powerweighted.jl index 1f6268e4..85b9194e 100644 --- a/src/combinators/powerweighted.jl +++ b/src/combinators/powerweighted.jl @@ -19,3 +19,15 @@ end (d::AbstractMeasure) ↑ α = powerweightedmeasure(d, α) insupport(d::PowerWeightedMeasure, x) = insupport(d.parent, x) + +function Base.show(io::IO, d::PowerWeightedMeasure) + print(io, d.parent, " ↑ ", d.exponent) +end + +function powerweightedmeasure(d::PowerWeightedMeasure, α) + powerweightedmeasure(d.parent, α * d.exponent) +end + +function powerweightedmeasure(d::WeightedMeasure, α) + weightedmeasure(α*d.logweight, powerweightedmeasure(d.base, α)) +end diff --git a/src/combinators/product.jl b/src/combinators/product.jl index 6069fc4c..50849cf3 100644 --- a/src/combinators/product.jl +++ b/src/combinators/product.jl @@ -174,7 +174,7 @@ using Random: rand!, GLOBAL_RNG, AbstractRNG end export rand! -using Random: rand!, GLOBAL_RNG, AbstractRNG +using Random: rand!, GLOBAL_RNG function _rand(rng::AbstractRNG, ::Type{T}, d::ProductMeasure, mar::AbstractArray) where {T} elT = typeof(rand(rng, T, first(mar))) From c3fff7e24bbe090a65f660849cf7670b38c83aff Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Thu, 28 Apr 2022 07:20:30 -0700 Subject: [PATCH 228/368] bugfix --- src/combinators/powerweighted.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/combinators/powerweighted.jl b/src/combinators/powerweighted.jl index 85b9194e..745318a8 100644 --- a/src/combinators/powerweighted.jl +++ b/src/combinators/powerweighted.jl @@ -7,7 +7,7 @@ end logdensity_def(d::PowerWeightedMeasure, x) = d.exponent * logdensity_def(d.parent, x) -basemeasure(d::PowerWeightedMeasure, x) = basemeasure(d.parent, x) +basemeasure(d::PowerWeightedMeasure, x) = basemeasure(d.parent, x) ↑ d.exponent basemeasure(d::PowerWeightedMeasure) = basemeasure(d.parent) ↑ d.exponent From a38da82e9e6bf6bd471af92e16019aecb1893eb3 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 2 May 2022 13:41:59 -0700 Subject: [PATCH 229/368] dropFactoredBase --- src/MeasureBase.jl | 1 - src/combinators/factoredbase.jl | 21 --------------------- 2 files changed, 22 deletions(-) delete mode 100644 src/combinators/factoredbase.jl diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index 8f6c39a1..d5016066 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -113,7 +113,6 @@ include("primitives/trivial.jl") include("combinators/conditional.jl") include("combinators/bind.jl") include("combinators/transformedmeasure.jl") -include("combinators/factoredbase.jl") include("combinators/weighted.jl") include("combinators/superpose.jl") include("combinators/product.jl") diff --git a/src/combinators/factoredbase.jl b/src/combinators/factoredbase.jl deleted file mode 100644 index 166a568b..00000000 --- a/src/combinators/factoredbase.jl +++ /dev/null @@ -1,21 +0,0 @@ -export FactoredBase - -struct FactoredBase{C,V,B} <: AbstractMeasure - constℓ::C - varℓ::V - base::B -end - -@inline function logdensity_def(d::FactoredBase, x) - d.constℓ + d.varℓ() -end - -function Pretty.tile(fb::FactoredBase) - result = Pretty.literal("FactoredBase") - result *= Pretty.list_layout(Pretty.tile.([fb.constℓ, fb.varℓ, fb.base])) - result -end - -basemeasure(d::FactoredBase) = d.base - -insupport(d::FactoredBase, x) = insupport(d.base, x) \ No newline at end of file From 7199c22dfab59e4d898726f9f11f68b40ad96f89 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 2 May 2022 15:42:05 -0700 Subject: [PATCH 230/368] drop FactoredBase --- src/combinators/smart-constructors.jl | 12 ------------ 1 file changed, 12 deletions(-) diff --git a/src/combinators/smart-constructors.jl b/src/combinators/smart-constructors.jl index 899b547a..77f55126 100644 --- a/src/combinators/smart-constructors.jl +++ b/src/combinators/smart-constructors.jl @@ -55,18 +55,6 @@ productmeasure(f, param_maps, pars) = ProductMeasure(kleisli(f, param_maps), par productmeasure(k::ParameterizedKleisli, pars) = productmeasure(k.f, k.param_maps, pars) - -function productmeasure(f::Returns{FB}, param_maps, pars) where {FB<:FactoredBase} - fb = f.value - dims = size(pars) - n = prod(dims) - inbounds(x) = all(fb.inbounds, x) - constℓ = n * fb.constℓ - varℓ() = n * fb.varℓ() - base = fb.base^dims - FactoredBase(inbounds, constℓ, varℓ, base) -end - function productmeasure(f::Returns{W}, ::typeof(identity), pars) where {W<:WeightedMeasure} ℓ = f.value.logweight base = f.value.base From a66c0700f54a93e03debb926afa5510829c9d068 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 3 May 2022 06:39:12 -0700 Subject: [PATCH 231/368] (::ProductMeasure) | constraint --- src/combinators/conditional.jl | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/src/combinators/conditional.jl b/src/combinators/conditional.jl index 7bcba1db..1c55cfab 100644 --- a/src/combinators/conditional.jl +++ b/src/combinators/conditional.jl @@ -25,4 +25,10 @@ upcoming changes. """ Base.:|(μ::AbstractMeasure, constraint) = ConditionalMeasure(μ, constraint) -@inline basemeasure(cm::ConditionalMeasure) = basemeasure(cm.parent) | cm.constraint \ No newline at end of file +@inline basemeasure(cm::ConditionalMeasure) = basemeasure(cm.parent) | cm.constraint + +@generated function Base.:|(μ::ProductMeasure{NamedTuple{M,T}}, constraint::NamedTuple{N}) where {N} + mar = marginals(μ) + newkeys = tuple(setdiff(keys(mar), N)...) + productmeasure(NamedTuple{newkeys}(mar)) +end \ No newline at end of file From 8eda66db5788a2138977f5f621b9015322e43be4 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 3 May 2022 14:22:45 -0700 Subject: [PATCH 232/368] update conditional measure --- src/combinators/conditional.jl | 16 +++++++++++----- src/utils.jl | 10 ++++++++++ 2 files changed, 21 insertions(+), 5 deletions(-) diff --git a/src/combinators/conditional.jl b/src/combinators/conditional.jl index 1c55cfab..2dc27ebd 100644 --- a/src/combinators/conditional.jl +++ b/src/combinators/conditional.jl @@ -27,8 +27,14 @@ Base.:|(μ::AbstractMeasure, constraint) = ConditionalMeasure(μ, constraint) @inline basemeasure(cm::ConditionalMeasure) = basemeasure(cm.parent) | cm.constraint -@generated function Base.:|(μ::ProductMeasure{NamedTuple{M,T}}, constraint::NamedTuple{N}) where {N} - mar = marginals(μ) - newkeys = tuple(setdiff(keys(mar), N)...) - productmeasure(NamedTuple{newkeys}(mar)) -end \ No newline at end of file +# @generated function Base.:|(μ::ProductMeasure{NamedTuple{M,T}}, constraint::NamedTuple{N}) where {M,T,N} +# newkeys = tuple(setdiff(M, N)...) +# quote +# mar = marginals(μ) +# productmeasure(NamedTuple{$newkeys}(mar)) +# end +# end + +function Base.:|(μ::ProductMeasure{NamedTuple{M,T}}, constraint::NamedTuple{N}) where {M,T,N} + productmeasure(merge(marginals(μ),rmap(Dirac, constraint))) +end diff --git a/src/utils.jl b/src/utils.jl index ffe67079..81ebbd99 100644 --- a/src/utils.jl +++ b/src/utils.jl @@ -133,3 +133,13 @@ end allequal(x::AbstractArray) = allequal(identity, x) + +rmap(f, x) = f(x) + +function rmap(f, t::Tuple) + map(x -> rmap(f,x), t) +end + +function rmap(f, nt::NamedTuple{N,T}) where {N,T} + NamedTuple{N}(map(x -> rmap(f,x), values(nt))) +end \ No newline at end of file From fa19d7313be169ab338e6094dc90f2f434e4ae2e Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 3 May 2022 14:22:51 -0700 Subject: [PATCH 233/368] update Dirac --- src/primitives/dirac.jl | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/src/primitives/dirac.jl b/src/primitives/dirac.jl index 9c3fe0aa..57067ec7 100644 --- a/src/primitives/dirac.jl +++ b/src/primitives/dirac.jl @@ -18,9 +18,7 @@ end basemeasure(d::Dirac) = CountingMeasure() -density_def(μ::Dirac, x) = x == μ.x - -logdensity_def(μ::Dirac, x) = (x == μ.x) ? 0.0 : -Inf +logdensity_def(μ::Dirac, x) = 0.0 Base.rand(::Random.AbstractRNG, T::Type, μ::Dirac) = μ.x @@ -31,5 +29,3 @@ dirac(d::AbstractMeasure) = Dirac(rand(d)) testvalue(d::Dirac) = d.x insupport(d::Dirac, x) = x == d.x - -logdensity_def(μ::Dirac, ν::Dirac, x) = logdensity_def(μ, x) - logdensity_def(ν, x) From 9b86a8df1836c25305be8f6cc4dfb59411aff4b9 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 3 May 2022 14:42:24 -0700 Subject: [PATCH 234/368] move conditional.jl down in the `include`s --- src/MeasureBase.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index d5016066..19201034 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -110,7 +110,6 @@ include("primitives/lebesgue.jl") include("primitives/dirac.jl") include("primitives/trivial.jl") -include("combinators/conditional.jl") include("combinators/bind.jl") include("combinators/transformedmeasure.jl") include("combinators/weighted.jl") @@ -123,6 +122,7 @@ include("combinators/pointwise.jl") include("combinators/restricted.jl") include("combinators/smart-constructors.jl") include("combinators/powerweighted.jl") +include("combinators/conditional.jl") include("rand.jl") From ceb310b1d958d1d2b73a1e1f1d0e7d3abd84aaec Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 4 May 2022 10:23:27 -0700 Subject: [PATCH 235/368] Kleisli => TransitionKernel --- src/MeasureBase.jl | 4 +- src/combinators/likelihood.jl | 10 ++-- src/combinators/product.jl | 2 +- src/combinators/smart-constructors.jl | 30 ++++++------ src/generated.jl | 24 --------- src/kleisli.jl | 70 +++++++++++---------------- src/parameterized.jl | 13 +++-- test/runtests.jl | 6 +-- 8 files changed, 61 insertions(+), 98 deletions(-) delete mode 100644 src/generated.jl diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index 19201034..6e505bfc 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -31,7 +31,7 @@ export AbstractMeasure import IfElse: ifelse export logdensity_def export basemeasure -export basekleisli +export basekernel """ inssupport(m, x) @@ -97,7 +97,7 @@ using Compat include("schema.jl") include("splat.jl") include("proxies.jl") -include("kleisli.jl") +include("kernel.jl") include("parameterized.jl") include("combinators/half.jl") include("domains.jl") diff --git a/src/combinators/likelihood.jl b/src/combinators/likelihood.jl index 93bbc5e1..4bd0c94e 100644 --- a/src/combinators/likelihood.jl +++ b/src/combinators/likelihood.jl @@ -11,7 +11,7 @@ abstract type AbstractLikelihood end # insupport(ℓ::AbstractLikelihood, p) = insupport(ℓ.k(p), ℓ.x) @doc raw""" - Likelihood(k::AbstractKleisli, x) + Likelihood(k::AbstractTransitionKernel, x) "Observe" a value `x`, yielding a function from the parameters to ℝ. @@ -115,9 +115,9 @@ struct Likelihood{K,X} <: AbstractLikelihood k::K x::X - Likelihood(k::K, x::X) where {K<:AbstractKleisli,X} = new{K,X}(k,x) + Likelihood(k::K, x::X) where {K<:AbstractTransitionKernel,X} = new{K,X}(k,x) Likelihood(k::K, x::X) where {K<:Function,X} = new{K,X}(k,x) - Likelihood(μ, x) = Likelihood(kleisli(μ), x) + Likelihood(μ, x) = Likelihood(kernel(μ), x) end # Not really a density, but this makes the code work @@ -148,9 +148,9 @@ likelihood(k, x, ::NamedTuple{()}) = Likelihood(k, x) likelihood(k, x; kwargs...) = likelihood(k, x, NamedTuple(kwargs)) -likelihood(k, x, pars::NamedTuple) = likelihood(kleisli(k, pars), x) +likelihood(k, x, pars::NamedTuple) = likelihood(kernel(k, pars), x) -likelihood(k::AbstractKleisli, x) = Likelihood(k, x) +likelihood(k::AbstractTransitionKernel, x) = Likelihood(k, x) """ log_likelihood_ratio(ℓ::Likelihood, p, q) diff --git a/src/combinators/product.jl b/src/combinators/product.jl index 50849cf3..68571588 100644 --- a/src/combinators/product.jl +++ b/src/combinators/product.jl @@ -133,7 +133,7 @@ end function _basemeasure(μ::ProductMeasure{Base.Generator{I,F}}, ::Type{B}, ::False) where {I,F,B} mar = marginals(μ) - productmeasure(Base.Generator(basekleisli(mar.f), mar.iter)) + productmeasure(Base.Generator(basekernel(mar.f), mar.iter)) end marginals(μ::ProductMeasure) = μ.marginals diff --git a/src/combinators/smart-constructors.jl b/src/combinators/smart-constructors.jl index 77f55126..752fb2c5 100644 --- a/src/combinators/smart-constructors.jl +++ b/src/combinators/smart-constructors.jl @@ -51,9 +51,9 @@ end productmeasure(nt::NamedTuple) = ProductMeasure(nt) productmeasure(tup::Tuple) = ProductMeasure(tup) -productmeasure(f, param_maps, pars) = ProductMeasure(kleisli(f, param_maps), pars) +productmeasure(f, param_maps, pars) = ProductMeasure(kernel(f, param_maps), pars) -productmeasure(k::ParameterizedKleisli, pars) = productmeasure(k.f, k.param_maps, pars) +productmeasure(k::ParameterizedTransitionKernel, pars) = productmeasure(k.f, k.param_maps, pars) function productmeasure(f::Returns{W}, ::typeof(identity), pars) where {W<:WeightedMeasure} ℓ = f.value.logweight @@ -100,30 +100,30 @@ function weightedmeasure(ℓ, b::WeightedMeasure) end ############################################################################### -# Kleisli +# TransitionKernel -kleisli(f, pars::NamedTuple) = ParameterizedKleisli(f, pars) +kernel(f, pars::NamedTuple) = ParameterizedTransitionKernel(f, pars) -# kleisli(Normal(μ=2)) -function kleisli(μ::M) where {M<:AbstractMeasure} - kleisli(M) +# kernel(Normal(μ=2)) +function kernel(μ::M) where {M<:AbstractMeasure} + kernel(M) end -function kleisli(d::PowerMeasure) - Base.Fix2(powermeasure, d.axes) ∘ kleisli(d.parent) +function kernel(d::PowerMeasure) + Base.Fix2(powermeasure, d.axes) ∘ kernel(d.parent) end -# kleisli(Normal{(:μ,), Tuple{Int64}}) -function kleisli(::Type{M}) where {M<:AbstractMeasure} +# kernel(Normal{(:μ,), Tuple{Int64}}) +function kernel(::Type{M}) where {M<:AbstractMeasure} constructorof(M) end -# kleisli(::Type{P}, op::O) where {O, N, P<:ParameterizedMeasure{N}} = kleisli{constructorof(P),O}(op) +# kernel(::Type{P}, op::O) where {O, N, P<:ParameterizedMeasure{N}} = kernel{constructorof(P),O}(op) -function kleisli(::Type{M}; param_maps...) where {M} +function kernel(::Type{M}; param_maps...) where {M} nt = NamedTuple(param_maps) - kleisli(M, nt) + kernel(M, nt) end -kleisli(k::ParameterizedKleisli) = k +kernel(k::ParameterizedTransitionKernel) = k diff --git a/src/generated.jl b/src/generated.jl deleted file mode 100644 index 7f1e2c66..00000000 --- a/src/generated.jl +++ /dev/null @@ -1,24 +0,0 @@ -@generated function _logdensityof(μ, x, ℓ, ::StaticInt{n}) where {n} - nsteps = max(n, 0) - quote - $(Expr(:meta, :inline)) - Base.Cartesian.@nexprs $nsteps i -> begin - Δℓ = logdensity_def(μ, x) - # @show μ - # @show Δℓ - # println() - μ = basemeasure(μ, x) - ℓ += Δℓ - end - return (ℓ,μ) - end -end - -@generated function _rootmeasure(μ, ::StaticInt{n}) where {n} - q = quote end - foreach(1:n) do _ - push!(q.args, :(μ = basemeasure(μ))) - end - return q -end - diff --git a/src/kleisli.jl b/src/kleisli.jl index 87b2d6f5..f99bded4 100644 --- a/src/kleisli.jl +++ b/src/kleisli.jl @@ -1,98 +1,86 @@ # TODO: Dangerous to export this - let's not -abstract type AbstractKleisli <: AbstractMeasure end +abstract type AbstractTransitionKernel <: AbstractMeasure end -struct ParameterizedKleisli{F,N,T} <: AbstractKleisli +struct ParameterizedTransitionKernel{F,N,T} <: AbstractTransitionKernel f::F param_maps::NamedTuple{N,T} - ParameterizedKleisli(::Type{F}, param_maps::NamedTuple{N,T}) where {F,N,T} = + ParameterizedTransitionKernel(::Type{F}, param_maps::NamedTuple{N,T}) where {F,N,T} = new{Type{F},N,T}(F, param_maps) - ParameterizedKleisli(f::F, param_maps::NamedTuple{N,T}) where {F,N,T} = + ParameterizedTransitionKernel(f::F, param_maps::NamedTuple{N,T}) where {F,N,T} = new{F,N,T}(f, param_maps) end """ - kleisli(f, M) - kleisli((f1, f2, ...), M) + kernel(f, M) + kernel((f1, f2, ...), M) -`kleisli` was originally called `kernel`, as in a *Markov kernel*. Such a kernel -can be considered to map each value in its domain to a probability measure. - -In the context of MeasureTheory, the codomain is not required to be a -*probability* measure; any measure will do. This makes "Markov" not really fit, -since the map need not be Markovian. - -This leaves us with "kernel", which can mean too wide a range of things to be -useful in such a general context as measure theory. See for example -https://github.com/JuliaGaussianProcesses/KernelFunctions.jl for one common use -of this term. - -We solve this problem by changing to a term from an even more general context. -In category theory, a *Kleisli arrow* is a function taking monadic values. -Since measures comprise a monad, our use is a special case of this. - -A kleisli `κ = kleisli(f, m)` returns a wrapper around a function `f` giving the +A kernel `κ = kernel(f, m)` returns a wrapper around a function `f` giving the parameters for a measure of type `M`, such that `κ(x) = M(f(x)...)` respective `κ(x) = M(f1(x), f2(x), ...)` If the argument is a named tuple `(;a=f1, b=f1)`, `κ(x)` is defined as `M(;a=f(x),b=g(x))`. +This function is not exported, because "kernel" can have so many other meanings. +See for example https://github.com/JuliaGaussianProcesses/KernelFunctions.jl for +another common use of this term. + # Reference * https://en.wikipedia.org/wiki/Markov_kernel """ -function kleisli end +function kernel end -# kleisli(Normal) do x +# kernel(Normal) do x # (μ=x,σ=x^2) # end -kleisli(f, ::Type{M}) where {M} = kleisli(M, f) +kernel(f, ::Type{M}) where {M} = kernel(M, f) mapcall(t, x) = map(func -> func(x), t) -# (k::Kleisli{Type{P},<:Tuple})(x) where {P<:ParameterizedMeasure} = k.f(mapcall(k.param_maps, x)...) +# (k::TransitionKernel{Type{P},<:Tuple})(x) where {P<:ParameterizedMeasure} = k.f(mapcall(k.param_maps, x)...) -(k::ParameterizedKleisli)(x) = k.f(; mapcall(k.param_maps, x)...) +(k::ParameterizedTransitionKernel)(x) = k.f(; mapcall(k.param_maps, x)...) -(k::ParameterizedKleisli)(x...) = k(x) +(k::ParameterizedTransitionKernel)(x...) = k(x) -function (k::ParameterizedKleisli)(x::Tuple) +function (k::ParameterizedTransitionKernel)(x::Tuple) k.f(NamedTuple{k.param_maps}(x)) end """ -For any `k::Kleisli`, `basekleisli` is expected to satisfy +For any `k::TransitionKernel`, `basekernel` is expected to satisfy ``` -basekleisli(k)(p) == (basemeasure ∘ k)(p) +basekernel(k)(p) == (basemeasure ∘ k)(p) ``` -The main purpose of `basekleisli` is to make it efficient to compute +The main purpose of `basekernel` is to make it efficient to compute ``` -basemeasure(d::ProductMeasure) = productmeasure(basekleisli(d.f), d.xs) +basemeasure(d::ProductMeasure) = productmeasure(basekernel(d.f), d.xs) ``` """ -function basekleisli end +function basekernel end # TODO: Find a way to do better than this -basekleisli(f) = basemeasure ∘ f +basekernel(f) = basemeasure ∘ f -basekleisli(k::ParameterizedKleisli) = kleisli(basekleisli(k.f), k.param_maps) +basekernel(k::ParameterizedTransitionKernel) = kernel(basekernel(k.f), k.param_maps) -basekleisli(f::Returns) = Returns(basemeasure(f.value)) +basekernel(f::Returns) = Returns(basemeasure(f.value)) -function Base.show(io::IO, μ::AbstractKleisli) +function Base.show(io::IO, μ::AbstractTransitionKernel) io = IOContext(io, :compact => true) Pretty.pprint(io, μ) end -function Pretty.quoteof(k::ParameterizedKleisli) +function Pretty.quoteof(k::ParameterizedTransitionKernel) qf = Pretty.quoteof(k.f) qg = Pretty.quoteof(k.param_maps) - :(ParameterizedKleisli($qf, $qg)) + :(ParameterizedTransitionKernel($qf, $qg)) end diff --git a/src/parameterized.jl b/src/parameterized.jl index fcaca087..03bc71cc 100644 --- a/src/parameterized.jl +++ b/src/parameterized.jl @@ -26,14 +26,13 @@ end # julia> Normal{(:μ,)}(2) # Normal(μ = 2,) # -export kleisli -function kleisli(::Type{P}) where {N,P<:ParameterizedMeasure{N}} +function kernel(::Type{P}) where {N,P<:ParameterizedMeasure{N}} C = constructorof(P) - _kleisli(C, Val(N)) + _kernel(C, Val(N)) end -@inline function _kleisli(::Type{C}, ::Val{N}) where {C,N} +@inline function _kernel(::Type{C}, ::Val{N}) where {C,N} @inline function(args::T) where {T<:Tuple} C(NamedTuple{N,T}(args))::C{N,T} end @@ -123,12 +122,12 @@ function paramnames(μ, constraints::NamedTuple{N}) where {N} end ############################################################################### -# kleislifactor +# kernelfactor -function kleislifactor(::Type{P}) where {N,P<:ParameterizedMeasure{N}} +function kernelfactor(::Type{P}) where {N,P<:ParameterizedMeasure{N}} (constructorof(P), N) end -function kleislifactor(::P) where {N,P<:ParameterizedMeasure{N}} +function kernelfactor(::P) where {N,P<:ParameterizedMeasure{N}} (constructorof(P), N) end diff --git a/test/runtests.jl b/test/runtests.jl index eab6722b..b8d067a2 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -65,8 +65,8 @@ testbroken_measures = [ end end -# @testset "Kleisli" begin -# κ = MeasureBase.kleisli(MeasureBase.Dirac, identity) +# @testset "TransitionKernel" begin +# κ = MeasureBase.kernel(MeasureBase.Dirac, identity) # @test rand(κ(1.1)) == 1.1 # end @@ -137,7 +137,7 @@ end # ℓs = [ # Likelihood(Normal{(:μ,)}, 3.0) -# Likelihood(kleisli(Normal, x -> (μ=x, σ=2.0)), 3.0) +# Likelihood(kernel(Normal, x -> (μ=x, σ=2.0)), 3.0) # ] # for (d,p) in dps From e4bb7ffa6b48d8ecde564b863c41c7bf3bee54bd Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 4 May 2022 16:00:06 -0700 Subject: [PATCH 236/368] simplify logdensity_def(::PowerMeasure, x) --- src/combinators/power.jl | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/src/combinators/power.jl b/src/combinators/power.jl index 0e823106..7d8a6fba 100644 --- a/src/combinators/power.jl +++ b/src/combinators/power.jl @@ -65,14 +65,10 @@ params(d::PowerMeasure) = params(first(marginals(d))) end @inline function logdensity_def(d::PowerMeasure{M}, x) where {M} - ℓ = 0.0 - # ℓ = zero(typeintersect(AbstractFloat,Core.Compiler.return_type(logdensity_def, Tuple{M,T}))) parent = d.parent - @simd for xj in x - Δℓ = logdensity_def(parent, xj) - ℓ += Δℓ + sum(x) do xj + @inline logdensity_def(parent, xj) end - ℓ end @generated function logdensity_def(d::PowerMeasure{M, Tuple{Base.OneTo{StaticInt{N}}}}, x) where {M,N} From a4b3f4452d1ae1ff8528281287199339bee0fdbf Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 4 May 2022 16:00:30 -0700 Subject: [PATCH 237/368] rename kleisli.jl to kernel.jl --- src/{kleisli.jl => kernel.jl} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename src/{kleisli.jl => kernel.jl} (100%) diff --git a/src/kleisli.jl b/src/kernel.jl similarity index 100% rename from src/kleisli.jl rename to src/kernel.jl From ed5a61dbc70a0c0a7d6d2742246fde772e746a8a Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 4 May 2022 16:15:39 -0700 Subject: [PATCH 238/368] update Dirac tests --- test/runtests.jl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/test/runtests.jl b/test/runtests.jl index b8d067a2..f8743e3a 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -77,8 +77,8 @@ end @testset "Dirac" begin @test rand(Dirac(0.2)) == 0.2 - @test logdensity_def(Dirac(0.3), 0.3) == 0.0 - @test logdensity_def(Dirac(0.3), 0.4) == -Inf + @test logdensityof(Dirac(0.3), 0.3) == 0.0 + @test logdensityof(Dirac(0.3), 0.4) == -Inf end # @testset "For" begin From 1f9eeaa6e758cdfc384a439c59de0ba7f01f9557 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 4 May 2022 16:15:44 -0700 Subject: [PATCH 239/368] update Half --- src/combinators/half.jl | 10 +++------- 1 file changed, 3 insertions(+), 7 deletions(-) diff --git a/src/combinators/half.jl b/src/combinators/half.jl index 9a2f275e..bc92774e 100644 --- a/src/combinators/half.jl +++ b/src/combinators/half.jl @@ -11,13 +11,8 @@ end unhalf(μ::Half) = μ.parent -isnonnegative(x) = x ≥ 0.0 - @inline function basemeasure(μ::Half) - constℓ = static(logtwo) - varℓ = Returns(0.0) - base = basemeasure(unhalf(μ)) - FactoredBase(constℓ, varℓ, base) + weightedmeasure(static(logtwo), basemeasure(unhalf(μ))) end function Base.rand(rng::AbstractRNG, ::Type{T}, μ::Half) where {T} @@ -27,7 +22,8 @@ end logdensity_def(μ::Half, x) = logdensity_def(unhalf(μ), x) @inline function insupport(d::Half, x) - ifelse(isnonnegative(x), insupport(unhalf(d), x), false) + x ≥ 0 || return false + insupport(unhalf(d), x) end testvalue(::Half) = 1.0 \ No newline at end of file From f98c7db31a703b9d433527e2d5828fa3eb386a7b Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 4 May 2022 16:57:44 -0700 Subject: [PATCH 240/368] get tests passing --- src/MeasureBase.jl | 1 + src/combinators/pointwise.jl | 17 ++++++++++++----- src/combinators/smart-constructors.jl | 1 - src/density.jl | 7 +++---- test/runtests.jl | 2 +- 5 files changed, 17 insertions(+), 11 deletions(-) diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index 6e505bfc..533292a7 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -13,6 +13,7 @@ import DensityInterface: densityof import DensityInterface: DensityKind using DensityInterface +import Base.iterate import ConstructionBase using ConstructionBase: constructorof diff --git a/src/combinators/pointwise.jl b/src/combinators/pointwise.jl index d1128f56..39264216 100644 --- a/src/combinators/pointwise.jl +++ b/src/combinators/pointwise.jl @@ -5,6 +5,10 @@ struct PointwiseProductMeasure{P,L} <: AbstractMeasure likelihood::L end + + +iterate(p::PointwiseProductMeasure, i=1) = iterate((p.prior, p.likelihood), i) + function Base.show(io::IO, μ::PointwiseProductMeasure) io = IOContext(io, :compact => true) print(io, μ.prior, " ⊙ ", μ.likelihood) @@ -25,16 +29,19 @@ end ⊙(μ, ℓ) = pointwiseproduct(μ, ℓ) @inline function logdensity_def(d::PointwiseProductMeasure, p) - (μ, ℓ) = (d.prior, d.likelihood) - logdensity_def(μ, p) + logdensityof(ℓ.k(p), ℓ.x) + μ, ℓ = d + logdensityof(ℓ.k(p), ℓ.x) end function gentype(d::PointwiseProductMeasure) gentype(d.prior) end -basemeasure(d::PointwiseProductMeasure, x) = basemeasure(d.prior, x) +@inbounds function insupport(d::PointwiseProductMeasure, p) + μ, ℓ = d + insupport(μ, p) && insupport(ℓ.k(p), ℓ.x) +end -basemeasure(d::PointwiseProductMeasure) = basemeasure(d.prior) +basemeasure(d::PointwiseProductMeasure, x) = d.prior -insupport(d::PointwiseProductMeasure, x) = insupport(d.prior, x) \ No newline at end of file +basemeasure(d::PointwiseProductMeasure) = basemeasure(d.prior) diff --git a/src/combinators/smart-constructors.jl b/src/combinators/smart-constructors.jl index 752fb2c5..9a393278 100644 --- a/src/combinators/smart-constructors.jl +++ b/src/combinators/smart-constructors.jl @@ -8,7 +8,6 @@ half(μ::AbstractMeasure) = Half(μ) # PointwiseProductMeasure function pointwiseproduct(μ::AbstractMeasure, ℓ::Likelihood) - @show μ T = Core.Compiler.return_type(ℓ.k, Tuple{gentype(μ)}) return pointwiseproduct(T, μ, ℓ) end diff --git a/src/density.jl b/src/density.jl index 8ca6d9e8..6ec14103 100644 --- a/src/density.jl +++ b/src/density.jl @@ -69,7 +69,7 @@ function _densitymeasure(f, base, _) end @inline function insupport(d::DensityMeasure, x) - ifelse(insupport(d.base, x), logdensityof(d.f, x) > -Inf, false) + insupport(d.base, x) == true && logdensityof(d.f, x) > -Inf end basemeasure(μ::DensityMeasure) = μ.base @@ -123,9 +123,8 @@ To compute a log-density relative to a specific base-measure, see `logdensity_rel`. """ @inline function logdensityof(μ::AbstractMeasure, x) - t() = dynamic(unsafe_logdensityof(μ, x)) - f() = -Inf - ifelse(insupport(μ, x), t, f)() + result = dynamic(unsafe_logdensityof(μ, x)) + ifelse(insupport(μ, x) == true, result, oftype(result, -Inf)) end export unsafe_logdensityof diff --git a/test/runtests.jl b/test/runtests.jl index f8743e3a..575febcd 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -126,7 +126,7 @@ end end end - @inferred logdensityof(ℓ, 2.0) + @inferred logdensityof(Lebesgue() ⊙ ℓ, 2.0) end # @testset "Likelihood" begin From 3bb68fe6a1a49b631239f456e378f6e74fe7a847 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Thu, 5 May 2022 07:52:36 -0700 Subject: [PATCH 241/368] update kernel --- src/parameterized.jl | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/src/parameterized.jl b/src/parameterized.jl index 03bc71cc..6ecb6df7 100644 --- a/src/parameterized.jl +++ b/src/parameterized.jl @@ -33,9 +33,15 @@ function kernel(::Type{P}) where {N,P<:ParameterizedMeasure{N}} end @inline function _kernel(::Type{C}, ::Val{N}) where {C,N} - @inline function(args::T) where {T<:Tuple} + @inline function f(args::T) where {T<:Tuple} C(NamedTuple{N,T}(args))::C{N,T} end + + @inline function f(arg::T) where {T} + C(NamedTuple{N,Tuple{T}}((arg,)))::C{N,Tuple{T}} + end + + f end function (::Type{P})(nt::NamedTuple) where {N,P<:ParameterizedMeasure{N}} From fafb3a2e57e0d33d189f0494b50547d3460cbed0 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Thu, 5 May 2022 08:20:47 -0700 Subject: [PATCH 242/368] Update Project.toml --- Project.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Project.toml b/Project.toml index d759b617..b492f7a4 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "MeasureBase" uuid = "fa1605e6-acd5-459c-a1e6-7e635759db14" authors = ["Chad Scherrer and contributors"] -version = "0.7.1" +version = "0.8.0" [deps] Compat = "34da2185-b29b-5c13-b0c7-acf172513d20" From 536992f6341f4c738ebbede7984e014239f00733 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Thu, 5 May 2022 09:13:00 -0700 Subject: [PATCH 243/368] no call-site inlining --- src/combinators/power.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/combinators/power.jl b/src/combinators/power.jl index 7d8a6fba..efb01d51 100644 --- a/src/combinators/power.jl +++ b/src/combinators/power.jl @@ -67,7 +67,7 @@ end @inline function logdensity_def(d::PowerMeasure{M}, x) where {M} parent = d.parent sum(x) do xj - @inline logdensity_def(parent, xj) + logdensity_def(parent, xj) end end From 3ae0f650b6c9c656909cc203551296f953f0d7e7 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Thu, 5 May 2022 14:19:05 -0700 Subject: [PATCH 244/368] restrict single-arg `kernel` to <:ParameterizedMeasure --- src/combinators/smart-constructors.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/combinators/smart-constructors.jl b/src/combinators/smart-constructors.jl index 938fabaf..bcf1ad13 100644 --- a/src/combinators/smart-constructors.jl +++ b/src/combinators/smart-constructors.jl @@ -104,7 +104,7 @@ end kernel(f, pars::NamedTuple) = ParameterizedTransitionKernel(f, pars) # kernel(Normal(μ=2)) -function kernel(μ::M) where {M<:AbstractMeasure} +function kernel(μ::M) where {M<:ParameterizedMeasure} kernel(M) end From 7364006d59837136fd34a65e50f010b2b0585aa2 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Fri, 6 May 2022 06:59:39 -0700 Subject: [PATCH 245/368] export log_likelihood_ratio --- src/combinators/likelihood.jl | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/combinators/likelihood.jl b/src/combinators/likelihood.jl index 4bd0c94e..58b77c71 100644 --- a/src/combinators/likelihood.jl +++ b/src/combinators/likelihood.jl @@ -152,6 +152,8 @@ likelihood(k, x, pars::NamedTuple) = likelihood(kernel(k, pars), x) likelihood(k::AbstractTransitionKernel, x) = Likelihood(k, x) +export log_likelihood_ratio + """ log_likelihood_ratio(ℓ::Likelihood, p, q) From 3eebcfb5d773ccf144093b1132603cf34e69a1a1 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Fri, 6 May 2022 07:00:26 -0700 Subject: [PATCH 246/368] Drop DensityKind(::Likelihood), at least for now --- src/combinators/likelihood.jl | 3 --- 1 file changed, 3 deletions(-) diff --git a/src/combinators/likelihood.jl b/src/combinators/likelihood.jl index 58b77c71..86c8236a 100644 --- a/src/combinators/likelihood.jl +++ b/src/combinators/likelihood.jl @@ -120,9 +120,6 @@ struct Likelihood{K,X} <: AbstractLikelihood Likelihood(μ, x) = Likelihood(kernel(μ), x) end -# Not really a density, but this makes the code work -@inline DensityKind(::Likelihood) = IsDensity() - function Pretty.quoteof(ℓ::Likelihood) k = Pretty.quoteof(ℓ.k) x = Pretty.quoteof(ℓ.x) From 38b26c7b6584fe5cb9da5295a98a960d492d2c62 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Fri, 6 May 2022 08:04:35 -0700 Subject: [PATCH 247/368] isfinite(x) instead of x>-Inf --- src/density.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/density.jl b/src/density.jl index 6ec14103..131413f2 100644 --- a/src/density.jl +++ b/src/density.jl @@ -69,7 +69,7 @@ function _densitymeasure(f, base, _) end @inline function insupport(d::DensityMeasure, x) - insupport(d.base, x) == true && logdensityof(d.f, x) > -Inf + insupport(d.base, x) == true && isfinite(logdensityof(d.f, x)) end basemeasure(μ::DensityMeasure) = μ.base From ba1eb20cc8ee6d35622243cd60ce0a1c46668dc0 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Fri, 6 May 2022 08:05:37 -0700 Subject: [PATCH 248/368] add `condition` constructor --- src/combinators/conditional.jl | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/src/combinators/conditional.jl b/src/combinators/conditional.jl index 2dc27ebd..030bd0e5 100644 --- a/src/combinators/conditional.jl +++ b/src/combinators/conditional.jl @@ -23,7 +23,9 @@ the notion of normalization may not even make sense. Because of this, this interface is not yet stable, and users should expect upcoming changes. """ -Base.:|(μ::AbstractMeasure, constraint) = ConditionalMeasure(μ, constraint) +Base.:|(μ::AbstractMeasure, constraint) = condition(μ, constraint) + +condition(μ, constraint) = ConditionalMeasure(μ, constraint) @inline basemeasure(cm::ConditionalMeasure) = basemeasure(cm.parent) | cm.constraint From 417b2d0f2153a88d2c629b608fd26904ff32c78f Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Fri, 6 May 2022 08:26:18 -0700 Subject: [PATCH 249/368] EOF newline --- src/combinators/half.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/combinators/half.jl b/src/combinators/half.jl index bc92774e..e9272fb5 100644 --- a/src/combinators/half.jl +++ b/src/combinators/half.jl @@ -26,4 +26,4 @@ logdensity_def(μ::Half, x) = logdensity_def(unhalf(μ), x) insupport(unhalf(d), x) end -testvalue(::Half) = 1.0 \ No newline at end of file +testvalue(::Half) = 1.0 From c81ca07d49645afeeab81bc948ed8ec3d5c96f0f Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 9 May 2022 07:24:58 -0700 Subject: [PATCH 250/368] simplify logdensity_def for power measures --- src/combinators/power.jl | 14 ++++---------- 1 file changed, 4 insertions(+), 10 deletions(-) diff --git a/src/combinators/power.jl b/src/combinators/power.jl index efb01d51..eca287ad 100644 --- a/src/combinators/power.jl +++ b/src/combinators/power.jl @@ -71,16 +71,10 @@ end end end -@generated function logdensity_def(d::PowerMeasure{M, Tuple{Base.OneTo{StaticInt{N}}}}, x) where {M,N} - quote - $(Expr(:meta, :inline)) - ℓ = 0.0 - parent = d.parent - @inbounds @simd for j in 1:$N - Δℓ = logdensity_def(parent, x[j]) - ℓ += Δℓ - end - ℓ +@inline function logdensity_def(d::PowerMeasure{M, Tuple{Base.OneTo{StaticInt{N}}}}, x) where {M,N} + parent = d.parent + sum(1:N) do j + @inbounds logdensity_def(parent, x[j]) end end From 11adfcf25dec687be68448a9ab41ba54f72cb208 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 9 May 2022 08:58:29 -0700 Subject: [PATCH 251/368] finishing up --- src/MeasureBase.jl | 6 ++---- src/combinators/conditional.jl | 4 ++++ src/combinators/likelihood.jl | 12 +++++++++++- src/combinators/pointwise.jl | 17 ++--------------- src/combinators/powerweighted.jl | 4 ++++ src/combinators/restricted.jl | 22 ++++++++++------------ src/combinators/smart-constructors.jl | 1 + src/combinators/superpose.jl | 8 ++++---- src/combinators/weighted.jl | 18 +++--------------- src/density.jl | 2 +- src/kernel.jl | 3 +++ 11 files changed, 45 insertions(+), 52 deletions(-) diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index 533292a7..bbe2da31 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -52,11 +52,9 @@ abstract type AbstractMeasure end using Static: @constprop -function Pretty.tile(d::M) where {M<:AbstractMeasure} +function Pretty.quoteof(d::M) where {M<:AbstractMeasure} the_names = fieldnames(typeof(d)) - result = Pretty.literal(repr(M)) - isempty(the_names) && return result * Pretty.literal("()") - Pretty.list_layout(Pretty.tile.([getfield(d, n) for n in the_names]); prefix=result) + :($M($([getfield(d, n) for n in the_names]...))) end @inline DensityKind(::AbstractMeasure) = HasDensity() diff --git a/src/combinators/conditional.jl b/src/combinators/conditional.jl index 030bd0e5..2230c748 100644 --- a/src/combinators/conditional.jl +++ b/src/combinators/conditional.jl @@ -40,3 +40,7 @@ condition(μ, constraint) = ConditionalMeasure(μ, constraint) function Base.:|(μ::ProductMeasure{NamedTuple{M,T}}, constraint::NamedTuple{N}) where {M,T,N} productmeasure(merge(marginals(μ),rmap(Dirac, constraint))) end + +function Pretty.tile(d::ConditionalMeasure) + Pretty.pair_layout(Pretty.tile(d.parent), Pretty.tile(d.constraint), sep=" | ") +end \ No newline at end of file diff --git a/src/combinators/likelihood.jl b/src/combinators/likelihood.jl index 86c8236a..780ce305 100644 --- a/src/combinators/likelihood.jl +++ b/src/combinators/likelihood.jl @@ -95,7 +95,8 @@ Finally, let's return to the expression for Bayes's Law, The product on the right side is computed pointwise. To work with this in MeasureBase, we have a "pointwise product" `⊙`, which takes a measure and a -likelihood, and returns a new measure, that is, the unnormalized posterior that has density ``P(θ) P(x|θ)`` with respect to the base measure of the prior. +likelihood, and returns a new measure, that is, the unnormalized posterior that +has density ``P(θ) P(x|θ)`` with respect to the base measure of the prior. For example, say we have @@ -141,6 +142,15 @@ end export likelihood +""" + likelihood(k::AbstractTransitionKernel, x; constraints...) + likelihood(k::AbstractTransitionKernel, x, constraints::NamedTuple) + +A likelihood is *not* a measure. Rather, a likelihood acts on a measure, through +the "pointwise product" `⊙`, yielding another measure. +""" +function likelihood end + likelihood(k, x, ::NamedTuple{()}) = Likelihood(k, x) likelihood(k, x; kwargs...) = likelihood(k, x, NamedTuple(kwargs)) diff --git a/src/combinators/pointwise.jl b/src/combinators/pointwise.jl index 39264216..9facf200 100644 --- a/src/combinators/pointwise.jl +++ b/src/combinators/pointwise.jl @@ -9,21 +9,8 @@ end iterate(p::PointwiseProductMeasure, i=1) = iterate((p.prior, p.likelihood), i) -function Base.show(io::IO, μ::PointwiseProductMeasure) - io = IOContext(io, :compact => true) - print(io, μ.prior, " ⊙ ", μ.likelihood) -end - -function Base.show_unquoted(io::IO, μ::PointwiseProductMeasure, indent::Int, prec::Int) - io = IOContext(io, :compact => true) - if Base.operator_precedence(:*) ≤ prec - print(io, "(") - show(io, μ) - print(io, ")") - else - show(io, μ) - end - return nothing +function Pretty.tile(d::PointwiseProductMeasure) + Pretty.pair_layout(Pretty.tile(d.prior), Pretty.tile(d.likelihood), sep=" ⊙ ") end ⊙(μ, ℓ) = pointwiseproduct(μ, ℓ) diff --git a/src/combinators/powerweighted.jl b/src/combinators/powerweighted.jl index 745318a8..4b45e4f4 100644 --- a/src/combinators/powerweighted.jl +++ b/src/combinators/powerweighted.jl @@ -31,3 +31,7 @@ end function powerweightedmeasure(d::WeightedMeasure, α) weightedmeasure(α*d.logweight, powerweightedmeasure(d.base, α)) end + +function Pretty.tile(d::PowerWeightedMeasure) + Pretty.pair_layout(Pretty.tile(d.parent), Pretty.tile(d.exponent), sep=" ↑ ") +end \ No newline at end of file diff --git a/src/combinators/restricted.jl b/src/combinators/restricted.jl index c0711efd..23cdfe64 100644 --- a/src/combinators/restricted.jl +++ b/src/combinators/restricted.jl @@ -1,18 +1,16 @@ -struct RestrictedMeasure{F,M} <: AbstractMeasure - f::F +struct RestrictedMeasure{P,M} <: AbstractMeasure + predicate::P base::M end -@inline function logdensity_def(d::RestrictedMeasure, x) - d.f(x) || return -Inf - return 0.0 -end - -function density_def(d::RestrictedMeasure, x) - d.f(x) || return 0.0 - return 1.0 -end +@inline logdensity_def(d::RestrictedMeasure, x) = logdensity_def(d.base, x) basemeasure(μ::RestrictedMeasure) = μ.base -insupport(μ::RestrictedMeasure, x) = μ.f(x) && insupport(μ.base, x) +insupport(μ::RestrictedMeasure, x) = μ.predicate(x) && insupport(μ.base, x) + +function Pretty.quoteof(d::RestrictedMeasure) + qf = Pretty.quoteof(d.predicate) + qbase = Pretty.quoteof(d.base) + :(RestrictedMeasure($qf, $qbase)) +end \ No newline at end of file diff --git a/src/combinators/smart-constructors.jl b/src/combinators/smart-constructors.jl index bcf1ad13..bc9468f4 100644 --- a/src/combinators/smart-constructors.jl +++ b/src/combinators/smart-constructors.jl @@ -63,6 +63,7 @@ end ############################################################################### # RestrictedMeasure +export restrict restrict(f, b) = RestrictedMeasure(f, b) diff --git a/src/combinators/superpose.jl b/src/combinators/superpose.jl index 58695b09..2ee83f39 100644 --- a/src/combinators/superpose.jl +++ b/src/combinators/superpose.jl @@ -89,15 +89,15 @@ end @inline function logdensity_def(s::SuperpositionMeasure{Tuple{A,B}}, β, x) where {A,B} (μ, ν) = s.components - insupport(μ, x) || return logdensity_rel(ν, β, x) - insupport(ν, x) || return logdensity_rel(μ, β, x) + insupport(μ, x) == true || return logdensity_rel(ν, β, x) + insupport(ν, x) == true || return logdensity_rel(μ, β, x) return logaddexp(logdensity_rel(μ, β, x), logdensity_rel(ν, β, x)) end @inline function logdensity_def(s::SuperpositionMeasure{Tuple{A,B}}, β::SuperpositionMeasure, x) where {A,B} (μ, ν) = s.components - insupport(μ, x) || return logdensity_rel(ν, β, x) - insupport(ν, x) || return logdensity_rel(μ, β, x) + insupport(μ, x) == true || return logdensity_rel(ν, β, x) + insupport(ν, x) == true || return logdensity_rel(μ, β, x) return logaddexp(logdensity_rel(μ, β, x), logdensity_rel(ν, β, x)) end diff --git a/src/combinators/weighted.jl b/src/combinators/weighted.jl index b364da7f..9b4d2feb 100644 --- a/src/combinators/weighted.jl +++ b/src/combinators/weighted.jl @@ -30,21 +30,9 @@ end _logweight(μ::WeightedMeasure) = μ.logweight basemeasure(μ::AbstractWeightedMeasure) = μ.base -function Base.show(io::IO, μ::WeightedMeasure) - io = IOContext(io, :compact => true) - print(io, exp(μ.logweight), " * ", μ.base) -end - -function Base.show_unquoted(io::IO, μ::WeightedMeasure, indent::Int, prec::Int) - io = IOContext(io, :compact => true) - if Base.operator_precedence(:*) ≤ prec - print(io, "(") - show(io, μ) - print(io, ")") - else - show(io, μ) - end - return nothing +function Pretty.tile(d::WeightedMeasure) + weight = round(exp(d.logweight), sigdigits=4) + Pretty.pair_layout(Pretty.tile(weight), Pretty.tile(d.base), sep=" * ") end function Base.:*(k::T, m::AbstractMeasure) where {T<:Number} diff --git a/src/density.jl b/src/density.jl index 131413f2..a439bde2 100644 --- a/src/density.jl +++ b/src/density.jl @@ -219,7 +219,7 @@ end # Note that this method assumes `μ` and `ν` to have the same type function logdensity_def(μ::T, ν::T, x) where {T} if μ === ν - return zero(return_type(logdensity_def, (μ, x))) + return zero(logdensity_def(μ, x)) else return logdensity_def(μ,x) - logdensity_def(ν, x) end diff --git a/src/kernel.jl b/src/kernel.jl index f99bded4..cce4146c 100644 --- a/src/kernel.jl +++ b/src/kernel.jl @@ -84,3 +84,6 @@ function Pretty.quoteof(k::ParameterizedTransitionKernel) :(ParameterizedTransitionKernel($qf, $qg)) end +const kleisli = kernel + +export kleisli \ No newline at end of file From 49981110286c4b578aae9d30d2e247638b53173b Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 18 May 2022 10:18:47 -0700 Subject: [PATCH 252/368] updates --- src/combinators/pointwise.jl | 22 ++++++++++------------ src/combinators/smart-constructors.jl | 10 ++++++++++ src/combinators/weighted.jl | 2 +- src/domains.jl | 2 +- 4 files changed, 22 insertions(+), 14 deletions(-) diff --git a/src/combinators/pointwise.jl b/src/combinators/pointwise.jl index aaf02f07..f6268188 100644 --- a/src/combinators/pointwise.jl +++ b/src/combinators/pointwise.jl @@ -11,22 +11,20 @@ function Pretty.tile(d::PointwiseProductMeasure) Pretty.pair_layout(Pretty.tile(d.prior), Pretty.tile(d.likelihood), sep = " ⊙ ") end -⊙(μ, ℓ) = pointwiseproduct(μ, ℓ) +⊙(prior, ℓ) = pointwiseproduct(prior, ℓ) + +@inbounds function insupport(d::PointwiseProductMeasure, p) + prior, ℓ = d + insupport(prior, p) && insupport(ℓ.k(p), ℓ.x) +end @inline function logdensity_def(d::PointwiseProductMeasure, p) - μ, ℓ = d - logdensityof(ℓ.k(p), ℓ.x) + prior, ℓ = d + unsafe_logdensityof(ℓ.k(p), ℓ.x) end +basemeasure(d::PointwiseProductMeasure) = d.prior + function gentype(d::PointwiseProductMeasure) gentype(d.prior) end - -@inbounds function insupport(d::PointwiseProductMeasure, p) - μ, ℓ = d - insupport(μ, p) && insupport(ℓ.k(p), ℓ.x) -end - -basemeasure(d::PointwiseProductMeasure, x) = d.prior - -basemeasure(d::PointwiseProductMeasure) = basemeasure(d.prior) diff --git a/src/combinators/smart-constructors.jl b/src/combinators/smart-constructors.jl index 86028b33..8783b93f 100644 --- a/src/combinators/smart-constructors.jl +++ b/src/combinators/smart-constructors.jl @@ -135,9 +135,19 @@ end # kernel(::Type{P}, op::O) where {O, N, P<:ParameterizedMeasure{N}} = kernel{constructorof(P),O}(op) +ntkeys(::Type{NT}) where {N, NT<:NamedTuple{N}} = N + function kernel(::Type{M}; param_maps...) where {M} nt = NamedTuple(param_maps) kernel(M, nt) end +function kernel(::Type{M}, f::F) where {M,F<:Function} + T = Base._return_type(f, Tuple{Any}) + @assert T<:NamedTuple + ks = ntkeys(T) + param_maps = NamedTuple{ks}(map(_ -> identity, values(ks))) + ParameterizedTransitionKernel(M, param_maps, f) +end + kernel(k::ParameterizedTransitionKernel) = k diff --git a/src/combinators/weighted.jl b/src/combinators/weighted.jl index 0b9c9b27..b31d1939 100644 --- a/src/combinators/weighted.jl +++ b/src/combinators/weighted.jl @@ -31,7 +31,7 @@ _logweight(μ::WeightedMeasure) = μ.logweight basemeasure(μ::AbstractWeightedMeasure) = μ.base function Pretty.tile(d::WeightedMeasure) - weight = round(exp(d.logweight), sigdigits = 4) + weight = round(dynamic(exp(d.logweight)), sigdigits = 4) Pretty.pair_layout(Pretty.tile(weight), Pretty.tile(d.base), sep = " * ") end diff --git a/src/domains.jl b/src/domains.jl index fd244147..492025cb 100644 --- a/src/domains.jl +++ b/src/domains.jl @@ -133,7 +133,7 @@ projectto!(x, ::Simplex) = normalize!(x, 1) struct Sphere <: CodimOne end function zeroset(::Sphere) - f(x::AbstractArray{T}) where {T} = sum(xⱼ -> xⱼ^2, x) - one(T) + f(x::AbstractArray{T}) where {T} = sum(abs2, x) - one(T) ∇f(x::AbstractArray{T}) where {T} = x ZeroSet(f, ∇f) end From 7408e6b8e9c28a3ba41dee71fa4acb38dfdd49e2 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 18 May 2022 14:57:45 -0700 Subject: [PATCH 253/368] kernel stuff --- src/kernel.jl | 58 +++++++++++++++++++++++++++++++++++++++------------ 1 file changed, 45 insertions(+), 13 deletions(-) diff --git a/src/kernel.jl b/src/kernel.jl index e2e2cc20..08c660bb 100644 --- a/src/kernel.jl +++ b/src/kernel.jl @@ -1,21 +1,32 @@ # TODO: Dangerous to export this - let's not abstract type AbstractTransitionKernel <: AbstractMeasure end -struct ParameterizedTransitionKernel{F,N,T} <: AbstractTransitionKernel - f::F +struct ParameterizedTransitionKernel{M,S,N,T} <: AbstractTransitionKernel + m::M + suff::S param_maps::NamedTuple{N,T} function ParameterizedTransitionKernel( - ::Type{F}, + ::Type{M}, + suff::S, param_maps::NamedTuple{N,T}, - ) where {F,N,T} - new{Type{F},N,T}(F, param_maps) + ) where {M,S,N,T} + new{Type{M},S,N,T}(M,suff, param_maps) end - function ParameterizedTransitionKernel(f::F, param_maps::NamedTuple{N,T}) where {F,N,T} - new{F,N,T}(f, param_maps) + function ParameterizedTransitionKernel(m::M, suff::S, param_maps::NamedTuple{N,T}) where {M,S,N,T} + new{M,S,N,T}(m, suff, param_maps) end end +struct GenericTransitionKernel{F} <: AbstractTransitionKernel + f::F +end + +struct TypedTransitionKernel{M,F} <: AbstractTransitionKernel + m::M + f::F +end + """ kernel(f, M) kernel((f1, f2, ...), M) @@ -41,20 +52,41 @@ function kernel end # (μ=x,σ=x^2) # end -kernel(f, ::Type{M}) where {M} = kernel(M, f) +kernel(f) = GenericTransitionKernel(f) + +kernel(f::F, ::Type{M}; kwargs...) where {F<:Function, M} = kernel(M,f) + +function kernel(::Type{M}, f::F) where {M,F<:Function} + T = Core.Compiler.return_type(f, Tuple{Any} ) + _kernel(M,f,T) +end + +function _kernel(::Type{M}, f::F, ::Type{NamedTuple{N,T}}) where {M,F<:Function,k,N<:NTuple{k,Symbol},T} + maps = ntuple(Val(k)) do i + x -> @inbounds x[i] + end + + kernel(M, values ∘ f, NamedTuple{N}(maps)) +end + +function _kernel(::Type{M}, f::F, ::Type{T}) where {M,F<:Function,T} + TypedTransitionKernel{Type{M},F}(M,f) +end + + +kernel(suff, ::Type{M}; kwargs...) where {M} = _kernel(M, f) mapcall(t, x) = map(func -> func(x), t) # (k::TransitionKernel{Type{P},<:Tuple})(x) where {P<:ParameterizedMeasure} = k.f(mapcall(k.param_maps, x)...) -(k::ParameterizedTransitionKernel)(x) = k.f(; mapcall(k.param_maps, x)...) +function (k::ParameterizedTransitionKernel)(x) + s = k.suff(x) + k.m(; mapcall(k.param_maps, s)...) +end (k::ParameterizedTransitionKernel)(x...) = k(x) -function (k::ParameterizedTransitionKernel)(x::Tuple) - k.f(NamedTuple{k.param_maps}(x)) -end - """ For any `k::TransitionKernel`, `basekernel` is expected to satisfy ``` From 2210d3d9d9236470c35caaae2102c5c2702573b8 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 23 May 2022 12:20:12 -0700 Subject: [PATCH 254/368] kernel stuff --- src/combinators/smart-constructors.jl | 68 +++++++---- src/kernel.jl | 155 ++++++++++++++------------ 2 files changed, 132 insertions(+), 91 deletions(-) diff --git a/src/combinators/smart-constructors.jl b/src/combinators/smart-constructors.jl index 8783b93f..173fbe2f 100644 --- a/src/combinators/smart-constructors.jl +++ b/src/combinators/smart-constructors.jl @@ -54,7 +54,7 @@ productmeasure(tup::Tuple) = ProductMeasure(tup) productmeasure(f, param_maps, pars) = ProductMeasure(kernel(f, param_maps), pars) function productmeasure(k::ParameterizedTransitionKernel, pars) - productmeasure(k.f, k.param_maps, pars) + productmeasure(k.suff, k.param_maps, pars) end function productmeasure(f::Returns{W}, ::typeof(identity), pars) where {W<:WeightedMeasure} @@ -117,37 +117,65 @@ end ############################################################################### # TransitionKernel -kernel(f, pars::NamedTuple) = ParameterizedTransitionKernel(f, pars) - # kernel(Normal(μ=2)) function kernel(μ::M) where {M<:ParameterizedMeasure} kernel(M) end -function kernel(d::PowerMeasure) - Base.Fix2(powermeasure, d.axes) ∘ kernel(d.parent) +# function kernel(d::PowerMeasure) +# Base.Fix2(powermeasure, d.axes) ∘ kernel(d.parent) +# end + + +# function kernel(f) +# T = Core.Compiler.return_type(f, Tuple{Any} ) +# _kernel(f, T) +# end + +# function _kernel(f, ::Type{T}) where {T} +# GenericTransitionKernel(f) +# end + +function _kernel(f, ::Type{P}) where {N,P<:ParameterizedMeasure{N}} + k = length(N) + C = constructorof(P) + maps = ntuple(Val(k)) do i + x -> @inbounds x[i] + end + + kernel(params ∘ f, C, NamedTuple{N}(maps)) end -# kernel(Normal{(:μ,), Tuple{Int64}}) -function kernel(::Type{M}) where {M<:AbstractMeasure} - constructorof(M) +kernel(f::F, ::Type{M}; kwargs...) where {F<:Function, M} = kernel(f, M, NamedTuple(kwargs)) + +kernel(f::F, ::Type{M}, nt::NamedTuple) where {F<:Function,M} = ParameterizedTransitionKernel(M,f,nt) + +function kernel(f::F, ::Type{M}, ::NamedTuple{()}) where {F<:Function, M} + T = Core.Compiler.return_type(f, Tuple{Any} ) + _kernel(f,M,T) end -# kernel(::Type{P}, op::O) where {O, N, P<:ParameterizedMeasure{N}} = kernel{constructorof(P),O}(op) +kernel(::Type{P}, nt::NamedTuple) where {P<:ParameterizedMeasure} = kernel(identity, P, nt) -ntkeys(::Type{NT}) where {N, NT<:NamedTuple{N}} = N +kernel(::Type{T}; kwargs...) where {T} = kernel(T, NamedTuple(kwargs)) -function kernel(::Type{M}; param_maps...) where {M} - nt = NamedTuple(param_maps) - kernel(M, nt) +function kernel(::Type{M}, ::NamedTuple{()}) where {M} + C = constructorof(M) + TypedTransitionKernel(C, identity) end -function kernel(::Type{M}, f::F) where {M,F<:Function} - T = Base._return_type(f, Tuple{Any}) - @assert T<:NamedTuple - ks = ntkeys(T) - param_maps = NamedTuple{ks}(map(_ -> identity, values(ks))) - ParameterizedTransitionKernel(M, param_maps, f) +function _kernel(f::F, ::Type{M}, ::Type{NT}) where {M,F,N,NT<:NamedTuple{N}} + k = length(N) + maps = ntuple(Val(k)) do i + x -> @inbounds x[i] + end + + ParameterizedTransitionKernel(M, values ∘ f, NamedTuple{N}(maps)) end + +kernel(f::F; kwargs...) where {F<:Function} = kernel(f, NamedTuple(kwargs)) -kernel(k::ParameterizedTransitionKernel) = k +function kernel(f::F, nt::NamedTuple{()}) where {F<:Function} + T = Core.Compiler.return_type(f, Tuple{Any} ) + _kernel(f, T) +end \ No newline at end of file diff --git a/src/kernel.jl b/src/kernel.jl index 08c660bb..2550b8ce 100644 --- a/src/kernel.jl +++ b/src/kernel.jl @@ -1,6 +1,22 @@ # TODO: Dangerous to export this - let's not abstract type AbstractTransitionKernel <: AbstractMeasure end +struct GenericTransitionKernel{F} <: AbstractTransitionKernel + f::F +end + + +(k::GenericTransitionKernel)(x) = k.f(x) +(k::GenericTransitionKernel)(x1, x2, xs...) = k.f((x1, x2, xs...)) + + + +struct TypedTransitionKernel{M,F} <: AbstractTransitionKernel + m::M + f::F +end + +(k::TypedTransitionKernel)(x) = (k.m ∘ k.f)(x) struct ParameterizedTransitionKernel{M,S,N,T} <: AbstractTransitionKernel m::M suff::S @@ -18,106 +34,103 @@ struct ParameterizedTransitionKernel{M,S,N,T} <: AbstractTransitionKernel end end -struct GenericTransitionKernel{F} <: AbstractTransitionKernel - f::F -end - -struct TypedTransitionKernel{M,F} <: AbstractTransitionKernel - m::M - f::F -end - -""" - kernel(f, M) - kernel((f1, f2, ...), M) -A kernel `κ = kernel(f, m)` returns a wrapper around a function `f` giving the -parameters for a measure of type `M`, such that `κ(x) = M(f(x)...)` respective -`κ(x) = M(f1(x), f2(x), ...)` -If the argument is a named tuple `(;a=f1, b=f1)`, `κ(x)` is defined as -`M(;a=f(x),b=g(x))`. +# """ +# kernel(f, M) +# kernel((f1, f2, ...), M) -This function is not exported, because "kernel" can have so many other meanings. -See for example https://github.com/JuliaGaussianProcesses/KernelFunctions.jl for -another common use of this term. +# A kernel `κ = kernel(f, m)` returns a wrapper around a function `f` giving the +# parameters for a measure of type `M`, such that `κ(x) = M(f(x)...)` respective +# `κ(x) = M(f1(x), f2(x), ...)` -# Reference +# If the argument is a named tuple `(;a=f1, b=f1)`, `κ(x)` is defined as +# `M(;a=f(x),b=g(x))`. -* https://en.wikipedia.org/wiki/Markov_kernel -""" -function kernel end +# This function is not exported, because "kernel" can have so many other meanings. +# See for example https://github.com/JuliaGaussianProcesses/KernelFunctions.jl for +# another common use of this term. -# kernel(Normal) do x -# (μ=x,σ=x^2) -# end +# # Reference -kernel(f) = GenericTransitionKernel(f) +# * https://en.wikipedia.org/wiki/Markov_kernel +# """ +# function kernel end -kernel(f::F, ::Type{M}; kwargs...) where {F<:Function, M} = kernel(M,f) +# # kernel(Normal) do x +# # (μ=x,σ=x^2) +# # end -function kernel(::Type{M}, f::F) where {M,F<:Function} - T = Core.Compiler.return_type(f, Tuple{Any} ) - _kernel(M,f,T) -end - -function _kernel(::Type{M}, f::F, ::Type{NamedTuple{N,T}}) where {M,F<:Function,k,N<:NTuple{k,Symbol},T} - maps = ntuple(Val(k)) do i - x -> @inbounds x[i] - end - - kernel(M, values ∘ f, NamedTuple{N}(maps)) -end - -function _kernel(::Type{M}, f::F, ::Type{T}) where {M,F<:Function,T} - TypedTransitionKernel{Type{M},F}(M,f) -end +# function _kernel(::Type{M}, f::F, ::Type{T}) where {M,F<:Function,T} +# TypedTransitionKernel{Type{M},F}(M,f) +# end -kernel(suff, ::Type{M}; kwargs...) where {M} = _kernel(M, f) mapcall(t, x) = map(func -> func(x), t) -# (k::TransitionKernel{Type{P},<:Tuple})(x) where {P<:ParameterizedMeasure} = k.f(mapcall(k.param_maps, x)...) +# # (k::TransitionKernel{Type{P},<:Tuple})(x) where {P<:ParameterizedMeasure} = k.f(mapcall(k.param_maps, x)...) function (k::ParameterizedTransitionKernel)(x) s = k.suff(x) k.m(; mapcall(k.param_maps, s)...) end -(k::ParameterizedTransitionKernel)(x...) = k(x) +# (k::AbstractTransitionKernel)(x1, x2, xs...) = k((x1, x2, xs...)) -""" -For any `k::TransitionKernel`, `basekernel` is expected to satisfy -``` -basekernel(k)(p) == (basemeasure ∘ k)(p) -``` +# """ +# For any `k::TransitionKernel`, `basekernel` is expected to satisfy +# ``` +# basekernel(k)(p) == (basemeasure ∘ k)(p) +# ``` -The main purpose of `basekernel` is to make it efficient to compute -``` -basemeasure(d::ProductMeasure) = productmeasure(basekernel(d.f), d.xs) -``` -""" -function basekernel end +# The main purpose of `basekernel` is to make it efficient to compute +# ``` +# basemeasure(d::ProductMeasure) = productmeasure(basekernel(d.f), d.xs) +# ``` +# """ +# function basekernel end # TODO: Find a way to do better than this basekernel(f) = basemeasure ∘ f -basekernel(k::ParameterizedTransitionKernel) = kernel(basekernel(k.f), k.param_maps) basekernel(f::Returns) = Returns(basemeasure(f.value)) -function Base.show(io::IO, μ::AbstractTransitionKernel) - io = IOContext(io, :compact => true) - Pretty.pprint(io, μ) -end +# function Base.show(io::IO, μ::AbstractTransitionKernel) +# io = IOContext(io, :compact => true) +# Pretty.pprint(io, μ) +# end + +# function Pretty.quoteof(k::ParameterizedTransitionKernel) +# qf = Pretty.quoteof(k.f) +# qg = Pretty.quoteof(k.param_maps) +# :(ParameterizedTransitionKernel($qf, $qg)) +# end + +# const kleisli = kernel + +# export kleisli + + + +# kernel(f, pars::NamedTuple) = ParameterizedTransitionKernel(f, pars) + + +# # kernel(Normal{(:μ,), Tuple{Int64}}) +# function kernel(::Type{M}) where {M<:AbstractMeasure} +# constructorof(M) +# end + +# # kernel(::Type{P}, op::O) where {O, N, P<:ParameterizedMeasure{N}} = kernel{constructorof(P),O}(op) + +# ntkeys(::Type{NT}) where {N, NT<:NamedTuple{N}} = N + +# function kernel(::Type{M}; param_maps...) where {M} +# nt = NamedTuple(param_maps) +# kernel(M, nt) +# end -function Pretty.quoteof(k::ParameterizedTransitionKernel) - qf = Pretty.quoteof(k.f) - qg = Pretty.quoteof(k.param_maps) - :(ParameterizedTransitionKernel($qf, $qg)) -end -const kleisli = kernel -export kleisli +# kernel(k::ParameterizedTransitionKernel) = k From c4ea293de92f5dae57850a0cf98db3e86fcc5db8 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 23 May 2022 12:21:14 -0700 Subject: [PATCH 255/368] update showe methods --- src/parameterized.jl | 30 ++++++++++++++++++++++-------- 1 file changed, 22 insertions(+), 8 deletions(-) diff --git a/src/parameterized.jl b/src/parameterized.jl index f8583394..f53cc689 100644 --- a/src/parameterized.jl +++ b/src/parameterized.jl @@ -10,17 +10,31 @@ function Base.propertynames(μ::ParameterizedMeasure{N}) where {N} return N end -function Base.show(io::IO, μ::ParameterizedMeasure{()}) - io = IOContext(io, :compact => true) - print(io, nameof(typeof(μ)), "()") +function Pretty.tile(d::ParameterizedMeasure) + result = Pretty.literal(nameof(typeof(d))) + par = getfield(d, :par) + result *= Pretty.literal(sprint(show, par; context=:compact => true)) + result end -function Base.show(io::IO, μ::ParameterizedMeasure{N}) where {N} - io = IOContext(io, :compact => true) - print(io, nameof(typeof(μ))) - print(io, getfield(μ, :par)) +function Pretty.tile(d::ParameterizedMeasure{()}) + result = Pretty.literal(nameof(typeof(d))) + par = getfield(d, :par) + result *= Pretty.literal("()") + result end +# function Base.show(io::IO, μ::ParameterizedMeasure{()}) +# io = IOContext(io, :compact => true) +# print(io, nameof(typeof(μ)), "()") +# end + +# function Base.show(io::IO, μ::ParameterizedMeasure{N}) where {N} +# io = IOContext(io, :compact => true) +# print(io, nameof(typeof(μ))) +# print(io, getfield(μ, :par)) +# end + # Allow things like # # julia> Normal{(:μ,)}(2) @@ -47,7 +61,7 @@ end function (::Type{P})(nt::NamedTuple) where {N,P<:ParameterizedMeasure{N}} C = constructorof(P) arg = NamedTuple{N}(nt) - return C(arg) + return C(arg)::P end function (::Type{P})(args...) where {N,P<:ParameterizedMeasure{N}} From a7ba3634ae11d95d81a6b24d59b334fa964e45ed Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 23 May 2022 12:43:28 -0700 Subject: [PATCH 256/368] ass a TODO --- src/parameterized.jl | 1 + 1 file changed, 1 insertion(+) diff --git a/src/parameterized.jl b/src/parameterized.jl index f53cc689..a501f887 100644 --- a/src/parameterized.jl +++ b/src/parameterized.jl @@ -46,6 +46,7 @@ function kernel(::Type{P}) where {N,P<:ParameterizedMeasure{N}} _kernel(C, Val(N)) end +# TODO: This should return a kernel @inline function _kernel(::Type{C}, ::Val{N}) where {C,N} @inline function f(args::T) where {T<:Tuple} C(NamedTuple{N,T}(args))::C{N,T} From bc08f16bc649ac3d905322efd95fceeaacfbc919 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 23 May 2022 13:05:53 -0700 Subject: [PATCH 257/368] use `dot` instead of `sum` --- src/domains.jl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/domains.jl b/src/domains.jl index 492025cb..2eed1719 100644 --- a/src/domains.jl +++ b/src/domains.jl @@ -114,7 +114,7 @@ export Simplex struct Simplex <: CodimOne end -function zeroset(::Simplex) +function zeroset(::Simplex)merge f(x::AbstractArray{T}) where {T} = sum(x) - one(T) ∇f(x::AbstractArray{T}) where {T} = Fill(one(T), size(x)) ZeroSet(f, ∇f) @@ -133,7 +133,7 @@ projectto!(x, ::Simplex) = normalize!(x, 1) struct Sphere <: CodimOne end function zeroset(::Sphere) - f(x::AbstractArray{T}) where {T} = sum(abs2, x) - one(T) + f(x::AbstractArray{T}) where {T} = dot(x,x) - one(T) ∇f(x::AbstractArray{T}) where {T} = x ZeroSet(f, ∇f) end From 20dafa964596a6d4d1c49c67e0fbf4788786ab82 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 23 May 2022 13:07:06 -0700 Subject: [PATCH 258/368] drop old code --- src/parameterized.jl | 13 ------------- 1 file changed, 13 deletions(-) diff --git a/src/parameterized.jl b/src/parameterized.jl index a501f887..30995e7d 100644 --- a/src/parameterized.jl +++ b/src/parameterized.jl @@ -24,23 +24,10 @@ function Pretty.tile(d::ParameterizedMeasure{()}) result end -# function Base.show(io::IO, μ::ParameterizedMeasure{()}) -# io = IOContext(io, :compact => true) -# print(io, nameof(typeof(μ)), "()") -# end - -# function Base.show(io::IO, μ::ParameterizedMeasure{N}) where {N} -# io = IOContext(io, :compact => true) -# print(io, nameof(typeof(μ))) -# print(io, getfield(μ, :par)) -# end - # Allow things like # # julia> Normal{(:μ,)}(2) # Normal(μ = 2,) -# - function kernel(::Type{P}) where {N,P<:ParameterizedMeasure{N}} C = constructorof(P) _kernel(C, Val(N)) From 11f78c47795eb443a06a9d19168a11ce1a9f0c1b Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 23 May 2022 13:07:50 -0700 Subject: [PATCH 259/368] typo --- src/domains.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/domains.jl b/src/domains.jl index 2eed1719..a920d87b 100644 --- a/src/domains.jl +++ b/src/domains.jl @@ -114,7 +114,7 @@ export Simplex struct Simplex <: CodimOne end -function zeroset(::Simplex)merge +function zeroset(::Simplex) f(x::AbstractArray{T}) where {T} = sum(x) - one(T) ∇f(x::AbstractArray{T}) where {T} = Fill(one(T), size(x)) ZeroSet(f, ∇f) From 8f9ab6b4fa3c764a6e3f9ee4f9b21393a032b5f3 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 23 May 2022 14:37:11 -0700 Subject: [PATCH 260/368] formatting --- src/combinators/smart-constructors.jl | 23 ++++++++++++++--------- src/domains.jl | 2 +- src/kernel.jl | 21 ++++++--------------- src/parameterized.jl | 8 ++++++-- 4 files changed, 27 insertions(+), 27 deletions(-) diff --git a/src/combinators/smart-constructors.jl b/src/combinators/smart-constructors.jl index 173fbe2f..f4d0084f 100644 --- a/src/combinators/smart-constructors.jl +++ b/src/combinators/smart-constructors.jl @@ -126,7 +126,6 @@ end # Base.Fix2(powermeasure, d.axes) ∘ kernel(d.parent) # end - # function kernel(f) # T = Core.Compiler.return_type(f, Tuple{Any} ) # _kernel(f, T) @@ -146,13 +145,19 @@ function _kernel(f, ::Type{P}) where {N,P<:ParameterizedMeasure{N}} kernel(params ∘ f, C, NamedTuple{N}(maps)) end -kernel(f::F, ::Type{M}; kwargs...) where {F<:Function, M} = kernel(f, M, NamedTuple(kwargs)) +function _kernel(f, ::Type{P}) where {N,P} + GenericTransitionKernel(f) +end + +kernel(f::F, ::Type{M}; kwargs...) where {F<:Function,M} = kernel(f, M, NamedTuple(kwargs)) -kernel(f::F, ::Type{M}, nt::NamedTuple) where {F<:Function,M} = ParameterizedTransitionKernel(M,f,nt) +function kernel(f::F, ::Type{M}, nt::NamedTuple) where {F<:Function,M} + ParameterizedTransitionKernel(M, f, nt) +end -function kernel(f::F, ::Type{M}, ::NamedTuple{()}) where {F<:Function, M} - T = Core.Compiler.return_type(f, Tuple{Any} ) - _kernel(f,M,T) +function kernel(f::F, ::Type{M}, ::NamedTuple{()}) where {F<:Function,M} + T = Core.Compiler.return_type(f, Tuple{Any}) + _kernel(f, M, T) end kernel(::Type{P}, nt::NamedTuple) where {P<:ParameterizedMeasure} = kernel(identity, P, nt) @@ -172,10 +177,10 @@ function _kernel(f::F, ::Type{M}, ::Type{NT}) where {M,F,N,NT<:NamedTuple{N}} ParameterizedTransitionKernel(M, values ∘ f, NamedTuple{N}(maps)) end - + kernel(f::F; kwargs...) where {F<:Function} = kernel(f, NamedTuple(kwargs)) function kernel(f::F, nt::NamedTuple{()}) where {F<:Function} - T = Core.Compiler.return_type(f, Tuple{Any} ) + T = Core.Compiler.return_type(f, Tuple{Any}) _kernel(f, T) -end \ No newline at end of file +end diff --git a/src/domains.jl b/src/domains.jl index a920d87b..ed4617b2 100644 --- a/src/domains.jl +++ b/src/domains.jl @@ -133,7 +133,7 @@ projectto!(x, ::Simplex) = normalize!(x, 1) struct Sphere <: CodimOne end function zeroset(::Sphere) - f(x::AbstractArray{T}) where {T} = dot(x,x) - one(T) + f(x::AbstractArray{T}) where {T} = dot(x, x) - one(T) ∇f(x::AbstractArray{T}) where {T} = x ZeroSet(f, ∇f) end diff --git a/src/kernel.jl b/src/kernel.jl index 2550b8ce..056f3e72 100644 --- a/src/kernel.jl +++ b/src/kernel.jl @@ -5,12 +5,9 @@ struct GenericTransitionKernel{F} <: AbstractTransitionKernel f::F end - (k::GenericTransitionKernel)(x) = k.f(x) (k::GenericTransitionKernel)(x1, x2, xs...) = k.f((x1, x2, xs...)) - - struct TypedTransitionKernel{M,F} <: AbstractTransitionKernel m::M f::F @@ -27,15 +24,17 @@ struct ParameterizedTransitionKernel{M,S,N,T} <: AbstractTransitionKernel suff::S, param_maps::NamedTuple{N,T}, ) where {M,S,N,T} - new{Type{M},S,N,T}(M,suff, param_maps) + new{Type{M},S,N,T}(M, suff, param_maps) end - function ParameterizedTransitionKernel(m::M, suff::S, param_maps::NamedTuple{N,T}) where {M,S,N,T} + function ParameterizedTransitionKernel( + m::M, + suff::S, + param_maps::NamedTuple{N,T}, + ) where {M,S,N,T} new{M,S,N,T}(m, suff, param_maps) end end - - # """ # kernel(f, M) # kernel((f1, f2, ...), M) @@ -65,8 +64,6 @@ end # TypedTransitionKernel{Type{M},F}(M,f) # end - - mapcall(t, x) = map(func -> func(x), t) # # (k::TransitionKernel{Type{P},<:Tuple})(x) where {P<:ParameterizedMeasure} = k.f(mapcall(k.param_maps, x)...) @@ -94,7 +91,6 @@ end # TODO: Find a way to do better than this basekernel(f) = basemeasure ∘ f - basekernel(f::Returns) = Returns(basemeasure(f.value)) # function Base.show(io::IO, μ::AbstractTransitionKernel) @@ -112,11 +108,8 @@ basekernel(f::Returns) = Returns(basemeasure(f.value)) # export kleisli - - # kernel(f, pars::NamedTuple) = ParameterizedTransitionKernel(f, pars) - # # kernel(Normal{(:μ,), Tuple{Int64}}) # function kernel(::Type{M}) where {M<:AbstractMeasure} # constructorof(M) @@ -131,6 +124,4 @@ basekernel(f::Returns) = Returns(basemeasure(f.value)) # kernel(M, nt) # end - - # kernel(k::ParameterizedTransitionKernel) = k diff --git a/src/parameterized.jl b/src/parameterized.jl index 30995e7d..5891e1f7 100644 --- a/src/parameterized.jl +++ b/src/parameterized.jl @@ -13,7 +13,7 @@ end function Pretty.tile(d::ParameterizedMeasure) result = Pretty.literal(nameof(typeof(d))) par = getfield(d, :par) - result *= Pretty.literal(sprint(show, par; context=:compact => true)) + result *= Pretty.literal(sprint(show, par; context = :compact => true)) result end @@ -49,7 +49,11 @@ end function (::Type{P})(nt::NamedTuple) where {N,P<:ParameterizedMeasure{N}} C = constructorof(P) arg = NamedTuple{N}(nt) - return C(arg)::P + return _parameterized(C, arg) +end + +function _parameterized(::Type{C}, arg::NamedTuple{N,T}) where {C,N,T} + return C(arg)::C{N,T} end function (::Type{P})(args...) where {N,P<:ParameterizedMeasure{N}} From 0e1ecf1a1d4eb9e686711661fe0a11734170492b Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 23 May 2022 15:05:56 -0700 Subject: [PATCH 261/368] cleanup --- src/combinators/smart-constructors.jl | 24 ++++++++++-------------- src/density.jl | 1 - src/parameterized.jl | 3 +-- 3 files changed, 11 insertions(+), 17 deletions(-) diff --git a/src/combinators/smart-constructors.jl b/src/combinators/smart-constructors.jl index f4d0084f..169196b7 100644 --- a/src/combinators/smart-constructors.jl +++ b/src/combinators/smart-constructors.jl @@ -122,18 +122,18 @@ function kernel(μ::M) where {M<:ParameterizedMeasure} kernel(M) end -# function kernel(d::PowerMeasure) -# Base.Fix2(powermeasure, d.axes) ∘ kernel(d.parent) -# end +function kernel(d::PowerMeasure) + Base.Fix2(powermeasure, d.axes) ∘ kernel(d.parent) +end -# function kernel(f) -# T = Core.Compiler.return_type(f, Tuple{Any} ) -# _kernel(f, T) -# end +function kernel(f) + T = Core.Compiler.return_type(f, Tuple{Any} ) + _kernel(f, T) +end -# function _kernel(f, ::Type{T}) where {T} -# GenericTransitionKernel(f) -# end +function _kernel(f, ::Type{T}) where {T} + GenericTransitionKernel(f) +end function _kernel(f, ::Type{P}) where {N,P<:ParameterizedMeasure{N}} k = length(N) @@ -145,10 +145,6 @@ function _kernel(f, ::Type{P}) where {N,P<:ParameterizedMeasure{N}} kernel(params ∘ f, C, NamedTuple{N}(maps)) end -function _kernel(f, ::Type{P}) where {N,P} - GenericTransitionKernel(f) -end - kernel(f::F, ::Type{M}; kwargs...) where {F<:Function,M} = kernel(f, M, NamedTuple(kwargs)) function kernel(f::F, ::Type{M}, nt::NamedTuple) where {F<:Function,M} diff --git a/src/density.jl b/src/density.jl index 06aa2834..1383985c 100644 --- a/src/density.jl +++ b/src/density.jl @@ -100,7 +100,6 @@ Define a new measure in terms of a log-density `f` over some measure `base`. """ ∫exp(f::Function, μ) = ∫(logfuncdensity(f), μ) -# TODO: `density` and `logdensity` functions for `DensityMeasure` """ logdensityof(m::AbstractMeasure, x) diff --git a/src/parameterized.jl b/src/parameterized.jl index 5891e1f7..ac3f537f 100644 --- a/src/parameterized.jl +++ b/src/parameterized.jl @@ -33,7 +33,6 @@ function kernel(::Type{P}) where {N,P<:ParameterizedMeasure{N}} _kernel(C, Val(N)) end -# TODO: This should return a kernel @inline function _kernel(::Type{C}, ::Val{N}) where {C,N} @inline function f(args::T) where {T<:Tuple} C(NamedTuple{N,T}(args))::C{N,T} @@ -43,7 +42,7 @@ end C(NamedTuple{N,Tuple{T}}((arg,)))::C{N,Tuple{T}} end - f + kernel(f) end function (::Type{P})(nt::NamedTuple) where {N,P<:ParameterizedMeasure{N}} From e2a1d8094ba7a244843e2fa7aa0062230ee91f10 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 23 May 2022 15:10:56 -0700 Subject: [PATCH 262/368] kernel updates --- src/kernel.jl | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/src/kernel.jl b/src/kernel.jl index 056f3e72..e5141c98 100644 --- a/src/kernel.jl +++ b/src/kernel.jl @@ -104,9 +104,9 @@ basekernel(f::Returns) = Returns(basemeasure(f.value)) # :(ParameterizedTransitionKernel($qf, $qg)) # end -# const kleisli = kernel +const kleisli = kernel -# export kleisli +export kleisli # kernel(f, pars::NamedTuple) = ParameterizedTransitionKernel(f, pars) @@ -125,3 +125,5 @@ basekernel(f::Returns) = Returns(basemeasure(f.value)) # end # kernel(k::ParameterizedTransitionKernel) = k + +kernel(k::AbstractTransitionKernel) = k \ No newline at end of file From 2392d8aba9a9b2f309e0d586de76347cea3b6874 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 23 May 2022 15:42:54 -0700 Subject: [PATCH 263/368] uncomment --- src/kernel.jl | 29 +++++++++++++---------------- 1 file changed, 13 insertions(+), 16 deletions(-) diff --git a/src/kernel.jl b/src/kernel.jl index e5141c98..66a3242f 100644 --- a/src/kernel.jl +++ b/src/kernel.jl @@ -73,20 +73,20 @@ function (k::ParameterizedTransitionKernel)(x) k.m(; mapcall(k.param_maps, s)...) end -# (k::AbstractTransitionKernel)(x1, x2, xs...) = k((x1, x2, xs...)) +(k::AbstractTransitionKernel)(x1, x2, xs...) = k((x1, x2, xs...)) -# """ -# For any `k::TransitionKernel`, `basekernel` is expected to satisfy -# ``` -# basekernel(k)(p) == (basemeasure ∘ k)(p) -# ``` - -# The main purpose of `basekernel` is to make it efficient to compute -# ``` -# basemeasure(d::ProductMeasure) = productmeasure(basekernel(d.f), d.xs) -# ``` -# """ -# function basekernel end +""" +For any `k::TransitionKernel`, `basekernel` is expected to satisfy +``` +basekernel(k)(p) == (basemeasure ∘ k)(p) +``` + +The main purpose of `basekernel` is to make it efficient to compute +``` +basemeasure(d::ProductMeasure) = productmeasure(basekernel(d.f), d.xs) +``` +""" +function basekernel end # TODO: Find a way to do better than this basekernel(f) = basemeasure ∘ f @@ -117,13 +117,10 @@ export kleisli # # kernel(::Type{P}, op::O) where {O, N, P<:ParameterizedMeasure{N}} = kernel{constructorof(P),O}(op) -# ntkeys(::Type{NT}) where {N, NT<:NamedTuple{N}} = N - # function kernel(::Type{M}; param_maps...) where {M} # nt = NamedTuple(param_maps) # kernel(M, nt) # end -# kernel(k::ParameterizedTransitionKernel) = k kernel(k::AbstractTransitionKernel) = k \ No newline at end of file From 90d4908f4051e8040714ac4f0e3f486946ee7788 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 23 May 2022 15:45:32 -0700 Subject: [PATCH 264/368] bugfix --- src/kernel.jl | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/kernel.jl b/src/kernel.jl index 66a3242f..db13ea65 100644 --- a/src/kernel.jl +++ b/src/kernel.jl @@ -104,6 +104,8 @@ basekernel(f::Returns) = Returns(basemeasure(f.value)) # :(ParameterizedTransitionKernel($qf, $qg)) # end +function kernel end + const kleisli = kernel export kleisli From dc74704e87e8fbab25236467825f17298d681d56 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 23 May 2022 16:30:38 -0700 Subject: [PATCH 265/368] drop old code --- src/kernel.jl | 5 ----- 1 file changed, 5 deletions(-) diff --git a/src/kernel.jl b/src/kernel.jl index db13ea65..64fb43a5 100644 --- a/src/kernel.jl +++ b/src/kernel.jl @@ -119,10 +119,5 @@ export kleisli # # kernel(::Type{P}, op::O) where {O, N, P<:ParameterizedMeasure{N}} = kernel{constructorof(P),O}(op) -# function kernel(::Type{M}; param_maps...) where {M} -# nt = NamedTuple(param_maps) -# kernel(M, nt) -# end - kernel(k::AbstractTransitionKernel) = k \ No newline at end of file From 71be3c5203b1cec732864906ae80991391faa436 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 23 May 2022 16:52:11 -0700 Subject: [PATCH 266/368] pretty printing --- src/kernel.jl | 63 ++++++++++++++++++++++++++++----------------------- 1 file changed, 35 insertions(+), 28 deletions(-) diff --git a/src/kernel.jl b/src/kernel.jl index 64fb43a5..12be071d 100644 --- a/src/kernel.jl +++ b/src/kernel.jl @@ -6,7 +6,6 @@ struct GenericTransitionKernel{F} <: AbstractTransitionKernel end (k::GenericTransitionKernel)(x) = k.f(x) -(k::GenericTransitionKernel)(x1, x2, xs...) = k.f((x1, x2, xs...)) struct TypedTransitionKernel{M,F} <: AbstractTransitionKernel m::M @@ -35,26 +34,34 @@ struct ParameterizedTransitionKernel{M,S,N,T} <: AbstractTransitionKernel end end -# """ -# kernel(f, M) -# kernel((f1, f2, ...), M) +""" +A *kernel* is a function that returns a measure. + + k1 = kernel() do x + Normal(x, x^2) + end + + k2 = kernel(Normal) do x + (μ = x, σ = x^2) + end + + k3 = kernel(Normal; μ = identity, σ = abs2) -# A kernel `κ = kernel(f, m)` returns a wrapper around a function `f` giving the -# parameters for a measure of type `M`, such that `κ(x) = M(f(x)...)` respective -# `κ(x) = M(f1(x), f2(x), ...)` + k4 = kernel(Normal; μ = first, σ = last) do x + (x, x^2) + end -# If the argument is a named tuple `(;a=f1, b=f1)`, `κ(x)` is defined as -# `M(;a=f(x),b=g(x))`. + x = randn(); k1(x) == k2(x) == k3(x) == k4(x) -# This function is not exported, because "kernel" can have so many other meanings. -# See for example https://github.com/JuliaGaussianProcesses/KernelFunctions.jl for -# another common use of this term. +This function is not exported, because "kernel" can have so many other meanings. +See for example https://github.com/JuliaGaussianProcesses/KernelFunctions.jl for +another common use of this term. -# # Reference +# Reference -# * https://en.wikipedia.org/wiki/Markov_kernel -# """ -# function kernel end +* https://en.wikipedia.org/wiki/Markov_kernel +""" +function kernel end # # kernel(Normal) do x # # (μ=x,σ=x^2) @@ -75,6 +82,9 @@ end (k::AbstractTransitionKernel)(x1, x2, xs...) = k((x1, x2, xs...)) +(k::AbstractTransitionKernel)(;kwargs...) = k(NamedTuple(kwargs)) + + """ For any `k::TransitionKernel`, `basekernel` is expected to satisfy ``` @@ -83,7 +93,7 @@ basekernel(k)(p) == (basemeasure ∘ k)(p) The main purpose of `basekernel` is to make it efficient to compute ``` -basemeasure(d::ProductMeasure) = productmeasure(basekernel(d.f), d.xs) +basemeasure(d::ProductMeasure) == productmeasure(basekernel(d.f), d.xs) ``` """ function basekernel end @@ -93,18 +103,15 @@ basekernel(f) = basemeasure ∘ f basekernel(f::Returns) = Returns(basemeasure(f.value)) -# function Base.show(io::IO, μ::AbstractTransitionKernel) -# io = IOContext(io, :compact => true) -# Pretty.pprint(io, μ) -# end +function Base.show(io::IO, μ::AbstractTransitionKernel) + io = IOContext(io, :compact => true) + Pretty.pprint(io, μ) +end -# function Pretty.quoteof(k::ParameterizedTransitionKernel) -# qf = Pretty.quoteof(k.f) -# qg = Pretty.quoteof(k.param_maps) -# :(ParameterizedTransitionKernel($qf, $qg)) -# end +function Pretty.tile(k::K) where {K<:AbstractTransitionKernel} + Pretty.list_layout(Pretty.tile.([getproperty(k, p) for p in propertynames(k)]), prefix=nameof(constructorof(K))) +end -function kernel end const kleisli = kernel @@ -120,4 +127,4 @@ export kleisli # # kernel(::Type{P}, op::O) where {O, N, P<:ParameterizedMeasure{N}} = kernel{constructorof(P),O}(op) -kernel(k::AbstractTransitionKernel) = k \ No newline at end of file +kernel(k::AbstractTransitionKernel) = k From 51d15a99d98a74fe430162b9dc376327d0701147 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 24 May 2022 06:02:41 -0700 Subject: [PATCH 267/368] exports, cleanup --- src/kernel.jl | 31 ++++++++----------------------- 1 file changed, 8 insertions(+), 23 deletions(-) diff --git a/src/kernel.jl b/src/kernel.jl index 12be071d..e3c81426 100644 --- a/src/kernel.jl +++ b/src/kernel.jl @@ -1,4 +1,6 @@ -# TODO: Dangerous to export this - let's not +export AbstractTransitionKernel, + GenericTransitionKernel, TypedTransitionKernel, ParameterizedTransitionKernel + abstract type AbstractTransitionKernel <: AbstractMeasure end struct GenericTransitionKernel{F} <: AbstractTransitionKernel @@ -63,18 +65,8 @@ another common use of this term. """ function kernel end -# # kernel(Normal) do x -# # (μ=x,σ=x^2) -# # end - -# function _kernel(::Type{M}, f::F, ::Type{T}) where {M,F<:Function,T} -# TypedTransitionKernel{Type{M},F}(M,f) -# end - mapcall(t, x) = map(func -> func(x), t) -# # (k::TransitionKernel{Type{P},<:Tuple})(x) where {P<:ParameterizedMeasure} = k.f(mapcall(k.param_maps, x)...) - function (k::ParameterizedTransitionKernel)(x) s = k.suff(x) k.m(; mapcall(k.param_maps, s)...) @@ -82,7 +74,7 @@ end (k::AbstractTransitionKernel)(x1, x2, xs...) = k((x1, x2, xs...)) -(k::AbstractTransitionKernel)(;kwargs...) = k(NamedTuple(kwargs)) +(k::AbstractTransitionKernel)(; kwargs...) = k(NamedTuple(kwargs)) """ @@ -109,7 +101,10 @@ function Base.show(io::IO, μ::AbstractTransitionKernel) end function Pretty.tile(k::K) where {K<:AbstractTransitionKernel} - Pretty.list_layout(Pretty.tile.([getproperty(k, p) for p in propertynames(k)]), prefix=nameof(constructorof(K))) + Pretty.list_layout( + Pretty.tile.([getproperty(k, p) for p in propertynames(k)]), + prefix = nameof(constructorof(K)), + ) end @@ -117,14 +112,4 @@ const kleisli = kernel export kleisli -# kernel(f, pars::NamedTuple) = ParameterizedTransitionKernel(f, pars) - -# # kernel(Normal{(:μ,), Tuple{Int64}}) -# function kernel(::Type{M}) where {M<:AbstractMeasure} -# constructorof(M) -# end - -# # kernel(::Type{P}, op::O) where {O, N, P<:ParameterizedMeasure{N}} = kernel{constructorof(P),O}(op) - - kernel(k::AbstractTransitionKernel) = k From 79dd2341ea239c8a7195194397f88230f69d41d7 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 24 May 2022 06:27:14 -0700 Subject: [PATCH 268/368] drop old for.jl --- src/combinators/for.jl | 1 - 1 file changed, 1 deletion(-) delete mode 100644 src/combinators/for.jl diff --git a/src/combinators/for.jl b/src/combinators/for.jl deleted file mode 100644 index 8b137891..00000000 --- a/src/combinators/for.jl +++ /dev/null @@ -1 +0,0 @@ - From 370c8d1aa46bf1ee131450a2267596e2385f7032 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 24 May 2022 06:28:01 -0700 Subject: [PATCH 269/368] Make DensityKind(::AbstractLikelihood) = IsDensity() --- src/combinators/likelihood.jl | 16 ++++++++++++---- src/combinators/pointwise.jl | 4 ++-- 2 files changed, 14 insertions(+), 6 deletions(-) diff --git a/src/combinators/likelihood.jl b/src/combinators/likelihood.jl index 871a841c..0c8c7dcb 100644 --- a/src/combinators/likelihood.jl +++ b/src/combinators/likelihood.jl @@ -121,6 +121,8 @@ struct Likelihood{K,X} <: AbstractLikelihood Likelihood(μ, x) = Likelihood(kernel(μ), x) end +DensityInterface.DensityKind(::AbstractLikelihood) = IsDensity() + function Pretty.quoteof(ℓ::Likelihood) k = Pretty.quoteof(ℓ.k) x = Pretty.quoteof(ℓ.x) @@ -132,11 +134,17 @@ function Base.show(io::IO, ℓ::Likelihood) Pretty.pprint(io, ℓ) end -# @inline function logdensity_def(ℓ::Likelihood, p) -# return logdensity_def(ℓ.k(p), ℓ.x) -# end +insupport(ℓ::AbstractLikelihood, p) = insupport(ℓ.k(p), ℓ.x) + +@inline function logdensityof(ℓ::AbstractLikelihood, p) + result = dynamic(unsafe_logdensityof(ℓ, p)) + ifelse(insupport(ℓ, p) == true, result, oftype(result, -Inf)) +end + +@inline function unsafe_logdensityof(ℓ::AbstractLikelihood, p) + return unsafe_logdensityof(ℓ.k(p), ℓ.x) +end -# basemeasure(ℓ::Likelihood, p) = basemeasure(ℓ.k(p), ℓ.x) # basemeasure(ℓ::Likelihood) = @error "Likelihood requires local base measure" diff --git a/src/combinators/pointwise.jl b/src/combinators/pointwise.jl index f6268188..25211fe6 100644 --- a/src/combinators/pointwise.jl +++ b/src/combinators/pointwise.jl @@ -15,12 +15,12 @@ end @inbounds function insupport(d::PointwiseProductMeasure, p) prior, ℓ = d - insupport(prior, p) && insupport(ℓ.k(p), ℓ.x) + insupport(prior, p) && insupport(ℓ, p) end @inline function logdensity_def(d::PointwiseProductMeasure, p) prior, ℓ = d - unsafe_logdensityof(ℓ.k(p), ℓ.x) + unsafe_logdensityof(ℓ, p) end basemeasure(d::PointwiseProductMeasure) = d.prior From c2fa848f8509ab42c79131300528cc5da675be66 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 24 May 2022 06:33:28 -0700 Subject: [PATCH 270/368] update Compat version --- Project.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Project.toml b/Project.toml index b492f7a4..80d345ad 100644 --- a/Project.toml +++ b/Project.toml @@ -23,7 +23,7 @@ Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" Tricks = "410a4b4d-49e4-4fbc-ab6d-cb71b17b3775" [compat] -Compat = "3.35" +Compat = "3.35, 4" ConstructionBase = "1.3" DensityInterface = "0.4" FillArrays = "0.12, 0.13" From 5b325819d1209efdbfbeb534746287e52c4c3e9b Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 24 May 2022 12:37:50 -0700 Subject: [PATCH 271/368] Make likelihoods work with Distributions --- Project.toml | 2 +- src/combinators/likelihood.jl | 4 +--- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/Project.toml b/Project.toml index f4b303cb..5d3cb105 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "MeasureBase" uuid = "fa1605e6-acd5-459c-a1e6-7e635759db14" authors = ["Chad Scherrer and contributors"] -version = "0.9.0" +version = "0.9.1" [deps] Compat = "34da2185-b29b-5c13-b0c7-acf172513d20" diff --git a/src/combinators/likelihood.jl b/src/combinators/likelihood.jl index 0c8c7dcb..66ddf6fe 100644 --- a/src/combinators/likelihood.jl +++ b/src/combinators/likelihood.jl @@ -137,15 +137,13 @@ end insupport(ℓ::AbstractLikelihood, p) = insupport(ℓ.k(p), ℓ.x) @inline function logdensityof(ℓ::AbstractLikelihood, p) - result = dynamic(unsafe_logdensityof(ℓ, p)) - ifelse(insupport(ℓ, p) == true, result, oftype(result, -Inf)) + logdensityof(ℓ.k(p), ℓ.x) end @inline function unsafe_logdensityof(ℓ::AbstractLikelihood, p) return unsafe_logdensityof(ℓ.k(p), ℓ.x) end - # basemeasure(ℓ::Likelihood) = @error "Likelihood requires local base measure" export likelihood From 4cb7e167248d665eb762424c43a176992871ed03 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 31 May 2022 19:15:07 -0700 Subject: [PATCH 272/368] _map(f, x::MappedArrays.ReadonlyMappedArray) --- src/combinators/product.jl | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/src/combinators/product.jl b/src/combinators/product.jl index 205e5331..877d21ab 100644 --- a/src/combinators/product.jl +++ b/src/combinators/product.jl @@ -157,7 +157,11 @@ end marginals(μ::ProductMeasure) = μ.marginals -testvalue(d::AbstractProductMeasure) = map(testvalue, marginals(d)) +# TODO: Better `map` support in MappedArrays +_map(f, args...) = map(f, args...) +_map(f, x::MappedArrays.ReadonlyMappedArray) = mappedarray(f ∘ x.f, x.data) + +testvalue(d::AbstractProductMeasure) = _map(testvalue, marginals(d)) export ⊗ From 8a6ef5c11ef35b326aad6450f86aa73cf9e1ac3d Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 1 Jun 2022 05:18:39 -0700 Subject: [PATCH 273/368] export productmeasure --- src/MeasureBase.jl | 1 + 1 file changed, 1 insertion(+) diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index 3cb735d0..63cd58ae 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -33,6 +33,7 @@ import IfElse: ifelse export logdensity_def export basemeasure export basekernel +export productmeasure """ inssupport(m, x) From e8a1be5bc63c7475d1bda019fa8a946c6c53994d Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Thu, 4 Aug 2022 11:59:02 -0700 Subject: [PATCH 274/368] AbstractMeasure(::AbstractMeasure) --- src/MeasureBase.jl | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index f2140846..35443833 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -59,6 +59,8 @@ include("insupport.jl") abstract type AbstractMeasure end +AbstractMeasure(m::AbstractMeasure) = m + using Static: @constprop function Pretty.quoteof(d::M) where {M<:AbstractMeasure} From d260e61b1bcc8eee31e324a08a5bcd823600bdbc Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Sun, 11 Sep 2022 16:44:30 -0700 Subject: [PATCH 275/368] fixedrng --- src/fixedrng.jl | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 src/fixedrng.jl diff --git a/src/fixedrng.jl b/src/fixedrng.jl new file mode 100644 index 00000000..232b0891 --- /dev/null +++ b/src/fixedrng.jl @@ -0,0 +1,19 @@ +export FixedRNG +struct FixedRNG <: AbstractRNG end + +Base.rand(::FixedRNG) = one(Float64) / 2 +Random.randn(::FixedRNG) = zero(Float64) +Random.randexp(::FixedRNG) = one(Float64) + +Base.rand(::FixedRNG, ::Type{T}) where {T<:Real} = one(T) / 2 +Random.randn(::FixedRNG, ::Type{T}) where {T<:Real} = zero(T) +Random.randexp(::FixedRNG, ::Type{T}) where {T<:Real} = one(T) + +# We need concrete type parameters to avoid amiguity for these cases +for T in [Float16, Float32, Float64] + @eval begin + Base.rand(::FixedRNG, ::Type{$T}) = one($T) / 2 + Random.randn(::FixedRNG, ::Type{$T}) = zero($T) + Random.randexp(::FixedRNG, ::Type{$T}) = one($T) + end +end From 3bd74a0e4cadeac2de276da7e2f6c8c55ed83d1f Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Sun, 11 Sep 2022 16:51:56 -0700 Subject: [PATCH 276/368] StdNormal --- src/standard/stdnormal.jl | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 src/standard/stdnormal.jl diff --git a/src/standard/stdnormal.jl b/src/standard/stdnormal.jl new file mode 100644 index 00000000..38b5ad7f --- /dev/null +++ b/src/standard/stdnormal.jl @@ -0,0 +1,18 @@ +struct StdNormal <: MeasureBase.StdMeasure end + +export StdNormal + +@inline MeasureBase.insupport(d::StdNormal, x) = true + +@inline MeasureBase.logdensity_def(::StdNormal, x) = -x^2 / 2 +@inline MeasureBase.basemeasure(::StdNormal) = WeightedMeasure(static(-0.5 * log2π), Lebesgue(ℝ)) + +@inline MeasureBase.getdof(::StdNormal) = static(1) + +@inline MeasureBase.transport_def(::StdUniform, μ::StdNormal, x) = StatsFuns.normcdf(x) +@inline MeasureBase.transport_def(::StdNormal, μ::StdUniform, x) = StatsFuns.norminvcdf(x) + +@inline Base.rand(rng::Random.AbstractRNG, ::Type{T}, ::StdNormal) where {T} = randn(rng, T) + + +@inline MeasureBase.StdMeasure(::typeof(randn)) = StdNormal() \ No newline at end of file From d309637790dc49a5e56bc2942f90803b297fe0e9 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Sun, 11 Sep 2022 16:52:12 -0700 Subject: [PATCH 277/368] add SpecialFunctions --- Project.toml | 1 + 1 file changed, 1 insertion(+) diff --git a/Project.toml b/Project.toml index 1c3f5c85..7ab9d020 100644 --- a/Project.toml +++ b/Project.toml @@ -21,6 +21,7 @@ NaNMath = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3" PrettyPrinting = "54e16d92-306c-5ea0-a30b-337be88ac337" Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" Reexport = "189a3867-3050-52da-a836-e630ba90ab69" +SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b" Static = "aedffcd0-7271-4cad-89d0-dc628f76c6d3" Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" From 1b9cec91087fd31cc2bea310b5262e6190be3a6e Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Sun, 11 Sep 2022 16:54:51 -0700 Subject: [PATCH 278/368] no need to qualify --- src/standard/stdnormal.jl | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/src/standard/stdnormal.jl b/src/standard/stdnormal.jl index 38b5ad7f..72c4e510 100644 --- a/src/standard/stdnormal.jl +++ b/src/standard/stdnormal.jl @@ -1,18 +1,18 @@ -struct StdNormal <: MeasureBase.StdMeasure end +struct StdNormal <: StdMeasure end export StdNormal -@inline MeasureBase.insupport(d::StdNormal, x) = true +@inline insupport(d::StdNormal, x) = true -@inline MeasureBase.logdensity_def(::StdNormal, x) = -x^2 / 2 -@inline MeasureBase.basemeasure(::StdNormal) = WeightedMeasure(static(-0.5 * log2π), Lebesgue(ℝ)) +@inline logdensity_def(::StdNormal, x) = -x^2 / 2 +@inline basemeasure(::StdNormal) = WeightedMeasure(static(-0.5 * log2π), Lebesgue(ℝ)) -@inline MeasureBase.getdof(::StdNormal) = static(1) +@inline getdof(::StdNormal) = static(1) -@inline MeasureBase.transport_def(::StdUniform, μ::StdNormal, x) = StatsFuns.normcdf(x) -@inline MeasureBase.transport_def(::StdNormal, μ::StdUniform, x) = StatsFuns.norminvcdf(x) +@inline transport_def(::StdUniform, μ::StdNormal, x) = StatsFuns.normcdf(x) +@inline transport_def(::StdNormal, μ::StdUniform, x) = StatsFuns.norminvcdf(x) @inline Base.rand(rng::Random.AbstractRNG, ::Type{T}, ::StdNormal) where {T} = randn(rng, T) -@inline MeasureBase.StdMeasure(::typeof(randn)) = StdNormal() \ No newline at end of file +@inline StdMeasure(::typeof(randn)) = StdNormal() \ No newline at end of file From aa22bef77b3f566f178344ce3bc8760e46ab9d43 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Sun, 11 Sep 2022 16:55:39 -0700 Subject: [PATCH 279/368] update basemeasure --- src/standard/stdnormal.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/standard/stdnormal.jl b/src/standard/stdnormal.jl index 72c4e510..f525aca6 100644 --- a/src/standard/stdnormal.jl +++ b/src/standard/stdnormal.jl @@ -5,7 +5,7 @@ export StdNormal @inline insupport(d::StdNormal, x) = true @inline logdensity_def(::StdNormal, x) = -x^2 / 2 -@inline basemeasure(::StdNormal) = WeightedMeasure(static(-0.5 * log2π), Lebesgue(ℝ)) +@inline basemeasure(::StdNormal) = WeightedMeasure(static(-0.5 * log2π), LebesgueMeasure()) @inline getdof(::StdNormal) = static(1) From 249b74e14aa1050c9fb559ba29c0ecae2f54d62d Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Sun, 11 Sep 2022 16:57:18 -0700 Subject: [PATCH 280/368] include stdnormal --- src/MeasureBase.jl | 1 + 1 file changed, 1 insertion(+) diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index b8e71555..41b1e250 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -144,6 +144,7 @@ include("standard/stdmeasure.jl") include("standard/stduniform.jl") include("standard/stdexponential.jl") include("standard/stdlogistic.jl") +include("standard/stdnormal.jl") include("latent-joint.jl") include("rand.jl") From ed83e128511ed5e089a9ddfe35806bf060089a67 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Sun, 11 Sep 2022 16:58:01 -0700 Subject: [PATCH 281/368] include fixedrng --- src/MeasureBase.jl | 1 + 1 file changed, 1 insertion(+) diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index 41b1e250..29d88139 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -148,6 +148,7 @@ include("standard/stdnormal.jl") include("latent-joint.jl") include("rand.jl") +include("fixedrng.jl") include("density.jl") From f60f85e12b3da5c9a0495af4fbf89a78691503f7 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Sun, 11 Sep 2022 16:59:18 -0700 Subject: [PATCH 282/368] update tests --- test/transport.jl | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/test/transport.jl b/test/transport.jl index da6377e5..70e1cd31 100644 --- a/test/transport.jl +++ b/test/transport.jl @@ -1,12 +1,12 @@ using Test using MeasureBase.Interface: transport_to, test_transport -using MeasureBase: StdUniform, StdExponential, StdLogistic +using MeasureBase: StdUniform, StdExponential, StdLogistic, StdNormal using MeasureBase: Dirac @testset "transport_to" begin - for μ0 in [StdUniform(), StdExponential(), StdLogistic()], - ν0 in [StdUniform(), StdExponential(), StdLogistic()] + for μ0 in [StdUniform(), StdExponential(), StdLogistic(), StdNormal()], + ν0 in [StdUniform(), StdExponential(), StdLogistic(), StdNormal()] @testset "transport_to (variations of) $(nameof(typeof(μ0))) to $(nameof(typeof(ν0)))" begin test_transport(ν0, μ0) From 4765887d312a0fec0bfdfdfd59d4fdc1c35849cb Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Sun, 11 Sep 2022 17:02:57 -0700 Subject: [PATCH 283/368] using SpecialFunctions --- Project.toml | 1 + src/standard/stdnormal.jl | 2 ++ 2 files changed, 3 insertions(+) diff --git a/Project.toml b/Project.toml index 7ab9d020..626e0f94 100644 --- a/Project.toml +++ b/Project.toml @@ -43,6 +43,7 @@ MappedArrays = "0.4" NaNMath = "0.3, 1" PrettyPrinting = "0.3, 0.4" Reexport = "1" +SpecialFunctions = "2" Static = "0.5, 0.6" Tricks = "0.1" julia = "1.3" diff --git a/src/standard/stdnormal.jl b/src/standard/stdnormal.jl index f525aca6..0fbe0b3c 100644 --- a/src/standard/stdnormal.jl +++ b/src/standard/stdnormal.jl @@ -1,3 +1,5 @@ +using SpecialFunctions + struct StdNormal <: StdMeasure end export StdNormal From 88e1ced872eb3cd13e75ed1703054b37ac956b08 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Sun, 11 Sep 2022 17:36:39 -0700 Subject: [PATCH 284/368] fixing transport_def --- src/standard/stdnormal.jl | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/src/standard/stdnormal.jl b/src/standard/stdnormal.jl index 0fbe0b3c..7d59a30d 100644 --- a/src/standard/stdnormal.jl +++ b/src/standard/stdnormal.jl @@ -1,4 +1,5 @@ -using SpecialFunctions +using SpecialFunctions: erfc, erfcinv +using IrrationalConstants: invsqrt2 struct StdNormal <: StdMeasure end @@ -11,10 +12,10 @@ export StdNormal @inline getdof(::StdNormal) = static(1) -@inline transport_def(::StdUniform, μ::StdNormal, x) = StatsFuns.normcdf(x) -@inline transport_def(::StdNormal, μ::StdUniform, x) = StatsFuns.norminvcdf(x) +@inline transport_def(::StdUniform, μ::StdNormal, x) = erfc(-z * invsqrt2) / 2 +@inline transport_def(::StdNormal, μ::StdUniform, x) = -erfcinv(2*p) * sqrt2 @inline Base.rand(rng::Random.AbstractRNG, ::Type{T}, ::StdNormal) where {T} = randn(rng, T) -@inline StdMeasure(::typeof(randn)) = StdNormal() \ No newline at end of file +@inline StdMeasure(::typeof(randn)) = StdNormal() From 023f3a44f98b5f0ad3212b653c2b50ea9054002c Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Sun, 11 Sep 2022 18:53:49 -0700 Subject: [PATCH 285/368] transport_def bugfix --- src/standard/stdnormal.jl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/standard/stdnormal.jl b/src/standard/stdnormal.jl index 7d59a30d..25e2a4ff 100644 --- a/src/standard/stdnormal.jl +++ b/src/standard/stdnormal.jl @@ -12,8 +12,8 @@ export StdNormal @inline getdof(::StdNormal) = static(1) -@inline transport_def(::StdUniform, μ::StdNormal, x) = erfc(-z * invsqrt2) / 2 -@inline transport_def(::StdNormal, μ::StdUniform, x) = -erfcinv(2*p) * sqrt2 +@inline transport_def(::StdUniform, μ::StdNormal, x) = erfc(-x * invsqrt2) / 2 +@inline transport_def(::StdNormal, μ::StdUniform, p) = -erfcinv(2*p) * sqrt2 @inline Base.rand(rng::Random.AbstractRNG, ::Type{T}, ::StdNormal) where {T} = randn(rng, T) From 7c6e4309e4f6bf08e99010bf537911f66e7660b5 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Sun, 11 Sep 2022 19:21:45 -0700 Subject: [PATCH 286/368] StdMeasure(::typeof(randn)) --- src/standard/stdmeasure.jl | 1 + src/standard/stdnormal.jl | 1 - 2 files changed, 1 insertion(+), 1 deletion(-) diff --git a/src/standard/stdmeasure.jl b/src/standard/stdmeasure.jl index 5af72106..59c21026 100644 --- a/src/standard/stdmeasure.jl +++ b/src/standard/stdmeasure.jl @@ -2,6 +2,7 @@ abstract type StdMeasure <: AbstractMeasure end StdMeasure(::typeof(rand)) = StdUniform() StdMeasure(::typeof(randexp)) = StdExponential() +StdMeasure(::typeof(randn)) = StdNormal() @inline check_dof(::StdMeasure, ::StdMeasure) = nothing diff --git a/src/standard/stdnormal.jl b/src/standard/stdnormal.jl index 25e2a4ff..f54c102c 100644 --- a/src/standard/stdnormal.jl +++ b/src/standard/stdnormal.jl @@ -18,4 +18,3 @@ export StdNormal @inline Base.rand(rng::Random.AbstractRNG, ::Type{T}, ::StdNormal) where {T} = randn(rng, T) -@inline StdMeasure(::typeof(randn)) = StdNormal() From d3f0076673d8feecb9ff116b5877d6333a9946ac Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Sun, 11 Sep 2022 19:50:02 -0700 Subject: [PATCH 287/368] checked_arg for LebesgueMeasure --- src/primitives/lebesgue.jl | 1 + 1 file changed, 1 insertion(+) diff --git a/src/primitives/lebesgue.jl b/src/primitives/lebesgue.jl index 52844708..c1aa8306 100644 --- a/src/primitives/lebesgue.jl +++ b/src/primitives/lebesgue.jl @@ -44,6 +44,7 @@ logdensity_def(::CountingMeasure, ::LebesgueMeasure, x) = Inf @inline getdof(::Lebesgue) = static(1) @inline checked_arg(::Lebesgue, x::Real) = x +@inline checked_arg(::LebesgueMeasure, x::Real) = x @propagate_inbounds function checked_arg(::Lebesgue, x::Any) @boundscheck throw(ArgumentError("Invalid variate type for measure")) From 7bfc18970fa534d24733563a3c03a5a9b494c4cd Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 13 Sep 2022 12:42:47 -0700 Subject: [PATCH 288/368] NoTransformOrigin => NoTransportOrigin --- src/transport.jl | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/src/transport.jl b/src/transport.jl index 08a6721c..652ddfcd 100644 --- a/src/transport.jl +++ b/src/transport.jl @@ -1,12 +1,12 @@ """ - struct MeasureBase.NoTransformOrigin{NU} + struct MeasureBase.NoTransportOrigin{NU} Indicates that no (default) pullback measure is available for measures of type `NU`. See [`MeasureBase.transport_origin`](@ref). """ -struct NoTransformOrigin{NU} end +struct NoTransportOrigin{NU} end """ MeasureBase.transport_origin(ν) @@ -16,7 +16,7 @@ between `ν` and another measure. """ function transport_origin end -transport_origin(ν::NU) where {NU} = NoTransformOrigin{NU}() +transport_origin(ν::NU) where {NU} = NoTransportOrigin{NU}() """ MeasureBase.from_origin(ν, x) @@ -25,7 +25,7 @@ Push `x` from `MeasureBase.transport_origin(μ)` forward to `ν`. """ function from_origin end -from_origin(ν::NU, ::Any) where {NU} = NoTransformOrigin{NU}() +from_origin(ν::NU, ::Any) where {NU} = NoTransportOrigin{NU}() """ MeasureBase.to_origin(ν, y) @@ -34,7 +34,7 @@ Pull `y` from `ν` back to `MeasureBase.transport_origin(ν)`. """ function to_origin end -to_origin(ν::NU, ::Any) where {NU} = NoTransformOrigin{NU}(ν) +to_origin(ν::NU, ::Any) where {NU} = NoTransportOrigin{NU}(ν) """ struct MeasureBase.NoTransport{NU,MU} end @@ -62,7 +62,7 @@ The resulting function `f` should support so that densities of `ν` can be derived from densities of `μ` via `f` (using appropriate base measures). -Returns NoTransformOrigin{typeof(ν),typeof(μ)} if no transformation from +Returns NoTransportOrigin{typeof(ν),typeof(μ)} if no transformation from `μ` to `ν` can be found. To add transformation rules for a measure type `MyMeasure`, specialize @@ -113,7 +113,7 @@ See [`transport_to`](@ref). """ function transport_def end -transport_def(::Any, ::Any, x::NoTransformOrigin) = x +transport_def(::Any, ::Any, x::NoTransportOrigin) = x transport_def(::Any, ::Any, x::NoTransport) = x function transport_def(ν, μ, x) @@ -144,20 +144,20 @@ function _transport_with_intermediate(ν, ν_o, μ_o, μ, x) return y end -function _transport_with_intermediate(ν, ν_o, ::NoTransformOrigin, μ, x) +function _transport_with_intermediate(ν, ν_o, ::NoTransportOrigin, μ, x) y_o = transport_def(ν_o, μ, x) y = from_origin(ν, y_o) return y end -function _transport_with_intermediate(ν, ::NoTransformOrigin, μ_o, μ, x) +function _transport_with_intermediate(ν, ::NoTransportOrigin, μ_o, μ, x) x_o = to_origin(μ, x) # If μ is a pushforward then checked_arg may have been bypassed, so check now: y = transport_def(ν, μ_o, checked_arg(μ_o, x_o)) return y end -function _transport_with_intermediate(ν, ::NoTransformOrigin, ::NoTransformOrigin, μ, x) +function _transport_with_intermediate(ν, ::NoTransportOrigin, ::NoTransportOrigin, μ, x) _transport_with_intermediate(ν, _transport_intermediate(ν, μ), μ, x) end From 07d2de83c4b13d33f9120151131d5f51e61f9d9f Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 13 Sep 2022 13:01:20 -0700 Subject: [PATCH 289/368] transport interface for pushforwards --- src/combinators/transformedmeasure.jl | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/src/combinators/transformedmeasure.jl b/src/combinators/transformedmeasure.jl index 35baf32d..bc7b57da 100644 --- a/src/combinators/transformedmeasure.jl +++ b/src/combinators/transformedmeasure.jl @@ -31,9 +31,31 @@ struct PushforwardMeasure{FF,IF,M,VC<:TransformVolCorr} <: AbstractPushforward volcorr::VC end + gettransform(ν::PushforwardMeasure) = ν.f parent(ν::PushforwardMeasure) = ν.origin +transport_origin(μ::PushforwardMeasure) = transport_origin(parent(μ)) + +from_origin(μ::PushforwardMeasure, x) = μ.f(from_origin(parent(μ), x)) +to_origin(μ::PushforwardMeasure, y) = μ.inv_f(to_origin(parent(f), y)) + +transport_def(ν::PushforwardMeasure{FF,IF,M}, μ::M, x) where {FF,IF,M} + if μ == parent(ν) + return ν.f(x) + else + invoke(transport_def, Tuple{Any, Any, Any}, ν, μ, x) + end +end + +transport_def(μ::M, ν::PushforwardMeasure{FF,IF,M}, y) where {FF,IF,M} + if μ == parent(ν) + return ν.inv_f(x) + else + invoke(transport_def, Tuple{Any, Any, Any}, μ, ν, x) + end +end + function Pretty.tile(ν::PushforwardMeasure) Pretty.list_layout(Pretty.tile.([ν.f, ν.inv_f, ν.origin]); prefix = :PushforwardMeasure) end From 1d52b132645d76f8bb3ab645be50c1242d2fc02e Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 13 Sep 2022 13:29:40 -0700 Subject: [PATCH 290/368] transporting pushforwards --- src/combinators/transformedmeasure.jl | 8 ++++---- test/transport.jl | 10 ++++++++++ 2 files changed, 14 insertions(+), 4 deletions(-) diff --git a/src/combinators/transformedmeasure.jl b/src/combinators/transformedmeasure.jl index bc7b57da..a11c3d6d 100644 --- a/src/combinators/transformedmeasure.jl +++ b/src/combinators/transformedmeasure.jl @@ -40,7 +40,7 @@ transport_origin(μ::PushforwardMeasure) = transport_origin(parent(μ)) from_origin(μ::PushforwardMeasure, x) = μ.f(from_origin(parent(μ), x)) to_origin(μ::PushforwardMeasure, y) = μ.inv_f(to_origin(parent(f), y)) -transport_def(ν::PushforwardMeasure{FF,IF,M}, μ::M, x) where {FF,IF,M} +function transport_def(ν::PushforwardMeasure{FF,IF,M}, μ::M, x) where {FF,IF,M} if μ == parent(ν) return ν.f(x) else @@ -48,11 +48,11 @@ transport_def(ν::PushforwardMeasure{FF,IF,M}, μ::M, x) where {FF,IF,M} end end -transport_def(μ::M, ν::PushforwardMeasure{FF,IF,M}, y) where {FF,IF,M} +function transport_def(μ::M, ν::PushforwardMeasure{FF,IF,M}, y) where {FF,IF,M} if μ == parent(ν) - return ν.inv_f(x) + return ν.inv_f(y) else - invoke(transport_def, Tuple{Any, Any, Any}, μ, ν, x) + invoke(transport_def, Tuple{Any, Any, Any}, μ, ν, y) end end diff --git a/test/transport.jl b/test/transport.jl index 70e1cd31..2ee12ed5 100644 --- a/test/transport.jl +++ b/test/transport.jl @@ -3,8 +3,18 @@ using Test using MeasureBase.Interface: transport_to, test_transport using MeasureBase: StdUniform, StdExponential, StdLogistic, StdNormal using MeasureBase: Dirac +using LogExpFunctions: logit @testset "transport_to" begin + for (f, μ) in [ + (logit, StdUniform()) + (log, StdExponential()) + (cbrt, StdNormal()) + ] + test_transport(μ, pushfwd(f, μ)) + test_transport(pushfwd(f, μ), μ) + end + for μ0 in [StdUniform(), StdExponential(), StdLogistic(), StdNormal()], ν0 in [StdUniform(), StdExponential(), StdLogistic(), StdNormal()] From af88a149e71190a59e4937d0cca4f2989b62be6d Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 13 Sep 2022 13:46:50 -0700 Subject: [PATCH 291/368] Use LebesgueMeasure for basemeasure --- src/standard/stdexponential.jl | 2 +- src/standard/stdlogistic.jl | 2 +- src/standard/stduniform.jl | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/standard/stdexponential.jl b/src/standard/stdexponential.jl index b038c587..f22f5038 100644 --- a/src/standard/stdexponential.jl +++ b/src/standard/stdexponential.jl @@ -5,7 +5,7 @@ export StdExponential insupport(d::StdExponential, x) = x ≥ zero(x) @inline logdensity_def(::StdExponential, x) = -x -@inline basemeasure(::StdExponential) = Lebesgue() +@inline basemeasure(::StdExponential) = LebesgueMeasure() @inline transport_def(::StdUniform, μ::StdExponential, x) = -expm1(-x) @inline transport_def(::StdExponential, μ::StdUniform, x) = -log1p(-x) diff --git a/src/standard/stdlogistic.jl b/src/standard/stdlogistic.jl index 31aa70f7..c246d5ec 100644 --- a/src/standard/stdlogistic.jl +++ b/src/standard/stdlogistic.jl @@ -5,7 +5,7 @@ export StdLogistic @inline insupport(d::StdLogistic, x) = true @inline logdensity_def(::StdLogistic, x) = (u = -abs(x); u - 2 * log1pexp(u)) -@inline basemeasure(::StdLogistic) = Lebesgue() +@inline basemeasure(::StdLogistic) = LebesgueMeasure() @inline transport_def(::StdUniform, μ::StdLogistic, x) = logistic(x) @inline transport_def(::StdLogistic, μ::StdUniform, x) = logit(x) diff --git a/src/standard/stduniform.jl b/src/standard/stduniform.jl index d29dce80..9cbc2b7b 100644 --- a/src/standard/stduniform.jl +++ b/src/standard/stduniform.jl @@ -5,6 +5,6 @@ export StdUniform insupport(d::StdUniform, x) = zero(x) ≤ x ≤ one(x) @inline logdensity_def(::StdUniform, x) = zero(x) -@inline basemeasure(::StdUniform) = Lebesgue() +@inline basemeasure(::StdUniform) = LebesgueMeasure() Base.rand(rng::Random.AbstractRNG, ::Type{T}, ::StdUniform) where {T} = rand(rng, T) From 03fa9fa22657c7188a93bf19ccde354a53a84531 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 13 Sep 2022 13:52:30 -0700 Subject: [PATCH 292/368] updates --- src/combinators/transformedmeasure.jl | 16 ++++++++-------- src/primitives/lebesgue.jl | 1 + 2 files changed, 9 insertions(+), 8 deletions(-) diff --git a/src/combinators/transformedmeasure.jl b/src/combinators/transformedmeasure.jl index a11c3d6d..3480308d 100644 --- a/src/combinators/transformedmeasure.jl +++ b/src/combinators/transformedmeasure.jl @@ -35,11 +35,6 @@ end gettransform(ν::PushforwardMeasure) = ν.f parent(ν::PushforwardMeasure) = ν.origin -transport_origin(μ::PushforwardMeasure) = transport_origin(parent(μ)) - -from_origin(μ::PushforwardMeasure, x) = μ.f(from_origin(parent(μ), x)) -to_origin(μ::PushforwardMeasure, y) = μ.inv_f(to_origin(parent(f), y)) - function transport_def(ν::PushforwardMeasure{FF,IF,M}, μ::M, x) where {FF,IF,M} if μ == parent(ν) return ν.f(x) @@ -108,9 +103,14 @@ end # Bypass `checked_arg`, would require potentially costly transformation: @inline checked_arg(::PushforwardMeasure, x) = x -@inline transport_origin(ν::PushforwardMeasure) = ν.origin -@inline from_origin(ν::PushforwardMeasure, x) = ν.f(x) -@inline to_origin(ν::PushforwardMeasure, y) = ν.inv_f(y) +# @inline transport_origin(ν::PushforwardMeasure) = ν.origin +# @inline from_origin(ν::PushforwardMeasure, x) = ν.f(x) +# @inline to_origin(ν::PushforwardMeasure, y) = ν.inv_f(y) + +@inline transport_origin(μ::PushforwardMeasure) = transport_origin(parent(μ)) +@inline from_origin(μ::PushforwardMeasure, x) = μ.f(from_origin(parent(μ), x)) +@inline to_origin(μ::PushforwardMeasure, y) = μ.inv_f(to_origin(parent(f), y)) + function Base.rand(rng::AbstractRNG, ::Type{T}, ν::PushforwardMeasure) where {T} return from_origin(ν, rand(rng, T, transport_origin(ν))) diff --git a/src/primitives/lebesgue.jl b/src/primitives/lebesgue.jl index c1aa8306..6623d56d 100644 --- a/src/primitives/lebesgue.jl +++ b/src/primitives/lebesgue.jl @@ -42,6 +42,7 @@ logdensity_def(::LebesgueMeasure, ::CountingMeasure, x) = -Inf logdensity_def(::CountingMeasure, ::LebesgueMeasure, x) = Inf @inline getdof(::Lebesgue) = static(1) +@inline getdof(::LebesgueMeasure) = static(1) @inline checked_arg(::Lebesgue, x::Real) = x @inline checked_arg(::LebesgueMeasure, x::Real) = x From 0ee3c5ae27198fb6ffcf6d577baa4a3282952b1c Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 13 Sep 2022 13:59:08 -0700 Subject: [PATCH 293/368] make testvalue fall back on FixedRNG approach --- src/utils.jl | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/src/utils.jl b/src/utils.jl index e93e1716..a48987a5 100644 --- a/src/utils.jl +++ b/src/utils.jl @@ -10,7 +10,15 @@ showparams(io::IO, ::EmptyNamedTuple) = print(io, "()") showparams(io::IO, nt::NamedTuple) = print(io, nt) export testvalue -testvalue(μ::AbstractMeasure) = testvalue(basemeasure(μ)) + +function testvalue(μ::M) where {M<:AbstractMeasure} + if Core.Compiler.return_type(rand, Tuple{M}) isa Core.TypeofBottom + return testvalue(basemeasure(μ)) + else + return rand(FixedRNG(), μ) + end +end + testvalue(::Type{T}) where {T} = zero(T) export rootmeasure From 853013ce858e7428bfdb897290f7b430ea07434d Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 13 Sep 2022 15:23:05 -0700 Subject: [PATCH 294/368] un-break testvalue --- src/combinators/half.jl | 2 +- src/combinators/product.jl | 2 +- src/combinators/spikemixture.jl | 2 +- src/combinators/superpose.jl | 2 +- src/combinators/transformedmeasure.jl | 4 ++-- src/combinators/weighted.jl | 2 ++ src/domains.jl | 6 +++--- src/primitives/counting.jl | 2 +- src/primitives/dirac.jl | 2 -- src/primitives/lebesgue.jl | 2 +- src/utils.jl | 10 +++------- 11 files changed, 16 insertions(+), 20 deletions(-) diff --git a/src/combinators/half.jl b/src/combinators/half.jl index 32dec91d..fe65357b 100644 --- a/src/combinators/half.jl +++ b/src/combinators/half.jl @@ -26,4 +26,4 @@ logdensity_def(μ::Half, x) = logdensity_def(unhalf(μ), x) insupport(unhalf(d), x) end -testvalue(::Half) = 1.0 +testvalue(::Type{T}, ::Half) where {T} = one(T) diff --git a/src/combinators/product.jl b/src/combinators/product.jl index 975ebcd1..e4c01713 100644 --- a/src/combinators/product.jl +++ b/src/combinators/product.jl @@ -161,7 +161,7 @@ marginals(μ::ProductMeasure) = μ.marginals _map(f, args...) = map(f, args...) _map(f, x::MappedArrays.ReadonlyMappedArray) = mappedarray(f ∘ x.f, x.data) -testvalue(d::AbstractProductMeasure) = _map(testvalue, marginals(d)) +testvalue(::Type{T}, d::AbstractProductMeasure) where {T} = _map(m -> testvalue(T, m), marginals(d)) export ⊗ diff --git a/src/combinators/spikemixture.jl b/src/combinators/spikemixture.jl index 6168907a..b1e3cf46 100644 --- a/src/combinators/spikemixture.jl +++ b/src/combinators/spikemixture.jl @@ -37,6 +37,6 @@ function Base.rand(rng::AbstractRNG, T::Type, μ::SpikeMixture) return (rand(rng, T) < μ.w) * rand(rng, T, μ.m) end -testvalue(μ::SpikeMixture) = testvalue(μ.m) +testvalue(::Type{T}, μ::SpikeMixture) where {T} = zero(T) insupport(μ::SpikeMixture, x) = dynamic(insupport(μ.m, x)) || iszero(x) diff --git a/src/combinators/superpose.jl b/src/combinators/superpose.jl index 53d49674..44eae6b4 100644 --- a/src/combinators/superpose.jl +++ b/src/combinators/superpose.jl @@ -34,7 +34,7 @@ function Pretty.tile(d::SuperpositionMeasure) result *= Pretty.literal(")") end -testvalue(μ::SuperpositionMeasure) = testvalue(first(μ.components)) +testvalue(::Type{T}, μ::SuperpositionMeasure) where {T} = testvalue(T, first(μ.components)) # SuperpositionMeasure(ms :: AbstractMeasure...) = SuperpositionMeasure{X,length(ms)}(ms) diff --git a/src/combinators/transformedmeasure.jl b/src/combinators/transformedmeasure.jl index 3480308d..f3810df6 100644 --- a/src/combinators/transformedmeasure.jl +++ b/src/combinators/transformedmeasure.jl @@ -84,7 +84,7 @@ end insupport(ν::PushforwardMeasure, y) = insupport(transport_origin(ν), to_origin(ν, y)) -testvalue(ν::PushforwardMeasure) = from_origin(ν, testvalue(transport_origin(ν))) +testvalue(::Type{T}, ν::PushforwardMeasure) where {T} = from_origin(ν, testvalue(T, transport_origin(ν))) @inline function basemeasure(ν::PushforwardMeasure) PushforwardMeasure(ν.f, ν.inv_f, basemeasure(transport_origin(ν)), NoVolCorr()) @@ -109,7 +109,7 @@ end @inline transport_origin(μ::PushforwardMeasure) = transport_origin(parent(μ)) @inline from_origin(μ::PushforwardMeasure, x) = μ.f(from_origin(parent(μ), x)) -@inline to_origin(μ::PushforwardMeasure, y) = μ.inv_f(to_origin(parent(f), y)) +@inline to_origin(μ::PushforwardMeasure, y) = μ.inv_f(to_origin(parent(μ), y)) function Base.rand(rng::AbstractRNG, ::Type{T}, ν::PushforwardMeasure) where {T} diff --git a/src/combinators/weighted.jl b/src/combinators/weighted.jl index aef9dbee..ec7095ad 100644 --- a/src/combinators/weighted.jl +++ b/src/combinators/weighted.jl @@ -20,6 +20,8 @@ function Base.rand(rng::AbstractRNG, ::Type{T}, μ::AbstractWeightedMeasure) whe rand(rng, T, basemeasure(μ)) end +testvalue(::Type{T}, μ::AbstractWeightedMeasure) where {T} = testvalue(T, basemeasure(μ)) + ############################################################################### struct WeightedMeasure{R,M} <: AbstractWeightedMeasure diff --git a/src/domains.jl b/src/domains.jl index ed4617b2..e4c7f5e7 100644 --- a/src/domains.jl +++ b/src/domains.jl @@ -32,9 +32,9 @@ Base.maximum(b::BoundedReals) = b.upper Base.show(io::IO, ::typeof(ℝ₊)) = print(io, "ℝ₊") Base.show(io::IO, ::typeof(𝕀)) = print(io, "𝕀") -testvalue(::typeof(ℝ)) = 0.0 -testvalue(::typeof(ℝ₊)) = 1.0 -testvalue(::typeof(𝕀)) = 0.5 +testvalue(::Type{T}, ::typeof(ℝ)) where {T} = zero(T) +testvalue(::Type{T}, ::typeof(ℝ₊)) where {T} = one(T) +testvalue(::Type{T}, ::typeof(𝕀)) where {T} = one(T) / 2 abstract type IntegerDomain <: AbstractDomain end diff --git a/src/primitives/counting.jl b/src/primitives/counting.jl index b9715f34..7e4b2cc2 100644 --- a/src/primitives/counting.jl +++ b/src/primitives/counting.jl @@ -20,7 +20,7 @@ basemeasure(::Counting) = CountingMeasure() Counting() = Counting(ℤ) -testvalue(d::Counting) = testvalue(d.support) +testvalue(::Type{T}, d::Counting) where {T} = testvalue(T, d.support) proxy(d::Counting) = restrict(in(d.support), CountingMeasure()) diff --git a/src/primitives/dirac.jl b/src/primitives/dirac.jl index 0c10e723..e6b5221b 100644 --- a/src/primitives/dirac.jl +++ b/src/primitives/dirac.jl @@ -26,8 +26,6 @@ export dirac dirac(d::AbstractMeasure) = Dirac(rand(d)) -testvalue(d::Dirac) = d.x - insupport(d::Dirac, x) = x == d.x @inline getdof(::Dirac) = static(0) diff --git a/src/primitives/lebesgue.jl b/src/primitives/lebesgue.jl index 6623d56d..1de2d462 100644 --- a/src/primitives/lebesgue.jl +++ b/src/primitives/lebesgue.jl @@ -24,7 +24,7 @@ Lebesgue() = Lebesgue(ℝ) # basemeasure(::Lebesgue) = LebesgueMeasure() -testvalue(d::Lebesgue) = testvalue(d.support) +testvalue(::Type{T}, d::Lebesgue) where {T} = testvalue(T, d.support)::T proxy(d::Lebesgue) = restrict(in(d.support), LebesgueMeasure()) @useproxy Lebesgue diff --git a/src/utils.jl b/src/utils.jl index a48987a5..10886d57 100644 --- a/src/utils.jl +++ b/src/utils.jl @@ -11,13 +11,9 @@ showparams(io::IO, nt::NamedTuple) = print(io, nt) export testvalue -function testvalue(μ::M) where {M<:AbstractMeasure} - if Core.Compiler.return_type(rand, Tuple{M}) isa Core.TypeofBottom - return testvalue(basemeasure(μ)) - else - return rand(FixedRNG(), μ) - end -end +@inline testvalue(μ) = testvalue(Float64, μ) + +@inline testvalue(::Type{T}, μ) where {T} = rand(FixedRNG(), T, μ) testvalue(::Type{T}) where {T} = zero(T) From 00fdfd7c4eb1dca8889b42bed593f4165685a01c Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 13 Sep 2022 15:40:19 -0700 Subject: [PATCH 295/368] CI for Juila 1.8 --- .github/workflows/CI.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index ee4ef71e..aa620f08 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -25,6 +25,7 @@ jobs: version: - '1.6' - '1.7' + - '1.8' - 'nightly' os: - ubuntu-latest From 3132af59d3f979d52e34f1f80527f58e613755a1 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 13 Sep 2022 15:56:06 -0700 Subject: [PATCH 296/368] fixes --- src/primitives/lebesgue.jl | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/src/primitives/lebesgue.jl b/src/primitives/lebesgue.jl index 1de2d462..baa476f2 100644 --- a/src/primitives/lebesgue.jl +++ b/src/primitives/lebesgue.jl @@ -41,12 +41,10 @@ logdensity_def(::LebesgueMeasure, ::CountingMeasure, x) = -Inf logdensity_def(::CountingMeasure, ::LebesgueMeasure, x) = Inf -@inline getdof(::Lebesgue) = static(1) @inline getdof(::LebesgueMeasure) = static(1) -@inline checked_arg(::Lebesgue, x::Real) = x @inline checked_arg(::LebesgueMeasure, x::Real) = x -@propagate_inbounds function checked_arg(::Lebesgue, x::Any) +@propagate_inbounds function checked_arg(::LebesgueMeasure, x::Any) @boundscheck throw(ArgumentError("Invalid variate type for measure")) end From 9bbf833506056962531edc7f48ab424589612e38 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 13 Sep 2022 16:15:39 -0700 Subject: [PATCH 297/368] `rand` on a pushforward calls rand on its parent --- src/combinators/transformedmeasure.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/combinators/transformedmeasure.jl b/src/combinators/transformedmeasure.jl index f3810df6..6ef6ebcd 100644 --- a/src/combinators/transformedmeasure.jl +++ b/src/combinators/transformedmeasure.jl @@ -113,7 +113,7 @@ end function Base.rand(rng::AbstractRNG, ::Type{T}, ν::PushforwardMeasure) where {T} - return from_origin(ν, rand(rng, T, transport_origin(ν))) + return ν.f(rand(rng, T, parent(ν))) end export pushfwd From d8b52c5347d2fbf27432eac18e0d8652a0ec6971 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 14 Sep 2022 05:42:48 -0700 Subject: [PATCH 298/368] LebesgueMeasure => LebesgueBase CountingMeasure => CountingBase --- src/primitives/counting.jl | 12 ++++++------ src/primitives/dirac.jl | 2 +- src/primitives/lebesgue.jl | 24 ++++++++++++------------ src/standard/stdexponential.jl | 2 +- src/standard/stdlogistic.jl | 2 +- src/standard/stdnormal.jl | 2 +- src/standard/stduniform.jl | 2 +- test/combinators/superpose.jl | 4 ++-- test/runtests.jl | 2 +- 9 files changed, 26 insertions(+), 26 deletions(-) diff --git a/src/primitives/counting.jl b/src/primitives/counting.jl index 7e4b2cc2..69476a05 100644 --- a/src/primitives/counting.jl +++ b/src/primitives/counting.jl @@ -1,10 +1,10 @@ # Counting measure -export Counting, CountingMeasure +export Counting, CountingBase -struct CountingMeasure <: PrimitiveMeasure end +struct CountingBase <: PrimitiveMeasure end -insupport(::CountingMeasure, x) = true +insupport(::CountingBase, x) = true struct Counting{T} <: AbstractMeasure support::T @@ -16,15 +16,15 @@ function logdensity_def(μ::Counting, x) insupport(μ, x) ? 0.0 : -Inf end -basemeasure(::Counting) = CountingMeasure() +basemeasure(::Counting) = CountingBase() Counting() = Counting(ℤ) testvalue(::Type{T}, d::Counting) where {T} = testvalue(T, d.support) -proxy(d::Counting) = restrict(in(d.support), CountingMeasure()) +proxy(d::Counting) = restrict(in(d.support), CountingBase()) -Base.:∘(::typeof(basemeasure), ::Type{Counting}) = CountingMeasure() +Base.:∘(::typeof(basemeasure), ::Type{Counting}) = CountingBase() Base.show(io::IO, d::Counting) = print(io, "Counting(", d.support, ")") diff --git a/src/primitives/dirac.jl b/src/primitives/dirac.jl index e6b5221b..69e1313e 100644 --- a/src/primitives/dirac.jl +++ b/src/primitives/dirac.jl @@ -16,7 +16,7 @@ function (μ::Dirac{X})(s) where {X} return 0 end -basemeasure(d::Dirac) = CountingMeasure() +basemeasure(d::Dirac) = CountingBase() logdensity_def(μ::Dirac, x) = 0.0 diff --git a/src/primitives/lebesgue.jl b/src/primitives/lebesgue.jl index baa476f2..93edd274 100644 --- a/src/primitives/lebesgue.jl +++ b/src/primitives/lebesgue.jl @@ -2,13 +2,13 @@ export Lebesgue -struct LebesgueMeasure <: PrimitiveMeasure end +struct LebesgueBase <: PrimitiveMeasure end -testvalue(::LebesgueMeasure) = 0.0 +testvalue(::LebesgueBase) = 0.0 -insupport(::LebesgueMeasure, x) = true +insupport(::LebesgueBase, x) = true -insupport(::LebesgueMeasure) = Returns(true) +insupport(::LebesgueBase) = Returns(true) struct Lebesgue{T} <: AbstractMeasure support::T @@ -22,14 +22,14 @@ gentype(::Lebesgue) = Float64 Lebesgue() = Lebesgue(ℝ) -# basemeasure(::Lebesgue) = LebesgueMeasure() +# basemeasure(::Lebesgue) = LebesgueBase() testvalue(::Type{T}, d::Lebesgue) where {T} = testvalue(T, d.support)::T -proxy(d::Lebesgue) = restrict(in(d.support), LebesgueMeasure()) +proxy(d::Lebesgue) = restrict(in(d.support), LebesgueBase()) @useproxy Lebesgue -Base.:∘(::typeof(basemeasure), ::Type{Lebesgue}) = LebesgueMeasure() +Base.:∘(::typeof(basemeasure), ::Type{Lebesgue}) = LebesgueBase() Base.show(io::IO, d::Lebesgue) = print(io, "Lebesgue(", d.support, ")") @@ -37,14 +37,14 @@ insupport(μ::Lebesgue, x) = x ∈ μ.support insupport(::Lebesgue{RealNumbers}, ::Real) = true -logdensity_def(::LebesgueMeasure, ::CountingMeasure, x) = -Inf +logdensity_def(::LebesgueBase, ::CountingBase, x) = -Inf -logdensity_def(::CountingMeasure, ::LebesgueMeasure, x) = Inf +logdensity_def(::CountingBase, ::LebesgueBase, x) = Inf -@inline getdof(::LebesgueMeasure) = static(1) +@inline getdof(::LebesgueBase) = static(1) -@inline checked_arg(::LebesgueMeasure, x::Real) = x +@inline checked_arg(::LebesgueBase, x::Real) = x -@propagate_inbounds function checked_arg(::LebesgueMeasure, x::Any) +@propagate_inbounds function checked_arg(::LebesgueBase, x::Any) @boundscheck throw(ArgumentError("Invalid variate type for measure")) end diff --git a/src/standard/stdexponential.jl b/src/standard/stdexponential.jl index f22f5038..a02c5765 100644 --- a/src/standard/stdexponential.jl +++ b/src/standard/stdexponential.jl @@ -5,7 +5,7 @@ export StdExponential insupport(d::StdExponential, x) = x ≥ zero(x) @inline logdensity_def(::StdExponential, x) = -x -@inline basemeasure(::StdExponential) = LebesgueMeasure() +@inline basemeasure(::StdExponential) = LebesgueBase() @inline transport_def(::StdUniform, μ::StdExponential, x) = -expm1(-x) @inline transport_def(::StdExponential, μ::StdUniform, x) = -log1p(-x) diff --git a/src/standard/stdlogistic.jl b/src/standard/stdlogistic.jl index c246d5ec..2247ca7b 100644 --- a/src/standard/stdlogistic.jl +++ b/src/standard/stdlogistic.jl @@ -5,7 +5,7 @@ export StdLogistic @inline insupport(d::StdLogistic, x) = true @inline logdensity_def(::StdLogistic, x) = (u = -abs(x); u - 2 * log1pexp(u)) -@inline basemeasure(::StdLogistic) = LebesgueMeasure() +@inline basemeasure(::StdLogistic) = LebesgueBase() @inline transport_def(::StdUniform, μ::StdLogistic, x) = logistic(x) @inline transport_def(::StdLogistic, μ::StdUniform, x) = logit(x) diff --git a/src/standard/stdnormal.jl b/src/standard/stdnormal.jl index f54c102c..24ce6441 100644 --- a/src/standard/stdnormal.jl +++ b/src/standard/stdnormal.jl @@ -8,7 +8,7 @@ export StdNormal @inline insupport(d::StdNormal, x) = true @inline logdensity_def(::StdNormal, x) = -x^2 / 2 -@inline basemeasure(::StdNormal) = WeightedMeasure(static(-0.5 * log2π), LebesgueMeasure()) +@inline basemeasure(::StdNormal) = WeightedMeasure(static(-0.5 * log2π), LebesgueBase()) @inline getdof(::StdNormal) = static(1) diff --git a/src/standard/stduniform.jl b/src/standard/stduniform.jl index 9cbc2b7b..8c386225 100644 --- a/src/standard/stduniform.jl +++ b/src/standard/stduniform.jl @@ -5,6 +5,6 @@ export StdUniform insupport(d::StdUniform, x) = zero(x) ≤ x ≤ one(x) @inline logdensity_def(::StdUniform, x) = zero(x) -@inline basemeasure(::StdUniform) = LebesgueMeasure() +@inline basemeasure(::StdUniform) = LebesgueBase() Base.rand(rng::Random.AbstractRNG, ::Type{T}, ::StdUniform) where {T} = rand(rng, T) diff --git a/test/combinators/superpose.jl b/test/combinators/superpose.jl index a77ff847..ed4c6996 100644 --- a/test/combinators/superpose.jl +++ b/test/combinators/superpose.jl @@ -10,13 +10,13 @@ using MeasureBase: superpose @test μs isa SuperpositionMeasure{<:Tuple{Dirac,Dirac}} @test μs == SuperpositionMeasure((μ, ν)) == superpose(μ, ν) @test density_def(μs, 0) == 1.0 - @test basemeasure(μs) == CountingMeasure() + CountingMeasure() + @test basemeasure(μs) == CountingBase() + CountingBase() μs = SuperpositionMeasure([μ, ν]) @test μs isa SuperpositionMeasure{<:AbstractVector{<:AbstractMeasure}} @test_throws ErrorException density_def(μs, 0) @test basemeasure(μs).components == - SuperpositionMeasure([CountingMeasure(), CountingMeasure()]).components + SuperpositionMeasure([CountingBase(), CountingBase()]).components μ2 = μ + μ @test μ2 isa WeightedMeasure diff --git a/test/runtests.jl b/test/runtests.jl index 3578043d..4aa91216 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -76,7 +76,7 @@ test_measures = [ testbroken_measures = [ # InverseGamma(2) # Not defined yet # MvNormal(I(3)) # Entirely broken for now - CountingMeasure() + CountingBase() Likelihood TrivialMeasure() ] From 9b6e0663d0907b70803ff400927e5fc3bd4f53a5 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 14 Sep 2022 07:35:49 -0700 Subject: [PATCH 299/368] tests passing! --- src/combinators/transformedmeasure.jl | 13 ++++--------- test/transport.jl | 2 +- 2 files changed, 5 insertions(+), 10 deletions(-) diff --git a/src/combinators/transformedmeasure.jl b/src/combinators/transformedmeasure.jl index 6ef6ebcd..c735b31e 100644 --- a/src/combinators/transformedmeasure.jl +++ b/src/combinators/transformedmeasure.jl @@ -47,7 +47,7 @@ function transport_def(μ::M, ν::PushforwardMeasure{FF,IF,M}, y) where {FF,IF,M if μ == parent(ν) return ν.inv_f(y) else - invoke(transport_def, Tuple{Any, Any, Any}, μ, ν, y) + invoke(transport_def, Tuple{Any, PushforwardMeasure, Any}, μ, ν, y) end end @@ -103,14 +103,9 @@ end # Bypass `checked_arg`, would require potentially costly transformation: @inline checked_arg(::PushforwardMeasure, x) = x -# @inline transport_origin(ν::PushforwardMeasure) = ν.origin -# @inline from_origin(ν::PushforwardMeasure, x) = ν.f(x) -# @inline to_origin(ν::PushforwardMeasure, y) = ν.inv_f(y) - -@inline transport_origin(μ::PushforwardMeasure) = transport_origin(parent(μ)) -@inline from_origin(μ::PushforwardMeasure, x) = μ.f(from_origin(parent(μ), x)) -@inline to_origin(μ::PushforwardMeasure, y) = μ.inv_f(to_origin(parent(μ), y)) - +@inline transport_origin(ν::PushforwardMeasure) = ν.origin +@inline from_origin(ν::PushforwardMeasure, x) = ν.f(x) +@inline to_origin(ν::PushforwardMeasure, y) = ν.inv_f(y) function Base.rand(rng::AbstractRNG, ::Type{T}, ν::PushforwardMeasure) where {T} return ν.f(rand(rng, T, parent(ν))) diff --git a/test/transport.jl b/test/transport.jl index 2ee12ed5..c81450ce 100644 --- a/test/transport.jl +++ b/test/transport.jl @@ -9,7 +9,7 @@ using LogExpFunctions: logit for (f, μ) in [ (logit, StdUniform()) (log, StdExponential()) - (cbrt, StdNormal()) + (exp, StdNormal()) ] test_transport(μ, pushfwd(f, μ)) test_transport(pushfwd(f, μ), μ) From ad279ce39063787100dd8d8c6a9da702f576db75 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 14 Sep 2022 07:41:25 -0700 Subject: [PATCH 300/368] change `invoke` type --- src/combinators/transformedmeasure.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/combinators/transformedmeasure.jl b/src/combinators/transformedmeasure.jl index c735b31e..0971d70b 100644 --- a/src/combinators/transformedmeasure.jl +++ b/src/combinators/transformedmeasure.jl @@ -39,7 +39,7 @@ function transport_def(ν::PushforwardMeasure{FF,IF,M}, μ::M, x) where {FF,IF,M if μ == parent(ν) return ν.f(x) else - invoke(transport_def, Tuple{Any, Any, Any}, ν, μ, x) + invoke(transport_def, Tuple{Any, PushforwardMeasure, Any}, ν, μ, x) end end From 0bf97b5d7f0eebbe1dfdd6f7ffb1badfd706b3e0 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 14 Sep 2022 11:56:40 -0700 Subject: [PATCH 301/368] Change `test_interface` to check for 2-arg testvalue --- src/interface.jl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/interface.jl b/src/interface.jl index 08a4b369..b4c2c4b1 100644 --- a/src/interface.jl +++ b/src/interface.jl @@ -54,7 +54,7 @@ function test_interface(μ::M) where {M} ########################################################################### # testvalue, logdensityof - x = @inferred testvalue(μ) + x = @inferred testvalue(Float64, μ) β = @inferred basemeasure(μ, x) ℓμ = @inferred logdensityof(μ, x) @@ -62,7 +62,7 @@ function test_interface(μ::M) where {M} @test ℓμ ≈ logdensity_def(μ, x) + ℓβ - @test logdensity_def(μ, testvalue(μ)) isa Real + @test logdensity_def(μ, testvalue(Float64, μ)) isa Real end end end From 4720e21a6393bdc9a961649c47fbc651fb16f943 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 14 Sep 2022 11:56:51 -0700 Subject: [PATCH 302/368] manually-specifed inverses --- src/combinators/transformedmeasure.jl | 31 +++++++++++++++++++++++---- 1 file changed, 27 insertions(+), 4 deletions(-) diff --git a/src/combinators/transformedmeasure.jl b/src/combinators/transformedmeasure.jl index 0971d70b..2977061e 100644 --- a/src/combinators/transformedmeasure.jl +++ b/src/combinators/transformedmeasure.jl @@ -114,9 +114,32 @@ end export pushfwd """ - pushfwd(f, μ, volcorr = WithVolCorr()) + pushfwd(f, [f_inverse,] μ, volcorr = WithVolCorr()) -Return the [pushforward measure](https://en.wikipedia.org/wiki/Pushforward_measure) -from `μ` the [measurable function](https://en.wikipedia.org/wiki/Measurable_function) `f`. +Return the [pushforward +measure](https://en.wikipedia.org/wiki/Pushforward_measure) from `μ` the +[measurable function](https://en.wikipedia.org/wiki/Measurable_function) `f`. + +If `f_inverse` is specified, it must be a valid inverse of the function given by +restricting `f` to the support of `μ`. """ -pushfwd(f, μ, volcorr = WithVolCorr()) = PushforwardMeasure(f, inverse(f), μ, volcorr) +pushfwd(f, μ, volcorr::TransformVolCorr = WithVolCorr()) = PushforwardMeasure(f, inverse(f), μ, volcorr) + +pushfwd(f, finv, μ, volcorr::TransformVolCorr = WithVolCorr()) = PushforwardMeasure(f, finv, μ, volcorr) + +@inline function pushfwd(f, μ::PushforwardMeasure, volcorr::TransformVolCorr = WithVolCorr()) + _pushfwd(f, inverse(f), μ, volcorr, μ.volcorr) +end + + +@inline function pushfwd(f, finv, μ::PushforwardMeasure, volcorr::TransformVolCorr = WithVolCorr()) + _pushfwd(f, finv, μ, volcorr, μ.volcorr) +end + +@inline function _pushfwd(f, finv, μ::PushforwardMeasure, vf::V, vμ::V) where {V<:TransformVolCorr} + pushfwd(f ∘ μ.f, μ.inv_f ∘ finv, v) +end + +@inline function _pushfwd(f, finv, μ::PushforwardMeasure, vf, vμ) + PushforwardMeasure(f, finv, μ, vf) +end \ No newline at end of file From d2c3858578ecd54d79212ba80261a893fd8cf886 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Fri, 16 Sep 2022 14:43:37 -0700 Subject: [PATCH 303/368] more pushfwd stuff --- src/combinators/transformedmeasure.jl | 39 ++++++++++++++++++++++++--- 1 file changed, 36 insertions(+), 3 deletions(-) diff --git a/src/combinators/transformedmeasure.jl b/src/combinators/transformedmeasure.jl index 2977061e..137df769 100644 --- a/src/combinators/transformedmeasure.jl +++ b/src/combinators/transformedmeasure.jl @@ -55,12 +55,45 @@ function Pretty.tile(ν::PushforwardMeasure) Pretty.list_layout(Pretty.tile.([ν.f, ν.inv_f, ν.origin]); prefix = :PushforwardMeasure) end +# TODO: Reduce code duplication +@inline function logdensityof( + ν::PushforwardMeasure{FF,IF,M,<:WithVolCorr}, + y, +) where {FF,IF,M} + x_orig, inv_ladj = with_logabsdet_jacobian(ν.inv_f, y) + μ = ν.origin + logd_orig = unsafe_logdensityof(ν.origin, x_orig) + logd = float(logd_orig + inv_ladj) + neginf = oftype(logd, -Inf) + insupport(μ, x_orig) || return oftype(logd, -Inf) + return ifelse( + # Zero density wins against infinite volume: + (isnan(logd) && logd_orig == -Inf && inv_ladj == +Inf) || + # Maybe also for (logd_orig == -Inf) && isfinite(inv_ladj) ? + # Return constant -Inf to prevent problems with ForwardDiff: + (isfinite(logd_orig) && (inv_ladj == -Inf)), + neginf, + logd, + ) +end + +# TODO: THIS IS ALMOST CERTAINLY WRONG +# @inline function logdensity_rel( +# ν::PushforwardMeasure{FF1,IF1,M1,<:WithVolCorr}, +# β::PushforwardMeasure{FF2,IF2,M2,<:WithVolCorr}, +# y, +# ) where {FF1,IF1,M1,FF2,IF2,M2} +# f = β.inv_f ∘ ν.f +# inv_f = ν.inv_f ∘ β.f +# logdensity_rel(pushfwd(f, inv_f, ν.origin, WithVolCorr()), β.origin, β.inv_f(y)) +# end + @inline function logdensity_def( ν::PushforwardMeasure{FF,IF,M,<:WithVolCorr}, y, ) where {FF,IF,M} x_orig, inv_ladj = with_logabsdet_jacobian(ν.inv_f, y) - logd_orig = logdensity_def(ν.origin, x_orig) + logd_orig = unsafe_logdensityof(ν.origin, x_orig) logd = float(logd_orig + inv_ladj) neginf = oftype(logd, -Inf) return ifelse( @@ -79,7 +112,7 @@ end y, ) where {FF,IF,M} x_orig = to_origin(ν, y) - return logdensity_def(ν.origin, x_orig) + return unsafe_logdensityof(ν.origin, x_orig) end insupport(ν::PushforwardMeasure, y) = insupport(transport_origin(ν), to_origin(ν, y)) @@ -137,7 +170,7 @@ end end @inline function _pushfwd(f, finv, μ::PushforwardMeasure, vf::V, vμ::V) where {V<:TransformVolCorr} - pushfwd(f ∘ μ.f, μ.inv_f ∘ finv, v) + pushfwd(f ∘ μ.f, μ.inv_f ∘ finv, μ, v) end @inline function _pushfwd(f, finv, μ::PushforwardMeasure, vf, vμ) From beb76183ca74a240a04b9b5ff88a3ccd40071666 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Fri, 16 Sep 2022 14:53:20 -0700 Subject: [PATCH 304/368] A little less wrong --- src/combinators/transformedmeasure.jl | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/src/combinators/transformedmeasure.jl b/src/combinators/transformedmeasure.jl index 137df769..1f39082b 100644 --- a/src/combinators/transformedmeasure.jl +++ b/src/combinators/transformedmeasure.jl @@ -83,9 +83,10 @@ end # β::PushforwardMeasure{FF2,IF2,M2,<:WithVolCorr}, # y, # ) where {FF1,IF1,M1,FF2,IF2,M2} -# f = β.inv_f ∘ ν.f -# inv_f = ν.inv_f ∘ β.f -# logdensity_rel(pushfwd(f, inv_f, ν.origin, WithVolCorr()), β.origin, β.inv_f(y)) +# x = β.inv_f(y) +# f = ν.inv_f ∘ β.f +# inv_f = β.inv_f ∘ ν.f +# logdensity_rel(pushfwd(f, inv_f, ν.origin, WithVolCorr()), β.origin, x) # end @inline function logdensity_def( From 806f31451c26f65621bef99f1712e01523dd9941 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 19 Sep 2022 09:43:51 -0700 Subject: [PATCH 305/368] add mass interface --- src/MeasureBase.jl | 1 + 1 file changed, 1 insertion(+) diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index 29d88139..8ec283e1 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -119,6 +119,7 @@ include("combinators/half.jl") include("domains.jl") include("primitive.jl") include("utils.jl") +include("mass-interface.jl") # include("absolutecontinuity.jl") include("primitives/counting.jl") From d05c044267f83bf380ad82f441c4785d4a5daa45 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 19 Sep 2022 09:58:59 -0700 Subject: [PATCH 306/368] pullback --- src/combinators/transformedmeasure.jl | 21 +++++++++++++++++++-- 1 file changed, 19 insertions(+), 2 deletions(-) diff --git a/src/combinators/transformedmeasure.jl b/src/combinators/transformedmeasure.jl index 1f39082b..c39988df 100644 --- a/src/combinators/transformedmeasure.jl +++ b/src/combinators/transformedmeasure.jl @@ -157,9 +157,26 @@ measure](https://en.wikipedia.org/wiki/Pushforward_measure) from `μ` the If `f_inverse` is specified, it must be a valid inverse of the function given by restricting `f` to the support of `μ`. """ -pushfwd(f, μ, volcorr::TransformVolCorr = WithVolCorr()) = PushforwardMeasure(f, inverse(f), μ, volcorr) +pushfwd(f, μ::AbstractMeasure, volcorr::TransformVolCorr = WithVolCorr()) = pushfwd(f, inverse(f), μ, volcorr) + +pushfwd(f, finv, μ::AbstractMeasure, volcorr::TransformVolCorr = WithVolCorr()) = PushforwardMeasure(f, finv, μ, volcorr) + +""" + pullback(f, [f_inverse,] μ, volcorr = WithVolCorr()) + +A _pullback_ is a dual concept to a _pushforward_. While a pushforward needs a +map _from_ the support of a measure, a pullback requires a map _into_ the +support of a measure. The log-density is then computed through function +composition, together with a volume correction as needed. + +This can be useful, since the log-density of a `PushforwardMeasure` is computing +in terms of the inverse function; the "forward" function is not used at all. In +some cases, we may be focusing on log-density (and not, for example, sampling). +""" +pullback(f, μ::AbstractMeasure, volcorr::TransformVolCorr = WithVolCorr()) = pushfwd(inverse(f), f, μ, volcorr) + +pullback(f, finv, μ::AbstractMeasure, volcorr::TransformVolCorr = WithVolCorr()) = pushfwd(finv, f, μ, volcorr) -pushfwd(f, finv, μ, volcorr::TransformVolCorr = WithVolCorr()) = PushforwardMeasure(f, finv, μ, volcorr) @inline function pushfwd(f, μ::PushforwardMeasure, volcorr::TransformVolCorr = WithVolCorr()) _pushfwd(f, inverse(f), μ, volcorr, μ.volcorr) From c0d5ba302b3df776512b1dce91a823709010e34a Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 19 Sep 2022 09:59:09 -0700 Subject: [PATCH 307/368] mass interface --- src/mass-interface.jl | 39 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 src/mass-interface.jl diff --git a/src/mass-interface.jl b/src/mass-interface.jl new file mode 100644 index 00000000..e0a11bb0 --- /dev/null +++ b/src/mass-interface.jl @@ -0,0 +1,39 @@ +import LinearAlgebra: normalize + +abstract type MeasureMass end + +struct KnownMass{M,MASS} <: MeasureMass + measure::M + mass::MASS +end + +struct UnknownFiniteMass{M} <: MeasureMass + measure::M +end + +struct UnknownMass{M} <: MeasureMass + measure::M +end + +massof(m::AbstractMeasure) = UnknownMass(m) + +struct NormalizedMeasure{P,M} <: AbstractMeasure + parent::P + parent_mass::M +end + +massof(m::NormalizedMeasure) = KnownMass(m, static(1)) + +normalize(m::AbstractMeasure) = normalize(m, massof(m)) +normalize(m::AbstractMeasure, mass) = NormalizedMeasure(m, mass) + +function normalize(m::AbstractMeasure, mass::KnownMass) + @assert m == mass.measure + isinf(m.mass) && error("Measure cannot be normalized: $m") + inv(mass.mass) * m +end + +isnormalized(m::AbstractMeasure) = isnormalized(massof(m)) +isnormalized(m::KnownMass) = m.mass == 1 +isnormalized(::MeasureMass) = false +isnormalized(::NormalizedMeasure) = true From c3e8a22b286c79f8e12eb823d5205bc43bfb71a6 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 19 Sep 2022 13:41:35 -0700 Subject: [PATCH 308/368] working on mass interface --- src/mass-interface.jl | 72 +++++++++++++++++++++++++++++++------------ 1 file changed, 53 insertions(+), 19 deletions(-) diff --git a/src/mass-interface.jl b/src/mass-interface.jl index e0a11bb0..4005efd6 100644 --- a/src/mass-interface.jl +++ b/src/mass-interface.jl @@ -1,18 +1,35 @@ import LinearAlgebra: normalize -abstract type MeasureMass end +import Base -struct KnownMass{M,MASS} <: MeasureMass - measure::M - mass::MASS + +export UnknownMass, UnknownFiniteMass + +abstract type AbstractUnknownMass <: Real end + +struct UnknownFiniteMass <: AbstractUnknownMass end -struct UnknownFiniteMass{M} <: MeasureMass - measure::M +struct UnknownMass <: AbstractUnknownMass end -struct UnknownMass{M} <: MeasureMass - measure::M +for T in (:UnknownFiniteMass, :UnknownMass) + @eval begin + Base.:+(::$T, ::$T) = $T() + Base.:*(::$T, ::$T) = $T() + Base.:^(::$T, k::Number) = isfinite(k) ? $T() : UnknownMass() + end +end + +for op in (:+, :*) + let + U = :UnknownMass + UF = :UnknownFiniteMass + @eval begin + Base.$op(::$U, ::$UF) = $U() + Base.$op(::$UF, ::$U) = $U() + end + end end massof(m::AbstractMeasure) = UnknownMass(m) @@ -22,18 +39,35 @@ struct NormalizedMeasure{P,M} <: AbstractMeasure parent_mass::M end -massof(m::NormalizedMeasure) = KnownMass(m, static(1)) +massof(m::NormalizedMeasure) = static(1) + +normalize(m::AbstractMeasure) = _normalize(m, massof(m)) + -normalize(m::AbstractMeasure) = normalize(m, massof(m)) -normalize(m::AbstractMeasure, mass) = NormalizedMeasure(m, mass) +_normalize(m::AbstractMeasure, mass::AbstractUnknownMass) = NormalizedMeasure(m, mass) -function normalize(m::AbstractMeasure, mass::KnownMass) - @assert m == mass.measure - isinf(m.mass) && error("Measure cannot be normalized: $m") - inv(mass.mass) * m +function _normalize(m::AbstractMeasure, mass) + isinf(mass) && error("Measure cannot be normalized: $m") + inv(mass) * m end -isnormalized(m::AbstractMeasure) = isnormalized(massof(m)) -isnormalized(m::KnownMass) = m.mass == 1 -isnormalized(::MeasureMass) = false -isnormalized(::NormalizedMeasure) = true +export isnormalized + +""" + isnormalized(m::AbstractMeasure) + +Checks whether the measure m is normalized, that is, whether `massof(m) == 1`. + +For convenience, we also provide a method on non-measures that only depends on +`norm`. +""" +isnormalized(m::AbstractMeasure) = isone(massof(m)) + +""" + isnormalized(x, p::Real=2) + +Check whether `norm(x, p) == 1`. +""" +isnormalized(x, p::Real=2) = isone(norm(x, p)) + +isone(::AbstractUnknownMass) = false \ No newline at end of file From 617ce41975107c5f861f5f4002fc146e6f7059e7 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 19 Sep 2022 13:42:22 -0700 Subject: [PATCH 309/368] add some `massof` methods --- src/combinators/half.jl | 2 ++ src/combinators/power.jl | 2 ++ src/combinators/powerweighted.jl | 2 ++ 3 files changed, 6 insertions(+) diff --git a/src/combinators/half.jl b/src/combinators/half.jl index fe65357b..77651d0f 100644 --- a/src/combinators/half.jl +++ b/src/combinators/half.jl @@ -27,3 +27,5 @@ logdensity_def(μ::Half, x) = logdensity_def(unhalf(μ), x) end testvalue(::Type{T}, ::Half) where {T} = one(T) + +massof(μ::Half) = massof(unhalf(μ)) diff --git a/src/combinators/power.jl b/src/combinators/power.jl index 94447844..ec754c8c 100644 --- a/src/combinators/power.jl +++ b/src/combinators/power.jl @@ -128,3 +128,5 @@ end function checked_arg(μ::PowerMeasure, x::Any) throw(ArgumentError("Size of variate doesn't match size of power measure")) end + +massof(m::PowerMeasure) = massof(m.parent) ^ product(m.axes) \ No newline at end of file diff --git a/src/combinators/powerweighted.jl b/src/combinators/powerweighted.jl index 47f50da4..323ce8cf 100644 --- a/src/combinators/powerweighted.jl +++ b/src/combinators/powerweighted.jl @@ -35,3 +35,5 @@ end function Pretty.tile(d::PowerWeightedMeasure) Pretty.pair_layout(Pretty.tile(d.parent), Pretty.tile(d.exponent), sep = " ↑ ") end + +massof(m::PowerWeightedMeasure) = massof(m.parent) ^ m.exponent \ No newline at end of file From 0490a257e070da570a24c1290b579d6ce7d4206d Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 19 Sep 2022 14:20:02 -0700 Subject: [PATCH 310/368] Maybe <:Number is better for invalidations? --- src/mass-interface.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/mass-interface.jl b/src/mass-interface.jl index 4005efd6..204719d0 100644 --- a/src/mass-interface.jl +++ b/src/mass-interface.jl @@ -5,7 +5,7 @@ import Base export UnknownMass, UnknownFiniteMass -abstract type AbstractUnknownMass <: Real end +abstract type AbstractUnknownMass <: Number end struct UnknownFiniteMass <: AbstractUnknownMass end From f68a9324789dd56748e797d52ad155a87b29f89b Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 19 Sep 2022 14:22:08 -0700 Subject: [PATCH 311/368] float instead of Int --- src/mass-interface.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/mass-interface.jl b/src/mass-interface.jl index 204719d0..49dbed1e 100644 --- a/src/mass-interface.jl +++ b/src/mass-interface.jl @@ -39,7 +39,7 @@ struct NormalizedMeasure{P,M} <: AbstractMeasure parent_mass::M end -massof(m::NormalizedMeasure) = static(1) +massof(m::NormalizedMeasure) = static(1.0) normalize(m::AbstractMeasure) = _normalize(m, massof(m)) From c05b5c40436d31e84c410ca685acc846f495c9ab Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 19 Sep 2022 14:22:17 -0700 Subject: [PATCH 312/368] logmassof --- src/mass-interface.jl | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/mass-interface.jl b/src/mass-interface.jl index 49dbed1e..3a05ef82 100644 --- a/src/mass-interface.jl +++ b/src/mass-interface.jl @@ -34,6 +34,8 @@ end massof(m::AbstractMeasure) = UnknownMass(m) +logmassof(m::AbstractMeasure) = log(massof(m)) + struct NormalizedMeasure{P,M} <: AbstractMeasure parent::P parent_mass::M From a2d3a3bbcfc9287bb6124c127be99555312d8cfd Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 20 Sep 2022 13:03:03 -0700 Subject: [PATCH 313/368] transports for proxies --- src/proxies.jl | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/src/proxies.jl b/src/proxies.jl index ae3bd6d2..cb34b5bc 100644 --- a/src/proxies.jl +++ b/src/proxies.jl @@ -19,5 +19,9 @@ macro useproxy(M) @inline $MeasureBase.basemeasure(μ::$M) = basemeasure(proxy(μ)) @inline $MeasureBase.basemeasure_depth(μ::$M) = basemeasure_depth(proxy(μ)) + + @inline $MeasureBase.transport_origin(μ::$M) = transport_origin(proxy(μ)) + @inline $MeasureBase.to_origin(μ::$M, y) = to_origin(proxy(μ), y) + @inline $MeasureBase.from_origin(μ::$M, x) = from_origin(proxy(μ), x) end end From ff7af02c20d9210c716c30858004c91e9ebe2324 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 20 Sep 2022 13:03:22 -0700 Subject: [PATCH 314/368] drop latent-joint.jl --- src/MeasureBase.jl | 1 - src/latent-joint.jl | 62 --------------------------------------------- 2 files changed, 63 deletions(-) delete mode 100644 src/latent-joint.jl diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index 8ec283e1..3d752e0d 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -146,7 +146,6 @@ include("standard/stduniform.jl") include("standard/stdexponential.jl") include("standard/stdlogistic.jl") include("standard/stdnormal.jl") -include("latent-joint.jl") include("rand.jl") include("fixedrng.jl") diff --git a/src/latent-joint.jl b/src/latent-joint.jl deleted file mode 100644 index 988c27cc..00000000 --- a/src/latent-joint.jl +++ /dev/null @@ -1,62 +0,0 @@ -_LATENT_DOCSTRING = """ -Some Probabilistic Programming Languages (PPLs) like Tilde.jl make a distinction -between a _latent space_, often a namespace represented as a named tuple, and -the space containing the return value, which we refer to as the _maifest space_. -The distinction is that computations are done in terms of the latent space, -while the resulting value is in the manifest space. - -To simplify many manipulations involving these concepts, we introduce the -concept of a _joint space_. For example, suppose `m()` is a measure with latent -space `NamedTuple{(:a, :b)}` that returns `a - b`, so the latent value `(a = 3, -b = 4)` is mapped to the manifest value `0.75`. Then the corresponding value in -the joint space is the pair `(a = 3, b = 4) => 0.75`. - -One of the many goals of probabilistic programming is to blur the line between -"built in" measures like `Normal()` and those defined in terms of a model from a -PPL. To accommodate this, we extend these concepts to general measures. - -For many measures, it's convenient to work directly in the manifest space, and -there's no need for such separation. However, it's important to be able to -manipulate measures programmatically, with minimal special cases. Because of -this, we introduce fall-back methods - - latentof(m) = m - manifestof(m) = m - -The default implementation of `jointof` is then a push-forward through the -function `x -> (x => x)`. For example, - - julia> rand(MeasureBase.jointof(StdUniform())) - 0.346439=>0.346439 -""" - -""" - latentof(m) - -$_LATENT_DOCSTRING -""" -latentof(m) = m - -""" - manifestof(m) - -$_LATENT_DOCSTRING -""" -manifestof(m) = m - -""" - jointof(m) - -$_LATENT_DOCSTRING -""" -function jointof(m) - fwd(x) = x => x - - function back(p::Pair) - x,y = p - @assert x === y - return x - end - - PushforwardMeasure(fwd, back, m, NoVolCorr()) -end From 8482cf3ea481d96474aa64bda3f08668fe51ad4b Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 21 Sep 2022 11:44:47 -0700 Subject: [PATCH 315/368] drop exports --- src/mass-interface.jl | 3 --- 1 file changed, 3 deletions(-) diff --git a/src/mass-interface.jl b/src/mass-interface.jl index 3a05ef82..7f14227e 100644 --- a/src/mass-interface.jl +++ b/src/mass-interface.jl @@ -2,9 +2,6 @@ import LinearAlgebra: normalize import Base - -export UnknownMass, UnknownFiniteMass - abstract type AbstractUnknownMass <: Number end struct UnknownFiniteMass <: AbstractUnknownMass From cdeb2a0eb8321ee9b634def8ca6a1b53894086c7 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 21 Sep 2022 11:45:55 -0700 Subject: [PATCH 316/368] Drop `logmassof` for now --- src/mass-interface.jl | 1 - 1 file changed, 1 deletion(-) diff --git a/src/mass-interface.jl b/src/mass-interface.jl index 7f14227e..a7654ac2 100644 --- a/src/mass-interface.jl +++ b/src/mass-interface.jl @@ -31,7 +31,6 @@ end massof(m::AbstractMeasure) = UnknownMass(m) -logmassof(m::AbstractMeasure) = log(massof(m)) struct NormalizedMeasure{P,M} <: AbstractMeasure parent::P From b15190ce510486fc33e072679341c0f591d241a4 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 21 Sep 2022 12:11:11 -0700 Subject: [PATCH 317/368] reorganize Lebesgue measure --- src/primitives/lebesgue.jl | 44 +++++++++++++++++++++++++++----------- 1 file changed, 31 insertions(+), 13 deletions(-) diff --git a/src/primitives/lebesgue.jl b/src/primitives/lebesgue.jl index 93edd274..58268e4f 100644 --- a/src/primitives/lebesgue.jl +++ b/src/primitives/lebesgue.jl @@ -4,12 +4,30 @@ export Lebesgue struct LebesgueBase <: PrimitiveMeasure end + +(::LebesgueBase)(s::Interval) = width(s) + testvalue(::LebesgueBase) = 0.0 insupport(::LebesgueBase, x) = true insupport(::LebesgueBase) = Returns(true) + + +logdensity_def(::LebesgueBase, ::CountingBase, x) = -Inf + +logdensity_def(::CountingBase, ::LebesgueBase, x) = Inf + +@inline getdof(::LebesgueBase) = static(1) + +@inline checked_arg(::LebesgueBase, x::Real) = x + +@propagate_inbounds function checked_arg(::LebesgueBase, x::Any) + @boundscheck throw(ArgumentError("Invalid variate type for measure")) +end + +########################################################## struct Lebesgue{T} <: AbstractMeasure support::T end @@ -22,8 +40,6 @@ gentype(::Lebesgue) = Float64 Lebesgue() = Lebesgue(ℝ) -# basemeasure(::Lebesgue) = LebesgueBase() - testvalue(::Type{T}, d::Lebesgue) where {T} = testvalue(T, d.support)::T proxy(d::Lebesgue) = restrict(in(d.support), LebesgueBase()) @@ -37,14 +53,16 @@ insupport(μ::Lebesgue, x) = x ∈ μ.support insupport(::Lebesgue{RealNumbers}, ::Real) = true -logdensity_def(::LebesgueBase, ::CountingBase, x) = -Inf - -logdensity_def(::CountingBase, ::LebesgueBase, x) = Inf - -@inline getdof(::LebesgueBase) = static(1) - -@inline checked_arg(::LebesgueBase, x::Real) = x - -@propagate_inbounds function checked_arg(::LebesgueBase, x::Any) - @boundscheck throw(ArgumentError("Invalid variate type for measure")) -end +(::Lebesgue{RealNumbers})(s::Interval) = width(s) + +# Example: +# julia> Lebesgue(𝕀)(0.2..5) +# 0.8 +function (μ::Lebesgue{<:BoundedReals})(s::Interval) + a = μ.support.lower + b = μ.support.upper + left = max(s.left, a) + right = min(s.right, b) + w = right - left + max(w, zero(w)) +end \ No newline at end of file From cccdaf701efb8bf1eb1527a83687f14a7d834b5f Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 21 Sep 2022 12:11:25 -0700 Subject: [PATCH 318/368] IntervalSets --- Project.toml | 1 + src/MeasureBase.jl | 6 ++++++ 2 files changed, 7 insertions(+) diff --git a/Project.toml b/Project.toml index 626e0f94..5e48b63e 100644 --- a/Project.toml +++ b/Project.toml @@ -11,6 +11,7 @@ ConstructionBase = "187b0558-2788-49d3-abe0-74a17ed4e7c9" DensityInterface = "b429d917-457f-4dbc-8f4c-0cc954292b1d" FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b" IfElse = "615f187c-cbe4-4ef1-ba3b-2fcf58d6d173" +IntervalSets = "8197267c-284f-5f27-9208-e0e47529a953" InverseFunctions = "3587e190-3f89-42d0-90ee-14403ec27112" IrrationalConstants = "92d709cd-6900-40b7-9082-c6be49f344b6" LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index 3d752e0d..dd437103 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -8,6 +8,12 @@ import Random: gentype using Statistics using LinearAlgebra +import IntervalSets +# This seems harder than it should be to get `IntervalSets.:(..)` +@eval (using IntervalSets: $(Symbol(IntervalSets.:(..)))) + +using IntervalSets: Interval, width + import DensityInterface: logdensityof import DensityInterface: densityof import DensityInterface: DensityKind From dffa2eccd903815cdfb445c8a6eb6abd175b701d Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 21 Sep 2022 12:29:25 -0700 Subject: [PATCH 319/368] proxy(::Lebesgue{MeasureBase.RealNumbers}) = LebesgueBase() --- src/primitives/lebesgue.jl | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/primitives/lebesgue.jl b/src/primitives/lebesgue.jl index 58268e4f..35574311 100644 --- a/src/primitives/lebesgue.jl +++ b/src/primitives/lebesgue.jl @@ -43,6 +43,8 @@ Lebesgue() = Lebesgue(ℝ) testvalue(::Type{T}, d::Lebesgue) where {T} = testvalue(T, d.support)::T proxy(d::Lebesgue) = restrict(in(d.support), LebesgueBase()) +proxy(::Lebesgue{MeasureBase.RealNumbers}) = LebesgueBase() + @useproxy Lebesgue Base.:∘(::typeof(basemeasure), ::Type{Lebesgue}) = LebesgueBase() From 44a151279c734d59399f34fe7bd268192c9d29a5 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 21 Sep 2022 12:34:19 -0700 Subject: [PATCH 320/368] calling a "useproxy" measure calls its proxy --- src/proxies.jl | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/proxies.jl b/src/proxies.jl index cb34b5bc..dbab1f93 100644 --- a/src/proxies.jl +++ b/src/proxies.jl @@ -23,5 +23,7 @@ macro useproxy(M) @inline $MeasureBase.transport_origin(μ::$M) = transport_origin(proxy(μ)) @inline $MeasureBase.to_origin(μ::$M, y) = to_origin(proxy(μ), y) @inline $MeasureBase.from_origin(μ::$M, x) = from_origin(proxy(μ), x) + + (μ::$M)(s) = proxy(μ)(s) end end From 590c933e6239331b2206bb45404daa8467d16d19 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 21 Sep 2022 12:35:04 -0700 Subject: [PATCH 321/368] StdUniform()(s::Interval) --- src/standard/stduniform.jl | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/standard/stduniform.jl b/src/standard/stduniform.jl index 8c386225..b091160f 100644 --- a/src/standard/stduniform.jl +++ b/src/standard/stduniform.jl @@ -8,3 +8,5 @@ insupport(d::StdUniform, x) = zero(x) ≤ x ≤ one(x) @inline basemeasure(::StdUniform) = LebesgueBase() Base.rand(rng::Random.AbstractRNG, ::Type{T}, ::StdUniform) where {T} = rand(rng, T) + +StdUniform()(s::Interval) = Lebesgue(𝕀)(s::Interval) \ No newline at end of file From d46afbf93e16b55b26100fe5db2265c1871f4e91 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 21 Sep 2022 12:47:17 -0700 Subject: [PATCH 322/368] typo --- src/standard/stduniform.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/standard/stduniform.jl b/src/standard/stduniform.jl index b091160f..2bd6a39c 100644 --- a/src/standard/stduniform.jl +++ b/src/standard/stduniform.jl @@ -9,4 +9,4 @@ insupport(d::StdUniform, x) = zero(x) ≤ x ≤ one(x) Base.rand(rng::Random.AbstractRNG, ::Type{T}, ::StdUniform) where {T} = rand(rng, T) -StdUniform()(s::Interval) = Lebesgue(𝕀)(s::Interval) \ No newline at end of file +(::StdUniform)(s::Interval) = Lebesgue(𝕀)(s::Interval) \ No newline at end of file From 0838fa2bdcd0c04cb5069e76ed730c8030d3c5a6 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 21 Sep 2022 13:04:45 -0700 Subject: [PATCH 323/368] (m::AbstractMeasure)(s::Interval) --- src/MeasureBase.jl | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index dd437103..06a206e7 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -162,4 +162,10 @@ include("interface.jl") using .Interface +function (m::AbstractMeasure)(s::Interval) + b = transport_def(StdUniform, m, s.right) + a = transport_def(StdUniform, m, s.left) + return abs(b - a) +end + end # module MeasureBase From 78cf303b10a0dda7fd55916410344a19b2f55d8f Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 21 Sep 2022 13:06:48 -0700 Subject: [PATCH 324/368] bugfix --- src/MeasureBase.jl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index 06a206e7..a7b174b2 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -163,8 +163,8 @@ include("interface.jl") using .Interface function (m::AbstractMeasure)(s::Interval) - b = transport_def(StdUniform, m, s.right) - a = transport_def(StdUniform, m, s.left) + b = transport_def(StdUniform(), m, s.right) + a = transport_def(StdUniform(), m, s.left) return abs(b - a) end From 20a8378c7a54c4119692af704d092a0824f34f8b Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Thu, 22 Sep 2022 11:47:39 -0700 Subject: [PATCH 325/368] comment --- src/MeasureBase.jl | 1 + 1 file changed, 1 insertion(+) diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index a7b174b2..ce31969d 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -162,6 +162,7 @@ include("interface.jl") using .Interface +# TODO: Make this work for non-unit-mass measures function (m::AbstractMeasure)(s::Interval) b = transport_def(StdUniform(), m, s.right) a = transport_def(StdUniform(), m, s.left) From a16d4876b00fa18b56d2ee3a6641f843a0812ff0 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Thu, 22 Sep 2022 11:53:28 -0700 Subject: [PATCH 326/368] IntervalSets version constraint --- Project.toml | 1 + 1 file changed, 1 insertion(+) diff --git a/Project.toml b/Project.toml index 5e48b63e..bc21d0ca 100644 --- a/Project.toml +++ b/Project.toml @@ -36,6 +36,7 @@ ConstructionBase = "1.3" DensityInterface = "0.4" FillArrays = "0.12, 0.13" IfElse = "0.1" +IntervalSets = "0.7" InverseFunctions = "0.1.7" IrrationalConstants = "0.1" LogExpFunctions = "0.3" From fcca30994cc016942c98402822a4edbb33685e06 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Thu, 22 Sep 2022 12:10:43 -0700 Subject: [PATCH 327/368] update dynamic_basemeasure_depth --- src/interface.jl | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/src/interface.jl b/src/interface.jl index b4c2c4b1..ecbc4ec2 100644 --- a/src/interface.jl +++ b/src/interface.jl @@ -22,7 +22,10 @@ export commonbase using Test -function dynamic_basemeasure_depth(μ) +function dynamic_basemeasure_depth(μ::M) where {M} + if hasmethod(proxy, Tuple{M}) + return dynamic_basemeasure_depth(proxy(μ)) + end β = basemeasure(μ) depth = 0 while μ ≠ β From c6c2bfffd4b71dd6651348153bcd73ae5371431a Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Thu, 22 Sep 2022 16:06:04 -0700 Subject: [PATCH 328/368] format --- src/combinators/likelihood.jl | 4 ++- src/combinators/power.jl | 2 +- src/combinators/powerweighted.jl | 2 +- src/combinators/product.jl | 4 ++- src/combinators/transformedmeasure.jl | 52 +++++++++++++++++++-------- src/mass-interface.jl | 12 +++---- src/primitives/lebesgue.jl | 5 +-- src/standard/stdnormal.jl | 4 +-- src/standard/stduniform.jl | 2 +- src/utils.jl | 2 +- test/runtests.jl | 2 +- 11 files changed, 54 insertions(+), 37 deletions(-) diff --git a/src/combinators/likelihood.jl b/src/combinators/likelihood.jl index d6da7ee1..6dfd164f 100644 --- a/src/combinators/likelihood.jl +++ b/src/combinators/likelihood.jl @@ -202,4 +202,6 @@ more efficient than logdensityof(ℓ.k(p), ℓ.x) - logdensityof(ℓ.k(q), ℓ.x) """ -likelihood_ratio(ℓ::Likelihood, p, q) = exp(ULogarithmic, logdensity_rel(ℓ.k(p), ℓ.k(q), ℓ.x)) \ No newline at end of file +function likelihood_ratio(ℓ::Likelihood, p, q) + exp(ULogarithmic, logdensity_rel(ℓ.k(p), ℓ.k(q), ℓ.x)) +end diff --git a/src/combinators/power.jl b/src/combinators/power.jl index ec754c8c..e3c7a3eb 100644 --- a/src/combinators/power.jl +++ b/src/combinators/power.jl @@ -129,4 +129,4 @@ function checked_arg(μ::PowerMeasure, x::Any) throw(ArgumentError("Size of variate doesn't match size of power measure")) end -massof(m::PowerMeasure) = massof(m.parent) ^ product(m.axes) \ No newline at end of file +massof(m::PowerMeasure) = massof(m.parent)^product(m.axes) diff --git a/src/combinators/powerweighted.jl b/src/combinators/powerweighted.jl index 323ce8cf..1d1a734b 100644 --- a/src/combinators/powerweighted.jl +++ b/src/combinators/powerweighted.jl @@ -36,4 +36,4 @@ function Pretty.tile(d::PowerWeightedMeasure) Pretty.pair_layout(Pretty.tile(d.parent), Pretty.tile(d.exponent), sep = " ↑ ") end -massof(m::PowerWeightedMeasure) = massof(m.parent) ^ m.exponent \ No newline at end of file +massof(m::PowerWeightedMeasure) = massof(m.parent)^m.exponent diff --git a/src/combinators/product.jl b/src/combinators/product.jl index e4c01713..39e4db2b 100644 --- a/src/combinators/product.jl +++ b/src/combinators/product.jl @@ -161,7 +161,9 @@ marginals(μ::ProductMeasure) = μ.marginals _map(f, args...) = map(f, args...) _map(f, x::MappedArrays.ReadonlyMappedArray) = mappedarray(f ∘ x.f, x.data) -testvalue(::Type{T}, d::AbstractProductMeasure) where {T} = _map(m -> testvalue(T, m), marginals(d)) +function testvalue(::Type{T}, d::AbstractProductMeasure) where {T} + _map(m -> testvalue(T, m), marginals(d)) +end export ⊗ diff --git a/src/combinators/transformedmeasure.jl b/src/combinators/transformedmeasure.jl index c39988df..f7f2c47c 100644 --- a/src/combinators/transformedmeasure.jl +++ b/src/combinators/transformedmeasure.jl @@ -31,7 +31,6 @@ struct PushforwardMeasure{FF,IF,M,VC<:TransformVolCorr} <: AbstractPushforward volcorr::VC end - gettransform(ν::PushforwardMeasure) = ν.f parent(ν::PushforwardMeasure) = ν.origin @@ -39,7 +38,7 @@ function transport_def(ν::PushforwardMeasure{FF,IF,M}, μ::M, x) where {FF,IF,M if μ == parent(ν) return ν.f(x) else - invoke(transport_def, Tuple{Any, PushforwardMeasure, Any}, ν, μ, x) + invoke(transport_def, Tuple{Any,PushforwardMeasure,Any}, ν, μ, x) end end @@ -47,7 +46,7 @@ function transport_def(μ::M, ν::PushforwardMeasure{FF,IF,M}, y) where {FF,IF,M if μ == parent(ν) return ν.inv_f(y) else - invoke(transport_def, Tuple{Any, PushforwardMeasure, Any}, μ, ν, y) + invoke(transport_def, Tuple{Any,PushforwardMeasure,Any}, μ, ν, y) end end @@ -118,7 +117,9 @@ end insupport(ν::PushforwardMeasure, y) = insupport(transport_origin(ν), to_origin(ν, y)) -testvalue(::Type{T}, ν::PushforwardMeasure) where {T} = from_origin(ν, testvalue(T, transport_origin(ν))) +function testvalue(::Type{T}, ν::PushforwardMeasure) where {T} + from_origin(ν, testvalue(T, transport_origin(ν))) +end @inline function basemeasure(ν::PushforwardMeasure) PushforwardMeasure(ν.f, ν.inv_f, basemeasure(transport_origin(ν)), NoVolCorr()) @@ -157,9 +158,13 @@ measure](https://en.wikipedia.org/wiki/Pushforward_measure) from `μ` the If `f_inverse` is specified, it must be a valid inverse of the function given by restricting `f` to the support of `μ`. """ -pushfwd(f, μ::AbstractMeasure, volcorr::TransformVolCorr = WithVolCorr()) = pushfwd(f, inverse(f), μ, volcorr) +function pushfwd(f, μ::AbstractMeasure, volcorr::TransformVolCorr = WithVolCorr()) + pushfwd(f, inverse(f), μ, volcorr) +end -pushfwd(f, finv, μ::AbstractMeasure, volcorr::TransformVolCorr = WithVolCorr()) = PushforwardMeasure(f, finv, μ, volcorr) +function pushfwd(f, finv, μ::AbstractMeasure, volcorr::TransformVolCorr = WithVolCorr()) + PushforwardMeasure(f, finv, μ, volcorr) +end """ pullback(f, [f_inverse,] μ, volcorr = WithVolCorr()) @@ -173,24 +178,41 @@ This can be useful, since the log-density of a `PushforwardMeasure` is computing in terms of the inverse function; the "forward" function is not used at all. In some cases, we may be focusing on log-density (and not, for example, sampling). """ -pullback(f, μ::AbstractMeasure, volcorr::TransformVolCorr = WithVolCorr()) = pushfwd(inverse(f), f, μ, volcorr) - -pullback(f, finv, μ::AbstractMeasure, volcorr::TransformVolCorr = WithVolCorr()) = pushfwd(finv, f, μ, volcorr) +function pullback(f, μ::AbstractMeasure, volcorr::TransformVolCorr = WithVolCorr()) + pushfwd(inverse(f), f, μ, volcorr) +end +function pullback(f, finv, μ::AbstractMeasure, volcorr::TransformVolCorr = WithVolCorr()) + pushfwd(finv, f, μ, volcorr) +end -@inline function pushfwd(f, μ::PushforwardMeasure, volcorr::TransformVolCorr = WithVolCorr()) +@inline function pushfwd( + f, + μ::PushforwardMeasure, + volcorr::TransformVolCorr = WithVolCorr(), +) _pushfwd(f, inverse(f), μ, volcorr, μ.volcorr) end - -@inline function pushfwd(f, finv, μ::PushforwardMeasure, volcorr::TransformVolCorr = WithVolCorr()) +@inline function pushfwd( + f, + finv, + μ::PushforwardMeasure, + volcorr::TransformVolCorr = WithVolCorr(), +) _pushfwd(f, finv, μ, volcorr, μ.volcorr) end -@inline function _pushfwd(f, finv, μ::PushforwardMeasure, vf::V, vμ::V) where {V<:TransformVolCorr} +@inline function _pushfwd( + f, + finv, + μ::PushforwardMeasure, + vf::V, + vμ::V, +) where {V<:TransformVolCorr} pushfwd(f ∘ μ.f, μ.inv_f ∘ finv, μ, v) end -@inline function _pushfwd(f, finv, μ::PushforwardMeasure, vf, vμ) +@inline function _pushfwd(f, finv, μ::PushforwardMeasure, vf, vμ) PushforwardMeasure(f, finv, μ, vf) -end \ No newline at end of file +end diff --git a/src/mass-interface.jl b/src/mass-interface.jl index a7654ac2..4eccc62d 100644 --- a/src/mass-interface.jl +++ b/src/mass-interface.jl @@ -4,11 +4,9 @@ import Base abstract type AbstractUnknownMass <: Number end -struct UnknownFiniteMass <: AbstractUnknownMass -end +struct UnknownFiniteMass <: AbstractUnknownMass end -struct UnknownMass <: AbstractUnknownMass -end +struct UnknownMass <: AbstractUnknownMass end for T in (:UnknownFiniteMass, :UnknownMass) @eval begin @@ -31,7 +29,6 @@ end massof(m::AbstractMeasure) = UnknownMass(m) - struct NormalizedMeasure{P,M} <: AbstractMeasure parent::P parent_mass::M @@ -41,7 +38,6 @@ massof(m::NormalizedMeasure) = static(1.0) normalize(m::AbstractMeasure) = _normalize(m, massof(m)) - _normalize(m::AbstractMeasure, mass::AbstractUnknownMass) = NormalizedMeasure(m, mass) function _normalize(m::AbstractMeasure, mass) @@ -66,6 +62,6 @@ isnormalized(m::AbstractMeasure) = isone(massof(m)) Check whether `norm(x, p) == 1`. """ -isnormalized(x, p::Real=2) = isone(norm(x, p)) +isnormalized(x, p::Real = 2) = isone(norm(x, p)) -isone(::AbstractUnknownMass) = false \ No newline at end of file +isone(::AbstractUnknownMass) = false diff --git a/src/primitives/lebesgue.jl b/src/primitives/lebesgue.jl index 35574311..39536326 100644 --- a/src/primitives/lebesgue.jl +++ b/src/primitives/lebesgue.jl @@ -4,7 +4,6 @@ export Lebesgue struct LebesgueBase <: PrimitiveMeasure end - (::LebesgueBase)(s::Interval) = width(s) testvalue(::LebesgueBase) = 0.0 @@ -13,8 +12,6 @@ insupport(::LebesgueBase, x) = true insupport(::LebesgueBase) = Returns(true) - - logdensity_def(::LebesgueBase, ::CountingBase, x) = -Inf logdensity_def(::CountingBase, ::LebesgueBase, x) = Inf @@ -67,4 +64,4 @@ function (μ::Lebesgue{<:BoundedReals})(s::Interval) right = min(s.right, b) w = right - left max(w, zero(w)) -end \ No newline at end of file +end diff --git a/src/standard/stdnormal.jl b/src/standard/stdnormal.jl index 24ce6441..76429b81 100644 --- a/src/standard/stdnormal.jl +++ b/src/standard/stdnormal.jl @@ -13,8 +13,6 @@ export StdNormal @inline getdof(::StdNormal) = static(1) @inline transport_def(::StdUniform, μ::StdNormal, x) = erfc(-x * invsqrt2) / 2 -@inline transport_def(::StdNormal, μ::StdUniform, p) = -erfcinv(2*p) * sqrt2 +@inline transport_def(::StdNormal, μ::StdUniform, p) = -erfcinv(2 * p) * sqrt2 @inline Base.rand(rng::Random.AbstractRNG, ::Type{T}, ::StdNormal) where {T} = randn(rng, T) - - diff --git a/src/standard/stduniform.jl b/src/standard/stduniform.jl index 2bd6a39c..621f090f 100644 --- a/src/standard/stduniform.jl +++ b/src/standard/stduniform.jl @@ -9,4 +9,4 @@ insupport(d::StdUniform, x) = zero(x) ≤ x ≤ one(x) Base.rand(rng::Random.AbstractRNG, ::Type{T}, ::StdUniform) where {T} = rand(rng, T) -(::StdUniform)(s::Interval) = Lebesgue(𝕀)(s::Interval) \ No newline at end of file +(::StdUniform)(s::Interval) = Lebesgue(𝕀)(s::Interval) diff --git a/src/utils.jl b/src/utils.jl index 10886d57..2b69e171 100644 --- a/src/utils.jl +++ b/src/utils.jl @@ -11,7 +11,7 @@ showparams(io::IO, nt::NamedTuple) = print(io, nt) export testvalue -@inline testvalue(μ) = testvalue(Float64, μ) +@inline testvalue(μ) = testvalue(Float64, μ) @inline testvalue(::Type{T}, μ) where {T} = rand(FixedRNG(), T, μ) diff --git a/test/runtests.jl b/test/runtests.jl index 4aa91216..4eee3c00 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -138,7 +138,7 @@ end # end @testset "broadcasting" begin - @test logdensityof.(Dirac(2), [1,2,3]) isa Vector{Float64} + @test logdensityof.(Dirac(2), [1, 2, 3]) isa Vector{Float64} end @testset "powers" begin From ef7f1abd673cd9e86cb360e287dc9644d9a60d11 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Fri, 23 Sep 2022 14:53:52 -0700 Subject: [PATCH 329/368] Calling a measure calls `massof` --- src/MeasureBase.jl | 7 +------ src/mass-interface.jl | 15 +++++++++++++++ src/primitives/lebesgue.jl | 6 +++--- src/standard/stduniform.jl | 2 +- 4 files changed, 20 insertions(+), 10 deletions(-) diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index ce31969d..792ba928 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -162,11 +162,6 @@ include("interface.jl") using .Interface -# TODO: Make this work for non-unit-mass measures -function (m::AbstractMeasure)(s::Interval) - b = transport_def(StdUniform(), m, s.right) - a = transport_def(StdUniform(), m, s.left) - return abs(b - a) -end + end # module MeasureBase diff --git a/src/mass-interface.jl b/src/mass-interface.jl index 4eccc62d..75c961dc 100644 --- a/src/mass-interface.jl +++ b/src/mass-interface.jl @@ -65,3 +65,18 @@ Check whether `norm(x, p) == 1`. isnormalized(x, p::Real = 2) = isone(norm(x, p)) isone(::AbstractUnknownMass) = false + +# TODO: Make this work for non-unit-mass measures +function massof(m::AbstractMeasure, s::Interval) + b = transport_def(StdUniform(), m, s.right) + a = transport_def(StdUniform(), m, s.left) + return abs(b - a) +end + +""" + (m::AbstractMeasure)(s) + +Convenience method for `massof(m, s)`. To make a user-defined measure callable +in this way, users should add the corresponding `massof` method. +""" +(m::AbstractMeasure)(s) = massof(m, s) \ No newline at end of file diff --git a/src/primitives/lebesgue.jl b/src/primitives/lebesgue.jl index 39536326..4d86e9ef 100644 --- a/src/primitives/lebesgue.jl +++ b/src/primitives/lebesgue.jl @@ -4,7 +4,7 @@ export Lebesgue struct LebesgueBase <: PrimitiveMeasure end -(::LebesgueBase)(s::Interval) = width(s) +massof(::LebesgueBase, s::Interval) = width(s) testvalue(::LebesgueBase) = 0.0 @@ -52,12 +52,12 @@ insupport(μ::Lebesgue, x) = x ∈ μ.support insupport(::Lebesgue{RealNumbers}, ::Real) = true -(::Lebesgue{RealNumbers})(s::Interval) = width(s) +massof(::Lebesgue{RealNumbers}, s::Interval) = width(s) # Example: # julia> Lebesgue(𝕀)(0.2..5) # 0.8 -function (μ::Lebesgue{<:BoundedReals})(s::Interval) +function massof(μ::Lebesgue{<:BoundedReals}, s::Interval) a = μ.support.lower b = μ.support.upper left = max(s.left, a) diff --git a/src/standard/stduniform.jl b/src/standard/stduniform.jl index 621f090f..32f4c62c 100644 --- a/src/standard/stduniform.jl +++ b/src/standard/stduniform.jl @@ -9,4 +9,4 @@ insupport(d::StdUniform, x) = zero(x) ≤ x ≤ one(x) Base.rand(rng::Random.AbstractRNG, ::Type{T}, ::StdUniform) where {T} = rand(rng, T) -(::StdUniform)(s::Interval) = Lebesgue(𝕀)(s::Interval) +massof(::StdUniform, s::Interval) = massof(Lebesgue(𝕀), s::Interval) From 0cfacfd41673bbb9e49a32ee29ecf3965382952f Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Fri, 23 Sep 2022 15:05:34 -0700 Subject: [PATCH 330/368] work on massof --- src/mass-interface.jl | 1 + src/primitives/counting.jl | 4 ++++ src/utils.jl | 2 ++ 3 files changed, 7 insertions(+) diff --git a/src/mass-interface.jl b/src/mass-interface.jl index 75c961dc..3b1ff1ad 100644 --- a/src/mass-interface.jl +++ b/src/mass-interface.jl @@ -27,6 +27,7 @@ for op in (:+, :*) end end +export massof massof(m::AbstractMeasure) = UnknownMass(m) struct NormalizedMeasure{P,M} <: AbstractMeasure diff --git a/src/primitives/counting.jl b/src/primitives/counting.jl index 69476a05..101ef8d0 100644 --- a/src/primitives/counting.jl +++ b/src/primitives/counting.jl @@ -31,3 +31,7 @@ Base.show(io::IO, d::Counting) = print(io, "Counting(", d.support, ")") insupport(μ::Counting, x) = x ∈ μ.support insupport(μ::Counting{T}, x) where {T<:Type} = x isa μ.support + +massof(c::Counting, s::Set) = massof(CountingBase(), filter(insupport(c), s)) + +massof(::CountingBase, s::Set) = length(s) \ No newline at end of file diff --git a/src/utils.jl b/src/utils.jl index 2b69e171..d9d28b0e 100644 --- a/src/utils.jl +++ b/src/utils.jl @@ -152,3 +152,5 @@ end function rmap(f, nt::NamedTuple{N,T}) where {N,T} NamedTuple{N}(map(x -> rmap(f, x), values(nt))) end + +insupport(m::AbstractMeasure) = Base.Fix1(insupport, m) \ No newline at end of file From 504936c616705c1b6ec87a79d1030bc28597bb06 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Fri, 23 Sep 2022 15:39:36 -0700 Subject: [PATCH 331/368] AbstractSuperpositionMeasure --- src/combinators/superpose.jl | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/src/combinators/superpose.jl b/src/combinators/superpose.jl index 44eae6b4..0b000150 100644 --- a/src/combinators/superpose.jl +++ b/src/combinators/superpose.jl @@ -4,6 +4,8 @@ using LogExpFunctions export SuperpositionMeasure +abstract type AbstractSuperpositionMeasure <: AbstractMeasure end + @doc raw""" struct SuperpositionMeasure{NT} <: AbstractMeasure components :: NT @@ -24,7 +26,7 @@ Superposition measures satisfy \end{aligned} ``` """ -struct SuperpositionMeasure{C} <: AbstractMeasure +struct SuperpositionMeasure{C} <: AbstractSuperpositionMeasure components::C end From 0e9a5637e82013dc0812cce9e445d5d130791743 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 26 Sep 2022 09:37:52 -0700 Subject: [PATCH 332/368] fix typo --- src/combinators/transformedmeasure.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/combinators/transformedmeasure.jl b/src/combinators/transformedmeasure.jl index f7f2c47c..2313d705 100644 --- a/src/combinators/transformedmeasure.jl +++ b/src/combinators/transformedmeasure.jl @@ -210,7 +210,7 @@ end vf::V, vμ::V, ) where {V<:TransformVolCorr} - pushfwd(f ∘ μ.f, μ.inv_f ∘ finv, μ, v) + pushfwd(f ∘ μ.f, μ.inv_f ∘ finv, μ, vf) end @inline function _pushfwd(f, finv, μ::PushforwardMeasure, vf, vμ) From e4147cfe1211be2a2dab51cc07ede4fca04960b3 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 26 Sep 2022 11:44:39 -0700 Subject: [PATCH 333/368] typo --- src/combinators/power.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/combinators/power.jl b/src/combinators/power.jl index e3c7a3eb..570e8b18 100644 --- a/src/combinators/power.jl +++ b/src/combinators/power.jl @@ -129,4 +129,4 @@ function checked_arg(μ::PowerMeasure, x::Any) throw(ArgumentError("Size of variate doesn't match size of power measure")) end -massof(m::PowerMeasure) = massof(m.parent)^product(m.axes) +massof(m::PowerMeasure) = massof(m.parent)^prod(m.axes) From 3eba519c828fc37f7498e4b98cf12d34cbfb1a34 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 26 Sep 2022 16:24:23 -0700 Subject: [PATCH 334/368] format --- src/MeasureBase.jl | 2 -- src/mass-interface.jl | 2 +- src/primitives/counting.jl | 2 +- src/utils.jl | 2 +- 4 files changed, 3 insertions(+), 5 deletions(-) diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index 792ba928..dd437103 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -162,6 +162,4 @@ include("interface.jl") using .Interface - - end # module MeasureBase diff --git a/src/mass-interface.jl b/src/mass-interface.jl index 3b1ff1ad..a6c1b19f 100644 --- a/src/mass-interface.jl +++ b/src/mass-interface.jl @@ -80,4 +80,4 @@ end Convenience method for `massof(m, s)`. To make a user-defined measure callable in this way, users should add the corresponding `massof` method. """ -(m::AbstractMeasure)(s) = massof(m, s) \ No newline at end of file +(m::AbstractMeasure)(s) = massof(m, s) diff --git a/src/primitives/counting.jl b/src/primitives/counting.jl index 101ef8d0..f101ca96 100644 --- a/src/primitives/counting.jl +++ b/src/primitives/counting.jl @@ -34,4 +34,4 @@ insupport(μ::Counting{T}, x) where {T<:Type} = x isa μ.support massof(c::Counting, s::Set) = massof(CountingBase(), filter(insupport(c), s)) -massof(::CountingBase, s::Set) = length(s) \ No newline at end of file +massof(::CountingBase, s::Set) = length(s) diff --git a/src/utils.jl b/src/utils.jl index d9d28b0e..b9f2cb29 100644 --- a/src/utils.jl +++ b/src/utils.jl @@ -153,4 +153,4 @@ function rmap(f, nt::NamedTuple{N,T}) where {N,T} NamedTuple{N}(map(x -> rmap(f, x), values(nt))) end -insupport(m::AbstractMeasure) = Base.Fix1(insupport, m) \ No newline at end of file +insupport(m::AbstractMeasure) = Base.Fix1(insupport, m) From 2393222f718e7a9a4df09c821bc2173d20b15690 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 27 Sep 2022 09:54:38 -0700 Subject: [PATCH 335/368] docstrings --- src/mass-interface.jl | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/src/mass-interface.jl b/src/mass-interface.jl index a6c1b19f..90831798 100644 --- a/src/mass-interface.jl +++ b/src/mass-interface.jl @@ -4,8 +4,18 @@ import Base abstract type AbstractUnknownMass <: Number end +""" + struct UnknownFiniteMass <: AbstractUnknownMass end + +See `massof` +""" struct UnknownFiniteMass <: AbstractUnknownMass end +""" + struct UnknownMass <: AbstractUnknownMass end + +See `massof` +""" struct UnknownMass <: AbstractUnknownMass end for T in (:UnknownFiniteMass, :UnknownMass) @@ -28,6 +38,33 @@ for op in (:+, :*) end export massof + +""" + massof(m) + +Get the _mass_ of a measure - that is, integrate the measure over its support. + +`massof` + +---------- + + massof(m, dom) + +Integrate the measure `m` over the "domain" `dom`. Note that domains are not +defined universally, but may be specific to a given measure. If `m` is +`<:AbstractMeasure`, users can also write `m(dom)`. For new measures, users +should *not* add new "call" methods, but instead extend `MeasureBase.massof`. + + +For example, for many univariate measures `m` with `rootmeasure(m) == +LebesgueBase()`, users can call `massof(m, a_b)` where +`a_b::IntervalSets.Interval`. + +`massof` often returns a `Real`. But in many cases we may only know the mass is +finite, or we may know nothing at all about it. For these cases, it will return +`UnknownFiniteMass` or `UnknownMass`, respectively. When no `massof` method +exists, it defaults to `UnknownMass`. +""" massof(m::AbstractMeasure) = UnknownMass(m) struct NormalizedMeasure{P,M} <: AbstractMeasure From 8ba4f5b9eb7c918a2a3f9d72bc5b9d0b32c0378b Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 27 Sep 2022 12:43:30 -0700 Subject: [PATCH 336/368] remove massof(::PowerWeightedMeasure) method --- src/combinators/powerweighted.jl | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/src/combinators/powerweighted.jl b/src/combinators/powerweighted.jl index 1d1a734b..68a4d50f 100644 --- a/src/combinators/powerweighted.jl +++ b/src/combinators/powerweighted.jl @@ -34,6 +34,4 @@ end function Pretty.tile(d::PowerWeightedMeasure) Pretty.pair_layout(Pretty.tile(d.parent), Pretty.tile(d.exponent), sep = " ↑ ") -end - -massof(m::PowerWeightedMeasure) = massof(m.parent)^m.exponent +end \ No newline at end of file From d4135443ca860a0d412b22aea92b1d6ec946d34f Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 27 Sep 2022 14:43:32 -0700 Subject: [PATCH 337/368] make `massof` better --- src/mass-interface.jl | 7 ++----- src/primitives/lebesgue.jl | 6 ++++++ 2 files changed, 8 insertions(+), 5 deletions(-) diff --git a/src/mass-interface.jl b/src/mass-interface.jl index 90831798..c141d076 100644 --- a/src/mass-interface.jl +++ b/src/mass-interface.jl @@ -104,11 +104,8 @@ isnormalized(x, p::Real = 2) = isone(norm(x, p)) isone(::AbstractUnknownMass) = false -# TODO: Make this work for non-unit-mass measures -function massof(m::AbstractMeasure, s::Interval) - b = transport_def(StdUniform(), m, s.right) - a = transport_def(StdUniform(), m, s.left) - return abs(b - a) +function massof(m, s) + _massof(m, s, rootmeasure(m)) end """ diff --git a/src/primitives/lebesgue.jl b/src/primitives/lebesgue.jl index 4d86e9ef..5f3610eb 100644 --- a/src/primitives/lebesgue.jl +++ b/src/primitives/lebesgue.jl @@ -24,6 +24,12 @@ logdensity_def(::CountingBase, ::LebesgueBase, x) = Inf @boundscheck throw(ArgumentError("Invalid variate type for measure")) end +function _massof(m, s::Interval, ::LebesgueBase) + b = transport_def(StdUniform(), m, s.right) + a = transport_def(StdUniform(), m, s.left) + return abs(b - a) +end + ########################################################## struct Lebesgue{T} <: AbstractMeasure support::T From 2164d7159c0b357d34a399e21233a86a5ea07888 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 28 Sep 2022 05:44:26 -0700 Subject: [PATCH 338/368] update testvalue --- src/utils.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/utils.jl b/src/utils.jl index b9f2cb29..88fec71d 100644 --- a/src/utils.jl +++ b/src/utils.jl @@ -11,7 +11,7 @@ showparams(io::IO, nt::NamedTuple) = print(io, nt) export testvalue -@inline testvalue(μ) = testvalue(Float64, μ) +@inline testvalue(μ) = rand(FixedRNG(), μ) @inline testvalue(::Type{T}, μ) where {T} = rand(FixedRNG(), T, μ) From 8e635261ae4636b4a20d8d805e71c5132a1440d4 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 28 Sep 2022 05:55:39 -0700 Subject: [PATCH 339/368] formatting --- src/combinators/powerweighted.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/combinators/powerweighted.jl b/src/combinators/powerweighted.jl index 68a4d50f..47f50da4 100644 --- a/src/combinators/powerweighted.jl +++ b/src/combinators/powerweighted.jl @@ -34,4 +34,4 @@ end function Pretty.tile(d::PowerWeightedMeasure) Pretty.pair_layout(Pretty.tile(d.parent), Pretty.tile(d.exponent), sep = " ↑ ") -end \ No newline at end of file +end From 4bc9d93bc4d457144161d82767c2a455ec904a24 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 28 Sep 2022 06:56:06 -0700 Subject: [PATCH 340/368] update _massof --- src/primitives/lebesgue.jl | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/src/primitives/lebesgue.jl b/src/primitives/lebesgue.jl index 5f3610eb..c1501963 100644 --- a/src/primitives/lebesgue.jl +++ b/src/primitives/lebesgue.jl @@ -25,9 +25,12 @@ logdensity_def(::CountingBase, ::LebesgueBase, x) = Inf end function _massof(m, s::Interval, ::LebesgueBase) - b = transport_def(StdUniform(), m, s.right) - a = transport_def(StdUniform(), m, s.left) - return abs(b - a) + mass = massof(m) + nu = mass * StdUniform() + f = transport_to(nu, m) + a = f(minimum(s)) + b = f(maximum(s)) + return mass * abs(b - a) end ########################################################## From 782c412b9fb9d7597ddded03b66769704027c9c8 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 28 Sep 2022 07:04:11 -0700 Subject: [PATCH 341/368] Update transports for weighted measures --- src/combinators/weighted.jl | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/src/combinators/weighted.jl b/src/combinators/weighted.jl index ec7095ad..8c63eb7c 100644 --- a/src/combinators/weighted.jl +++ b/src/combinators/weighted.jl @@ -51,6 +51,8 @@ gentype(μ::WeightedMeasure) = gentype(μ.base) insupport(μ::WeightedMeasure, x) = insupport(μ.base, x) -transport_origin(ν::WeightedMeasure) = ν.base -to_origin(::WeightedMeasure, y) = y -from_origin(::WeightedMeasure, x) = x +# Transports must preserve mass +transport_origin(ν::WeightedMeasure) = weightedmeasure(ν.logweight, transport_origin(ν.base)) + +to_origin(w::WeightedMeasure, y) = to_origin(w.base, y) +from_origin(w::WeightedMeasure, x) = from_origin(w.base, x) From bb092d50472ca735b7f69c51893e26a86029455b Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 28 Sep 2022 17:02:46 -0700 Subject: [PATCH 342/368] add chain rules --- src/density.jl | 21 +++++++++++++++++---- 1 file changed, 17 insertions(+), 4 deletions(-) diff --git a/src/density.jl b/src/density.jl index c5cdc9fe..282ded86 100644 --- a/src/density.jl +++ b/src/density.jl @@ -121,7 +121,18 @@ To compute a log-density relative to a specific base-measure, see """ @inline function logdensityof(μ::AbstractMeasure, x) result = dynamic(unsafe_logdensityof(μ, x)) - ifelse(insupport(μ, x) == true, result, oftype(result, -Inf)) + _checksupport(insupport(μ, x), result) +end + +_checksupport(cond, result) = ifelse(cond == true, result, oftype(result, -Inf)) + +import ChainRulesCore +@inline function ChainRulesCore.rrule(::typeof(_checksupport), cond, result) + y = _checksupport(cond, result) + function _checksupport_pullback(ȳ) + return NoTangent(), ZeroTangent(), one(ȳ) + end + y, _checksupport_pullback end export unsafe_logdensityof @@ -140,9 +151,11 @@ See also `logdensityof`. b_0 = μ Base.Cartesian.@nexprs 10 i -> begin # 10 is just some "big enough" number b_{i} = basemeasure(b_{i - 1}, x) - if b_{i} isa typeof(b_{i - 1}) - return ℓ_{i - 1} - end + + # The below makes the evaluated code shorter, but screws up Zygote + # if b_{i} isa typeof(b_{i - 1}) + # return ℓ_{i - 1} + # end ℓ_{i} = let Δℓ_{i} = logdensity_def(b_{i}, x) ℓ_{i - 1} + Δℓ_{i} end From be8251a4cb6fdb9439a264a292d43e360fd36832 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Wed, 28 Sep 2022 18:53:37 -0700 Subject: [PATCH 343/368] invariant mass under transport --- test/transport.jl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/test/transport.jl b/test/transport.jl index c81450ce..080ed397 100644 --- a/test/transport.jl +++ b/test/transport.jl @@ -20,12 +20,12 @@ using LogExpFunctions: logit @testset "transport_to (variations of) $(nameof(typeof(μ0))) to $(nameof(typeof(ν0)))" begin test_transport(ν0, μ0) - test_transport(2.2 * ν0, 3 * μ0) + test_transport(2.2 * ν0, 2.2 * μ0) test_transport(ν0, μ0^1) test_transport(ν0^1, μ0) test_transport(ν0^3, μ0^3) test_transport(ν0^(2, 3, 2), μ0^(3, 4)) - test_transport(2.2 * ν0^(2, 3, 2), 3 * μ0^(3, 4)) + test_transport(2.2 * ν0^(2, 3, 2), 2.2 * μ0^(3, 4)) @test_throws ArgumentError transport_to(ν0, μ0)(rand(μ0^12)) @test_throws ArgumentError transport_to(ν0^3, μ0^3)(rand(μ0^(3, 4))) end From 38f0fe2d579a8828a3977a9b88d4038e9642eabf Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Thu, 29 Sep 2022 05:46:26 -0700 Subject: [PATCH 344/368] typo --- src/transport.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/transport.jl b/src/transport.jl index 652ddfcd..d8753e51 100644 --- a/src/transport.jl +++ b/src/transport.jl @@ -34,7 +34,7 @@ Pull `y` from `ν` back to `MeasureBase.transport_origin(ν)`. """ function to_origin end -to_origin(ν::NU, ::Any) where {NU} = NoTransportOrigin{NU}(ν) +to_origin(ν::NU, ::Any) where {NU} = NoTransportOrigin{NU}() """ struct MeasureBase.NoTransport{NU,MU} end From 93804cf9093dce7d91ef1259373ff08ec97a7ecf Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Fri, 30 Sep 2022 11:41:17 -0700 Subject: [PATCH 345/368] bugfix --- src/density.jl | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/src/density.jl b/src/density.jl index 282ded86..d69e1e1e 100644 --- a/src/density.jl +++ b/src/density.jl @@ -236,7 +236,9 @@ function logdensity_def(μ::T, ν::T, x) where {T} if μ === ν return zero(logdensity_def(μ, x)) else - return logdensity_def(μ, x) - logdensity_def(ν, x) + α = basemeasure(μ) + β = basemeasure(ν) + return logdensity_def(μ, x) - logdensity_def(ν, x) + logdensity_rel(α, β, x) end end From 4aa2b4495579f07f3968ab69a36aeeb110eb18fc Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Fri, 30 Sep 2022 15:11:49 -0700 Subject: [PATCH 346/368] hasmethod => Tricks.static_hasmethod --- src/interface.jl | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/interface.jl b/src/interface.jl index ecbc4ec2..0ad64b5b 100644 --- a/src/interface.jl +++ b/src/interface.jl @@ -11,6 +11,7 @@ using MeasureBase: transport_to, NoTransport using DensityInterface: logdensityof using InverseFunctions: inverse using ChangesOfVariables: with_logabsdet_jacobian +using Tricks: static_hasmethod export test_interface export test_transport @@ -23,7 +24,7 @@ export commonbase using Test function dynamic_basemeasure_depth(μ::M) where {M} - if hasmethod(proxy, Tuple{M}) + if static_hasmethod(proxy, Tuple{M}) return dynamic_basemeasure_depth(proxy(μ)) end β = basemeasure(μ) From 6e5526f0a80191dfc398c1f37ee567eaeacf079d Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Sat, 1 Oct 2022 16:22:11 -0700 Subject: [PATCH 347/368] `massof` methods --- src/combinators/product.jl | 2 ++ src/combinators/smart-constructors.jl | 2 +- src/combinators/superpose.jl | 2 ++ src/combinators/weighted.jl | 2 ++ src/primitives/dirac.jl | 2 ++ src/primitives/lebesgue.jl | 2 ++ src/primitives/trivial.jl | 2 ++ 7 files changed, 13 insertions(+), 1 deletion(-) diff --git a/src/combinators/product.jl b/src/combinators/product.jl index 39e4db2b..4f310d5f 100644 --- a/src/combinators/product.jl +++ b/src/combinators/product.jl @@ -16,6 +16,8 @@ function Pretty.tile(μ::AbstractProductMeasure) result *= Pretty.literal(")") end +massof(m::AbstractProductMeasure) = prod(massof, marginals(m)) + export marginals function Base.:(==)(a::AbstractProductMeasure, b::AbstractProductMeasure) diff --git a/src/combinators/smart-constructors.jl b/src/combinators/smart-constructors.jl index 775b1d93..11d7bbbb 100644 --- a/src/combinators/smart-constructors.jl +++ b/src/combinators/smart-constructors.jl @@ -85,7 +85,7 @@ superpose(nt::NamedTuple) = SuperpositionMeasure(nt) function superpose(μ::T, ν::T) where {T<:AbstractMeasure} if μ == ν - return weightedmeasure(logtwo, μ) + return weightedmeasure(static(float(logtwo)), μ) else return superpose((μ, ν)) end diff --git a/src/combinators/superpose.jl b/src/combinators/superpose.jl index 0b000150..2d385636 100644 --- a/src/combinators/superpose.jl +++ b/src/combinators/superpose.jl @@ -30,6 +30,8 @@ struct SuperpositionMeasure{C} <: AbstractSuperpositionMeasure components::C end +massof(m::SuperpositionMeasure) = sum(massof, m.components) + function Pretty.tile(d::SuperpositionMeasure) result = Pretty.literal("SuperpositionMeasure(") result *= Pretty.list_layout([Pretty.tile.(d.components)...]) diff --git a/src/combinators/weighted.jl b/src/combinators/weighted.jl index 8c63eb7c..10f79af2 100644 --- a/src/combinators/weighted.jl +++ b/src/combinators/weighted.jl @@ -29,6 +29,8 @@ struct WeightedMeasure{R,M} <: AbstractWeightedMeasure base::M end +massof(w::WeightedMeasure) = exp(w.logweight) * massof(w.base) + _logweight(μ::WeightedMeasure) = μ.logweight basemeasure(μ::AbstractWeightedMeasure) = μ.base diff --git a/src/primitives/dirac.jl b/src/primitives/dirac.jl index 69e1313e..77727605 100644 --- a/src/primitives/dirac.jl +++ b/src/primitives/dirac.jl @@ -18,6 +18,8 @@ end basemeasure(d::Dirac) = CountingBase() +massof(::Dirac) = static(1.0) + logdensity_def(μ::Dirac, x) = 0.0 Base.rand(::Random.AbstractRNG, T::Type, μ::Dirac) = μ.x diff --git a/src/primitives/lebesgue.jl b/src/primitives/lebesgue.jl index c1501963..b12a80c0 100644 --- a/src/primitives/lebesgue.jl +++ b/src/primitives/lebesgue.jl @@ -24,6 +24,8 @@ logdensity_def(::CountingBase, ::LebesgueBase, x) = Inf @boundscheck throw(ArgumentError("Invalid variate type for measure")) end +massof(::LebesgueBase) = static(Inf) + function _massof(m, s::Interval, ::LebesgueBase) mass = massof(m) nu = mass * StdUniform() diff --git a/src/primitives/trivial.jl b/src/primitives/trivial.jl index e82b4ffc..6f73eb78 100644 --- a/src/primitives/trivial.jl +++ b/src/primitives/trivial.jl @@ -5,3 +5,5 @@ struct TrivialMeasure <: PrimitiveMeasure end gentype(::TrivialMeasure) = Nothing insupport(::TrivialMeasure, x) = False + +massof(::TrivialMeasure) = static(0.0) \ No newline at end of file From d0530c3bc2891243d21a052139aaeb9d99f381a8 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 3 Oct 2022 09:09:54 -0700 Subject: [PATCH 348/368] roll back tranports for WeightedMeasure --- src/combinators/weighted.jl | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/combinators/weighted.jl b/src/combinators/weighted.jl index 10f79af2..db239b50 100644 --- a/src/combinators/weighted.jl +++ b/src/combinators/weighted.jl @@ -53,8 +53,8 @@ gentype(μ::WeightedMeasure) = gentype(μ.base) insupport(μ::WeightedMeasure, x) = insupport(μ.base, x) -# Transports must preserve mass -transport_origin(ν::WeightedMeasure) = weightedmeasure(ν.logweight, transport_origin(ν.base)) +# TODO: Transports must preserve mass +transport_origin(ν::WeightedMeasure) = ν.base -to_origin(w::WeightedMeasure, y) = to_origin(w.base, y) -from_origin(w::WeightedMeasure, x) = from_origin(w.base, x) +to_origin(w::WeightedMeasure, y) = y +from_origin(w::WeightedMeasure, x) = x From e9cffcdd02608edf705af84ee8faf6fd6ebd6865 Mon Sep 17 00:00:00 2001 From: Oliver Schulz Date: Mon, 3 Oct 2022 18:37:59 +0200 Subject: [PATCH 349/368] Improve transport implementation and add product support (#97) * Improve default transport implementation Increases type stability. * Rename NoTransformOrigin to NoTransportOrigin * Add rrule for _origin_depth * Fix ambiguities when forwarding NoTransportOrigin and NoTransportOrigin * Define getdof for product measures * Generalize test_transport to tuple-valued measures * Implement transport for tuple-based products Co-authored-by: Chad Scherrer --- src/combinators/product.jl | 12 +++++ src/interface.jl | 12 +++-- src/standard/stdmeasure.jl | 47 ++++++++++++++++++++ src/transport.jl | 89 +++++++++++++++++++++----------------- test/transport.jl | 12 +++++ 5 files changed, 130 insertions(+), 42 deletions(-) diff --git a/src/combinators/product.jl b/src/combinators/product.jl index 4f310d5f..fefce863 100644 --- a/src/combinators/product.jl +++ b/src/combinators/product.jl @@ -224,3 +224,15 @@ end end return true end + + +getdof(d::AbstractProductMeasure) = mapreduce(getdof, +, marginals(d)) + + +function checked_arg(μ::ProductMeasure{<:NTuple{N,Any}}, x::NTuple{N,Any}) where N + map(checked_arg, marginals(μ), x) +end + +function checked_arg(μ::ProductMeasure{<:NamedTuple{names}}, x::NamedTuple{names}) where names + NamedTuple{names}(map(checked_arg, values(marginals(μ)), values(x))) +end diff --git a/src/interface.jl b/src/interface.jl index 0ad64b5b..4a1bda5b 100644 --- a/src/interface.jl +++ b/src/interface.jl @@ -71,22 +71,28 @@ function test_interface(μ::M) where {M} end end + function test_transport(ν, μ) + supertype(x) = Any supertype(x::Real) = Real supertype(x::AbstractArray{<:Real,N}) where {N} = AbstractArray{<:Real,N} + structisapprox(a, b) = isapprox(a, b) + structisapprox(a::NTuple{N,Any}, b::NTuple{N,Any}) where N = all(map(structisapprox, a, b)) + structisapprox(a::NamedTuple{names}, b::NamedTuple{names}) where names = all(map(structisapprox, values(a), values(b))) + @testset "transport_to $μ to $ν" begin x = rand(μ) @test !(@inferred(transport_to(ν, μ)(x)) isa NoTransport) f = transport_to(ν, μ) y = f(x) - @test @inferred(inverse(f)(y)) ≈ x + @test structisapprox(@inferred(inverse(f)(y)), x) @test @inferred(with_logabsdet_jacobian(f, x)) isa Tuple{supertype(y),Real} @test @inferred(with_logabsdet_jacobian(inverse(f), y)) isa Tuple{supertype(x),Real} y2, ladj_fwd = with_logabsdet_jacobian(f, x) x2, ladj_inv = with_logabsdet_jacobian(inverse(f), y) - @test x ≈ x2 - @test y ≈ y2 + @test structisapprox(x, x2) + @test structisapprox(y, y2) @test ladj_fwd ≈ -ladj_inv @test ladj_fwd ≈ logdensityof(μ, x) - logdensityof(ν, y) end diff --git a/src/standard/stdmeasure.jl b/src/standard/stdmeasure.jl index 59c21026..316f97b0 100644 --- a/src/standard/stdmeasure.jl +++ b/src/standard/stdmeasure.jl @@ -53,3 +53,50 @@ end @inline function transport_def(ν::PowerMeasure{<:StdMeasure}, ::Dirac, ::Any) Zeros{Bool}(map(_ -> 0, ν.axes)) end + + +# Helpers for product transforms and similar: + +struct _TransportToStd{NU<:StdMeasure} <: Function end +_TransportToStd{NU}(μ, x) where NU = transport_to(NU()^getdof(μ), μ)(x) + +struct _TransportFromStd{MU<:StdMeasure} <: Function end +_TransportFromStd{MU}(ν, x) where MU = transport_to(ν, MU()^getdof(ν))(x) + + +function _tuple_transport_def(ν::PowerMeasure{NU}, μs::Tuple, xs::Tuple) where {NU<:StdMeasure} + reshape(vcat(map(_TransportToStd{NU}, μs, xs)...), ν.axes) +end + +function transport_def(ν::PowerMeasure{NU}, μ::ProductMeasure{<:Tuple}, x) where {NU<:StdMeasure} + _tuple_transport_def(ν, marginals(μ), x) +end + +function transport_def(ν::PowerMeasure{NU}, μ::ProductMeasure{<:NamedTuple{names}}, x) where {NU<:StdMeasure,names} + _tuple_transport_def(ν, values(marginals(μ)), values(x)) +end + + +@inline _offset_cumsum(s, x, y, rest...) = (s, _offset_cumsum(s+x, y, rest...)...) +@inline _offset_cumsum(s,x) = (s,) +@inline _offset_cumsum(s) = () + +function _stdvar_viewranges(μs::Tuple, startidx::Integer) + N = map(getdof, μs) + offs = _offset_cumsum(startidx, N...) + map((o, n) -> o:o+n-1, offs, N) +end + +function _tuple_transport_def(νs::Tuple, μ::PowerMeasure{MU}, x::AbstractArray{<:Real}) where {MU<:StdMeasure} + vrs = _stdvar_viewranges(νs, firstindex(x)) + xs = map(r -> view(x, r), vrs) + map(_TransportFromStd{MU}, νs, xs) +end + +function transport_def(ν::ProductMeasure{<:Tuple}, μ::PowerMeasure{MU}, x) where {MU<:StdMeasure} + _tuple_transport_def(marginals(ν), μ, x) +end + +function transport_def(ν::ProductMeasure{<:NamedTuple{names}}, μ::PowerMeasure{MU}, x) where {MU<:StdMeasure,names} + NamedTuple{names}(_tuple_transport_def(values(marginals(ν)), μ, x)) +end diff --git a/src/transport.jl b/src/transport.jl index d8753e51..ff3f4bed 100644 --- a/src/transport.jl +++ b/src/transport.jl @@ -113,61 +113,72 @@ See [`transport_to`](@ref). """ function transport_def end -transport_def(::Any, ::Any, x::NoTransportOrigin) = x -transport_def(::Any, ::Any, x::NoTransport) = x - function transport_def(ν, μ, x) - _transport_with_intermediate( - ν, - _checked_transport_origin(ν), - _checked_transport_origin(μ), - μ, - x, - ) + _transport_between_origins(ν, _origin_depth(ν), _origin_depth(μ), μ, x) end -@inline _origin_must_have_separate_type(::Type{MU}, μ_o) where {MU} = μ_o -function _origin_must_have_separate_type(::Type{MU}, μ_o::MU) where {MU} - throw(ArgumentError("Measure of type $MU and its origin must have separate types")) -end -@inline function _checked_transport_origin(μ::MU) where {MU} - μ_o = transport_origin(μ) - _origin_must_have_separate_type(MU, μ_o) +@inline function _origin_depth(ν::NU) where {NU} + ν_0 = ν + Base.Cartesian.@nexprs 10 i -> begin # 10 is just some "big enough" number + ν_{i} = transport_origin(ν_{i - 1}) + if ν_{i} isa NoTransportOrigin + return static(i - 1) + end + end + return static(10) end -function _transport_with_intermediate(ν, ν_o, μ_o, μ, x) - x_o = to_origin(μ, x) - # If μ is a pushforward then checked_arg may have been bypassed, so check now: - y_o = transport_def(ν_o, μ_o, checked_arg(μ_o, x_o)) - y = from_origin(ν, y_o) - return y -end +_origin_depth_pullback(ΔΩ) = NoTangent(), NoTangent() +ChainRulesCore.rrule(::typeof(_origin_depth), ν) = _origin_depth(ν), _origin_depth_pullback -function _transport_with_intermediate(ν, ν_o, ::NoTransportOrigin, μ, x) - y_o = transport_def(ν_o, μ, x) - y = from_origin(ν, y_o) - return y -end -function _transport_with_intermediate(ν, ::NoTransportOrigin, μ_o, μ, x) - x_o = to_origin(μ, x) - # If μ is a pushforward then checked_arg may have been bypassed, so check now: - y = transport_def(ν, μ_o, checked_arg(μ_o, x_o)) - return y +# If both both measures have no origin: +function _transport_between_origins(ν, ::StaticInt{0}, ::StaticInt{0}, μ, x) + _transport_with_intermediate(ν, _transport_intermediate(ν, μ), μ, x) end -function _transport_with_intermediate(ν, ::NoTransportOrigin, ::NoTransportOrigin, μ, x) - _transport_with_intermediate(ν, _transport_intermediate(ν, μ), μ, x) +@generated function _transport_between_origins(ν, ::StaticInt{n_ν}, ::StaticInt{n_μ}, μ, x) where {n_ν, n_μ} + prog = quote + μ0 = μ + x0 = x + ν0 = ν + end + for i in 1:n_μ + μ_i = Symbol(:μ,i); μ_last = Symbol(:μ,i-1) + push!(prog.args, :($μ_i = transport_origin($μ_last))) + end + for i in 1:n_μ + x_i = Symbol(:x,i); x_last = Symbol(:x,i-1); μ_last = Symbol(:μ,i-1) + push!(prog.args, :($x_i = to_origin($μ_last, $x_last))) + end + for i in 1:(n_ν) + ν_i = Symbol(:ν,i); ν_last = Symbol(:ν,i-1); + push!(prog.args, :($ν_i = transport_origin($ν_last))) + end + μ_im = Symbol(:μ,n_μ); x_im = Symbol(:x,n_μ) + ν_im = Symbol(:ν,n_ν); y_im = Symbol(:y,n_ν) + push!(prog.args, :($y_im = transport_def($ν_im, $μ_im, $x_im))) + for i in (n_ν-1):-1:0 + y_i = Symbol(:y,i); y_last = Symbol(:y,i+1); ν_last = Symbol(:ν,i) + push!(prog.args, :($y_i = from_origin($ν_last, $y_last))) + end + push!(prog.args, :(return y0)) + return prog end + @inline _transport_intermediate(ν, μ) = _transport_intermediate(getdof(ν), getdof(μ)) @inline _transport_intermediate(::Integer, n_μ::Integer) = StdUniform()^n_μ @inline _transport_intermediate(::StaticInt{1}, ::StaticInt{1}) = StdUniform() +_call_transport_def(ν, μ, x) = transport_def(ν, μ, x) +_call_transport_def(::Any, ::Any, x::NoTransportOrigin) = x +_call_transport_def(::Any, ::Any, x::NoTransport) = x + function _transport_with_intermediate(ν, m, μ, x) - z = transport_def(m, μ, x) - y = transport_def(ν, m, z) + z = _call_transport_def(m, μ, x) + y = _call_transport_def(ν, m, z) return y end @@ -208,7 +219,7 @@ function Base.:(==)(a::TransportFunction, b::TransportFunction) end Base.@propagate_inbounds function (f::TransportFunction)(x) - return transport_def(f.ν, f.μ, checked_arg(f.μ, x)) + return _call_transport_def(f.ν, f.μ, checked_arg(f.μ, x)) end @inline function InverseFunctions.inverse(f::TransportFunction{NU,MU}) where {NU,MU} diff --git a/test/transport.jl b/test/transport.jl index 080ed397..c1907f18 100644 --- a/test/transport.jl +++ b/test/transport.jl @@ -5,7 +5,11 @@ using MeasureBase: StdUniform, StdExponential, StdLogistic, StdNormal using MeasureBase: Dirac using LogExpFunctions: logit +using ChainRulesTestUtils + @testset "transport_to" begin + test_rrule(MeasureBase._origin_depth, pushfwd(exp, StdUniform())) + for (f, μ) in [ (logit, StdUniform()) (log, StdExponential()) @@ -51,4 +55,12 @@ using LogExpFunctions: logit @test @inferred(transport_to(StdUniform()^(2, 3), StdExponential)) == transport_to(StdUniform()^(2, 3), StdExponential()^6) end + + @testset "transport for products" begin + test_transport(StdUniform()^(2, 2), productmeasure((StdExponential(), StdLogistic()^3))) + test_transport(productmeasure((StdExponential(), StdLogistic()^3)), StdUniform()^(2, 2)) + + test_transport(StdUniform()^(2, 2), productmeasure((a = StdExponential(), b = StdLogistic()^3))) + test_transport(productmeasure((a = StdExponential(), b = StdLogistic()^3)), StdUniform()^(2, 2)) + end end From 57ececedd1aadb22812013e248590e31a20f80c5 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 3 Oct 2022 15:14:06 -0700 Subject: [PATCH 350/368] `@useproxy` delegates `massof` --- src/proxies.jl | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/proxies.jl b/src/proxies.jl index dbab1f93..8dc4d3a3 100644 --- a/src/proxies.jl +++ b/src/proxies.jl @@ -24,6 +24,8 @@ macro useproxy(M) @inline $MeasureBase.to_origin(μ::$M, y) = to_origin(proxy(μ), y) @inline $MeasureBase.from_origin(μ::$M, x) = from_origin(proxy(μ), x) + @inline $MeasureBase.massof(μ::$M) = massof(proxy(μ)) + @inline $MeasureBase.massof(μ::$M, s) = massof(proxy(μ), s) (μ::$M)(s) = proxy(μ)(s) end end From 2201dc90a37d8405a84742b4433aa319d9d9cb98 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 4 Oct 2022 09:16:55 -0700 Subject: [PATCH 351/368] drop CI for nightly --- .github/workflows/CI.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index aa620f08..97bfc55a 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -26,7 +26,6 @@ jobs: - '1.6' - '1.7' - '1.8' - - 'nightly' os: - ubuntu-latest arch: From f58dfd4236efc8ca1c4715235c9e08383596c78a Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 4 Oct 2022 15:11:46 -0700 Subject: [PATCH 352/368] callable densities (#85) * callable densities * separate `Density` and `LogDensity`, etc * bugfix * move some code around * format * updates * working on densities * update CI * bugfix * formatting * reorg * fix typos * Drop LogDensityMeasure and refactor * docstring * inner type constructor with assertion * type parameters * 2-arg density_rel and logdensity_rel * oops * properties * typo * fix ambiguity * bugfix * bugfix * updates * drop densityof and logdensityof for AbstractDensity * updates * update tests * update * formatting * bad calls throw errors * drop CI for nightly --- src/MeasureBase.jl | 2 + src/density-core.jl | 27 ++++--- src/density.jl | 153 +++++++++++++++++++++++++++----------- src/primitives/trivial.jl | 2 +- test/runtests.jl | 17 ++--- 5 files changed, 133 insertions(+), 68 deletions(-) diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index ed7ac40b..3022b0d7 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -17,6 +17,7 @@ using IntervalSets: Interval, width import DensityInterface: logdensityof import DensityInterface: densityof import DensityInterface: DensityKind +using DensityInterface: FuncDensity, LogFuncDensity using DensityInterface using InverseFunctions @@ -114,6 +115,7 @@ using Compat using IrrationalConstants +include("density-core.jl") include("getdof.jl") include("transport.jl") include("schema.jl") diff --git a/src/density-core.jl b/src/density-core.jl index 1be9d888..5b75f2f9 100644 --- a/src/density-core.jl +++ b/src/density-core.jl @@ -1,3 +1,14 @@ +export logdensityof +export logdensity_rel +export logdensity_def + +export unsafe_logdensityof +export unsafe_logdensity_rel + +export densityof +export density_rel +export density_def + """ logdensityof(m::AbstractMeasure, x) @@ -22,7 +33,7 @@ To compute a log-density relative to a specific base-measure, see _checksupport(insupport(μ, x), result) end -_checksupport(cond, result) = ifelse(cond == true, result, oftype(result, -Inf)) +_checksupport(cond, result) = ifelse(cond == true, result, oftype(result, -Inf)) import ChainRulesCore @inline function ChainRulesCore.rrule(::typeof(_checksupport), cond, result) @@ -61,12 +72,6 @@ See also `logdensityof`. return ℓ_10 end -export density_rel - -@inline density_rel(μ, ν, x) = exp(logdensity_rel(μ, ν, x)) - -export logdensity_rel - """ logdensity_rel(m1, m2, x) @@ -165,10 +170,8 @@ end return q end -export densityof -export logdensityof - -export density_def +@inline density_rel(μ, ν, x) = exp(logdensity_rel(μ, ν, x)) +# TODO: Do we need this method? density_def(μ, ν::AbstractMeasure, x) = exp(logdensity_def(μ, ν, x)) -density_def(μ, x) = exp(logdensity_def(μ, x)) \ No newline at end of file +density_def(μ, x) = exp(logdensity_def(μ, x)) diff --git a/src/density.jl b/src/density.jl index 360210bf..05e5a70f 100644 --- a/src/density.jl +++ b/src/density.jl @@ -1,53 +1,122 @@ -abstract type AbstractDensity end +################################################################### +# Abstract types and methods + +abstract type AbstractDensity <: Function end @inline DensityKind(::AbstractDensity) = IsDensity() +import DensityInterface + +#################################################################################### +# Density + """ - struct Density{M,B} + struct Density{M,B} <: AbstractDensity μ::M base::B end -For measures μ and ν with μ≪ν, the density of μ with respect to ν (also called -the Radon-Nikodym derivative dμ/dν) is a function f defined on the support of ν -with the property that for any measurable a ⊂ supp(ν), μ(a) = ∫ₐ f dν. - -Because this function is often difficult to express in closed form, there are -many different ways of computing it. We therefore provide a formal -representation to allow comptuational flexibilty. +For measures `μ` and `ν`, `Density(μ,ν)` represents the _density function_ +`dμ/dν`, also called the _Radom-Nikodym derivative_: +https://en.wikipedia.org/wiki/Radon%E2%80%93Nikodym_theorem#Radon%E2%80%93Nikodym_derivative + +Instead of calling this directly, users should call `density_rel(μ, ν)` or +its abbreviated form, `𝒹(μ,ν)`. """ struct Density{M,B} <: AbstractDensity μ::M base::B end +Base.:∘(::typeof(log), d::Density) = logdensity_rel(d.μ, d.base) + +Base.log(d::Density) = log ∘ d + export 𝒹 """ - 𝒹(μ::AbstractMeasure, base::AbstractMeasure) + 𝒹(μ, base) + +Compute the density (Radom-Nikodym derivative) of μ with respect to `base`. This +is a shorthand form for `density_rel(μ, base)`. +""" +𝒹(μ, base) = density_rel(μ, base) + +density_rel(μ, base) = Density(μ, base) + +(f::Density)(x) = density_rel(f.μ, f.base, x) + +DensityInterface.logfuncdensity(d::Density) = throw(MethodError(logfuncdensity, (d,))) + +#################################################################################### +# LogDensity -Compute the Radom-Nikodym derivative of μ with respect to `base`. """ -function 𝒹(μ::AbstractMeasure, base::AbstractMeasure) - return Density(μ, base) + struct LogDensity{M,B} <: AbstractDensity + μ::M + base::B + end + +For measures `μ` and `ν`, `LogDensity(μ,ν)` represents the _log-density function_ +`log(dμ/dν)`, also called the _Radom-Nikodym derivative_: +https://en.wikipedia.org/wiki/Radon%E2%80%93Nikodym_theorem#Radon%E2%80%93Nikodym_derivative + +Instead of calling this directly, users should call `logdensity_rel(μ, ν)` or +its abbreviated form, `log𝒹(μ,ν)`. +""" +struct LogDensity{M,B} <: AbstractDensity + μ::M + base::B end -logdensityof(d::Density, x) = logdensity_rel(d.μ, d.base, x) +Base.:∘(::typeof(exp), d::LogDensity) = density(d.μ, d.base) -logdensity_def(d::Density, x) = logdensityof(d, x) +Base.exp(d::LogDensity) = exp ∘ d +export log𝒹 + +""" + log𝒹(μ, base) + +Compute the log-density (Radom-Nikodym derivative) of μ with respect to `base`. +This is a shorthand form for `logdensity_rel(μ, base)` """ - struct DensityMeasure{F,B} <: AbstractMeasure +log𝒹(μ, base) = logdensity_rel(μ, base) + +logdensity_rel(μ, base) = LogDensity(μ, base) + +(f::LogDensity)(x) = logdensity_rel(f.μ, f.base, x) + +DensityInterface.funcdensity(d::LogDensity) = throw(MethodError(funcdensity, (d,))) + +####################################################################################### +# DensityMeasure + +""" + struct DensityMeasure{F,B} <: AbstractDensityMeasure density :: F base :: B end -A `DensityMeasure` is a measure defined by a density with respect to some other -"base" measure +A `DensityMeasure` is a measure defined by a density or log-density with respect +to some other "base" measure. + +Users should not call `DensityMeasure` directly, but should instead call `∫(f, +base)` (if `f` is a density function or `DensityInterface.IsDensity` object) or +`∫exp(f, base)` (if `f` is a log-density function). """ struct DensityMeasure{F,B} <: AbstractMeasure f::F base::B + + function DensityMeasure(f::F, base::B) where {F,B} + @assert DensityKind(f) isa IsDensity + new{F,B}(f, base) + end +end + +@inline function insupport(d::DensityMeasure, x) + insupport(d.base, x) == true && isfinite(logdensityof(getfield(d, :f), x)) end function Pretty.tile(μ::DensityMeasure{F,B}) where {F,B} @@ -56,28 +125,6 @@ function Pretty.tile(μ::DensityMeasure{F,B}) where {F,B} result *= Pretty.literal(")") end -densitymeasure(f, base) = _densitymeasure(f, base, DensityKind(f)) - -_densitymeasure(f, base, ::IsDensity) = DensityMeasure(f, base) - -function _densitymeasure(f, base, _) - @error """ - The first argument of `DensityMeasure`" must be `::IsDensity`. To pass a - function, first wrap it in `DensityInterface.funcdensity` or - `DensityInterface.logfuncdensity`. - """ -end - -@inline function insupport(d::DensityMeasure, x) - insupport(d.base, x) == true && isfinite(logdensityof(d.f, x)) -end - -basemeasure(μ::DensityMeasure) = μ.base - -logdensity_def(μ::DensityMeasure, x) = logdensityof(μ.f, x) - -density_def(μ::DensityMeasure, x) = densityof(μ.f, x) - export ∫ """ @@ -85,11 +132,13 @@ export ∫ Define a new measure in terms of a density `f` over some measure `base`. """ -∫(f::Function, base::AbstractMeasure) = DensityMeasure(funcdensity(f), base) - -∫(f, base::AbstractMeasure) = _densitymeasure(f, base, DensityKind(f)) +∫(f, base) = _densitymeasure(f, base, DensityKind(f)) -# ∫(μ::AbstractMeasure, base::AbstractMeasure) = ∫(𝒹(μ, base), base) +_densitymeasure(f, base, ::IsDensity) = DensityMeasure(f, base) +function _densitymeasure(f, base, ::HasDensity) + @error "`∫(f, base)` requires `DensityKind(f)` to be `IsDensity()` or `NoDensity()`." +end +_densitymeasure(f, base, ::NoDensity) = DensityMeasure(funcdensity(f), base) export ∫exp @@ -98,7 +147,21 @@ export ∫exp Define a new measure in terms of a log-density `f` over some measure `base`. """ -∫exp(f::Function, μ) = ∫(logfuncdensity(f), μ) +∫exp(f, base) = _logdensitymeasure(f, base, DensityKind(f)) + +function _logdensitymeasure(f, base, ::IsDensity) + @error "`∫exp(f, base)` is not valid when `DensityKind(f) == IsDensity()`. Use `∫(f, base)` instead." +end +function _logdensitymeasure(f, base, ::HasDensity) + @error "`∫exp(f, base)` is not valid when `DensityKind(f) == HasDensity()`." +end +_logdensitymeasure(f, base, ::NoDensity) = DensityMeasure(logfuncdensity(f), base) + +basemeasure(μ::DensityMeasure) = μ.base + +logdensity_def(μ::DensityMeasure, x) = logdensityof(μ.f, x) + +density_def(μ::DensityMeasure, x) = densityof(μ.f, x) """ rebase(μ, ν) diff --git a/src/primitives/trivial.jl b/src/primitives/trivial.jl index 6f73eb78..f224ccd0 100644 --- a/src/primitives/trivial.jl +++ b/src/primitives/trivial.jl @@ -6,4 +6,4 @@ gentype(::TrivialMeasure) = Nothing insupport(::TrivialMeasure, x) = False -massof(::TrivialMeasure) = static(0.0) \ No newline at end of file +massof(::TrivialMeasure) = static(0.0) diff --git a/test/runtests.jl b/test/runtests.jl index 4eee3c00..7601aecb 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -146,8 +146,9 @@ end @test logdensityof(Lebesgue()^3, 2) == logdensityof(Lebesgue()^(3, 1), (2, 0)) end +Normal() = ∫exp(x -> -0.5x^2, Lebesgue(ℝ)) + @testset "Half" begin - Normal() = ∫exp(x -> -0.5x^2, Lebesgue(ℝ)) HalfNormal() = Half(Normal()) @test logdensityof(HalfNormal(), -0.2) == -Inf @test logdensity_def(HalfNormal(), 0.2) == logdensity_def(Normal(), 0.2) @@ -233,19 +234,15 @@ end @testset "Density measures and Radon-Nikodym" begin x = randn() f(x) = x^2 - @test logdensityof(𝒹(∫exp(f, Lebesgue()), Lebesgue()), x) ≈ f(x) + @test log(𝒹(∫exp(f, Lebesgue()), Lebesgue())(x)) ≈ f(x) let f = 𝒹(∫exp(x -> x^2, Lebesgue()), Lebesgue()) - @test logdensityof(f, x) ≈ x^2 + @test log(f(x)) ≈ x^2 end - # let d = ∫exp(log𝒹(Cauchy(), Normal()), Normal()) - # @test logdensity_def(d, x) ≈ logdensity_def(Cauchy(), x) - # end - - # let f = log𝒹(∫exp(x -> x^2, Normal()), Normal()) - # @test f(x) ≈ x^2 - # end + let f = log𝒹(∫exp(x -> x^2, Normal()), Normal()) + @test f(x) ≈ x^2 + end end include("getdof.jl") From 304163d1f1ed4d59c8d4c1c9805f00ccd59e0346 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Thu, 6 Oct 2022 15:27:33 -0700 Subject: [PATCH 353/368] Pushfwd-inverses (#98) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * use InverseFunctions.setinverse * bug fixes * bugfix * bugfix * pushfwd of a pushfwd * format * drop old comment * drop CI for nightly * working on pushfwd * bugfix * inverse(f) => ν.finv * separate logdensity functions from transport API * format * don't unwrap FunctionWithInverse * drop redundant method * leave logdensityof alone, instead write unsafe_logdensityof * more tests * more work on tests * tests * tests * still messing with tests * tests passing * small edits * formatting * add some more failing tests * add atol to isapprox in test * getdof(μ::PushforwardMeasure) = getdof(transport_origin(μ)) * update atol * small fix * drop ((-) ∘ log1p ∘ (-), StdUniform(), StdExponential()) --- Project.toml | 2 +- src/combinators/product.jl | 9 +- src/combinators/transformedmeasure.jl | 170 +++++++++++-------------- src/interface.jl | 13 +- src/standard/stdmeasure.jl | 47 +++++-- src/transport.jl | 31 +++-- test/combinators/transformedmeasure.jl | 75 +++++++++-- test/transport.jl | 20 ++- 8 files changed, 220 insertions(+), 147 deletions(-) diff --git a/Project.toml b/Project.toml index bc21d0ca..86005f65 100644 --- a/Project.toml +++ b/Project.toml @@ -37,7 +37,7 @@ DensityInterface = "0.4" FillArrays = "0.12, 0.13" IfElse = "0.1" IntervalSets = "0.7" -InverseFunctions = "0.1.7" +InverseFunctions = "0.1.8" IrrationalConstants = "0.1" LogExpFunctions = "0.3" LogarithmicNumbers = "1" diff --git a/src/combinators/product.jl b/src/combinators/product.jl index fefce863..ee0ae2b6 100644 --- a/src/combinators/product.jl +++ b/src/combinators/product.jl @@ -225,14 +225,15 @@ end return true end - getdof(d::AbstractProductMeasure) = mapreduce(getdof, +, marginals(d)) - -function checked_arg(μ::ProductMeasure{<:NTuple{N,Any}}, x::NTuple{N,Any}) where N +function checked_arg(μ::ProductMeasure{<:NTuple{N,Any}}, x::NTuple{N,Any}) where {N} map(checked_arg, marginals(μ), x) end -function checked_arg(μ::ProductMeasure{<:NamedTuple{names}}, x::NamedTuple{names}) where names +function checked_arg( + μ::ProductMeasure{<:NamedTuple{names}}, + x::NamedTuple{names}, +) where {names} NamedTuple{names}(map(checked_arg, values(marginals(μ)), values(x))) end diff --git a/src/combinators/transformedmeasure.jl b/src/combinators/transformedmeasure.jl index 2313d705..d85e0791 100644 --- a/src/combinators/transformedmeasure.jl +++ b/src/combinators/transformedmeasure.jl @@ -1,5 +1,7 @@ # TODO: Compare with ChangesOfVariables.jl +using InverseFunctions: FunctionWithInverse + abstract type AbstractTransformedMeasure <: AbstractMeasure end abstract type AbstractPushforward <: AbstractTransformedMeasure end @@ -17,16 +19,15 @@ function parent(::AbstractTransformedMeasure) end export PushforwardMeasure """ - struct PushforwardMeasure{FF,IF,MU,VC<:TransformVolCorr} <: AbstractPushforward - f :: FF - inv_f :: IF - origin :: MU - volcorr :: VC - end + struct PushforwardMeasure{F,I,MU,VC<:TransformVolCorr} <: + AbstractPushforward f :: F finv :: I origin :: MU volcorr :: VC end + + Users should not call `PushforwardMeasure` directly. Instead call or add + methods to `pushfwd`. """ -struct PushforwardMeasure{FF,IF,M,VC<:TransformVolCorr} <: AbstractPushforward - f::FF - inv_f::IF +struct PushforwardMeasure{F,I,M,VC<:TransformVolCorr} <: AbstractPushforward + f::F + finv::I origin::M volcorr::VC end @@ -34,46 +35,24 @@ end gettransform(ν::PushforwardMeasure) = ν.f parent(ν::PushforwardMeasure) = ν.origin -function transport_def(ν::PushforwardMeasure{FF,IF,M}, μ::M, x) where {FF,IF,M} - if μ == parent(ν) +function transport_def(ν::PushforwardMeasure{F,I,M}, μ::M, x) where {F,I,M} + if μ === parent(ν) return ν.f(x) else - invoke(transport_def, Tuple{Any,PushforwardMeasure,Any}, ν, μ, x) + invoke(transport_def, Tuple{PushforwardMeasure,Any,Any}, ν, μ, x) end end -function transport_def(μ::M, ν::PushforwardMeasure{FF,IF,M}, y) where {FF,IF,M} - if μ == parent(ν) - return ν.inv_f(y) +function transport_def(μ::M, ν::PushforwardMeasure{F,I,M}, y) where {F,I,M} + if μ === parent(ν) + return ν.finv(y) else invoke(transport_def, Tuple{Any,PushforwardMeasure,Any}, μ, ν, y) end end function Pretty.tile(ν::PushforwardMeasure) - Pretty.list_layout(Pretty.tile.([ν.f, ν.inv_f, ν.origin]); prefix = :PushforwardMeasure) -end - -# TODO: Reduce code duplication -@inline function logdensityof( - ν::PushforwardMeasure{FF,IF,M,<:WithVolCorr}, - y, -) where {FF,IF,M} - x_orig, inv_ladj = with_logabsdet_jacobian(ν.inv_f, y) - μ = ν.origin - logd_orig = unsafe_logdensityof(ν.origin, x_orig) - logd = float(logd_orig + inv_ladj) - neginf = oftype(logd, -Inf) - insupport(μ, x_orig) || return oftype(logd, -Inf) - return ifelse( - # Zero density wins against infinite volume: - (isnan(logd) && logd_orig == -Inf && inv_ladj == +Inf) || - # Maybe also for (logd_orig == -Inf) && isfinite(inv_ladj) ? - # Return constant -Inf to prevent problems with ForwardDiff: - (isfinite(logd_orig) && (inv_ladj == -Inf)), - neginf, - logd, - ) + Pretty.list_layout(Pretty.tile.([ν.f, ν.origin]); prefix = :PushforwardMeasure) end # TODO: THIS IS ALMOST CERTAINLY WRONG @@ -88,12 +67,11 @@ end # logdensity_rel(pushfwd(f, inv_f, ν.origin, WithVolCorr()), β.origin, x) # end -@inline function logdensity_def( - ν::PushforwardMeasure{FF,IF,M,<:WithVolCorr}, - y, -) where {FF,IF,M} - x_orig, inv_ladj = with_logabsdet_jacobian(ν.inv_f, y) - logd_orig = unsafe_logdensityof(ν.origin, x_orig) +@inline function logdensity_def(ν::PushforwardMeasure{F,I,M,<:WithVolCorr}, y) where {F,I,M} + f = ν.f + finv = ν.finv + x_orig, inv_ladj = with_logabsdet_jacobian(finv.f, y) + logd_orig = logdensity_def(ν.origin, x_orig) logd = float(logd_orig + inv_ladj) neginf = oftype(logd, -Inf) return ifelse( @@ -107,22 +85,19 @@ end ) end -@inline function logdensity_def( - ν::PushforwardMeasure{FF,IF,M,<:NoVolCorr}, - y, -) where {FF,IF,M} - x_orig = to_origin(ν, y) - return unsafe_logdensityof(ν.origin, x_orig) +@inline function logdensity_def(ν::PushforwardMeasure{F,I,M,<:NoVolCorr}, y) where {F,I,M} + x = ν.finv(y) + return logdensity_def(ν.origin, x) end -insupport(ν::PushforwardMeasure, y) = insupport(transport_origin(ν), to_origin(ν, y)) +insupport(ν::PushforwardMeasure, y) = insupport(ν.origin, ν.finv(y)) function testvalue(::Type{T}, ν::PushforwardMeasure) where {T} - from_origin(ν, testvalue(T, transport_origin(ν))) + ν.f(testvalue(T, parent(ν))) end @inline function basemeasure(ν::PushforwardMeasure) - PushforwardMeasure(ν.f, ν.inv_f, basemeasure(transport_origin(ν)), NoVolCorr()) + pushfwd(ν.f, basemeasure(parent(ν)), NoVolCorr()) end _pushfwd_dof(::Type{MU}, ::Type, dof) where {MU} = NoDOF{MU}() @@ -140,34 +115,63 @@ end @inline transport_origin(ν::PushforwardMeasure) = ν.origin @inline from_origin(ν::PushforwardMeasure, x) = ν.f(x) -@inline to_origin(ν::PushforwardMeasure, y) = ν.inv_f(y) +@inline to_origin(ν::PushforwardMeasure, y) = ν.finv(y) function Base.rand(rng::AbstractRNG, ::Type{T}, ν::PushforwardMeasure) where {T} return ν.f(rand(rng, T, parent(ν))) end +############################################################################### +# pushfwd + export pushfwd +function pushfwd(f::FunctionWithInverse, μ, volcorr::TransformVolCorr) + PushforwardMeasure(f, inverse(f), μ, volcorr) +end + """ - pushfwd(f, [f_inverse,] μ, volcorr = WithVolCorr()) + pushfwd(f, μ, volcorr = WithVolCorr()) Return the [pushforward measure](https://en.wikipedia.org/wiki/Pushforward_measure) from `μ` the [measurable function](https://en.wikipedia.org/wiki/Measurable_function) `f`. -If `f_inverse` is specified, it must be a valid inverse of the function given by -restricting `f` to the support of `μ`. +To manually specify an inverse, call +`pushfwd(InverseFunctions.setinverse(f, finv), μ, volcorr)`. """ -function pushfwd(f, μ::AbstractMeasure, volcorr::TransformVolCorr = WithVolCorr()) - pushfwd(f, inverse(f), μ, volcorr) +function pushfwd(f, μ, volcorr::TransformVolCorr = WithVolCorr()) + pushfwd(setinverse(f, inverse(f)), μ, volcorr) +end + +function pushfwd(f, μ::PushforwardMeasure, volcorr::TransformVolCorr = WithVolCorr()) + _pushfwd(f, μ, μ.volcorr, volcorr) +end + +function pushfwd(f, μ::PushforwardMeasure, ::WithVolCorr) + _pushfwd(f, μ, μ.volcorr, WithVolCorr()) +end + +# Either both WithVolCorr or both NoVolCorr, so we can merge them +function _pushfwd(f, μ, ::V, v::V) where {V} + pushfwd(setinverse(f ∘ μ.f, μ.finv ∘ inverse(f)), μ.origin, v) end -function pushfwd(f, finv, μ::AbstractMeasure, volcorr::TransformVolCorr = WithVolCorr()) - PushforwardMeasure(f, finv, μ, volcorr) +function _pushfwd(f::FunctionWithInverse, μ, ::V, v::V) where {V} + pushfwd(setinverse(f.f ∘ μ.f, μ.finv ∘ f.invf), μ.origin, v) end +function _pushfwd(f, μ, _, v) + pushfwd(setinverse(f, inverse(f)), μ, v) +end + +getdof(μ::PushforwardMeasure) = getdof(transport_origin(μ)) + +############################################################################### +# pullback + """ - pullback(f, [f_inverse,] μ, volcorr = WithVolCorr()) + pullback(f, μ, volcorr = WithVolCorr()) A _pullback_ is a dual concept to a _pushforward_. While a pushforward needs a map _from_ the support of a measure, a pullback requires a map _into_ the @@ -177,42 +181,10 @@ composition, together with a volume correction as needed. This can be useful, since the log-density of a `PushforwardMeasure` is computing in terms of the inverse function; the "forward" function is not used at all. In some cases, we may be focusing on log-density (and not, for example, sampling). -""" -function pullback(f, μ::AbstractMeasure, volcorr::TransformVolCorr = WithVolCorr()) - pushfwd(inverse(f), f, μ, volcorr) -end - -function pullback(f, finv, μ::AbstractMeasure, volcorr::TransformVolCorr = WithVolCorr()) - pushfwd(finv, f, μ, volcorr) -end - -@inline function pushfwd( - f, - μ::PushforwardMeasure, - volcorr::TransformVolCorr = WithVolCorr(), -) - _pushfwd(f, inverse(f), μ, volcorr, μ.volcorr) -end -@inline function pushfwd( - f, - finv, - μ::PushforwardMeasure, - volcorr::TransformVolCorr = WithVolCorr(), -) - _pushfwd(f, finv, μ, volcorr, μ.volcorr) -end - -@inline function _pushfwd( - f, - finv, - μ::PushforwardMeasure, - vf::V, - vμ::V, -) where {V<:TransformVolCorr} - pushfwd(f ∘ μ.f, μ.inv_f ∘ finv, μ, vf) -end - -@inline function _pushfwd(f, finv, μ::PushforwardMeasure, vf, vμ) - PushforwardMeasure(f, finv, μ, vf) +To manually specify an inverse, call +`pullback(InverseFunctions.setinverse(f, finv), μ, volcorr)`. +""" +function pullback(f, μ, volcorr::TransformVolCorr = WithVolCorr()) + pushfwd(setinverse(inverse(f), f), μ, volcorr) end diff --git a/src/interface.jl b/src/interface.jl index 4a1bda5b..bb0e022a 100644 --- a/src/interface.jl +++ b/src/interface.jl @@ -71,16 +71,19 @@ function test_interface(μ::M) where {M} end end - function test_transport(ν, μ) supertype(x) = Any supertype(x::Real) = Real supertype(x::AbstractArray{<:Real,N}) where {N} = AbstractArray{<:Real,N} structisapprox(a, b) = isapprox(a, b) - structisapprox(a::NTuple{N,Any}, b::NTuple{N,Any}) where N = all(map(structisapprox, a, b)) - structisapprox(a::NamedTuple{names}, b::NamedTuple{names}) where names = all(map(structisapprox, values(a), values(b))) - + function structisapprox(a::NTuple{N,Any}, b::NTuple{N,Any}) where {N} + all(map(structisapprox, a, b)) + end + function structisapprox(a::NamedTuple{names}, b::NamedTuple{names}) where {names} + all(map(structisapprox, values(a), values(b))) + end + @testset "transport_to $μ to $ν" begin x = rand(μ) @test !(@inferred(transport_to(ν, μ)(x)) isa NoTransport) @@ -93,7 +96,7 @@ function test_transport(ν, μ) x2, ladj_inv = with_logabsdet_jacobian(inverse(f), y) @test structisapprox(x, x2) @test structisapprox(y, y2) - @test ladj_fwd ≈ -ladj_inv + @test isapprox(ladj_fwd, -ladj_inv, atol=1e-10) @test ladj_fwd ≈ logdensityof(μ, x) - logdensityof(ν, y) end end diff --git a/src/standard/stdmeasure.jl b/src/standard/stdmeasure.jl index 316f97b0..2b50c1e5 100644 --- a/src/standard/stdmeasure.jl +++ b/src/standard/stdmeasure.jl @@ -54,31 +54,40 @@ end Zeros{Bool}(map(_ -> 0, ν.axes)) end - # Helpers for product transforms and similar: struct _TransportToStd{NU<:StdMeasure} <: Function end -_TransportToStd{NU}(μ, x) where NU = transport_to(NU()^getdof(μ), μ)(x) +_TransportToStd{NU}(μ, x) where {NU} = transport_to(NU()^getdof(μ), μ)(x) struct _TransportFromStd{MU<:StdMeasure} <: Function end -_TransportFromStd{MU}(ν, x) where MU = transport_to(ν, MU()^getdof(ν))(x) - +_TransportFromStd{MU}(ν, x) where {MU} = transport_to(ν, MU()^getdof(ν))(x) -function _tuple_transport_def(ν::PowerMeasure{NU}, μs::Tuple, xs::Tuple) where {NU<:StdMeasure} +function _tuple_transport_def( + ν::PowerMeasure{NU}, + μs::Tuple, + xs::Tuple, +) where {NU<:StdMeasure} reshape(vcat(map(_TransportToStd{NU}, μs, xs)...), ν.axes) end -function transport_def(ν::PowerMeasure{NU}, μ::ProductMeasure{<:Tuple}, x) where {NU<:StdMeasure} +function transport_def( + ν::PowerMeasure{NU}, + μ::ProductMeasure{<:Tuple}, + x, +) where {NU<:StdMeasure} _tuple_transport_def(ν, marginals(μ), x) end -function transport_def(ν::PowerMeasure{NU}, μ::ProductMeasure{<:NamedTuple{names}}, x) where {NU<:StdMeasure,names} +function transport_def( + ν::PowerMeasure{NU}, + μ::ProductMeasure{<:NamedTuple{names}}, + x, +) where {NU<:StdMeasure,names} _tuple_transport_def(ν, values(marginals(μ)), values(x)) end - -@inline _offset_cumsum(s, x, y, rest...) = (s, _offset_cumsum(s+x, y, rest...)...) -@inline _offset_cumsum(s,x) = (s,) +@inline _offset_cumsum(s, x, y, rest...) = (s, _offset_cumsum(s + x, y, rest...)...) +@inline _offset_cumsum(s, x) = (s,) @inline _offset_cumsum(s) = () function _stdvar_viewranges(μs::Tuple, startidx::Integer) @@ -87,16 +96,28 @@ function _stdvar_viewranges(μs::Tuple, startidx::Integer) map((o, n) -> o:o+n-1, offs, N) end -function _tuple_transport_def(νs::Tuple, μ::PowerMeasure{MU}, x::AbstractArray{<:Real}) where {MU<:StdMeasure} +function _tuple_transport_def( + νs::Tuple, + μ::PowerMeasure{MU}, + x::AbstractArray{<:Real}, +) where {MU<:StdMeasure} vrs = _stdvar_viewranges(νs, firstindex(x)) xs = map(r -> view(x, r), vrs) map(_TransportFromStd{MU}, νs, xs) end -function transport_def(ν::ProductMeasure{<:Tuple}, μ::PowerMeasure{MU}, x) where {MU<:StdMeasure} +function transport_def( + ν::ProductMeasure{<:Tuple}, + μ::PowerMeasure{MU}, + x, +) where {MU<:StdMeasure} _tuple_transport_def(marginals(ν), μ, x) end -function transport_def(ν::ProductMeasure{<:NamedTuple{names}}, μ::PowerMeasure{MU}, x) where {MU<:StdMeasure,names} +function transport_def( + ν::ProductMeasure{<:NamedTuple{names}}, + μ::PowerMeasure{MU}, + x, +) where {MU<:StdMeasure,names} NamedTuple{names}(_tuple_transport_def(values(marginals(ν)), μ, x)) end diff --git a/src/transport.jl b/src/transport.jl index ff3f4bed..49d99e1f 100644 --- a/src/transport.jl +++ b/src/transport.jl @@ -117,7 +117,6 @@ function transport_def(ν, μ, x) _transport_between_origins(ν, _origin_depth(ν), _origin_depth(μ), μ, x) end - @inline function _origin_depth(ν::NU) where {NU} ν_0 = ν Base.Cartesian.@nexprs 10 i -> begin # 10 is just some "big enough" number @@ -132,42 +131,54 @@ end _origin_depth_pullback(ΔΩ) = NoTangent(), NoTangent() ChainRulesCore.rrule(::typeof(_origin_depth), ν) = _origin_depth(ν), _origin_depth_pullback - # If both both measures have no origin: function _transport_between_origins(ν, ::StaticInt{0}, ::StaticInt{0}, μ, x) _transport_with_intermediate(ν, _transport_intermediate(ν, μ), μ, x) end -@generated function _transport_between_origins(ν, ::StaticInt{n_ν}, ::StaticInt{n_μ}, μ, x) where {n_ν, n_μ} +@generated function _transport_between_origins( + ν, + ::StaticInt{n_ν}, + ::StaticInt{n_μ}, + μ, + x, +) where {n_ν,n_μ} prog = quote μ0 = μ x0 = x ν0 = ν end for i in 1:n_μ - μ_i = Symbol(:μ,i); μ_last = Symbol(:μ,i-1) + μ_i = Symbol(:μ, i) + μ_last = Symbol(:μ, i - 1) push!(prog.args, :($μ_i = transport_origin($μ_last))) end for i in 1:n_μ - x_i = Symbol(:x,i); x_last = Symbol(:x,i-1); μ_last = Symbol(:μ,i-1) + x_i = Symbol(:x, i) + x_last = Symbol(:x, i - 1) + μ_last = Symbol(:μ, i - 1) push!(prog.args, :($x_i = to_origin($μ_last, $x_last))) end for i in 1:(n_ν) - ν_i = Symbol(:ν,i); ν_last = Symbol(:ν,i-1); + ν_i = Symbol(:ν, i) + ν_last = Symbol(:ν, i - 1) push!(prog.args, :($ν_i = transport_origin($ν_last))) end - μ_im = Symbol(:μ,n_μ); x_im = Symbol(:x,n_μ) - ν_im = Symbol(:ν,n_ν); y_im = Symbol(:y,n_ν) + μ_im = Symbol(:μ, n_μ) + x_im = Symbol(:x, n_μ) + ν_im = Symbol(:ν, n_ν) + y_im = Symbol(:y, n_ν) push!(prog.args, :($y_im = transport_def($ν_im, $μ_im, $x_im))) for i in (n_ν-1):-1:0 - y_i = Symbol(:y,i); y_last = Symbol(:y,i+1); ν_last = Symbol(:ν,i) + y_i = Symbol(:y, i) + y_last = Symbol(:y, i + 1) + ν_last = Symbol(:ν, i) push!(prog.args, :($y_i = from_origin($ν_last, $y_last))) end push!(prog.args, :(return y0)) return prog end - @inline _transport_intermediate(ν, μ) = _transport_intermediate(getdof(ν), getdof(μ)) @inline _transport_intermediate(::Integer, n_μ::Integer) = StdUniform()^n_μ @inline _transport_intermediate(::StaticInt{1}, ::StaticInt{1}) = StdUniform() diff --git a/test/combinators/transformedmeasure.jl b/test/combinators/transformedmeasure.jl index 4cdf7f0f..1c6d9073 100644 --- a/test/combinators/transformedmeasure.jl +++ b/test/combinators/transformedmeasure.jl @@ -1,21 +1,74 @@ using Test +using MeasureBase using MeasureBase: pushfwd, StdUniform, StdExponential, StdLogistic using MeasureBase: pushfwd, PushforwardMeasure -using MeasureBase: transport_to -using Statistics: var +using MeasureBase: transport_to, unsafe_logdensityof +import Statistics: var using DensityInterface: logdensityof +using LogExpFunctions +using SpecialFunctions: erfc, erfcinv +import InverseFunctions: inverse, FunctionWithInverse +using IrrationalConstants: invsqrt2, sqrt2 +import ChangesOfVariables: with_logabsdet_jacobian -@testset "transformedmeasure.jl" begin - μ = StdUniform() - @test @inferred(pushfwd((-) ∘ log1p ∘ (-), μ)) isa PushforwardMeasure - ν = pushfwd((-) ∘ log1p ∘ (-), μ) - ν_ref = StdExponential() +Φ(z) = erfc(-z * invsqrt2)/2 +Φinv(p) = -erfcinv(2*p) * sqrt2 + +with_logabsdet_jacobian(f::FunctionWithInverse, x) = with_logabsdet_jacobian(f.f, x) + +with_logabsdet_jacobian(::typeof(Φ), z) = (Φ(z), logdensityof(StdNormal(), z)) + +function with_logabsdet_jacobian(::typeof(Φinv), p) + z = Φinv(p) + (z, -logdensityof(StdNormal(), z)) +end + +inverse(::typeof(Φ)) = Φinv +inverse(::typeof(Φinv)) = Φ + +var(::StdNormal) = 1.0 +var(::StdExponential) = 1.0 +var(::StdUniform) = 1/12 +var(::StdLogistic) = π^2/3 - y = rand(ν_ref) - @test @inferred(logdensityof(ν, y)) ≈ logdensityof(ν_ref, y) +function test_pushfwd(f, μ, ν_ref) + @testset "pushfwd($f, $μ)" begin + @inferred(pushfwd(f, μ)) + ν = pushfwd(f, μ) - @test isapprox(var(rand(ν^(10^5))), 1, rtol = 0.05) + test_transport(ν, ν_ref) + test_transport(ν_ref, ν) + + y = rand(ν_ref) + @test isapprox(@inferred(logdensityof(ν, y)), logdensityof(ν_ref, y), atol=1e-10) + @test isapprox(@inferred(unsafe_logdensityof(ν, y)), unsafe_logdensityof(ν_ref, y), atol=1e-10) + + @test isapprox(var(rand(ν^(10^5))), var(ν_ref), rtol = 0.05) + + @test abs(transport_to(StdLogistic(), ν)(y)) ≈ abs(transport_to(StdLogistic(), ν_ref)(y)) + end +end + +@testset "transformedmeasure.jl" begin + # (f, μ, ν_ref), so that pushfwd(f, μ) ≅ ν_ref + triples = [ + ((-) ∘ log, StdUniform(), StdExponential()) + (exp ∘ (-), StdExponential(), StdUniform()) + (logit, StdUniform(), StdLogistic()) + (logistic, StdLogistic(), StdUniform()) + (Φ, StdNormal(), StdUniform()) + (Φinv, StdUniform(), StdNormal()) + ] + + for (f, μ, ν_ref) in triples + test_pushfwd(f, μ, ν_ref) + end - @test transport_to(StdLogistic(), ν)(y) ≈ transport_to(StdLogistic(), ν)(y) + @testset "Pushforward-of-pushforward" begin + for (f, μ, ν_ref) in triples + finv = inverse(f) + test_pushfwd(finv, pushfwd(f, μ), μ) + end + end end diff --git a/test/transport.jl b/test/transport.jl index c1907f18..874cb88b 100644 --- a/test/transport.jl +++ b/test/transport.jl @@ -57,10 +57,22 @@ using ChainRulesTestUtils end @testset "transport for products" begin - test_transport(StdUniform()^(2, 2), productmeasure((StdExponential(), StdLogistic()^3))) - test_transport(productmeasure((StdExponential(), StdLogistic()^3)), StdUniform()^(2, 2)) + test_transport( + StdUniform()^(2, 2), + productmeasure((StdExponential(), StdLogistic()^3)), + ) + test_transport( + productmeasure((StdExponential(), StdLogistic()^3)), + StdUniform()^(2, 2), + ) - test_transport(StdUniform()^(2, 2), productmeasure((a = StdExponential(), b = StdLogistic()^3))) - test_transport(productmeasure((a = StdExponential(), b = StdLogistic()^3)), StdUniform()^(2, 2)) + test_transport( + StdUniform()^(2, 2), + productmeasure((a = StdExponential(), b = StdLogistic()^3)), + ) + test_transport( + productmeasure((a = StdExponential(), b = StdLogistic()^3)), + StdUniform()^(2, 2), + ) end end From 5d1807d64598b02b4551241fb552866c30becd34 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 10 Oct 2022 15:56:51 -0700 Subject: [PATCH 354/368] remove duplicate method --- src/combinators/transformedmeasure.jl | 2 -- 1 file changed, 2 deletions(-) diff --git a/src/combinators/transformedmeasure.jl b/src/combinators/transformedmeasure.jl index d85e0791..4fa3e211 100644 --- a/src/combinators/transformedmeasure.jl +++ b/src/combinators/transformedmeasure.jl @@ -165,8 +165,6 @@ function _pushfwd(f, μ, _, v) pushfwd(setinverse(f, inverse(f)), μ, v) end -getdof(μ::PushforwardMeasure) = getdof(transport_origin(μ)) - ############################################################################### # pullback From 29e00401efa5ba9fe0a7bf4fb8b33522a4cfa97d Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Mon, 10 Oct 2022 15:58:21 -0700 Subject: [PATCH 355/368] remove duplicate `include` --- src/MeasureBase.jl | 1 - 1 file changed, 1 deletion(-) diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index 3022b0d7..c279730a 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -115,7 +115,6 @@ using Compat using IrrationalConstants -include("density-core.jl") include("getdof.jl") include("transport.jl") include("schema.jl") From d44ead036c9a255c303bc8602c623ac766ef1583 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Tue, 11 Oct 2022 05:38:25 -0700 Subject: [PATCH 356/368] simplify getdof(::PushforwardMeasure) --- src/combinators/transformedmeasure.jl | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/src/combinators/transformedmeasure.jl b/src/combinators/transformedmeasure.jl index 4fa3e211..0242a79a 100644 --- a/src/combinators/transformedmeasure.jl +++ b/src/combinators/transformedmeasure.jl @@ -103,12 +103,7 @@ end _pushfwd_dof(::Type{MU}, ::Type, dof) where {MU} = NoDOF{MU}() _pushfwd_dof(::Type{MU}, ::Type{<:Tuple{Any,Real}}, dof) where {MU} = dof -# Assume that DOF are preserved if with_logabsdet_jacobian is functional: -@inline function getdof(ν::MU) where {MU<:PushforwardMeasure} - T = Core.Compiler.return_type(testvalue, Tuple{typeof(ν.origin)}) - R = Core.Compiler.return_type(with_logabsdet_jacobian, Tuple{typeof(ν.f),T}) - _pushfwd_dof(MU, R, getdof(ν.origin)) -end +@inline getdof(ν::MU) where {MU<:PushforwardMeasure} = getdof(ν.origin) # Bypass `checked_arg`, would require potentially costly transformation: @inline checked_arg(::PushforwardMeasure, x) = x From 6d5955520dcf1d63334d69f2d21fc767f35ae601 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Fri, 14 Oct 2022 05:58:10 -0700 Subject: [PATCH 357/368] Stieltjes measure function (#100) * smf * more smf stuff * transport_to * Lebesgue smf * smf for std measures * format * transport_to * oops * smfinv * bugfix * more fixes * minor refactoring * formatting * change x to p * bugfix * smfinv(::StdLogistic, p) * add NoSMF and NoSMFInverse * roll back some changes * transport_def methods * formatting * another rollback * make transport_def depend on smf(inv) * update smf and transports for ::Half * change `include` order * test_smf * more tests * tests * add tests * formatting * Drop unneeded type parameters * smfinv => invsmf * add some inverses * Base.Fix1 versions * some more methods --- src/MeasureBase.jl | 4 ++- src/combinators/half.jl | 12 ++++++++ src/density.jl | 2 +- src/interface.jl | 30 ++++++++++++++++++- src/mass-interface.jl | 2 ++ src/primitives/lebesgue.jl | 14 +++++++++ src/smf.jl | 40 ++++++++++++++++++++++++++ src/standard/stdlogistic.jl | 10 +++++-- src/standard/stdnormal.jl | 18 ++++++++++-- src/standard/stduniform.jl | 7 +++++ src/transport.jl | 7 +++++ test/combinators/transformedmeasure.jl | 22 ++++++++------ test/runtests.jl | 3 +- test/smf.jl | 14 +++++++++ 14 files changed, 168 insertions(+), 17 deletions(-) create mode 100644 src/smf.jl create mode 100644 test/smf.jl diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index c279730a..f96ac86c 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -26,6 +26,7 @@ using ChangesOfVariables import Base.iterate import ConstructionBase using ConstructionBase: constructorof +using IntervalSets using PrettyPrinting const Pretty = PrettyPrinting @@ -115,6 +116,7 @@ using Compat using IrrationalConstants +include("smf.jl") include("getdof.jl") include("transport.jl") include("schema.jl") @@ -122,7 +124,6 @@ include("splat.jl") include("proxies.jl") include("kernel.jl") include("parameterized.jl") -include("combinators/half.jl") include("domains.jl") include("primitive.jl") include("utils.jl") @@ -153,6 +154,7 @@ include("standard/stduniform.jl") include("standard/stdexponential.jl") include("standard/stdlogistic.jl") include("standard/stdnormal.jl") +include("combinators/half.jl") include("rand.jl") include("fixedrng.jl") diff --git a/src/combinators/half.jl b/src/combinators/half.jl index 77651d0f..c713193a 100644 --- a/src/combinators/half.jl +++ b/src/combinators/half.jl @@ -29,3 +29,15 @@ end testvalue(::Type{T}, ::Half) where {T} = one(T) massof(μ::Half) = massof(unhalf(μ)) + +function smf(μ::Half, x) + 2 * smf(μ.parent, max(x, zero(x))) - 1 +end + +function invsmf(μ::Half, p) + @assert zero(p) ≤ p ≤ one(p) + invsmf(μ.parent, (p + 1) / 2) +end + +transport_def(μ::Half, ::StdUniform, p) = invsmf(μ, p) +transport_def(::StdUniform, μ::Half, x) = smf(μ, x) diff --git a/src/density.jl b/src/density.jl index 05e5a70f..4862dcb1 100644 --- a/src/density.jl +++ b/src/density.jl @@ -69,7 +69,7 @@ struct LogDensity{M,B} <: AbstractDensity base::B end -Base.:∘(::typeof(exp), d::LogDensity) = density(d.μ, d.base) +Base.:∘(::typeof(exp), d::LogDensity) = density_rel(d.μ, d.base) Base.exp(d::LogDensity) = exp ∘ d diff --git a/src/interface.jl b/src/interface.jl index bb0e022a..06b836ba 100644 --- a/src/interface.jl +++ b/src/interface.jl @@ -12,9 +12,11 @@ using DensityInterface: logdensityof using InverseFunctions: inverse using ChangesOfVariables: with_logabsdet_jacobian using Tricks: static_hasmethod +using IntervalSets: Interval export test_interface export test_transport +export test_smf export basemeasure_depth export proxy export insupport @@ -96,9 +98,35 @@ function test_transport(ν, μ) x2, ladj_inv = with_logabsdet_jacobian(inverse(f), y) @test structisapprox(x, x2) @test structisapprox(y, y2) - @test isapprox(ladj_fwd, -ladj_inv, atol=1e-10) + @test isapprox(ladj_fwd, -ladj_inv, atol = 1e-10) @test ladj_fwd ≈ logdensityof(μ, x) - logdensityof(ν, y) end end +function test_smf(μ, n = 100) + # Get `n` sorted uniforms in O(n) time + p = rand(n) + p .+= 0:n-1 + p .*= inv(n) + + F(x) = smf(μ, x) + Finv(p) = invsmf(μ, p) + + @assert issorted(p) + x = invsmf.(μ, p) + @test issorted(x) + @test all(insupport(μ), x) + + @test all((Finv ∘ F).(x) .≈ x) + + for j in 1:n + a = rand() + b = rand() + a, b = minmax(a, b) + x = Finv(a) + y = Finv(b) + @test μ(Interval{:open,:closed}(x, y)) ≈ (F(y) - F(x)) + end +end + end # module Interface diff --git a/src/mass-interface.jl b/src/mass-interface.jl index c141d076..7b0518f9 100644 --- a/src/mass-interface.jl +++ b/src/mass-interface.jl @@ -115,3 +115,5 @@ Convenience method for `massof(m, s)`. To make a user-defined measure callable in this way, users should add the corresponding `massof` method. """ (m::AbstractMeasure)(s) = massof(m, s) + +massof(μ, a_b::AbstractInterval) = smf(μ, rightendpoint(a_b)) - smf(μ, leftendpoint(a_b)) diff --git a/src/primitives/lebesgue.jl b/src/primitives/lebesgue.jl index b12a80c0..e11db884 100644 --- a/src/primitives/lebesgue.jl +++ b/src/primitives/lebesgue.jl @@ -76,3 +76,17 @@ function massof(μ::Lebesgue{<:BoundedReals}, s::Interval) w = right - left max(w, zero(w)) end + +function smf(μ::Lebesgue{<:BoundedReals}, x) + clamp(x, μ.support.lower, μ.support.upper) +end + +smf(::Lebesgue{RealNumbers}, x) = x +smf(::Lebesgue{RealNumbers}) = identity +invsmf(::Lebesgue{RealNumbers}, x) = x +invsmf(::Lebesgue{RealNumbers}) = identity + +smf(::LebesgueBase, x) = x +smf(::LebesgueBase) = identity +invsmf(::LebesgueBase, x) = x +invsmf(::LebesgueBase) = identity \ No newline at end of file diff --git a/src/smf.jl b/src/smf.jl new file mode 100644 index 00000000..1d499d2c --- /dev/null +++ b/src/smf.jl @@ -0,0 +1,40 @@ +@doc raw""" + smf(μ, x::Real) ::Real + +Compute the _Stieltjes measure function (SMF)_ of the measure `μ` at the point +`x`. + +The SMF is the measure-theoretic generalization of the _cumulative distribution +function (CDF)_ from probability theory. An SMF `F(x) = smf(μ, x)` must have the +following properties: + +1. F is _nondecreasing_ +2. F is _right-continuous_: `F(x)` should be the same as `lim_{δ→0} F(x + |δ|)`. +3. μ((a,b]) = F(b) - F(a) + +Note that unlike the CDF, an SMF is only determined up to addition by a +constant. For many applications, this leads to a need to evaluate an SMF at -∞. +It's therefore important that `smf(μ, -Inf)` be fast. In practice, this will +usually be called as `smf(μ, static(-Inf))`. It's then easy to ensure speed and +avoid complex control flow by adding a method `smf(μ::M, ::StaticFloat64{-Inf})`. + +Users who pronounce `sinh` as "sinch" are advised to pronounce `smf` as "smurf". +""" +function smf end + +export smf + +function invsmf end + +export invsmf + +struct NoSMF end + +struct NoSMFInverse end + +smf(μ, x) = NoSMF() + +invsmf(μ, p) = NoSMFInverse() + +smf(μ) = Base.Fix1(smf, μ) +invsmf(μ) = Base.Fix1(invsmf, μ) \ No newline at end of file diff --git a/src/standard/stdlogistic.jl b/src/standard/stdlogistic.jl index 2247ca7b..a3a351c3 100644 --- a/src/standard/stdlogistic.jl +++ b/src/standard/stdlogistic.jl @@ -7,9 +7,15 @@ export StdLogistic @inline logdensity_def(::StdLogistic, x) = (u = -abs(x); u - 2 * log1pexp(u)) @inline basemeasure(::StdLogistic) = LebesgueBase() -@inline transport_def(::StdUniform, μ::StdLogistic, x) = logistic(x) -@inline transport_def(::StdLogistic, μ::StdUniform, x) = logit(x) +@inline transport_def(::StdUniform, μ::StdLogistic, x) = smf(StdLogistic(), x) +@inline transport_def(::StdLogistic, μ::StdUniform, p) = invsmf(StdLogistic(), p) @inline function Base.rand(rng::Random.AbstractRNG, ::Type{T}, ::StdLogistic) where {T} logit(rand(rng, T)) end + +smf(::StdLogistic, x) = logistic(x) +smf(::StdLogistic) = logistic + +invsmf(::StdLogistic, p) = logit(p) +invsmf(::StdLogistic) = logit \ No newline at end of file diff --git a/src/standard/stdnormal.jl b/src/standard/stdnormal.jl index 76429b81..dbb89ed0 100644 --- a/src/standard/stdnormal.jl +++ b/src/standard/stdnormal.jl @@ -12,7 +12,19 @@ export StdNormal @inline getdof(::StdNormal) = static(1) -@inline transport_def(::StdUniform, μ::StdNormal, x) = erfc(-x * invsqrt2) / 2 -@inline transport_def(::StdNormal, μ::StdUniform, p) = -erfcinv(2 * p) * sqrt2 - @inline Base.rand(rng::Random.AbstractRNG, ::Type{T}, ::StdNormal) where {T} = randn(rng, T) + +Φ(z) = erfc(-z * invsqrt2) / 2 +Φinv(p) = -erfcinv(2 * p) * sqrt2 + +InverseFunctions.inverse(::typeof(Φ)) = Φinv +InverseFunctions.inverse(::typeof(Φinv)) = Φ + +smf(::StdNormal, x) = Φ(x) +invsmf(::StdNormal, p) = Φinv(p) + +smf(::StdNormal) = Φ +invsmf(::StdNormal) = Φinv + +transport_def(::StdNormal, ::StdUniform, p) = invsmf(StdNormal(), p) +transport_def(::StdUniform, ::StdNormal, x) = smf(StdNormal(), x) diff --git a/src/standard/stduniform.jl b/src/standard/stduniform.jl index 32f4c62c..8817561e 100644 --- a/src/standard/stduniform.jl +++ b/src/standard/stduniform.jl @@ -10,3 +10,10 @@ insupport(d::StdUniform, x) = zero(x) ≤ x ≤ one(x) Base.rand(rng::Random.AbstractRNG, ::Type{T}, ::StdUniform) where {T} = rand(rng, T) massof(::StdUniform, s::Interval) = massof(Lebesgue(𝕀), s::Interval) + +smf(::StdUniform, x) = clamp(x, zero(x), one(x)) + +function invsmf(::StdUniform, p) + @assert zero(p) ≤ p ≤ one(p) + p +end diff --git a/src/transport.jl b/src/transport.jl index 49d99e1f..cc73c07d 100644 --- a/src/transport.jl +++ b/src/transport.jl @@ -92,6 +92,13 @@ distribution itself or a power of it (e.g. `StdUniform()` or """ function transport_to end +""" + transport_to(ν, μ, x) + +Transport `x` from the measure `μ` to the measure `ν` +""" +transport_to(ν, μ, x) = transport_to(ν, μ)(x) + """ transport_def(ν, μ, x) diff --git a/test/combinators/transformedmeasure.jl b/test/combinators/transformedmeasure.jl index 1c6d9073..342edbed 100644 --- a/test/combinators/transformedmeasure.jl +++ b/test/combinators/transformedmeasure.jl @@ -11,9 +11,10 @@ using SpecialFunctions: erfc, erfcinv import InverseFunctions: inverse, FunctionWithInverse using IrrationalConstants: invsqrt2, sqrt2 import ChangesOfVariables: with_logabsdet_jacobian +using MeasureBase.Interface: transport_to, test_transport -Φ(z) = erfc(-z * invsqrt2)/2 -Φinv(p) = -erfcinv(2*p) * sqrt2 +Φ(z) = erfc(-z * invsqrt2) / 2 +Φinv(p) = -erfcinv(2 * p) * sqrt2 with_logabsdet_jacobian(f::FunctionWithInverse, x) = with_logabsdet_jacobian(f.f, x) @@ -29,8 +30,8 @@ inverse(::typeof(Φinv)) = Φ var(::StdNormal) = 1.0 var(::StdExponential) = 1.0 -var(::StdUniform) = 1/12 -var(::StdLogistic) = π^2/3 +var(::StdUniform) = 1 / 12 +var(::StdLogistic) = π^2 / 3 function test_pushfwd(f, μ, ν_ref) @testset "pushfwd($f, $μ)" begin @@ -41,12 +42,17 @@ function test_pushfwd(f, μ, ν_ref) test_transport(ν_ref, ν) y = rand(ν_ref) - @test isapprox(@inferred(logdensityof(ν, y)), logdensityof(ν_ref, y), atol=1e-10) - @test isapprox(@inferred(unsafe_logdensityof(ν, y)), unsafe_logdensityof(ν_ref, y), atol=1e-10) + @test isapprox(@inferred(logdensityof(ν, y)), logdensityof(ν_ref, y), atol = 1e-10) + @test isapprox( + @inferred(unsafe_logdensityof(ν, y)), + unsafe_logdensityof(ν_ref, y), + atol = 1e-10, + ) @test isapprox(var(rand(ν^(10^5))), var(ν_ref), rtol = 0.05) - @test abs(transport_to(StdLogistic(), ν)(y)) ≈ abs(transport_to(StdLogistic(), ν_ref)(y)) + @test abs(transport_to(StdLogistic(), ν)(y)) ≈ + abs(transport_to(StdLogistic(), ν_ref)(y)) end end @@ -60,7 +66,7 @@ end (Φ, StdNormal(), StdUniform()) (Φinv, StdUniform(), StdNormal()) ] - + for (f, μ, ν_ref) in triples test_pushfwd(f, μ, ν_ref) end diff --git a/test/runtests.jl b/test/runtests.jl index 7601aecb..f10bde45 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -5,7 +5,7 @@ using LinearAlgebra import LogarithmicNumbers using MeasureBase -using MeasureBase: test_interface +using MeasureBase: test_interface, test_smf using Aqua Aqua.test_all(MeasureBase; ambiguities = false) @@ -247,6 +247,7 @@ end include("getdof.jl") include("transport.jl") +include("smf.jl") include("combinators/weighted.jl") include("combinators/transformedmeasure.jl") diff --git a/test/smf.jl b/test/smf.jl new file mode 100644 index 00000000..e4b0905e --- /dev/null +++ b/test/smf.jl @@ -0,0 +1,14 @@ +smf_measures = [ + StdNormal() + StdLogistic() + StdUniform() + Half(StdNormal()) + Half(StdLogistic()) + Half(StdUniform()) +] + +@testset "smf" begin + for μ in smf_measures + test_smf(μ) + end +end From aa50a0d0a60e002ffb325ef37f8e8be4d67d32d8 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Sat, 15 Oct 2022 13:31:55 -0700 Subject: [PATCH 358/368] drop redundant `transport_def`s --- src/combinators/transformedmeasure.jl | 16 ---------------- 1 file changed, 16 deletions(-) diff --git a/src/combinators/transformedmeasure.jl b/src/combinators/transformedmeasure.jl index 0242a79a..3b887fe1 100644 --- a/src/combinators/transformedmeasure.jl +++ b/src/combinators/transformedmeasure.jl @@ -35,22 +35,6 @@ end gettransform(ν::PushforwardMeasure) = ν.f parent(ν::PushforwardMeasure) = ν.origin -function transport_def(ν::PushforwardMeasure{F,I,M}, μ::M, x) where {F,I,M} - if μ === parent(ν) - return ν.f(x) - else - invoke(transport_def, Tuple{PushforwardMeasure,Any,Any}, ν, μ, x) - end -end - -function transport_def(μ::M, ν::PushforwardMeasure{F,I,M}, y) where {F,I,M} - if μ === parent(ν) - return ν.finv(y) - else - invoke(transport_def, Tuple{Any,PushforwardMeasure,Any}, μ, ν, y) - end -end - function Pretty.tile(ν::PushforwardMeasure) Pretty.list_layout(Pretty.tile.([ν.f, ν.origin]); prefix = :PushforwardMeasure) end From 3dbbddfffa08eafef683821462c77b7a2b43820f Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Sat, 15 Oct 2022 13:57:12 -0700 Subject: [PATCH 359/368] update `pushfwd` --- src/combinators/transformedmeasure.jl | 16 +++++----------- 1 file changed, 5 insertions(+), 11 deletions(-) diff --git a/src/combinators/transformedmeasure.jl b/src/combinators/transformedmeasure.jl index 3b887fe1..ef73f5c4 100644 --- a/src/combinators/transformedmeasure.jl +++ b/src/combinators/transformedmeasure.jl @@ -54,7 +54,7 @@ end @inline function logdensity_def(ν::PushforwardMeasure{F,I,M,<:WithVolCorr}, y) where {F,I,M} f = ν.f finv = ν.finv - x_orig, inv_ladj = with_logabsdet_jacobian(finv.f, y) + x_orig, inv_ladj = with_logabsdet_jacobian(finv, y) logd_orig = logdensity_def(ν.origin, x_orig) logd = float(logd_orig + inv_ladj) neginf = oftype(logd, -Inf) @@ -105,9 +105,7 @@ end export pushfwd -function pushfwd(f::FunctionWithInverse, μ, volcorr::TransformVolCorr) - PushforwardMeasure(f, inverse(f), μ, volcorr) -end + """ pushfwd(f, μ, volcorr = WithVolCorr()) @@ -120,7 +118,7 @@ To manually specify an inverse, call `pushfwd(InverseFunctions.setinverse(f, finv), μ, volcorr)`. """ function pushfwd(f, μ, volcorr::TransformVolCorr = WithVolCorr()) - pushfwd(setinverse(f, inverse(f)), μ, volcorr) + PushforwardMeasure(f, inverse(f), μ, volcorr) end function pushfwd(f, μ::PushforwardMeasure, volcorr::TransformVolCorr = WithVolCorr()) @@ -133,15 +131,11 @@ end # Either both WithVolCorr or both NoVolCorr, so we can merge them function _pushfwd(f, μ, ::V, v::V) where {V} - pushfwd(setinverse(f ∘ μ.f, μ.finv ∘ inverse(f)), μ.origin, v) -end - -function _pushfwd(f::FunctionWithInverse, μ, ::V, v::V) where {V} - pushfwd(setinverse(f.f ∘ μ.f, μ.finv ∘ f.invf), μ.origin, v) + pushfwd(f ∘ μ.f, μ.origin, v) end function _pushfwd(f, μ, _, v) - pushfwd(setinverse(f, inverse(f)), μ, v) + PushforwardMeasure(f, inverse(f), μ, v) end ############################################################################### From d245978bc143f5bedca4038bce564d380b3d8a9e Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Sat, 15 Oct 2022 14:34:02 -0700 Subject: [PATCH 360/368] change name --- src/combinators/transformedmeasure.jl | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/combinators/transformedmeasure.jl b/src/combinators/transformedmeasure.jl index ef73f5c4..eb6b7ff2 100644 --- a/src/combinators/transformedmeasure.jl +++ b/src/combinators/transformedmeasure.jl @@ -122,19 +122,19 @@ function pushfwd(f, μ, volcorr::TransformVolCorr = WithVolCorr()) end function pushfwd(f, μ::PushforwardMeasure, volcorr::TransformVolCorr = WithVolCorr()) - _pushfwd(f, μ, μ.volcorr, volcorr) + _pushfwd_of_pushfwd(f, μ, μ.volcorr, volcorr) end function pushfwd(f, μ::PushforwardMeasure, ::WithVolCorr) - _pushfwd(f, μ, μ.volcorr, WithVolCorr()) + _pushfwd_of_pushfwd(f, μ, μ.volcorr, WithVolCorr()) end # Either both WithVolCorr or both NoVolCorr, so we can merge them -function _pushfwd(f, μ, ::V, v::V) where {V} +function _pushfwd_of_pushfwd(f, μ, ::V, v::V) where {V} pushfwd(f ∘ μ.f, μ.origin, v) end -function _pushfwd(f, μ, _, v) +function _pushfwd_of_pushfwd(f, μ, _, v) PushforwardMeasure(f, inverse(f), μ, v) end From 868c34899aa08bf7d802e2a99bfc0a96a4c56f0c Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Sat, 15 Oct 2022 14:35:41 -0700 Subject: [PATCH 361/368] add type --- src/combinators/transformedmeasure.jl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/combinators/transformedmeasure.jl b/src/combinators/transformedmeasure.jl index eb6b7ff2..32e461ec 100644 --- a/src/combinators/transformedmeasure.jl +++ b/src/combinators/transformedmeasure.jl @@ -130,11 +130,11 @@ function pushfwd(f, μ::PushforwardMeasure, ::WithVolCorr) end # Either both WithVolCorr or both NoVolCorr, so we can merge them -function _pushfwd_of_pushfwd(f, μ, ::V, v::V) where {V} +function _pushfwd_of_pushfwd(f, μ::PushforwardMeasure, ::V, v::V) where {V} pushfwd(f ∘ μ.f, μ.origin, v) end -function _pushfwd_of_pushfwd(f, μ, _, v) +function _pushfwd_of_pushfwd(f, μ::PushforwardMeasure, _, v) PushforwardMeasure(f, inverse(f), μ, v) end From 00b128a671b61e4ee88efee74b6ea4ce24bac58f Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Sat, 15 Oct 2022 15:31:27 -0700 Subject: [PATCH 362/368] formatting --- src/combinators/transformedmeasure.jl | 2 -- src/primitives/lebesgue.jl | 2 +- src/smf.jl | 2 +- src/standard/stdlogistic.jl | 2 +- 4 files changed, 3 insertions(+), 5 deletions(-) diff --git a/src/combinators/transformedmeasure.jl b/src/combinators/transformedmeasure.jl index 32e461ec..e0caf854 100644 --- a/src/combinators/transformedmeasure.jl +++ b/src/combinators/transformedmeasure.jl @@ -105,8 +105,6 @@ end export pushfwd - - """ pushfwd(f, μ, volcorr = WithVolCorr()) diff --git a/src/primitives/lebesgue.jl b/src/primitives/lebesgue.jl index e11db884..8c42766f 100644 --- a/src/primitives/lebesgue.jl +++ b/src/primitives/lebesgue.jl @@ -89,4 +89,4 @@ invsmf(::Lebesgue{RealNumbers}) = identity smf(::LebesgueBase, x) = x smf(::LebesgueBase) = identity invsmf(::LebesgueBase, x) = x -invsmf(::LebesgueBase) = identity \ No newline at end of file +invsmf(::LebesgueBase) = identity diff --git a/src/smf.jl b/src/smf.jl index 1d499d2c..6ffa6f41 100644 --- a/src/smf.jl +++ b/src/smf.jl @@ -37,4 +37,4 @@ smf(μ, x) = NoSMF() invsmf(μ, p) = NoSMFInverse() smf(μ) = Base.Fix1(smf, μ) -invsmf(μ) = Base.Fix1(invsmf, μ) \ No newline at end of file +invsmf(μ) = Base.Fix1(invsmf, μ) diff --git a/src/standard/stdlogistic.jl b/src/standard/stdlogistic.jl index a3a351c3..d7e0430a 100644 --- a/src/standard/stdlogistic.jl +++ b/src/standard/stdlogistic.jl @@ -18,4 +18,4 @@ smf(::StdLogistic, x) = logistic(x) smf(::StdLogistic) = logistic invsmf(::StdLogistic, p) = logit(p) -invsmf(::StdLogistic) = logit \ No newline at end of file +invsmf(::StdLogistic) = logit From 97cbb33482ae7b95dcfaab742b880837753bfd7a Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Sat, 15 Oct 2022 15:33:04 -0700 Subject: [PATCH 363/368] fix docstring --- src/combinators/transformedmeasure.jl | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/src/combinators/transformedmeasure.jl b/src/combinators/transformedmeasure.jl index e0caf854..c78e4e45 100644 --- a/src/combinators/transformedmeasure.jl +++ b/src/combinators/transformedmeasure.jl @@ -19,8 +19,12 @@ function parent(::AbstractTransformedMeasure) end export PushforwardMeasure """ - struct PushforwardMeasure{F,I,MU,VC<:TransformVolCorr} <: - AbstractPushforward f :: F finv :: I origin :: MU volcorr :: VC end + struct PushforwardMeasure{F,I,M,VC<:TransformVolCorr} <: AbstractPushforward + f :: F + finv :: I + origin :: M + volcorr :: VC + end Users should not call `PushforwardMeasure` directly. Instead call or add methods to `pushfwd`. From b6c039ffd4f048a2a6a6005b2bfbd581fc61cc0a Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Sat, 15 Oct 2022 15:36:07 -0700 Subject: [PATCH 364/368] depend on FunctinoChains --- Project.toml | 2 ++ src/MeasureBase.jl | 1 + 2 files changed, 3 insertions(+) diff --git a/Project.toml b/Project.toml index 86005f65..1c9139e4 100644 --- a/Project.toml +++ b/Project.toml @@ -10,6 +10,7 @@ Compat = "34da2185-b29b-5c13-b0c7-acf172513d20" ConstructionBase = "187b0558-2788-49d3-abe0-74a17ed4e7c9" DensityInterface = "b429d917-457f-4dbc-8f4c-0cc954292b1d" FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b" +FunctionChains = "8e6b2b91-af83-483e-ba35-d00930e4cf9b" IfElse = "615f187c-cbe4-4ef1-ba3b-2fcf58d6d173" IntervalSets = "8197267c-284f-5f27-9208-e0e47529a953" InverseFunctions = "3587e190-3f89-42d0-90ee-14403ec27112" @@ -35,6 +36,7 @@ Compat = "3.35, 4" ConstructionBase = "1.3" DensityInterface = "0.4" FillArrays = "0.12, 0.13" +FunctionChains = "0.1" IfElse = "0.1" IntervalSets = "0.7" InverseFunctions = "0.1.8" diff --git a/src/MeasureBase.jl b/src/MeasureBase.jl index f96ac86c..dcfe7464 100644 --- a/src/MeasureBase.jl +++ b/src/MeasureBase.jl @@ -34,6 +34,7 @@ const Pretty = PrettyPrinting using ChainRulesCore using FillArrays using Static +using FunctionChains export ≪ export gentype From f96b54695c06f9e8ebc18ccf70d6f58b5b0cd04d Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Sat, 15 Oct 2022 15:40:19 -0700 Subject: [PATCH 365/368] Use fchain --- src/combinators/product.jl | 2 +- src/combinators/transformedmeasure.jl | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/combinators/product.jl b/src/combinators/product.jl index ee0ae2b6..97db166b 100644 --- a/src/combinators/product.jl +++ b/src/combinators/product.jl @@ -161,7 +161,7 @@ marginals(μ::ProductMeasure) = μ.marginals # TODO: Better `map` support in MappedArrays _map(f, args...) = map(f, args...) -_map(f, x::MappedArrays.ReadonlyMappedArray) = mappedarray(f ∘ x.f, x.data) +_map(f, x::MappedArrays.ReadonlyMappedArray) = mappedarray(fchain((x.f, f)), x.data) function testvalue(::Type{T}, d::AbstractProductMeasure) where {T} _map(m -> testvalue(T, m), marginals(d)) diff --git a/src/combinators/transformedmeasure.jl b/src/combinators/transformedmeasure.jl index c78e4e45..8217ff3e 100644 --- a/src/combinators/transformedmeasure.jl +++ b/src/combinators/transformedmeasure.jl @@ -133,7 +133,7 @@ end # Either both WithVolCorr or both NoVolCorr, so we can merge them function _pushfwd_of_pushfwd(f, μ::PushforwardMeasure, ::V, v::V) where {V} - pushfwd(f ∘ μ.f, μ.origin, v) + pushfwd(fchain((μ.f, f)), μ.origin, v) end function _pushfwd_of_pushfwd(f, μ::PushforwardMeasure, _, v) From 0a216725666ccc7990ec9d32dea0976c029114fb Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Sat, 15 Oct 2022 15:42:53 -0700 Subject: [PATCH 366/368] simplify transport_def for StdLogistic --- src/standard/stdlogistic.jl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/standard/stdlogistic.jl b/src/standard/stdlogistic.jl index d7e0430a..0d502ec6 100644 --- a/src/standard/stdlogistic.jl +++ b/src/standard/stdlogistic.jl @@ -7,8 +7,8 @@ export StdLogistic @inline logdensity_def(::StdLogistic, x) = (u = -abs(x); u - 2 * log1pexp(u)) @inline basemeasure(::StdLogistic) = LebesgueBase() -@inline transport_def(::StdUniform, μ::StdLogistic, x) = smf(StdLogistic(), x) -@inline transport_def(::StdLogistic, μ::StdUniform, p) = invsmf(StdLogistic(), p) +@inline transport_def(::StdUniform, μ::StdLogistic, x) = logistic(x) +@inline transport_def(::StdLogistic, μ::StdUniform, p) = logit(p) @inline function Base.rand(rng::Random.AbstractRNG, ::Type{T}, ::StdLogistic) where {T} logit(rand(rng, T)) From 046b48cf69b5624d5303155b7e7283ba4d2511a4 Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Sat, 15 Oct 2022 15:44:14 -0700 Subject: [PATCH 367/368] simplify transport_def for StdNormal --- src/standard/stdnormal.jl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/standard/stdnormal.jl b/src/standard/stdnormal.jl index dbb89ed0..dc9cac74 100644 --- a/src/standard/stdnormal.jl +++ b/src/standard/stdnormal.jl @@ -26,5 +26,5 @@ invsmf(::StdNormal, p) = Φinv(p) smf(::StdNormal) = Φ invsmf(::StdNormal) = Φinv -transport_def(::StdNormal, ::StdUniform, p) = invsmf(StdNormal(), p) -transport_def(::StdUniform, ::StdNormal, x) = smf(StdNormal(), x) +transport_def(::StdNormal, ::StdUniform, p) = Φinv(p) +transport_def(::StdUniform, ::StdNormal, x) = Φ(x) From 18a9f99d938f79b49e46138df241a285d958f04e Mon Sep 17 00:00:00 2001 From: Chad Scherrer Date: Sat, 15 Oct 2022 15:57:51 -0700 Subject: [PATCH 368/368] drop redundant method --- src/combinators/transformedmeasure.jl | 4 ---- 1 file changed, 4 deletions(-) diff --git a/src/combinators/transformedmeasure.jl b/src/combinators/transformedmeasure.jl index 8217ff3e..b00065a1 100644 --- a/src/combinators/transformedmeasure.jl +++ b/src/combinators/transformedmeasure.jl @@ -127,10 +127,6 @@ function pushfwd(f, μ::PushforwardMeasure, volcorr::TransformVolCorr = WithVolC _pushfwd_of_pushfwd(f, μ, μ.volcorr, volcorr) end -function pushfwd(f, μ::PushforwardMeasure, ::WithVolCorr) - _pushfwd_of_pushfwd(f, μ, μ.volcorr, WithVolCorr()) -end - # Either both WithVolCorr or both NoVolCorr, so we can merge them function _pushfwd_of_pushfwd(f, μ::PushforwardMeasure, ::V, v::V) where {V} pushfwd(fchain((μ.f, f)), μ.origin, v)