API: Turing.Inference
Turing.Inference.CSMC — TypeCSMC(...)Equivalent to PG.
Turing.Inference.ESS — TypeESSElliptical slice sampling algorithm.
Examples
julia> @model function gdemo(x)
+Inference · Turing API: Turing.Inference
Turing.Inference.CSMC — TypeCSMC(...)
Equivalent to PG.
sourceTuring.Inference.ESS — TypeESS
Elliptical slice sampling algorithm.
Examples
julia> @model function gdemo(x)
m ~ Normal()
x ~ Normal(m, 0.5)
end
@@ -469,14 +11,14 @@
│ Row │ parameters │ mean │
│ │ Symbol │ Float64 │
├─────┼────────────┼──────────┤
-│ 1 │ m │ 0.824853 │
sourceTuring.Inference.Emcee — TypeEmcee(n_walkers::Int, stretch_length=2.0)
Affine-invariant ensemble sampling algorithm.
Reference
Foreman-Mackey, D., Hogg, D. W., Lang, D., & Goodman, J. (2013). emcee: The MCMC Hammer. Publications of the Astronomical Society of the Pacific, 125 (925), 306. https://doi.org/10.1086/670067
sourceTuring.Inference.ExternalSampler — TypeExternalSampler{S<:AbstractSampler,AD<:ADTypes.AbstractADType,Unconstrained}
Represents a sampler that is not an implementation of InferenceAlgorithm.
The Unconstrained type-parameter is to indicate whether the sampler requires unconstrained space.
Fields
sampler::AbstractMCMC.AbstractSampler: the sampler to wrap
adtype::ADTypes.AbstractADType: the automatic differentiation (AD) backend to use
sourceTuring.Inference.Gibbs — TypeGibbs
A type representing a Gibbs sampler.
Fields
varnames::Any: varnames representing variables for each sampler
samplers::Any: samplers for each entry in varnames
sourceTuring.Inference.GibbsContext — TypeGibbsContext{VNs}(global_varinfo, context)
A context used in the implementation of the Turing.jl Gibbs sampler.
There will be one GibbsContext for each iteration of a component sampler.
VNs is a a tuple of symbols for VarNames that the current component sampler is sampling. For those VarNames, GibbsContext will just pass tilde_assume calls to its child context. For other variables, their values will be fixed to the values they have in global_varinfo.
The naive implementation of GibbsContext would simply have a field target_varnames that would be a collection of VarNames that the current component sampler is sampling. The reason we instead have a Tuple type parameter listing Symbols is to allow is_target_varname to benefit from compile time constant propagation. This is important for type stability of tilde_assume.
Fields
global_varinfo: a Ref to the global AbstractVarInfo object that holds values for all variables, both those fixed and those being sampled. We use a Ref because this field may need to be updated if new variables are introduced.
context: the child context that tilde calls will eventually be passed onto.
sourceTuring.Inference.HMC — TypeHMC(ϵ::Float64, n_leapfrog::Int; adtype::ADTypes.AbstractADType = AutoForwardDiff())
Hamiltonian Monte Carlo sampler with static trajectory.
Arguments
ϵ: The leapfrog step size to use.n_leapfrog: The number of leapfrog steps to use.adtype: The automatic differentiation (AD) backend. If not specified, ForwardDiff is used, with its chunksize automatically determined.
Usage
HMC(0.05, 10)
Tips
If you are receiving gradient errors when using HMC, try reducing the leapfrog step size ϵ, e.g.
# Original step size
+│ 1 │ m │ 0.824853 │
sourceTuring.Inference.Emcee — TypeEmcee(n_walkers::Int, stretch_length=2.0)
Affine-invariant ensemble sampling algorithm.
Reference
Foreman-Mackey, D., Hogg, D. W., Lang, D., & Goodman, J. (2013). emcee: The MCMC Hammer. Publications of the Astronomical Society of the Pacific, 125 (925), 306. https://doi.org/10.1086/670067
sourceTuring.Inference.ExternalSampler — TypeExternalSampler{S<:AbstractSampler,AD<:ADTypes.AbstractADType,Unconstrained}
Represents a sampler that is not an implementation of InferenceAlgorithm.
The Unconstrained type-parameter is to indicate whether the sampler requires unconstrained space.
Fields
sampler::AbstractMCMC.AbstractSampler: the sampler to wrap
adtype::ADTypes.AbstractADType: the automatic differentiation (AD) backend to use
sourceTuring.Inference.Gibbs — TypeGibbs
A type representing a Gibbs sampler.
Fields
varnames::Any: varnames representing variables for each sampler
samplers::Any: samplers for each entry in varnames
sourceTuring.Inference.GibbsContext — TypeGibbsContext{VNs}(global_varinfo, context)
A context used in the implementation of the Turing.jl Gibbs sampler.
There will be one GibbsContext for each iteration of a component sampler.
VNs is a a tuple of symbols for VarNames that the current component sampler is sampling. For those VarNames, GibbsContext will just pass tilde_assume calls to its child context. For other variables, their values will be fixed to the values they have in global_varinfo.
The naive implementation of GibbsContext would simply have a field target_varnames that would be a collection of VarNames that the current component sampler is sampling. The reason we instead have a Tuple type parameter listing Symbols is to allow is_target_varname to benefit from compile time constant propagation. This is important for type stability of tilde_assume.
Fields
global_varinfo: a Ref to the global AbstractVarInfo object that holds values for all variables, both those fixed and those being sampled. We use a Ref because this field may need to be updated if new variables are introduced.
context: the child context that tilde calls will eventually be passed onto.
sourceTuring.Inference.HMC — TypeHMC(ϵ::Float64, n_leapfrog::Int; adtype::ADTypes.AbstractADType = AutoForwardDiff())
Hamiltonian Monte Carlo sampler with static trajectory.
Arguments
ϵ: The leapfrog step size to use.n_leapfrog: The number of leapfrog steps to use.adtype: The automatic differentiation (AD) backend. If not specified, ForwardDiff is used, with its chunksize automatically determined.
Usage
HMC(0.05, 10)
Tips
If you are receiving gradient errors when using HMC, try reducing the leapfrog step size ϵ, e.g.
# Original step size
sample(gdemo([1.5, 2]), HMC(0.1, 10), 1000)
# Reduced step size
-sample(gdemo([1.5, 2]), HMC(0.01, 10), 1000)
sourceTuring.Inference.HMCDA — TypeHMCDA(
+sample(gdemo([1.5, 2]), HMC(0.01, 10), 1000)
sourceTuring.Inference.HMCDA — TypeHMCDA(
n_adapts::Int, δ::Float64, λ::Float64; ϵ::Float64 = 0.0;
adtype::ADTypes.AbstractADType = AutoForwardDiff(),
-)
Hamiltonian Monte Carlo sampler with Dual Averaging algorithm.
Usage
HMCDA(200, 0.65, 0.3)
Arguments
n_adapts: Numbers of samples to use for adaptation.δ: Target acceptance rate. 65% is often recommended.λ: Target leapfrog length.ϵ: Initial step size; 0 means automatically search by Turing.adtype: The automatic differentiation (AD) backend. If not specified, ForwardDiff is used, with its chunksize automatically determined.
Reference
For more information, please view the following paper (arXiv link):
Hoffman, Matthew D., and Andrew Gelman. "The No-U-turn sampler: adaptively setting path lengths in Hamiltonian Monte Carlo." Journal of Machine Learning Research 15, no. 1 (2014): 1593-1623.
sourceTuring.Inference.IS — TypeIS()
Importance sampling algorithm.
Usage:
IS()
Example:
# Define a simple Normal model with unknown mean and variance.
+)
Hamiltonian Monte Carlo sampler with Dual Averaging algorithm.
Usage
HMCDA(200, 0.65, 0.3)
Arguments
n_adapts: Numbers of samples to use for adaptation.δ: Target acceptance rate. 65% is often recommended.λ: Target leapfrog length.ϵ: Initial step size; 0 means automatically search by Turing.adtype: The automatic differentiation (AD) backend. If not specified, ForwardDiff is used, with its chunksize automatically determined.
Reference
For more information, please view the following paper (arXiv link):
Hoffman, Matthew D., and Andrew Gelman. "The No-U-turn sampler: adaptively setting path lengths in Hamiltonian Monte Carlo." Journal of Machine Learning Research 15, no. 1 (2014): 1593-1623.
sourceTuring.Inference.IS — TypeIS()
Importance sampling algorithm.
Usage:
IS()
Example:
# Define a simple Normal model with unknown mean and variance.
@model function gdemo(x)
s² ~ InverseGamma(2,3)
m ~ Normal(0,sqrt.(s))
@@ -485,7 +27,7 @@
return s², m
end
-sample(gdemo([1.5, 2]), IS(), 1000)
sourceTuring.Inference.MH — MethodMH(space...)
Construct a Metropolis-Hastings algorithm.
The arguments space can be
- Blank (i.e.
MH()), in which case MH defaults to using the prior for each parameter as the proposal distribution. - An iterable of pairs or tuples mapping a
Symbol to a AdvancedMH.Proposal, Distribution, or Function that generates returns a conditional proposal distribution. - A covariance matrix to use as for mean-zero multivariate normal proposals.
Examples
The default MH will draw proposal samples from the prior distribution using AdvancedMH.StaticProposal.
@model function gdemo(x, y)
+sample(gdemo([1.5, 2]), IS(), 1000)
sourceTuring.Inference.MH — MethodMH(space...)
Construct a Metropolis-Hastings algorithm.
The arguments space can be
- Blank (i.e.
MH()), in which case MH defaults to using the prior for each parameter as the proposal distribution. - An iterable of pairs or tuples mapping a
Symbol to a AdvancedMH.Proposal, Distribution, or Function that generates returns a conditional proposal distribution. - A covariance matrix to use as for mean-zero multivariate normal proposals.
Examples
The default MH will draw proposal samples from the prior distribution using AdvancedMH.StaticProposal.
@model function gdemo(x, y)
s² ~ InverseGamma(2,3)
m ~ Normal(0, sqrt(s²))
x ~ Normal(m, sqrt(s²))
@@ -533,22 +75,22 @@
),
1_000
)
-mean(chain)
sourceTuring.Inference.MHLogDensityFunction — TypeMHLogDensityFunction
A log density function for the MH sampler.
This variant uses the set_namedtuple! function to update the VarInfo.
sourceTuring.Inference.NUTS — TypeNUTS(n_adapts::Int, δ::Float64; max_depth::Int=10, Δ_max::Float64=1000.0, init_ϵ::Float64=0.0; adtype::ADTypes.AbstractADType=AutoForwardDiff()
No-U-Turn Sampler (NUTS) sampler.
Usage:
NUTS() # Use default NUTS configuration.
-NUTS(1000, 0.65) # Use 1000 adaption steps, and target accept ratio 0.65.
Arguments:
n_adapts::Int : The number of samples to use with adaptation.δ::Float64 : Target acceptance rate for dual averaging.max_depth::Int : Maximum doubling tree depth.Δ_max::Float64 : Maximum divergence during doubling tree.init_ϵ::Float64 : Initial step size; 0 means automatically searching using a heuristic procedure.adtype::ADTypes.AbstractADType : The automatic differentiation (AD) backend. If not specified, ForwardDiff is used, with its chunksize automatically determined.
sourceTuring.Inference.PG — TypePG(n, space...)
+mean(chain)
sourceTuring.Inference.MHLogDensityFunction — TypeMHLogDensityFunction
A log density function for the MH sampler.
This variant uses the set_namedtuple! function to update the VarInfo.
sourceTuring.Inference.NUTS — TypeNUTS(n_adapts::Int, δ::Float64; max_depth::Int=10, Δ_max::Float64=1000.0, init_ϵ::Float64=0.0; adtype::ADTypes.AbstractADType=AutoForwardDiff()
No-U-Turn Sampler (NUTS) sampler.
Usage:
NUTS() # Use default NUTS configuration.
+NUTS(1000, 0.65) # Use 1000 adaption steps, and target accept ratio 0.65.
Arguments:
n_adapts::Int : The number of samples to use with adaptation.δ::Float64 : Target acceptance rate for dual averaging.max_depth::Int : Maximum doubling tree depth.Δ_max::Float64 : Maximum divergence during doubling tree.init_ϵ::Float64 : Initial step size; 0 means automatically searching using a heuristic procedure.adtype::ADTypes.AbstractADType : The automatic differentiation (AD) backend. If not specified, ForwardDiff is used, with its chunksize automatically determined.
sourceTuring.Inference.PG — TypePG(n, space...)
PG(n, [resampler = AdvancedPS.ResampleWithESSThreshold(), space = ()])
-PG(n, [resampler = AdvancedPS.resample_systematic, ]threshold[, space = ()])
Create a Particle Gibbs sampler of type PG with n particles for the variables in space.
If the algorithm for the resampling step is not specified explicitly, systematic resampling is performed if the estimated effective sample size per particle drops below 0.5.
sourceTuring.Inference.PG — Typestruct PG{space, R} <: Turing.Inference.ParticleInference
Particle Gibbs sampler.
Fields
nparticles::Int64: Number of particles.
resampler::Any: Resampling algorithm.
sourceTuring.Inference.PolynomialStepsize — MethodPolynomialStepsize(a[, b=0, γ=0.55])
Create a polynomially decaying stepsize function.
At iteration t, the step size is
\[a (b + t)^{-γ}.\]
sourceTuring.Inference.Prior — TypePrior()
Algorithm for sampling from the prior.
sourceTuring.Inference.RepeatSampler — TypeRepeatSampler <: AbstractMCMC.AbstractSampler
A RepeatSampler is a container for a sampler and a number of times to repeat it.
Fields
sampler: The sampler to repeat
num_repeat: The number of times to repeat the sampler
Examples
repeated_sampler = RepeatSampler(sampler, 10)
-AbstractMCMC.step(rng, model, repeated_sampler) # take 10 steps of `sampler`
sourceTuring.Inference.SGHMC — TypeSGHMC{AD,space}
Stochastic Gradient Hamiltonian Monte Carlo (SGHMC) sampler.e
Fields
learning_rate::Real
momentum_decay::Real
adtype::Any
Reference
Tianqi Chen, Emily Fox, & Carlos Guestrin (2014). Stochastic Gradient Hamiltonian Monte Carlo. In: Proceedings of the 31st International Conference on Machine Learning (pp. 1683–1691).
sourceTuring.Inference.SGHMC — MethodSGHMC(
+PG(n, [resampler = AdvancedPS.resample_systematic, ]threshold[, space = ()])
Create a Particle Gibbs sampler of type PG with n particles for the variables in space.
If the algorithm for the resampling step is not specified explicitly, systematic resampling is performed if the estimated effective sample size per particle drops below 0.5.
sourceTuring.Inference.PG — Typestruct PG{space, R} <: Turing.Inference.ParticleInference
Particle Gibbs sampler.
Fields
nparticles::Int64: Number of particles.
resampler::Any: Resampling algorithm.
sourceTuring.Inference.PolynomialStepsize — MethodPolynomialStepsize(a[, b=0, γ=0.55])
Create a polynomially decaying stepsize function.
At iteration t, the step size is
\[a (b + t)^{-γ}.\]
sourceTuring.Inference.Prior — TypePrior()
Algorithm for sampling from the prior.
sourceTuring.Inference.RepeatSampler — TypeRepeatSampler <: AbstractMCMC.AbstractSampler
A RepeatSampler is a container for a sampler and a number of times to repeat it.
Fields
sampler: The sampler to repeat
num_repeat: The number of times to repeat the sampler
Examples
repeated_sampler = RepeatSampler(sampler, 10)
+AbstractMCMC.step(rng, model, repeated_sampler) # take 10 steps of `sampler`
sourceTuring.Inference.SGHMC — TypeSGHMC{AD,space}
Stochastic Gradient Hamiltonian Monte Carlo (SGHMC) sampler.e
Fields
learning_rate::Real
momentum_decay::Real
adtype::Any
Reference
Tianqi Chen, Emily Fox, & Carlos Guestrin (2014). Stochastic Gradient Hamiltonian Monte Carlo. In: Proceedings of the 31st International Conference on Machine Learning (pp. 1683–1691).
sourceTuring.Inference.SGHMC — MethodSGHMC(
space::Symbol...;
learning_rate::Real,
momentum_decay::Real,
adtype::ADTypes.AbstractADType = AutoForwardDiff(),
-)
Create a Stochastic Gradient Hamiltonian Monte Carlo (SGHMC) sampler.
If the automatic differentiation (AD) backend adtype is not provided, ForwardDiff with automatically determined chunksize is used.
Reference
Tianqi Chen, Emily Fox, & Carlos Guestrin (2014). Stochastic Gradient Hamiltonian Monte Carlo. In: Proceedings of the 31st International Conference on Machine Learning (pp. 1683–1691).
sourceTuring.Inference.SGLD — TypeSGLD
Stochastic gradient Langevin dynamics (SGLD) sampler.
Fields
stepsize::Any: Step size function.
adtype::Any
Reference
Max Welling & Yee Whye Teh (2011). Bayesian Learning via Stochastic Gradient Langevin Dynamics. In: Proceedings of the 28th International Conference on Machine Learning (pp. 681–688).
sourceTuring.Inference.SGLD — MethodSGLD(
+)
Create a Stochastic Gradient Hamiltonian Monte Carlo (SGHMC) sampler.
If the automatic differentiation (AD) backend adtype is not provided, ForwardDiff with automatically determined chunksize is used.
Reference
Tianqi Chen, Emily Fox, & Carlos Guestrin (2014). Stochastic Gradient Hamiltonian Monte Carlo. In: Proceedings of the 31st International Conference on Machine Learning (pp. 1683–1691).
sourceTuring.Inference.SGLD — TypeSGLD
Stochastic gradient Langevin dynamics (SGLD) sampler.
Fields
stepsize::Any: Step size function.
adtype::Any
Reference
Max Welling & Yee Whye Teh (2011). Bayesian Learning via Stochastic Gradient Langevin Dynamics. In: Proceedings of the 28th International Conference on Machine Learning (pp. 681–688).
sourceTuring.Inference.SGLD — MethodSGLD(
space::Symbol...;
stepsize = PolynomialStepsize(0.01),
adtype::ADTypes.AbstractADType = AutoForwardDiff(),
-)
Stochastic gradient Langevin dynamics (SGLD) sampler.
By default, a polynomially decaying stepsize is used.
If the automatic differentiation (AD) backend adtype is not provided, ForwardDiff with automatically determined chunksize is used.
Reference
Max Welling & Yee Whye Teh (2011). Bayesian Learning via Stochastic Gradient Langevin Dynamics. In: Proceedings of the 28th International Conference on Machine Learning (pp. 681–688).
See also: PolynomialStepsize
sourceTuring.Inference.SMC — TypeSMC(space...)
+)
Stochastic gradient Langevin dynamics (SGLD) sampler.
By default, a polynomially decaying stepsize is used.
If the automatic differentiation (AD) backend adtype is not provided, ForwardDiff with automatically determined chunksize is used.
Reference
Max Welling & Yee Whye Teh (2011). Bayesian Learning via Stochastic Gradient Langevin Dynamics. In: Proceedings of the 28th International Conference on Machine Learning (pp. 681–688).
See also: PolynomialStepsize
sourceTuring.Inference.SMC — TypeSMC(space...)
SMC([resampler = AdvancedPS.ResampleWithESSThreshold(), space = ()])
-SMC([resampler = AdvancedPS.resample_systematic, ]threshold[, space = ()])
Create a sequential Monte Carlo sampler of type SMC for the variables in space.
If the algorithm for the resampling step is not specified explicitly, systematic resampling is performed if the estimated effective sample size per particle drops below 0.5.
sourceTuring.Inference.SMC — Typestruct SMC{space, R} <: Turing.Inference.ParticleInference
Sequential Monte Carlo sampler.
Fields
resampler::Any
sourceStatsAPI.predict — Methodpredict([rng::AbstractRNG,] model::Model, chain::MCMCChains.Chains; include_all=false)
Execute model conditioned on each sample in chain, and return the resulting Chains.
If include_all is false, the returned Chains will contain only those variables sampled/not present in chain.
Details
Internally calls Turing.Inference.transitions_from_chain to obtained the samples and then converts these into a Chains object using AbstractMCMC.bundle_samples.
Example
julia> using Turing; Turing.setprogress!(false);
+SMC([resampler = AdvancedPS.resample_systematic, ]threshold[, space = ()])
Create a sequential Monte Carlo sampler of type SMC for the variables in space.
If the algorithm for the resampling step is not specified explicitly, systematic resampling is performed if the estimated effective sample size per particle drops below 0.5.
sourceTuring.Inference.SMC — Typestruct SMC{space, R} <: Turing.Inference.ParticleInference
Sequential Monte Carlo sampler.
Fields
resampler::Any
sourceStatsAPI.predict — Methodpredict([rng::AbstractRNG,] model::Model, chain::MCMCChains.Chains; include_all=false)
Execute model conditioned on each sample in chain, and return the resulting Chains.
If include_all is false, the returned Chains will contain only those variables sampled/not present in chain.
Details
Internally calls Turing.Inference.transitions_from_chain to obtained the samples and then converts these into a Chains object using AbstractMCMC.bundle_samples.
Example
julia> using Turing; Turing.setprogress!(false);
[ Info: [Turing]: progress logging is disabled globally
julia> @model function linear_reg(x, y, σ = 0.1)
@@ -596,10 +138,11 @@
y[1] 20.0342 20.1188 20.2135 20.2588 20.4188
y[2] 20.1870 20.3178 20.3839 20.4466 20.5895
+
julia> ys_pred = vec(mean(Array(group(predictions, :y)); dims = 1));
julia> sum(abs2, ys_test - ys_pred) ≤ 0.1
-true
sourceTuring.Inference.dist_val_tuple — Methoddist_val_tuple(spl::Sampler{<:MH}, vi::VarInfo)
Return two NamedTuples.
The first NamedTuple has symbols as keys and distributions as values. The second NamedTuple has model symbols as keys and their stored values as values.
sourceTuring.Inference.drop_space — Functiondrop_space(alg::InferenceAlgorithm)
Return an InferenceAlgorithm like alg, but with all space information removed.
sourceTuring.Inference.externalsampler — Methodexternalsampler(sampler::AbstractSampler; adtype=AutoForwardDiff(), unconstrained=true)
Wrap a sampler so it can be used as an inference algorithm.
Arguments
sampler::AbstractSampler: The sampler to wrap.
Keyword Arguments
adtype::ADTypes.AbstractADType=ADTypes.AutoForwardDiff(): The automatic differentiation (AD) backend to use.unconstrained::Bool=true: Whether the sampler requires unconstrained space.
sourceTuring.Inference.getparams — Methodgetparams(model, t)
Return a named tuple of parameters.
sourceTuring.Inference.group_varnames_by_symbol — Methodgroup_varnames_by_symbol(vns)
Group the varnames by their symbol.
Arguments
vns: Iterable of VarName.
Returns
OrderedDict{Symbol, Vector{VarName}}: A dictionary mapping symbol to a vector of varnames.
sourceTuring.Inference.isgibbscomponent — Methodisgibbscomponent(alg::Union{InferenceAlgorithm, AbstractMCMC.AbstractSampler})
Return a boolean indicating whether alg is a valid component for a Gibbs sampler.
Defaults to false if no method has been defined for a particular algorithm type.
sourceTuring.Inference.make_conditional — Methodmake_conditional(model, target_variables, varinfo)
Return a new, conditioned model for a component of a Gibbs sampler.
Arguments
model::DynamicPPL.Model: The model to condition.target_variables::AbstractVector{<:VarName}: The target variables of the component
sampler. These will not be conditioned.
varinfo::DynamicPPL.AbstractVarInfo: Values for all variables in the model. All the
values in varinfo but not in target_variables will be conditioned to the values they have in varinfo.
Returns
- A new model with the variables not in
target_variables conditioned. - The
GibbsContext object that will be used to condition the variables. This is necessary
because evaluation can mutate its global_varinfo field, which we need to access later.
sourceTuring.Inference.match_linking!! — Methodmatch_linking!!(varinfo_local, prev_state_local, model)
Make sure the linked/invlinked status of varinfo_local matches that of the previous state for this sampler. This is relevant when multilple samplers are sampling the same variables, and one might need it to be linked while the other doesn't.
sourceTuring.Inference.mh_accept — Methodmh_accept(logp_current::Real, logp_proposal::Real, log_proposal_ratio::Real)
Decide if a proposal $x'$ with log probability $\log p(x') = logp_proposal$ and log proposal ratio $\log k(x', x) - \log k(x, x') = log_proposal_ratio$ in a Metropolis-Hastings algorithm with Markov kernel $k(x_t, x_{t+1})$ and current state $x$ with log probability $\log p(x) = logp_current$ is accepted by evaluating the Metropolis-Hastings acceptance criterion
\[\log U \leq \log p(x') - \log p(x) + \log k(x', x) - \log k(x, x')\]
for a uniform random number $U \in [0, 1)$.
sourceTuring.Inference.requires_unconstrained_space — Methodrequires_unconstrained_space(sampler::ExternalSampler)
Return true if the sampler requires unconstrained space, and false otherwise.
sourceTuring.Inference.set_namedtuple! — Methodset_namedtuple!(vi::VarInfo, nt::NamedTuple)
Places the values of a NamedTuple into the relevant places of a VarInfo.
sourceTuring.Inference.setparams_varinfo!! — Methodsetparams_varinfo!!(model, sampler::Sampler, state, params::AbstractVarInfo)
A lot like AbstractMCMC.setparams!!, but instead of taking a vector of parameters, takes an AbstractVarInfo object. Also takes the sampler as an argument. By default, falls back to AbstractMCMC.setparams!!(model, state, params[:]).
model is typically a DynamicPPL.Model, but can also be e.g. an AbstractMCMC.LogDensityModel.
sourceTuring.Inference.transitions_from_chain — Methodtransitions_from_chain(
+true
sourceTuring.Inference.dist_val_tuple — Methoddist_val_tuple(spl::Sampler{<:MH}, vi::VarInfo)
Return two NamedTuples.
The first NamedTuple has symbols as keys and distributions as values. The second NamedTuple has model symbols as keys and their stored values as values.
sourceTuring.Inference.drop_space — Functiondrop_space(alg::InferenceAlgorithm)
Return an InferenceAlgorithm like alg, but with all space information removed.
sourceTuring.Inference.externalsampler — Methodexternalsampler(sampler::AbstractSampler; adtype=AutoForwardDiff(), unconstrained=true)
Wrap a sampler so it can be used as an inference algorithm.
Arguments
sampler::AbstractSampler: The sampler to wrap.
Keyword Arguments
adtype::ADTypes.AbstractADType=ADTypes.AutoForwardDiff(): The automatic differentiation (AD) backend to use.unconstrained::Bool=true: Whether the sampler requires unconstrained space.
sourceTuring.Inference.getparams — Methodgetparams(model, t)
Return a named tuple of parameters.
sourceTuring.Inference.group_varnames_by_symbol — Methodgroup_varnames_by_symbol(vns)
Group the varnames by their symbol.
Arguments
vns: Iterable of VarName.
Returns
OrderedDict{Symbol, Vector{VarName}}: A dictionary mapping symbol to a vector of varnames.
sourceTuring.Inference.isgibbscomponent — Methodisgibbscomponent(alg::Union{InferenceAlgorithm, AbstractMCMC.AbstractSampler})
Return a boolean indicating whether alg is a valid component for a Gibbs sampler.
Defaults to false if no method has been defined for a particular algorithm type.
sourceTuring.Inference.make_conditional — Methodmake_conditional(model, target_variables, varinfo)
Return a new, conditioned model for a component of a Gibbs sampler.
Arguments
model::DynamicPPL.Model: The model to condition.target_variables::AbstractVector{<:VarName}: The target variables of the component
sampler. These will not be conditioned.
varinfo::DynamicPPL.AbstractVarInfo: Values for all variables in the model. All the
values in varinfo but not in target_variables will be conditioned to the values they have in varinfo.
Returns
- A new model with the variables not in
target_variables conditioned. - The
GibbsContext object that will be used to condition the variables. This is necessary
because evaluation can mutate its global_varinfo field, which we need to access later.
sourceTuring.Inference.match_linking!! — Methodmatch_linking!!(varinfo_local, prev_state_local, model)
Make sure the linked/invlinked status of varinfo_local matches that of the previous state for this sampler. This is relevant when multilple samplers are sampling the same variables, and one might need it to be linked while the other doesn't.
sourceTuring.Inference.mh_accept — Methodmh_accept(logp_current::Real, logp_proposal::Real, log_proposal_ratio::Real)
Decide if a proposal $x'$ with log probability $\log p(x') = logp_proposal$ and log proposal ratio $\log k(x', x) - \log k(x, x') = log_proposal_ratio$ in a Metropolis-Hastings algorithm with Markov kernel $k(x_t, x_{t+1})$ and current state $x$ with log probability $\log p(x) = logp_current$ is accepted by evaluating the Metropolis-Hastings acceptance criterion
\[\log U \leq \log p(x') - \log p(x) + \log k(x', x) - \log k(x, x')\]
for a uniform random number $U \in [0, 1)$.
sourceTuring.Inference.requires_unconstrained_space — Methodrequires_unconstrained_space(sampler::ExternalSampler)
Return true if the sampler requires unconstrained space, and false otherwise.
sourceTuring.Inference.set_namedtuple! — Methodset_namedtuple!(vi::VarInfo, nt::NamedTuple)
Places the values of a NamedTuple into the relevant places of a VarInfo.
sourceTuring.Inference.setparams_varinfo!! — Methodsetparams_varinfo!!(model, sampler::Sampler, state, params::AbstractVarInfo)
A lot like AbstractMCMC.setparams!!, but instead of taking a vector of parameters, takes an AbstractVarInfo object. Also takes the sampler as an argument. By default, falls back to AbstractMCMC.setparams!!(model, state, params[:]).
model is typically a DynamicPPL.Model, but can also be e.g. an AbstractMCMC.LogDensityModel.
sourceTuring.Inference.transitions_from_chain — Methodtransitions_from_chain(
[rng::AbstractRNG,]
model::Model,
chain::MCMCChains.Chains;
@@ -625,5 +168,4 @@
julia> [first(t.θ.x) for t in transitions] # extract samples for `x`
2-element Array{Array{Float64,1},1}:
[-2.0844148956440796]
- [-1.704630494695469]
sourceSettings
This document was generated with Documenter.jl version 1.8.0 on Thursday 19 December 2024. Using Julia version 1.11.2.