feature request: gp_sampler and opt_gp_sampler

[oxinabox]

Target functionality

Currently Cobrexa implements 1 method for flux sampling:
ACHR.
This is set by passing the method argument to flux_sample but there is no other options provid)ed in the package other than sample_chain_achr.

There are two methods which sucessively build on ACHR:

• gp_sampler
• opt_gp_sampler (https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0086587

Desired output

• flux_sample(model, method=gp_sampler)
• flux_sample(model, method=opt_gp_sampler)

[exaexa]

Hi,
because of the general magic involved in the sampling algorithms we chose to offload this to other packages, thus the pluggable method interface.

Some GPU accelerated ones were made for cobrexa1 here https://github.com/LCSB-BioCore/CuFluxSampler.jl and I still have to finish the port to cobrexa2, should be available soon. I'll be adding one extra such package with CPU counterparts so this might fit there nicely.

(Anyway, TBH, I somehow got to the opinion that there isn't much point in implementing more complicated things than ACHR (or the faster-mixing partial-mean ACHR that we have there too), because most of the benefits of the more complex algorithms are completely outweighted on literally any GPU...)

I'll keep this open here as a reminder for later. PRs accepted (if the code is sufficiently small).

[exaexa]

@stelmo is it just me or (opt)gpSampler improvements are so negligible that our ACHR impl already does them? In the paper I can't detect anything that we don't do already.

[oxinabox]

Once that update/port is done, updating the docs on that page to reference that package.
It would be nice to have docs on what the API for the method argument is meant to tag.
Though not pressing

[stelmo]

@stelmo is it just me or (opt)gpSampler improvements are so negligible that our ACHR impl already does them? In the paper I can't detect anything that we don't do already.

Yep, I am not sure there is much benefit in extending sampling functionality beyond what we have right now.