tobias-liaudat/proxnest

Proximal Nested Sampling for high-dimensional Bayesian model selection

Proximal nested sampling for high-dimensional Bayesian model selection

ProxNest is an open source, well tested and documented Python implementation of the proximal nested sampling framework (Cai et al. 2022) to compute the Bayesian model evidence or marginal likelihood in high-dimensional log-convex settings. Furthermore, non-smooth sparsity-promoting priors are also supported.

This is achieved by exploiting tools from proximal calculus and Moreau-Yosida regularisation (Moreau 1962) to efficiently sample from the prior subject to the hard likelihood constraint. The resulting Markov chain iterations include a gradient step, approximating (with arbitrary precision) an overdamped Langevin SDE that can scale to very high-dimensional applications.

Basic Usage

The following is a straightforward example application to image denoising (Phi = I), regularised with Daubechies wavelets (DB6).

# Import relevant modules.
import numpy as np
import ProxNest

# Load your data and set parameters.
data = np.load(<path to your data.npy>)
params = params    # Parameters of the prior resampling optimisation problem.
options = options  # Options associated with the sampling strategy.

# Construct your forward model (phi) and wavelet operators (psi).
phi = ProxNest.operators.sensing_operators.Identity()
psi = ProxNest.operators.wavelet_operators.db_wavelets(["db6"], 2, (dim, dim))

# Define proximal operators for both your likelihood and prior.
proxH = lambda x, T : ProxNest.operators.proximal_operators.l1_projection(x, T, delta, Psi=psi)
proxB = lambda x, tau: ProxNest.optimisations.l2_ball_proj.sopt_fast_proj_B2(x, tau, params)

# Write a lambda function to evaluate your likelihood term (here a Gaussian)
LogLikeliL = lambda sol : - np.linalg.norm(y-phi.dir_op(sol), 'fro')**2/(2*sigma**2)

# Perform proximal nested sampling
BayEvi, XTrace = ProxNest.sampling.proximal_nested.ProxNestedSampling(
    np.abs(phi.adj_op(data)), LogLikeliL, proxH, proxB, params, options
    )

At this point you have recovered the tuple BayEvi and dict Xtrace which contain

Live = options["samplesL"] # Number of live samples
Disc = options["samplesD"] # Number of discarded samples

# BayEvi is a tuple containing two values:
BayEvi[0] = 'Estimate of Bayesian evidence (float).'
BayEvi[1] = 'Variance of Bayesian evidence estimate (float).'

# XTrace is a dictionary containing the np.ndarrays:
XTrace['Liveset'] = 'Set of live samples (shape: Live, dim, dim).'
XTrace['LivesetL'] = 'Likelihood of live samples (shape: Live).'

XTrace['Discard'] = 'Set of discarded samples (shape: Disc, dim, dim).'
XTrace['DiscardL'] = 'Likelihood of discarded samples (shape: Disc).'
XTrace['DiscardW'] = 'Weights of discarded samples (shape: Disc).'

XTrace['DiscardPostProb'] = 'Posterior probability of discarded samples (shape: Disc)'
XTrace['DiscardPostMean'] = 'Posterior mean solution (shape: dim, dim)'

from which one can perform e.g. Bayesian model comparison.

Installation

Brief installation instructions are given below (for further details see the full installation documentation).

Quick install (PyPi)

The ProxNest package can be installed by running

pip install ProxNest

Install from source (GitHub)

The ProxNest package can also be installed from source by running

git clone https://github.com/astro-informatics/proxnest
cd harmonic

and running the install script, within the root directory, with one command

bash build_proxnest.sh

To check the install has worked correctly run the unit tests with

pytest --black ProxNest/tests/

Contributors

Matthew Price, Xiaohao Cai, Jason McEwen, Marcelo Pereyra, and contributors.

Attribution

A BibTeX entry for ProxNest is:

@article{Cai:ProxNest:2021,
   author = {Cai, Xiaohao and McEwen, Jason~D. and Pereyra, Marcelo},
    title = {"High-dimensional Bayesian model selection by proximal nested sampling"},
  journal = {ArXiv},
   eprint = {arXiv:2106.03646},
     year = {2021}
}

License

ProxNest is released under the GPL-3 license (see LICENSE.txt), subject to the non-commercial use condition (see LICENSE_EXT.txt)

ProxNest
Copyright (C) 2022 Matthew Price, Xiaohao Cai, Jason McEwen, Marcelo Pereyra & contributors

This program is released under the GPL-3 license (see LICENSE.txt),
subject to a non-commercial use condition (see LICENSE_EXT.txt).

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.