Literature DB >> 25422442

A general construction for parallelizing Metropolis-Hastings algorithms.

Ben Calderhead1.   

Abstract

Markov chain Monte Carlo methods (MCMC) are essential tools for solving many modern-day statistical and computational problems; however, a major limitation is the inherently sequential nature of these algorithms. In this paper, we propose a natural generalization of the Metropolis-Hastings algorithm that allows for parallelizing a single chain using existing MCMC methods. We do so by proposing multiple points in parallel, then constructing and sampling from a finite-state Markov chain on the proposed points such that the overall procedure has the correct target density as its stationary distribution. Our approach is generally applicable and straightforward to implement. We demonstrate how this construction may be used to greatly increase the computational speed and statistical efficiency of a variety of existing MCMC methods, including Metropolis-Adjusted Langevin Algorithms and Adaptive MCMC. Furthermore, we show how it allows for a principled way of using every integration step within Hamiltonian Monte Carlo methods; our approach increases robustness to the choice of algorithmic parameters and results in increased accuracy of Monte Carlo estimates with little extra computational cost.

Entities:  

Keywords:  Bayesian inference; Hamiltonian dynamics; Markov chain Monte Carlo; parallel computation

Year:  2014        PMID: 25422442      PMCID: PMC4267367          DOI: 10.1073/pnas.1408184111

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  3 in total

1.  Understanding GPU Programming for Statistical Computation: Studies in Massively Parallel Massive Mixtures.

Authors:  Marc A Suchard; Quanli Wang; Cliburn Chan; Jacob Frelinger; Andrew Cron; Mike West
Journal:  J Comput Graph Stat       Date:  2010-06-01       Impact factor: 2.302

2.  Searching for efficient Markov chain Monte Carlo proposal kernels.

Authors:  Ziheng Yang; Carlos E Rodríguez
Journal:  Proc Natl Acad Sci U S A       Date:  2013-11-11       Impact factor: 11.205

3.  On the utility of graphics cards to perform massively parallel simulation of advanced Monte Carlo methods.

Authors:  Anthony Lee; Christopher Yau; Michael B Giles; Arnaud Doucet; Christopher C Holmes
Journal:  J Comput Graph Stat       Date:  2010-12-01       Impact factor: 2.302

  3 in total
  7 in total

1.  MultiBUGS: A Parallel Implementation of the BUGS Modelling Framework for Faster Bayesian Inference.

Authors:  Robert J B Goudie; Rebecca M Turner; Daniela De Angelis; Andrew Thomas
Journal:  J Stat Softw       Date:  2020-10-07       Impact factor: 6.440

2.  Statistical methods and computing for big data.

Authors:  Chun Wang; Ming-Hui Chen; Elizabeth Schifano; Jing Wu; Jun Yan
Journal:  Stat Interface       Date:  2016       Impact factor: 0.582

3.  Parallel Prefetching for Canonical Ensemble Monte Carlo Simulations.

Authors:  Harold W Hatch
Journal:  J Phys Chem A       Date:  2020-08-25       Impact factor: 2.781

4.  Phylodynamic analysis to inform prevention efforts in mixed HIV epidemics.

Authors:  Erik M Volz; Nicaise Ndembi; Rebecca Nowak; Gustavo H Kijak; John Idoko; Patrick Dakum; Walter Royal; Stefan Baral; Mark Dybul; William A Blattner; Man Charurat
Journal:  Virus Evol       Date:  2017-07-28

5.  Phylogenetic Tools for Generalized HIV-1 Epidemics: Findings from the PANGEA-HIV Methods Comparison.

Authors:  Oliver Ratmann; Emma B Hodcroft; Michael Pickles; Anne Cori; Matthew Hall; Samantha Lycett; Caroline Colijn; Bethany Dearlove; Xavier Didelot; Simon Frost; A S Md Mukarram Hossain; Jeffrey B Joy; Michelle Kendall; Denise Kühnert; Gabriel E Leventhal; Richard Liang; Giacomo Plazzotta; Art F Y Poon; David A Rasmussen; Tanja Stadler; Erik Volz; Caroline Weis; Andrew J Leigh Brown; Christophe Fraser
Journal:  Mol Biol Evol       Date:  2016-10-07       Impact factor: 16.240

6.  Annealed Importance Sampling for Neural Mass Models.

Authors:  Will Penny; Biswa Sengupta
Journal:  PLoS Comput Biol       Date:  2016-03-04       Impact factor: 4.475

Review 7.  Accelerating MCMC algorithms.

Authors:  Christian P Robert; Víctor Elvira; Nick Tawn; Changye Wu
Journal:  Wiley Interdiscip Rev Comput Stat       Date:  2018-06-13
  7 in total

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