Literature DB >> 33800743

Approximate Bayesian Computation for Discrete Spaces.

Ilze A Auzina1, Jakub M Tomczak1.   

Abstract

Many real-life processes are black-box problems, i.e., the internal workings are inaccessible or a closed-form mathematical expression of the likelihood function cannot be defined. For continuous random variables, likelihood-free inference problems can be solved via Approximate Bayesian Computation (ABC). However, an optimal alternative for discrete random variables is yet to be formulated. Here, we aim to fill this research gap. We propose an adjusted population-based MCMC ABC method by re-defining the standard ABC parameters to discrete ones and by introducing a novel Markov kernel that is inspired by differential evolution. We first assess the proposed Markov kernel on a likelihood-based inference problem, namely discovering the underlying diseases based on a QMR-DTnetwork and, subsequently, the entire method on three likelihood-free inference problems: (i) the QMR-DT network with the unknown likelihood function, (ii) the learning binary neural network, and (iii) neural architecture search. The obtained results indicate the high potential of the proposed framework and the superiority of the new Markov kernel.

Entities:  

Keywords:  Approximate Bayesian Computation; MCMC; Markov kernels; differential evolution; discrete state space

Year:  2021        PMID: 33800743      PMCID: PMC7998962          DOI: 10.3390/e23030312

Source DB:  PubMed          Journal:  Entropy (Basel)        ISSN: 1099-4300            Impact factor:   2.524


  11 in total

1.  Population growth of human Y chromosomes: a study of Y chromosome microsatellites.

Authors:  J K Pritchard; M T Seielstad; A Perez-Lezaun; M W Feldman
Journal:  Mol Biol Evol       Date:  1999-12       Impact factor: 16.240

2.  Using Bayesian networks to analyze expression data.

Authors:  N Friedman; M Linial; I Nachman; D Pe'er
Journal:  J Comput Biol       Date:  2000       Impact factor: 1.479

3.  Markov chain Monte Carlo without likelihoods.

Authors:  Paul Marjoram; John Molitor; Vincent Plagnol; Simon Tavare
Journal:  Proc Natl Acad Sci U S A       Date:  2003-12-08       Impact factor: 11.205

4.  Approximate Bayesian computation in population genetics.

Authors:  Mark A Beaumont; Wenyang Zhang; David J Balding
Journal:  Genetics       Date:  2002-12       Impact factor: 4.562

5.  The Monte Carlo method.

Authors:  N METROPOLIS; S ULAM
Journal:  J Am Stat Assoc       Date:  1949-09       Impact factor: 5.033

6.  The frontier of simulation-based inference.

Authors:  Kyle Cranmer; Johann Brehmer; Gilles Louppe
Journal:  Proc Natl Acad Sci U S A       Date:  2020-05-29       Impact factor: 11.205

7.  Fundamentals and Recent Developments in Approximate Bayesian Computation.

Authors:  Jarno Lintusaari; Michael U Gutmann; Ritabrata Dutta; Samuel Kaski; Jukka Corander
Journal:  Syst Biol       Date:  2017-01-01       Impact factor: 15.683

8.  Approximate Bayesian computation scheme for parameter inference and model selection in dynamical systems.

Authors:  Tina Toni; David Welch; Natalja Strelkowa; Andreas Ipsen; Michael P H Stumpf
Journal:  J R Soc Interface       Date:  2009-02-06       Impact factor: 4.118

9.  Approximate Bayesian Inference.

Authors:  Pierre Alquier
Journal:  Entropy (Basel)       Date:  2020-11-10       Impact factor: 2.524

10.  Using likelihood-free inference to compare evolutionary dynamics of the protein networks of H. pylori and P. falciparum.

Authors:  Oliver Ratmann; Ole Jørgensen; Trevor Hinkley; Michael Stumpf; Sylvia Richardson; Carsten Wiuf
Journal:  PLoS Comput Biol       Date:  2007-10-09       Impact factor: 4.475

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