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A comparison of Monte Carlo-based Bayesian parameter estimation methods for stochastic models of genetic networks

We compare three state-of-the-art Bayesian inference methods for the estimation of the unknown parameters in a stochastic model of a genetic network. In particular, we introduce a stochastic version of the paradigmatic synthetic multicellular clock model proposed by Ullner et al., 2007. By introduci...

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Detalles Bibliográficos
Autores principales: Mariño, Inés P., Zaikin, Alexey, Míguez, Joaquín
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5552360/
https://www.ncbi.nlm.nih.gov/pubmed/28797087
http://dx.doi.org/10.1371/journal.pone.0182015
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author Mariño, Inés P.
Zaikin, Alexey
Míguez, Joaquín
author_facet Mariño, Inés P.
Zaikin, Alexey
Míguez, Joaquín
author_sort Mariño, Inés P.
collection PubMed
description We compare three state-of-the-art Bayesian inference methods for the estimation of the unknown parameters in a stochastic model of a genetic network. In particular, we introduce a stochastic version of the paradigmatic synthetic multicellular clock model proposed by Ullner et al., 2007. By introducing dynamical noise in the model and assuming that the partial observations of the system are contaminated by additive noise, we enable a principled mechanism to represent experimental uncertainties in the synthesis of the multicellular system and pave the way for the design of probabilistic methods for the estimation of any unknowns in the model. Within this setup, we tackle the Bayesian estimation of a subset of the model parameters. Specifically, we compare three Monte Carlo based numerical methods for the approximation of the posterior probability density function of the unknown parameters given a set of partial and noisy observations of the system. The schemes we assess are the particle Metropolis-Hastings (PMH) algorithm, the nonlinear population Monte Carlo (NPMC) method and the approximate Bayesian computation sequential Monte Carlo (ABC-SMC) scheme. We present an extensive numerical simulation study, which shows that while the three techniques can effectively solve the problem there are significant differences both in estimation accuracy and computational efficiency.
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spelling pubmed-55523602017-08-25 A comparison of Monte Carlo-based Bayesian parameter estimation methods for stochastic models of genetic networks Mariño, Inés P. Zaikin, Alexey Míguez, Joaquín PLoS One Research Article We compare three state-of-the-art Bayesian inference methods for the estimation of the unknown parameters in a stochastic model of a genetic network. In particular, we introduce a stochastic version of the paradigmatic synthetic multicellular clock model proposed by Ullner et al., 2007. By introducing dynamical noise in the model and assuming that the partial observations of the system are contaminated by additive noise, we enable a principled mechanism to represent experimental uncertainties in the synthesis of the multicellular system and pave the way for the design of probabilistic methods for the estimation of any unknowns in the model. Within this setup, we tackle the Bayesian estimation of a subset of the model parameters. Specifically, we compare three Monte Carlo based numerical methods for the approximation of the posterior probability density function of the unknown parameters given a set of partial and noisy observations of the system. The schemes we assess are the particle Metropolis-Hastings (PMH) algorithm, the nonlinear population Monte Carlo (NPMC) method and the approximate Bayesian computation sequential Monte Carlo (ABC-SMC) scheme. We present an extensive numerical simulation study, which shows that while the three techniques can effectively solve the problem there are significant differences both in estimation accuracy and computational efficiency. Public Library of Science 2017-08-10 /pmc/articles/PMC5552360/ /pubmed/28797087 http://dx.doi.org/10.1371/journal.pone.0182015 Text en © 2017 Mariño et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Mariño, Inés P.
Zaikin, Alexey
Míguez, Joaquín
A comparison of Monte Carlo-based Bayesian parameter estimation methods for stochastic models of genetic networks
title A comparison of Monte Carlo-based Bayesian parameter estimation methods for stochastic models of genetic networks
title_full A comparison of Monte Carlo-based Bayesian parameter estimation methods for stochastic models of genetic networks
title_fullStr A comparison of Monte Carlo-based Bayesian parameter estimation methods for stochastic models of genetic networks
title_full_unstemmed A comparison of Monte Carlo-based Bayesian parameter estimation methods for stochastic models of genetic networks
title_short A comparison of Monte Carlo-based Bayesian parameter estimation methods for stochastic models of genetic networks
title_sort comparison of monte carlo-based bayesian parameter estimation methods for stochastic models of genetic networks
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5552360/
https://www.ncbi.nlm.nih.gov/pubmed/28797087
http://dx.doi.org/10.1371/journal.pone.0182015
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