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

PloS One
Inés P MariñoJoaquín Míguez

Abstract

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 th...Continue Reading

References

Feb 5, 2000·Nature·M B Elowitz, S Leibler
Jul 17, 2004·Proceedings of the National Academy of Sciences of the United States of America·J García-OjalvoSteven H Strogatz
Oct 15, 2008·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Ekkehard UllnerJ García-Ojalvo
Feb 11, 2009·Journal of the Royal Society, Interface·Tina ToniMichael P H Stumpf
Nov 26, 2009·Journal of Theoretical Biology·A KoseskaJ García-Ojalvo
Jul 31, 2012·Journal of the Royal Statistical Society. Series B, Statistical Methodology·Steven N Evans, Frederick A Matsen
Nov 28, 2013·PloS One·Inés P MariñoAlexey Zaikin
Apr 2, 2014·Nature Reviews. Microbiology·D Ewen CameronJames J Collins

Methods Mentioned

BETA
random draws

Related Concepts

Dorsal
Particle
Simulation
Population Group
Computed (Procedure)
Homeostasis of Number of Cells

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