Bayesian parameter inference for stochastic biochemical network models using particle Markov chain Monte Carlo
TLDR
Inference for the parameters of complex nonlinear multivariate stochastic process models is a challenging problem, but it is found here that algorithms based on particle Markov chain Monte Carlo turn out to be a very effective computationally intensive approach to the problem.Abstract:
Computational systems biology is concerned with the development of detailed mechanistic models of biological processes. Such models are often stochastic and analytically intractable, containing uncertain parameters that must be estimated from time course data. In this article, we consider the task of inferring the parameters of a stochastic kinetic model defined as a Markov (jump) process. Inference for the parameters of complex nonlinear multivariate stochastic process models is a challenging problem, but we find here that algorithms based on particle Markov chain Monte Carlo turn out to be a very effective computationally intensive approach to the problem. Approximations to the inferential model based on stochastic differential equations (SDEs) are considered, as well as improvements to the inference scheme that exploit the SDE structure. We apply the methodology to a Lotka–Volterra system and a prokaryotic auto-regulatory network.read more
Citations
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Approximation and inference methods for stochastic biochemical kinetics—a tutorial review
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Stochastic mechano-chemical kinetics of molecular motors: A multidisciplinary enterprise from a physicist’s perspective
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A framework for parameter estimation and model selection from experimental data in systems biology using approximate Bayesian computation
TL;DR: An approximate Bayesian computation framework and software environment, ABC-SysBio, which is a Python package that runs on Linux and Mac OS X systems and that enables parameter estimation and model selection in the Bayesian formalism by using sequential Monte Carlo (SMC) approaches is presented.
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On the efficiency of pseudo-marginal random walk Metropolis algorithms
TL;DR: In this paper, the authors examined the behavior of the pseudo-marginal random walk Metropolis algorithm, where evaluations of the target density for the accept/reject probability are estimated rather than computed precisely.
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Particle Gibbs with Ancestor Sampling
TL;DR: Particle Markov chain Monte Carlo (PMCMC) as discussed by the authors is a systematic way of combining the two main tools used for Monte Carlo statistical inference: SMC and MCMC.
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