Bayesian parameter estimation for the Wnt pathway: an infinite mixture models approach

Abstract : Motivation: Likelihood-free methods, like Approximate Bayesian Computation (ABC), have been extensively used in model-based statistical inference with intractable likelihood functions. When combined with Sequential Monte Carlo (SMC) algorithms they constitute a powerful approach for parameter estimation and model selection of mathematical models of complex biological systems. A crucial step in the ABC–SMC algorithms, significantly affecting their performance, is the propagation of a set of parameter vectors through a sequence of intermediate distributions using Markov kernels. Results: In this article, we employ Dirichlet process mixtures (DPMs) to design optimal transition kernels and we present an ABC–SMC algorithm with DPM kernels. We illustrate the use of the proposed methodology using real data for the canonical Wnt signaling pathway. A multi-compartment model of the pathway is developed and it is compared to an existing model. The results indicate that DPMs are more efficient in the exploration of the parameter space and can significantly improve ABC–SMC performance. In comparison to alternative sampling schemes that are commonly used, the proposed approach can bring potential benefits in the estimation of complex multimodal distributions. The method is used to estimate the parameters and the initial state of two models of the Wnt pathway and it is shown that the multi-compartment model fits better the experimental data. Availability and Implementation: Python scripts for the Dirichlet Process Gaussian Mixture model and the Gibbs sampler are available at https://sites.google.com/site/kkoutroumpas/software.
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Konstantinos Koutroumpas, Paolo Ballarini, Irene Votsi, Paul-Henry Cournède. Bayesian parameter estimation for the Wnt pathway: an infinite mixture models approach. Bioinformatics, Oxford University Press (OUP), 2016, 32 (17), pp.i781 - i789. ⟨https://academic.oup.com/bioinformatics/article/32/17/i781/2450800/Bayesian-parameter-estimation-for-the-Wnt-pathway⟩. ⟨10.1093/bioinformatics/btw471⟩. ⟨hal-01817488⟩

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