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Bayesian parameter estimation for biochemical reaction networks using region-based adaptive parallel tempering.

Bioinformatics 34, 494-501 (2018)
Publishers Version Research data DOI PMC
Open Access Gold (Paid Option)
Creative Commons Lizenzvertrag
as soon as is submitted to ZB.
Motivation: Mathematical models have become standard tools for the investigation of cellular processes and the unraveling of signal processing mechanisms. The parameters of these models are usually derived from the available data using optimization and sampling methods. However, the efficiency of these methods is limited by the properties of the mathematical model, e.g. nonidentifiabilities, and the resulting posterior distribution. In particular, multi-modal distributions with long valleys or pronounced tails are difficult to optimize and sample. Thus, the developement or improvement of optimization and sampling methods is subject to ongoing research. Results: We suggest a region-based adaptive parallel tempering algorithm which adapts to the problem-specific posterior distributions, i.e. modes and valleys. The algorithm combines several established algorithms to overcome their individual shortcomings and to improve sampling efficiency. We assessed its properties for established benchmark problems and two ordinary differential equation models of biochemical reaction networks. The proposed algorithm outperformed state-of-the-art methods in terms of calculation efficiency and mixing. Since the algorithm does not rely on a specific problem structure, but adapts to the posterior distribution, it is suitable for a variety of model classes.
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Publication type Article: Journal article
Document type Scientific Article
Keywords Hamiltonian Monte-carlo; Dynamical-systems; Mcmc; Algorithm; Chain; Inference; Kinetics
Reviewing status