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

Ballnus B, Schaper S, Theis FJ, Hasenauer J (2018)

Publication Type: Journal article

Publication year: 2018

Journal

Bioinformatics Oxford University Press (OUP): Policy B - Oxford Open Option B

Book Volume: 34

Pages Range: i494-i501

Journal Issue: 13

DOI: 10.1093/bioinformatics/bty229

Abstract

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.

Involved external institutions

Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt (HMGU) / Helmholtz Munich DE Germany (DE) Bayer AG DE Germany (DE)

How to cite

APA:

Ballnus, B., Schaper, S., Theis, F.J., & Hasenauer, J. (2018). Bayesian parameter estimation for biochemical reaction networks using region-based adaptive parallel tempering. Bioinformatics, 34(13), i494-i501. https://doi.org/10.1093/bioinformatics/bty229

MLA:

Ballnus, Benjamin, et al. "Bayesian parameter estimation for biochemical reaction networks using region-based adaptive parallel tempering." Bioinformatics 34.13 (2018): i494-i501.

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