Robustly simulating biochemical reaction kinetics using multi-level Monte Carlo approaches

Christopher Lester, Christian A. Yates, Ruth E. Baker

Research output: Contribution to journalArticle

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Abstract

In this work, we consider the problem of estimating summary statistics to characterise biochemical reaction networks of interest. Such networks are often described using the framework of the Chemical Master Equation (CME). For physically-realistic models, the CME is widely considered to be analytically intractable. A variety of Monte Carlo algorithms have therefore been developed to explore the dynamics of such networks empirically. Amongst them is the multi-level method, which uses estimates from multiple ensembles of sample paths of different accuracies to estimate a summary statistic of interest. In this work, we develop the multi-level method in two directions: (1) to increase the robustness, reliability and performance of the multi-level method, we implement an improved variance reduction method for generating the sample paths of each ensemble; and (2) to improve computational performance, we demonstrate the successful use of a different mechanism for choosing which ensembles should be included in the multi-level algorithm.

Original languageEnglish
Pages (from-to)1401-1423
Number of pages23
JournalJournal of Computational Physics
Volume375
DOIs
Publication statusPublished - 15 Dec 2018

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Reaction kinetics
reaction kinetics
Statistics
statistics
estimates
estimating

Keywords

  • Biochemical reaction networks
  • Multi-level Monte Carlo approaches
  • Stochastic simulation
  • Variance reduction

ASJC Scopus subject areas

  • Physics and Astronomy (miscellaneous)
  • Computer Science Applications

Cite this

Robustly simulating biochemical reaction kinetics using multi-level Monte Carlo approaches. / Lester, Christopher; Yates, Christian A.; Baker, Ruth E.

In: Journal of Computational Physics, Vol. 375, 15.12.2018, p. 1401-1423.

Research output: Contribution to journalArticle

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