An adaptive multi-level simulation algorithm for stochastic biological systems

Christopher Lester, Christian Adam Yates, Ruth E. Baker

Research output: Contribution to journalArticle

11 Citations (Scopus)
133 Downloads (Pure)

Abstract

Discrete-state, continuous-time Markov models are widely used in the modeling of biochemical reaction networks. Their complexity often precludes analytic solution, and we rely on stochastic simulation algorithms to estimate system statistics. The Gillespie algorithm is exact, but computationally costly as it simulates every single reaction. As such, approximate stochastic simulation algorithms such as the tau-leap algorithm are often used. Potentially computationally more efficient, the system statistics generated suffer from significant bias unless tau is relatively small, in which case the computational time can be comparable to that of the Gillespie algorithm.

The multi-level method (Anderson and Higham, Multiscale Model. Simul. 10:146--179, 2012) tackles this problem. A base estimator is computed using many (cheap) sample paths at low accuracy. The bias inherent in this estimator is then reduced using a number of corrections. Each correction term is estimated using a collection of paired sample paths where one path of each pair is generated at a higher accuracy compared to the other (and so more expensive). By sharing random variables between these paired paths the variance of each correction estimator can be reduced. This renders the multi-level method very efficient as only a relatively small number of paired paths are required to calculate each correction term.

In the original multi-level method, each sample path is simulated using the tau-leap algorithm with a fixed value of $\tau$. This approach can result in poor performance when the reaction activity of a system changes substantially over the timescale of interest. By introducing a novel, adaptive time-stepping approach where $\tau$ is chosen according to the stochastic behaviour of each sample path we extend the applicability of the multi-level method to such cases. We demonstrate the efficiency of our method using a number of examples.
Original languageEnglish
Article number024113
Number of pages10
JournalJournal of Chemical Physics
Volume142
Issue number2
DOIs
Publication statusPublished - 14 Jan 2015

Keywords

  • stochastic siulation, multilevel

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