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Weighted next reaction method and parameter selection for efficient simulation of rare events in biochemical reaction systems

Authors
  • Xu, Zhouyi1
  • Cai, Xiaodong1
  • 1 University of Miami, Department of Electrical and Computer Engineering, 1251 Memorial Drive, Coral Gables, FL, 33124, USA , Coral Gables (United States)
Type
Published Article
Journal
EURASIP Journal on Bioinformatics and Systems Biology
Publisher
Springer International Publishing
Publication Date
Jul 25, 2011
Volume
2011
Issue
1
Identifiers
DOI: 10.1186/1687-4153-2011-797251
Source
Springer Nature
Keywords
License
Green

Abstract

The weighted stochastic simulation algorithm (wSSA) recently developed by Kuwahara and Mura and the refined wSSA proposed by Gillespie et al. based on the importance sampling technique open the door for efficient estimation of the probability of rare events in biochemical reaction systems. In this paper, we first apply the importance sampling technique to the next reaction method (NRM) of the stochastic simulation algorithm and develop a weighted NRM (wNRM). We then develop a systematic method for selecting the values of importance sampling parameters, which can be applied to both the wSSA and the wNRM. Numerical results demonstrate that our parameter selection method can substantially improve the performance of the wSSA and the wNRM in terms of simulation efficiency and accuracy.

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