Unbiased τ-leap methods for stochastic simulation of biochemical systems

Zhouyi Xu, Xiaodong Cai

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Stochastic simulation of biological systems has received much attention recently. A very promising stochastic simulation method is the τ-leap method, which can significantly accelerate simulation with controllable accuracy. However, all current τ-leap methods produce biased results, which can cause large simulation errors. In this paper, we analyze the expected number of reactions occurring during each leap. Relying on the analytical results, we develop an unbiased Poisson τ-leap method and an unbiased binomial τ-leap method. Simulations demonstrate that our new unbiased τ-leap method can significantly improve simulation accuracy without sacrificing simulation speed.

Original languageEnglish
Title of host publicationICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings
Pages657-660
Number of pages4
DOIs
StatePublished - Sep 17 2008
Event2008 IEEE International Conference on Acoustics, Speech and Signal Processing, ICASSP - Las Vegas, NV, United States
Duration: Mar 31 2008Apr 4 2008

Other

Other2008 IEEE International Conference on Acoustics, Speech and Signal Processing, ICASSP
CountryUnited States
CityLas Vegas, NV
Period3/31/084/4/08

Fingerprint

Biological systems
simulation
causes

Keywords

  • Biological system modeling
  • Cell signalling pathway
  • Parameter estimation
  • Stochastic simulation

ASJC Scopus subject areas

  • Electrical and Electronic Engineering
  • Signal Processing
  • Acoustics and Ultrasonics

Cite this

Xu, Z., & Cai, X. (2008). Unbiased τ-leap methods for stochastic simulation of biochemical systems. In ICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings (pp. 657-660). [4517695] https://doi.org/10.1109/ICASSP.2008.4517695

Unbiased τ-leap methods for stochastic simulation of biochemical systems. / Xu, Zhouyi; Cai, Xiaodong.

ICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings. 2008. p. 657-660 4517695.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Xu, Z & Cai, X 2008, Unbiased τ-leap methods for stochastic simulation of biochemical systems. in ICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings., 4517695, pp. 657-660, 2008 IEEE International Conference on Acoustics, Speech and Signal Processing, ICASSP, Las Vegas, NV, United States, 3/31/08. https://doi.org/10.1109/ICASSP.2008.4517695
Xu Z, Cai X. Unbiased τ-leap methods for stochastic simulation of biochemical systems. In ICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings. 2008. p. 657-660. 4517695 https://doi.org/10.1109/ICASSP.2008.4517695
Xu, Zhouyi ; Cai, Xiaodong. / Unbiased τ-leap methods for stochastic simulation of biochemical systems. ICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings. 2008. pp. 657-660
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