Literature DB >> 21054005

State-dependent biasing method for importance sampling in the weighted stochastic simulation algorithm.

Min K Roh1, Dan T Gillespie, Linda R Petzold.   

Abstract

The weighted stochastic simulation algorithm (wSSA) was developed by Kuwahara and Mura [J. Chem. Phys. 129, 165101 (2008)] to efficiently estimate the probabilities of rare events in discrete stochastic systems. The wSSA uses importance sampling to enhance the statistical accuracy in the estimation of the probability of the rare event. The original algorithm biases the reaction selection step with a fixed importance sampling parameter. In this paper, we introduce a novel method where the biasing parameter is state-dependent. The new method features improved accuracy, efficiency, and robustness.

Mesh:

Year:  2010        PMID: 21054005      PMCID: PMC3188645          DOI: 10.1063/1.3493460

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  3 in total

1.  Refining the weighted stochastic simulation algorithm.

Authors:  Dan T Gillespie; Min Roh; Linda R Petzold
Journal:  J Chem Phys       Date:  2009-05-07       Impact factor: 3.488

2.  An efficient and exact stochastic simulation method to analyze rare events in biochemical systems.

Authors:  Hiroyuki Kuwahara; Ivan Mura
Journal:  J Chem Phys       Date:  2008-10-28       Impact factor: 3.488

3.  The diffusive finite state projection algorithm for efficient simulation of the stochastic reaction-diffusion master equation.

Authors:  Brian Drawert; Michael J Lawson; Linda Petzold; Mustafa Khammash
Journal:  J Chem Phys       Date:  2010-02-21       Impact factor: 3.488

  3 in total
  7 in total

1.  State-dependent doubly weighted stochastic simulation algorithm for automatic characterization of stochastic biochemical rare events.

Authors:  Min K Roh; Bernie J Daigle; Dan T Gillespie; Linda R Petzold
Journal:  J Chem Phys       Date:  2011-12-21       Impact factor: 3.488

2.  Adaptively biased sequential importance sampling for rare events in reaction networks with comparison to exact solutions from finite buffer dCME method.

Authors:  Youfang Cao; Jie Liang
Journal:  J Chem Phys       Date:  2013-07-14       Impact factor: 3.488

3.  Efficient stochastic simulation of chemical kinetics networks using a weighted ensemble of trajectories.

Authors:  Rory M Donovan; Andrew J Sedgewick; James R Faeder; Daniel M Zuckerman
Journal:  J Chem Phys       Date:  2013-09-21       Impact factor: 3.488

4.  The stochastic quasi-steady-state assumption: reducing the model but not the noise.

Authors:  Rishi Srivastava; Eric L Haseltine; Ethan Mastny; James B Rawlings
Journal:  J Chem Phys       Date:  2011-04-21       Impact factor: 3.488

5.  Comparison of finite difference based methods to obtain sensitivities of stochastic chemical kinetic models.

Authors:  Rishi Srivastava; David F Anderson; James B Rawlings
Journal:  J Chem Phys       Date:  2013-02-21       Impact factor: 3.488

6.  Perspective: Stochastic algorithms for chemical kinetics.

Authors:  Daniel T Gillespie; Andreas Hellander; Linda R Petzold
Journal:  J Chem Phys       Date:  2013-05-07       Impact factor: 3.488

7.  Data-Driven Method for Efficient Characterization of Rare Event Probabilities in Biochemical Systems.

Authors:  Min K Roh
Journal:  Bull Math Biol       Date:  2018-09-17       Impact factor: 1.758

  7 in total

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