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Fast Exact Stochastic Simulation Algorithms Using Partial Propensities


Ramaswamy, Rajesh; Sbalzarini, Ivo F (2010). Fast Exact Stochastic Simulation Algorithms Using Partial Propensities. In: International Conference of Numerical Analysis and Applied Mathematics, Rhodes, Greece, 19 September 2010 - 25 September 2010, 1338-1341.

Abstract

We review the class of partial-propensity exact stochastic simulation algorithms (SSA) for chemical reaction networks. We show which modules partial-propensity SSAs are composed of and how partial-propensity variants of known SSAs can be constructed by adjusting the sampling strategy used. We demonstrate this on the example of two instances, namely the partial-propensity variant of Gillespie’s original direct method and that of the SSA with composition-rejection sampling (SSA-CR). Partial-propensity methods may outperform the corresponding classical SSA, particularly on strongly coupled reaction networks. Changing the different modules of partial-propensity SSAs provides flexibility in tuning them to perform particularly well on certain classes of reaction networks. The framework presented here defines the design space of such adaptations.

Abstract

We review the class of partial-propensity exact stochastic simulation algorithms (SSA) for chemical reaction networks. We show which modules partial-propensity SSAs are composed of and how partial-propensity variants of known SSAs can be constructed by adjusting the sampling strategy used. We demonstrate this on the example of two instances, namely the partial-propensity variant of Gillespie’s original direct method and that of the SSA with composition-rejection sampling (SSA-CR). Partial-propensity methods may outperform the corresponding classical SSA, particularly on strongly coupled reaction networks. Changing the different modules of partial-propensity SSAs provides flexibility in tuning them to perform particularly well on certain classes of reaction networks. The framework presented here defines the design space of such adaptations.

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Additional indexing

Item Type:Conference or Workshop Item (Paper), refereed, original work
Communities & Collections:Special Collections > SystemsX.ch
Special Collections > SystemsX.ch > Research, Technology and Development Projects > WingX
Dewey Decimal Classification:570 Life sciences; biology
Language:English
Event End Date:25 September 2010
Deposited On:11 Jul 2013 12:00
Last Modified:07 Aug 2017 06:17
Publisher:American Institute of Physics
Series Name:AIP Conference Proceedings
ISSN:0094-243X
Free access at:Publisher DOI. An embargo period may apply.
Publisher DOI:https://doi.org/10.1063/1.3497968

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