Efficient Parallel Statistical Model Checking of Biochemical Networks

Paolo Ballarini
(CoSBi)
Michele Forlin
(CoSBi)
Tommaso Mazza
(CoSBi)
Davide Prandi
(CoSBi)

We consider the problem of verifying stochastic models of biochemical networks against behavioral properties expressed in temporal logic terms. Exact probabilistic verification approaches such as, for example, CSL/PCTL model checking, are undermined by a huge computational demand which rule them out for most real case studies. Less demanding approaches, such as statistical model checking, estimate the likelihood that a property is satisfied by sampling executions out of the stochastic model. We propose a methodology for efficiently estimating the likelihood that a LTL property P holds of a stochastic model of a biochemical network. As with other statistical verification techniques, the methodology we propose uses a stochastic simulation algorithm for generating execution samples, however there are three key aspects that improve the efficiency: first, the sample generation is driven by on-the-fly verification of P which results in optimal overall simulation time. Second, the confidence interval estimation for the probability of P to hold is based on an efficient variant of the Wilson method which ensures a faster convergence. Third, the whole methodology is designed according to a parallel fashion and a prototype software tool has been implemented that performs the sampling/verification process in parallel over an HPC architecture.

In Lubos Brim and Jaco van de Pol: Proceedings 8th International Workshop on Parallel and Distributed Methods in verifiCation (PDMC 2009), Eindhoven, The Netherlands, 4th November 2009, Electronic Proceedings in Theoretical Computer Science 14, pp. 47–61.
Published: 15th December 2009.

ArXived at: http://dx.doi.org/10.4204/EPTCS.14.4 bibtex PDF

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