Home // International Journal On Advances in Systems and Measurements, volume 8, numbers 1 and 2, 2015 // View article

A Rare Event Method Applied to Signalling Cascades

Authors:
Benoit Barbot
Serge Haddad
Monika Heiner
Claudine Picaronny

Keywords: rare event problem; importance sampling; regulatory biological systems; stochastic Petri nets.

Abstract:
Formal models have been shown useful for analysis of regulatory systems. Here we focus on signalling cascades, a recurrent pattern of biological regulatory systems. We choose the formalism of stochastic Petri nets for this modelling and we express the properties of interest by formulas of a temporal logic. Such properties can be evaluated with either numeric or simulation based methods. The former one suffers from the combinatorial state space explosion problem, while the latter suffers from time explosion due to rare event phenomena. In this paper, we demonstrate the use of rare event techniques to tackle the analysis of signalling cascades. We compare the effectiveness of the COSMOS statistical model checker, which implements importance sampling methods to speed up rare event simulations, with the numerical model checker MARCIE on several properties. More precisely, we study three properties that characterise the ordering of events in the signalling cascade. We establish an interesting dependency between quantitative parameters of the regulatory system and its transient behaviour. Summarising, our experiments establish that simulation is the only appropriate method when parameters values increase and that importance sampling is effective when dealing with rare events.

Pages: 69 to 79

Copyright: Copyright (c) to authors, 2015. Used with permission.

Publication date: June 30, 2015

Published in: journal

ISSN: 1942-261x