Concurrency in Boolean networks

Thomas Chatain 1, 2, 3 Stefan Haar 2, 3 Juraj Kolčák 2, 3 Aalok Thakkar 4 Loïc Paulevé 5, 6
2 MEXICO - Modeling and Exploitation of Interaction and Concurrency
LSV - Laboratoire Spécification et Vérification [Cachan], ENS Cachan - École normale supérieure - Cachan, Inria Saclay - Ile de France, CNRS - Centre National de la Recherche Scientifique : UMR8643
6 BioInfo - LRI - Bioinformatique (LRI)
LRI - Laboratoire de Recherche en Informatique
Abstract : Boolean networks (BNs) are widely used to model the qualitative dynamics of biological systems. Besides the logical rules determining the evolution of each component with respect to the state of its regulators, the scheduling of components updates can have a dramatic impact on the predicted behaviours. In this paper, we explore the use of Contextual Petri Nets (CPNs) to study dynamics of BNs with a concurrency theory perspective. After showing bi-directional translations between CPNs and BNs and analogies between results on synchronism sensitivies, we illustrate that usual updating modes for BNs can miss plausible behaviours, i.e., incorrectly conclude on the absence/impossibility of reaching specific configurations. Taking advantage of CPN semantics enabling more behaviour than the generalized asynchronous updating mode, we propose an encoding of BNs ensuring a correct abstraction of any multivalued refinement, as one may expect to achieve when modelling biological systems with no assumption on its time features.
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https://hal.inria.fr/hal-01893106
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Submitted on : Thursday, October 11, 2018 - 10:04:05 AM
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  • HAL Id : hal-01893106, version 1

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Thomas Chatain, Stefan Haar, Juraj Kolčák, Aalok Thakkar, Loïc Paulevé. Concurrency in Boolean networks. 2018. ⟨hal-01893106⟩

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