Unfolding of Parametric Boolean Networks

Juraj Kolčák 1, 2 David Šafránek 1 Stefan Haar 2 Loïc Paulevé 3
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
3 BioInfo - LRI - Bioinformatique (LRI)
LRI - Laboratoire de Recherche en Informatique
Abstract : In systems biology, models of cellular regulatory processes such as gene regulatory networks or signalling pathways are crucial to understanding the behaviour of living cells. Available biological data are however often insufficient for full model specification. In this paper, we focus on partially specified models where the missing information is abstracted in the form of parameters. We introduce a novel approach to analysis of parametric logical regulatory networks addressing both sources of combinatoric explosion native to the model. First, we introduce a new compact representation of admissible parameters using Boolean lattices. Then, we define the unfolding of parametric Boolean networks. The resulting structure provides a partial-order reduction of concurrent transitions, and factorises the common transitions among the concrete models. A comparison is performed against state-of-the-art approaches to parametric model analysis.
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Juraj Kolčák, David Šafránek, Stefan Haar, Loïc Paulevé. Unfolding of Parametric Boolean Networks. 7th International Workshop on Static Analysis and Systems Biology (SASB 2016), Sep 2016, Edimbourg, United Kingdom. pp.67-90, ⟨10.1016/j.entcs.2018.03.009⟩. ⟨hal-01354109v2⟩



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