Parameter space abstraction and unfolding semantics of discrete regulatory networks

DOI10.1016/J.TCS.2018.03.009MaRDI QIDQ2422012zbMATH OpenOpenAlexWikidataFDO

Authors Juraj Kolčák, D. Šafránek, Stefan Haar, Loïc Paulevé

Publication date 18 June 2019

Published in Theoretical Computer Science (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1803.06157

zbMATH Keywords

systems biologyconcurrencyBoolean networksasynchronous systemsparametrised discrete dynamicsThomas networks

Mathematics Subject Classification ID

Systems biology, networks (92C42) Models and methods for concurrent and distributed computing (process algebras, bisimulation, transition nets, etc.) (68Q85)

Abstract: The modelling of discrete regulatory networks combines a graph specifying the pairwise influences between the variables of the system, and a parametrisation from which can be derived a discrete transition system. Given the influence graph only, the exploration of admissible parametrisations and the behaviours they enable is computationally demanding due to the combinatorial explosions of both parametrisation and reachable state space. This article introduces an abstraction of the parametrisation space and its refinement to account for the existence of given transitions, and for constraints on the sign and observability of influences. The abstraction uses a convex sublattice containing the concrete parametrisation space specified by its infimum and supremum parametrisations. It is shown that the computed abstractions are optimal, i.e., no smaller convex sublattice exists. Although the abstraction may introduce over-approximation, it has been proven to be conservative with respect to reachability of states. Then, an unfolding semantics for Parametric Regulatory Networks is defined, taking advantage of concurrency between transitions to provide a compact representation of reachable transitions. A prototype implementation is provided: it has been applied to several examples of Boolean and multi-valued networks, showing its tractability for networks with numerous components.

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Cited in

(4)

• Static analysis and stochastic search for reachability problem
• Static analysis of biological regulatory networks dynamics using abstract interpretation
• Property Preservation along Embedding of Biological Regulatory Networks
• Combining refinement of parametric models with goal-oriented reduction of dynamics

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