Boolean Networks: Beyond Generalized Asynchronicity

Thomas Chatain 1 Stefan Haar 1 Loïc Paulevé 2
1 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
2 BioInfo - LRI - Bioinformatique (LRI)
LRI - Laboratoire de Recherche en Informatique
Abstract : Boolean networks are commonly used in systems biology to model dynamics of biochemical networks by abstracting away many (and often unknown) parameters related to speed and species activity thresholds. It is then expected that Boolean networks produce an over-approximation of behaviours (reachable configurations), and that subsequent refinements would only prune some impossible transitions. However, we show that even generalized asynchronous updating of Boolean networks, which subsumes the usual updating modes including synchronous and fully asynchronous, does not capture all transitions doable in a multi-valued or timed refinement. We define a structural model transformation which takes a Boolean network as input and outputs a new Boolean network whose asynchronous updating simulates both synchronous and asynchronous updating of the original network, and exhibits even more behaviours than the generalized asynchronous updating. We argue that these new behaviours should not be ignored when analyzing Boolean networks, unless some knowledge about the characteristics of the system explicitly allows one to restrict its behaviour.
Type de document :
Communication dans un congrès
Baetens, Jan M. and Kutrib, Martin. AUTOMATA 2018 - 24th IFIP WG 1.5 International Workshop on Cellular Automata and Discrete Complex Systems, Jun 2018, Ghent, Belgium. Springer, 10875, pp.29-42, 2018, Lecture Notes in Computer Science. 〈http://www.automata2018.ugent.be〉. 〈10.1007/978-3-319-92675-9_3〉
Liste complète des métadonnées

Littérature citée [28 références]  Voir  Masquer  Télécharger

https://hal.archives-ouvertes.fr/hal-01768359
Contributeur : Loïc Paulevé <>
Soumis le : jeudi 21 juin 2018 - 09:10:26
Dernière modification le : mercredi 27 juin 2018 - 17:16:41

Fichier

main.pdf
Fichiers produits par l'(les) auteur(s)

Identifiants

Citation

Thomas Chatain, Stefan Haar, Loïc Paulevé. Boolean Networks: Beyond Generalized Asynchronicity. Baetens, Jan M. and Kutrib, Martin. AUTOMATA 2018 - 24th IFIP WG 1.5 International Workshop on Cellular Automata and Discrete Complex Systems, Jun 2018, Ghent, Belgium. Springer, 10875, pp.29-42, 2018, Lecture Notes in Computer Science. 〈http://www.automata2018.ugent.be〉. 〈10.1007/978-3-319-92675-9_3〉. 〈hal-01768359v2〉

Partager

Métriques

Consultations de la notice

187

Téléchargements de fichiers

335