Minimal trap spaces of Logical models are maximal siphons of their Petri net encoding - Inria - Institut national de recherche en sciences et technologies du numérique Accéder directement au contenu
Communication Dans Un Congrès Année : 2022

Minimal trap spaces of Logical models are maximal siphons of their Petri net encoding

Résumé

Boolean modelling of gene regulation but also of post-transcriptomic systems has proven over the years that it can bring powerful analyses and corresponding insight to the many cases where precise biological data is not sufficiently available to build a detailed quantitative model. This is even more true for very large models where such data is frequently missing and led to a constant increase in size of logical models à la Thomas. Besides simulation, the analysis of such models is mostly based on attractor computation, since those correspond roughly to observable biological phenotypes. The recent use of trap spaces made a real breakthrough in that field allowing to consider medium-sized models that used to be out of reach. However, with the continuing increase in model-size, the state-of-the-art computation of minimal trap spaces based on prime-implicants shows its limits as there can be a huge number of implicants. In this article we present an alternative method to compute minimal trap spaces, and hence complex attractors, of a Boolean model. It replaces the need for prime-implicants by a completely different technique, namely the enumeration of maximal siphons in the Petri net encoding of the original model. After some technical preliminaries, we expose the concrete need for such a method and detail its implementation using Answer Set Programming. We then demonstrate its efficiency and compare it to implicant-based methods on some large Boolean models from the literature.
Fichier principal
Vignette du fichier
cmsb22.pdf (478.5 Ko) Télécharger le fichier
Origine Fichiers produits par l'(les) auteur(s)

Dates et versions

hal-03721508 , version 1 (12-07-2022)

Identifiants

Citer

Van-Giang Trinh, Belaid Benhamou, Kunihiko Hiraishi, Sylvain Soliman. Minimal trap spaces of Logical models are maximal siphons of their Petri net encoding. CMSB 2022 - International Conference on Computational Methods in Systems Biology, Sep 2022, Bucarest, Romania. pp.158--176, ⟨10.1007/978-3-031-15034-0_8⟩. ⟨hal-03721508⟩
316 Consultations
174 Téléchargements

Altmetric

Partager

Gmail Mastodon Facebook X LinkedIn More