Model Revision from Temporal Logic Properties in Computational Systems Biology

Abstract : Systems biologists build models of bio-molecular processes from knowledge acquired both at the gene and protein levels, and at the phenotype level through experiments done in wildlife and mutated organisms. In this chapter, we present qualitative and quantitative logic learning tools, and illustrate how they can be useful to the modeler. We focus on biochemical reaction models written in the Systems Biology Markup Language SBML, and interpreted in the Biochemical Abstract Machine BIOCHAM. We first present a model revision algorithm for inferring reaction rules from biological properties expressed in temporal logic. Then we discuss the representations of kinetic models with ordinary differential equations (ODEs) and with stochastic logic programs (SLPs), and describe a parameter search algorithm for finding parameter values satisfying quantitative temporal properties. These methods are illustrated by a simple model of the cell cycle control, and by an application to the modelling of the conditions of synchronization in period of the cell cycle by the circadian cycle.
Type de document :
Chapitre d'ouvrage
Luc de Raedt and Paolo Frasconi and Kristian Kersting and Stephen Muggleton. Probabilistic Inductive Logic Programming, pp.287--304, 2008, 〈10.1007/978-3-540-78652-8_11〉
Liste complète des métadonnées

Littérature citée [28 références]  Voir  Masquer  Télécharger

https://hal.inria.fr/hal-01431378
Contributeur : Sylvain Soliman <>
Soumis le : mardi 10 janvier 2017 - 17:14:32
Dernière modification le : lundi 24 septembre 2018 - 14:00:04
Document(s) archivé(s) le : mardi 11 avril 2017 - 16:26:00

Fichier

FS07april.pdf
Fichiers produits par l'(les) auteur(s)

Identifiants

Collections

Citation

Francois Fages, Sylvain Soliman. Model Revision from Temporal Logic Properties in Computational Systems Biology. Luc de Raedt and Paolo Frasconi and Kristian Kersting and Stephen Muggleton. Probabilistic Inductive Logic Programming, pp.287--304, 2008, 〈10.1007/978-3-540-78652-8_11〉. 〈hal-01431378〉

Partager

Métriques

Consultations de la notice

284

Téléchargements de fichiers

32