Francois Fages

Reifying Global Constraints

Global constraints were introduced two decades ago as a means to model some core aspects of combinatorial problems with one single constraint for which an efficient domain …

Inferring Reaction Models from ODEs

A Boolean Model for Enumerating Minimal Siphons and Traps in Petri Nets

Automatic Curation of SBML Models based on their ODE Semantics

SBGN support in BIOCHAM

On Coupling Models Using Model-Checking: Effects of Irinotecan Injections on the Mammalian Cell Cycle

In systems biology, the number of models of cellular processes increases rapidly, but re-using models in different contexts or for different questions remains a challenging issue. …

Model-based Predictions of the Influence of Circadian Clock Genes Knock-Outs on the Cell Cycle

The existence of links between the cell division cycle and the circadian clock has been recently discovered. In this research report, we perform a small in silico analysis of how …

Dynamics of the interlocked positive feedback loops explaining the robust epigenetic switching in Candida albicans

On Coupling Models Using Model-Checking: Effects of Irinotecan Injections on the Mammalian Cell Cycle

A general computational method for robustness analysis with applications to synthetic gene networks

Model Revision from Temporal Logic Properties in Computational Systems Biology

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 …

On a Continuous Degree of Satisfaction of Temporal Logic Formulae with Applications to Systems Biology

Formal Cell Biology in Biocham

From reaction models to influence graphs and back: a theorem

Proceedings of CSCLP 2007: Annual ERCIM Workshop on Constraint Solving and Constraint Logic Programming

Constraints are a natural way to represent knowledge, and constraint programming is a declarative programming paradigm that has been successfully used to express and solve many …

On Internalizing Modules as Agents in Concurrent Constraint Programming

Module systems are an essential feature of programming languages as they facilitate the re-use of existing code and the development of general purpose libraries. There are however …

Learning Transition Rules from Temporal Logic Properties

Most of the work on temporal representation issues in Machine Learning deals with the problem of learning/mining temporal patterns from a large set of temporal data. In this paper …

A Machine Learning approach to Biochemical Reaction Rules Discovery

Beyond numerical simulation, the possibility of performing symbolic computation on bio-molecular interaction networks opens the way to the design of new automated reasoning tools …

Apprentissage de règles de réactions biochimiques à partir de propriétés en logique temporelle

Machine Learning Bio-molecular Interactions from Temporal Logic Properties

With the advent of formal languages for modeling bio-molecu-lar interaction systems, the design of automated reasoning tools to assist the biologist becomes possible. The …