Section: New Results

Petri Net Analyses of Biochemical Reaction Networks using Constraint Logic Programming

Participants : François Fages, Thierry Martinez, Faten Nabli, Sylvain Soliman.

The Thesis of Faten Nabli [1] marks our achievements on the static analysis of biochemical reaction networks using Petri Net concepts and Constraint Logic Programming algorithms. This Thesis presents a Boolean model and two constraint-based methods for enumerating all minimal siphons and traps of a Petri net, by iterating the resolution of Boolean satisfiability problems executed with either a SAT solver or a CLP(B) program. The performances of these methods are compared with respect to a state-of-the-art algorithm from the Petri net community. On a benchmark with 80 Petri nets from the Petriweb database and 403 Petri nets from curated biological models of the Biomodels database, we show that miniSAT and CLP(B) solvers are overall both faster by two orders of magnitude with respect to the dedicated algorithm. Furthermore, we analyse why these programs perform so well on even very large biological models and show a polynomial time complexity result for Petri nets of fixed treewidth, using a similar theorem for constraint satisfaction problems with bounded treewidth constraint graphs. Faten Nabli has been hired with a Post-Doc position at Sanofi Paris.