Section: Research Program
Constraint solving and optimization
Optimization methods are important in our research.
On the one hand, static analysis of biochemical reaction networks involves solving
hard combinatorial optimization problems,
for which constraint programming techniques
have shown particularly successful,
often beating dedicated algorithms
and allowing to solve large instances from model repositories. On the other hand, parameter search and model calibration problems involve similarly solving hard continuous optimization problems,
for which evolutionary algorithms such as the covariance matrix evolution strategy (CMA-ES ) (N. Hansen, A. Ostermeier (2001). Completely derandomized self-adaptation in evolution strategies. Evolutionary Computation, 9(2) pp. 159–195.)
has shown to provide best results in our context, for up to 100 parameters,
for building challenging
quantitative models, gaining model-based insights, revisiting admitted assumptions and contributing to biological knowledge (Domitille Heitzler, Guillaume Durand, Nathalie Gallay, Aurélien Rizk, Seungkirl Ahn, Jihee Kim, Jonathan D. Violin, Laurence Dupuy, Christophe Gauthier, Vincent Piketty, Pascale Crépieux, Anne Poupon, Frédérique Clément, François Fages, Robert J. Lefkowitz, Eric Reiter. Competing G protein-coupled receptor kinases balance G protein and