- Artificial intelligence: mainly focused on algorithms for answering complex queries on and learning discrete graphical models, both probabilistic (Markov Random Fields, Bayes Nets,...), and deterministic (Constraint networks, Constraint Programming and Cost Function Networks). My current focus lies in the interaction of such models with Deep Learning: how can a probabilistic Graphical Model be learned from natural inputs influencing observed realizations of this model, or how can the criteria and constraints of a deterministic Graphical Model be similarly learned from natural inputs influencing observed feasible high quality solutions. Eventually, the aim is to use several (learned or hand built) Graphical Models to combine learned information (intuition) with knowledge (Logic), especillay in the context of Design new physical objetcs. This is the topic of my chair in the Artificial and Natural Intelligence Toulouse Institute (ANITI) entitled Design with Intuition and Logic.
- Bioinformatics: the application of Discrete Graphical Models and Machine/Deep learning technologies mostly to constrained optimisation problems arising in computational biology. Initially, this was mainly genetic markers ordering, genetic map joining, then RNA secondary structure prediction and also RNA/protein gene finding and prediction (with frameshift detection, using Conditional Random Field models) both for prokaryotic and eukaryotic organisms, then biological network inference (by learning parameters and structures of probabilistic graphical models). My current application domain of inetrest is Computational Protein Design, with applications in health and green chemistry.
RESEARCH THEMES
EXTERNAL COLLABORATIONS
- With Sophie Barbe of the CIMES team in Toulouse Biotech Institute for designing and applying Computational Protein Design algorithms and tools.
- With Juan Cortés in LAAS/CNRS for the use of robotics-inspired flexible protein modeling.
- With the Combinatorial optimization group of CERT (Centre d'Études et de Recherches de Toulouse de l'ONERA) on algorithms for CSP.
- With Hélène Fargier, Jérôme Lang, Martin Cooper from the Institut de Recherches en Informatique de Toulouse for extensions of the CSP formalism and valued constraint network properties and algorithms.
- With the team of F. Rossi, University of Padova, Italy, for the comparison of Valued CSP and Semi-ring CSP.
- With Pedro Meseguer and Javier Larrosa (Polytechnic University of Catalunya, Spain), for the algorithmic of Valued and weighted CSP.
- With P. Rouzé (University of Ghent, Belgium) for gene finding in Arabidopsis thaliana. and other plants.
- With Marie-France Sagot on the algorithmic of gene finding.