Genomic and post-genomic studies

Previous studies of the DOLPHIN project mainly deal with genomic and postgenomic applications. These have been realized in collaboration with academic and industrial partners (IBL: Biology Institute of Lille; IPL: Pasteur Institute of Lille; IT-Omics firm).

First, genomic studies aim at analyzing genetic factors which may explain multi-factorial diseases such as diabetes, obesity or cardiovascular diseases. The scientific goal was to formulate hypotheses describing associations that may have any influence on diseases under study.

Secondly, in the context of post-genomic, a very large amount of data are obtained thanks to advanced technologies and have to be analyzed. Hence, one of the goals of the project was to develop analysis methods in order to discover knowledge in data coming from biological experiments.

These problems can be modeled as classical data mining tasks (Association rules, feature selection). As the combinatoric of such problems is very high and the quality criteria not unique, we proposed to model these problems as multi-objective combinatorial optimization problems. Evolutionary approaches have been adopted in order to cope with large scale problems.

Nowadays the technology is still going fast and the amount of data increases rapidly. Within the collaboration with Genes Diffusion, specialized in genetics and animal reproduction for bovine, swine, equine and rabbit species, we study combinations of Single Nucleotide Polymorphisms (SNP) that can explain some phenotypic characteristics. Therefore feature selection for regression is addressed using metaheuristics.

Optimization for health care

The collaboration with the Alicante company, a major actor in the hospital decision making, deals with knowledge extraction by optimization methods for improving the process of inclusion in clinical trials. Indeed, conducting a clinical trial, allowing for example to measure the effectiveness of a treatment, involves selecting a set of patients likely to participate to this test. Currently existing selection processes are far from optimal, and many potential patients are not considered. The objective of this collaboration consists in helping the practitioner to quickly determine if a patient is interesting for a clinical trial or not. Exploring different data sources (from a hospital information system, patient data...), a set of decision rules have to be generated. For this, approaches from multi-objective combinatorial optimization are implemented, requiring extensive work to model the problem, to define criteria optimization and to design specific optimization methods.

Molecular sampling and docking on large hybrid clusters

A Phd thesis is started in September 2015 in this context in collaboration with UMONS and University of Strasbourg. Flexible molecular docking is a very complex combinatorial opitmization problem especially when two components (ligand and protein) involved in the mechanism are together flexible. To deal in a reasonable time with such highly combinatorial process approximate optimization methods and massively parallel computing are absolutely The focus of the Ph.D thesis is on the flexibility-aware modeling and the design and implementation of near-approached optimization methods for solving the docking problem on large hybrid clusters including GPU accelerators and MIC coprocessors.