Section: Application Domains

Life Sciences: Biology, Chemistry and Medicine

Participants : Miguel Couceiro, Adrien Coulet, Nicolas Jay, Joël Legrand, Jean Lieber, Pierre Monnin, Amedeo Napoli, Abdelkader Ouali, Chedy Raïssi, Malika Smaïl-Tabbone, Yannick Toussaint.

Keywords:

knowledge discovery in life sciences, biology, chemistry, medicine, pharmacogenomics and precision medicine.

One major application domain which is currently investigated by the Orpailleur team is related to life sciences, with particular emphasis on biology, medicine, and chemistry. The understanding of biological systems provides complex problems for computer scientists, and the developed solutions bring new research ideas or possibilities for biologists and for computer scientists as well. Indeed, the interactions between researchers in biology and researchers in computer science improve not only knowledge about systems in biology, chemistry, and medicine, but knowledge about computer science as well.

Knowledge discovery is gaining more and more interest and importance in life sciences for mining either homogeneous databases such as protein sequences and structures, or heterogeneous databases for discovering interactions between genes and environment, or between genetic and phenotypic data, especially for public health and precision medicine (pharmacogenomics). Pharmacogenomics is one main challenge for the Orpailleur team as it considers a large panel of complex data ranging from biological to medical data, and various kinds of encoded domain knowledge ranging from texts to formal ontologies.

On the same line as biological data, chemical data are presenting important challenges w.r.t. knowledge discovery, for example for mining collections of molecular structures and collections of chemical reactions in organic chemistry. The mining of such collections is an important task for various reasons among which the challenge of graph mining and the industrial needs (especially in drug design, pharmacology and toxicology). Molecules and chemical reactions are complex data that can be modeled as labeled graphs. Graph mining methods may play an important role in this framework and Formal Concept Analysis can also be used in an efficient and well-founded way [81]. Graph mining as considered in the framework of FCA is an important task on which we are working, whose results can be transferred to text mining as well.

Finally, the so called “projet de recherche exploratoire” (PRE) HyGraMi for “Hybrid Graph Mining for the Design of New Antibacterials” is about the fight against resistance of bacteria to antibiotics. The objective of HyGraMi is to design a hybrid data mining system for discovering new antibacterial agents. This system should rely on a combination of numeric and symbolic classifiers, that will be guided by expert domain knowledge. The analysis and classification of the chemical structures is based on an interaction between symbolic methods e.g. graph mining techniques, and numerical supervised classifiers based on exact and approximate matching.