Research in text algorithmics focuses on comparing, analyzing, handling or indexing sequences of characters. Working since 2016 as a CNRS researcher in computer science in the LIFL laboratory, now CRIStAL (UMR 9189, Université de Lille), Mathieu Giraud plays with sequence comparisons. This habilitation thesis focuses on two projects he worked on the last five years. In the Bonsai team, joint with Inria, Mathieu leads with Mikaël Salson a project on bioinformatics applied to hematology and immunology on the analysis of lymphocytes through their V(D)J recombinations (« Counting white blood cells »). This project, started by a collaboration with bioinformaticians and hematologists in the Lille hospital, combines research in algorithmics for immunology and hematology, software engineering and fundamental and clinical applications. The Vidjil software developed by Mathieu and his colleagues is now used by several labs in France and worldwide, sometimes in a routine hospital practice as in the Lille hospital. Mathieu also leads a projet on computer music (« Analyzing music scores »). Digital humanities link computational methods to cultural heritage and humanities research. Can computers understand music? The Algomus emergent team, shared between the CRIStAL and the MIS (Université de Picardie Jules Verne, Amiens) labs, combines musicological knowledge and computer science methods to propose algorithms analyzing music scores – with focus on patterns, chords and chord progressions, music texture and high-level structure of music. Algomus collaborates with music theorists, music teachers and artists, and contributes to science and art projects. This thesis concludes by the description of some popular science events.
defended on 30/03/2016