Expertise: Machine Learning and Image Analysis. I'm particularly interested in Interpretability, Accountability and Robustness in machine learning. Strong experience in Image Registration.
Engineering: Project supervision and algorithmical expertise for the valorization of novel mathematical strategies in machine learning. Supervision of engineers or students from all levels in applied mathematics and computer science. Program and package development using C++ or Python. GPU computing using OpenCL or CUDA. Machine learning using PyTorch and Scikit-Learn.
Teaching: Machine Learning, Image Analysis, Optimization, Python, GPU programming, Statistics.
Career:2019-.: CNRS member of the 3IA Artificial and Natural Intelligence Toulouse Institute (ANITI).
2012-.: CNRS Research Engineer at Mathematics Institute of Toulouse (IMT), France. Statistics and Optimization (SO) team. Learning, Optimization, Complex data (AOC) team-projet.
2011: Research fellow at the Biomedical Image Analysis Laboratory with Julia A. Schnabel (then invited fellow until 2014). Institute of Biomedical Engineering, University of Oxford, UK.
2009-2010: Research assistant at the Biomedical Image Analysis Group and the Institute for Mathematical Sciences with Daniel Rueckert and Darryl Holm. Imperial College, London, UK.
2007-2008: Researcher/Engineer at the Computer Assisted Neuroimaging Laboratory with Philippe Ciuciu. Neurospin, CEA Saclay, France.
2003-2006: Junior lecturer in Fluid Mechanics. Department of Mathematics and Computer science, Paul Sabatier University, Toulouse, France.
Studies - qualifications:2018: HDR (French accreditation to supervise research): Mathematical Models and Numerical Methods for the Analysis of Medical Images and Complex Data (manuscript). Institut de Mathématiques de Toulouse (IMT, UMR 5219); Paul Sabatier University, France.
Jury: X. Pennec (DR INRIA Sophia-Antipolis), J.F. Aujol (Pr Univ. Bordeaux), G. Peyré (DR ENS Paris), L. Younes (Pr Johns Hopkins University), A. Desolneux (DR ENS Cachan), F. Gamboa (Pr Univ. Toulouse), J.M. Loubes (Pr Univ. Toulouse).
2003-2007: PhD thesis: Quantitative Analysis of Micro-vascular Networks from Computed Tomography Images. Advisor: F. Plouraboué. Fluid Mechanics Institute of Toulouse (IMFT, UMR 5502); Paul Sabatier University, France.
Jury: G. Malandain (DR INRIA Sophia-Antipolis), I. Magnin (DR INSERM, CREATIS Lyon), F. Estève (ESRF Grenoble), M. Zagzoule (Pr Univ. Toulouse), A.R. Pries (Pr Univ. Berlin), F. Plouraboué (DR CNRS IMFT Toulouse), C. Fonta (DR CNRS CerCo Toulouse), X. Descombes (DR INRIA Sophia-Antipolis).
2002-2003: Master 2 in Computer Science. Major in Image analysis. Paul Sabatier university (IRIT, UMR 5505), Toulouse, France.
2000-2002: Licence 3, Master 1 in Mathematical Engineering. Major in Scientific Computing (PDEs and optimization). Paul Sabatier university, Toulouse, France.
1998-2000: Licence 1,2 in Mathematics, Computer Science and applications. Paul Sabatier university, Toulouse, France.
Responsibilities:2020 - .: Co-responsible for the team-project Learning, Optimization, Complex data with Edouard Pauwel (IRIT). This team-project of Labex CIMI gathers 24 researchers interested by Machine Learning from the Mathematics Institute of Toulouse (IMT), the Toulouse Research Institute in Computer Science (IRIT) and some parts of the Laboratory for Analysis and Architecture of Systems (LAAS).
2020 - .: Local correspondant of the SMAI (French Society for Applied and Industrial Mathematics) in Toulouse.
2017 - .: Member of the valorization group at the Mathematics Institute of Toulouse (link).
2015 - 2019: Representative of the technical and administrative personnel at the Mathematics Institute of Toulouse laboratory Council.
2014 - 2020: Member of the editorial board of AIMS Medical Science (link).
Distributed codes:Gems-AI: Interpretability of black-box decision rules in A.I.: https://www.gems-ai.com/ (granted by CNRS-Innovation)
uTIlzreg: Diffeomorphic registration of 3D images (see the Papers webpage for specific citations): https://sourceforge.net/projects/utilzreg/. Explanations about uTIlzreg are given here.
LargeGraphCenterEstimator: Barycenter esimation of observed events on large weighted graphs (citation): https://sourceforge.net/projects/largegraphcenterestimator/.
CORE-clustering: Scalable graph or variables clustering with interpretable decision rules (see the Papers webpage for specific citations): https://sourceforge.net/projects/core-clustering/.
SlicerRegularizedFastMarching: Semi-interactive 3D image segmentation in Slicer3D https://github.com/AldrickF/SlicerRegularizedFastMarching (internship of Aldrick Faure -- Univ. Toulouse).
GeoShoot: GPU implementation in C++/OpenCL of the Geodesic shooting algorithm here for 3D medical images (internship of Alexandre Martin -- ENS Lyon): https://github.com/scalexm/GeoShoot.
CoordinatesLayout: Cytoscape App for the defintion of graph layouts with pre-defined coordinates (internship of Noémy Artigouha -- INSA Toulouse): http://apps.cytoscape.org/apps/coordinateslayout.
Sanssouci.python (Main developer: Pierre Neuvial): Post hoc inference via multiple testing https://github.com/pneuvial/sanssouci.python.
ImpecBrainSeg: Segmentation of MR brain images: https://sourceforge.net/projects/impecbrainseg/.
Disclaimer: All these codes should be used for research purposes only.
Organizing committees:2021: Workshop on AI based surrogate models SURDAY (Surrogate day), with J. Morlier (ISAE-Supaero) and E. Gondet (OMP)
2021: CIMI-ANITI summer school on optimization, with E. Cazelles, C. Févotte and E. Soubies (CNRS, IRIT)
2020: Co-organiser of the ICML workshop Law and Machine Learning, with C. Castets-Renard (U. Ottawa/Law) and S. Cussat-Blanc (U. Toulouse/IRIT).
2020: Guest Editor of the Special Issue Interpretability, Accountability and Robustness in Machine Learning of the journal Algorithms.
2020: Co-organiser of the 8th thematic of JDEV 2020 with E. Gondet (CNRS/OMP). It deals with Programming and Deploying AI.
2018: Co-organiser of the CIMI Optimization and Learning workshop, which focuses on current challenges in optimization for machine learning.
2016: Co-organiser of the MASCOT-NUM 2016 meeting, dealing with stochastic methods for the analysis of numerical codes.
2015 : Co-organiser of the French conference Journées de probabilités 2015, dealing with probability.
2014: Co-organiser of the French conference Journées MAS 2014, dealing with stochastic modelling and statistics. Proceedings are here.
Awards and Grants:2019: Member of the 3IA-ANITI chair Law, Accountability and Social Trust in Artificial Intelligence of the Integrative Program A (Acceptability, Fair Representative Data For AI). Obtained with C. Castets-Renard (PI) and S. Cussat-Blanc (picture). Additionally member of the Integrative Program B (Certifiable Al Toward Autonomous Critical Systems) to make links between these complementary programs.
2019: CNRS innovation grant obtained on the project Ethik-IA, in order to develop a reference Python package dealing with Interpretability, Fairness and Robustness in Machine Learning. Obtained with J.-M. Loubes (IMT, Univ. Toulouse).
2019: Grant from the Del Duca foundation on the project OpSiMorE, dealing with Stochastic Optimization. Grant in association with Fort G. (P.I.), Huang L. and Gadat S.
2018: Maturation program with Toulouse Tech Transfert, in order to work on practical strategies to detect selection biases in Machine Learning. Obtained with J.-M. Loubes (IMT, Univ. Toulouse) and P. Besse (IMT, INSA Toulouse).
2016: Grant for a PhD thesis Regression models for non-Euclidean and high-dimensional data founded by Region Midi-Pyrénées (now Occitanie). Obtained with J.-M. Loubes (IMT, Univ. Toulouse) and P. Balaresque (AMIS, CNRS).
2016: Member of the ANR granted project Voice4PD-MSA (Differential diagnosis between Parkinson's disease and Multiple System Atrophy using digital speech analysis) with K. Daoudi (INRIA Bordeaux, PI), J. Mauclair (IRIT, Univ. Toulouse), W. Meissner (CHU Bordeaux), A. Pavy-Le-Traon (CHU Toulouse), S. Déjean (IMT - Univ. Toulouse). Co-responsible for statistical analyses with S. Déjean.
2015: Member of the project Fluidbrain founded by the Midi-Pyrénées region and INSERM with E. Schmidt (PI, INSERM 825 - CHU Toulouse), P. Celsis (INSERM 825 - CHU Toulouse), P. Payoux (INSERM 825 - CHU Toulouse), P. Swider (IMFT), P. Besse (IMT - INSA), S. Déjean (IMT - UPS). Responsible for the work package dealing with data integration.
2015: Member of the project SysBio founded by INSERM with E. Dupré (PI, INSERM 1043 - CHU Toulouse), L. Ysebaert (CHU Toulouse), E. Chatelut (Institut Claudius Regaud), F. Courbon (CHU Toulouse), F. Malgouyres (UPS - IMT), S. Gadat (UT1/TSE - associate IMT). Responsible for the development of image analysis strategies on 3D Slicer.
2014: Member of the ANR granted project Numerical Schemes using Lattice Basis Reduction with J.-M. Mirebeau (PI, Univ. Paris Dauphine), L. Cohen (Univ. Paris Dauphine) and J. Fehrenbach (Univ. Paul Sabatier, Institut de Mathématiques de Toulouse) (website).
2014: Travel grant CNRS / University of Oxford collaboration scheme. Grant obtained in collaboration with Julia A. Schnabel.
2013: PI of an AO1/Université Paul Sabatier grant. Grant obtained in collaboration with CerCo Toulouse (in particular M. Mescam and C. Fonta).
2012: Travel grant CNRS / University of Oxford collaboration scheme. Grant obtained in collaboration with Julia A. Schnabel.
2010: Co-author with Darryl D. Holm (Principal Investigator) and François-Xavier Vialard of the ERC projet: Five Grand Challenges in Computational Anatomy.
2008: French national prize "La recherche" 2008 - human health mention. Prize obtained with the team members Franck Plouraboué, Caroline Fonta, Peter Cloetens and Xavier Descombes on my PhD work. This prize rewards pluridisciplinary research works.
2006: PI of a grant to fund an extension of one year to my PhD work. Grant from the Fondation pour la Recherche Médicale (French Foundation for Medical Research) with F. Plouraboué and C. Fonta.
Links:Google scholar profile: link.
DBLP profile: link.
French Society for Applied and Industrial Mathematics (SMAI): link.
French academic network for Software Development (DevLog): link.
French academic network for Scientific Computation / HPC (groupe Calcul): link.
French research network for Data Science and Machine Learning (GdR MaDICS): link.
French research network for Information, Signal, Image et ViSion processing/analysis (GdR ISIS): link.
Toulouse Data Science meetup group: link.