Curriculum vitae
A concise HTML CV for reading on the web. CV – English (PDF)
Profile
I am an applied mathematician and AI researcher based in Toulouse, France. My early research focused on probabilistic models for reconstructing demographic history from genomic data, with particular attention to population structure, coalescent processes, and the limits of statistical inference. Since then, I have worked across natural-language processing, medical imaging, signal processing, generative models, and AI agents, both in academic collaborations and in industry. I am especially interested in methods that combine mathematical structure, statistical reasoning, and machine learning to produce systems that are scientifically meaningful and practically useful. Alongside my research and engineering work, I teach, mentor student research, and have been president of Toulouse Data Science since 2024.
Research interests
- Probabilistic modelling and statistical inference
- Population genetics and demographic inference
- Representation learning and natural-language processing
- Machine learning for scientific and medical data
- Hybrid model-based and learning-based systems
Education
PhD in Applied Mathematics and Statistics
INSA Toulouse / Institut de Mathématiques de Toulouse, 2012–2016
Thesis on reconstructing the demographic history of populations from genomic data.
Research and professional appointments
PhD in Applied Mathematics and Statistics
INSA Toulouse / Institut de Mathématiques de Toulouse · 2012–2016
Probabilistic modelling of demographic history from genomic data, with emphasis on coalescent processes, population structure, and identifiability.
Research engineer
INRAE · 2016–2017
Genetic linkage maps and related computational genetics.
Research engineer
Institut de Mathématiques de Toulouse · 2017–2019
Probabilistic modelling in genetics.
Research engineer
ENAC · 2019–2021
Natural-language processing for aviation safety, described here only at a non-confidential level.
AI Researcher
Torus · 2023–present
Medical imaging, signal processing, generative models, and agentic systems, presented as selected applied research rather than commercial case studies.
Publications
See the publications page for BibTeX, DOIs, and preprints.
2022
SeSAM: software for automatic construction of order-robust linkage maps
Adrien Vidal, Franck Gauthier, , Nadège Guiglielmoni, Damien Leroux, Nicolas Chevrolier, Sylvain Jasson, Elise Tourrette, Olivier C. Martin, Matthieu Falque
BMC Bioinformatics, 23, article 499, 2022
BibTeX
@article{vidal2022sesam, title = {SeSAM: software for automatic construction of order-robust linkage maps}, author = {Vidal, Adrien and Gauthier, Franck and Rodrigez, Willy and Guiglielmoni, Nad{\`e}ge and Leroux, Damien and Chevrolier, Nicolas and Jasson, Sylvain and Tourrette, Elise and Martin, Olivier C. and Falque, Matthieu}, journal = {BMC Bioinformatics}, volume = {23}, pages = {499}, year = {2022}, doi = {10.1186/s12859-022-05045-7} }2021
Inferring number of populations and changes in connectivity under the n-island model
Armando Arredondo, Beatriz Mourato, Khoa Nguyen, Simon Boitard, , Olivier Mazet, Lounès Chikhi
Heredity, 126(6), 896-912, 2021
BibTeX
@article{arredondo2021nisland, title = {Inferring number of populations and changes in connectivity under the n-island model}, author = {Arredondo, Armando and Mourato, Beatriz and Nguyen, Khoa and Boitard, Simon and Rodr{\'i}guez, Willy and Mazet, Olivier and Chikhi, Loun{\`e}s}, journal = {Heredity}, volume = {126}, number = {6}, pages = {896--912}, year = {2021}, doi = {10.1038/s41437-021-00426-9} }2020
Epidemic Dynamics via Wavelet Theory and Machine Learning with Applications to Covid-19
Tô Tat Dat, Frédéric Protin, Nguyen T. T. Hang, Jules Martel, Nguyen Duc Thang, Charles Piffault, , Susely Figueroa, Hông Vân Lê, Wilderich Tuschmann, Tien Zung Nguyen
Biology, 9(12), article 477, 2020
DOI ·
BibTeX
@article{to2020epidemic, title = {Epidemic Dynamics via Wavelet Theory and Machine Learning with Applications to Covid-19}, author = {T{\^o}, Tat Dat and Protin, Fr{\'e}d{\'e}ric and Hang, Nguyen T. T. and Martel, Jules and Nguyen, Duc Thang and Piffault, Charles and Rodr{\'i}guez, Willy and Figueroa, Susely and L{\^e}, H{\^o}ng V{\^a}n and Tuschmann, Wilderich and Nguyen, Tien Zung}, journal = {Biology}, volume = {9}, number = {12}, pages = {477}, year = {2020}, doi = {10.3390/biology9120477} }2019
Coalescence times for three genes provide sufficient information to distinguish population structure from population size changes
Simona Grusea, , Didier Pinchon, Lounès Chikhi, Simon Boitard, Olivier Mazet
Journal of Mathematical Biology, 78(1), 189-224, 2019
BibTeX
@article{grusea2019coalescence, title = {Coalescence times for three genes provide sufficient information to distinguish population structure from population size changes}, author = {Grusea, Simona and Rodr{\'i}guez, Willy and Pinchon, Didier and Chikhi, Loun{\`e}s and Boitard, Simon and Mazet, Olivier}, journal = {Journal of Mathematical Biology}, volume = {78}, number = {1}, pages = {189--224}, year = {2019}, doi = {10.1007/s00285-018-1272-4} }2018
The IICR and the non-stationary structured coalescent: towards demographic inference with arbitrary changes in population structure
, Olivier Mazet, Simona Grusea, Armando Arredondo, Josué M. Corujo, Simon Boitard, Lounès Chikhi
Heredity, 121(6), 663-678, 2018
BibTeX
@article{rodriguez2018nssc, title = {The IICR and the non-stationary structured coalescent: towards demographic inference with arbitrary changes in population structure}, author = {Rodr{\'i}guez, Willy and Mazet, Olivier and Grusea, Simona and Arredondo, Armando and Corujo, Josu{\'e} M. and Boitard, Simon and Chikhi, Loun{\`e}s}, journal = {Heredity}, volume = {121}, number = {6}, pages = {663--678}, year = {2018}, doi = {10.1038/s41437-018-0148-0} }2018
The IICR (inverse instantaneous coalescence rate) as a summary of genomic diversity: insights into demographic inference and model choice
Lounès Chikhi, , Simona Grusea, Patrícia Santos, Simon Boitard, Olivier Mazet
Heredity, 120(1), 13-24, 2018
BibTeX
@article{chikhi2018iicr, title = {The IICR (inverse instantaneous coalescence rate) as a summary of genomic diversity: insights into demographic inference and model choice}, author = {Chikhi, Loun{\`e}s and Rodr{\'i}guez, Willy and Grusea, Simona and Santos, Patr{\'i}cia and Boitard, Simon and Mazet, Olivier}, journal = {Heredity}, volume = {120}, number = {1}, pages = {13--24}, year = {2018}, doi = {10.1038/s41437-017-0005-6} }2016
On the importance of being structured: instantaneous coalescence rates and human evolution—lessons for ancestral population size inference?
Olivier Mazet, , Simona Grusea, Simon Boitard, Lounès Chikhi
Heredity, 116, 362-371, 2016
DOI ·
BibTeX
@article{mazet2016structured, title = {On the importance of being structured: instantaneous coalescence rates and human evolution—lessons for ancestral population size inference?}, author = {Mazet, Olivier and Rodr{\'i}guez, Willy and Grusea, Simona and Boitard, Simon and Chikhi, Loun{\`e}s}, journal = {Heredity}, volume = {116}, pages = {362--371}, year = {2016}, doi = {10.1038/hdy.2015.104} }2016
Inferring Population Size History from Large Samples of Genome-Wide Molecular Data - An Approximate Bayesian Computation Approach
Simon Boitard, , Flora Jay, Stefano Mona, Frédéric Austerlitz
PLOS Genetics, 12(3), article e1005877, 2016
DOI ·
BibTeX
@article{boitard2016popsize, title = {Inferring Population Size History from Large Samples of Genome-Wide Molecular Data - An Approximate Bayesian Computation Approach}, author = {Boitard, Simon and Rodr{\'i}guez, Willy and Jay, Flora and Mona, Stefano and Austerlitz, Fr{\'e}d{\'e}ric}, journal = {PLOS Genetics}, volume = {12}, number = {3}, pages = {e1005877}, year = {2016}, doi = {10.1371/journal.pgen.1005877} }2015
Demographic inference using genetic data from a single individual: Separating population size variation from population structure
Olivier Mazet, , Lounès Chikhi
Theoretical Population Biology, 104, 46-58, 2015
DOI ·
BibTeX
@article{mazet2015demographic, title = {Demographic inference using genetic data from a single individual: Separating population size variation from population structure}, author = {Mazet, Olivier and Rodr{\'i}guez, Willy and Chikhi, Loun{\`e}s}, journal = {Theoretical Population Biology}, volume = {104}, pages = {46--58}, year = {2015}, doi = {10.1016/j.tpb.2015.06.003} }
Teaching and mentoring
Teaching interests include Applied mathematics, Probability and statistics, Machine learning, Natural-language processing, Generative AI and AI agents, Scientific computing. Confirmed course records appear on the teaching page.
Talks and scientific service
Verified talks are listed on the talks page. I have been president of Toulouse Data Science since 2024.
Selected software and projects
See selected projects, including IICR-related research software and SeSAM.