Alexandre Chaussard

Affiliations. Université Paris-Saclay, AgroParisTech, INRAE, UMR MIA Paris-Saclay, F-91120 Palaiseau, France.

prof_pic.jpg

E4.226

22 place de l’Agronomie

91120 Palaiseau

Welcome to my personal page! I am an assistant professor at AgroParisTech, working in machine learning for multiomics applications. Previously, I did my PhD at LPSM (Sorbonne Université) under the supervision of Sylvain Le Corff, Anna Bonnet and Harry Sokol. You can find my PhD manuscript here.

My current research topics include:

  • Generative models
  • Variational inference in structured probabilistic models
  • Microbiome analysis
  • Deep learning for biology

Publications

  1. Stats. & Comp.
    Tree-based variational inference for Poisson log-normal models
    Alexandre Chaussard, Anna Bonnet, Elisabeth Gassiat, and Sylvain Le Corff
    Statistics and Computing, 2025
    DOI arXiv
  2. BMC Bioinfo.
    TaxaPLN: a taxonomy-aware augmentation strategy for microbiome-trait classification including metadata
    Alexandre Chaussard, Anna Bonnet, Sylvain Le Corff, and Harry Sokol
    BMC Bioinformatics, 2025
    DOI
  3. Gastroenterology
    Uncovering the dynamics of mucosa-associated microbiota in post-operative recurrence of Crohn’s disease
    Léonard Dubois, Alexandre Chaussard, Philippe Seksik, Stéphane Nancey, and 21 more authors
    Gastroenterology, 2026
    DOI
  4. Independent Component Discovery in Temporal Count Data
    Alexandre Chaussard, Anna Bonnet, and Sylvain Le Corff
    ICML, 2026
    DOI arXiv

Events

Jul 07, 2026 Poster at ICML 2026, Seoul on “Independent Component Analysis in Temporal Count data”.
Jan 15, 2026 Seminar at MIA Paris-Saclay - 1 hour talk on “Independent components discovery in longitudinal microbiome data”.
Dec 10, 2025 15 minutes talk at 6th edition of “Mathematical Foundations of AI” - Identifiability in Poisson Log-Normal models and its applications.
Aug 27, 2025 30 minutes talk on microbiome modelling using Poisson Log-Normal models and applications to disease diagnosis at “IA & Alimentation” Summer School 2025 at Sorbonne Université, SCAI.
Jun 05, 2025 15 minutes talk at the 56th Journées de Statistique de la SFdS, Marseille on TaxaPLN applications for microbiome-trait association.
Mar 20, 2025 Seminar at Mines de Paris, Fontainebleau - 45 minutes talk on “TaxaPLN: a taxonomy-aware augmentation strategy for microbiome-trait classification including metadata”.
Dec 01, 2024 GT LEGO 2024 Machine Learning for genomics - Research Day 2024: 15 minutes talk Presenting early results on “TaxaPLN: a taxonomy-aware augmentation strategy for microbiome-trait classification including metadata”.
Jul 01, 2024 15 minutes talk at 55th Journée de statistique de la SFdS on theoretical foundations and practical interest of “Tree-based variational inference for Poisson log-normal models”.
Feb 01, 2024 15 minutes talk at SMPGD 2024 on microbial applications of “Tree-based variational inference for Poisson log-normal models”.
Nov 01, 2023 SCAI workshop “AI and nutrition health” - Practical sessions on microbial applications.