Ecole thématique AI4BioMed 2026

31 mars 2026, 13:00 → 3 avr. 2026, 18:00 Europe/Paris

Polytech Lyon

Spring School on AI and Machine Learning and their Applications to Biology and Health -  Université Lyon 1, La Doua, Villeurbanne.

Artificial intelligence and machine learning are rapidly transforming our research activity in biological sciences and health. As a result, there is a critical need for making machine learning and AI accessible to everyone currently working in these scientific and applied domains.

 

To meet those challenges, the DIgitBioMed initiative proposes a 4-day spring school, March 31 - April 3, 2026, on machine learning and AI in Biological and Health sciences. This spring school will provide a basic introduction to machine learning, deep learning, AI, and their applications to biology and health.

 

In terms of the practical outline, the three days will consist of a combination of basic courses, hands-on sessions, conferences on principles and on applications, round-tables and discussions. Two parallel tracks of hands-on session will be proposed, depending on the level of skills in basic programming and in mathematics and statistics. This is meant to give everyone an opportunity to get an entry point to basic understanding and practical manipulations in machine learning and AI in research today.

 

Prerequisites: knowledge of scripting in Python. Some acquaintance with biological and/or health related sciences (applicants can come from a math, stat or computer science background, but they should then either have at least some courses related to biology and/or health in their current training programs, or should be involved in at least some research activities related to biology and/or health). 

 

Eligibility: All MSc, PhD students, post-docs, permanent members are eligible. A priority will be given to MSc and PhD students of the masters, doctoral schools and laboratories associated with the DigitBioMed initiative. For more information about DigitBioMed, its programs and its member labs: https://graduate-plus.fr/digital-sciences-forbiology-and-health/

 

Registration: Registration is free but mandatory. Deadline March 13, 2026.

 

Programme

 

Tuesday, March 31, 2026

 

13.00 - 14.00: Welcome 

14.00 - 15.00: Course 1 - Philippe Veber - Introduction and general principles

15.00 - 18.00: Hands-on session

 

Wednesday, April 1, 2026

 

09:00-10:00: Course 2 - Stefan Duffner - Neural architectures

10:00-13:00: Hands-on session

 

13:00-14:00: lunch

 

14:00 - 15:00: Course 3 - Nicolas Lartillot - Transformers and foundation models

15.00 - 18.00: Hands-on session

 

Thursday, April 2, 2026

 

09:00 - 9:30: Conference - Romain Déleat Besson, CREATIS, INSA Université Lyon 1

Title: TBA

 

10:00 - 13:00: Hands-on session

 

13:00 - 14:00: lunch

 

14:00 - 15:00: Conference - Élodie Laine, CQSB, IBPS, Sorbonne Université

Protein Language Models: Principles and Applications to Mutations and Protein Dynamics

 

15.00 - 18.00: Hands-on session

 

18:00 - 19:00: cocktail

 

Friday, April 3, 2026

 

09:00 - 10:00: Conference - Stéphane Chrétien. ERIC, Université Lyon 2

SigBERT: Combining Narrative Medical Reports and Rough Path Signature Theory for Survival Risk Estimation in Oncology

 

10.00 - 13.00 Parallel hands-on sessions: applications 

• TP1 -  Protein language models and their application to protein structure prediction - Nicolas Lartillot 
• TP2 - The autoencoder - Stefan Duffner
• TP3 - Penalized splines for flexible modelling and anaalyis of survival in cancer patients - Mathieu Fauvernier and Pascal Roy

 

13:00 - 14:00: lunch

 

14:00 - 15:00: Conference - Ernest Mordret, Institut Pasteur, Paris

Protein and genomic language models uncover the unexplored diversity of bacterial immunity

 

15.00 - 18.00: Parallel hands-on sessions: applications 

• TP1 -  Predicting functional annotations of protein coding genes - Nicolas Lartillot 
• TP2 - The autoencoder - Stefan Duffner
• TP3 -  Deep-learning approach to modelling and analysis of survival in cancer patients - Philippe Veber 

 

 

Speakers and teaching staff

 

Speakers:

 

Romain Déleat Besson, Post Doc, CREATIS, INSA Université Lyon 1

 

Élodie Laine, Full Professor in Computational Biology and Artificial Intelligence. CQSB, IBPS, Sorbonne Université

https://www.lcqb.upmc.fr/laine/

 

Stéphane Chrétien., Full Professor,  ERIC, Université Lyon 2

https://sites.google.com/site/stephanegchretien/home

 

Ernest Mordret, Post Doc, Institut Pasteur, Paris

https://research.pasteur.fr/fr/member/ernest-mordret/

 

Teaching staff:

 

Julien Barnier, 

Stefan Duffner, 

Gaspard Dussert

Mathieu Fauvernier, 

Laurent Jacob

Nicolas Lartillot, 

Pascal Roy,

Philippe Veber,

 

Scientific committee:

 

Julien Barnier, Laboratoire de Biométrie et Biologie Évolutive, Université Claude Bernard Lyon 1, CNRS.

Stefan Duffner, Laboratoire d'InfoRmatique en Image et Systèmes d'information, INSA Lyon

Gaspard Dussert, Laboratoire de Biométrie et Biologie Évolutive, Université Claude Bernard Lyon 1, CNRS

Nicolas Lartillot, Laboratoire de Biométrie et Biologie Évolutive, Université Claude Bernard Lyon 1, CNRS.

Pascal Roy, Laboratoire de Biométrie et Biologie Évolutive, Université Claude Bernard Lyon 1, Hospices Civils de Lyon

Philippe Veber, Laboratoire de Biométrie et Biologie Évolutive, Université Claude Bernard Lyon 1, CNRS