Planning
| Time |
Event |
|
|
19:15 - 19:30
|
Dinner (1st service at 19:15, 2nd service at 20:00 when the rest of the people arrived) (CPL restaurant) |
|
Tuesday, December 9, 2025
| Time |
Event |
|
|
07:30 - 08:45
|
Breakfast (CPL restaurant) |
|
|
08:45 - 09:00
|
Welcome Remarks (La Parrachée) |
|
|
09:00 - 10:00
|
Keynote: Predicting interaction partners and generating protein sequences using protein language models (La Parrachée) - Anne-Florence Bitbol |
|
|
10:00 - 10:30
|
Contributed Talks (La Parrachée) |
|
|
10:00 - 10:30 |
› Protein and genomic language models chart a vast landscape of antiphage defenses - Mordret Ernest, Institut Pasteur [Paris], Institut National de la Santé et de la Recherche Médicale |
|
|
10:30 - 11:00
|
Coffee (mezzanine) |
|
|
11:00 - 12:00
|
Contributed Talks (La Parrachée) |
|
|
11:00 - 11:30 |
› Language Models Outperform Supervised-Only Approaches for Conserved Element Comprehension - Eyes Robson, University of California [Berkeley] |
|
|
11:30 - 12:00 |
› An attention-based model for studying bacterial evolution and epidemiology - Samuel Horsfield, EMBL-EBI |
|
|
12:00 - 13:30
|
Lunch (CPL restaurant) |
|
|
13:30 - 15:00
|
Contributed Talks (La Parrachée) |
|
|
13:30 - 14:00 |
› Identification and Classification of Orphan Genes, Spurious Orphan Genes, and Conserved Genes from the human microbiome - Chen Chen, Chen Chen, Wageningen University |
|
|
14:00 - 14:30 |
› A differentiable model for detecting diversifying selection directly from alignments in large-scale bacterial datasets - Leonie Lorenz, European Bioinformatics Institute [Hinxton] |
|
|
14:30 - 15:00 |
› Detecting interspecific positive selection using transformers - Charlotte West, European Bioinformatics Institute [Hinxton] |
|
|
15:00 - 15:30
|
Coffee (mezzanine) |
|
|
15:30 - 16:30
|
Contributed Talks (La Parrachée) |
|
|
15:30 - 16:00 |
› Exploring the space of self-reproducing RNA using generative models - Martin Weigt, Sorbonne University |
|
|
16:00 - 16:30 |
› Generative continuous time model reveals epistatic signatures in protein evolution - Barrat-Charlaix Pierre, Laboratoire de Biologie Computationnelle Quantitative et Synthétique |
|
|
16:30 - 18:30
|
Poster Session (mezzanine) |
|
|
19:15 - 19:15
|
Dinner (CPL restaurant) |
|
Wednesday, December 10, 2025
| Time |
Event |
|
|
07:30 - 08:30
|
Breakfast |
|
|
08:30 - 09:30
|
Keynote: A perspective on generative neural networks in genomics with applications in synthetic data generation (La Parrachée) - Burak Yelmen |
|
|
09:30 - 10:30
|
Contributed Talks (La Parrachée) |
|
|
09:30 - 10:00 |
› PRIVET: PRIVacy metric based on Extreme value Theory - Antoine Szatkownik, LISN |
|
|
10:00 - 10:30 |
› Generative models for inferring the evolutionary history of the malaria vector Anopheles gambiae - Sara Mathieson, University of Pennsylvania |
|
|
10:30 - 11:00
|
Coffee break (mezzanine) |
|
|
11:00 - 12:30
|
Contributed Talks (La Parrachée) |
|
|
11:00 - 11:30 |
› Contrastive Learning for Population Structure and Trait Prediction - Carl Nettelblad, Uppsala Universitet [Uppsala] |
|
|
11:30 - 12:00 |
› Neural posterior estimation for high-dimensional genomic data from complex population genetic models - Yuxin Ning, Eberhard Karls Universität Tübingen = University of Tübingen |
|
|
12:00 - 12:30 |
› Popformer: learning general signatures of genetic variation and natural selection with a self-supervised transformer - Leon Zong, University of Pennsylvania |
|
|
12:30 - 14:00
|
Lunch (CPL restaurant) |
|
|
13:30 - 17:00
|
Excursions - (outside) |
|
|
14:00 - 18:00
|
Board Games - (downstairs café) |
|
|
14:30 - 16:00
|
Yoga session - (Scolette room) |
|
|
19:30 - 19:30
|
Conference Dinner (CPL restaurant) |
|
Thursday, December 11, 2025
| Time |
Event |
|
|
07:30 - 09:00
|
Breakfast (CPL restaurant) |
|
|
09:00 - 10:30
|
Contributed Talks (La Parrachée) |
|
|
09:00 - 09:30 |
› Likelihood-free inference of phylogenetic tree posterior distributions - Luc Blassel, Département écologie évolutive [LBBE] |
|
|
09:30 - 10:00 |
› Graph Neural Networks for Likelihood-Free Inference in Diversification Models - Amélie Leroy, Biologie Computationnelle, Quantitative et Synthétique, Modélisation de la biologie - Ismaël Lajaaiti, Institut des Sciences de l'Évolution de Montpellier, Theoretical Ecology Lab - Sophia Lambert, Modélisation de la biologie - Jakub Voznica, Modélisation de la biologie - Maximilian Pichler, Theoretical Ecology Lab - Hélène Morlon, Modélisation de la biologie - Florian Hartig, Theoretical Ecology Lab - Laurent Jacob, Biologie Computationnelle, Quantitative et Synthétique |
|
|
10:00 - 10:30 |
› Phylodynamic modeling with unsupervised Bayesian neural networks - Marino Gabriele, ETH Zürich, Swiss Institute of Bioinformatics |
|
|
10:30 - 11:00
|
Coffee break (mezzanine) |
|
|
11:00 - 12:30
|
Contributed Talks (La Parrachée) |
|
|
11:00 - 11:30 |
› Predicting Multiple Sequence Alignment Uncertainty via Machine Learning - Lucia Martin-Fernandez, Biodiversity Computing Group, Institute of Computer Science, Foundation for Research and Technology - Hellas |
|
|
11:30 - 12:00 |
› Species Identification and aDNA Read Mapping Using k-mer Embeddings - Filip Thor, Uppsala Universitet [Uppsala] - Carl Nettelblad, Uppsala Universitet [Uppsala] |
|
|
12:00 - 12:30 |
› The Phylogenomics and Sparse Learning of Trait Innovations - Gaurav Diwan, Bioquant, Ruprecht-Karls Universität Heidelberg = Ruprecht-Karls University = Universität Heidelberg = Heidelberg University |
|
|
12:30 - 14:00
|
Lunch (CPL restaurant) |
|
|
14:00 - 16:00
|
Workshop - Neural Posterior Estimation for Population Genetics |
|
|
16:00 - 16:30
|
Coffee break (mezzanine) |
|
|
16:30 - 17:30
|
Keynote: The good, the bad and the ugly of deep learning in phylogenetic inference (La Parrachée) - Claudia Solís-Lemus |
|
|
17:30 - 18:30
|
Contributed Talks (La Parrachée) |
|
|
17:30 - 18:00 |
› Predicting natural variation in the yeast phenotypic landscape with machine learning - Sakshi Khaiwal, Institut de Recherche sur le Cancer et le Vieillissement |
|
|
18:00 - 18:30 |
› Exploring the archaic introgression landscape of admixed populations through joint ancestry inference |
|
|
18:30 - 18:45
|
Conclusion (La Parrachée) |
|
|
19:15 - 19:15
|
Dinner (CPL restaurant) |
|
Friday, December 12, 2025
| Time |
Event |
|
|
07:30 - 09:15
|
Breakfast (CPL restaurant) |
|
|
