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Monday, December 8, 2025
| 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) |
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