Planning

Week Mon. 08 Tue. 09 Wed. 10 Thu. 11 Fri. 12 List

	Mon. 08	Tue. 09	Wed. 10	Thu. 11	Fri. 12
07:00 08:00 09:00 10:00 11:00 12:00 13:00 14:00 15:00 16:00 17:00 18:00 19:00	Dinner (1st service at 19:15, 2nd service at 20:00 when the rest of the people arrived) 19:15 - 19:30 (15min) Dinner (1st service at 19:15, 2nd service at 20:00 when the rest of the people arrived) CPL restaurant	Breakfast 7:30 - 8:45 (1h15) Breakfast CPL restaurant Welcome Remarks 8:45 - 9:00 (15min) Welcome Remarks La Parrachée Keynote: Predicting interaction partners and generating protein sequences using protein language models 9:00 - 10:00 (1h) Keynote: Predicting interaction partners and generating protein sequences using protein language models La Parrachée Anne-Florence Bitbol Contributed Talks 10:00 - 10:30 (30min) Contributed Talks La Parrachée › 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 10:00-10:30 (30min) Coffee 10:30 - 11:00 (30min) Coffee mezzanine Contributed Talks 11:00 - 12:00 (1h) Contributed Talks La Parrachée › Language Models Outperform Supervised-Only Approaches for Conserved Element Comprehension - Eyes Robson, University of California [Berkeley] 11:00-11:30 (30min) › An attention-based model for studying bacterial evolution and epidemiology - Samuel Horsfield, EMBL-EBI 11:30-12:00 (30min) Lunch 12:00 - 13:30 (1h30) Lunch CPL restaurant Contributed Talks 13:30 - 15:00 (1h30) Contributed Talks La Parrachée › Identification and Classification of Orphan Genes, Spurious Orphan Genes, and Conserved Genes from the human microbiome - Chen Chen, Chen Chen, Wageningen University 13:30-14:00 (30min) › A differentiable model for detecting diversifying selection directly from alignments in large-scale bacterial datasets - Leonie Lorenz, European Bioinformatics Institute [Hinxton] 14:00-14:30 (30min) › Detecting interspecific positive selection using transformers - Charlotte West, European Bioinformatics Institute [Hinxton] 14:30-15:00 (30min) Coffee 15:00 - 15:30 (30min) Coffee mezzanine Contributed Talks 15:30 - 16:30 (1h) Contributed Talks La Parrachée › Exploring the space of self-reproducing RNA using generative models - Martin Weigt, Sorbonne University 15:30-16:00 (30min) › Generative continuous time model reveals epistatic signatures in protein evolution - Barrat-Charlaix Pierre, Laboratoire de Biologie Computationnelle Quantitative et Synthétique 16:00-16:30 (30min) Poster Session 16:30 - 18:30 (2h) Poster Session mezzanine Dinner 19:15 - 19:15 () Dinner CPL restaurant	Breakfast 7:30 - 8:30 (1h) Breakfast Keynote: A perspective on generative neural networks in genomics with applications in synthetic data generation 8:30 - 9:30 (1h) Keynote: A perspective on generative neural networks in genomics with applications in synthetic data generation La Parrachée Burak Yelmen Contributed Talks 9:30 - 10:30 (1h) Contributed Talks La Parrachée › PRIVET: PRIVacy metric based on Extreme value Theory - Antoine Szatkownik, LISN 09:30-10:00 (30min) › Generative models for inferring the evolutionary history of the malaria vector Anopheles gambiae - Sara Mathieson, University of Pennsylvania 10:00-10:30 (30min) Coffee break 10:30 - 11:00 (30min) Coffee break mezzanine Contributed Talks 11:00 - 12:30 (1h30) Contributed Talks La Parrachée › Contrastive Learning for Population Structure and Trait Prediction - Carl Nettelblad, Uppsala Universitet [Uppsala] 11:00-11:30 (30min) › Neural posterior estimation for high-dimensional genomic data from complex population genetic models - Yuxin Ning, Eberhard Karls Universität Tübingen = University of Tübingen 11:30-12:00 (30min) › Popformer: learning general signatures of genetic variation and natural selection with a self-supervised transformer - Leon Zong, University of Pennsylvania 12:00-12:30 (30min) Lunch Excursions Board Games Yoga session 12:30 - 14:00 (1h30) Lunch CPL restaurant 13:30 - 17:00 (3h30) Excursions (outside) 14:00 - 18:00 (4h) Board Games (downstairs café) 14:30 - 16:00 (1h30) Yoga session (Scolette room) Conference Dinner 19:30 - 19:30 () Conference Dinner CPL restaurant	Breakfast 7:30 - 9:00 (1h30) Breakfast CPL restaurant Contributed Talks 9:00 - 10:30 (1h30) Contributed Talks La Parrachée › Likelihood-free inference of phylogenetic tree posterior distributions - Luc Blassel, Département écologie évolutive [LBBE] 09:00-09:30 (30min) › 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 09:30-10:00 (30min) › Phylodynamic modeling with unsupervised Bayesian neural networks - Marino Gabriele, ETH Zürich, Swiss Institute of Bioinformatics 10:00-10:30 (30min) Coffee break 10:30 - 11:00 (30min) Coffee break mezzanine Contributed Talks 11:00 - 12:30 (1h30) Contributed Talks La Parrachée › Predicting Multiple Sequence Alignment Uncertainty via Machine Learning - Lucia Martin-Fernandez, Biodiversity Computing Group, Institute of Computer Science, Foundation for Research and Technology - Hellas 11:00-11:30 (30min) › Species Identification and aDNA Read Mapping Using k-mer Embeddings - Filip Thor, Uppsala Universitet [Uppsala] - Carl Nettelblad, Uppsala Universitet [Uppsala] 11:30-12:00 (30min) › The Phylogenomics and Sparse Learning of Trait Innovations - Gaurav Diwan, Bioquant, Ruprecht-Karls Universität Heidelberg = Ruprecht-Karls University = Universität Heidelberg = Heidelberg University 12:00-12:30 (30min) Lunch 12:30 - 14:00 (1h30) Lunch CPL restaurant Workshop 14:00 - 16:00 (2h) Workshop Neural Posterior Estimation for Population Genetics Coffee break 16:00 - 16:30 (30min) Coffee break mezzanine Keynote: The good, the bad and the ugly of deep learning in phylogenetic inference 16:30 - 17:30 (1h) Keynote: The good, the bad and the ugly of deep learning in phylogenetic inference La Parrachée Claudia Solís-Lemus Contributed Talks 17:30 - 18:30 (1h) Contributed Talks La Parrachée › Predicting natural variation in the yeast phenotypic landscape with machine learning - Sakshi Khaiwal, Institut de Recherche sur le Cancer et le Vieillissement 17:30-18:00 (30min) › Exploring the archaic introgression landscape of admixed populations through joint ancestry inference - 18:00-18:30 (30min) Conclusion 18:30 - 18:45 (15min) Conclusion La Parrachée Dinner 19:15 - 19:15 () Dinner CPL restaurant	Breakfast 7:30 - 9:15 (1h45) Breakfast CPL restaurant

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