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
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
7:30 - 8:45 (1h15)
Breakfast
CPL restaurant
8:45 - 9:00 (15min)
Welcome Remarks
La Parrachée
9:00 - 10:00 (1h)
Keynote: Predicting interaction partners and generating protein sequences using protein language models
La Parrachée
Anne-Florence Bitbol
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)
10:30 - 11:00 (30min)
Coffee
mezzanine
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)
12:00 - 13:30 (1h30)
Lunch
CPL restaurant
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)
15:00 - 15:30 (30min)
Coffee
mezzanine
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)
16:30 - 18:30 (2h)
Poster Session
mezzanine
19:15 - 19:15 ()
Dinner
CPL restaurant
7:30 - 8:30 (1h)
Breakfast
8:30 - 9:30 (1h)
Keynote: A perspective on generative neural networks in genomics with applications in synthetic data generation
La Parrachée
Burak Yelmen
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)
10:30 - 11:00 (30min)
Coffee break
mezzanine
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)
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)
19:30 - 19:30 ()
Conference Dinner
CPL restaurant
7:30 - 9:00 (1h30)
Breakfast
CPL restaurant
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)
10:30 - 11:00 (30min)
Coffee break
mezzanine
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)
12:30 - 14:00 (1h30)
Lunch
CPL restaurant
14:00 - 16:00 (2h)
Workshop
Neural Posterior Estimation for Population Genetics
16:00 - 16:30 (30min)
Coffee break
mezzanine
16:30 - 17:30 (1h)
Keynote: The good, the bad and the ugly of deep learning in phylogenetic inference
La Parrachée
Claudia Solís-Lemus
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)
18:30 - 18:45 (15min)
Conclusion
La Parrachée
19:15 - 19:15 ()
Dinner
CPL restaurant
7:30 - 9:15 (1h45)
Breakfast
CPL restaurant
