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Monday, May 13, 2024
| Time | Event | (+) |
| 09:45 - 10:00 | Introduction | |
| 10:00 - 11:00 | Keynote: Harnessing AI in phylogenomics - Tal Pupko | |
| 11:00 - 11:30 | Realistic data simulation - Franz Baumdicker | (+) |
| 11:00 - 11:30 | › Assessing usefulness of artificial genomes via local ancestry inference - Antoine Szatkownik, Laboratoire Interdisciplinaire des Sciences du Numérique | |
| 11:30 - 12:00 | Coffee break | |
| 12:00 - 13:00 | Realistic data simulation - Franz Baumdicker | (+) |
| 12:00 - 12:30 | › Simulations of Sequence Evolution: How (Un)realistic They Are and Why - Johanna Trost, Université Claude Bernard Lyon 1 - Julia Haag, Heidelberg Institute for Theoretical Studies - Dimitri Höhler, Heidelberg Institute for Theoretical Studies - Laurent Jacob, Sorbonne Université | |
| 12:30 - 13:00 | › Fitting Indel Evolution Model Parameters to PFam Protein Alignments with a GPU-accelerated Framework - Annabel Large, Department of Bioengineering; University of California, Berkeley, Joint Bioengineering Graduate Group; University of California, Berkeley and University of California, San Francisco | |
| 13:00 - 14:30 | Lunch | |
| 14:30 - 15:30 | Keynote: Deep learning for the phylogenetic inference of species diversification - Hélène Morlon | |
| 15:30 - 16:30 | Phylogenetics - Alexandros Stamatakis | (+) |
| 15:30 - 16:00 | › Phyloformer: Towards fast and accurate phylogeny reconstruction with self-attention networks - Luca Nesterenko, Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 | |
| 16:00 - 16:30 | › Learning from an Artificial Neural Network in Phylogenetics - Alina Leuchtenberger, Max Perutz Labs, Medical University of Vienna | |
| 16:30 - 17:00 | Coffee break | |
| 17:00 - 18:00 | Phylogenetics - Alexandros Stamatakis | (+) |
| 17:00 - 17:30 | › Neural networks can predict ghost species diversity from gene transfers - Enzo Marsot, Max-Planck-Institut für Biochemie = Max Planck Institute of Biochemistry | |
| 17:30 - 18:00 | › Predicting Phylogenetic Bootstrap Values via Machine Learning - Julius Wiegert, Heidelberg Institute for Theoretical Studies | |
| 18:00 - 19:00 | Poster session |
Tuesday, May 14, 2024
| Time | Event | (+) |
| 09:00 - 10:00 | Keynote: Generative adversarial networks, transfer learning, and interpretability for evolutionary inference - Sara Mathieson | |
| 10:00 - 11:00 | Predictions on a single sequence - Laurent Jacob | (+) |
| 10:00 - 10:30 | › Illuminating the functional landscape of the dark proteome across the Animal Tree of Life through natural language processing models - Gemma I. Martínez-Redondo, Institute of Evolutionary Biology (CSIC-UPF), Passeig marítim de la Barceloneta 37-49, 08003 Barcelona, Spain | |
| 10:30 - 11:00 | › Deciphering Deep Phylogeny and Evolution of Protein Families through Protein Language Models - Ivan Koludarov, Institut für Informatik | |
| 11:00 - 11:30 | Coffee break | |
| 11:30 - 13:30 | Predictions on a single sequence - Laurent Jacob | (+) |
| 11:30 - 12:00 | › Classification of the evolutionary origin of orphan genes using machine learning approaches - Nikolaos Vakirlis, Biomedical Sciences Research Centre Alexander Fleming [Vari, Greece] | |
| 12:00 - 12:30 | › Unsupervised learning as a tool to retrieve genomes from undersampled taxa: Fast and slow evolution in myxozoans - Claudia Weber, Wellcome Sanger Institute | |
| 12:30 - 13:00 | › Long context windows improve deep learning methods for predicting genomic regulation - Ian Holmes, University of California [Berkeley], Calico Life Sciences LLC, Lawrence Berkeley National Laboratory [Berkeley] | |
| 13:00 - 13:30 | › Interpreting artificial neural networks for detecting genome-wide association signals for complex traits - Burak Yelmen, Institute of Genomics [Tartu, Estonia], LISN | |
| 13:30 - 14:30 | Lunch | |
| 14:30 - 17:30 | Hike at Sroumpoulas - Hike at Sroumpoulas |
Wednesday, May 15, 2024
| Time | Event | (+) |
| 09:00 - 10:00 | Keynote: Inference of Coalescence Times and Variant Ages Using Convolutional Neural Networks - Pier Palamara | |
| 10:00 - 11:00 | Population genetics - Nikolaos Alachiotis | (+) |
| 10:00 - 10:30 | › Using supervised machine learning methods to infer demographic history from genomic data - Arnaud Quelin, Éco-Anthropologie, Laboratoire Interdisciplinaire des Sciences du Numérique | |
| 10:30 - 11:00 | › Unifying Ideas from the Sequentially Markovian Coalescence with Deep Learning for Population Genomic Inference - Kevin Korfmann, Technische Universität München = Technical University of Munich | |
| 11:00 - 11:30 | Coffee break | |
| 11:30 - 13:00 | Detecting positive selection - Flora Jay | (+) |
| 11:30 - 12:00 | › Scalable CNN-based classification of selective sweeps using derived allele frequencies - Sjoerd Van den Belt, University of Twente | |
| 11:30 - 12:00 | › Detecting selective sweeps using FPGA-accelerated spiking convolutional neural networks - Hanqing Zhao, University of Twente | |
| 12:30 - 13:00 | › Detecting Positive Selection using Convolutional Neural Networks - Charlotte West, European Bioinformatics Institute [Hinxton] | |
| 13:00 - 14:30 | Lunch | |
| 14:30 - 16:00 | Phylodynamics - Flora Jay | (+) |
| 14:30 - 15:00 | › Improving tree representation and neural network architecture for deep learning from phylogenies in phylodynamics and diversification studies - Manolo Perez, Muséum national d'Histoire naturelle, Imperial College London | |
| 15:00 - 15:30 | › Transformers for EpiDemiological DYnamics: from genomic data to epidemiological parameters - Vincent GAROT, Biologie Computationnelle et Quantitative = Laboratory of Computational and Quantitative Biology, Centre interdisciplinaire de recherche en biologie | |
| 15:30 - 16:00 | › Assessing the power of artificial intelligence approaches for birth-death model classification - Pablo Gutiérrez de la Peña, Real Jardín Botánico - CSIC | |
| 16:00 - 16:15 | Closing comments | |
| 16:15 - 18:00 | After conference chill out (posters can still hang until 18h) | |
| 20:00 - 22:00 | Conference dinner downtown Heraklion |
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