Please note all times are listed as Pacific Standard Time.

Monday November 23

8:30-8:35 PST: Introduction

8:35-9:20: Keynote: Aviv Regev. "Design for Inference for Tissue Biology"

9:20-9:40: Oral 1: Convolutional Additive Models: a full interpretable approach to deep learning in genomics (Gherman E Novakovsky* ; Manu Saraswat*; Etienne Meunier ; Oriol Fornes; Sara Mostafavi; Wyeth Wasserman)

9:40-10:00: Oral 2: Benchmarking Reverse-Complement Strategies for Deep Learning Models in Genomics (Hannah Zhou; Avanti Shrikumar*; Anshul Kundaje)

10:00-10:20: Oral 3: Detecting higher-order structural changes in 3D genome organization with multi-task matrix factorization (Da-Inn Lee; Sushmita Roy)

10:20-10:40: Coffee Break

10:40-11:00: Oral 4: Variational Combinatorial Sequential Monte Carlo for Bayesian Phylogenetic Inference (Antonio K Moretti ; Liyi Zhang; Itsik Pe'er)

11:00-11:20: Oral 5: JIND: Joint Integration and Discrimination for Automated Single-Cell Annotation (Mohit Goyal; Guillermo Serrano; Ilan Shomorony; Mikel Hernaez; Idoia Ochoa)

11:20 - 11:40: Oral 6: Gromov-Wasserstein to align single-cell multi-omics data (Pinar Demetci; Rebecca Santorella; Bjorn Sandstede; William Stafford Noble; Ritambhara Singh)

11:40 - 12:00: Oral 7: Transformer protein language models are unsupervised structure learners (Roshan M Rao; Joshua Meier; Tom Sercu; Sergey Ovchinnikov; Alexander Rives)

12:00-12:40: Lunch Break

12:40-1:10: Spotlight presentations (9 orals, 3 min each; see here)

1:10-3:00: Poster session/social using gather.town (poster list)

Tuesday November 24

8:30-8:35 PST: Introduction

8:35-9:20: Keynote: Eran Segal. "Personalised medicine based on gut microbiome and clinical data"

9:20-9:40: Oral 8: Molecular Matchmaker: selecting binding peptide-aptamer pairs using machine learning (Aishwarya Mandyam; Yuhao Wan; Jeff Nivala ; Kevin Jamieson)

9:40-10:00: Oral 9: fastISM: Performant in-silico saturation mutagenesis for convolutional neural networks (Surag Nair; Avanti Shrikumar; Anshul Kundaje)

10:00-10:20: Oral 10: Drug Repurposing Efficacy Estimation based on Morphological Analysis of SARS-CoV-2 Infected Cells within a Multiple Instance Learning Framework (Mohammadsadegh Saberian; Kathleen P. Moriarty; Max Libbrecht; Ghassan Hamarneh)

10:20-10:40: Coffee Break

10:40-11:00: Oral 11: Neural Potts Model (Tom Sercu*, Robert Verkuil*, Joshua Meier, Brandon Amos, Zeming Lin, Caroline Chen, Jason Liu, Yann LeCun, Alexander Rives)

11:00-11:20: Oral 12: SplitStrains, a tool to identify and separate mixed Mycobacterium tuberculosis infections from WGS data (Einar Gabbassov, Miguel Moreno-Molina, Inaki Comas, Maxwell Libbrecht, Leonid Chindelevitch)

11:20 - 11:40: Oral 13: AMBIENT: Accelerated Convolutional Neural Network Architecture Search for Regulatory Genomics (Evan Cofer; Zijun Zhang; Olga Troyanskaya)

11:40 - 12:00: Oral 14: Causal Network Models of SARS-CoV-2 Expression and Aging Identify Candidates for Drug Repurposing (Anastasiya Belyaeva; Louis V Cammarata; Adityanarayanan Radhakrishnan; Chandler Squires; Karren D Yang ; G. V. Shivashankar; Caroline Uhler)

12:00-12:30: Lunch Break

12:30-1:30: Panel Discussion. ML for proteins, molecules and drug discovery. Panel members: Richard Bonneau, Mohamed AlQuarishi, and Lucy Colwell.

1:30-2:15: Keynote: Marinka Zitnik. "Graph Neural Networks for Biomedical Data"

2:20-2:30: Closing remarks