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Day 1September 5
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9:00-9:50Keynote 1: Jian Zhou - Sequence basis of transcription initiation in the human genome
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9:50-10:10Oral 1: The Nucleotide Transformer: building and evaluating robust foundation models for genomicsBernardo Almeida (InstaDeep)*; Guillaume Richard (InstaDeep); Hugo Dalla-Torre (InstaDeep); Javier Mendoza-Revilla (InstaDeep); Marie Lopez (InstaDeep); Alexandre Laterre (InstaDeep); Karim Beguir (InstaDeep); Thomas Pierrot (InstaDeep)
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10:10-10:40Coffee break
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10:40-11:00Oral 2: DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNAAman Patel (Stanford University)*; Arpita Singhal (Stanford University); Austin T Wang (Stanford University); Anusri Pampari (Stanford University); Maya Kasowski (Stanford University); Anshul Kundaje (Stanford University)
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11:00-11:20Oral 3: Designing DNA With Tunable Regulatory Activity Using Discrete DiffusionSarkar, Anirban*; Tang, Ziqi; Zhao, Chris; Koo, Peter K.
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11:20-11:40Oral 4: gReLU: A Comprehensive Python Framework for DNA Sequence Modeling and DesignAvantika Lal (Genentech)*; Laura Gunsalus (Genentech); Surag Nair (Genentech); Tommaso Biancalani (Genentech); Gokcen Eraslan (Genentech)
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11:40-12:00Oral 5: A deep learning model of tumor cell architecture elucidates response and resistance to CDK4/6 inhibitorsSungjoon Park (University of California, San Diego); Erica Silva (University of California, San Diego); Akshat Singhal (University of California, San Diego)*; Trey Ideker (University of California, San Diego)
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12:00-1:00Lunch
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1:00-1:30Spotlights 1
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1:30-2:20
Keynote 2: Sergey Ovchinnikov - Decomposing protein and genomic language models to understand what they are learning
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2:20-2:40Oral 6: Computational design of target-specific linear peptide binders with TransformerBeta (remote via Zoom)Haowen Zhao (University of Cambridge)*; Barbara Bravi (Imperial College London); Francesco Aprile (Imperial College London)
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2:40-3:00Oral 7: Predicting cell cycle stage from 3D single-cell nuclear-stained imagesGang Li (University of Washington)*; Valentino E. Browning (University of Washington); Nicolas J. Longhi (University of Washington); Eva K. Nichols (University of Washington); Brian J. Beliveau (University of Washington); William S Noble (University of Washington)
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3:00-3:15Coffee break
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3:15-4:00Panel: foundation models for biology; when is it useful or not useful?Panelist: Maria Chikina, Anshul Kundaje, Su-In Lee, Jian Zhou, Sergey Ovchinnikov. Moderator: James Zou
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4:00-4:30Spotlights 2
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4:45-6:30Posters: List of posters is here
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Day2September 6
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8:30-9:20Keynote 3: Nilah Ioannidis - Personal genome interpretation with sequence-to-function models
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9:20-9:40Oral 8: Regulatory sequence analysis of RNA-seq via parameter-efficient fine tuning a multi-task sequence modelRegulatory sequence analysis of RNA-seq via parameter-efficient fine tuning a multi-task sequence model
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9:40-10:00Oral 9: Decima: Decoding sequence determinants of gene expression in diverse cellular and disease statesAvantika Lal (Genentech); Alex M Tseng (Genentech); Surag Nair (Genentech); Nathaniel Diamant (Genentech); Tommaso Biancalani (Genentech); Gabriele Scalia (Genentech); Gokcen Eraslan (Genentech)*
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10:00-10:20Oral 10: Fine-tuning on Personal Genomes Improves Expression Prediction Deep Learning ModelsShiron Drusinsky (Gladstone Institutes)*; Katherine Pollard (Gladstone Institutes); Sean Whalen (Gladstone Institutes)
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10:20-10:50Coffee break
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10:50-11:40Keynote 4: Maria Chikina - Towards biophysically interpretable sequence to function models
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11:40-12:00Oral 11: SLIDE: Significant Latent Factor Interaction Discovery and Exploration across biological domainsRahimikollu, Javad; Xiao, Hanxi; Rosengart, AnnaElaine; Rosen, Aaron; Tabib, Tracy; Zdinak, Paul; He, Kun; Bing, Xin; Bunea, Florentina; Wegkamp, Marten; Poholek, Amanda; Joglekar, Alok; Lafyatis, Robert; Das, Jishnu*
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12:00-1:00Lunch
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1:00-1:20Oral 12: IsoCLR: Contrastive learning for RNA foundation modelsPhilip Fradkin (Vector Institute)*; Ruian Shi (University of Toronto and Vector Institute); Keren Isaev (Columbia University ); Quaid Morris (Memorial Sloan Kettering Cancer Center, Vector Institute, University of Toronto); Bo Wang (Vector Institute); Brendan Frey (U. Toronto); Leo J Lee (University of Toronto)
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1:20-1:40Oral 13: RNA-FrameFlow: Flow Matching for de novo 3D RNA Backbone Design (remote via Zoom)
Rishabh Anand (National University of Singapore)*; Chaitanya K Joshi (University of Cambridge); Alex Morehead (University of Missouri-Columbia); Arian Jamasb (Prescient Design, Genentech, Roche); Charles Harris (University of Cambridge); Simon V Mathis (University of Cambridge); Kieran Didi (University of Cambridge); Bryan Hooi (National University of Singapore); Pietro Lió (University of Cambridge)
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1:40-2:00Oral 14: Approximating mutual information of high-dimensional variables using learned representationsGokul Gowri (Harvard University)*; Xiao-Kang Lun (Harvard University); Allon Klein (Harvard University); Peng Yin (Harvard University)
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2:00-2:30Coffee break
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2:30-3:20Keynote 5: Ava Amini - Bridging biophysics & AI for generative protein design
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3:20-3:40
Oral 15: Cross-modality Matching and Prediction of Perturbation Responses with Labeled Gromov-Wasserstein Optimal Transport
Jayoung Ryu (Harvard University)*; Charlotte Bunne (Genentech); Luca Pinello (Massachusetts General Hospital); Aviv Regev (Genentech); Romain Lopez (Genentech)
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3:40-4:00Oral 16: Multi-marginal Schrödinger Bridges with Iterative Reference RefinementYunyi Shen (MIT)*; Renato Berlinghieri (MIT); Tamara Broderick (MIT)
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4:00-4:20Oral 17: RegDiffusion: Fast Gene Regulatory Networks using Diffusion Probabilistic ModelHao Zhu (Tufts University)*; Donna Slonim (Tufts University)
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