Workshop
ICML 2022 Workshop on Computational Biology
Cassandra Burdziak · Yubin Xie · Amine Remita · Mauricio Tec · Achille O R Nazaret · Pascal Notin · Mafalda Dias · Steffan Paul · Cameron Park · Dana Pe'er · Debora Marks · Alexander Anderson · Elham Azizi · Abdoulaye Baniré Diallo · Wesley Tansey · Julia Vogt · Sandhya Prabhakaran
Room 310
Fri 22 Jul, 5:30 a.m. PDT
Machine learning advances are used in self-driving cars, speech recognition systems, and translation software. However, the COVID-19 pandemic has highlighted the urgency of translating such advances to the domain of biomedicine. Such a pivot requires new machine learning methods to build long-term vaccines and therapeutic strategies, predict immune avoidance, and better repurpose small molecules as drugs.The ICML Workshop on Computational Biology (WCB) will highlight how machine learning approaches can be tailored to making both translational and basic scientific discoveries with biological data. Practitioners at the intersection of computation, machine learning, and biology are in a unique position to frame problems in biomedicine, from drug discovery to vaccination risk scores, and WCB will showcase such recent research. Commodity lab techniques lead to the proliferation of large complex datasets and require new methods to interpret these collections of high-dimensional biological data, such as genetic sequences, cellular features or protein structures and imaging datasets. These data can be used to make new predictions towards clinical response, uncover new biology, or aid in drug discovery.This workshop aims to bring together interdisciplinary machine learning researchers working in areas such as computational genomics; neuroscience; metabolomics; proteomics; bioinformatics; cheminformatics; pathology; radiology; evolutionary biology; population genomics; phenomics; ecology, cancer biology; causality; representation learning and disentanglement to present recent advances and open questions to the machine learning community. We especially encourage interdisciplinary submissions that might not neatly fit into one of these categories.
Schedule
Fri 5:30 a.m. - 5:40 a.m.
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Opening remarks
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Talk
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SlidesLive Video |
Cassandra Burdziak 🔗 |
Fri 5:40 a.m. - 6:10 a.m.
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Predicting and maximizing genomic variant discovery via Bayesian nonparametrics
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Invited Talk
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SlidesLive Video |
🔗 |
Fri 6:10 a.m. - 6:20 a.m.
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Predicting and maximizing genomic variant discovery via Bayesian nonparametrics
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Q&A
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🔗 |
Fri 6:20 a.m. - 6:40 a.m.
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Generative power of a protein language model trained on multiple sequence alignments
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Contributed Talk
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SlidesLive Video |
Damiano Sgarbossa 🔗 |
Fri 6:40 a.m. - 6:45 a.m.
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Generative power of a protein language model trained on multiple sequence alignments
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Q&A
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Damiano Sgarbossa 🔗 |
Fri 6:45 a.m. - 6:50 a.m.
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RITA: a Study on Scaling Up Generative Protein Sequence Models
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Spotlight
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SlidesLive Video |
Daniel Hesslow 🔗 |
Fri 6:50 a.m. - 6:55 a.m.
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Learning Batch-Invariant Representations with Domain Adaptation in Large Scale Proteomics Data
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Spotlight
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SlidesLive Video |
Amir Alavi 🔗 |
Fri 6:55 a.m. - 7:00 a.m.
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COEM: Cross-Modal Embedding for MetaCell Identification
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Spotlight
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SlidesLive Video |
Haiyi Mao · Minxue Jia 🔗 |
Fri 7:00 a.m. - 7:30 a.m.
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Break
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🔗 |
Fri 7:30 a.m. - 8:00 a.m.
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Towards a Common Coordinate Framework: Alignment of Spatially Resolved Omics Data
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Invited Talk
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SlidesLive Video |
Jean Fan 🔗 |
Fri 8:00 a.m. - 8:10 a.m.
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Towards a Common Coordinate Framework: Alignment of Spatially Resolved Omics Data
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Q&A
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Jean Fan 🔗 |
Fri 8:10 a.m. - 8:30 a.m.
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BayesTME: A reference-free Bayesian method for end-to-end analysis of spatial transcriptomic data
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Contributed Talk
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SlidesLive Video |
Haoran Zhang 🔗 |
Fri 8:30 a.m. - 8:35 a.m.
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BayesTME: A reference-free Bayesian method for end-to-end analysis of spatial transcriptomic data
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Q&A
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Haoran Zhang 🔗 |
Fri 8:35 a.m. - 8:40 a.m.
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EquiBind: Geometric Deep Learning for Drug Binding Structure Prediction
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Spotlight
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SlidesLive Video |
Hannes Stärk 🔗 |
Fri 8:40 a.m. - 8:45 a.m.
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Learning to rank metabolites across datasets
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Spotlight
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SlidesLive Video |
Sophie Jaro 🔗 |
Fri 8:45 a.m. - 8:50 a.m.
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7-UP: generating in silico CODEX from a small set of immunofluorescence markers
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Spotlight
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SlidesLive Video |
James Zou 🔗 |
Fri 8:50 a.m. - 8:55 a.m.
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RTfold: RNA secondary structure prediction using deep learning with domain inductive bias
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Spotlight
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SlidesLive Video |
Jongho Jung 🔗 |
Fri 8:55 a.m. - 9:00 a.m.
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A Deep Learning Framework for Estimating Cell-specific Kinetic Rates of RNA Velocity
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Spotlight
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SlidesLive Video |
Haotian Cui 🔗 |
Fri 9:00 a.m. - 10:30 a.m.
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Poster session #1 / Lunch break
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Poster Session
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🔗 |
Fri 10:30 a.m. - 11:20 a.m.
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Panel: ML for drug discovery
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Panel Discussion
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SlidesLive Video |
Mohammed AlQuraishi · Elana Fertig · Patrick Schwab · Neeha Zaidi · Pascal Notin 🔗 |
Fri 11:20 a.m. - 11:25 a.m.
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Probabilistic basis decomposition for characterizing temporal dynamics of gene expression
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Spotlight
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SlidesLive Video |
Achille Nazaret 🔗 |
Fri 11:25 a.m. - 11:30 a.m.
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SNVformer: An Attention-based Deep Neural Network for GWAS Data
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Spotlight
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SlidesLive Video |
Kieran Elmes 🔗 |
Fri 11:30 a.m. - 11:35 a.m.
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Extracting Part of Signal Representation from Direct RNA Squiggle for Modification Detection
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Spotlight
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SlidesLive Video |
Christopher Hendra 🔗 |
Fri 11:35 a.m. - 11:40 a.m.
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A mechanistic probabilistic model of genomic compartments
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Spotlight
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SlidesLive Video |
Hagai Kariti 🔗 |
Fri 11:40 a.m. - 11:45 a.m.
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TCR-BERT: learning the grammar of T-cell receptors for flexible antigen-binding analyses
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Spotlight
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SlidesLive Video |
Kevin Wu 🔗 |
Fri 11:45 a.m. - 11:50 a.m.
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Interpretable RNA Foundation Model from Unannotated Data for Highly Accurate RNA Structure and Function Predictions
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Spotlight
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SlidesLive Video |
Yu Li 🔗 |
Fri 11:50 a.m. - 11:55 a.m.
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Assessing the utility of genomic deep learning models for disease-relevant variant effect prediction
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Spotlight
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SlidesLive Video |
Pooja Kathail 🔗 |
Fri 11:55 a.m. - 12:00 p.m.
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Molecular Fingerprints Are a Simple Yet Effective Solution to the Drug–Drug Interaction Problem
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Spotlight
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SlidesLive Video |
Yanan Long 🔗 |
Fri 12:00 p.m. - 1:30 p.m.
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Poster session #2 / Break
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Poster Session
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🔗 |
Fri 1:30 p.m. - 1:50 p.m.
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DIISCO: Dynamic Intercellular Interactions in Single Cell transcriptOmics
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Talk
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SlidesLive Video |
Cameron Park 🔗 |
Fri 1:50 p.m. - 1:55 p.m.
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DIISCO: Dynamic Intercellular Interactions in Single Cell transcriptOmics
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Q&A
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Cameron Park 🔗 |
Fri 1:55 p.m. - 2:15 p.m.
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SPACE-GM: geometric deep learning of disease-associated microenvironments from multiplex spatial protein profiles.
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Contributed Talk
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SlidesLive Video |
Zhenqin Wu 🔗 |
Fri 2:15 p.m. - 2:20 p.m.
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SPACE-GM: geometric deep learning of disease-associated microenvironments from multiplex spatial protein profiles
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Q&A
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Zhenqin Wu 🔗 |
Fri 2:20 p.m. - 2:30 p.m.
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Concluding remarks
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Talk
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SlidesLive Video |
🔗 |