Workshop
ICML 2021 Workshop on Computational Biology
Yubin Xie · Cassandra Burdziak · Amine Remita · Elham Azizi · Abdoulaye Baniré Diallo · Sandhya Prabhakaran · Debora Marks · Dana Pe'er · Wesley Tansey · Julia Vogt · Engelbert MEPHU NGUIFO · Jaan Altosaar · Anshul Kundaje · Sabeur Aridhi · Bishnu Sarker · Wajdi Dhifli · Alexander Anderson
Sat 24 Jul, 5:43 a.m. PDT
The ICML Workshop on Computational Biology will highlight how machine learning approaches can be tailored to making 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 the Workshop 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, to uncover new biology, or to aid in drug discovery.
This workshop aims to bring together interdisciplinary machine learning researchers working at the intersection of machine learning and biology that includes 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.
The workshop is a sequel to the WCB workshops we organized in the last five years at ICML, which had excellent line-ups of talks and were well-received by the community. Every year, we received 60+ submissions. After multiple rounds of rigorous reviewing, around 50 submissions were selected from which the best set of papers were chosen for Contributed talks and Spotlights and the rest were invited for Poster presentations. We have a steadfast and growing base of reviewers making up the Program Committee. For two of the previous editions, a special issue of Journal of Computational Biology has been released with extended versions of a selected set of accepted papers.
Schedule
Sat 5:45 a.m. - 5:50 a.m.
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Opening Remarks
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Opening Remarks
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Sat 5:50 a.m. - 6:25 a.m.
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Invited talk 1 - Lessons from the Pandemic for Machine Learning and Medical Imaging
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Talk
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SlidesLive Video |
Workshop CompBio · Carola-Bibiane Schönlieb · Michael Roberts 🔗 |
Sat 6:25 a.m. - 6:30 a.m.
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Invited Talk 1 Q&A
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Q&A
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Sat 6:30 a.m. - 6:45 a.m.
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Contributed Talk 1 - Multigrate: single-cell multi-omic data integration
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Contributed Talk
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SlidesLive Video |
Workshop CompBio · Mohammad Lotfollahi 🔗 |
Sat 6:45 a.m. - 6:50 a.m.
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Contributed Talk 1 Q&A
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Q&A
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Sat 6:50 a.m. - 6:55 a.m.
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Spotlight Set 1-1 | Statistical correction of input gradients for black box models trained with categorical input features
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Spotlight
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SlidesLive Video |
Workshop CompBio · Antonio Majdandzic 🔗 |
Sat 6:55 a.m. - 7:00 a.m.
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Spotlight Set 1-2 | Opportunities and Challenges in Designing Genomic Sequences
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Spotlight
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SlidesLive Video |
Workshop CompBio · Mengyan Zhang 🔗 |
Sat 7:00 a.m. - 7:05 a.m.
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Spotlight Set 1-3 | pmVAE: Learning Interpretable Single-Cell Representations with Pathway Modules
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Spotlight
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SlidesLive Video |
Workshop CompBio · Stefan Stark 🔗 |
Sat 7:05 a.m. - 7:10 a.m.
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Spotlight Set 1-5 | Deep Contextual Learners for Protein Networks
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Spotlight
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SlidesLive Video |
Workshop CompBio · Michelle Li 🔗 |
Sat 7:10 a.m. - 7:15 a.m.
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Spotlight Set 1-4 | Multimodal data visualization, denoising and clustering with integrated diffusion
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Spotlight
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SlidesLive Video |
Workshop CompBio · MANIK KUCHROO 🔗 |
Sat 7:15 a.m. - 7:30 a.m.
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Break 1
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🔗 |
Sat 7:30 a.m. - 7:31 a.m.
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Introduction for Session 2
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Introduction
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Sat 7:31 a.m. - 7:56 a.m.
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Invited talk 2 - Anomaly detection to find rare phenotypes
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Talk
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SlidesLive Video |
Workshop CompBio · Quaid Morris 🔗 |
Sat 7:56 a.m. - 8:00 a.m.
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Invited Talk 2 Q&A
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Q&A
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Sat 8:00 a.m. - 8:15 a.m.
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Contributed Talk 2 - Light Attention Predicts Protein Location from the Language of Life
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Contributed Talk
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SlidesLive Video |
Workshop CompBio · Hannes Stärk 🔗 |
Sat 8:15 a.m. - 8:20 a.m.
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Contributed Talk 2 Q&A
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Q&A
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Sat 8:20 a.m. - 8:25 a.m.
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Highlight 1 | Representation of Features as Images with Neighborhood Dependencies forCompatibility with Convolutional Neural Networks
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Paper Highlight
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SlidesLive Video |
Workshop CompBio · Omid Bazgir 🔗 |
Sat 8:25 a.m. - 8:30 a.m.
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Highlight 2 | VoroCNN: Deep Convolutional Neural Network Built on 3D Voronoi Tessellation of Protein Structures
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Paper Highlight
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SlidesLive Video |
Workshop CompBio · Ilia Igashov 🔗 |
Sat 8:30 a.m. - 8:35 a.m.
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Highlight 3 | DIVERSE: Bayesian Data IntegratiVE learning for precise drug ResponSE prediction
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Paper Highlight
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SlidesLive Video |
Workshop CompBio · Betul Guvenc Paltun 🔗 |
Sat 8:35 a.m. - 8:40 a.m.
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Highlight 4 | Spherical Convolutions on Molecular Graphs for Protein Model Quality Assessment
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Paper Highlight
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SlidesLive Video |
Workshop CompBio · Nikita Pavlichenko 🔗 |
Sat 8:40 a.m. - 8:45 a.m.
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Highlight 5 | Data-driven Experimental Prioritization via Imputation and Submodular Optimization
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Paper Highlight
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SlidesLive Video |
Workshop CompBio · Jacob Schreiber 🔗 |
Sat 8:45 a.m. - 8:50 a.m.
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Highlight 6 | Data Inequality, Machine Learning and Health Disparity
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Paper Highlight
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SlidesLive Video |
Workshop CompBio · Yan Gao 🔗 |
Sat 8:50 a.m. - 8:55 a.m.
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Highlight 7 | Deep neural networks identify sequence context features predictive of transcription factor binding
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Paper Highlight
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SlidesLive Video |
Workshop CompBio · AN ZHENG 🔗 |
Sat 9:00 a.m. - 10:00 a.m.
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Poster Session 1 and Break ( Poster session and lunch break ) > link | 🔗 |
Sat 10:00 a.m. - 11:00 a.m.
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Poster Session 2 and Break ( Poster session and lunch break ) > link | 🔗 |
Sat 11:00 a.m. - 11:01 a.m.
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Introduction for Session 3
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Introduction
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🔗 |
Sat 11:01 a.m. - 11:26 a.m.
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Invited talk 3 - Every Patient Deserves Their Own Equation
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Talk
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SlidesLive Video |
Workshop CompBio 🔗 |
Sat 11:26 a.m. - 11:30 a.m.
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Invited Talk 3 Q&A
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Q&A
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Sat 11:30 a.m. - 11:45 a.m.
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Contributed Talk 3 - Reconstructing unobserved cellular states from paired single-cell lineage tracing and transcriptomics data
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Contributed Talk
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SlidesLive Video |
Workshop CompBio · Khalil Ouardini 🔗 |
Sat 11:45 a.m. - 11:50 a.m.
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Contributed Talk 3 Q&A
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Q&A
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Sat 11:50 a.m. - 11:55 a.m.
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Spotlight Set 2-1 | Equivariant Graph Neural Networks for 3D Macromolecular Structure
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Spotlight
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SlidesLive Video |
Workshop CompBio · Bowen Jing 🔗 |
Sat 11:55 a.m. - 12:00 p.m.
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Spotlight Set 2-2 | Viral Evolution and Antibody Escape Mutations using Deep Generative Models
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Spotlight
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SlidesLive Video |
Workshop CompBio · Nicole Thadani 🔗 |
Sat 12:00 p.m. - 12:05 p.m.
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Spotlight Set 2-3 | Multi-Scale Representation Learning on Proteins
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Spotlight
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SlidesLive Video |
Workshop CompBio · Charlotte Bunne 🔗 |
Sat 12:05 p.m. - 12:10 p.m.
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Spotlight Set 2-4 | Immuno-mimetic Deep Neural Networks (Immuno-Net)
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Spotlight
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SlidesLive Video |
Workshop CompBio · Ren Wang 🔗 |
Sat 12:10 p.m. - 12:15 p.m.
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Spotlight Set 2-5 | Gene expression evolution across species, organs and sexes in Drosophila
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Spotlight
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SlidesLive Video |
Workshop CompBio · Soumitra Pal 🔗 |
Sat 12:15 p.m. - 1:15 p.m.
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Poster Session 3 and Break ( Poster session and break ) > link | 🔗 |
Sat 1:15 p.m. - 1:16 p.m.
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Introduction for Session 4
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Introduction
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Sat 1:16 p.m. - 1:41 p.m.
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Invited talk 4 - Learning from evolution
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Talk
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SlidesLive Video |
Workshop CompBio · 🔗 |
Sat 1:41 p.m. - 1:45 p.m.
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Invited Talk 4 Q&A
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Q&A
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Sat 1:45 p.m. - 2:00 p.m.
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Contributed Talk 4 - A Bayesian Mutation-Selection Model of Evolutionary Constraints on Coding Sequences
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Contributed Talk
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SlidesLive Video |
Workshop CompBio · Berk Alpay 🔗 |
Sat 2:00 p.m. - 2:05 p.m.
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Contributed Talk 4 Q&A
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Q&A
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🔗 |
Sat 2:05 p.m. - 2:20 p.m.
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Closing Remarks & Awards Ceremony
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Closing Remarks
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SlidesLive Video |
🔗 |
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Immuno-mimetic Deep Neural Networks (Immuno-Net)
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Workshop Poster
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Ren Wang 🔗 |
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Improving confident peptide identifications across mass spectrometry runs by learning deep representations of TIMS-MS1 features
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Workshop Poster
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Soroor Hediyeh-zadeh 🔗 |
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Semi-supervised Deconvolution of Spatial Transcriptomics in Breast Tumors
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Workshop Poster
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xueer chen 🔗 |
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VoroCNN: Deep Convolutional Neural Network Built on 3D Voronoi Tessellation of Protein Structures
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Workshop Poster
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Ilia Igashov 🔗 |
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Epiphany: Predicting the Hi-C Contact Map from 1D Epigenomic Data
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Workshop Poster
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Rui Yang 🔗 |
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MultImp: Multiomics Generative Models for Data Imputation
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Workshop Poster
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Yining Jiao 🔗 |
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Spherical Convolutions on Molecular Graphs for Protein Model Quality Assessment
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Workshop Poster
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Nikita Pavlichenko 🔗 |
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Multigrate: single-cell multi-omic data integration
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Workshop Poster
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Anastasia Litinetskaya 🔗 |
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Deconvolution of the T cell immune response using multi-modal learning
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Workshop Poster
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Felix Drost 🔗 |
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Deep Contextual Learners for Protein Networks
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Workshop Poster
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Michelle Li 🔗 |
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Integrating unpaired scRNA-seq and scATAC-seq with unequal cell type compositions
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Workshop Poster
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Ziqi Zhang 🔗 |
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Fingerprint VAE
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Workshop Poster
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Andrea Karlova · Andrea Karlova 🔗 |
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Identifying systematic variation in gene-gene interactions at the single-cell level by leveraging low-resolution population-level data
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Workshop Poster
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Elior Rahmani 🔗 |
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Distance-Enhanced Graph Neural Network for Link Prediction
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Workshop Poster
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Yingce Xia 🔗 |
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Viral Evolution and Antibody Escape Mutations using Deep Generative Models
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Workshop Poster
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Nicole Thadani 🔗 |
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Statistical correction of input gradients for black box models trained with categorical input features
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Workshop Poster
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Antonio Majdandzic 🔗 |
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Light Attention Predicts Protein Location from the Language of Life
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Workshop Poster
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Hannes Stärk 🔗 |
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Data-driven Experimental Prioritization via Imputation and Submodular Optimization
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Workshop Poster
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Jacob Schreiber 🔗 |
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Opportunities and Challenges in Designing Genomic Sequences
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Workshop Poster
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Mengyan Zhang 🔗 |
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Data Inequality, Machine Learning and Health Disparity
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Workshop Poster
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Yan Gao 🔗 |
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VEGN: variant effect prediction with graph neural network
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Workshop Poster
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Carolin Lawrence 🔗 |
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NeuRL: Closed-form Inverse Reinforcement Learning for Neural Decoding
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Workshop Poster
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Joschka Boedecker 🔗 |
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Prediction of RNA-protein Interactions Using a Nucleotide Language Model
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Workshop Poster
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Keisuke Yamada 🔗 |
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Synthetic COVID-19 Chest X-ray Dataset for Computer-Aided Diagnosis
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Workshop Poster
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Hasib Zunair 🔗 |
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Equivariant Graph Neural Networks for 3D Macromolecular Structure
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Workshop Poster
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Bowen Jing 🔗 |
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Reference-free cell type annotation and phenotype characterisation in single cell RNA sequencing by learning geneset representations
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Workshop Poster
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Soroor Hediyeh-zadeh 🔗 |
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Graph Representation Learning on Tissue-Specific Multi-Omics
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Workshop Poster
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Amine Amor 🔗 |
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Simultaneous Selection of Multiple Important Single Nucleotide Polymorphisms in Familial Genome Wide Association Studies Data
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Workshop Poster
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Subhabrata Majumdar 🔗 |
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Deep neural networks identify sequence context features predictive of transcription factor binding
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Workshop Poster
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AN ZHENG 🔗 |
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Neural message passing for joint paratope-epitope prediction
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Workshop Poster
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Alice Del Vecchio 🔗 |
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Designing Interpretable Convolution-Based Hybrid Networks for Genomics
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Workshop Poster
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Rohan Ghotra 🔗 |
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APObind: A Dataset of Ligand Unbound Protein Conformations for Machine Learning Applications in De Novo Drug Design
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Workshop Poster
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Rishal Aggarwal 🔗 |
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Reconstructing unobserved cellular states from paired single-cell lineage tracing and transcriptomics data
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Workshop Poster
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Khalil Ouardini 🔗 |
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Gene expression evolution across species, organs and sexes in Drosophila
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Workshop Poster
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Soumitra Pal 🔗 |
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Effective Surrogate Models for Protein Design with Bayesian Optimization
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Workshop Poster
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Nate Gruver 🔗 |
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Drug Repurposing using Link Prediction on Knowledge Graphs
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Workshop Poster
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Martin Taraz 🔗 |
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Exploring the latent space of deep generative models: Applications to G-protein coupled receptors
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Workshop Poster
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Lood van Niekerk 🔗 |
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MultiMAP: Dimensionality Reduction and Integration of Multimodal Data
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Workshop Poster
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Mika Jain 🔗 |
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Towards better understanding of developmental disorders from integration of spatial single-cell transcriptomics and epigenomics
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Workshop Poster
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Guojie Zhong 🔗 |
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Representation of Features as Images with Neighborhood Dependencies forCompatibility with Convolutional Neural Networks
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Workshop Poster
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Omid Bazgir 🔗 |
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pmVAE: Learning Interpretable Single-Cell Representations with Pathway Modules
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Workshop Poster
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Stefan Stark 🔗 |
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DynaMorph: self-supervised learning of morphodynamic states of live cells
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Workshop Poster
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Zhenqin Wu 🔗 |
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Graph attribution methods applied to understanding immunogenicity in glycans
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Workshop Poster
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Somesh Mohapatra 🔗 |
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Prot-A-GAN: Automatic Protein Function Annotation using GAN-inspired Knowledge Graph Embedding
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Workshop Poster
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Bishnu Sarker 🔗 |
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Representation learning of genomic sequence motifs via information maximization
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Workshop Poster
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Nicholas Lee 🔗 |
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TCR-epitope binding affinity prediction using multi-head self attention model
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Workshop Poster
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Michael Cai 🔗 |
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Multi-target optimization for drug discovery using generative models
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Workshop Poster
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Anirudh jain 🔗 |
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Multimodal data visualization, denoising and clustering with integrated diffusion
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Workshop Poster
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Abhinav Godavarthi 🔗 |