Workshop
Generative AI and Biology (GenBio@NeurIPS2023)
Minkai Xu · Regina Barzilay · Jure Leskovec · Wenxian Shi · Menghua Wu · Zhenqiao Song · Lei Li · Fan Yang · Stefano Ermon
Room 265 - 268
Sat 16 Dec, 6:15 a.m. PST
Advancing biological discovery, therapeutic design, and pharma development through generative AI.
Chat is not available.
Timezone: America/Los_Angeles
Schedule
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Sat 6:15 a.m. - 6:30 a.m.
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Opening Remarks
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Opening Remarks
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SlidesLive Video |
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Sat 6:30 a.m. - 6:50 a.m.
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Geometric deep learning for protein understanding
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Invited talk
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link
SlidesLive Video |
Jian Tang 🔗 |
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Sat 6:50 a.m. - 7:10 a.m.
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Invited talk | Ellen Zhong
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Invited talk
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link
SlidesLive Video |
Ellen Zhong 🔗 |
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Sat 7:10 a.m. - 7:30 a.m.
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Invited talk | Ron Dror
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Invited talk
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link
SlidesLive Video |
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Sat 7:30 a.m. - 7:40 a.m.
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Contributed talk | The Discovery of Binding Modes Requires Rethinking Docking Generalization
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Spotlight
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link
SlidesLive Video |
Gabriele Corso · Arthur Deng · Nicholas Polizzi · Regina Barzilay · Tommi Jaakkola 🔗 |
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Sat 7:40 a.m. - 7:50 a.m.
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Contributed talk | Exploring the building blocks of cell organization as high-order network motifs with graph isomorphism network
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Spotlight
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link
SlidesLive Video |
Yang Yu · Shuang Wang · Dong Xu · Juexin Wang 🔗 |
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Sat 7:50 a.m. - 8:00 a.m.
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Contributed talk | CodonBERT: Large Language Models for mRNA design and optimization
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Spotlight
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link
SlidesLive Video |
24 presentersSizhen Li · Saeed Moayedpour · Ruijiang Li · Michael Bailey · Saleh Riahi · Milad Miladi · Jacob Miner · Dinghai Zheng · Jun Wang · Akshay Balsubramani · Khang Tran · Minnie · Monica Wu · Xiaobo Gu · Ryan Clinton · Carla Asquith · Joseph Skaleski · Lianne Boeglin · Sudha Chivukula · Anusha Dias · Fernando Ulloa Montoya · Vikram Agarwal · Ziv Bar-Joseph · Sven Jager |
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Sat 8:00 a.m. - 8:30 a.m.
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Break
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Sat 8:30 a.m. - 9:30 a.m.
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Panel discussion
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Panel discussion: AI and biology in industry
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SlidesLive Video |
Max Welling · Kyunghyun Cho · Evan Feinberg · SONG LE 🔗 |
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Sat 9:30 a.m. - 11:30 a.m.
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Poster session 1
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Poster session 1
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Sat 11:30 a.m. - 11:50 a.m.
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Invited talk | Debora Marks
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Invited talk
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link
SlidesLive Video |
Debora Marks 🔗 |
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Sat 11:50 a.m. - 12:10 p.m.
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Invited talk | Shuiwang Ji
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Invited talk
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link
SlidesLive Video |
Shuiwang Ji 🔗 |
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Sat 12:10 p.m. - 12:30 p.m.
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Invited talk | Anima Anandkumar
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Invited talk
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link
SlidesLive Video |
Anima Anandkumar 🔗 |
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Sat 12:30 p.m. - 12:50 p.m.
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Neural ODEs and Flows to generate cell fate and regulatory network rewiring
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Invited talk
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>
link
SlidesLive Video |
Smita Krishnaswamy 🔗 |
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Sat 12:50 p.m. - 1:00 p.m.
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Contributed talk | AntiFold: Improved antibody structure design using inverse folding
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Spotlight
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link
SlidesLive Video |
Magnus H Høie · Alissa M Hummer · Tobias Olsen · Morten Nielsen · Charlotte Deane 🔗 |
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Sat 1:00 p.m. - 1:30 p.m.
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Break
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Sat 1:30 p.m. - 1:40 p.m.
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Contributed talk | Binding Oracle: Fine-Tuning From Stability to Binding Free Energy
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Spotlight
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link
SlidesLive Video |
Chengyue Gong · Adam Klivans · Jordan Wells · James Loy · Qiang Liu · Alex Dimakis · Daniel Diaz 🔗 |
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Sat 1:40 p.m. - 1:50 p.m.
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Contributed talk | Protein Discovery with Discrete Walk-Jump Sampling
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Spotlight
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SlidesLive Video |
12 presentersNathan Frey · Dan Berenberg · Karina Zadorozhny · Joseph Kleinhenz · Julien Lafrance-Vanasse · Isidro Hotzel · Yan Wu · Stephen Ra · Richard Bonneau · Kyunghyun Cho · Vladimir Gligorijevic · Saeed Saremi |
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Sat 1:50 p.m. - 2:00 p.m.
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Contributed talk | Amalga: Designable Protein Backbone Generation with Folding and Inverse Folding Guidance
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Spotlight
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link
SlidesLive Video |
Shugao Chen · Ziyao Li · xiangxiang Zeng · Guolin Ke 🔗 |
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Sat 2:00 p.m. - 2:15 p.m.
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Closing Remarks
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Closing Remarks
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SlidesLive Video |
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Sat 2:15 p.m. - 3:30 p.m.
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Poster session 2
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Poster session 2
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AlphaFold Meets Flow Matching for Generating Protein Ensembles ( Poster ) > link | Bowen Jing · Bonnie Berger · Tommi Jaakkola 🔗 |
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AlphaFold Meets Flow Matching for Generating Protein Ensembles ( Spotlight ) > link | Bowen Jing · Bonnie Berger · Tommi Jaakkola 🔗 |
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Protein Discovery with Discrete Walk-Jump Sampling ( Poster ) > link |
12 presentersNathan Frey · Dan Berenberg · Karina Zadorozhny · Joseph Kleinhenz · Julien Lafrance-Vanasse · Isidro Hotzel · Yan Wu · Stephen Ra · Richard Bonneau · Kyunghyun Cho · Vladimir Gligorijevic · Saeed Saremi |
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SecretoGen: towards prediction of signal peptides for efficient protein secretion ( Poster ) > link | Felix Teufel · Carsten Stahlhut · Jan Refsgaard · Henrik Nielsen · Ole Winther · Dennis Madsen 🔗 |
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ProteinRL: Reinforcement learning with generative protein language models for property-directed sequence design ( Poster ) > link | Matt Sternke · Joel Karpiak 🔗 |
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Protein generation with evolutionary diffusion ( Poster ) > link | Sarah Alamdari · Nitya Thakkar · Rianne van den Berg · Alex X Lu · Nicolo Fusi · Ava Amini · Kevin Yang 🔗 |
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$\textit{In vitro}$ validated antibody design against multiple therapeutic antigens using generative inverse folding ( Poster ) > link | Amir Shanehsazzadeh 🔗 |
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Unexplored regions of the protein sequence-structure map revealed at scale by a library of “foldtuned” language models ( Poster ) > link | Arjuna Subramanian · Matt Thomson 🔗 |
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Targeting tissues via dynamic human systems modeling in generative design ( Poster ) > link | Zachary Fox · Nolan English · Belinda S Akpa 🔗 |
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Transition Path Sampling with Boltzmann Generator-based MCMC Moves ( Poster ) > link | Michael Plainer · Hannes Stärk · Charlotte Bunne · Stephan Günnemann 🔗 |
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Transition Path Sampling with Boltzmann Generator-based MCMC Moves ( Spotlight ) > link | Michael Plainer · Hannes Stärk · Charlotte Bunne · Stephan Günnemann 🔗 |
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Causal Inference in Gene Regulatory Networks with GFlowNet: Towards Scalability in Large Systems ( Poster ) > link | Trang Nguyen · Alexander Tong · Kanika Madan · Yoshua Bengio · Dianbo Liu 🔗 |
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Masked autoencoders are scalable learners of cellular morphology ( Poster ) > link |
16 presentersOren Kraus · Kian Kenyon-Dean · Saber Saberian · Maryam Fallah · Peter McLean · Jess Leung · Vasudev Sharma · Ayla Khan · Jia Balakrishnan · Safiye Celik · Maciej Sypetkowski · Chi Cheng · Kristen Morse · Maureen Makes · Ben Mabey · Berton Earnshaw |
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Masked autoencoders are scalable learners of cellular morphology ( Spotlight ) > link |
16 presentersOren Kraus · Kian Kenyon-Dean · Saber Saberian · Maryam Fallah · Peter McLean · Jess Leung · Vasudev Sharma · Ayla Khan · Jia Balakrishnan · Safiye Celik · Maciej Sypetkowski · Chi Cheng · Kristen Morse · Maureen Makes · Ben Mabey · Berton Earnshaw |
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DSMBind: an unsupervised generative modeling framework for binding energy prediction ( Poster ) > link | Wengong Jin · Caroline Uhler · Nir HaCohen 🔗 |
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Analysis of cellular phenotypes with image-based generative models ( Poster ) > link | Ruben Fonnegra · Mohammad Vali Sanian · Zitong Sam Chen · Lassi Paavolainen · Juan C. Caicedo 🔗 |
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Analysis of cellular phenotypes with image-based generative models ( Spotlight ) > link | Ruben Fonnegra · Mohammad Vali Sanian · Zitong Sam Chen · Lassi Paavolainen · Juan C. Caicedo 🔗 |
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Delta Score: Improving the Binding Assessment of Structure-Based Drug Design Methods ( Poster ) > link | Minsi Ren · Bowen Gao · Bo Qiang · Yanyan Lan 🔗 |
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On Complex Network Dynamics of an In-Vitro Neuronal System during Rest and Gameplay ( Poster ) > link | Moein Khajehnejad · Forough Habibollahi · Alon Loeffler · Brett J. Kagan · Adeel Razi 🔗 |
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Contextualized Networks Reveal Heterogeneous Transcriptomic Regulation in Tumors at Sample-Specific Resolution ( Poster ) > link | Caleb Ellington · Ben Lengerich · Thomas Watkins · Jiekun Yang · Hanxi Xiao · Manolis Kellis · Eric Xing 🔗 |
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Target Conditioned GFlowNet for Drug Design ( Poster ) > link | Tony Shen · Mohit Pandey · Martin Ester 🔗 |
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Target Conditioned GFlowNet for Drug Design ( Spotlight ) > link | Tony Shen · Mohit Pandey · Martin Ester 🔗 |
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Microenvironment Flows as Protein Engineers ( Poster ) > link | Chengyue Gong · Lemeng Wu · Daniel Diaz · Xingchao Liu · James Loy · Adam Klivans · Qiang Liu 🔗 |
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AntiFold: Improved antibody structure design using inverse folding ( Poster ) > link | Magnus H Høie · Alissa M Hummer · Tobias Olsen · Morten Nielsen · Charlotte Deane 🔗 |
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DynamicBind: Predicting ligand-specific protein-ligand complex structure with a deep equivariant generative model ( Poster ) > link | Wei Lu · Jixian Zhang · Huang Weifeng · Ziqiao Zhang · Chengtao Li · Shuangjia Zheng 🔗 |
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Guiding diffusion models for antibody sequence and structure co-design with developability properties ( Poster ) > link | Amelia Villegas-Morcillo · Jana M. Weber · Marcel Reinders 🔗 |
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Improving few-shot learning-based protein engineering with evolutionary sampling ( Poster ) > link | Muhammad Zaki Jawaid · Aayushma Gautam · T. Gainous · Dan Hart · Robin Yeo · Timothy Daley 🔗 |
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Protein Inpainting Co-Design with ProtFill ( Poster ) > link | Elizaveta Kozlova · Arthur Valentin · Daniel Nakhaee-Zadeh Gutierrez 🔗 |
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Accelerating Inference in Molecular Diffusion Models with Latent Representations of Protein Structure ( Poster ) > link | Ian Dunn · David Koes 🔗 |
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Accelerating Inference in Molecular Diffusion Models with Latent Representations of Protein Structure ( Spotlight ) > link | Ian Dunn · David Koes 🔗 |
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Evaluating Zero-Shot Scoring for In Vitro Antibody Binding Prediction with Experimental Validation ( Poster ) > link | Divya Nori · Simon Mathis · Amir Shanehsazzadeh 🔗 |
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Evaluating Zero-Shot Scoring for In Vitro Antibody Binding Prediction with Experimental Validation ( Spotlight ) > link | Divya Nori · Simon Mathis · Amir Shanehsazzadeh 🔗 |
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Fine-tuned protein language models capture T cell receptor stochasticity ( Poster ) > link | Lewis Cornwall · Grisha Szep · James Day · S R Gokul Krishnan · David Carter · Jamie Blundell · Lilly Wollman · Neil Dalchau · Aaron Sim 🔗 |
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Harmonic Prior Self-conditioned Flow Matching for Multi-Ligand Docking and Binding Site Design ( Poster ) > link | Hannes Stärk · Bowen Jing · Regina Barzilay · Tommi Jaakkola 🔗 |
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Exploring the building blocks of cell organization as high-order network motifs with graph isomorphism network ( Poster ) > link | Yang Yu · Shuang Wang · Dong Xu · Juexin Wang 🔗 |
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Conditional Generation of Antigen Specific T-cell Receptor Sequences ( Poster ) > link | Dhuvarakesh Karthikeyan · Colin Raffel · Benjamin Vincent · Alex Rubinsteyn 🔗 |
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Enhancing Language Models for Technical Domains with Dynamic Token Injection ( Poster ) > link | Giorgio Giannone · Neil Tenenholtz · James B Hall · Nicolo Fusi · David Alvarez-Melis 🔗 |
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Scalable Multimer Structure Prediction using Diffusion Models ( Poster ) > link | Peter Pao-Huang · Bowen Jing · Bonnie Berger 🔗 |
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Generative Antibody Design for Complementary Chain Pairing Sequences through Encoder-Decoder Language Model ( Poster ) > link | Kit Sang Chu · Kathy Wei 🔗 |
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Generative design for gene therapy: An $\textit{in vivo}$ validated method ( Poster ) > link | Farhan Damani · David Brookes · Jeffrey Chan · Rishi Jajoo · Alexander Mijalis · Joyce Samson · Flaviu Vadan · Cameron Webster · Stephen Malina · Sam Sinai 🔗 |
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Bending and Binding: Predicting Protein Flexibility upon Ligand Interaction using Diffusion Models ( Poster ) > link | Xuejin Zhang · Tomas Geffner · Matt McPartlon · Mehmet Akdel · Dylan Abramson · Graham Holt · Alexander Goncearenco · Luca Naef · Michael Bronstein 🔗 |
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Generating Molecular Conformer Fields ( Poster ) > link | Yuyang Wang · Ahmed Elhag · Navdeep Jaitly · Joshua Susskind · Miguel Angel Bautista 🔗 |
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PoseCheck: Generative Models for 3D Structure-based Drug Design Produce Unrealistic Poses ( Poster ) > link | Charles Harris · Kieran Didi · Arian Jamasb · Chaitanya K. Joshi · Simon Mathis · Pietro Lió · Tom Blundell 🔗 |
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A deep generative model of single-cell methylomic data ( Poster ) > link | Ethan Weinberger · Su-In Lee 🔗 |
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Shape-conditioned 3D Molecule Generation via Equivariant Diffusion Models ( Poster ) > link | Ziqi Chen · Bo Peng · Srinivasan Parthasarathy · Xia Ning 🔗 |
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Sampling Protein Language Models for Functional Protein Design ( Poster ) > link | Jeremie Theddy Darmawan · Yarin Gal · Pascal Notin 🔗 |
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Parameter-Efficient Fine-Tune on Open Pre-trained Transformers for Genomic Sequence ( Poster ) > link | Huixin Zhan · Zijun Frank Zhang 🔗 |
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Approximation of Intractable Likelihood Functions in Systems Biology via Normalizing Flows ( Poster ) > link | Vincent Zaballa · Elliot Hui 🔗 |
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The Discovery of Binding Modes Requires Rethinking Docking Generalization ( Poster ) > link | Gabriele Corso · Arthur Deng · Nicholas Polizzi · Regina Barzilay · Tommi Jaakkola 🔗 |
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regLM: Designing realistic regulatory DNA with autoregressive language models ( Poster ) > link | Avantika Lal · Tommaso Biancalani · Gokcen Eraslan 🔗 |
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Epitope-specific antibody design using diffusion models on the latent space of ESM embeddings ( Poster ) > link | Tomer Cohen · Dina Schneidman 🔗 |
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An Energy Based Model for Incorporating Sequence Priors for Target-Specific Antibody Design ( Poster ) > link | Steffanie Paul · Yining Huang · Debora Marks 🔗 |
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Preference Optimization for Molecular Language Models ( Poster ) > link | Ryan Park · Ryan Theisen · Rayees Rahman · Anna Cichonska · Marcel Patek · Navriti Sahni 🔗 |
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Genomic language model predicts protein co-regulation and function ( Poster ) > link | Yunha Hwang · Andre Cornman · Sergey Ovchinnikov · Peter Girguis 🔗 |
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Fine-tuning protein Language Models by ranking protein fitness ( Poster ) > link | Minji Lee · Kyungmin Lee · Jinwoo Shin 🔗 |
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Amalga: Designable Protein Backbone Generation with Folding and Inverse Folding Guidance ( Poster ) > link | Shugao Chen · Ziyao Li · xiangxiang Zeng · Guolin Ke 🔗 |
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Integrating Protein Structure Prediction and Bayesian Optimization for Peptide Design ( Poster ) > link | Negin Manshour · Fei He · Duolin Wang · Dong Xu 🔗 |
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Binding Oracle: Fine-Tuning From Stability to Binding Free Energy ( Poster ) > link | Chengyue Gong · Adam Klivans · Jordan Wells · James Loy · Qiang Liu · Alex Dimakis · Daniel Diaz 🔗 |
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Generative AI for designing and validating easily synthesizable and structurally novel antibiotics ( Poster ) > link | Kyle Swanson · Gary Liu · Denise Catacutan · James Zou · Jonathan Stokes 🔗 |
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UMD-fit: Generating Realistic Ligand Conformations for Distance-Based Deep Docking Models ( Poster ) > link | Eric Alcaide · Ziyao Li · Hang Zheng · Zhifeng Gao · Guolin Ke 🔗 |
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DiffDock-Site: A Novel Paradigm for Enhanced Protein-Ligand Predictions through Binding Site Identification ( Poster ) > link | Huanlei Guo · Song LIU · Mingdi HU · Yilun Lou · Bingyi Jing 🔗 |
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DiffDock-Site: A Novel Paradigm for Enhanced Protein-Ligand Predictions through Binding Site Identification ( Spotlight ) > link | Huanlei Guo · Song LIU · Mingdi HU · Yilun Lou · Bingyi Jing 🔗 |
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Through the looking glass: navigating in latent space to optimize over combinatorial synthesis libraries ( Poster ) > link | Aryan Pedawi · Saulo de Oliveira · Henry van den Bedem 🔗 |
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Generative Flow Networks Assisted Biological Sequence Editing ( Poster ) > link | Pouya M. Ghari · Alex Tseng · Gokcen Eraslan · Romain Lopez · Tommaso Biancalani · Gabriele Scalia · Ehsan Hajiramezanali 🔗 |
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Generative Flow Networks Assisted Biological Sequence Editing ( Spotlight ) > link | Pouya M. Ghari · Alex Tseng · Gokcen Eraslan · Romain Lopez · Tommaso Biancalani · Gabriele Scalia · Ehsan Hajiramezanali 🔗 |
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Combining Structure and Sequence for Superior Fitness Prediction ( Poster ) > link | Steffanie Paul · Aaron Kollasch · Pascal Notin · Debora Marks 🔗 |
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Improving Precision in Language Models Learning from Invalid Samples ( Poster ) > link | Niels Larsen · Giorgio Giannone · Ole Winther · Kai Blin 🔗 |
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Machine learning derived embeddings of bulk multi-omics data enable clinically significant representations in a pan-cancer cohort ( Poster ) > link | Sanjay Nagaraj · ZACHARY MCCAW · Theofanis Karaletsos · Daphne Koller · Anna Shcherbina 🔗 |
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Target-Aware Variational Auto-Encoders for Ligand Generation with Multi-Modal Protein Modeling ( Poster ) > link | Khang Ngo · Truong Son Hy 🔗 |
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TopoDiff: Improve Protein Backbone Generation with Topology-aware Latent Encoding ( Poster ) > link | Yuyang Zhang · Zinnia Ma · Haipeng Gong 🔗 |
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TopoDiff: Improve Protein Backbone Generation with Topology-aware Latent Encoding ( Spotlight ) > link | Yuyang Zhang · Zinnia Ma · Haipeng Gong 🔗 |
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CodonBERT: Large Language Models for mRNA design and optimization ( Poster ) > link |
24 presentersSizhen Li · Saeed Moayedpour · Ruijiang Li · Michael Bailey · Saleh Riahi · Milad Miladi · Jacob Miner · Dinghai Zheng · Jun Wang · Akshay Balsubramani · Khang Tran · Minnie · Monica Wu · Xiaobo Gu · Ryan Clinton · Carla Asquith · Joseph Skaleski · Lianne Boeglin · Sudha Chivukula · Anusha Dias · Fernando Ulloa Montoya · Vikram Agarwal · Ziv Bar-Joseph · Sven Jager |
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CoarsenConf: Equivariant Coarsening with Aggregated Attention for Molecular Conformer Generation ( Poster ) > link | Danny Reidenbach · Aditi Krishnapriyan 🔗 |
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De Novo Drug Design with Joint Transformers ( Poster ) > link | Adam Izdebski · Ewelina Weglarz-Tomczak · Ewa Szczurek · Jakub Tomczak 🔗 |
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DGFN: Double Generative Flow Networks ( Poster ) > link | Elaine Lau · Nikhil Murali Vemgal · Doina Precup · Emmanuel Bengio 🔗 |
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AMP-Diffusion: Integrating Latent Diffusion with Protein Language Models for Antimicrobial Peptide Generation ( Poster ) > link | Tianlai Chen · Pranay Vure · Rishab Pulugurta · Pranam Chatterjee 🔗 |
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Identifying Neglected Hypotheses in Neurodegenerative Disease with Large Language Models ( Poster ) > link | Spencer Hey · Darren Angle · Christopher Chatham 🔗 |
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Autoregressive fragment-based diffusion for pocket-aware ligand design ( Poster ) > link | Mahdi Ghorbani · Leo Gendelev · Paul Beroza · Michael Keiser 🔗 |