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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
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Abstract

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Schedule

Timezone: America/Los_Angeles
6:15 AM
Opening Remarks
6:50 AM
Invited talk | Ellen Zhong
Ellen Zhong
7:30 AM
Contributed talk | The Discovery of Binding Modes Requires Rethinking Docking Generalization
Gabriele Corso ⋅ Arthur Deng ⋅ Nicholas Polizzi ⋅ Regina Barzilay ⋅ Tommi Jaakkola
7:50 AM
Contributed talk | CodonBERT: Large Language Models for mRNA design and optimization
Sizhen 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
8:00 AM
Break
8:30 AM
Panel discussion
Max Welling ⋅ Kyunghyun Cho ⋅ Evan Feinberg ⋅ SONG LE
11:30 AM
Invited talk | Debora Marks
Debora Marks
11:50 AM
Invited talk | Shuiwang Ji
Shuiwang Ji
12:10 PM
Invited talk | Anima Anandkumar
Anima Anandkumar
12:50 PM
Contributed talk | AntiFold: Improved antibody structure design using inverse folding
Magnus H Høie ⋅ Alissa M Hummer ⋅ Tobias Olsen ⋅ Morten Nielsen ⋅ Charlotte Deane
1:00 PM
Break
1:30 PM
Contributed talk | Binding Oracle: Fine-Tuning From Stability to Binding Free Energy
Chengyue Gong ⋅ Adam Klivans ⋅ Jordan Wells ⋅ James Loy ⋅ Qiang Liu ⋅ Alex Dimakis ⋅ Daniel Diaz
1:40 PM
Contributed talk | Protein Discovery with Discrete Walk-Jump Sampling
Nathan Frey ⋅ Dan Berenberg ⋅ Karina Zadorozhny ⋅ Joseph Kleinhenz ⋅ Julien Lafrance-Vanasse ⋅ Isidro Hotzel ⋅ Yan Wu ⋅ Stephen Ra ⋅ Richard Bonneau ⋅ Kyunghyun Cho ⋅ Vladimir Gligorijevic ⋅ Saeed Saremi
2:00 PM
Closing Remarks
AlphaFold Meets Flow Matching for Generating Protein Ensembles
Bowen Jing ⋅ Bonnie Berger ⋅ Tommi Jaakkola
AlphaFold Meets Flow Matching for Generating Protein Ensembles
Bowen Jing ⋅ Bonnie Berger ⋅ Tommi Jaakkola
Protein Discovery with Discrete Walk-Jump Sampling
Nathan Frey ⋅ Dan Berenberg ⋅ Karina Zadorozhny ⋅ Joseph Kleinhenz ⋅ Julien Lafrance-Vanasse ⋅ Isidro Hotzel ⋅ Yan Wu ⋅ Stephen Ra ⋅ Richard Bonneau ⋅ Kyunghyun Cho ⋅ Vladimir Gligorijevic ⋅ Saeed Saremi
SecretoGen: towards prediction of signal peptides for efficient protein secretion
Felix Teufel ⋅ Carsten Stahlhut ⋅ Jan Refsgaard ⋅ Henrik Nielsen ⋅ Ole Winther ⋅ Dennis Madsen
Protein generation with evolutionary diffusion
Sarah Alamdari ⋅ Nitya Thakkar ⋅ Rianne van den Berg ⋅ Alex X Lu ⋅ Nicolo Fusi ⋅ Ava Amini ⋅ Kevin Yang
Targeting tissues via dynamic human systems modeling in generative design
Zachary Fox ⋅ Nolan English ⋅ Belinda S Akpa
Transition Path Sampling with Boltzmann Generator-based MCMC Moves
Michael Plainer ⋅ Hannes Stärk ⋅ Charlotte Bunne ⋅ Stephan Günnemann
Transition Path Sampling with Boltzmann Generator-based MCMC Moves
Michael Plainer ⋅ Hannes Stärk ⋅ Charlotte Bunne ⋅ Stephan Günnemann
Causal Inference in Gene Regulatory Networks with GFlowNet: Towards Scalability in Large Systems
Trang Nguyen ⋅ Alexander Tong ⋅ Kanika Madan ⋅ Yoshua Bengio ⋅ Dianbo Liu
Masked autoencoders are scalable learners of cellular morphology
Oren 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
Masked autoencoders are scalable learners of cellular morphology
Oren 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
Analysis of cellular phenotypes with image-based generative models
Ruben Fonnegra ⋅ Mohammad Vali Sanian ⋅ Zitong Sam Chen ⋅ Lassi Paavolainen ⋅ Juan C. Caicedo
Analysis of cellular phenotypes with image-based generative models
Ruben Fonnegra ⋅ Mohammad Vali Sanian ⋅ Zitong Sam Chen ⋅ Lassi Paavolainen ⋅ Juan C. Caicedo
On Complex Network Dynamics of an In-Vitro Neuronal System during Rest and Gameplay
Moein Khajehnejad ⋅ Forough Habibollahi ⋅ Alon Loeffler ⋅ Brett J. Kagan ⋅ Adeel Razi
Contextualized Networks Reveal Heterogeneous Transcriptomic Regulation in Tumors at Sample-Specific Resolution
Caleb Ellington ⋅ Ben Lengerich ⋅ Thomas Watkins ⋅ Jiekun Yang ⋅ Hanxi Xiao ⋅ Manolis Kellis ⋅ Eric Xing
Target Conditioned GFlowNet for Drug Design
Tony Shen ⋅ Mohit Pandey ⋅ Martin Ester
Target Conditioned GFlowNet for Drug Design
Tony Shen ⋅ Mohit Pandey ⋅ Martin Ester
Microenvironment Flows as Protein Engineers
Chengyue Gong ⋅ Lemeng Wu ⋅ Daniel Diaz ⋅ Xingchao Liu ⋅ James Loy ⋅ Adam Klivans ⋅ Qiang Liu
AntiFold: Improved antibody structure design using inverse folding
Magnus H Høie ⋅ Alissa M Hummer ⋅ Tobias Olsen ⋅ Morten Nielsen ⋅ Charlotte Deane
DynamicBind: Predicting ligand-specific protein-ligand complex structure with a deep equivariant generative model
Wei Lu ⋅ Jixian Zhang ⋅ Huang Weifeng ⋅ Ziqiao Zhang ⋅ Chengtao Li ⋅ Shuangjia Zheng
Improving few-shot learning-based protein engineering with evolutionary sampling
Muhammad Zaki Jawaid ⋅ Aayushma Gautam ⋅ T. Gainous ⋅ Dan Hart ⋅ Robin Yeo ⋅ Timothy Daley
Protein Inpainting Co-Design with ProtFill
Elizaveta Kozlova ⋅ Arthur Valentin ⋅ Daniel Nakhaee-Zadeh Gutierrez
Fine-tuned protein language models capture T cell receptor stochasticity
Lewis Cornwall ⋅ Grisha Szep ⋅ James Day ⋅ S R Gokul Krishnan ⋅ David Carter ⋅ Jamie Blundell ⋅ Lilly Wollman ⋅ Neil Dalchau ⋅ Aaron Sim
Harmonic Prior Self-conditioned Flow Matching for Multi-Ligand Docking and Binding Site Design
Hannes Stärk ⋅ Bowen Jing ⋅ Regina Barzilay ⋅ Tommi Jaakkola
Conditional Generation of Antigen Specific T-cell Receptor Sequences
Dhuvarakesh Karthikeyan ⋅ Colin Raffel ⋅ Benjamin Vincent ⋅ Alex Rubinsteyn
Enhancing Language Models for Technical Domains with Dynamic Token Injection
Giorgio Giannone ⋅ Neil Tenenholtz ⋅ James B Hall ⋅ Nicolo Fusi ⋅ David Alvarez-Melis
Scalable Multimer Structure Prediction using Diffusion Models
Peter Pao-Huang ⋅ Bowen Jing ⋅ Bonnie Berger
Generative design for gene therapy: An $\textit{in vivo}$ validated method
Farhan Damani ⋅ David Brookes ⋅ Jeffrey Chan ⋅ Rishi Jajoo ⋅ Alexander Mijalis ⋅ Joyce Samson ⋅ Flaviu Vadan ⋅ Cameron Webster ⋅ Stephen Malina ⋅ Sam Sinai
Bending and Binding: Predicting Protein Flexibility upon Ligand Interaction using Diffusion Models
Xuejin Zhang ⋅ Tomas Geffner ⋅ Matt McPartlon ⋅ Mehmet Akdel ⋅ Dylan Abramson ⋅ Graham Holt ⋅ Alexander Goncearenco ⋅ Luca Naef ⋅ Michael Bronstein
Generating Molecular Conformer Fields
Yuyang Wang ⋅ Ahmed Elhag ⋅ Navdeep Jaitly ⋅ Joshua Susskind ⋅ Miguel Angel Bautista
PoseCheck: Generative Models for 3D Structure-based Drug Design Produce Unrealistic Poses
Charles Harris ⋅ Kieran Didi ⋅ Arian Jamasb ⋅ Chaitanya K. Joshi ⋅ Simon Mathis ⋅ Pietro Lió ⋅ Tom Blundell
Shape-conditioned 3D Molecule Generation via Equivariant Diffusion Models
Ziqi Chen ⋅ Bo Peng ⋅ Srinivasan Parthasarathy ⋅ Xia Ning
Sampling Protein Language Models for Functional Protein Design
Jeremie Theddy Darmawan ⋅ Yarin Gal ⋅ Pascal Notin
The Discovery of Binding Modes Requires Rethinking Docking Generalization
Gabriele Corso ⋅ Arthur Deng ⋅ Nicholas Polizzi ⋅ Regina Barzilay ⋅ Tommi Jaakkola
regLM: Designing realistic regulatory DNA with autoregressive language models
Avantika Lal ⋅ Tommaso Biancalani ⋅ Gokcen Eraslan
Preference Optimization for Molecular Language Models
Ryan Park ⋅ Ryan Theisen ⋅ Rayees Rahman ⋅ Anna Cichonska ⋅ Marcel Patek ⋅ Navriti Sahni
Genomic language model predicts protein co-regulation and function
Yunha Hwang ⋅ Andre Cornman ⋅ Sergey Ovchinnikov ⋅ Peter Girguis
Fine-tuning protein Language Models by ranking protein fitness
Minji Lee ⋅ Kyungmin Lee ⋅ Jinwoo Shin
Amalga: Designable Protein Backbone Generation with Folding and Inverse Folding Guidance
Shugao Chen ⋅ Ziyao Li ⋅ xiangxiang Zeng ⋅ Guolin Ke
Binding Oracle: Fine-Tuning From Stability to Binding Free Energy
Chengyue Gong ⋅ Adam Klivans ⋅ Jordan Wells ⋅ James Loy ⋅ Qiang Liu ⋅ Alex Dimakis ⋅ Daniel Diaz
Generative AI for designing and validating easily synthesizable and structurally novel antibiotics
Kyle Swanson ⋅ Gary Liu ⋅ Denise Catacutan ⋅ James Zou ⋅ Jonathan Stokes
UMD-fit: Generating Realistic Ligand Conformations for Distance-Based Deep Docking Models
Eric Alcaide ⋅ Ziyao Li ⋅ Hang Zheng ⋅ Zhifeng Gao ⋅ Guolin Ke
Generative Flow Networks Assisted Biological Sequence Editing
Pouya M. Ghari ⋅ Alex Tseng ⋅ Gokcen Eraslan ⋅ Romain Lopez ⋅ Tommaso Biancalani ⋅ Gabriele Scalia ⋅ Ehsan Hajiramezanali
Generative Flow Networks Assisted Biological Sequence Editing
Pouya M. Ghari ⋅ Alex Tseng ⋅ Gokcen Eraslan ⋅ Romain Lopez ⋅ Tommaso Biancalani ⋅ Gabriele Scalia ⋅ Ehsan Hajiramezanali
Combining Structure and Sequence for Superior Fitness Prediction
Steffanie Paul ⋅ Aaron Kollasch ⋅ Pascal Notin ⋅ Debora Marks
Improving Precision in Language Models Learning from Invalid Samples
Niels Larsen ⋅ Giorgio Giannone ⋅ Ole Winther ⋅ Kai Blin
Machine learning derived embeddings of bulk multi-omics data enable clinically significant representations in a pan-cancer cohort
Sanjay Nagaraj ⋅ ZACHARY MCCAW ⋅ Theofanis Karaletsos ⋅ Daphne Koller ⋅ Anna Shcherbina
CodonBERT: Large Language Models for mRNA design and optimization
Sizhen 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
De Novo Drug Design with Joint Transformers
Adam Izdebski ⋅ Ewelina Weglarz-Tomczak ⋅ Ewa Szczurek ⋅ Jakub Tomczak
DGFN: Double Generative Flow Networks
Elaine Lau ⋅ Nikhil Murali Vemgal ⋅ Doina Precup ⋅ Emmanuel Bengio
AMP-Diffusion: Integrating Latent Diffusion with Protein Language Models for Antimicrobial Peptide Generation
Tianlai Chen ⋅ Pranay Vure ⋅ Rishab Pulugurta ⋅ Pranam Chatterjee
Autoregressive fragment-based diffusion for pocket-aware ligand design
Mahdi Ghorbani ⋅ Leo Gendelev ⋅ Paul Beroza ⋅ Michael Keiser