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

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8:00 AM

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8:30 AM

Panel discussion Panel discussion: AI and biology in industry

Max Welling · Kyunghyun Cho · Evan Feinberg · SONG LE

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9:30 AM

Poster session 1 Poster session 1

11:30 AM

Invited talk | Debora Marks Invited talk

Debora Marks

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11:50 AM

Invited talk | Shuiwang Ji Invited talk

Shuiwang Ji

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12:10 PM

Invited talk | Anima Anandkumar Invited talk

Anima Anandkumar

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12:30 PM

Neural ODEs and Flows to generate cell fate and regulatory network rewiring Invited talk

Smita Krishnaswamy

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12:50 PM

Contributed talk | AntiFold: Improved antibody structure design using inverse folding Spotlight

Magnus H Høie · Alissa M Hummer · Tobias Olsen · Morten Nielsen · Charlotte Deane

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1:00 PM

Break

1:30 PM

Contributed talk | Binding Oracle: Fine-Tuning From Stability to Binding Free Energy Spotlight

Chengyue Gong · Adam Klivans · Jordan Wells · James Loy · Qiang Liu · Alex Dimakis · Daniel Diaz

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1:40 PM

Contributed talk | Protein Discovery with Discrete Walk-Jump Sampling Spotlight

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

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1:50 PM

Contributed talk | Amalga: Designable Protein Backbone Generation with Folding and Inverse Folding Guidance Spotlight

Shugao Chen · Ziyao Li · xiangxiang Zeng · Guolin Ke

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2:00 PM

Closing Remarks Closing Remarks

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2:15 PM

Poster session 2 Poster session 2

AlphaFold Meets Flow Matching for Generating Protein Ensembles Poster

Bowen Jing · Bonnie Berger · Tommi Jaakkola

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AlphaFold Meets Flow Matching for Generating Protein Ensembles Spotlight

Bowen Jing · Bonnie Berger · Tommi Jaakkola

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Protein Discovery with Discrete Walk-Jump Sampling Poster

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SecretoGen: towards prediction of signal peptides for efficient protein secretion Poster

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

Matt Sternke · Joel Karpiak

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Protein generation with evolutionary diffusion Poster

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

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

Arjuna Subramanian · Matt Thomson

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Targeting tissues via dynamic human systems modeling in generative design Poster

Zachary Fox · Nolan English · Belinda S Akpa

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Transition Path Sampling with Boltzmann Generator-based MCMC Moves Poster

Michael Plainer · Hannes Stärk · Charlotte Bunne · Stephan Günnemann

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Transition Path Sampling with Boltzmann Generator-based MCMC Moves Spotlight

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

Trang Nguyen · Alexander Tong · Kanika Madan · Yoshua Bengio · Dianbo Liu

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Masked autoencoders are scalable learners of cellular morphology Poster

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

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Masked autoencoders are scalable learners of cellular morphology Spotlight

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DSMBind: an unsupervised generative modeling framework for binding energy prediction Poster

Wengong Jin · Caroline Uhler · Nir HaCohen

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Analysis of cellular phenotypes with image-based generative models Poster

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

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

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

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

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

Tony Shen · Mohit Pandey · Martin Ester

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Target Conditioned GFlowNet for Drug Design Spotlight

Tony Shen · Mohit Pandey · Martin Ester

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Microenvironment Flows as Protein Engineers Poster

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

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

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

Amelia Villegas-Morcillo · Jana M. Weber · Marcel Reinders

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Improving few-shot learning-based protein engineering with evolutionary sampling Poster

Muhammad Zaki Jawaid · Aayushma Gautam · T. Gainous · Dan Hart · Robin Yeo · Timothy Daley

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Protein Inpainting Co-Design with ProtFill Poster

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

Ian Dunn · David Koes

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Accelerating Inference in Molecular Diffusion Models with Latent Representations of Protein Structure Spotlight

Ian Dunn · David Koes

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Evaluating Zero-Shot Scoring for In Vitro Antibody Binding Prediction with Experimental Validation Poster

Divya Nori · Simon Mathis · Amir Shanehsazzadeh

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Evaluating Zero-Shot Scoring for In Vitro Antibody Binding Prediction with Experimental Validation Spotlight

Divya Nori · Simon Mathis · Amir Shanehsazzadeh

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Fine-tuned protein language models capture T cell receptor stochasticity Poster

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

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

Yang Yu · Shuang Wang · Dong Xu · Juexin Wang

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Conditional Generation of Antigen Specific T-cell Receptor Sequences Poster

Dhuvarakesh Karthikeyan · Colin Raffel · Benjamin Vincent · Alex Rubinsteyn

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Enhancing Language Models for Technical Domains with Dynamic Token Injection Poster

Giorgio Giannone · Neil Tenenholtz · James B Hall · Nicolo Fusi · David Alvarez-Melis

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Scalable Multimer Structure Prediction using Diffusion Models Poster

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

Kit Sang Chu · Kathy Wei

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Generative design for gene therapy: An $\textit{in vivo}$ validated method Poster

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

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

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

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

Ethan Weinberger · Su-In Lee

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Shape-conditioned 3D Molecule Generation via Equivariant Diffusion Models Poster

Ziqi Chen · Bo Peng · Srinivasan Parthasarathy · Xia Ning

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Sampling Protein Language Models for Functional Protein Design Poster

Jeremie Theddy Darmawan · Yarin Gal · Pascal Notin

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Parameter-Efficient Fine-Tune on Open Pre-trained Transformers for Genomic Sequence Poster

Huixin Zhan · Zijun Frank Zhang

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Approximation of Intractable Likelihood Functions in Systems Biology via Normalizing Flows Poster

Vincent Zaballa · Elliot Hui

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The Discovery of Binding Modes Requires Rethinking Docking Generalization Poster

Gabriele Corso · Arthur Deng · Nicholas Polizzi · Regina Barzilay · Tommi Jaakkola

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regLM: Designing realistic regulatory DNA with autoregressive language models Poster

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

Tomer Cohen · Dina Schneidman

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An Energy Based Model for Incorporating Sequence Priors for Target-Specific Antibody Design Poster

Steffanie Paul · Yining Huang · Debora Marks

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Preference Optimization for Molecular Language Models Poster

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

Yunha Hwang · Andre Cornman · Sergey Ovchinnikov · Peter Girguis

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Fine-tuning protein Language Models by ranking protein fitness Poster

Minji Lee · Kyungmin Lee · Jinwoo Shin

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Amalga: Designable Protein Backbone Generation with Folding and Inverse Folding Guidance Poster

Shugao Chen · Ziyao Li · xiangxiang Zeng · Guolin Ke

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Integrating Protein Structure Prediction and Bayesian Optimization for Peptide Design Poster

Negin Manshour · Fei He · Duolin Wang · Dong Xu

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Binding Oracle: Fine-Tuning From Stability to Binding Free Energy Poster

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

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

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

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

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

Aryan Pedawi · Saulo de Oliveira · Henry van den Bedem

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Generative Flow Networks Assisted Biological Sequence Editing Poster

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

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

Steffanie Paul · Aaron Kollasch · Pascal Notin · Debora Marks

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Improving Precision in Language Models Learning from Invalid Samples Poster

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

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

Khang Ngo · Truong Son Hy

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TopoDiff: Improve Protein Backbone Generation with Topology-aware Latent Encoding Poster

Yuyang Zhang · Zinnia Ma · Haipeng Gong

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TopoDiff: Improve Protein Backbone Generation with Topology-aware Latent Encoding Spotlight

Yuyang Zhang · Zinnia Ma · Haipeng Gong

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CodonBERT: Large Language Models for mRNA design and optimization Poster

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CoarsenConf: Equivariant Coarsening with Aggregated Attention for Molecular Conformer Generation Poster

Danny Reidenbach · Aditi Krishnapriyan

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De Novo Drug Design with Joint Transformers Poster

Adam Izdebski · Ewelina Weglarz-Tomczak · Ewa Szczurek · Jakub Tomczak

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DGFN: Double Generative Flow Networks Poster

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

Tianlai Chen · Pranay Vure · Rishab Pulugurta · Pranam Chatterjee

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Identifying Neglected Hypotheses in Neurodegenerative Disease with Large Language Models Poster

Spencer Hey · Darren Angle · Christopher Chatham

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Autoregressive fragment-based diffusion for pocket-aware ligand design Poster

Mahdi Ghorbani · Leo Gendelev · Paul Beroza · Michael Keiser

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