Workshop
AI for New Drug Modalities
Masatoshi Uehara · Su-In Lee · Mengdi Wang · Le Song · Nicola Richmond · Xiner Li · Maria Brbic · Mohammad Lotfollahi · Ehsan Hajiramezanali
West Meeting Room 109, 110
Sun 15 Dec, 8:50 a.m. PST
The primary objective of this workshop is to bridge the gap between AI and emerging drug modalities, such as gene and cell therapies, and RNA-based drugs. These modalities are important for disease mechanisms which were previously considered difficult, if not impossible, to target. They offer novel mechanisms of action, target previously undruggable proteins, and can address unmet medical needs with higher precision and efficacy. Traditional modalities such as small-molecule drugs, recombinant proteins, and monoclonal antibodies have formed the basis of numerous existing treatments. Recently, there has been growing recognition that AI methods have the potential to expedite breakthroughs in these established modalities. This same potential extends to the emerging field of new drug modalities, where AI can play a transformative role in accelerating the discovery and development process, overcoming challenges, and ultimately bringing innovative therapies to patients more efficiently and effectively. We aim to bring specialists in these modalities and ML communities together to discuss and investigate how AI can accelerate drug development in these emerging modalities.
Schedule
Sun 8:50 a.m. - 9:00 a.m.
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Opening remark
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Opening remark
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SlidesLive Video |
Ehsan Hajiramezanali 🔗 |
Sun 9:00 a.m. - 9:30 a.m.
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Multi scale modeling for drug discovery
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Invited Talk
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SlidesLive Video |
Animashree Anandkumar 🔗 |
Sun 9:30 a.m. - 10:00 a.m.
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Machine learning-guided sequence design for mRNA and gene therapy
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Invited Talk
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SlidesLive Video |
Georg Seelig 🔗 |
Sun 10:00 a.m. - 10:30 a.m.
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Old Friends & New Partners: Accelerating Genome Engineering with Fine-tuned LLMs and CRISPR-GPT Agent
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Invited Talk
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SlidesLive Video |
Le Cong 🔗 |
Sun 10:30 a.m. - 10:45 a.m.
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Break
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Sun 10:45 a.m. - 10:55 a.m.
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Spotlight
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Spotlight
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SlidesLive Video |
Talip Ucar 🔗 |
Sun 10:55 a.m. - 11:40 a.m.
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Panel 1: AI for New Drug Modalities
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Panel
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SlidesLive Video |
Grace (Xinying) Zheng · Ali Madani · Edith Hessel · Le Cong · Georg Seelig 🔗 |
Sun 11:40 a.m. - 12:20 p.m.
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Poster Session
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Poster
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Sun 12:50 p.m. - 1:00 p.m.
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Hackson
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Hackson
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Sun 1:00 p.m. - 1:30 p.m.
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Toward AI-Driven Digital Organism: Multiscale Foundation Models for Predicting, Simulating, and Programming Biology at All Levels
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Invited Talk
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SlidesLive Video |
Eric Xing 🔗 |
Sun 1:30 p.m. - 2:00 p.m.
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Conditional Generative Modeling on Discrete State Spaces
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Invited Talk
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SlidesLive Video |
Jennifer Listgarten 🔗 |
Sun 2:15 p.m. - 3:00 p.m.
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Gap Between Theory and Practice in AI for Drug Discovery + Future Potentials of Foundational Models in Drug Discovery
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Panel
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SlidesLive Video |
Ryan Peckner · Janet Paulsen · Bruno Trentini · Lindsay Edwards · Kyunghyun Cho 🔗 |
Sun 3:00 p.m. - 3:30 p.m.
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Break
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🔗 |
Sun 3:30 p.m. - 3:50 p.m.
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Hackson
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Presentation
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SlidesLive Video |
Masatoshi Uehara · Julian Englert 🔗 |
Sun 3:50 p.m. - 4:30 p.m.
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Spotlight
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Spotlight
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SlidesLive Video |
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Sun 4:30 p.m. - 5:10 p.m.
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Poster 2
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Poster Session
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Sun 5:20 p.m. - 5:30 p.m.
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Closing remark
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Closing remark
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SlidesLive Video |
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Generalized Flow Matching for Transition Dynamics Modeling ( Poster ) > link | Haibo Wang · Yuxuan Qiu · Yanze Wang · Rob Brekelmans · Yuanqi Du 🔗 |
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DeepRNA-DTI: A Deep Learning Approach for RNA-Compound Interaction Prediction with Binding Site Interpretability ( Poster ) > link | Haelee Bae · Hojung Nam 🔗 |
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PQA: Zero-shot Protein Question Answering for Free-form Scientific Enquiry with Large Language Models ( Poster ) > link | Eli Carrami · Sahand Sharifzadeh 🔗 |
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IgBlend: Unifying 3D Structure and Sequence for Antibody LLMs ( Poster ) > link | Cédric Malherbe · Talip Ucar 🔗 |
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Fine-Tuning Discrete Diffusion Models via Reward Optimization with Applications to DNA and Protein Design ( Poster ) > link | Chenyu Wang · Masatoshi Uehara · Yichun He · Amy Wang · Tommaso Biancalani · Avantika Lal · Tommi Jaakkola · Sergey Levine · Hanchen Wang · Aviv Regev 🔗 |
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Improving Antibody Design with Force-Guided Sampling in Diffusion Models ( Poster ) > link | Paulina Kulyte · Francisco Vargas · Simon Mathis · Yuguang Wang · José Miguel Hernández-Lobato · Pietro Lió 🔗 |
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AptaBLE: A Deep Learning Platform for SELEX Optimization ( Poster ) > link | Sawan Patel · Keith Fraser · Zhangzhi Peng · Adam Friedman · Owen Yao · Pranam Chatterjee · Sherwood Yao 🔗 |
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Molphenix: A Multimodal Foundation Model for PhenoMolecular Retrieval ( Poster ) > link | Philip Fradkin · Puria Azadi Moghadam · Karush Suri · Frederik Wenkel · Maciej Sypetkowski · Dominique Beaini 🔗 |
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Scaling Dense Representations for Single Cell Gene Expression with Transcriptome-Scale Context ( Poster ) > link |
11 presentersNicholas Ho · Caleb Ellington · Jinyu Hou · Sohan Addagudi · Shentong Mo · Tianhua Tao · Yonghao Zhuang · Hongyi Wang · Xingyi Cheng · Eric Xing · Le Song |
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FluxGAT: Integrating Flux Sampling with Graph Neural Networks for Unbiased Gene Essentiality Classification ( Poster ) > link | Kieren Sharma · Zahraa Abdallah · Lucia Marucci 🔗 |
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MOFFlow: Flow Matching for Structure Prediction of Metal-Organic Frameworks ( Poster ) > link | Nayoung Kim · SEONGSU KIM · Minsu Kim · Jinkyoo Park · Sungsoo Ahn 🔗 |
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Generative Model for Synthesizing Ionizable Lipids: A Monte Carlo Tree Search Approach ( Poster ) > link | Jingyi Zhao · Yuxuan Ou · Austin Tripp · Morteza Rasoulianboroujeni · José Miguel Hernández-Lobato 🔗 |
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Harnessing Preference Optimisation in Protein LMs for Hit Maturation in Cell Therapy ( Poster ) > link | Katarzyna Janocha · Annabel Ling · Alice Godson · Yulia Lampi · Simon Bornschein · Nils Hammerla 🔗 |
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EnzymeFlow: Generating Reaction-specific Enzyme Catalytic Pockets through Flow Matching and Co-Evolutionary Dynamics ( Poster ) > link | Chenqing Hua · Yong Liu · Dinghuai Zhang · Odin Zhang · Sitao Luan · Kevin Yang · Guy Wolf · Doina Precup · Shuangjia Zheng 🔗 |
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Probing the Embedding Space of Protein Foundation Models through Intrinsic Dimension Analysis ( Poster ) > link | Soojung Yang · Juno Nam · Tynan Perez · Jinyeop Song · Xiaochen Du · Rafael Gomez-Bombarelli 🔗 |
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Deep Interactions for Multimodal Molecular Property Prediction ( Poster ) > link | Patrick Soga · Zhenyu Lei · Camille Bilodeau · Jundong Li 🔗 |
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Modeling CAR Response at the Single-Cell Level Using Conditional OT ( Poster ) > link | Alice Driessen · Jannis Born · Rocío Rueda · Sai Reddy · Marianna Rapsomaniki 🔗 |
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PertEval-scFM: Benchmarking Single-Cell Foundation Models for Perturbation Effect Prediction ( Poster ) > link |
11 presentersAaron Wenteler · Martina Occhetta · Nikhil Branson · Magdalena Huebner · William Dee · Victor Curean · William Connell · Siu Chung · Yasha Ektefaie · Amaya Gallagher-Syed · César Córdova |
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Directly Optimizing for Synthesizability in Generative Molecular Design using Retrosynthesis Models ( Poster ) > link | Jeff Guo · Philippe Schwaller 🔗 |
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Discrete Diffusion Schrödinger Bridge Matching for Graph Transformation ( Poster ) > link | Jun Hyeong Kim · SEONGHWAN KIM · Seokhyun Moon · Hyeongwoo Kim · Jeheon Woo · Woo Youn Kim 🔗 |
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HELM: Hierarchical Encoding for mRNA Language Modeling ( Poster ) > link | Mehdi Yazdani-Jahromi · Mangal Prakash · Tommaso Mansi · Artem Moskalev · Rui Liao 🔗 |
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Beyond Sequence: Impact of Geometric Context for RNA Property Prediction ( Poster ) > link | Junjie Xu · Artem Moskalev · Tommaso Mansi · Mangal Prakash · Rui Liao 🔗 |
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CancerGPT: A single-cell RNA sequencing foundation model to decipher drug resistance in cancer ( Poster ) > link | Alexander Theus · Florian Barkmann · David Wissel · Valentina Boeva 🔗 |
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Improving Structural Plausibility in 3D Molecule Generation via Property-Conditioned Training with Distorted Molecules ( Poster ) > link | Lucy Vost · Vijil Chenthamarakshan · Payel Das · Charlotte Deane 🔗 |
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Reinforcement Learning for Enhanced Targeted Molecule Generation Via Language Models ( Poster ) > link | Salma J. Ahmed · Emad Mohammed 🔗 |
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Leveraging Disease-Specific Topologies and Counterfactual Relationships in Knowledge Graphs for Inductive Reasoning in Drug Repurposing ( Poster ) > link | Cerag Oguztuzun · Zhenxiang Gao · Hui Li · Rong Xu 🔗 |
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DiffER: Categorical Diffusion Models for Chemical Retrosynthesis ( Poster ) > link | Sean Current · Ziqi Chen · Xia Ning · Srinivasan Parthasarathy 🔗 |
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TCRGenesis: Generation of SIINFEKL-specific T-cell receptor sequences using autoregressive Transformer ( Poster ) > link | Yang An · Felix Drost · Adrian Straub · Annalisa Marsico · Dirk Busch · Benjamin Schubert 🔗 |
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Signals in the Cells: Multimodal and Contextualized Machine Learning Foundations for Therapeutics ( Poster ) > link | Alejandro Velez-Arce · Kexin Huang · Michelle Li · xiang lin · Wenhao Gao · Bradley Pentelute · Tianfan Fu · Manolis Kellis · Marinka Zitnik 🔗 |
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Language Models for Text-guided Protein Evolution ( Poster ) > link | Zhanghan Ni · Shengchao Liu · Hongyu Guo · Animashree Anandkumar 🔗 |
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Latent Diffusion Models for Controllable RNA Sequence Generation ( Poster ) > link | Kaixuan Huang · Yukang Yang · Kaidi Fu · Yanyi Chu · Le Cong · Mengdi Wang 🔗 |
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Weighted Diversified Sampling for Efficient Data-Driven Single-Cell Gene-Gene Interaction Discovery ( Poster ) > link | Yifan Wu · Yuntao Yang · Zirui Liu · Zhao Li · Khushbu Pahwa · Rongbin Li · W. Jim Zheng · Xia Hu · Zhaozhuo Xu 🔗 |
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Training-Free Guidance with Applications to Protein Engineering ( Poster ) > link | Lewis Cornwall · Joshua Meyers · James Day · Lilly Wollman · Neil Dalchau · Aaron Sim 🔗 |
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Pharmacophore-based design by learning on voxel grids ( Poster ) > link | Omar Mahmood · Pedro O. Pinheiro · Richard Bonneau · Saeed Saremi · Vishnu Sresht 🔗 |
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Correlational Lagrangian Schrodinger Bridge: Learning Dynamics with Population-Level Regularization ( Poster ) > link | Yuning You · Ruida Zhou · Yang Shen 🔗 |
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Learning to refine domain knowledge for biological network inference ( Poster ) > link | Peiwen Li · Menghua Wu 🔗 |
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Best Practices for Multi-Fidelity Bayesian Optimization in Materials and Molecular Research ( Poster ) > link | Victor Sabanza Gil · Riccardo Barbano · Daniel Gutiérrez · Jeremy Luterbacher · José Miguel Hernández-Lobato · Philippe Schwaller · Loïc Roch 🔗 |
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Video Representation Learning of Cardiac MRI for Genetic Discovery ( Poster ) > link | Matt Sooknah · Sivaramakrishnan Sankarapandian · Ramprakash Srinivasan · Johannes Riegler · Jun Xu 🔗 |
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Generative Flows on Synthetic Pathway for Drug Design ( Poster ) > link | Seonghwan Seo · Minsu Kim · Tony Shen · Martin Ester · Jinkyoo Park · Sungsoo Ahn · Woo Youn Kim 🔗 |
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Alignment-based and protein foundation models for viral evolution, vaccines and vectors ( Poster ) > link | Noor Youssef · Sarah Gurev · Debora Marks 🔗 |
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Understanding the Sources of Performance in Deep Drug Response Models Reveals Insights and Improvements ( Poster ) > link | Nikhil Branson · Pedro Cutillas · Conrad Bessant 🔗 |
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Representation Learning based Target Discovery from UKBB MRI data ( Poster ) > link | Sivaramakrishnan Sankarapandian · Ramprakash Srinivasan · Matt Sooknah · Elena Sorokin · Jun Xu 🔗 |
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Cell ontology guided transcriptome foundation model ( Poster ) > link | XINYU YUAN · Zhihao Zhan · Zuobai Zhang · Manqi Zhou · Jianan Zhao · Boyu Han · Yue Li · Jian Tang 🔗 |
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Chain-of-thoughts for molecular understanding ( Poster ) > link | Yunhui Jang · Jaehyung Kim · Sungsoo Ahn 🔗 |
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Benchmarking Transcriptomics Foundation Models for Perturbation Analysis : one PCA still rules them all ( Poster ) > link | Ihab Bendidi · Shawn Whitfield · Kian Kenyon-Dean · Hanene Ben Yedder · Yassir El Mesbahi · Emmanuel Noutahi · Alisandra Denton 🔗 |
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Benchmarking Generative Models for Antibody Design ( Poster ) > link | Talip Ucar · Cédric Malherbe · Ferran Gonzalez 🔗 |
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Saturn: Sample-efficient Generative Molecular Design using Memory Manipulation ( Poster ) > link | Jeff Guo · Philippe Schwaller 🔗 |
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SMORE-DRL: Scalable Multi-Objective Robust and Efficient Deep Reinforcement Learning for Molecular Optimization ( Poster ) > link | Aws Al Jumaily · Nicholas Aksamit · Yage Zhang · Sajjad Ghaemi · Jinqiang Hou · Hsu Kiang Ooi · Yifeng Li 🔗 |
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Learning Molecular Representation in a Cell ( Poster ) > link | Gang Liu · Srijit Seal · John Arevalo · Zhenwen Liang · Anne Carpenter · Meng Jiang · Shantanu Singh 🔗 |
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ML-driven design of 3’ untranslated regions for mRNA stability ( Poster ) > link |
12 presentersAlyssa Morrow · Elise Flynn · Emily Hoelzli · Ashley Thornal · Meimei Shan · Aniketh Janardhan Reddy · Gorkem Garipler · Rory Kirchner · Sophia Tabchouri · Ankit Gupta · Jean-Baptiste Michel · Uri Laserson |
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BindingGYM: A Large-Scale Mutational Dataset Toward Deciphering Protein-Protein Interactions ( Poster ) > link | Wei Lu · Jixian Zhang · Ming Gu · Shuangjia Zheng 🔗 |
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Learning Protocols for Non-Equilibrium Conformational Free-Energy Estimation Using Optimal Transport and Conditional Flow Matching ( Poster ) > link | Lars Holdijk · Max Welling · Michael Bronstein 🔗 |
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A Foundational Multi-Modal Knowledge Graph for Pancreatic Cancer Drug Effects Prediction ( Poster ) > link | Jingwen (Steven) Hui · Shengchao Liu · Xiaohua Huang · Animashree Anandkumar 🔗 |
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Evaluating synergies among generative design models for multi-objective optimization of drug-like proteins ( Poster ) > link |
12 presentersJune Shin · Nathan Rollins · Jordan Anderson · Grace Carey · Allison Colthart · Thomas Hopf · Ivan Mascanfroni · Jyothsna Visweswaraiah · Yi Xing · Kevin Otipoby · Nathan Higginson-Scott · Ryan Peckner |
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Machine learning enables engineering of potent, specific, and therapeutically developable proteases ( Poster ) > link |
14 presentersJune Shin · Nathan Rollins · Purvi Mande · Jordan Anderson · Allison Colthart · Soumya Bengeri · Emily Hoyt · Alex Pellerin · Ivan Mascanfroni · Jyothsna Visweswaraiah · Yi Xing · Kevin Otipoby · Nathan Higginson-Scott · Ryan Peckner |
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Improved Off-policy Reinforcement Learning in Biological Sequence Design ( Poster ) > link | Hyeonah Kim · Minsu Kim · Taeyoung Yun · Sanghyeok Choi · Emmanuel Bengio · Alex Hernandez-Garcia · Jinkyoo Park 🔗 |
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GeneGench: Systematic Evaluation of Genomic Foundation Models and Beyond ( Poster ) > link |
11 presentersZicheng Liu · Jiahui Li · Lei Xin · Siyuan Li · Chang Yu · Zelin Zang · Cheng Tan · Yufei Huang · yajing bai · Jun Xia · Stan Z. Li |
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Imporving Molecular Graph Generation with Flow Matching and Optimal Transport ( Poster ) > link | Xiaoyang Hou · Tian Zhu · Milong Ren · Dongbo Bu · Xin Gao · Chunming Zhang · Shiwei Sun 🔗 |
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GNNAS-Dock: Budget Aware Algorithm Selection with Graph Neural Networks for Molecular Docking ( Poster ) > link | Yiliang Yuan · Mustafa Misir 🔗 |
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TaxDiff: Taxonomic-Guided Diffusion Model for Protein Sequence Generation ( Poster ) > link | lin zongying · Li Hao · Liuzhenghao Lv · Yu Wang · lin bin · Junwu Zhang · Zijun Chen · Calvin Yu-Chian Chen · Li Yuan · Yonghong Tian 🔗 |
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Diverse Genomic Embedding Benchmark for functional evaluation across the tree of life. ( Poster ) > link | Jacob West-Roberts · Joshua Kravitz · Nishant Jha · Andre Cornman · Yunha Hwang 🔗 |
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Learning multi-cellular representations of single-cell transcriptomics data enables characterization of patient-level disease states ( Poster ) > link |
11 presentersTianyu Liu · Edward De Brouwer · Tony Kuo · Nathaniel Diamant · Missarova Alsu · Minsheng Hao · Hanchen Wang · Hector Corrada Bravo · Gabriele Scalia · Aviv Regev · Graham Heimberg |
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Detection of RNA Editing Sites by GPT Fine-tuning ( Poster ) > link | Zohar Rosenwasser · Erez Levanon · Michael Levitt · Gal Oren 🔗 |
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ProtPainter: Draw or Drag Protein via Topology-guided Diffusion ( Poster ) > link | Zhengxi Lu · Shizhuo Cheng · Tintin Jiang · Xiaoyin Xu · Yan Zhang · Min Zhang 🔗 |
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MolKD: Distilling Cross-Modal Knowledge in Chemical Reactions for Molecular Property Prediction ( Poster ) > link | Liang Zeng 🔗 |
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LLMs are Highly-Constrained Biophysical Sequence Optimizers ( Poster ) > link | Angelica Chen · Robert Alberstein · Andrew Watkins · Kyunghyun Cho · Nathan Frey · Samuel Stanton 🔗 |
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Modeling variable guide efficiency in pooled CRISPR screens with ContrastiveVI+ ( Poster ) > link | Ethan Weinberger · Tal Ashuach · Ryan Conrad 🔗 |
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MeMDLM: De Novo Membrane Protein Design with Masked Discrete Diffusion Protein Language Models ( Poster ) > link | Shrey Goel · Vishrut Thoutam · Edgar Marroquin · Aaron Gokaslan · Arash Firouzbakht · Sophia Vincoff · Volodymyr Kuleshov · Huong Kratochvil · Pranam Chatterjee 🔗 |
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Effective Protein-Protein Interaction Exploration with PPIretrieval ( Poster ) > link | Chenqing Hua · Connor Coley · Guy Wolf · Doina Precup · Shuangjia Zheng 🔗 |
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Antibody Library Design by Seeding Linear Programming with Inverse Folding and Protein Language Models ( Poster ) > link | Conor Hayes · Andre Goncalves · Steven Magana-Zook · Ahmet Solak · Daniel faissol · Mikel Landajuela 🔗 |
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MV-CLAM: Multi-View Molecular Interpretation with Cross-Modal Projection via Language Model ( Poster ) > link | Sumin Ha · Jun Kim · Yinhua Piao · Sun Kim 🔗 |
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Orthrus: Towards Evolutionary and Functional RNA Foundation Models ( Poster ) > link | Philip Fradkin · Ruian (Ian) Shi · Karin Isaev · Brendan Frey · Quaid Morris · Leo J Lee · Bo Wang 🔗 |
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Interpretable Causal Representation Learning for Biological Data in the Pathway Space ( Poster ) > link |
11 presentersJesus de la Fuente Cedeño · Robert Lehmann · Carlos Ruiz-Arenas · Irene Marín Goñi · Jan Voges · Xabier Martíneznez-de-Morentin · David Gomez-Cabrero · Idoia Ochoa · Jesper Tegner · Vincenzo Lagani · Mikel Hernaez |
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Distilling Structural Representations into Protein Sequence Models ( Poster ) > link | Jeffrey Ouyang-Zhang · Chengyue Gong · Yue Zhao · Philipp Kraehenbuehl · Adam Klivans · Daniel Diaz 🔗 |
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Bridging the Gap between Database Search and \emph{De Novo} Peptide Sequencing with SearchNovo ( Poster ) > link | Jun Xia · Sizhe Liu · Jingbo Zhou · Shaorong Chen · hongxin xiang · Zicheng Liu · Yue Liu · Stan Z. Li 🔗 |
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SmileyLlama: Modifying Large Language Models \\for Directed Chemical Space Exploration ( Poster ) > link | Joe Cavanagh · Kunyang Sun · Andrew Gritsevskiy · Dorian Bagni · Teresa Head-Gordon · Thomas Bannister 🔗 |
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Small-cohort GWAS discovery with AI over massive functional genomics knowledge graph ( Poster ) > link | Kexin Huang · Tony Zeng · Soner Koc · Alexandra Pettet · Martin Zhang · Jure Leskovec 🔗 |
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Natural Language Prompts Guide the Design of Novel Functional Protein Sequences ( Poster ) > link | Niksa Praljak · Hugh Yeh · Miranda Moore · Michael Socolich · Rama Ranganathan · Andrew Ferguson 🔗 |
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Accurate and General DNA Representations Emerge from Genome Foundation Models at Scale ( Poster ) > link | Caleb Ellington · Ning Sun · Nicholas Ho · Tianhua Tao · Sazan Mahbub · Yonghao Zhuang · Hongyi Wang · Eric Xing · Le Song 🔗 |
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Applications of Modular Co-Design for De Novo 3D Molecule Generation ( Poster ) > link | Danny Reidenbach · Filipp Nikitin · Olexandr Isayev · Saee Paliwal 🔗 |
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Modeling Complex System Dynamics with Flow Matching Across Time and Conditions ( Poster ) > link | Martin Rohbeck · Charlotte Bunne · Edward De Brouwer · Jan-Christian Huetter · Anne Biton · Kelvin Chen · Aviv Regev · Romain Lopez 🔗 |
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Designing DNA With Tunable Regulatory Activity Using Discrete Diffusion ( Poster ) > link | Anirban Sarkar · Ziqi Tang · Chris Zhao · Peter Koo 🔗 |
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Epitope Generation for Peptide-based Cancer Vaccine using Goal-directed Wasserstein Generative Adversarial Network with Gradient Penalty ( Poster ) > link | Yen-Che Hsiao · Abhishek Dutta 🔗 |
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A Foundation Model for RNA Function and Structure Prediction ( Poster ) > link | Shuxian Zou · Tianhua Tao · Sazan Mahbub · Caleb Ellington · Robin Algayres · Yonghao Zhuang · Hongyi Wang · Eric Xing · Le Song 🔗 |
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Derivative-Free Guidance in Continuous and Discrete Diffusion Models with Soft Value-Based Decoding ( Poster ) > link |
11 presentersXiner Li · Yulai Zhao · Chenyu Wang · Gabriele Scalia · Gokcen Eraslan · Surag Nair · Tommaso Biancalani · Shuiwang Ji · Aviv Regev · Sergey Levine · Masatoshi Uehara |
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Similarity-Aware Relative Difference Learning for Improved Molecular Activity Prediction ( Poster ) > link | Karina Zadorozhny · Kangway Chuang · Bharath Sathappan · Ewan Wallace · Vishnu Sresht · Colin Grambow 🔗 |
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Homomorphism Counts as Structural Encodings for Molecular Property Prediction ( Poster ) > link | Emily Jin · Linus Bao · Matthias Lanzinger · Ismail Ceylan · Michael Bronstein 🔗 |
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Understanding Protein-DNA Interactions by Paying Attention to Protein and Genomics Foundation Models ( Poster ) > link | Dhruva Rajwade · Erica Wang · Aryan Satpathy · Alexander Brace · Hongyu Guo · Arvind Ramanathan · Shengchao Liu · Animashree Anandkumar 🔗 |
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Disentangling the Peptide Space: A Contrastive Approach with Wasserstein Autoencoders ( Poster ) > link | Mihir Agarwal · Progyan Das 🔗 |
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GFlowNet Pretraining with Inexpensive Rewards ( Poster ) > link | Mohit Pandey · Gopeshh Subbaraj · Emmanuel Bengio 🔗 |
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PepDoRA: A Unified Peptide Language Model via Weight-Decomposed Low-Rank Adaptation ( Poster ) > link | Leyao Wang · Rishab Pulugurta · Pranay Vure · Aastha Pal · Yinuo Zhang · Pranam Chatterjee 🔗 |
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DeepProtein: Deep Learning Library and Benchmark for Protein Sequence Learning ( Poster ) > link | Jiaqing Xie · Yue Zhao · Tianfan Fu 🔗 |
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DeepADAR: A deep learning approach to model regulatory elements of ADAR-based RNA editing and its application to gRNA design ( Poster ) > link | Andrew Jung · Jiexin Gao · Leo J Lee · Brendan Frey 🔗 |
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A Deep Generative Model for the Design of Synthesizable Ionizable Lipids ( Poster ) > link | Yuxuan Ou · Jingyi Zhao · Austin Tripp · Morteza Rasoulianboroujeni · José Miguel Hernández-Lobato 🔗 |
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Bayesian Optimization of Antibodies Informed by a Generative Model of Evolving Sequences ( Poster ) > link | Alan Amin · Nate Gruver · Yucen Li · Yilun Kuang · Hunter Elliott · Calvin McCarter · Aniruddh Raghu · Peyton Greenside · Andrew Wilson 🔗 |
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An Efficient Tokenization for Molecular Language Models ( Poster ) > link | Seojin Kim · Jaehyun Nam · Jinwoo Shin 🔗 |
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JAMUN: Transferable Molecular Conformational Ensemble Generation with Walk-Jump Sampling ( Poster ) > link | Bodhi Vani · Ameya Daigavane · Joshua Rackers · Joseph Kleinhenz 🔗 |
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Geometry-text Multi-modal Foundation Model for Reactivity-oriented Molecule Editing ( Poster ) > link | Haorui Li · Shengchao Liu · Hongyu Guo · Animashree Anandkumar 🔗 |
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LatentDE: Latent-based Directed Evolution accelerated by Gradient Ascent for Protein Sequence Design ( Poster ) > link | Thanh Tran · Nhat Ngo · Viet Thanh Duy Nguyen · Truong Son Hy 🔗 |
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Active learning for efficient discovery of optimal gene combinations in the combinatorial perturbation space ( Poster ) > link | Jason Qin · Hans-Hermann Wessels · Carlos Fernandez-Granda · Yuhan Hao 🔗 |
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Mixture of Experts Enable Efficient and Effective Protein Understanding and Design ( Poster ) > link | Ning Sun · Shuxian Zou · Tianhua Tao · Sazan Mahbub · Xingyi Cheng · Yonghao Zhuang · Hongyi Wang · Eric Xing · Le Song 🔗 |
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3D Interaction Geometric Pre-training for Molecular Relational Learning ( Poster ) > link | Namkyeong Lee · Yunhak Oh · Heewoong Noh · Gyoung S. Na · Tianfan Fu · Chanyoung Park 🔗 |
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PLMFit: Benchmarking Transfer Learning with Protein Language Models for Protein Engineering ( Poster ) > link | Thomas Bikias · Evangelos Stamkopoulos · Sai Reddy 🔗 |
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Foundational Model-aided Automatic High-throughput Drug Screening Using Self-controlled Cohort Study ( Poster ) > link | Shenbo Xu · Raluca Cobzaru · Stan Finkelstein · Roy Welsch · Kenney Ng 🔗 |
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TrialDura: Multimodal Hierarchical Attentive Transformer for Explainable Clinical Trial Duration Prediction ( Poster ) > link | Ling YUE · Sixue Xing · Jonathan Li · MD ZABIRUL ISLAM · Bolun Xia · Jintai Chen · Tianfan Fu 🔗 |
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MF-LAL: Drug Compound Generation Using Multi-Fidelity Latent Space Active Learning ( Poster ) > link | Peter Eckmann · Dongxia Wu · Germano Heinzelmann · Michael Gilson · Rose Yu 🔗 |
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Molecular Generation with State Space Sequence Models ( Poster ) > link | Anri Lombard · Shane Acton · Ulrich Armel Mbou Sob · Jan Buys 🔗 |
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PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis ( Poster ) > link | Yan Wu · Esther Wershof · Sebastian Schmon · Marcel Nassar · Błażej Osiński · Ridvan Eksi · Kun Zhang · Thore Graepel 🔗 |
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Structure Language Models for Protein Conformation Generation ( Poster ) > link | Jiarui Lu · Xiaoyin Chen · Stephen Lu · Chence Shi · Hongyu Guo · Yoshua Bengio · Jian Tang 🔗 |
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AlphaFold3, a secret sauce for predicting mutational effects on protein-protein interactions ( Poster ) > link | Wei Lu · Jixian Zhang · Jiahua Rao · Zhongyue Zhang · Shuangjia Zheng 🔗 |
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Computational Antigen Optimization through Symbolic Optimization and Affinity Maturation Simulation ( Poster ) > link | Jonathan Faris · Mikel Landajuela · Kayla Sprenger · Daniel faissol · Felipe Leno da Silva 🔗 |