Workshop
2nd Generative AI for Biology Workshop
Minkai Xu · Zhenqiao Song · Tingyang Yu · Wenxian Shi · Seul Lee · Aditi Krishnapriyan · Maria Brbic · Regina Barzilay · Stefano Ermon · Lei Li
East Exhibition Hall A
Fri 18 Jul, 8:30 a.m. PDT
The 2024 Nobel Prize in Chemistry was awarded to AI-based protein structure prediction and protein design. It highlights the immense potential of AI in basic science and health research. In the meantime, generative AI models such as large language models (LLMs) and diffusion models are acquiring impressive capabilities in generating language, creating artwork, solving complex reasoning problems, writing computer programs, etc. To further facilitate the dialog between machine learning and biology, we propose to organize a workshop at ICML 2025, focusing on generative AI for biological discovery and therapeutic design. By fostering connections among preeminent researchers from both industry and academia, we aim to gain critical insights into the future of generative-AI-driven biology. Moreover, we hope to bridge the gap between machine learning and biological disciplines by focusing on three central themes that encapsulate innovative research as well as practical implications, which span both cutting-edge research and translational impact.
Schedule
Fri 8:30 a.m. - 8:45 a.m.
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Opening remark
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Fri 8:45 a.m. - 9:25 a.m.
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Invited speaker: James J. Collins (Generative AI for Antibiotic Discovery and Synthetic Biology)
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Fri 9:25 a.m. - 9:35 a.m.
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Spotlight1
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Fri 9:35 a.m. - 10:00 a.m.
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Poster and break
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Poster
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Fri 10:00 a.m. - 11:00 a.m.
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Invited speaker: David Baker (Design of new protein functions using deep learning) ( Talk ) > link | 🔗 |
Fri 11:00 a.m. - 11:40 a.m.
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Invited speaker: Martin Renqiang Min (Agentic Generative Biomedicine)
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Fri 11:40 a.m. - 12:00 p.m.
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Spotlight2
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Fri 12:00 p.m. - 1:00 p.m.
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Poster and lunch
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Poster
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Fri 1:00 p.m. - 1:40 p.m.
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Invited speaker: Mengdi Wang ( From Genome to Theorem: Can AI Agents Do Science?)
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Fri 1:40 p.m. - 2:20 p.m.
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Invited speaker: Marinka Zitnik (Empowering biomedical discovery with "AI scientists”)
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Fri 2:20 p.m. - 2:35 p.m.
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Invited speaker: Maruan Al-Shedivat (Driving Small Molecule Drug Discovery with Generative Modeling)
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Fri 2:35 p.m. - 2:55 p.m.
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Spotlight3
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Fri 2:55 p.m. - 3:30 p.m.
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Poster and break
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Poster
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Fri 3:30 p.m. - 4:10 p.m.
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Invited speaker: Eric P. Xing (Multiscale Foundation Models for Predicting, Simulating, and Programming Biology at All Levels)
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Fri 4:10 p.m. - 5:40 p.m.
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Panel discussion: Arash Vahdat, David Li-Bland, Eric P. Xing, Mengdi Wang, Martin Renqiang Min and Marinka Zitnik
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Fri 5:40 p.m. - 6:00 p.m.
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Award and Closing
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TABASCO: A Fast, Simplified Model for Molecular Generation with Improved Physical Quality ( Poster ) > link | Carlos Vonessen · Charles Harris · Miruna Cretu · Pietro Lió 🔗 |
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Towards Molecular Conformer Generation with Language Models ( Poster ) > link | Menua Bedrosian · Hrant Khachatrian 🔗 |
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Unifying Force Prediction and Molecular Conformation Generation Through Representation Alignment ( Poster ) > link | Lucas Pinede · Soojung Yang · Juno Nam · Rafael Gomez-Bombarelli 🔗 |
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Spatial Cell-Guided Pretraining for Scalable Spatial Transcriptomics Foundation Model ( Poster ) > link | Jing Gong · Yixuan Wang · Nicholas Ho · Xingyi Cheng · Le Song · Eric Xing 🔗 |
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MINT: Multimodal Integrated Knowledge Transfer to Large Language Models through Preference Optimization with Biomedical Applications ( Spotlight ) > link | Da Wu · Zhanliang Wang · Quan Nguyen · Zhuoran Xu · Kai Wang 🔗 |
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SurfProp: A surface-based property prediction framework for antibody developability and screening ( Poster ) > link | Pranav Rao · Henry Isaacson · Jennifer Hofmann · Darcy Davidson · Amy Wang · Andrew Watkins · Richard Bonneau · Saeed Izadi · Jae Hyeon Lee 🔗 |
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AntiDIF: Accurate and Diverse Antibody Specific Inverse Folding with Discrete Diffusion ( Poster ) > link | Nikhil Branson · Charlotte Deane 🔗 |
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A framework to extract and interpret biological concepts from scRNAseq generative foundation models ( Poster ) > link | Charlotte Claye · Pierre Marschall · Wassila Ouerdane · Céline Hudelot · Julien Duquesne 🔗 |
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FORT: Forward-Only Regression Training of Normalizing Flows ( Spotlight ) > link | Danyal Rehman · Oscar Davis · Jiarui Lu · Jian Tang · Michael Bronstein · Yoshua Bengio · Alexander Tong · Joey Bose 🔗 |
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LapDDPM: A Conditional Graph Diffusion Model for scRNA-seq Generation with Spectral Adversarial Perturbations ( Poster ) > link | Lorenzo Bini · Stephane Marchand-Maillet 🔗 |
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Pi-SAGE: Permutation-invariant surface-aware graph encoder for binding affinity prediction ( Poster ) > link | Sharmi Banerjee · Mostafa Karimi · Melih Yilmaz · Tommi Jaakkola · Bella Dubrov · Shang Shang · Ron Benson 🔗 |
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Retrieval Augmented Protein Language Models for Protein Structure Prediction ( Spotlight ) > link | Pan Li · Xingyi Cheng · Le Song · Eric Xing 🔗 |
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Progressive Inference-Time Annealing of Diffusion Models for Sampling from Boltzmann Densities ( Spotlight ) > link | Tara Akhound-Sadegh · Jungyoon Lee · Joey Bose · Valentin De Bortoli · Arnaud Doucet · Michael Bronstein · Dominique Beaini · Siamak Ravanbakhsh · Kirill Neklyudov · Alexander Tong 🔗 |
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Molecular Cues to Smart Sequences: Optimizing Early Aptamers from SELEX ( Poster ) > link | Soniya · Runjhun Narayan · Apurva Narayan 🔗 |
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Enhancing AlphaFold3 for Protein-Ligand Co-Folding via Reinforcement Learning ( Poster ) > link | YU PEI · Yuxuan Song · Zhilong Zhang · Keyue Qiu · Hao Zhou · Wei-Ying Ma 🔗 |
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Integrating Bilinear Transduction with Message Passing Neural Networks for Improved ADMET Property Prediction ( Poster ) > link | Claire Suen · Alan Cheng 🔗 |
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Generating readily synthesizable dye scaffolds with SyntheFluor ( Poster ) > link | Ruhi Sayana · Jennifer Xu · Kate Callon · Jonathan Deutsch · James Zou · John Janetzko · Rabindra Shivnaraine · Kyle Swanson 🔗 |
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Measuring Scientific Capabilities of Language Models with a Systems Biology Dry Lab ( Poster ) > link | Haonan Duan · Stephen Lu · Caitlin Harrigan · Nishkrit Desai · Jiarui Lu · Michał Koziarski · Leonardo Cotta · Chris Maddison 🔗 |
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PhenoGraph: A Multi-Agent Framework for Phenotype-driven Discovery in Spatial Transcriptomics Data Augmented with Knowledge Graphs ( Poster ) > link | Seyednami Niyakan · Xiaoning Qian 🔗 |
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Sparse Autoencoders in Protein Engineering Campaigns: Steering and Model Diffing ( Poster ) > link | Gerard Corominas · Filippo Stocco · Noelia Ferruz 🔗 |
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SIMBA-GNN: Simulation-augmented Microbiome Abundance Graph Neural Network ( Poster ) > link | Mohammad Parsa · Javad Aminian-Dehkordi · Mohammad Mofrad 🔗 |
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Teddy: A FAMILY OF FOUNDATION MODELS FOR UNDERSTANDING SINGLE CELL BIOLOGY ( Poster ) > link |
18 presentersAlexis Chevalier · Soumya Ghosh · Urvi Awasthi · James Watkins · Julia Bieniewska · Nichita Mitrea · Olga Kotova · Kirill Shkura · Andrew Noble · Michael Steinbaugh · Vijay Sadashivaiah · George Dasoulas · Julien Delile · Christoph Meier · Leonid Zhukov · Iya Khalil · Srayanta Mukherjee · Judith Mueller |
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Modeling Molecular Sequences with Learning-Order Autoregressive Models ( Poster ) > link | Zhe Wang · Jiaxin Shi · Nicolas Heess · Michalis Titsias · Arthur Gretton · Yee-Whye Teh 🔗 |
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Bures-Wasserstein Flow Matching for Graph Generation ( Spotlight ) > link | Keyue Jiang · Jiahao Cui · Xiaowen Dong · Laura Toni 🔗 |
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Two-Stage Pretraining for Molecular Property Prediction in the Wild ( Poster ) > link | Kevin Tirta Wijaya · Minghao Guo · Michael Sun · Hans-peter Seidel · Wojciech Matusik · Vahid Babaei 🔗 |
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TACTIC: An Explainable Multi-Agent Architecture for Classification & Interpretable Reasoning in Spatial Transcriptomics ( Poster ) > link | Abdel Rahman Alsabbagh · Mahmoud Zahran · Ali Balubaid · Sumeer Khan · Robert Lehmann · Xabier Martínez de Morentin · Vincenzo Lagani · Narsis Kiani · David Gomez-Cabrero · jesper tegner 🔗 |
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Representing local protein environments with atomistic foundation models ( Poster ) > link | Meital Bojan · Sanketh Vedula · Sai Advaith Maddipatla · Nadav Bojan · Federico Napoli · Paul Schanda · Alexander Bronstein 🔗 |
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EpitopeGen: Learning to Generate T Cell Epitopes: A Semi-Supervised Approach with Biological Constraints ( Poster ) > link | Minuk Ma · Wilson Tu · Carlos Vasquez-Rios · Jiarui Ding 🔗 |
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Scaling and Saturation Protein Language Models with Biological Data ( Poster ) > link | Aviv Spinner · Erika DeBenedictis 🔗 |
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Do we need equivariant models for molecule generation? ( Poster ) > link | Ewa M. Nowara · Joshua Rackers · Patricia Suriana · Pan Kessel · Max Shen · Andrew Watkins · Michael Maser 🔗 |
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Learning Diffusion Models with Flexible Representation Guidance ( Poster ) > link | Chenyu Wang · Cai Zhou · Sharut Gupta · Zongyu Lin · Stefanie Jegelka · Stephen Bates · Tommi Jaakkola 🔗 |
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Straight but not so fast: Challenges with Rectified Flows in Protein Design. ( Poster ) > link | Junhua Chen · Simon Mathis · Charles Harris · Kieran Didi · Pietro Lió 🔗 |
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Bimodal masked language modeling for bulk RNA-seq and DNA methylation representation learning ( Poster ) > link | Maxence Gélard · Hakim Benkirane · Thomas Pierrot · Guillaume Richard · Paul-Henry Cournède 🔗 |
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ProteinCrow: A Language Model Agent That Can Design Proteins ( Poster ) > link |
11 presentersRaghava Manvitha Reddy Ponnapati · Sam Cox · Cade Gordon · Michael Hammerling · Siddharth Narayanan · Jon Laurent · James Braza · Michaela Hinks · Michael Skarlinski · Sam Rodriques · Andrew White |
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Unlocking Non-Invasive Brain-to-Text ( Poster ) > link | Dulhan Jayalath · Gilad Landau · ʻŌiwi Parker Jones 🔗 |
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HM-GIM: A Probabilistic Neural Model for Discovering Heterogeneous Microbiome or Human Gene Groupings and Their Interactions ( Poster ) > link | Jiening Zhu · Isin Comba · Shakti Bhattarai · Vanni Bucci · Georg Gerber 🔗 |
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Importance-Weighted Training of Diffusion Samplers ( Poster ) > link | Sanghyeok Choi · Sarthak Mittal · Víctor Elvira · Jinkyoo Park · Nikolay Malkin 🔗 |
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No Clear Winner at Small Scale: Comparing Modern Sequence Architectures and Training Strategies for Genomic Language Models ( Poster ) > link | Vera Milovanović · Antonio Orvieto 🔗 |
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MolFORM: Multi-modal Flow Matching for Structure-Based Drug Design ( Poster ) > link | Daiheng Zhang · Jie Huang · Zhao Zhang 🔗 |
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In silico design of epigenetic reprogramming payloads ( Poster ) > link | Lucas Seninge · Conner Kummerlowe · David Reynolds · Nicholas Bernstein · Jacob Kimmel 🔗 |
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ProxelGen: Generating Proteins as 3D Densities ( Spotlight ) > link | Felix Faltings · Hannes Stärk · Regina Barzilay · Tommi Jaakkola 🔗 |
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Bridging Quantum and Classical Computing in Drug Design: Architecture Principles for Improved Molecule Generation ( Poster ) > link | Andrew Smith · Erhan Guven 🔗 |
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Fast and Scalable Gene Embedding Search: A Comparative Study of FAISS and ScaNN ( Poster ) > link | Mohammadsaleh Refahi · Gavin Hearne · Harrison Muller · Kieran Lynch · Bahrad Sokhansanj · James Brown · Gail Rosen 🔗 |
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Benchmark of Diffusion and Flow Matching Models for Unconditional Protein Structure Design ( Poster ) > link | Wenran LI · Xavier Cadet · Cédric Damour · Yu LI · Alexandre G. de BREVERN · Alain Miranville · Frederic CADET 🔗 |
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Chemical Reaction Network Implementation of Logic Gates and Neural Networks Using a Molecular Exchange Mechanism ( Poster ) > link | Muhtasim Ishmum Khan · Moshiur Rahman · Md. Shahriar Karim 🔗 |
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Improving Genomic Models via Task-Specific Self-Pretraining ( Poster ) > link | Sohan Mupparapu · Parameswari Krishnamurthy · Ratish Surendran Puduppully 🔗 |
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Partition Generative Modeling: Masked Modeling Without Masks ( Poster ) > link | Justin Deschenaux · Lan Tran · Caglar Gulcehre 🔗 |
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Straight-Line Diffusion Model for Efficient 3D Molecular Generation ( Poster ) > link | Yuyan Ni · Shikun Feng · Haohan Chi · Bowen Zheng · Huan-ang Gao · Wei-Ying Ma · Zhi-Ming Ma · Yanyan Lan 🔗 |
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An Iterative Framework for Generative Backmapping of Coarse Grained Proteins ( Poster ) > link | Georgios Kementzidis · Erin Wong · John Nicholson · Ruichen Xu · Yuefan Deng 🔗 |
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OrthoGraphRAG: Enhancing Clinical Decision Making with Multi-Level Knowledge Graphs ( Poster ) > link | Venkatesh Tata · Zohra Bouchamaoui · Nagavaishnavi Bhaskara 🔗 |
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DisProtEdit: Exploring Disentangled Representations for Multi-Attribute Protein Editing ( Poster ) > link | Max KU · Sun Sun · Hongyu Guo · Wenhu Chen 🔗 |
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Active Leaning-Guided Seq2Seq Variational Autoencoder for Multi-target Inhibitor Generation ( Poster ) > link | Júlia Vilalta Mor · Alexis Molina · Laura Varga · Isaac Filella-Merce · VICTOR GUALLAR 🔗 |
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Rapidash: Scalable Molecular Modeling Through Controlled Equivariance Breaking ( Poster ) > link | Sharvaree Vadgama · Erik Bekkers 🔗 |
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AbFlowNet: Optimizing Antibody-Antigen Binding Energy via Diffusion-GFlowNet Fusion ( Poster ) > link | Abrar Abir · Haz Shahgir · Rownok Ratul · Toki Tahmid · Greg Ver Steeg · Yue Dong 🔗 |
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A Diffusion-Based Autoencoder for Learning Patient-Level Representations from Single-Cell Data ( Poster ) > link | Rebecca Boiarsky · Johann Wenckstern · Nicholas Haradhvala · Gad Getz · David Sontag 🔗 |
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CryoSAMU: Enhancing 3D Cryo-EM Density Maps of Protein Structures at Intermediate Resolution with Structure-Aware Multimodal U-Nets ( Poster ) > link | Chenwei Zhang · Khanh Dao Duc 🔗 |
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Align Your Structures: Generating Trajectories with Structure Pretraining for Molecular Dynamics ( Poster ) > link | Aniketh Iyengar · Jiaqi Han · Pengwei Sun · Mingjian Jiang · Jianwen Xie · Stefano Ermon 🔗 |
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An Improved Systematic Method for Constructing Enzyme-Constrained Genome-Scale Metabolic Models Using a Protein-Chemical Transformer ( Poster ) > link | Anna Schooneveld · Shafiat Dewan · Will Addison · David Berman · Navot Arad · Sam Genway · Sonya Kalsi · Kotryna Bloznelyte 🔗 |
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BC-Design: A Biochemistry-Aware Framework for Highly Accurate Inverse Protein Folding ( Poster ) > link | Robert Tang · Xinwu Ye · Fang Wu · Daniel Shao · Dong Xu · Mark Gerstein 🔗 |
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Self-Supervised Representation Learning for Microbiome Improves Downstream Prediction in Data-Limited Settings and Cross-Cohort Generalizability ( Poster ) > link | Liron Zahavi · Zachary Levine · Eran Segal 🔗 |
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Balancing Speed and Precision in Protein Folding: A Comparison of AlphaFold2, ESMFold, and OmegaFold ( Poster ) > link | Petr Simecek 🔗 |
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LLMs for Experiment Design in Scientific Domains: Are We There Yet? ( Poster ) > link | Rushil Gupta · Jason Hartford · Bang Liu 🔗 |
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ATOMICA: Learning Universal Representations of Molecular Interactions ( Spotlight ) > link | Ada Fang · ZAIXI ZHANG · Marinka Zitnik 🔗 |
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Drug Discovery SMILES-to-Pharmacokinetics Diffusion Models with Deep Molecular Understanding ( Poster ) > link | Bing Hu · Anita Layton · Helen Chen 🔗 |
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Foreground-aware Virtual Staining for Accurate 3D Cell Morphological Profiling ( Poster ) > link |
14 presentersAlexandr A. Kalinin · Paula Llanos · Theresa Sommer · Giovanni Sestini · Xinhai Hou · Jonathan Sexton · Xiang Wan · Ivo Dinov · Brian Athey · nicolas rivron · Anne Carpenter · Beth Cimini · Shantanu Singh · Matthew O'Meara |
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Self-supervised learning predicts plant growth trajectories from multi-modal industrial greenhouse data ( Poster ) > link | Adam Riesselman · Evan Cofer · Therese LaRue · Wim Meeussen 🔗 |
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Pullback Flow Matching on Data Manifolds ( Poster ) > link | Friso de Kruiff · Erik Bekkers · Ozan Öktem · Carola-Bibiane Schönlieb · Willem Diepeveen 🔗 |
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Predicting Microbial Ontology and Pathogen Risk from Environmental Metadata with Large Language Models ( Poster ) > link | Hyunwoo Yoo · Gail Rosen 🔗 |
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Modeling Microenvironment Trajectories on Spatial Transcriptomics with NicheFlow ( Poster ) > link | Kristiyan Sakalyan · Alessandro Palma · Filippo Guerranti · Fabian Theis · Stephan Günnemann 🔗 |
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Predicting function of evolutionarily implausible DNA sequences ( Poster ) > link | Shiyu Jiang · Xuyin Liu · Zitong Jerry Wang 🔗 |
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Beyond Visual Inspection: Principled Benchmarking of Single-Cell Trajectory Representations with scTRAM ( Poster ) > link | Kemal Inecik · Malte Luecken · Fabian Theis 🔗 |
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Diversity by Design: Addressing Mode Collapse Improves scRNA-seq Perturbation Modeling on Well-Calibrated Metrics ( Poster ) > link | Gabriel Mejia · Henry Miller · Francis Leblanc · BO WANG · Brendan Swain · Lucas Paulo de Lima Camillo 🔗 |
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MolGuidance: A Comparative Study of Guidance Methods for Conditional Molecule Generation ( Poster ) > link | Cheng Zeng · Jirui Jin · Pawan Prakash · George Karypis · Mark Transtrum · Ellad Tadmor · Richard Hennig · Adrian Roitberg · Stefano Martiniani · Mingjie Liu 🔗 |
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Torsional-GFN: a conditional conformation generator for small molecules ( Poster ) > link | Lena Nehale Ezzine · Alexandra Volokhova · Piotr Gaiński · Luca Scimeca · Emmanuel Bengio · Prudencio Tossou · Yoshua Bengio · Alex Hernandez-Garcia 🔗 |
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Automated Neuron Labels For Protein Language Models Enable Generative Steering ( Spotlight ) > link | Arjun Banerjee · David Martinez · Camille Dang · Ethan Tam 🔗 |
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SynCoGen: Synthesizable 3D Molecule Generation via Joint Reaction and Coordinate Modeling ( Poster ) > link | Andrei Rekesh · Miruna Cretu · Dmytro Shevchuk · Vignesh Ram Somnath · Pietro Lió · Robert Batey · Mike Tyers · Michał Koziarski · Chenghao Liu 🔗 |
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SynPair: Pairing Unpaired Antibody Chains at Billion-Sequence Scale With Contrastive Learning ( Poster ) > link | Ollie Turnbull · Charlotte Deane 🔗 |
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Calibrating Generative Models ( Spotlight ) > link | Henry Smith · Brian Trippe 🔗 |
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From Fragments to Geometry: A Unified Graph Transformer for Molecular Representation from Conformer Ensembles ( Poster ) > link |
14 presentersDuy Nguyen · Trung Nguyen · Ha Le · Mai Thanh Nhat Truong · TrungTin Nguyen · Nhat Ho · Khoa Doan · Duy Duong-Tran · Li Shen · Daniel Sonntag · James Zou · Mathias Niepert · Hyojin Kim · Jonathan Allen |
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Intrinsic Evaluation of DNA Embeddings in Genome Language Models: Insights from Yeast Genomic Sequences ( Poster ) > link | Ruhaib Muhammad · Rajeeva Madhan · Roshan Balaji · Nirav Bhatt 🔗 |
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Robust Molecular Property Prediction via Densifying Scarce Labeled Data ( Poster ) > link | Jina Kim · Jeffrey Willette · Bruno Andreis · Sung Ju Hwang 🔗 |
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A Zero-shot LLM-based Framework for Descriptive Gene-gene Interaction Network Generation ( Poster ) > link | Bingjun Li · Mason Ritchotte · Sihong He · Sheida Nabavi 🔗 |
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Trustworthy Inverse Molecular Design via Alignment with Molecular Dynamics ( Poster ) > link | Kevin Tirta Wijaya · Navid Ansari · Hans-peter Seidel · Vahid Babaei 🔗 |
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Analytic Gaussian Convolution for Faster Molecular Optimization and Sampling ( Poster ) > link | Soumya Ram · Akhila Ram 🔗 |
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DePO: Elicit Chemical Reasoning Capability via Demonstration-Guided Policy Optimization ( Spotlight ) > link | Xuan Li · Zhanke Zhou · Zongze Li · Jiangchao Yao · Yu Rong · Lu Zhang · Bo Han 🔗 |
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Minimum-Excess-Work Guidance ( Poster ) > link | Christopher Kolloff · Tobias Höppe · Emmanouil Angelis · Mathias Schreiner · Stefan Bauer · Andrea Dittadi · Simon Olsson 🔗 |
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Constrained Molecular Generation via Sequential Flow Model Fine-Tuning ( Poster ) > link | Sven Gutjahr · Riccardo De Santi · Luca Schaufelberger · Kjell Jorner · Andreas Krause 🔗 |
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DIVER-0 : A Fully Channel Equivariant EEG Foundation Model ( Spotlight ) > link | Danny D Han · Ahhyun Lee · Taeyang Lee · Yonghyeon Gwon · Sebin Lee · Seong Lee · David K Park · Shinjae Yoo · Chun Kee Chung · Jiook Cha 🔗 |
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Multi-Granular Contrastive Alignment and Fusion for Fragment-Enhanced Virtual Screening ( Poster ) > link |
11 presentersHaichuan Tan · Bowen Gao · Jiaxin Li · Yanwen Huang · Wenyu Zhu · Jianhui Wang · Yinjun Jia · Yuanhuan Mo · Ya-Qin Zhang · Wei-Ying Ma · Yanyan Lan |
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AtoMAE: Learning Protein Structure Representations from Atomic Voxel Grids via Masked Autoencoders ( Poster ) > link | Namuk Park · Pedro O. Pinheiro · Nathan Frey · Sidney Lisanza · Andrew Watkins · Arian Jamasb · Matthieu Kirchmeyer · Richard Bonneau · Saeed Saremi · Vladimir Gligorijevic 🔗 |
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Guided Generation for Developable Antibodies ( Poster ) > link | Siqi Zhao · Joshua Moller · Lood van Niekerk 🔗 |
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A Diffusion Model to Shrink Proteins While Maintaining their Function ( Spotlight ) > link | Ethan Baron · Alan Amin · Ruben Weitzman · Debora Marks · Andrew Wilson 🔗 |
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Consistent Sampling and Simulation: Molecular Dynamics with Energy-Based Diffusion Models ( Poster ) > link | Michael Plainer · Hao Wu · Leon Klein · Stephan Günnemann · Frank Noe 🔗 |
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KODA: An Agentic Framework for KEGG Orthology-Driven Discovery of Antimicrobial Drug Targets in Gut Microbiome ( Poster ) > link | Javad Aminian-Dehkordi · Mohammad Parsa · Mohsen Naghipourfar · Mohammad Mofrad 🔗 |
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ProVADA: Generation of Subcellular Protein Variants via Ensemble-Guided Test-Time Steering ( Spotlight ) > link | Wenhui Lu · Xiaowei Zhang · L. Mille-Fragoso · Haoyu Dai · Xiaojing Gao · Wong 🔗 |
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Towards functional annotation with latent protein language model features ( Poster ) > link | Jake Silberg · Elana Simon · James Zou 🔗 |
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SMICE: enhanced conformational sampling using AlphaFold and coevolutionary information ( Poster ) > link | Yongkai Chen · Samuel Wong · Samuel Kou 🔗 |
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Generation of structure-guided pMHC-I libraries using Diffusion Models ( Poster ) > link | Sergio Mares · Ariel Espinoza · Nilah Ioannidis 🔗 |
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STRAND: Structure Refinement of RNA-Protein Complexes via Diffusion ( Poster ) > link | Mohsen Al-zeqri · Jörg Franke · Frederic Runge 🔗 |
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Diffusion models with group symmetries for biomolecule generation ( Poster ) > link | Wenran LI · Xavier Cadet · David Medina · Mehdi D. Davari · Ramanathan Sowdhamini · Cédric Damour · Yu LI · Alain Miranville · Frederic CADET 🔗 |
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Connecting Gene Expression and Tissue Morphology with Conditional Generative Models ( Spotlight ) > link | Frederieke Lohmann · Alberto Valdeolivas · Jelica Vasiljević 🔗 |
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Biological Reasoning with Reinforcement Learning through Natural Language Enables Generalizable Zero-Shot Cell Type Annotations ( Poster ) > link | Xi Wang · Runzi Tan · Simona Cristea 🔗 |
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Learning Collective Variables from Time-lagged Generation ( Poster ) > link | Seonghyun Park · Kiyoung Seong · Soojung Yang · Rafael Gomez-Bombarelli · Sungsoo Ahn 🔗 |
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A Genomic Language Model for Zero-Shot Prediction of Promoter Indel Effects ( Spotlight ) > link |
12 presentersCourtney Shearer · Felix Teufel · Rose Orenbuch · Christian Steinmetz · Daniel Ritter · Erik Xie · Artem Gazizov · Aviv Spinner · Jonathan Frazer · Mafalda Dias · Pascal Notin · Debora Marks |
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Multi-Objective-Guided Generative Design of mRNA with Therapeutic Properties ( Poster ) > link | Sawan Patel · Sophia Tang · Yinuo Zhang · Pranam Chatterjee, PhD · Sherwood Yao 🔗 |
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Joint Probabilistic Modeling of Pseudobulk and Single-Cell Transcriptomics Enables Accurate Estimation of Cell Type Composition ( Poster ) > link | Simon Grouard · Khalil Ouardini · Yann Rodriguez · Jean-Philippe Vert · Almudena Espin-Perez 🔗 |
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Promoter Sequence Generation using Homology Prompting ( Poster ) > link | Erik Xie · Courtney Shearer · Ruben Weitzman · Pascal Notin · Debora Marks 🔗 |
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Efficient Models for molecular property prediction ( Poster ) > link | Sairam Babu · Rishabh Bhattacharya 🔗 |
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Revisiting Sampling Strategies for Molecular Generation ( Poster ) > link | Yuyan Ni · Shikun Feng · Wei-Ying Ma · Zhi-Ming Ma · Yanyan Lan 🔗 |
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HybridLinker: Topology-Guided Posterior Sampling for Enhanced Diversity and Validity in 3D Molecular Linker Generation ( Poster ) > link | Minyeong Hwang · Ziseok Lee · Kwang-Soo Kim · Kyungsu Kim · Eunho Yang 🔗 |
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FIGRDock: Fast Interaction-Guided Regression for Flexible Docking ( Poster ) > link | Shikun Feng · Bicheng Lin · Yuanhuan Mo · Yuyan Ni · Wenyu Zhu · Bowen Gao · Wei-Ying Ma · haitao li · Yanyan Lan 🔗 |
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Forecasting H1N1 Influenza Pandemic and Seasonal Evolution ( Poster ) > link | Aarushi Mehrotra · Sarah Gurev · Noor Youssef · Debora Marks 🔗 |
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scAgents: A Multi-Agent Framework for Fully Autonomous End-to-End Single-Cell Perturbation Analysis ( Poster ) > link |
13 presentersRobert Tang · Zhuoyun Yu · Jiapeng Chen · Yan Cui · Daniel Shao · Fang Wu · Kexu Li · Wangchunshu Zhou · Weixu Wang · Zhi Huang · Arman Cohan · Smita Krishnaswamy · Mark Gerstein |
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Improving Inverse Folding for Peptide Design with Diversity-regularized Direct Preference Optimization ( Spotlight ) > link | Ryan Park · Darren Hsu · C. Roland · Maria Korshunova · Chen Tessler · Shie Mannor · Olivia Viessmann · Bruno Trentini 🔗 |
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Mixtures of Neural Cellular Automata: A Stochastic Framework for Biological Growth Modelling ( Poster ) > link | Salvatore Milite · Giulio Caravagna · Andrea Sottoriva 🔗 |
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BoltzNCE: Learning Likelihoods for Boltzmann Generation with Stochastic Interpolants and Noise Contrastive Estimation ( Poster ) > link | Rishal Aggarwal · Jacky Chen · Nicholas Boffi · David Koes 🔗 |
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BindEnergyCraft: Casting Protein Structure Predictors as Energy-Based Models for Binder Design ( Spotlight ) > link | Divya Nori · Anisha Parsan · Caroline Uhler · Wengong Jin 🔗 |
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EpiBinder: a multimodal deep learning model at base-resolution to analyze in vivo Transcription Factor-DNA Binding ( Poster ) > link | Rubén Solozabal · Albert Baichorov · Tamir Avioz · Le Song · Martin Takac · Ariel Afek 🔗 |
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Ibex: Pan-immunoglobulin structure prediction ( Poster ) > link | Frederic Dreyer · Karolis Martinkus · Jan Ludwiczak · Brennan Abanades · Robert Alberstein · Pranav Rao · Jae Hyeon Lee · Richard Bonneau · Andrew Watkins · Franziska Seeger 🔗 |
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JAMUN: Bridging Smoothed Molecular Dynamics and Score-Based Learning for Conformational Ensemble Generation ( Poster ) > link | Ameya Daigavane · Bodhi Vani · Darcy Davidson · Saeed Saremi · Joshua Rackers · Joseph Kleinhenz 🔗 |
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Flow Density Control: Generative Optimization Beyond Entropy-Regularized Fine-Tuning ( Spotlight ) > link | Riccardo De Santi · Marin Vlastelica · Ya-Ping Hsieh · Zebang Shen · Niao He · Andreas Krause 🔗 |
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ControllableGPT: A Ground-Up Designed Controllable GPT for Molecule Optimization ( Poster ) > link | Xuefeng Liu · Songhao Jiang · Bo Li · Rick Stevens 🔗 |
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CoFM: Molecular Conformation Generation via Flow Matching in SE(3)-Invariant Latent Space ( Poster ) > link | Guikun Xu · Yankai Yu · Yongquan Jiang · Yan Yang · Yatao Bian 🔗 |
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Simultaneous Modeling of Protein Conformation and Dynamics via Autoregression ( Poster ) > link | Yuning Shen · Lihao Wang · Huizhuo Yuan · YAN WANG · Bangji Yang · Quanquan Gu 🔗 |
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SOAPIA: Siamese-Guided Generation of Off Target-Avoiding Protein Interactions with High Target Affinity ( Poster ) > link | Sophia Vincoff · Oscar Davis · Ismail Ceylan · Alexander Tong · Joey Bose · Pranam Chatterjee, PhD 🔗 |
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Protein Generator with Ribosomal Origin and Folding ( Poster ) > link | MinGyu Choi · Derek Chen · Tommi Jaakkola · Regina Barzilay 🔗 |
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Multi-state Protein Design with DynamicMPNN ( Poster ) > link | Alex Abrudan · Sebastian Pujalte Ojeda · Chaitanya Joshi · Matthew Greenig · Felipe Engelberger · Alena Khmelinskaia · Jens Meiler · Michele Vendruscolo · Tuomas Knowles 🔗 |
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To Optimize, Not to Invent: Controlled On-Manifold Diffusion Walk for mRNA Sequence Generation and Optimization Without $\textit{de novo}$ Design ( Spotlight ) > link | Danqi Liao · Chen Liu · Xingzhi Sun · Die Tang · Haochen Wang · Scott Youlten · Antonio Giraldez · Smita Krishnaswamy 🔗 |
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Tissue Reassembly with Generative AI ( Poster ) > link | Tingyang Yu · Chanakya Ekbote · Nikita Morozov · Jiashuo Fan · Pascal Frossard · Stéphane d'Ascoli · Maria Brbic 🔗 |
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Multi-Objective-Guided Discrete Flow Matching for Controllable Biological Sequence Design ( Spotlight ) > link | Tong Chen · Yinuo Zhang · Sophia Tang · Pranam Chatterjee, PhD 🔗 |
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ScaffoldGPT: A Scaffold-based GPT Model for Drug Optimization ( Poster ) > link | Xuefeng Liu · Songhao Jiang · Ian Foster · Jinbo Xu · Rick Stevens 🔗 |
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Diffusion-Free Graph Generation with Next-Scale Prediction ( Poster ) > link | Samuel Belkadi · Dat Hong · Marian Chen · Miruna Cretu · Charles Harris · Pietro Lió 🔗 |
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Design in Voxel Space Decode in SMILES Space: Plixer Generates Drug-Like Molecules for Protein Pockets ( Poster ) > link | Jude Wells · Brooks Paige 🔗 |
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Electrostatics from Laplacian Eigenbasis for Neural Network Interatomic Potentials ( Poster ) > link | Maksim Zhdanov · Vladislav Kurenkov 🔗 |
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Exploring Adversarial Robustness in Classification tasks using DNA Language Models ( Poster ) > link | Hyunwoo Yoo · Haebin Shin · Kaidi Xu · Gail Rosen 🔗 |
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Rapid and Reproducible Multimodal Biological Foundation Model Development with AIDO.ModelGenerator ( Spotlight ) > link | Caleb Ellington · Dian Li · Shuxian Zou · Elijah Cole · Ning Sun · Sohan Addagudi · Le Song · Eric Xing 🔗 |
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ToxBench: A Binding Affinity Prediction Benchmark with AB-FEP-Calculated Labels for Human Estrogen Receptor Alpha ( Poster ) > link |
22 presentersMeng Liu · Karl Leswing · Simon Chu · FARHAD RAMEZANGHORBANI · Griffin Young · Gabriel Marques · Prerna Das · Anjali Panikar · Esther Jamir · Mohammed Sulaiman Shamsudeen · K. Watts · Ananya Sen · Hari Devannagari · Edward Miller · Muyun Lihan · Howook Hwang · Janet Paulsen · Xin Yu · Kyle Gion · Timur Rvachov · Emine Kucukbenli · Saee Paliwal |
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Riemannian generative decoder ( Poster ) > link | Andreas Bjerregaard · Søren Hauberg · Anders Krogh 🔗 |
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NovoMolGen: Rethinking Molecular Language Model Pretraining ( Poster ) > link | Kamran Chitsaz · Roshan Balaji · Quentin Fournier · Nirav Bhatt · Sarath Chandar 🔗 |
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eccDNAMamba: A Pre-Trained Model for Ultra-Long eccDNA Sequence Analysis ( Poster ) > link | zhenke liu · Jien Li · Ziqi Zhang 🔗 |
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Ligand Iterative Sampling for Affinity Refinement and Drug Discovery (LISARDD) ( Poster ) > link | Valentin BADEA · Shyam Chandra · John Lin 🔗 |
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Multimodal Benchmarking of Foundation Model Representations for Cellular Perturbation Response Prediction ( Poster ) > link | Euxhen Hasanaj · Elijah Cole · Shahin Mohammadi · Sohan Addagudi · Xingyi Zhang · Le Song · Eric Xing 🔗 |
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Amortized Sampling with Transferable Normalizing Flows ( Spotlight ) > link | Charlie Tan · Majdi Hassan · Leon Klein · Saifuddin Syed · Dominique Beaini · Michael Bronstein · Alexander Tong · Kirill Neklyudov 🔗 |
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NucleoBench: A Large-Scale Benchmark of Neural Nucleic Acid Design Algorithms ( Poster ) > link | Joel Shor · Erik Strand · Cory McLean 🔗 |
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How Good is AlphaFold3 at Ranking Drug Binding Affinities? ( Poster ) > link | Xin Hong · Bowen Gao · Yinjun Jia · Wenyu Zhu · Qixuan Chen · Xiaohe Tian · Zhenyi Zhong · Jianhui Wang · Yanyan Lan 🔗 |