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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
Project Page [ OpenReview] 

Abstract

Video

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Schedule

Timezone: Asia/Seoul
12:30 AM
Opening remark
1:25 AM
Spotlight1
3:40 AM
Spotlight2
6:35 AM
Spotlight3
TABASCO: A Fast, Simplified Model for Molecular Generation with Improved Physical Quality
Carlos Vonessen ⋅ Charles Harris ⋅ Miruna Cretu ⋅ Pietro Lió
Towards Molecular Conformer Generation with Language Models
Menua Bedrosian ⋅ Hrant Khachatrian
Unifying Force Prediction and Molecular Conformation Generation Through Representation Alignment
Lucas Pinede ⋅ Soojung Yang ⋅ Juno Nam ⋅ Rafael Gomez-Bombarelli
Spatial Cell-Guided Pretraining for Scalable Spatial Transcriptomics Foundation Model
Jing Gong ⋅ Yixuan Wang ⋅ Nicholas Ho ⋅ Xingyi Cheng ⋅ Le Song ⋅ Eric Xing
SurfProp: A surface-based property prediction framework for antibody developability and screening
Pranav Rao ⋅ Henry Isaacson ⋅ Jennifer Hofmann ⋅ Darcy Davidson ⋅ Amy Wang ⋅ Andrew Watkins ⋅ Richard Bonneau ⋅ Saeed Izadi ⋅ Jae Hyeon Lee
A framework to extract and interpret biological concepts from scRNAseq generative foundation models
Charlotte Claye ⋅ Pierre Marschall ⋅ Wassila Ouerdane ⋅ Céline Hudelot ⋅ Julien Duquesne
FORT: Forward-Only Regression Training of Normalizing Flows
Danyal Rehman ⋅ Oscar Davis ⋅ Jiarui Lu ⋅ Jian Tang ⋅ Michael Bronstein ⋅ Yoshua Bengio ⋅ Alexander Tong ⋅ Joey Bose
Pi-SAGE: Permutation-invariant surface-aware graph encoder for binding affinity prediction
Sharmi Banerjee ⋅ Mostafa Karimi ⋅ Melih Yilmaz ⋅ Tommi Jaakkola ⋅ Bella Dubrov ⋅ Shang Shang ⋅ Ron Benson
Retrieval Augmented Protein Language Models for Protein Structure Prediction
Pan Li ⋅ Xingyi Cheng ⋅ Le Song ⋅ Eric Xing
Progressive Inference-Time Annealing of Diffusion Models for Sampling from Boltzmann Densities
Tara Akhound-Sadegh ⋅ Jungyoon Lee ⋅ Joey Bose ⋅ Valentin De Bortoli ⋅ Arnaud Doucet ⋅ Michael Bronstein ⋅ Dominique Beaini ⋅ Siamak Ravanbakhsh ⋅ Kirill Neklyudov ⋅ Alexander Tong
Molecular Cues to Smart Sequences: Optimizing Early Aptamers from SELEX
Soniya ⋅ Runjhun Narayan ⋅ Apurva Narayan
Enhancing AlphaFold3 for Protein-Ligand Co-Folding via Reinforcement Learning
YU PEI ⋅ Yuxuan Song ⋅ Zhilong Zhang ⋅ Keyue Qiu ⋅ Hao Zhou ⋅ Wei-Ying Ma
Generating readily synthesizable dye scaffolds with SyntheFluor
Ruhi Sayana ⋅ Jennifer Xu ⋅ Kate Callon ⋅ Jonathan Deutsch ⋅ James Zou ⋅ John Janetzko ⋅ Rabindra Shivnaraine ⋅ Kyle Swanson
Measuring Scientific Capabilities of Language Models with a Systems Biology Dry Lab
Haonan Duan ⋅ Stephen Lu ⋅ Caitlin Harrigan ⋅ Nishkrit Desai ⋅ Jiarui Lu ⋅ Michał Koziarski ⋅ Leonardo Cotta ⋅ Chris Maddison
Sparse Autoencoders in Protein Engineering Campaigns: Steering and Model Diffing
Gerard Corominas ⋅ Filippo Stocco ⋅ Noelia Ferruz
SIMBA-GNN: Simulation-augmented Microbiome Abundance Graph Neural Network
Mohammad Parsa ⋅ Javad Aminian-Dehkordi ⋅ Mohammad Mofrad
Teddy: A FAMILY OF FOUNDATION MODELS FOR UNDERSTANDING SINGLE CELL BIOLOGY
Alexis 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
Modeling Molecular Sequences with Learning-Order Autoregressive Models
Zhe Wang ⋅ Jiaxin Shi ⋅ Nicolas Heess ⋅ Michalis Titsias ⋅ Arthur Gretton ⋅ Yee-Whye Teh
Bures-Wasserstein Flow Matching for Graph Generation
Keyue Jiang ⋅ Jiahao Cui ⋅ Xiaowen Dong ⋅ Laura Toni
Two-Stage Pretraining for Molecular Property Prediction in the Wild
Kevin Tirta Wijaya ⋅ Minghao Guo ⋅ Michael Sun ⋅ Hans-peter Seidel ⋅ Wojciech Matusik ⋅ Vahid Babaei
TACTIC: An Explainable Multi-Agent Architecture for Classification & Interpretable Reasoning in Spatial Transcriptomics
Abdel Rahman Alsabbagh ⋅ Mahmoud Zahran ⋅ Ali Balubaid ⋅ Sumeer Khan ⋅ Robert Lehmann ⋅ Xabier Martínez de Morentin ⋅ Vincenzo Lagani ⋅ Narsis Kiani ⋅ David Gomez-Cabrero ⋅ jesper tegner
Representing local protein environments with atomistic foundation models
Meital Bojan ⋅ Sanketh Vedula ⋅ Sai Advaith Maddipatla ⋅ Nadav Bojan ⋅ Federico Napoli ⋅ Paul Schanda ⋅ Alexander Bronstein
Do we need equivariant models for molecule generation?
Ewa M. Nowara ⋅ Joshua Rackers ⋅ Patricia Suriana ⋅ Pan Kessel ⋅ Max Shen ⋅ Andrew Watkins ⋅ Michael Maser
Learning Diffusion Models with Flexible Representation Guidance
Chenyu Wang ⋅ Cai Zhou ⋅ Sharut Gupta ⋅ Zongyu Lin ⋅ Stefanie Jegelka ⋅ Stephen Bates ⋅ Tommi Jaakkola
Straight but not so fast: Challenges with Rectified Flows in Protein Design.
Junhua Chen ⋅ Simon Mathis ⋅ Charles Harris ⋅ Kieran Didi ⋅ Pietro Lió
Bimodal masked language modeling for bulk RNA-seq and DNA methylation representation learning
Maxence Gélard ⋅ Hakim Benkirane ⋅ Thomas Pierrot ⋅ Guillaume Richard ⋅ Paul-Henry Cournède
ProteinCrow: A Language Model Agent That Can Design Proteins
Raghava Manvitha Reddy Ponnapati ⋅ Sam Cox ⋅ Cade Gordon ⋅ Michael Hammerling ⋅ Siddharth Narayanan ⋅ Jon Laurent ⋅ James Braza ⋅ Michaela Hinks ⋅ Michael Skarlinski ⋅ Sam Rodriques ⋅ Andrew White
Unlocking Non-Invasive Brain-to-Text
Dulhan Jayalath ⋅ Gilad Landau ⋅ ʻŌiwi Parker Jones
HM-GIM: A Probabilistic Neural Model for Discovering Heterogeneous Microbiome or Human Gene Groupings and Their Interactions
Jiening Zhu ⋅ Isin Comba ⋅ Shakti Bhattarai ⋅ Vanni Bucci ⋅ Georg Gerber
Importance-Weighted Training of Diffusion Samplers
Sanghyeok Choi ⋅ Sarthak Mittal ⋅ Víctor Elvira ⋅ Jinkyoo Park ⋅ Nikolay Malkin
MolFORM: Multi-modal Flow Matching for Structure-Based Drug Design
Daiheng Zhang ⋅ Jie Huang ⋅ Zhao Zhang
In silico design of epigenetic reprogramming payloads
Lucas Seninge ⋅ Conner Kummerlowe ⋅ David Reynolds ⋅ Nicholas Bernstein ⋅ Jacob Kimmel
ProxelGen: Generating Proteins as 3D Densities
Felix Faltings ⋅ Hannes Stärk ⋅ Regina Barzilay ⋅ Tommi Jaakkola
Fast and Scalable Gene Embedding Search: A Comparative Study of FAISS and ScaNN
Mohammadsaleh Refahi ⋅ Gavin Hearne ⋅ Harrison Muller ⋅ Kieran Lynch ⋅ Bahrad Sokhansanj ⋅ James Brown ⋅ Gail Rosen
Benchmark of Diffusion and Flow Matching Models for Unconditional Protein Structure Design
Wenran LI ⋅ Xavier Cadet ⋅ Cédric Damour ⋅ Yu LI ⋅ Alexandre G. de BREVERN ⋅ Alain Miranville ⋅ Frederic CADET
Improving Genomic Models via Task-Specific Self-Pretraining
Sohan Mupparapu ⋅ Parameswari Krishnamurthy ⋅ Ratish Surendran Puduppully
Partition Generative Modeling: Masked Modeling Without Masks
Justin Deschenaux ⋅ Lan Tran ⋅ Caglar Gulcehre
Straight-Line Diffusion Model for Efficient 3D Molecular Generation
Yuyan Ni ⋅ Shikun Feng ⋅ Haohan Chi ⋅ Bowen Zheng ⋅ Huan-ang Gao ⋅ Wei-Ying Ma ⋅ Zhi-Ming Ma ⋅ Yanyan Lan
An Iterative Framework for Generative Backmapping of Coarse Grained Proteins
Georgios Kementzidis ⋅ Erin Wong ⋅ John Nicholson ⋅ Ruichen Xu ⋅ Yuefan Deng
OrthoGraphRAG: Enhancing Clinical Decision Making with Multi-Level Knowledge Graphs
Venkatesh Tata ⋅ Zohra Bouchamaoui ⋅ Nagavaishnavi Bhaskara
Active Leaning-Guided Seq2Seq Variational Autoencoder for Multi-target Inhibitor Generation
Júlia Vilalta Mor ⋅ Alexis Molina ⋅ Laura Varga ⋅ Isaac Filella-Merce ⋅ VICTOR GUALLAR
AbFlowNet: Optimizing Antibody-Antigen Binding Energy via Diffusion-GFlowNet Fusion
Abrar Abir ⋅ Haz Shahgir ⋅ Rownok Ratul ⋅ Toki Tahmid ⋅ Greg Ver Steeg ⋅ Yue Dong
A Diffusion-Based Autoencoder for Learning Patient-Level Representations from Single-Cell Data
Rebecca Boiarsky ⋅ Johann Wenckstern ⋅ Nicholas Haradhvala ⋅ Gad Getz ⋅ David Sontag
Align Your Structures: Generating Trajectories with Structure Pretraining for Molecular Dynamics
Aniketh Iyengar ⋅ Jiaqi Han ⋅ Pengwei Sun ⋅ Mingjian Jiang ⋅ Jianwen Xie ⋅ Stefano Ermon
An Improved Systematic Method for Constructing Enzyme-Constrained Genome-Scale Metabolic Models Using a Protein-Chemical Transformer
Anna Schooneveld ⋅ Shafiat Dewan ⋅ Will Addison ⋅ David Berman ⋅ Navot Arad ⋅ Sam Genway ⋅ Sonya Kalsi ⋅ Kotryna Bloznelyte
BC-Design: A Biochemistry-Aware Framework for Highly Accurate Inverse Protein Folding
Robert Tang ⋅ Xinwu Ye ⋅ Fang Wu ⋅ Daniel Shao ⋅ Dong Xu ⋅ Mark Gerstein
LLMs for Experiment Design in Scientific Domains: Are We There Yet?
Rushil Gupta ⋅ Jason Hartford ⋅ Bang Liu
ATOMICA: Learning Universal Representations of Molecular Interactions
Ada Fang ⋅ ZAIXI ZHANG ⋅ Marinka Zitnik
Foreground-aware Virtual Staining for Accurate 3D Cell Morphological Profiling
Alexandr 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
Pullback Flow Matching on Data Manifolds
Friso de Kruiff ⋅ Erik Bekkers ⋅ Ozan Öktem ⋅ Carola-Bibiane Schönlieb ⋅ Willem Diepeveen
Modeling Microenvironment Trajectories on Spatial Transcriptomics with NicheFlow
Kristiyan Sakalyan ⋅ Alessandro Palma ⋅ Filippo Guerranti ⋅ Fabian Theis ⋅ Stephan Günnemann
Predicting function of evolutionarily implausible DNA sequences
Shiyu Jiang ⋅ Xuyin Liu ⋅ Zitong Jerry Wang
Diversity by Design: Addressing Mode Collapse Improves scRNA-seq Perturbation Modeling on Well-Calibrated Metrics
Gabriel Mejia ⋅ Henry Miller ⋅ Francis Leblanc ⋅ BO WANG ⋅ Brendan Swain ⋅ Lucas Paulo de Lima Camillo
MolGuidance: A Comparative Study of Guidance Methods for Conditional Molecule Generation
Cheng Zeng ⋅ Jirui Jin ⋅ Pawan Prakash ⋅ George Karypis ⋅ Mark Transtrum ⋅ Ellad Tadmor ⋅ Richard Hennig ⋅ Adrian Roitberg ⋅ Stefano Martiniani ⋅ Mingjie Liu
Torsional-GFN: a conditional conformation generator for small molecules
Lena Nehale Ezzine ⋅ Alexandra Volokhova ⋅ Piotr Gaiński ⋅ Luca Scimeca ⋅ Emmanuel Bengio ⋅ Prudencio Tossou ⋅ Yoshua Bengio ⋅ Alex Hernandez-Garcia
Automated Neuron Labels For Protein Language Models Enable Generative Steering
Arjun Banerjee ⋅ David Martinez ⋅ Camille Dang ⋅ Ethan Tam
SynCoGen: Synthesizable 3D Molecule Generation via Joint Reaction and Coordinate Modeling
Andrei Rekesh ⋅ Miruna Cretu ⋅ Dmytro Shevchuk ⋅ Vignesh Ram Somnath ⋅ Pietro Lió ⋅ Robert Batey ⋅ Mike Tyers ⋅ Michał Koziarski ⋅ Chenghao Liu
Calibrating Generative Models
Henry Smith ⋅ Brian Trippe
From Fragments to Geometry: A Unified Graph Transformer for Molecular Representation from Conformer Ensembles
Duy 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
Intrinsic Evaluation of DNA Embeddings in Genome Language Models: Insights from Yeast Genomic Sequences
Ruhaib Muhammad ⋅ Rajeeva Madhan ⋅ Roshan Balaji ⋅ Nirav Bhatt
Robust Molecular Property Prediction via Densifying Scarce Labeled Data
Jina Kim ⋅ Jeffrey Willette ⋅ Bruno Andreis ⋅ Sung Ju Hwang
A Zero-shot LLM-based Framework for Descriptive Gene-gene Interaction Network Generation
Bingjun Li ⋅ Mason Ritchotte ⋅ Sihong He ⋅ Sheida Nabavi
Trustworthy Inverse Molecular Design via Alignment with Molecular Dynamics
Kevin Tirta Wijaya ⋅ Navid Ansari ⋅ Hans-peter Seidel ⋅ Vahid Babaei
DePO: Elicit Chemical Reasoning Capability via Demonstration-Guided Policy Optimization
Xuan Li ⋅ Zhanke Zhou ⋅ Zongze Li ⋅ Jiangchao Yao ⋅ Yu Rong ⋅ Lu Zhang ⋅ Bo Han
Minimum-Excess-Work Guidance
Christopher Kolloff ⋅ Tobias Höppe ⋅ Emmanouil Angelis ⋅ Mathias Schreiner ⋅ Stefan Bauer ⋅ Andrea Dittadi ⋅ Simon Olsson
Constrained Molecular Generation via Sequential Flow Model Fine-Tuning
Sven Gutjahr ⋅ Riccardo De Santi ⋅ Luca Schaufelberger ⋅ Kjell Jorner ⋅ Andreas Krause
DIVER-0 : A Fully Channel Equivariant EEG Foundation Model
Danny D Han ⋅ Ahhyun Lee ⋅ Taeyang Lee ⋅ Yonghyeon Gwon ⋅ Sebin Lee ⋅ Seong Lee ⋅ David K Park ⋅ Shinjae Yoo ⋅ Chun Kee Chung ⋅ Jiook Cha
Multi-Granular Contrastive Alignment and Fusion for Fragment-Enhanced Virtual Screening
Haichuan Tan ⋅ Bowen Gao ⋅ Jiaxin Li ⋅ Yanwen Huang ⋅ Wenyu Zhu ⋅ Jianhui Wang ⋅ Yinjun Jia ⋅ Yuanhuan Mo ⋅ Ya-Qin Zhang ⋅ Wei-Ying Ma ⋅ Yanyan Lan
AtoMAE: Learning Protein Structure Representations from Atomic Voxel Grids via Masked Autoencoders
Namuk Park ⋅ Pedro O. Pinheiro ⋅ Nathan Frey ⋅ Sidney Lisanza ⋅ Andrew Watkins ⋅ Arian Jamasb ⋅ Matthieu Kirchmeyer ⋅ Richard Bonneau ⋅ Saeed Saremi ⋅ Vladimir Gligorijevic
Guided Generation for Developable Antibodies
Siqi Zhao ⋅ Joshua Moller ⋅ Lood van Niekerk
A Diffusion Model to Shrink Proteins While Maintaining their Function
Ethan Baron ⋅ Alan Amin ⋅ Ruben Weitzman ⋅ Debora Marks ⋅ Andrew Wilson
Consistent Sampling and Simulation: Molecular Dynamics with Energy-Based Diffusion Models
Michael Plainer ⋅ Hao Wu ⋅ Leon Klein ⋅ Stephan Günnemann ⋅ Frank Noe
KODA: An Agentic Framework for KEGG Orthology-Driven Discovery of Antimicrobial Drug Targets in Gut Microbiome
Javad Aminian-Dehkordi ⋅ Mohammad Parsa ⋅ Mohsen Naghipourfar ⋅ Mohammad Mofrad
ProVADA: Generation of Subcellular Protein Variants via Ensemble-Guided Test-Time Steering
Wenhui Lu ⋅ Xiaowei Zhang ⋅ L. Mille-Fragoso ⋅ Haoyu Dai ⋅ Xiaojing Gao ⋅ Wong
Generation of structure-guided pMHC-I libraries using Diffusion Models
Sergio Mares ⋅ Ariel Espinoza ⋅ Nilah Ioannidis
STRAND: Structure Refinement of RNA-Protein Complexes via Diffusion
Mohsen Al-zeqri ⋅ Jörg Franke ⋅ Frederic Runge
Diffusion models with group symmetries for biomolecule generation
Wenran LI ⋅ Xavier Cadet ⋅ David Medina ⋅ Mehdi D. Davari ⋅ Ramanathan Sowdhamini ⋅ Cédric Damour ⋅ Yu LI ⋅ Alain Miranville ⋅ Frederic CADET
Connecting Gene Expression and Tissue Morphology with Conditional Generative Models
Frederieke Lohmann ⋅ Alberto Valdeolivas ⋅ Jelica Vasiljević
Learning Collective Variables from Time-lagged Generation
Seonghyun Park ⋅ Kiyoung Seong ⋅ Soojung Yang ⋅ Rafael Gomez-Bombarelli ⋅ Sungsoo Ahn
A Genomic Language Model for Zero-Shot Prediction of Promoter Indel Effects
Courtney Shearer ⋅ Felix Teufel ⋅ Rose Orenbuch ⋅ Christian Steinmetz ⋅ Daniel Ritter ⋅ Erik Xie ⋅ Artem Gazizov ⋅ Aviv Spinner ⋅ Jonathan Frazer ⋅ Mafalda Dias ⋅ Pascal Notin ⋅ Debora Marks
Multi-Objective-Guided Generative Design of mRNA with Therapeutic Properties
Sawan Patel ⋅ Sophia Tang ⋅ Yinuo Zhang ⋅ Pranam Chatterjee, PhD ⋅ Sherwood Yao
Joint Probabilistic Modeling of Pseudobulk and Single-Cell Transcriptomics Enables Accurate Estimation of Cell Type Composition
Simon Grouard ⋅ Khalil Ouardini ⋅ Yann Rodriguez ⋅ Jean-Philippe Vert ⋅ Almudena Espin-Perez
Promoter Sequence Generation using Homology Prompting
Erik Xie ⋅ Courtney Shearer ⋅ Ruben Weitzman ⋅ Pascal Notin ⋅ Debora Marks
Efficient Models for molecular property prediction
Sairam Babu ⋅ Rishabh Bhattacharya
Revisiting Sampling Strategies for Molecular Generation
Yuyan Ni ⋅ Shikun Feng ⋅ Wei-Ying Ma ⋅ Zhi-Ming Ma ⋅ Yanyan Lan
HybridLinker: Topology-Guided Posterior Sampling for Enhanced Diversity and Validity in 3D Molecular Linker Generation
Minyeong Hwang ⋅ Ziseok Lee ⋅ Kwang-Soo Kim ⋅ Kyungsu Kim ⋅ Eunho Yang
FIGRDock: Fast Interaction-Guided Regression for Flexible Docking
Shikun Feng ⋅ Bicheng Lin ⋅ Yuanhuan Mo ⋅ Yuyan Ni ⋅ Wenyu Zhu ⋅ Bowen Gao ⋅ Wei-Ying Ma ⋅ haitao li ⋅ Yanyan Lan
Forecasting H1N1 Influenza Pandemic and Seasonal Evolution
Aarushi Mehrotra ⋅ Sarah Gurev ⋅ Noor Youssef ⋅ Debora Marks
scAgents: A Multi-Agent Framework for Fully Autonomous End-to-End Single-Cell Perturbation Analysis
Robert 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
Improving Inverse Folding for Peptide Design with Diversity-regularized Direct Preference Optimization
Ryan Park ⋅ Darren Hsu ⋅ C. Roland ⋅ Maria Korshunova ⋅ Chen Tessler ⋅ Shie Mannor ⋅ Olivia Viessmann ⋅ Bruno Trentini
BindEnergyCraft: Casting Protein Structure Predictors as Energy-Based Models for Binder Design
Divya Nori ⋅ Anisha Parsan ⋅ Caroline Uhler ⋅ Wengong Jin
EpiBinder: a multimodal deep learning model at base-resolution to analyze in vivo Transcription Factor-DNA Binding
Rubén Solozabal ⋅ Albert Baichorov ⋅ Tamir Avioz ⋅ Le Song ⋅ Martin Takac ⋅ Ariel Afek
Ibex: Pan-immunoglobulin structure prediction
Frederic Dreyer ⋅ Karolis Martinkus ⋅ Jan Ludwiczak ⋅ Brennan Abanades ⋅ Robert Alberstein ⋅ Pranav Rao ⋅ Jae Hyeon Lee ⋅ Richard Bonneau ⋅ Andrew Watkins ⋅ Franziska Seeger
JAMUN: Bridging Smoothed Molecular Dynamics and Score-Based Learning for Conformational Ensemble Generation
Ameya Daigavane ⋅ Bodhi Vani ⋅ Darcy Davidson ⋅ Saeed Saremi ⋅ Joshua Rackers ⋅ Joseph Kleinhenz
Flow Density Control: Generative Optimization Beyond Entropy-Regularized Fine-Tuning
Riccardo De Santi ⋅ Marin Vlastelica ⋅ Ya-Ping Hsieh ⋅ Zebang Shen ⋅ Niao He ⋅ Andreas Krause
ControllableGPT: A Ground-Up Designed Controllable GPT for Molecule Optimization
Xuefeng Liu ⋅ Songhao Jiang ⋅ Bo Li ⋅ Rick Stevens
CoFM: Molecular Conformation Generation via Flow Matching in SE(3)-Invariant Latent Space
Guikun Xu ⋅ Yankai Yu ⋅ Yongquan Jiang ⋅ Yan Yang ⋅ Yatao Bian
Simultaneous Modeling of Protein Conformation and Dynamics via Autoregression
Yuning Shen ⋅ Lihao Wang ⋅ Huizhuo Yuan ⋅ YAN WANG ⋅ Bangji Yang ⋅ Quanquan Gu
SOAPIA: Siamese-Guided Generation of Off Target-Avoiding Protein Interactions with High Target Affinity
Sophia Vincoff ⋅ Oscar Davis ⋅ Ismail Ceylan ⋅ Alexander Tong ⋅ Joey Bose ⋅ Pranam Chatterjee, PhD
Protein Generator with Ribosomal Origin and Folding
MinGyu Choi ⋅ Derek Chen ⋅ Tommi Jaakkola ⋅ Regina Barzilay
Multi-state Protein Design with DynamicMPNN
Alex Abrudan ⋅ Sebastian Pujalte Ojeda ⋅ Chaitanya Joshi ⋅ Matthew Greenig ⋅ Felipe Engelberger ⋅ Alena Khmelinskaia ⋅ Jens Meiler ⋅ Michele Vendruscolo ⋅ Tuomas Knowles
To Optimize, Not to Invent: Controlled On-Manifold Diffusion Walk for mRNA Sequence Generation and Optimization Without $\textit{de novo}$ Design
Danqi Liao ⋅ Chen Liu ⋅ Xingzhi Sun ⋅ Die Tang ⋅ Haochen Wang ⋅ Scott Youlten ⋅ Antonio Giraldez ⋅ Smita Krishnaswamy
Tissue Reassembly with Generative AI
Tingyang Yu ⋅ Chanakya Ekbote ⋅ Nikita Morozov ⋅ Jiashuo Fan ⋅ Pascal Frossard ⋅ Stéphane d'Ascoli ⋅ Maria Brbic
Multi-Objective-Guided Discrete Flow Matching for Controllable Biological Sequence Design
Tong Chen ⋅ Yinuo Zhang ⋅ Sophia Tang ⋅ Pranam Chatterjee, PhD
ScaffoldGPT: A Scaffold-based GPT Model for Drug Optimization
Xuefeng Liu ⋅ Songhao Jiang ⋅ Ian Foster ⋅ Jinbo Xu ⋅ Rick Stevens
Diffusion-Free Graph Generation with Next-Scale Prediction
Samuel Belkadi ⋅ Dat Hong ⋅ Marian Chen ⋅ Miruna Cretu ⋅ Charles Harris ⋅ Pietro Lió
Exploring Adversarial Robustness in Classification tasks using DNA Language Models
Hyunwoo Yoo ⋅ Haebin Shin ⋅ Kaidi Xu ⋅ Gail Rosen
Rapid and Reproducible Multimodal Biological Foundation Model Development with AIDO.ModelGenerator
Caleb Ellington ⋅ Dian Li ⋅ Shuxian Zou ⋅ Elijah Cole ⋅ Ning Sun ⋅ Sohan Addagudi ⋅ Le Song ⋅ Eric Xing
ToxBench: A Binding Affinity Prediction Benchmark with AB-FEP-Calculated Labels for Human Estrogen Receptor Alpha
Meng 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
Riemannian generative decoder
Andreas Bjerregaard ⋅ Søren Hauberg ⋅ Anders Krogh
NovoMolGen: Rethinking Molecular Language Model Pretraining
Kamran Chitsaz ⋅ Roshan Balaji ⋅ Quentin Fournier ⋅ Nirav Bhatt ⋅ Sarath Chandar
Multimodal Benchmarking of Foundation Model Representations for Cellular Perturbation Response Prediction
Euxhen Hasanaj ⋅ Elijah Cole ⋅ Shahin Mohammadi ⋅ Sohan Addagudi ⋅ Xingyi Zhang ⋅ Le Song ⋅ Eric Xing
Amortized Sampling with Transferable Normalizing Flows
Charlie Tan ⋅ Majdi Hassan ⋅ Leon Klein ⋅ Saifuddin Syed ⋅ Dominique Beaini ⋅ Michael Bronstein ⋅ Alexander Tong ⋅ Kirill Neklyudov
How Good is AlphaFold3 at Ranking Drug Binding Affinities?
Xin Hong ⋅ Bowen Gao ⋅ Yinjun Jia ⋅ Wenyu Zhu ⋅ Qixuan Chen ⋅ Xiaohe Tian ⋅ Zhenyi Zhong ⋅ Jianhui Wang ⋅ Yanyan Lan