ICML 2025 Workshop GenBio Submissions

Calibrating Generative Models
Henry Smith, Brian L. Trippe
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Spotlight
- Readers: Everyone
Design in Voxel Space Decode in SMILES Space: Plixer Generates Drug-Like Molecules for Protein Pockets
Jude Wells, Brooks Paige
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
Scaffold-Driven GPT Model for Drug Optimization
Xuefeng Liu, Songhao Jiang, Ian Foster, Jinbo Xu, Rick L. Stevens
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
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 Hernández-García
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
Modeling Molecular Sequences with Learning-Order Autoregressive Models
Zhe Wang, Jiaxin Shi, Nicolas Heess, Michalis Titsias, Arthur Gretton, Yee Whye Teh
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
STRAND: Structure Refinement of RNA-Protein Complexes via Diffusion
Mohsen Al-zeqri, Jörg K.H. Franke, Frederic Runge
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
Unifying Force Prediction and Molecular Conformation Generation Through Representation Alignment
Lucas Pinede, Soojung Yang, Juno Nam, Rafael Gomez-Bombarelli
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
MolFORM: Multi-modal Flow Matching for Structure-Based Drug Design
Jie Huang, Daiheng Zhang
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
Generation of structure-guided pMHC-I libraries using Diffusion Models
Sergio Emilio Mares, Ariel Espinoza Weinberger, Nilah M Ioannidis
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
A Ground-Up Designed Controllable GPT for Molecule Optimization
Xuefeng Liu, Songhao Jiang, Bo Li, Rick L. Stevens
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
SurfProp: A surface-based property prediction framework for antibody developability and screening
Pranav Rao, Henry Isaacson, Jennifer L. Hofmann, Darcy Davidson, Amy Wang, Andrew Martin Watkins, Richard Bonneau, Saeed Izadi, Jae Hyeon Lee
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
A Zero-shot LLM-based Framework for Descriptive Gene-gene Interaction Network Generation
Bingjun Li, Mason Zito Ritchotte, Sihong He, Sheida Nabavi
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
Foreground-aware Virtual Staining for Accurate 3D Cell Morphological Profiling
Alexandr A. Kalinin, Paula Llanos, Theresa Maria Sommer, Giovanni Sestini, Xinhai Hou, Jonathan Z. Sexton, Xiang Wan, Ivo Dinov, Brian Athey, nicolas clement rivron, Anne E Carpenter, Beth A Cimini, Shantanu Singh, Matthew J. O'Meara
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
Analytic Gaussian Convolution for Faster Molecular Optimization and Sampling
Soumya Ram, Akhila Ram
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
Generating readily synthesizable dye scaffolds with SyntheFluor
Ruhi Sayana, Jennifer Xu, Kate Callon, Jonathan Deutsch, James Zou, John Janetzko, Rabindra V. Shivnaraine, Kyle Swanson
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
Forecasting H1N1 Influenza Pandemic and Seasonal Evolution
Aarushi Mehrotra, Sarah Gurev, Noor Youssef, Debora Susan Marks
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
Towards functional annotation with latent protein language model features
Jake Silberg, Elana Simon, James Zou
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
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
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
FORT: Forward-Only Regression Training of Normalizing Flows
Danyal Rehman, Oscar Davis, Jiarui Lu, Jian Tang, Michael M. Bronstein, Yoshua Bengio, Alexander Tong, Joey Bose
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Spotlight
- Readers: Everyone
Rapidash: Scalable Molecular Modeling Through Controlled Equivariance Breaking
Sharvaree Vadgama, Erik J Bekkers
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
SIMBA-GNN: Simulation-augmented Microbiome Abundance Graph Neural Network
Mohammad S. Parsa, Javad Aminian Dehkordi, Mohammad Mofrad
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
Biological Reasoning with Reinforcement Learning through Natural Language Enables Generalizable Zero-Shot Cell Type Annotations
Xi Wang, Runzi Tan, Simona Cristea
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
AbFlowNet: Optimizing Antibody-Antigen Binding Energy via Diffusion-GFlowNet Fusion
Abrar Rahman Abir, Haz Sameen Shahgir, Md. Rownok Zahan Ratul, Md Toki Tahmid, Greg Ver Steeg, Yue Dong
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
A Diffusion-Based Autoencoder for Learning Patient-Level Representations from Single-Cell Data
Rebecca Boiarsky, Johann Wenckstern, Nicholas J Haradhvala, Gad Getz, David Sontag
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
Multimodal Benchmarking of Foundation Model Representations for Cellular Perturbation Response Prediction
Euxhen Hasanaj, Elijah Cole, Shahin Mohammadi, Sohan Addagudi, Xingyi Zhang, Le Song, Eric P. Xing
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone