ICML 2025 Workshop GenBio Submissions

From Fragments to Geometry: A Unified Graph Transformer for Molecular Representation from Conformer Ensembles
Duy Minh Ho Nguyen, Trung Quoc Nguyen, Ha Thi Hong Le, Mai Thanh Nhat Truong, TrungTin Nguyen, Nhat Ho, Khoa D Doan, Duy Duong-Tran, Li Shen, Daniel Sonntag, James Zou, Mathias Niepert, Hyojin Kim, Jonathan E Allen
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
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 M. Bronstein, Dominique Beaini, Siamak Ravanbakhsh, Kirill Neklyudov, Alexander Tong
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Spotlight
- Readers: Everyone
Riemannian generative decoder
Andreas Bjerregaard, Søren Hauberg, Anders Krogh
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
Benchmark of Diffusion and Flow Matching Models for Unconditional Protein Structure Design
Wenran LI, Xavier Cadet, Cédric Damour, Yu LI, Alexandre de BREVERN, Alain Miranville, Frederic CADET
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
Active Leaning-Guided Seq2Seq Variational Autoencoder for Multi-target Inhibitor Generation
Júlia Vilalta-Mor, Alexis Molina, Laura Ortega Varga, Isaac Filella-Merce, VICTOR GUALLAR
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
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
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
Two-Stage Pretraining for Molecular Property Prediction in the Wild
Kevin Tirta Wijaya, Minghao Guo, Michael Sun, Hans-peter Seidel, Wojciech Matusik, Vahid Babaei
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
Connecting Gene Expression and Tissue Morphology with Conditional Generative Models
Frederieke Lohmann, Alberto Valdeolivas, Jelica Vasiljević
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Spotlight
- Readers: Everyone
Trustworthy Inverse Molecular Design via Alignment with Molecular Dynamics
Kevin Tirta Wijaya, Navid Ansari, Hans-peter Seidel, Vahid Babaei
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
Mixtures of Neural Cellular Automata: A Stochastic Framework for Biological Growth Modelling
Salvatore Milite, Giulio Caravagna, Andrea Sottoriva
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
Predicting function of evolutionarily implausible DNA sequences
Shiyu Jiang, Xuyin Liu, Zitong Jerry Wang
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
Representing local protein environments with atomistic foundation models
Meital Bojan, Sanketh Vedula, Sai Advaith Maddipatla, Nadav Bojan, Federico Napoli, Paul Schanda, Alexander Bronstein
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
TABASCO: A Fast, Simplified Model for Molecular Generation with Improved Physical Quality
Carlos Vonessen, Charles Harris, Miruna Cretu, Pietro Lio
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
Improving Inverse Folding for Peptide Design with Diversity-regularized Direct Preference Optimization
Ryan Park, Darren J. Hsu, C. Brian Roland, Maria Korshunova, Chen Tessler, Shie Mannor, Olivia Viessmann, Bruno Trentini
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Spotlight
- Readers: Everyone
Learning Collective Variables from Time-lagged Generation
Seonghyun Park, Kiyoung Seong, Soojung Yang, Rafael Gomez-Bombarelli, Sungsoo Ahn
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
JAMUN: Bridging Smoothed Molecular Dynamics and Score-Based Learning for Conformational Ensemble Generation
Ameya Daigavane, Bodhi P. Vani, Darcy Davidson, Saeed Saremi, Joshua A Rackers, Joseph Kleinhenz
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
Spatial Cell-Guided Pretraining for Scalable Spatial Transcriptomics Foundation Model
Jing Gong, Yixuan Wang, Nicholas Ho, Xingyi Cheng, Le Song, Eric P. Xing
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
Retrieval Augmented Protein Language Models for Protein Structure Prediction
Pan Li, Xingyi Cheng, Le Song, Eric P. Xing
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Spotlight
- Readers: Everyone
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
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
Modeling Microenvironment Trajectories on Spatial Transcriptomics with NicheFlow
Kristiyan Sakalyan, Alessandro Palma, Filippo Guerranti, Fabian J Theis, Stephan Günnemann
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
Improving Genomic Models via Task-Specific Self-Pretraining
Sohan Mupparapu, Parameswari Krishnamurthy, Ratish Puduppully
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
Revisiting Sampling Strategies for Molecular Generation
Yuyan Ni, Shikun Feng, Wei-Ying Ma, Zhi-Ming Ma, Yanyan Lan
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
Learning Diffusion Models with Flexible Representation Guidance
Chenyu Wang, Cai Zhou, Sharut Gupta, Zongyu Lin, Stefanie Jegelka, Stephen Bates, Tommi Jaakkola
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
An Iterative Framework for Generative Backmapping of Coarse Grained Proteins
Georgios Kementzidis, Erin Wong, John Nicholson, Ruichen Xu, Yuefan Deng
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
CoFM: Molecular Conformation Generation via Flow Matching in SE(3)-Invariant Latent Space
Guikun Xu, Yankai Yu, Yongquan Jiang, Yan Yang, Yatao Bian
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone