ICML 2025 Workshop GenBio Submissions

ATOMICA: Learning Universal Representations of Molecular Interactions
Ada Fang, ZAIXI ZHANG, Marinka Zitnik
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Spotlight
- Readers: Everyone
scAgents: A Multi-Agent Framework for Fully Autonomous End-to-End Single-Cell Perturbation Analysis
Xiangru 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
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
Chemical Reaction Network Implementation of Logic Gates and Neural Networks Using a Molecular Exchange Mechanism
Muhtasim Ishmum Khan, Moshiur Rahman, Md. Shahriar Karim
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
Intrinsic Evaluation of DNA Embeddings in Genome Language Models: Insights from Yeast Genomic Sequences
Ruhaib Muhammad, Rajeeva Lokshanan Reguna Madhan, Roshan Balaji, Nirav Pravinbhai Bhatt
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
Electrostatics from Laplacian Eigenbasis for Neural Network Interatomic Potentials
Maksim Zhdanov, Vladislav Kurenkov
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
Self-Supervised Representation Learning for Microbiome Improves Downstream Prediction in Data-Limited Settings and Cross-Cohort Generalizability
Liron Zahavi, Zachary Levine, Eran Segal
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
SynPair: Pairing Unpaired Antibody Chains at Billion-Sequence Scale With Contrastive Learning
Oliver M. Turnbull, Charlotte Deane
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
DIVER-0 : A Fully Channel Equivariant EEG Foundation Model
Danny Dongyeop Han, Ahhyun Lucy Lee, Taeyang Lee, Yonghyeon Gwon, Sebin Lee, Seong Jin Lee, David Keetae Park, Shinjae Yoo, Chun Kee Chung, Jiook Cha
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Spotlight
- Readers: Everyone
Balancing Speed and Precision in Protein Folding: A Comparison of AlphaFold2, ESMFold, and OmegaFold
Petr Simecek
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
Importance-Weighted Training of Diffusion Samplers
Sanghyeok Choi, Sarthak Mittal, Víctor Elvira, Jinkyoo Park, Nikolay Malkin
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
Sparse Autoencoders in Protein Engineering Campaigns: Steering and Model Diffing
Gerard Boxo Corominas, Filippo Stocco, Noelia Ferruz
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
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
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
Automated Neuron Labelling Enables Generative Steering and Interpretability in Protein Language Models
Arjun Banerjee, David Martinez, Camille Dang, Ethan Tam
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Spotlight
- Readers: Everyone
Molecular Cues to Smart Sequences: Optimizing Early Round SELEX Sequences
Soniya, Runjhun Saran Narayan, Nived Ambadipudi, Apurva Narayan
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
EpiBinder: a multimodal deep learning model at base-resolution to analyze in vivo Transcription Factor-DNA Binding
Ruben Solozabal, Albert Baichorov, Tamir Avioz, Le Song, Martin Takáč, Ariel Afek
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
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
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
No Clear Winner at Small Scale: Comparing Modern Sequence Architectures and Training Strategies for Genomic Language Models
Vera Milovanović, Antonio Orvieto
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
ProVADA: Generating Subcellular Protein Variants via Ensemble-Guided Test-Time Steering
Wenhui Sophia Lu, Xiaowei Zhang, L. Santiago Mille-Fragoso, Haoyu Dai, Xiaojing J Gao, Wing Hung Wong
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Spotlight
- Readers: Everyone
SOAPIA: Siamese-Guided Generation of Off Target-Avoiding Protein Interactions with High Target Affinity
Sophia Vincoff, Oscar Davis, Ismail Ilkan Ceylan, Alexander Tong, Joey Bose, Pranam Chatterjee
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
Robust Molecular Property Prediction via Densifying Scarce Labeled Data
Jina Kim, Jeffrey Willette, Bruno Andreis, Sung Ju Hwang
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
Constrained Molecular Generation via Sequential Flow Model Fine-Tuning
Sven Gutjahr, Riccardo De Santi, Luca Schaufelberger, Kjell Jorner, Andreas Krause
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
Diffusion-Free Graph Generation with Next-Scale Prediction
Samuel Belkadi, Dat Minh Hong, Marian Chen, Miruna Cretu, Charles Harris, Pietro Lio
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
BC-Design: A Biochemistry-Aware Framework for Highly Accurate Inverse Protein Folding
Xiangru Tang, Xinwu Ye, Fang Wu, Daniel Shao, Dong Xu, Mark Gerstein
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
Multi-state Protein Design with DynamicMPNN
Alex Abrudan, Sebastian Pujalte Ojeda, Chaitanya K. Joshi, Matthew Greenig, Felipe Engelberger, Alena Khmelinskaia, Jens Meiler, Michele Vendruscolo, Tuomas Knowles
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
Diversity by Design: Addressing Mode Collapse Improves scRNA-seq Perturbation Modeling on Well-Calibrated Metrics
Gabriel Mateo Mejia, Henry E Miller, Francis J.A. Leblanc, BO WANG, Brendan Swain, Lucas Paulo de Lima Camillo
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone