ICML 2025 Workshop GenBio Submissions

To Optimize, Not to Invent: RNAGenScape for mRNA Sequence Generation and Optimization Without de novo Design
Danqi Liao, Chen Liu, Xingzhi Sun, Die Tang, Haochen Wang, Scott Elliot Youlten, Antonio J. Giraldez, Smita Krishnaswamy
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Spotlight
- Readers: Everyone
SynCoGen: Synthesizable 3D Molecule Generation via Joint Reaction and Coordinate Modeling
Andrei Rekesh, Miruna Cretu, Dmytro Shevchuk, Vignesh Ram Somnath, Pietro Lio, Robert A. Batey, Mike Tyers, Michał Koziarski, Cheng-Hao Liu
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
A Genomic Language Model for Zero-Shot Prediction of Promoter Indel Effects
Courtney A. Shearer, Felix Teufel, Rose Orenbuch, Christian J. Steinmetz, Daniel Ritter, Erik Xie, Artem Gazizov, Aviv Spinner, Jonathan Frazer, Mafalda Dias, Pascal Notin, Debora Susan Marks
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Spotlight
- Readers: Everyone
ProxelGen: Generating Proteins as 3D Densities
Felix Faltings, Hannes Stark, Regina Barzilay, Tommi Jaakkola
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Spotlight
- Readers: Everyone
Minimum-Excess-Work Guidance
Christopher Kolloff, Tobias Höppe, Emmanouil Angelis, Mathias Jacob Schreiner, Stefan Bauer, Andrea Dittadi, Simon Olsson
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
Protein Generator with Ribosomal Origin and Folding
MinGyu Choi, Derek Chen, Tommi Jaakkola, Regina Barzilay
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
Multi-Objective-Guided Generative Design of mRNA with Therapeutic Properties
Sawan Patel, Sophia Tang, Yinuo Zhang, Pranam Chatterjee, Sherwood Yao
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
Exploring Adversarial Robustness in Classification tasks using DNA Language Models
Hyunwoo Yoo, Haebin Shin, Kaidi Xu, Gail Rosen
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
Tissue Reassembly with Generative AI
Tingyang Yu, Chanakya Ekbote, Nikita Morozov, Jiashuo Fan, Pascal Frossard, Stéphane d'Ascoli, Maria Brbic
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Spotlight
- Readers: Everyone
Efficient Models For Molecular Property Prediction
Sairam Narendra Babu, Rishabh Bhattacharya
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
eccDNAMamba: A Pre-Trained Model for Ultra-Long eccDNA Sequence Analysis
Zhenke Liu, Jien Li, Ziqi Zhang
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
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 P. Xing
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Spotlight
- Readers: Everyone
Towards Molecular Conformer Generation with Language Models
Menua Bedrosian, Hrant Khachatrian
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
Ligand Iterative Sampling for Affinity Refinement and Drug Discovery (LISARDD)
Valentin BADEA, Shyam Chandra, John Lin
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
Predicting Microbial Ontology and Pathogen Risk from Environmental Metadata with Large Language Models
Hyunwoo Yoo, Gail Rosen
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
PhenoGraph: A Multi-Agent Framework for Phenotype-driven Discovery in Spatial Transcriptomics Data Augmented with Knowledge Graphs
Seyednami Niyakan, Xiaoning Qian
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
EpitopeGen: Learning to Generate T Cell Epitopes: A Semi-Supervised Approach with Biological Constraints
Minuk Ma, Wilson Tu, Carlos Vasquez-Rios, Jiarui Ding
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
TACTIC: An Explainable Multi-Agent Architecture for Classification & Interpretable Reasoning in Spatial Transcriptomics
Abdel Rahman Alsabbagh, Mahmoud Zahran, Ali Balubaid, Sumeer Ahmad Khan, Robert Lehmann, Xabier Martinez de Morentin, Vincenzo Lagani, Narsis A. Kiani, David Gomez-Cabrero, Jesper Tegnér
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
NucleoBench: A Large-Scale Benchmark of Neural Nucleic Acid Design Algorithms
Joel Shor, Erik Strand, Cory Y McLean
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
Amortized Sampling with Transferable Normalizing Flows
Charlie B. Tan, Majdi Hassan, Leon Klein, Saifuddin Syed, Dominique Beaini, Michael M. Bronstein, Alexander Tong, Kirill Neklyudov
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Spotlight
- Readers: Everyone
Beyond Visual Inspection: Principled Benchmarking of Single-Cell Trajectory Representations with scTRAM
Kemal Inecik, Malte D Luecken, Fabian J Theis
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
LLMs for Experiment Design in Scientific Domains: Are We There Yet?
Rushil Gupta, Jason Hartford, Bang Liu
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
MolGuidance: A Comparative Study of Guidance Methods for Conditional Molecule Generation
Cheng Zeng, Jirui Jin, Pawan Prakash, George Karypis, Mark Transtrum, Ellad B. Tadmor, Richard Hennig, Adrian Roitberg, Stefano Martiniani, Mingjie Liu
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
Straight but not so fast: Challenges with Rectified Flows in Protein Design.
Junhua Chen, Simon V Mathis, Charles Harris, Kieran Didi, Pietro Lio
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone
LapDDPM: A Conditional Graph Diffusion Model for scRNA-seq Generation with Spectral Adversarial Perturbations
Lorenzo Bini, Stephane Marchand-Maillet
- Published: 11 Jun 2025, Last Modified: 18 Jul 2025
- GenBio 2025 Poster
- Readers: Everyone