ICLR 2025 Workshop GEM Submissions

A Mammalian High-Throughput Assay to Screen AI-Designed Protein Degraders
Lin Zhao, Aastha Pal, Tong Chen, Pranam Chatterjee
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
AffinityFlow: Guided Flows for Antibody Affinity Maturation
Can Chen, Karla-Luise Herpoldt, Chenchao Zhao, Zichen Wang, Marcus D. Collins, Shang Shang, Ron Benson
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
GLID$^2$E: A Gradient-Free Lightweight Fine-tune Approach for Discrete Sequence Design
Hanqun Cao, Haosen Shi, Chenyu Wang, Sinno Jialin Pan, Pheng-Ann Heng
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
Structural modeling of antibody variant epitope specificity with complementary experimental and computational techniques
Eva Smorodina, Oliver Crook, Johannes R. Loeffler, Monica Lisa Fernandez Quintero, Lucas Matthias Weissenborn, Hannah L Turner, Aleksandar Antanasijevic, Rahmad Akbar, Puneet Rawat, Khang Lê Quý, Brij Bhushan Mehta, Ole Magnus Fløgstad, Dario Segura-Peña, Nikolina Sekulić, Andrew B. Ward, Fridtjof Lund-Johansen, Jan Terje Andersen, Victor Greiff
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
Guided Sequence-Structure Generative Modeling for Iterative Antibody Optimization
Aniruddh Raghu, Sebastian W. Ober, Maxwell Kazman, Hunter Elliott
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
MeMDLM: De Novo Membrane Protein Design with Property-Guided Discrete Diffusion
Shrey Goel, Vishrut Thoutam, Edgar Mariano Marroquin, Aaron Gokaslan, Arash Firouzbakht, Sophia Vincoff, Volodymyr Kuleshov, Huong T. Kratochvil, Pranam Chatterjee
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
Repurposing AlphaFold3-like Protein Folding Models for Antibody Sequence and Structure Co-design
Nianzu Yang, Jian Ma, Songlin Jiang, Huaijin Wu, Shuangjia Zheng, Wengong Jin, Junchi Yan
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
Efficient Molecular Conformer Generation with SO(3) Averaged Flow-Matching and Reflow
Zhonglin Cao, Mario Geiger, Allan Dos Santos Costa, Danny Reidenbach, Karsten Kreis, Tomas Geffner, Franco Pellegrini, Guoqing Zhou, Emine Kucukbenli
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
Programmable Protein Stabilization with Language Model-Derived Peptide Guides
Lauren Hong, Tian Zi Wang, Divya Srijay, Howard Liu, Rio Watson, Lin Zhao, Sophia Vincoff, Leo Chen, Kseniia Kholina, Shrey Goel, Matthew DeLisa, Pranam Chatterjee
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
Compositional Flows for 3D Molecule and Synthesis Pathway Co-design
Tony Shen, Seonghwan Seo, Ross Irwin, Kieran Didi, Simon Olsson, Woo Youn Kim, Martin Ester
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
Piloting Structure-Based Drug Design via Modality-Specific Optimal Schedule
Keyue Qiu, Yuxuan Song, Zhehuan Fan, Peidong Liu, Zhe Zhang, Mingyue Zheng, Hao Zhou, Wei-Ying Ma
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
ESM-Effect: An Effective and Efficient Fine-Tuning Framework towards accurate prediction of Mutation's Functional Effect
Moritz Glaser
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
moPPIt: De Novo Generation of Motif-Specific Peptide Binders via Conditional Uniform Discrete Diffusion
Tong Chen, Yinuo Zhang, Zachary Quinn, Pranam Chatterjee
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
Implicit Bayesian Markov Decision Process for Resource-Efficient Experimental Design in Drug Discovery
Tianchi Chen, Jan Bíma, Sean L. Wu, Otto Ritter, Bo Yuan, Bingjia Yang, Xiang Yu
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
Metalorian: De Novo Generation of Heavy Metal-Binding Peptides with Classifier-Guided Diffusion Sampling
Yinuo Zhang, Divya Srijay, Pranam Chatterjee
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
Path Planning for Masked Diffusion Models with Applications to Biological Sequence Generation
Fred Zhangzhi Peng, Zachary Bezemek, Sawan Patel, Jarrid Rector-Brooks, Sherwood Yao, Alexander Tong, Pranam Chatterjee
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
Reinforcement learning on structure-conditioned categorical diffusion for protein inverse folding
Yasha Ektefaie, Olivia Viessmann, Siddharth Narayanan, Drew Dresser, J. Mark Kim, Armen Mkrtchyan
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
It Takes Two to Tango: Directly Optimizing for Constrained Synthesizability in Generative Molecular Design
Jeff Guo, Philippe Schwaller
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
Preferential Multi-Objective Bayesian Optimization for Drug Discovery
Tai Dang, Long-Hung Pham, Sang T. Truong, Ari Glenn, Wendy Nguyen, Edward A Pham, Jeffrey S. Glenn, Sanmi Koyejo, Thang Luong
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
Aligning Chemical and Protein Language Models with Continuous Feedback using Energy Rank Alignment
Shriram Chennakesavalu, Frank Hu, Sebastian Ibarraran, Grant M. Rotskoff
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
Few-shot active learning for de novo dual-target peptide design with high bio-activity
Tianxu Lv, Bing He, Yuran Jia, Xiang pan, Jianhua Yao
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
PepTune: De Novo Generation of Therapeutic Peptides with Multi-Objective-Guided Discrete Diffusion
Sophia Tang, Yinuo Zhang, Pranam Chatterjee
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone