ICLR 2025 Workshop GEM Submissions

Preventing cell-to-cell tranmission of disordered proto-fibrils of $\alpha$-Synuclein
Akshay Chenna
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
Structure-Aware Language Models Trained on Ultra-Mega-Scale Metagenomic Data Improve Protein Folding Stability Prediction
Yehlin Cho, Kotaro Tsuboyama, Gabriel J. Rocklin, Sergey Ovchinnikov
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
AI-guided data-scarce engineering of RfxCas13d to create a cell selection tool
Aviv Spinner, Ayush Noori, Debora Susan Marks, George Church, Lisa Maria Riedmayr
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
An evaluation of unconditional 3D molecular generation methods
Martin Buttenschoen, Yael Ziv, Garrett M Morris, Charlotte Deane
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
Towards Scaling Laws for Language Model Powered Evolutionary Algorithms: Case Study on Molecular Optimization
Tigran Fahradyan, Filya Geikyan, Philipp Guevorguian, Hrant Khachatrian
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
TCR-TRANSLATE: CONDITIONAL GENERATION OF REAL ANTIGEN- SPECIFIC T-CELL RECEPTOR SEQUENCES
Dhuvarakesh Karthikeyan, Colin Raffel, Benjamin Garrett Vincent, Alex Rubinsteyn
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
All-Atom Protein Generation with Latent Diffusion
Amy X. Lu, Wilson Yan, Sarah A Robinson, Simon Kelow, Kevin K Yang, Vladimir Gligorijevic, Kyunghyun Cho, Richard Bonneau, Pieter Abbeel, Nathan C. Frey
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
GROQ-seq: A Collaborative, Open Data Approach to Addressing Protein Function Prediction
David Ross, Aviv Spinner, Simon d'Oelsnitz, Svetlana P Ikonomova, Olga Vasilyeva, Nina Alperovich, Kristen Sheldon, Courtney Tretheway, Dana Cortade, Erika DeBenedictis, Peter J Kelly
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
A data guided approach to building an ML ready protein expression dataset
Catherine Baranowski, Aviv Spinner, Peter J Kelly
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
Gumbel-Softmax Score and Flow Matching for Discrete Biological Sequence Generation
Sophia Tang, Yinuo Zhang, Alexander Tong, Pranam Chatterjee
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
EquiJump: Protein Dynamics Simulation via SO(3)-Equivariant Stochastic Interpolants
Allan Dos Santos Costa, Ilan Mitnikov, Franco Pellegrini, Ameya Daigavane, Mario Geiger, Zhonglin Cao, Karsten Kreis, Tess Smidt, Emine Kucukbenli, JOSEPH JACOBSON
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
Gradient GA: Gradient Genetic Algorithm for Drug Molecular Design
Chris Zhuang, Debadyuti Mukherjee, Yingzhou Lu, Tianfan Fu, Ruqi Zhang
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
Decoding the Mechanistic Impact of Genetic Variation on Regulatory Sequences with Deep Learning
Evan Seitz, David M. McCandlish, Justin Kinney, Peter K Koo
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
Tensor-DTI: Enhancing Biomolecular Interaction Prediction with Contrastive Embedding Learning
Manel Gil-Sorribes, Alvaro Ciudad Serrano, Alexis Molina
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
Scalable and Cost-Efficient de Novo Template-Based Molecular Generation
Piotr Gaiński, Oussama Boussif, Dmytro Shevchuk, Andrei Rekesh, Ali Parviz, Mike Tyers, Robert A. Batey, Michał Koziarski
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
OPUS-GO: Unlocking Residue-level Insights from Sequence-level Annotations Using Biological Language Models
Gang Xu, Ying Lv, Ruoxi Zhang, Xinyuan Xia, Qinghua Wang, Jianpeng Ma
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
SOAPI: Siamese-guided generation of Off-Target-Avoiding Protein Interactions
Sophia Vincoff, Oscar Davis, Alexander Tong, Joey Bose, Pranam Chatterjee
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
Guided Generation of B-cell Receptors with Conditional Walk-Jump Sampling
Taylor Joren, Sarah A Robinson, Homa MohammadiPeyhani, Sai Pooja Mahajan, Edith Lee, Stephen Lillington, Qixin Bei, Saeed Saremi, Jae Hyeon Lee, Richard Bonneau, Isidro Hotzel, Vladimir Gligorijevic, Simon Kelow, Nathan C. Frey
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
Molecular design using graph Bayesian optimization with shortest-path kernels
Yilin Xie, Shiqiang Zhang, Jixiang Qing, Ruth Misener, Calvin Tsay
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
Towards Interpretable Protein Structure Prediction with Sparse Autoencoders
Nithin Parsan, David J Yang, John Jingxuan Yang
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
Towards More Accurate Full-Atom Antibody Co-Design
Jiayang Wu, Xingyi Zhang, Xiangyu Dong, Kun XIE, Ziqi Liu, Wensheng Gan, Sibo Wang, Le Song
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
FragFM: Efficient Fragment-Based Molecular Generation via Discrete Flow Matching
Joongwon Lee, Seonghwan Kim, Woo Youn Kim
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
Design of Ligand-Binding Proteins with Atomic Flow Matching
Junqi Liu, Shaoning Li, Chence Shi, Zhi Yang, Jian Tang
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
Active Learning on Synthons for Molecular Design
Tom George Grigg, Mason Burlage, Oliver Brook Scott, Dominique Sydow, Liam Wilbraham
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
Reframing Retreival-Augmented Generation for *in silico* optimization of antibody solubility
Lena Erlach, Rohit Singh, Bonnie Berger, Sai T. Reddy
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone