ICLR 2025 Workshop GEM Submissions

Molecular Property Prediction using Pretrained-BERT and Bayesian Active Learning: A Data-Efficient Approach to Drug Design
Muhammad Arslan Masood, Samuel Kaski, Tianyu Cui
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
Structure-based synthetic data augmentation for protein language models
Alex Jihun Lee, Ava P Amini, Kevin K Yang, Sarah Alamdari, Chentong Wang, Reza Abbasi-Asl
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
Steering Generative Models with Experimental Data for Protein Fitness Optimization
Jason Yang, Wenda Chu, Daniel Khalil, Raul Astudillo, Bruce James Wittmann, Frances H. Arnold, Yisong Yue
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
Learning Representations of Instruments for Partial Identification of Treatment Effects
Jonas Schweisthal, Dennis Frauen, Maresa Schröder, Konstantin Hess, Niki Kilbertus, Stefan Feuerriegel
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
Residue-level text conditioning for protein language model mutation effect prediction
Dan Berenberg, Nate Gruver, Alan Nawzad Amin, Peter Mørch Groth, Leo Chen, Harsh R. Srivastava, Pascal Notin, Debora Susan Marks, Andrew Gordon Wilson, Kyunghyun Cho, Richard Bonneau
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
Large Drug Discovery Model
Ilia Igashov, Arne Schneuing, Adrian W. Dobbelstein, Irina Morozova, Rebecca Manuela Neeser, Evgenia Elizarova, Philippe Schwaller, Michael M. Bronstein, Bruno Correia
- Published: 06 Mar 2025, Last Modified: 04 May 2025
- GEM
- Readers: Everyone
Scaling Deep Learning Solutions for Transition Path Sampling
Jungyoon Lee, Michael Plainer, Yuanqi Du, Lars Holdijk, Rob Brekelmans, Carla P Gomes, Dominique Beaini, Kirill Neklyudov
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
Bio2Token: All-atom tokenization of any biomolecular structure with Mamba
Andrew Liu, Axel Elaldi, Nathan Russell, Olivia Viessmann
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
SweetBERT: exploring BERT-based models for IUPAC glycan nomenclature modeling
Irene Rubia-Rodríguez, Henrik Nielsen, Garry P. Gippert, Kristian Barrett, Bernard Henrissat, Ole Winther
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
A generalized protein design ML model enables generation of functional de novo proteins
Timothy P Riley, Oleg Matusovsky, Mohammad S. Parsa, Pourya Kalantari, Kooshiar Azimian, Kathy Y Wei
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
Action-Minimization Meets Generative Modeling: Efficient Transition Path Sampling with the Onsager-Machlup Functional
Sanjeev Raja, Martin Sipka, Michael Psenka, Tobias Kreiman, Michal Pavelka, Aditi S. Krishnapriyan
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
Flow-Based Fragment Identification via Contrastive Learning of Binding Site-Specific Latent Representations
Rebecca Manuela Neeser, Ilia Igashov, Arne Schneuing, Michael M. Bronstein, Philippe Schwaller, Bruno Correia
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
Protein structure predictors implicitly define binding energy functions
Divya Nori, Anisha Parsan, Caroline Uhler, Wengong Jin
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
Mol-MoE: Training Preference-Guided Routers for Molecule Generation
Diego Calanzone, Pierluca D'Oro, Pierre-Luc Bacon
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
Programming co-folding to design binders for intrinsically disordered epitopes
Jakub Lála, Daniele Visco, Stefano Angioletti-Uberti
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
Interpreting and Steering Protein Language Models through Sparse Autoencoders
Edith Natalia Villegas Garcia, Alessio ansuini
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
Fast and Accurate Antibody Sequence Design via Structure Retrieval
Xingyi Zhang, Kun XIE, Ningqiao Huang, Wei Liu, Peilin Zhao, Sibo Wang, Kangfei Zhao, Biaobin Jiang
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
Why risk matters for protein binder design
Tudor-Stefan Cotet, Igor Krawczuk
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
De Novo Design of Antigen-Specific Antibodies Using Structural Constraint-Based Generative Language Model
Yuran Jia, Bing He, Tianxu Lv, YangXiao, Tianyi Zhao, Jianhua Yao
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
RNA-EFM : Energy based Flow Matching for Protein-conditioned RNA Sequence-Structure Co-design
Abrar Rahman Abir, Liqing Zhang
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
GENERATIVE PROTEIN DESIGN FOR OVERLAPPING GENES
Chenling Xu, Jennifer Lynn Chlebek, Jonathan E Allen, Hunter Nisonoff, Dan Mcfarland Park
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
Hierarchical Protein Backbone Generation with Latent and Structure Diffusion
Jason Yim, Marouane Jaakik, Ge Liu, Jacob Gershon, Karsten Kreis, David Baker, Regina Barzilay, Tommi Jaakkola
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
Sampling Protein Language Models for Functional Protein Design
Jeremie Theddy Darmawan, Yarin Gal, Pascal Notin
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
Targeting Aggregating Proteins with Language Model-Designed Degraders
Rio Watson, Kishan Patel, Tong Chen, Pranam Chatterjee
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone
Towards Protein Sequence & Structure Co-Design with Multi-Modal Language Models
Stephen Zhewen Lu, Jiarui Lu, Hongyu Guo, Jian Tang
- Published: 06 Mar 2025, Last Modified: 26 Apr 2025
- GEM
- Readers: Everyone