ICLR 2025 Workshop LMRL Submissions

Interpreting and Steering Protein Language Models through Sparse Autoencoders
Edith Natalia Villegas Garcia, Alessio ansuini
- Published: 06 Mar 2025, Last Modified: 21 Jul 2025
- ICLR 2025 Workshop LMRL
- Readers: Everyone
Learning to Predict Ensembles of Protein Conformations from Molecular Dynamics Simulation Trajectories
Bongjin Koo, Patrick Jiang, Soumya Dutta, I. Can Kazan, S. Banu Ozkan, Paul T Kim, Abhishek Singharoy, Tristan Bepler
- Published: 06 Mar 2025, Last Modified: 21 Jul 2025
- ICLR 2025 Workshop LMRL
- Readers: Everyone
Exploring Query-to-reference Mapping Challenges for Automated Single-Cell Atlas-based Diagnostics
Francesco Craighero, Davide Maspero, Laura Jiménez-Gracia, Sergio Aguilar-Fernández, Maria Boulougouri, Juan C. Nieto, Holger Heyn
- Published: 06 Mar 2025, Last Modified: 21 Jul 2025
- ICLR 2025 Workshop LMRL
- Readers: Everyone
HARMONY: A Multi-Representation Framework for RNA Property Prediction
Junjie Xu, Artem Moskalev, Tommaso Mansi, Mangal Prakash, Rui Liao
- Published: 06 Mar 2025, Last Modified: 18 Apr 2025
- ICLR 2025 Workshop LMRL Withdrawn Submission
- Readers: Everyone
Universally Applicable And Tunable Graph-Based Coarse-Graining For Machine Learning Force Fields
Christoph Brunken, Sebastien Boyer, Mustafa Omar, Martin Maarand, Olivier Peltre, Solal Attias, Bakary N'tji Diallo, Anastasia Markina, Olaf Othersen, Oliver Bent
- Published: 06 Mar 2025, Last Modified: 21 Jul 2025
- ICLR 2025 Workshop LMRL
- Readers: Everyone
Cellular-Guided Graph Generative Model
Yiming Huang, Tolga Birdal
- Published: 06 Mar 2025, Last Modified: 21 Jul 2025
- ICLR 2025 Workshop LMRL
- Readers: Everyone
Beyond Schrödinger Bridges: A Least-Squares Approach for Learning Stochastic Dynamics with Unknown Volatility
Renato Berlinghieri, Yunyi Shen, Tamara Broderick
- Published: 06 Mar 2025, Last Modified: 21 Jul 2025
- ICLR 2025 Workshop LMRL
- Readers: Everyone
A pretrained SCVI model for 60,000 drug perturbation experiments in 100 million cells
Valentine Svensson
- Published: 06 Mar 2025, Last Modified: 21 Jul 2025
- ICLR 2025 Workshop LMRL
- Readers: Everyone
Spatially-Informed Sampling Enables Accurate Prediction of Large-Scale Mutational Effects
Maxime Basse, Dianzhuo Wang, Eugene Shakhnovich
- Published: 06 Mar 2025, Last Modified: 21 Jul 2025
- ICLR 2025 Workshop LMRL
- Readers: Everyone
Decision Tree Induction with Dynamic Feature Generation: A Framework for Interpretable DNA Sequence Analysis
Nicolas Huynh, Krzysztof Kacprzyk, Ryan M Sheridan, David L. Bentley, Mihaela van der Schaar
- Published: 06 Mar 2025, Last Modified: 21 Jul 2025
- ICLR 2025 Workshop LMRL
- Readers: Everyone
Using Autoregressive-Transformer Model for Protein-Ligand Binding Site Prediction
Mahdi Pourmirzaei, Salhuldin Alqarghuli, Farzaneh Esmaili, Mohammadreza Pourmirzaeioliaei, Mohsen Rezaei, Dong Xu
- Published: 06 Mar 2025, Last Modified: 21 Jul 2025
- ICLR 2025 Workshop LMRL
- Readers: Everyone
Roll-AE: A Spatiotemporal Invariant Autoencoder for Uncovering Neuronal Electrophysiological Patterns
Tommaso Dreossi, Rounak Dey, Emily Fox, Daphne Koller
- Published: 06 Mar 2025, Last Modified: 21 Jul 2025
- ICLR 2025 Workshop LMRL
- Readers: Everyone
From Medical Literature to Predictive Features: An Evidence-based Knowledge Graph Approach
Donghee Choi, Antoine D Lain, Joram M. Posma, Mark Kozdoba, Binyamin Perets, Shie Mannor
- Published: 06 Mar 2025, Last Modified: 21 Jul 2025
- ICLR 2025 Workshop LMRL
- Readers: Everyone
Metabolically Constrained Neural Networks for Bioprocess Optimization
Remy Kusters
- Published: 06 Mar 2025, Last Modified: 21 Jul 2025
- ICLR 2025 Workshop LMRL
- Readers: Everyone
Omni-Mol: Exploring Universal Convergent Space for Omni-Molecular Tasks
Chengxin Hu, Hao Li, Yihe Yuan, Zezheng Song, Haixin Wang
- Published: 06 Mar 2025, Last Modified: 21 Jul 2025
- ICLR 2025 Workshop LMRL
- 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: 21 Jul 2025
- ICLR 2025 Workshop LMRL
- Readers: Everyone
muPPIt: De Novo Generation of Mutant-Specific Peptide Binders via Conditional Uniform Discrete Diffusion
Tong Chen, Pranam Chatterjee
- Published: 06 Mar 2025, Last Modified: 21 Jul 2025
- ICLR 2025 Workshop LMRL
- 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: 21 Jul 2025
- ICLR 2025 Workshop LMRL
- 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: 21 Jul 2025
- ICLR 2025 Workshop LMRL
- 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: 21 Jul 2025
- ICLR 2025 Workshop LMRL
- Readers: Everyone
Flexible Models of Functional Annotations to Variant Effects using Accelerated Linear Algebra
Alan Nawzad Amin, Andres Potapczynski, Andrew Gordon Wilson
- Published: 06 Mar 2025, Last Modified: 21 Jul 2025
- ICLR 2025 Workshop LMRL
- Readers: Everyone
AI Foundation Models for Personalized Health Monitoring: Learning Meaningful Representations of Metabolic Profiles
Raphael Kozlovsky
- Published: 21 Jul 2025, Last Modified: 21 Jul 2025
- ICLR 2025 Workshop LMRL
- Readers: Everyone
InfoSEM: A Deep Generative Model with Informative Priors for Gene Regulatory Network Inference
Tianyu Cui, Song-Jun Xu, Artem Moskalev, Shuwei Li, Tommaso Mansi, Mangal Prakash, Rui Liao
- Published: 06 Mar 2025, Last Modified: 18 Apr 2025
- ICLR 2025 Workshop LMRL Withdrawn Submission
- Readers: Everyone
Leveraging State Space Models in Long Range Genomics
Matvei Popov, Aymen Kallala, Anirudha Ramesh, Narimane Hennouni, Shivesh Khaitan, Rick Gentry, Alain-Sam Cohen
- Published: 06 Mar 2025, Last Modified: 21 Jul 2025
- ICLR 2025 Workshop LMRL
- Readers: Everyone
Weakly Supervised Latent Variable Inference of Proximity Bias in CRISPR Gene Knockouts from Single-Cell Images
Aditya Ravuri, Kristina Ulicna, Jana Osea, Konstantin Donhauser, Jason Hartford
- Published: 06 Mar 2025, Last Modified: 21 Jul 2025
- ICLR 2025 Workshop LMRL
- Readers: Everyone