ICLR 2025 Workshop MLGenX Submissions

Building Foundation Models to Characterize Cellular Interactions via Geometric Self-Supervised Learning on Spatial Genomics
Yuning You, Zitong Jerry Wang, Kevin Fleisher, Rex Liu, Matt Thomson
- Published: 05 Mar 2025, Last Modified: 21 Apr 2025
- MLGenX 2025
- Readers: Everyone
Enhancing DNA Foundation Models to Address Masking Inefficiencies
Monireh Safari, Pablo Andres Millan Arias, Scott C. Lowe, Lila Kari, Angel X Chang, Graham W. Taylor
- Published: 05 Mar 2025, Last Modified: 23 Apr 2025
- MLGenX 2025
- Readers: Everyone
Featurization of single cell trajectories through kernel mean embedding of optimal transport maps
Alec Plotkin, Justin Milner, Natalie Stanley
- Published: 05 Mar 2025, Last Modified: 07 May 2025
- MLGenX 2025
- Readers: Everyone
AI AGENT FOR DATA-DRIVEN HYPOTHESIS EXPLORATION IN SINGLE-CELL TRANSCRIPTOMICS
Artemy Bakulin, Pierre Boyeau, Nir Yosef
- Published: 05 Mar 2025, Last Modified: 05 Mar 2025
- MLGenX 2025 Spotlight
- Readers: Everyone
NOLAN: SELF-SUPERVISED FRAMEWORK FOR MAPPING CONTINUOUS TISSUE ORGANIZATION
Artemy Bakulin, Nathan Levy, Can Ergen, Jonas Maaskola, Nir Yosef
- Published: 05 Mar 2025, Last Modified: 05 Mar 2025
- MLGenX 2025
- Readers: Everyone
RAG-Enhanced Collaborative LLM Agents for Drug Discovery
Namkyeong Lee, Edward De Brouwer, Ehsan Hajiramezanali, Tommaso Biancalani, Chanyoung Park, Gabriele Scalia
- Published: 05 Mar 2025, Last Modified: 07 May 2025
- MLGenX 2025 Spotlight
- Readers: Everyone
ECG-Nest-FM: A Frequency-Focused ECG Foundation Model with Nested Embeddings
Abhishek Sharma, Lin Yang, Cory Y McLean, Justin Cosentino, Farhad I Hormozdiari
- Published: 05 Mar 2025, Last Modified: 19 Apr 2025
- MLGenX 2025
- Readers: Everyone
GraphPINE: Graph importance propagation for interpretable drug response prediction
Yoshitaka Inoue, Tianfan Fu, Augustin Luna
- Published: 05 Mar 2025, Last Modified: 24 Apr 2025
- MLGenX 2025
- Readers: Everyone
SpaceDX: A Bayesian test for localized differential expression in population-level spatial transcriptomics datasets
Niklas Stotzem, Simon Chang, Na Cai, Francesco Paolo Casale
- Published: 05 Mar 2025, Last Modified: 23 Apr 2025
- MLGenX 2025
- Readers: Everyone
DrugAgent: Multi-Agent Large Language Model-Based Reasoning for Drug-Target Interaction Prediction
Yoshitaka Inoue, Tianci Song, Xinling Wang, Augustin Luna, Tianfan Fu
- Published: 05 Mar 2025, Last Modified: 24 Apr 2025
- MLGenX 2025 TinyPapers
- Readers: Everyone
RNAGym: Benchmarks for RNA Fitness and Structure Prediction
Rohit Arora, Murphy Angelo, Christian Andrew Choe, Aaron W Kollasch, Fiona Qu, Courtney A. Shearer, Ruben Weitzman, Artem Gazizov, Sarah Gurev, Erik Xie, Debora Susan Marks, Pascal Notin
- Published: 05 Mar 2025, Last Modified: 05 Mar 2025
- MLGenX 2025
- 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: 05 Mar 2025, Last Modified: 15 Apr 2025
- MLGenX 2025 Spotlight
- Readers: Everyone
Aligning Molecules and Fragments in a Shared Embedding Space for RL-Based Molecule Generation
Youngkuk Kim, Yinhua Piao, Sangseon Lee, Sun Kim
- Published: 05 Mar 2025, Last Modified: 24 Apr 2025
- MLGenX 2025 TinyPapers
- Readers: Everyone
PREDICTING TIME-VARYING METABOLIC DYNAMICS USING STRUCTURED NEURAL ODE PROCESSES
Santanu Rathod, Pietro Lio, Xiao Zhang
- Published: 05 Mar 2025, Last Modified: 21 Apr 2025
- MLGenX 2025
- Readers: Everyone
Gradient-Based Gene Selection for Multimodal scRNA-seq Foundation Models
Pakaphol Thadawasin, Farhan khodaee, Rohola Zandie, Elazer R Edelman
- Published: 05 Mar 2025, Last Modified: 07 May 2025
- MLGenX 2025 TinyPapers
- Readers: Everyone
CellMemory: Hierarchical Interpretation of Out-of-Distribution Cells Using Bottlenecked Transformer
Qifei Wang
- Published: 05 Mar 2025, Last Modified: 21 Apr 2025
- MLGenX 2025
- Readers: Everyone
COLOR: A COMPOSITIONAL LINEAR OPERATION BASED REPRESENTATION OF PROTEIN SEQUENCES FOR IDENTIFICATION OF MONOMER CONTRIBUTIONS TO PROPERTIES
Akash Pandey, Wei Chen, Sinan Keten
- Published: 05 Mar 2025, Last Modified: 24 Apr 2025
- MLGenX 2025
- Readers: Everyone
Searching for Phenotypic Needles in Genomic Haystacks: DNA Language Models for Sex Prediction
Alla Chepurova, Yuri Kuratov, Polina Belokopytova, Mikhail Burtsev, Veniamin Fishman
- Published: 05 Mar 2025, Last Modified: 24 Apr 2025
- MLGenX 2025 TinyPapers
- Readers: Everyone
Leveraging GPT Continual Fine-Tuning for Improved RNA Editing Site Prediction
Zohar Rosenwasser, Erez Levanon, Michael Levitt, Gal Oren
- Published: 05 Mar 2025, Last Modified: 07 May 2025
- MLGenX 2025
- Readers: Everyone
GENATATOR: de novo Gene Annotation With DNA Language Model
Aleksei Shmelev, Artem Shadskiy, Yuri Kuratov, Mikhail Burtsev, Olga Kardymon, Veniamin Fishman
- Published: 05 Mar 2025, Last Modified: 21 Apr 2025
- MLGenX 2025
- Readers: Everyone
PIONEER: a virtual platform for iterative improvement of genomic deep learning
Alessandro Crnjar, John J Desmarais, Justin Kinney, Peter K Koo
- Published: 05 Mar 2025, Last Modified: 03 Apr 2025
- MLGenX 2025
- Readers: Everyone
2DE: a probabilistic method for differential expression across niches in spatial transcriptomics data
Nathan Levy, Florian Ingelfinger, Artemy Bakulin, Giacomo Cinnirella, Pierre Boyeau, Can Ergen, Nir Yosef
- Published: 05 Mar 2025, Last Modified: 22 Apr 2025
- MLGenX 2025 TinyPapers
- Readers: Everyone
AI-Powered Virtual Tissues from Spatial Proteomics for Clinical Diagnostics and Biomedical Discovery
Johann Wenckstern, Eeshaan Jain, Kiril Vasilev, Matteo Pariset, Andreas Wicki, Gabriele Gut, Charlotte Bunne
- Published: 05 Mar 2025, Last Modified: 25 Mar 2025
- MLGenX 2025 Spotlight
- Readers: Everyone
Multi-omic Causal Discovery using Genotypes and Gene Expression
Stephen M. Asiedu, David Watson
- Published: 05 Mar 2025, Last Modified: 07 May 2025
- MLGenX 2025 TinyPapers
- Readers: Everyone
Curly Flow Matching for Learning Non-gradient Field Dynamics
Katarina Petrović, Lazar Atanackovic, Kacper Kapusniak, Michael M. Bronstein, Joey Bose, Alexander Tong
- Published: 05 Mar 2025, Last Modified: 05 Mar 2025
- MLGenX 2025
- Readers: Everyone