ICLR 2025 Workshop MLGenX Submissions

Learning Non-Equilibrium Signaling Dynamics in Single-Cell Perturbation Dynamics
Heman Shakeri
- Published: 05 Mar 2025, Last Modified: 05 Mar 2025
- MLGenX 2025 Spotlight
- Readers: Everyone
Reference-free cell-type annotation with LLM agents
Yidi Huang, Ivan Cohen, Van Quynh-Thi Truong, Pedram B Bayat, Sameer A Bhatti, Luca Paruzzo, Mark M. Painter, Shirong Zheng, Derek Alan Oldridge, Joost Wagenaar, Allison R Greenplate, Dokyoon Kim
- Published: 05 Mar 2025, Last Modified: 24 Apr 2025
- MLGenX 2025 TinyPapers
- Readers: Everyone
Integrating Protein Language Model and Active Learning for Few-Shot Viral Variant Detection
Marian Huot, Dianzhuo Wang, Jiacheng Liu, Eugene Shakhnovich
- Published: 05 Mar 2025, Last Modified: 07 May 2025
- MLGenX 2025
- Readers: Everyone
BEYOND SEQUENCE-ONLY MODELS: LEVERAGING STRUCTURAL CONSTRAINTS FOR ANTIBIOTIC RESISTANCE PREDICTION IN SPARSE GENOMIC DATASETS
Mahbuba Tasmin, Anna G. Green
- Published: 05 Mar 2025, Last Modified: 21 Apr 2025
- MLGenX 2025 TinyPapers
- Readers: Everyone
A data-driven recommendation framework for genomic discovery
Ying Yang, Zhaoying Pan, Jinge Ma, Daniel J. Klionsky
- Published: 05 Mar 2025, Last Modified: 17 Apr 2025
- MLGenX 2025
- Readers: Everyone
Multi-modal single-cell foundation models via dynamic token adaptation
Wenmin Zhao, Ana Solaguren-Beascoa, Grant Neilson, Louwai Muhammed, Liisi Laaniste, Aylin Cakiroglu
- Published: 05 Mar 2025, Last Modified: 17 Apr 2025
- MLGenX 2025 TinyPapers
- Readers: Everyone
LLM4GRN: Discovering Causal Gene Regulatory Networks with LLMs – Evaluation through Synthetic Data Generation
Tejumade Afonja, Ivaxi Sheth, Ruta Binkyte, Waqar Hanif, Shubhi Ambast, Charles Mwangi Kaumbutha, Matthias Becker, Mario Fritz
- Published: 05 Mar 2025, Last Modified: 25 Mar 2025
- MLGenX 2025
- Readers: Everyone
Large Language Models for Zero-shot Inference of Causal Structures in Biology
Izzy Newsham, Luka Kovačević, Richard Moulange, Nan Rosemary Ke, Sach Mukherjee
- Published: 05 Mar 2025, Last Modified: 24 Apr 2025
- MLGenX 2025
- Readers: Everyone
Predicting Drug-likeness via Biomedical Knowledge Alignment and EM-like One-Class Boundary Optimization
Dongmin Bang, Inyoung Sung, Yinhua Piao, Sangseon Lee, Sun Kim
- Published: 05 Mar 2025, Last Modified: 24 Apr 2025
- MLGenX 2025
- Readers: Everyone
ShortListing Model: A Streamlined Simplex Diffusion for Biological Sequence Generation
Yuxuan Song, Zhe Zhang, Yu Pei, Jingjing Gong, Mingxuan Wang, Hao Zhou, Jingjing Liu, Wei-Ying Ma
- Published: 05 Mar 2025, Last Modified: 05 Mar 2025
- MLGenX 2025
- Readers: Everyone
MutEmbed: Self-Supervised Learning of Biological Latent Embeddings from Cancer Mutational Profiles
Aakansha Narain, Wu Jialun Andy, Hannan Wong, Vedant Sandhu, Jason J. Pitt
- Published: 05 Mar 2025, Last Modified: 24 Apr 2025
- MLGenX 2025 TinyPapers
- Readers: Everyone
HybriDNA: A Hybird Transformer-Mamba2 Long-Range DNA Language Model
Mingqian Ma, Guoqing Liu, Chuan Cao, Pan Deng, Tri Dao, Albert Gu, Peiran Jin, Zhao Yang, Yingce Xia, Renqian Luo, Pipi Hu, Zun Wang, Yuan-Jyue Chen, Haiguang Liu, Tao Qin
- Published: 05 Mar 2025, Last Modified: 23 Apr 2025
- MLGenX 2025
- Readers: Everyone
A Scalable LLM Framework for Therapeutic Biomarker Discovery: Grounding Q/A Generation in Knowledge Graphs and Literature
Marc Boubnovski Martell, Kaspar Märtens, Lawrence Phillips, Daniel Keitley, Maria Dermit, Julien Fauqueur
- Published: 05 Mar 2025, Last Modified: 25 Apr 2025
- MLGenX 2025
- Readers: Everyone
MolCap-Arena: A Comprehensive Captioning Benchmark on Language-Enhanced Molecular Property Prediction
Carl Edwards, Ziqing Lu, Ehsan Hajiramezanali, Tommaso Biancalani, Heng Ji, Gabriele Scalia
- Published: 05 Mar 2025, Last Modified: 23 Apr 2025
- MLGenX 2025
- Readers: Everyone
Detecting cell level transcriptomic changes of Perturb-seq using Contrastive Fine-tuning of Single-Cell Foundation Models
Wenmin Zhao, Ana Solaguren-Beascoa, Grant Neilson, Regina Reynolds, Louwai Muhammed, Liisi Laaniste, Sera Aylin Cakiroglu
- Published: 05 Mar 2025, Last Modified: 17 Apr 2025
- MLGenX 2025
- 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: 05 Mar 2025, Last Modified: 24 Apr 2025
- MLGenX 2025
- Readers: Everyone
Relaxed Equivariance via Multitask Learning
Ahmed A. A. Elhag, T. Konstantin Rusch, Francesco Di Giovanni, Michael M. Bronstein
- Published: 05 Mar 2025, Last Modified: 23 Apr 2025
- MLGenX 2025 Spotlight
- Readers: Everyone
Spatially-Informed Sampling Enables Accurate Prediction of Large-Scale Mutational Effects
Maxime Basse, Dianzhuo Wang, Eugene Shakhnovich
- Published: 05 Mar 2025, Last Modified: 02 Apr 2025
- MLGenX 2025
- 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: 05 Mar 2025, Last Modified: 14 Apr 2025
- MLGenX 2025 Spotlight
- Readers: Everyone
Structure-based metabolite function prediction using graph neural networks
Tancredi Cogne, Mariam Ait Oumelloul, Ali Saadat, Janna Hastings, Jacques Fellay
- Published: 05 Mar 2025, Last Modified: 09 Apr 2025
- MLGenX 2025
- Readers: Everyone
Graph Pseudotime Analysis and Neural Stochastic Differential Equations for Analyzing Retinal Degeneration Dynamics and Beyond
Dai Shi, Kuan Yan, Lequan Lin, Yue Zeng, Ting Zhang, Jialing zhang, Matsypura Dmytro, Mark C. Gillies, Ling Zhu, Junbin Gao
- Published: 05 Mar 2025, Last Modified: 23 Mar 2025
- MLGenX 2025
- Readers: Everyone
HARMONY: A Multi-Representation Framework for RNA Property Prediction
Junjie Xu, Artem Moskalev, Tommaso Mansi, Mangal Prakash, Rui Liao
- Published: 05 Mar 2025, Last Modified: 25 Mar 2025
- MLGenX 2025 TinyPapers
- Readers: Everyone
Supervised Contrastive Block Disentanglement
Taro Makino, Ji Won Park, Natasa Tagasovska, TAKAMASA KUDO, Paula Coelho, Heming Yao, Jan-Christian Huetter, Ana Carolina Leote, Burkhard Hoeckendorf, Stephen Ra, David Richmond, Kyunghyun Cho, Aviv Regev, Romain Lopez
- Published: 05 Mar 2025, Last Modified: 24 Apr 2025
- MLGenX 2025
- Readers: Everyone
Benchmarking Fine-Tuned RNA Language Models for Intronic Branch Point Prediction
Pablo Rodenas Ruiz, Ali Saadat, Timothy T. Tran, Oliver Müller Smedt, Peng Zhang, Jacques Fellay
- Published: 05 Mar 2025, Last Modified: 07 May 2025
- MLGenX 2025 TinyPapers
- Readers: Everyone
RAG-ESM: Improving pretrained protein language models via sequence retrieval
Damiano Sgarbossa, Anne-Florence Bitbol
- Published: 05 Mar 2025, Last Modified: 02 Apr 2025
- MLGenX 2025 Spotlight
- Readers: Everyone