ICLR 2025 Workshop MLGenX Submissions

Talk2Biomodels and Talk2KnowledgeGraph: AI agent-based application for prediction of patient biomarkers and reasoning over biomedical knowledge graphs
Gurdeep Singh, Lilija Wehling, Ahmad Wisnu Mulyadi, Rakesh Hadne Sreenath, Thomas Klabunde, Tommaso Andreani, Douglas McCloskey
- Published: 05 Mar 2025, Last Modified: 08 Apr 2025
- MLGenX 2025
- Readers: Everyone
Pathway-Attentive GAN for Interpretable Biomolecular Design
Azmine Toushik Wasi, Mahfuz Ahmed Anik
- Published: 05 Mar 2025, Last Modified: 15 Apr 2025
- MLGenX 2025 TinyPapers
- Readers: Everyone
WASSERSTEIN CYCLEGAN FOR SINGLE-CELL RNA- SEQ DATA GENERATION USING CROSS-MODALITY TRANSLATION
Sajib Acharjee Dip, Liqing Zhang
- Published: 05 Mar 2025, Last Modified: 25 Apr 2025
- MLGenX 2025 TinyPapers
- Readers: Everyone
BirdieDNA: Reward-Based Pre-Training for Genomic Sequence Modeling
Sam Blouir, Defne Circi, Asher Moldwin, Amarda Shehu
- Published: 05 Mar 2025, Last Modified: 23 Apr 2025
- MLGenX 2025 TinyPapers
- Readers: Everyone
FACA-GEN: Investigating Bias and Generalization in Active Learning for Genomics AI
Amber Qayum Hawabaz
- Published: 05 Mar 2025, Last Modified: 24 Apr 2025
- MLGenX 2025 TinyPapers
- Readers: Everyone
Gene Set Function Discovery with LLM-Based Agents and Knowledge Retrieval
Daniela Pinto Veizaga, Aécio Santos, Juliana Freire, Wenke Liu, Sarah Keegan, David Fenyo
- Published: 05 Mar 2025, Last Modified: 24 Apr 2025
- MLGenX 2025 TinyPapers
- Readers: Everyone
To trap or not to trap--analyzing the trade-offs in diffusion transport models
Rushmila Shehreen Khan, Md. Shahriar Karim
- Published: 05 Mar 2025, Last Modified: 25 Apr 2025
- MLGenX 2025 TinyPapers
- Readers: Everyone
What do single-cell models already know about perturbations?
Andreas Bjerregaard, Vivek Das, Anders Krogh
- Published: 05 Mar 2025, Last Modified: 07 May 2025
- MLGenX 2025 TinyPapers
- Readers: Everyone
Interpretable prediction of DNA replication origins in S. cerevisiae using attention-based motif discovery
Zohreh Piroozeh, Ildem Akerman, Stefan Kesselheim, Olga Kalinina, Alina Bazarova
- Published: 05 Mar 2025, Last Modified: 21 Apr 2025
- MLGenX 2025 TinyPapers
- Readers: Everyone
PRISM: Enhancing Protein Inverse Folding through Fine-Grained Retrieval on Structure-Sequence Multimodal Representations
Sazan Mahbub, Souvik Kundu, Eric P. Xing
- Published: 05 Mar 2025, Last Modified: 07 May 2025
- MLGenX 2025 TinyPapers
- Readers: Everyone
Transferring Preclinical Drug Response to Patient via Tumor Heterogeneity-Aware Alignment and Perturbation Modeling
Inyoung Sung, Dongmin Bang, Sun Kim, Sangseon Lee
- Published: 05 Mar 2025, Last Modified: 24 Apr 2025
- MLGenX 2025 TinyPapers
- Readers: Everyone
Enhancing E. coli Genomic Analysis with Retrieval-Augmented Generation
KRITIKA CHUGH
- Published: 05 Mar 2025, Last Modified: 23 Mar 2025
- MLGenX 2025 TinyPapers
- Readers: Everyone
Hallucinations vs. Predictions: Reframing Uncertainty in LLM-Generated Medical Responses
Saleh Afroogh, Yasser Poreesmaiel, Junfeng Jiao
- Published: 07 May 2025, Last Modified: 07 May 2025
- MLGenX 2025 TinyPapers
- Readers: Everyone
SPELL: Spatial Prompting with Chain-of-Thought for Zero-Shot Learning in Spatial Transcriptomics
Sumeer Ahmad Khan, Xabier Martinez de Morentin, Vincenzo Lagani, Robert Lehmann, Abdel Rahman Alsabbagh, Mahmoud Zahran, Narsis A. Kiani, David Gomez-Cabrero, Jesper Tegnér
- Published: 05 Mar 2025, Last Modified: 17 Apr 2025
- MLGenX 2025 TinyPapers
- Readers: Everyone
stDiffusion: A Diffusion Based Model for Generative Spatial Transcriptomics
Sumeer Ahmad Khan, Xabier Martínez de Morentin, Vincenzo Lagani, Robert Lehmann, Narsis A. Kiani, David Gomez-Cabrero, Jesper Tegnér
- Published: 05 Mar 2025, Last Modified: 21 Apr 2025
- MLGenX 2025 TinyPapers
- Readers: Everyone
Helix-mRNA: A Hybrid Foundation Model For Full Sequence mRNA Therapeutics
Matthew Wood, Mathieu Klop, Maxime Allard
- Published: 05 Mar 2025, Last Modified: 24 Apr 2025
- MLGenX 2025 TinyPapers
- Readers: Everyone
LIMEADE: Local Interpretable Manifold Explanations for Dimension Evaluations
Tarek M Zikry, Genevera I. Allen
- Published: 05 Mar 2025, Last Modified: 07 Apr 2025
- MLGenX 2025 TinyPapers
- Readers: Everyone
LangPert: LLM-Driven Contextual Synthesis for Unseen Perturbation Prediction
Kaspar Märtens, Marc Boubnovski Martell, Cesar A. Prada-Medina, Rory Donovan-Maiye
- Published: 05 Mar 2025, Last Modified: 25 Apr 2025
- MLGenX 2025 Spotlight
- Readers: Everyone
When repeats drive the vocabulary: a Byte-Pair Encoding analysis of T2T primate genomes
Marina Popova, Iaroslav Chelombitko, Aleksey Komissarov
- Published: 05 Mar 2025, Last Modified: 23 Apr 2025
- MLGenX 2025
- Readers: Everyone
Hierarchical Assembly of Long DNA Libraries from Short Oligonucleotide Pools
Shaozhong Zou, zhien wu, Chunfu Xu
- Published: 05 Mar 2025, Last Modified: 07 May 2025
- MLGenX 2025
- Readers: Everyone
Test-Time View Selection for Multi-Modal Decision Making
Eeshaan Jain, Johann Wenckstern, Benedikt von Querfurth, Charlotte Bunne
- Published: 05 Mar 2025, Last Modified: 03 Apr 2025
- MLGenX 2025 Spotlight
- Readers: Everyone
A Topologically Guided Machine Learning Framework for Enhanced Fine-Mapping in Whole-Genome Bacterial Studies
Tamsin Emily James, Peter Tino, Nicole E Wheeler
- Published: 05 Mar 2025, Last Modified: 24 Apr 2025
- MLGenX 2025
- Readers: Everyone
Capturing functional context of genetic pathways through hyperedge disentanglement
Yoonho Lee, Junseok Lee, Sangwoo Seo, Sungwon Kim, Yeongmin Kim, Chanyoung Park
- Published: 05 Mar 2025, Last Modified: 17 Apr 2025
- MLGenX 2025
- Readers: Everyone
LoFTPat: Low-Rank Subspace Optimization for Parameter-Efficient Fine-Tuning of Genomic Language Models in Pathogenicity Identification
Sajib Acharjee Dip
- Published: 05 Mar 2025, Last Modified: 25 Apr 2025
- MLGenX 2025
- Readers: Everyone
Uncovering BioLOGICAL Motifs and Syntax via Sufficient and Necessary Explanations
Beepul Bharti, Gabriele Scalia, Tommaso Biancalani, Alex M Tseng
- Published: 05 Mar 2025, Last Modified: 07 May 2025
- MLGenX 2025
- Readers: Everyone