NeurIPS 2025 Workshop FM4LS Submissions

Virtual Screening on Cellular Systems
Caleb Ellington, Sohan Addagudi, Jiaqi Wang, Ben Lengerich, Eric P. Xing
- 16 Sept 2025 (modified: 16 Oct 2025)
- Submitted to NeurIPS 2025 2nd Workshop FM4LS
- Readers: Everyone
Predicting cellular responses to perturbation across diverse contexts with State
Abhinav Adduri, Dhruv Gautam, Beatrice Bevilacqua, Alishba Imran, Rohan Shah, Mohsen Naghipourfar, Noam Teyssier, Rajesh Ilango, Sanjay Nagaraj, Chiara Ricci-Tam, Chris Carpenter, Vishvak Subramanyam, Aidan Winters, Mingze Dong, Sravya Tirukkovalur, Jeremy Sullivan, Brian Plosky, Basak Eraslan, Nicholas D. Youngblut, Jure Leskovec et al. (7 additional authors not shown)
- Published: 06 Oct 2025, Last Modified: 06 Oct 2025
- NeurIPS 2025 2nd Workshop FM4LS Poster
- Readers: Everyone
Predicting Influenza Reassortment Potential Using Foundation Models and Genetic Algorithms for Pandemic Preparedness
Seeraja Konnur
- Published: 06 Oct 2025, Last Modified: 07 Oct 2025
- NeurIPS 2025 2nd Workshop FM4LS Poster
- Readers: Everyone
HIP-HOP: Invariants for 2D Tilings with Biomedical Case Study
Madhava Gaikwad, Ashwini Ramchandra Doke
- Published: 06 Oct 2025, Last Modified: 06 Oct 2025
- NeurIPS 2025 2nd Workshop FM4LS Poster
- Readers: Everyone
Learning In-Silico Maps of Transcription Factor Binding and Cooperativity interactions
Ruben Solozabal, Albert Baichorov, Tamir Avioz, Le Song, Ariel Afek, Martin Takáč
- Published: 06 Oct 2025, Last Modified: 06 Oct 2025
- NeurIPS 2025 2nd Workshop FM4LS Poster
- Readers: Everyone
Towards Optimized Use of LLMs in Drug Discovery
Andrew Y. Zhou, Peter Eckmann, Sumanth Varambally, Michael K Gilson, Rose Yu
- 07 Sept 2025 (modified: 16 Oct 2025)
- Submitted to NeurIPS 2025 2nd Workshop FM4LS
- Readers: Everyone
Optimization and Tokenization Strategies for Biological Foundation Models: Evaluating H-Net and Muon
Krithik Ramesh, Nauman Javed, Frederick Hoffman, Yash Semlani, Sameed Muneeb Siddiqui
- 07 Sept 2025 (modified: 16 Oct 2025)
- Submitted to NeurIPS 2025 2nd Workshop FM4LS
- Readers: Everyone
Multimodal Alignment Reveals Interpretable Gene–Morphology Links in Perineuronal Net Pathology
Wenjun Liu, Saeed Hassanpour
- Published: 06 Oct 2025, Last Modified: 06 Oct 2025
- NeurIPS 2025 2nd Workshop FM4LS Poster
- Readers: Everyone
Complementarity-Driven Distillation from Multiple Foundation Models for DNA Classification
Dohoon Kim, Jihwan Kwak, Sunghwan Joo, Jung Yoon Hwang, Taesup Moon
- 07 Sept 2025 (modified: 16 Oct 2025)
- Submitted to NeurIPS 2025 2nd Workshop FM4LS
- Readers: Everyone
Disentangling Protein Family Signals in Protein Language Models: Composition or Motifs?
Sohel Bashar, M Saifur Rahman
- Published: 06 Oct 2025, Last Modified: 06 Oct 2025
- NeurIPS 2025 2nd Workshop FM4LS Poster
- Readers: Everyone
Multimodal Fusion of CNN and LLM Embeddings for Chest X-Ray Classification
Shriya Ramesh, Smarak Patnaik, Sreedath Panat
- 07 Sept 2025 (modified: 16 Oct 2025)
- Submitted to NeurIPS 2025 2nd Workshop FM4LS
- Readers: Everyone
Multitask Asynchronous Bidirectional Multimodal Agent for Personalized Treatment Companions
Muhamad Iqbal Januadi Putra, Raka Admiral Abdurrahman, Vincent Alexander
- Published: 06 Oct 2025, Last Modified: 06 Oct 2025
- NeurIPS 2025 2nd Workshop FM4LS Poster
- Readers: Everyone
Aligning Protein Language Models to Stability Preferences using 1M+ Experimental Mutant Effects
Niksa Praljak, Sung-Won Hwang, Cheng-Yen Lin, Allen Po-Chih Liu, Andrew Ferguson
- Published: 06 Oct 2025, Last Modified: 06 Oct 2025
- NeurIPS 2025 2nd Workshop FM4LS Poster
- Readers: Everyone
Weakly Supervised Contrastive Alignment of scRNA-seq to CNV Anchors
Garv Goswami, David Xu, Hwi Joo Park
- 07 Sept 2025 (modified: 16 Oct 2025)
- Submitted to NeurIPS 2025 2nd Workshop FM4LS
- Readers: Everyone
Thin Bridges for Drug Text Alignment: Lightweight Contrastive Learning for Target Specific Drug Retrieval
Mallikarjuna Tupakula
- Published: 06 Oct 2025, Last Modified: 06 Oct 2025
- NeurIPS 2025 2nd Workshop FM4LS Poster
- Readers: Everyone
Temporal Protein Evolution Prediction for Proactive Pathogen Surveillance
Bin Hu, Martha Dix, Kaetlyn Gibson
- 06 Sept 2025 (modified: 16 Oct 2025)
- Submitted to NeurIPS 2025 2nd Workshop FM4LS
- Readers: Everyone
A Multi-Modal Deep Learning Model for Drug Potency Prediction: Leveraging Features from Physics-Based Docking and Advanced Co-Folding Methods
Claire Suen, BoRam Lee, Matthew Adrian, Jeffrey Zhou, Hyeyun Jung, David He, Gean Hu, Kelly Hui, Aditi Jain, Qamil Mirza Bin Abdullah, Milena Novakovic, Joseph Park, Winston Qian, Aarav Shah, Xina Wang, Yunsie Chung, Alan C Cheng
- Published: 06 Oct 2025, Last Modified: 06 Oct 2025
- NeurIPS 2025 2nd Workshop FM4LS Poster
- Readers: Everyone
Enhancing Splice Site Detection Through Deep Learning and Retrieval-Augmented Generation
Yogesh Mahendran, Julia Olivieri
- 06 Sept 2025 (modified: 16 Oct 2025)
- Submitted to NeurIPS 2025 2nd Workshop FM4LS
- Readers: Everyone
Predicting and generating antibiotics against future pathogens with ApexOracle
Tianang Leng, Fangping Wan, Marcelo Der Torossian Torres, Cesar de la Fuente-Nunez
- Published: 06 Oct 2025, Last Modified: 06 Oct 2025
- NeurIPS 2025 2nd Workshop FM4LS Poster
- Readers: Everyone
MolVision: Molecular Property Prediction with Vision Language Models
Deepan Adak, Yogesh S Rawat, Shruti Vyas
- Published: 06 Oct 2025, Last Modified: 06 Oct 2025
- NeurIPS 2025 2nd Workshop FM4LS Poster
- Readers: Everyone
Contrastive MIM: A Contrastive Mutual Information Framework for Unified Generative and Discriminative Representation Learning
Micha Livne
- 06 Sept 2025 (modified: 16 Oct 2025)
- Submitted to NeurIPS 2025 2nd Workshop FM4LS
- Readers: Everyone
BaggingCPP: An Inductive PU-Learning Framework for Discovering Cell-Penetrating Peptides
Omri Yakir, Chieh Chang, Maayan Gal, Jerome Tubiana
- Published: 06 Oct 2025, Last Modified: 06 Oct 2025
- NeurIPS 2025 2nd Workshop FM4LS Poster
- Readers: Everyone
Multimodal Survival Analysis with Locally Deployable Large Language Models
Moritz Gögl, Peter Watkinson, Christopher Yau
- Published: 06 Oct 2025, Last Modified: 07 Oct 2025
- NeurIPS 2025 2nd Workshop FM4LS Poster
- Readers: Everyone
Positioning Multi-Agent Large Language Models as the Future of Bulk Gene Expression Analysis and Cancer Prediction
SeyedMohsen Hosseini, Divya Sharma
- 06 Sept 2025 (modified: 16 Oct 2025)
- Submitted to NeurIPS 2025 2nd Workshop FM4LS
- Readers: Everyone
Double Vision: Unifying Morphology and Gene Expression with a Multimodal Transformer
Adriano Martinelli, Bernd Illing, Alice Driessen, Robert Berke, Raphael Gottardo, Marianna Rapsomaniki, Fei Tang
- 06 Sept 2025 (modified: 16 Oct 2025)
- Submitted to NeurIPS 2025 2nd Workshop FM4LS
- Readers: Everyone