NeurIPS 2025 Past Large language modelsAI for scienceMultimodal

NeurIPS 2025 2nd Workshop on Multi-modal Foundation Models and Large Language Models for Life Sciences

NeurIPS 2025 2nd Workshop FM4LS

Submission deadline
Sep 7, 2025, 12:00 UTC
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Submission portal
OpenReview
Notes
Auto-imported from the OpenReview venue record on 2026-06-10 — please verify and enrich (topics are keyword-guessed).

Accepted papers (53)

Fetched from OpenReview (v2) on 2026-06-10.

  1. A Comparative Study of Semi-supervised Deep Anomaly Detection and LLMs for Monitoring Patients with Severe Health Status Undergoing Radiotherapy

    Yang Yan, Xinglei Shen, Ronald Chen, Hao Gao, Chen Zhao, Guihong Wan, Yi He, Zhong Chen · PDF
  2. A multi-domain EHR foundation model for predicting Hepatitis B liver disease: a clinical perspective

    Caroline V Weis, Max Horn, Max F Burg, Filippo Grazioli, Adam Kania, Giovanni Visona, Jonathan Golob, Patrick Schwab · PDF
  3. 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 · PDF
  4. A Multi-Modal Foundation Model Across Species for Interpreting Gene Functions

    Tianyu Liu · PDF
  5. 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 · PDF
  6. BaggingCPP: An Inductive PU-Learning Framework for Discovering Cell-Penetrating Peptides

    Omri Yakir, Chieh Chang, Maayan Gal, Jerome Tubiana · PDF
  7. Benchmarking Biomolecular Foundation Models for Cross-Modal Genomics-Proteomics

    Joseph G. Wakim, Vinayak Gupta, Jose Manuel Marti, Jonathan E Allen, Brian R. Bartoldson, Bhavya Kailkhura · PDF
  8. Beyond Labels: Explanatory Collapse due to Instruction Tuning in Protein LLMs

    Yining Yang, Ruihong Huang, Yang Shen · PDF
  9. BiDoRA: Bi-level Optimization-Based Weight-Decomposed Low-Rank Adaptation for Overfitting-Resilient Fine-Tuning of Biological Foundation Models

    Peijia Qin, Ruiyi Zhang, Pengtao Xie · PDF
  10. BioCLIP 2: Emergent Properties from Scaling Hierarchical Contrastive Learning

    Jianyang Gu, Samuel Stevens, Elizabeth G Campolongo, Matthew J Thompson, Net Zhang, Jiaman Wu, Andrei Kopanev, Zheda Mai, Alexander E. White, James Balhoff, Wasila Dahdul, Daniel Rubenstein, Hilmar Lapp, Tanya Berger-Wolf, Wei-Lun Chao, Yu Su · PDF
  11. Boundary Guidance for Efficient 3D CT Vision–Language Reasoning

    Soo Yong Kim · PDF
  12. CellSpliceNet: Explainable Multimodal Transformers for Splicing in C. elegans Neurons

    Arman Afrasiyabi, Jake Kovalic, Chen Liu, Egbert Castro, Alexis Weinreb, Erdem Varol, David M. Miller III, Marc Hammarlund, Smita Krishnaswamy · PDF
  13. Challenges in Leveraging Functional Information to Evaluate Predicted Protein-Ligand Interactions

    Joseph G. Wakim, Jose Manuel Marti, Jonathan E Allen, Adam T. Zemla · PDF
  14. CHEMSETS: How Capable Are Chemistry LLMs?

    Christoph Bartmann, Mykyta Ielanskyi, Johannes Schimunek, Philipp Seidl, Günter Klambauer, Sohvi Luukkonen · PDF
  15. Decoding Histone Modification Signatures of Non-Coding RNAs via Foundation Models

    Nishant Sharma, Mohammad Atif Quamar, Pengtao Xie · PDF
  16. DeepSpot2Cell: Predicting Virtual Single-Cell Spatial Transcriptomics from H&E images using Spot-Level Supervision

    Kalin Nonchev, Glib Manaiev, Viktor Koelzer, Gunnar Ratsch · PDF
  17. Disentangling Protein Family Signals in Protein Language Models: Composition or Motifs?

    Sohel Bashar, M Saifur Rahman · PDF
  18. Explainable Insulin Pump Control with LLM Controllers for Type 1 Diabetes

    Maya Sarkar · PDF
  19. FlashRNA: an efficient model for regulatory genomics

    Andrew J Jung, ALICE J. GAO, Leo J Lee, Brendan Frey · PDF
  20. From Base Pairs to Functions: Rich RNA Representations via Multimodal Language Modeling

    Joel Bonnie, Tin Vlašić, Mile Sikic · PDF
  21. g-DPO: Scalable Preference Optimization for Protein Language Models

    Constance Ferragu, Cradle ML Team · PDF
  22. GLM-Prior: A Genomic Language Model for Sequence-Derived Prior Knowledge in GRN Inference

    Claudia Skok Gibbs, Angelica Chen, Richard Bonneau, Kyunghyun Cho · PDF
  23. GRAM-DTI: Adaptive Multimodal Representation Learning for Drug–Target Interaction Prediction

    Feng Jiang, Amina Mollaysa, Hehuan Ma, Tommaso Mansi, Junzhou Huang, Mangal Prakash, Rui Liao · PDF
  24. Harnessing biomedical foundation models for genomic feature engineering to investigate patient drug response

    Laura-Jayne Gardiner, Jennifer Kelly, Stephen Checkley, Karen Bingham, Graeme Macluskie, David Bunton · PDF
  25. HIP-HOP: Invariants for 2D Tilings with Biomedical Case Study

    Madhava Gaikwad, Ashwini Ramchandra Doke · PDF
  26. Horizon-Aware Vision–Language Forecasting of Diabetic Retinopathy with Text Prototypes

    Gongyu Zhang, YT, Zengxiang Li, Timothy L Jackson, Christos Bergeles · PDF
  27. Hyperbolic Multimodal Representation Learning for Biological Taxonomies

    ZeMing Gong, Chuanqi Tang, Xiaoliang Huo, Nicholas Pellegrino, Austin Wang, Graham W. Taylor, Angel X Chang, Scott C. Lowe, Joakim Bruslund Haurum · PDF
  28. Improved Therapeutic Antibody Reformatting through Multimodal Machine Learning

    Jiayi Xin, Aniruddh Raghu, Nick Bhattacharya, Adam Carr, Melanie Montgomery, Hunter Elliott · PDF
  29. Learning In-Silico Maps of Transcription Factor Binding and Cooperativity interactions

    Ruben Solozabal, Albert Baichorov, Tamir Avioz, Le Song, Ariel Afek, Martin Takáč · PDF
  30. Learning monosemantic features in multitask DNA regulatory sequence models via sparse autoencoder decomposition

    Anya Korsakova, David Roy Kelley · PDF
  31. Learning to Align Molecules and Proteins: A Geometry-Aware Approach to Binding Affinity

    Mohammadsaleh Refahi, Bahrad A. Sokhansanj, James R. Brown, Gail Rosen · PDF
  32. LINKER: Learning Interactions Between Functional Groups and Residues With Chemical Knowledge-Enhanced Reasoning and Explainability

    PhucPhamHuyThien, Viet Thanh Duy Nguyen, Truong-Son Hy · PDF
  33. LLM-Integrated Representative Path Selection for Context-Aware Drug Repurposing on Biomedical Knowledge Graphs

    Haerin Song, Dongmin Bang, Bonil Koo, Sun Kim, Sangseon Lee · PDF
  34. LLMGEN: Evolving Interpretable Surrogate Programs for Genomics with LLMs

    Chandana Rajesh, Wilson Ho, Ziqi Tang, Peter K Koo, Thomas Pierrot · PDF
  35. Mechanistic Interpretability of Semantic Abstraction in Biomedical Texts

    Nikhil Gourisetty, Snata Mohanty, Vishnu Srinivas, Soumil Jain, Sunith Vallabhaneni, Kevin Zhu, Sunishchal Dev · PDF
  36. MoAgent: A Hypothesis-Driven Multi-Agent Framework for Drug Mechanism of Action Discovery

    Jun Hyeong Kim, Seokhyun Moon, Seonghwan Kim, Junhyeok Jeon, Taein Kim, Jisu Seo, Songmi Kim, Woo Youn Kim · PDF
  37. MolVision: Molecular Property Prediction with Vision Language Models

    Deepan Adak, Yogesh S Rawat, Shruti Vyas · PDF
  38. Motif-aware Tokenization of the Genome: Towards Interpretable Modeling of Gene Regulation

    Parmida Davarmanesh, Adityanarayanan Radhakrishnan, Ashia C. Wilson, Ruochi Zhang, Jimin Tan, Joshua Pereira, Bo Xia · PDF
  39. Multi-Modal Foundation Models for Computational Pathology: A Survey

    Dong Li, Guihong Wan, Xintao Wu, Xinyu Wu, Xiaohui Chen, Yi He, Zhong Chen, Ninghui Hao, Chen Zhao · PDF
  40. Multimodal Alignment Reveals Interpretable Gene–Morphology Links in Perineuronal Net Pathology

    Wenjun Liu, Saeed Hassanpour · PDF
  41. Multimodal Survival Analysis with Locally Deployable Large Language Models

    Moritz Gögl, Peter Watkinson, Christopher Yau · PDF
  42. Multitask Asynchronous Bidirectional Multimodal Agent for Personalized Treatment Companions

    Muhamad Iqbal Januadi Putra, Raka Admiral Abdurrahman, Vincent Alexander · PDF
  43. Not all representations are equal: Comparing protein language models for antibody thermostability prediction

    Rudrasis Chakraborty, Jacob Pettit, Mary S Silva, Emily Alipio Lyon, Anastassya Davis, Emilia Solomon, Joseph Sanchez, Colin Singer Kruse, Corey Quackenbush, Yuliya Kunde, Antonietta M. Lillo, Tavish Malcolm McDonald, T.S. Jayram, Barry Y. Chen, Daniel faissol, Ana Paula De Oliveira Sales · PDF
  44. Position: Adjacent Technologies Are the Key Enablers of Scalable and Safe Clinical MLLM Deployment

    Azmine Toushik Wasi, Md. Iqramul Hoque · PDF
  45. Predicting and generating antibiotics against future pathogens with ApexOracle

    Tianang Leng, Fangping Wan, Marcelo Der Torossian Torres, Cesar de la Fuente-Nunez · PDF
  46. 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, Luke A. Gilbert, Silvana Konermann, Patrick D Hsu, Alexander Dobin, Dave P. Burke, Hani Goodarzi, Yusuf H Roohani · PDF
  47. Predicting Influenza Reassortment Potential Using Foundation Models and Genetic Algorithms for Pandemic Preparedness

    Seeraja Konnur · PDF
  48. Quantifying the Role of OpenFold Components in Protein Structure Prediction

    Tyler L. Hayes, Giri P Krishnan · PDF
  49. Revealing bias in antibody language models through systematic training data processing with OAS-explore

    Wiona Sophie Glänzer, Sai T. Reddy, Alexander Yermanos · PDF
  50. The Exposome Interpreter: A Multi-Modal Framework for Personalized Autoimmune Care

    KRITIKA CHUGH · PDF
  51. Thin Bridges for Drug Text Alignment: Lightweight Contrastive Learning for Target Specific Drug Retrieval

    Mallikarjuna Tupakula · PDF
  52. Token-Level Guided Discrete Diffusion for Membrane Protein Design

    Shrey Goel, Peregrine Michael Schray, Yinuo Zhang, Sophia Vincoff, Huong T. Kratochvil, Pranam Chatterjee · PDF
  53. Uncertainty-Guided Model Selection for Tabular Foundation Models in Biomolecule Efficacy Prediction

    Jie Li, Andrew McCarthy, Zhizhuo Zhang · PDF