| A Multi-Modal Foundation Model Across Species for Interpreting Gene Functions Tianyu Liu [Paper Link] |
| Token-Level Guided Discrete Diffusion for Membrane Protein Design Shrey Goel, Peregrine Michael Schray, Yinuo Zhang, Sophia Vincoff, Huong T. Kratochvil, Pranam Chatterjee [Paper Link] |
| GLM-Prior: A Genomic Language Model for Sequence-Derived Prior Knowledge in GRN Inference Claudia Skok Gibbs, Angelica Chen, Richard Bonneau, Kyunghyun Cho [Paper Link] |
| Explainable Insulin Pump Control with LLM Controllers for Type 1 Diabetes Maya Sarkar [Paper Link] |
| LINKER: Learning Interactions Between Functional Groups and Residues With Chemical Knowledge-Enhanced Reasoning and Explainability PhucPhamHuyThien, Viet Thanh Duy Nguyen, Truong-Son Hy [Paper Link] |
| 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 [Paper Link] |
| From Base Pairs to Functions: Rich RNA Representations via Multimodal Language Modeling Joel Bonnie, Tin Vlašić, Mile Sikic [Paper Link] |
| 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 [Paper Link] |
| 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, Wasla Dahdul, Daniel Rubenstein, Hilmar Lapp, Tanya Berger-Wolf, Wei-Lun Chao, Yu Su [Paper Link] |
| The Exposome Interpreter: A Multi-Modal Framework for Personalized Autoimmune Care KRITIKA CHUGH [Paper Link] |
| 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 [Paper Link] |
| CHEMSETS: How Capable Are Chemistry LLMs? Christoph Bartmann, Mykyta Ielanskyi, Johannes Schimunek, Philipp Seidl, Günter Klambauer, Sohvi Luukkonen [Paper Link] |
| 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 [Paper Link] |
| 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 [Paper Link] |
| 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 [Paper Link] |
| 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 [Paper Link] |
| 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 [Paper Link] |
| Learning to Align Molecules and Proteins: A Geometry-Aware Approach to Binding Affinity Mohammadsaleh Refahi, Bahrad A. Sokhansanj, James R. Brown, Gail Rosen [Paper Link] |
| Horizon-Aware Vision–Language Forecasting of Diabetic Retinopathy with Text Prototypes Gongyu Zhang, YT, Zengxiang Li, Timothy L Jackson, Christos Bergeles [Paper Link] |
| LLM-Integrated Representative Path Selection for Context-Aware Drug Repurposing on Biomedical Knowledge Graphs Haerin Song, Dongmin Bang, Bonil Koo, Sun Kim, Sangseon Lee [Paper Link] |
| DeepSpot2Cell: Predicting Virtual Single-Cell Spatial Transcriptomics from H&E images using Spot-Level Supervision Kalin Nonchev, Glib Manaiev, Viktor Koelzer, Gunnar Ratsch [Paper Link] |
| Boundary Guidance for Efficient 3D CT Vision–Language Reasoning Soo Yong Kim [Paper Link] |
| Improved Therapeutic Antibody Reformatting through Multimodal Machine Learning Jiayi Xin, Aniruddh Raghu, Nick Bhattacharya, Adam Carr, Melanie Montgomery, Hunter Elliott [Paper Link] |
| 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 [Paper Link] |
| Revealing bias in antibody language models through systematic training data processing with OAS-explore Wiona Sophie Glänzer, Sai T. Reddy, Alexander Yermanos [Paper Link] |
| 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 [Paper Link] |
| Challenges in Leveraging Functional Information to Evaluate Predicted Protein-Ligand Interactions Joseph G. Wakim, Jose Manuel Marti, Jonathan E Allen, Adam T. Zemla [Paper Link] |
| g-DPO: Scalable Preference Optimization for Protein Language Models Constance Ferragu, Cradle ML Team [Paper Link] |
| Position: Adjacent Technologies Are the Key Enablers of Scalable and Safe Clinical MLLM Deployment Azmine Toushik Wasi, Md. Iqramul Hoque [Paper Link] |
| FlashRNA: an efficient model for regulatory genomics Andrew J Jung, ALICE J. GAO, Leo J Lee, Brendan Frey [Paper Link] |
| Decoding Histone Modification Signatures of Non-Coding RNAs via Foundation Models Nishant Sharma, Mohammad Atif Quamar, Pengtao Xie [Paper Link] |
| Beyond Labels: Explanatory Collapse due to Instruction Tuning in Protein LLMs Yining Yang, Ruihong Huang, Yang Shen [Paper Link] |
| Learning monosemantic features in multitask DNA regulatory sequence models via sparse autoencoder decomposition Anya Korsakova, David Roy Kelley [Paper Link] |
| 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 [Paper Link] |
| Mechanistic Interpretability of Semantic Abstraction in Biomedical Texts Nikhil Gourisetty, Snata Mohanty, Vishnu Srinivas, Soumil Jain, Sunith Vallabhaneni, Kevin Zhu, Sunishchal Dev [Paper Link] |
| Quantifying the Role of OpenFold Components in Protein Structure Prediction Tyler L. Hayes, Giri P Krishnan [Paper Link] |
| Uncertainty-Guided Model Selection for Tabular Foundation Models in Biomolecule Efficacy Prediction Jie Li, Andrew McCarthy, Zhizhuo Zhang [Paper Link] |
| LLMGEN: Evolving Interpretable Surrogate Programs for Genomics with LLMs Chandana Rajesh, Wilson Ho, Ziqi Tang, Peter K Koo, Thomas Pierrot [Paper Link] |
| 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 [Paper Link] |
| Multimodal Survival Analysis with Locally Deployable Large Language Models Moritz Gögl, Peter Watkinson, Christopher Yau [Paper Link] |
| BaggingCPP: An Inductive PU-Learning Framework for Discovering Cell-Penetrating Peptides Omri Yakir, Chieh Chang, Maayan Gal, Jerome Tubiana [Paper Link] |
| MolVision: Molecular Property Prediction with Vision Language Models Deepan Adak, Yogesh S Rawat, Shruti Vyas [Paper Link] |
| Predicting and generating antibiotics against future pathogens with ApexOracle Tianang Leng, Fangping Wan, Marcelo Der Torossian Torres, Cesar de la Fuente-Nunez [Paper Link] |
| 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 [Paper Link] |
| Thin Bridges for Drug Text Alignment: Lightweight Contrastive Learning for Target Specific Drug Retrieval Mallikarjuna Tupakula [Paper Link] |
| 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 [Paper Link] |
| Multitask Asynchronous Bidirectional Multimodal Agent for Personalized Treatment Companions Muhamad Iqbal Januadi Putra, Raka Admiral Abdurrahman, Vincent Alexander [Paper Link] |
| Disentangling Protein Family Signals in Protein Language Models: Composition or Motifs? Sohel Bashar, M Saifur Rahman [Paper Link] |
| Multimodal Alignment Reveals Interpretable Gene–Morphology Links in Perineuronal Net Pathology Wenjun Liu, Saeed Hassanpour [Paper Link] |
| Learning In-Silico Maps of Transcription Factor Binding and Cooperativity interactions Ruben Solozabal, Albert Baichorov, Tamir Avioz, Le Song, Ariel Afek, Martin Takáč [Paper Link] |
| HIP-HOP: Invariants for 2D Tilings with Biomedical Case Study Madhava Gaikwad, Ashwini Ramchandra Doke [Paper Link] |
| Predicting Influenza Reassortment Potential Using Foundation Models and Genetic Algorithms for Pandemic Preparedness Seeraja Konnur [Paper Link] |
| 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 [Paper Link] |