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Workshop Sun, Dec 7, 2025 • 8:00 AM – 5:00 PM PST Upper Level Room 31ABC

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

Pengtao Xie · James Zou · Le Song · Ruishan Liu · Aidong Zhang · Eran Segal · Wei Wang · Li Zhang
Project Page [ OpenReview] 

Video

Chat is not available.

Schedule

Timezone: America/Los_Angeles
8:30 AM
Opening Remarks
8:40 AM
Invited Talk 1
9:05 AM
Invited Talk 2
9:30 AM
Invited Talk 3
11:10 AM
Invited Talk 4
11:35 AM
Invited Talk 5
12:00 PM
Lunch Break
1:00 PM
Invited Talk 6
1:25 PM
Invited Talk 7
1:50 PM
Invited Talk 8
2:15 PM
Invited Talk 9
4:55 PM
Closing Remark
Hyperbolic Multimodal Representation Learning for Biological Taxonomies
ZeMing Gong · Chuanqi Tang · Xiaoliang Huo · Nicholas Pellegrino · Austin T. Wang · Graham Taylor · Angel Chang · Scott C. Lowe · Joakim Bruslund Haurum
FlashRNA: an efficient model for regulatory genomics
Andrew Jung · Jiexin Gao · Leo J Lee · Brendan Frey
Horizon-Aware Vision–Language Forecasting of Diabetic Retinopathy with Text Prototypes
Gongyu Zhang · YT · Zengxiang Li · Timothy Jackson · Christos Bergeles
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
BaggingCPP: An Inductive PU-Learning Framework for Discovering Cell-Penetrating Peptides
Omri Yakir · Chieh Chang · Maayan Gal · Jerome Tubiana
Not all representations are equal: Comparing protein language models for antibody thermostability prediction
Rudrasis Chakraborty · Jacob Pettit · Mary Silva · Emily Lyon · Anastassya Davis · Emilia Solomon · Joseph Sanchez · Colin Kruse · Corey Quackenbush · Yuliya Kunde · Antonietta Lillo · Tavish McDonald · T.S. Jayram · Barry Chen · Daniel faissol · Ana De Oliveira Sales
Mechanistic Interpretability of Semantic Abstraction in Biomedical Texts
Nikhil Gourisetty · Snata Mohanty · Vishnu Srinivas · Soumil Jain · Sunith Vallabhaneni · Kevin Zhu · Sunishchal Dev
CHEMSETS: How Capable Are Chemistry LLMs?
Christoph Bartmann · Mykyta Ielanskyi · Johannes Schimunek · Philipp Seidl · Günter Klambauer · Sohvi Luukkonen
Predicting and generating antibiotics against future pathogens with ApexOracle
Tianang Leng · Fangping Wan · Marcelo Der Torossian Torres · Cesar de la Fuente-Nunez
CellSpliceNet: Explainable Multimodal Transformers for Splicing in C. elegans Neurons
Arman Afrasiyabi · Jake Kovalic · Chen Liu · Egbert Castro · Alexis Weinreb · Erdem Varol · David Miller · Marc Hammarlund · Smita Krishnaswamy
Improved Therapeutic Antibody Reformatting through Multimodal Machine Learning
Jiayi Xin · Aniruddh Raghu · Nicholas Bhattacharya · Adam Carr · Melanie Montgomery · Hunter Elliott
Learning In-Silico Maps of Transcription Factor Binding and Cooperativity interactions
Ruben Solozabal · Albert Baichorov · Tamir Avioz · Le Song · Ariel Afek · Martin Takac
Learning to Align Molecules and Proteins: A Geometry-Aware Approach to Binding Affinity
Mohammad Saleh Refahi · Bahrad Sokhansanj · James R Brown · Gail Rosen
A Comparative Study of Semi-supervised Deep Anomaly Detection and LLMs for Monitoring Patients with Severe Health Status Undergoing Radiotherapy
Yan Yang · Xinglei Shen · Ronald Chen · Hao Gao · Chen Zhao · Guihong Wan · Yi He · Zhong Chen
Benchmarking Biomolecular Foundation Models for Cross-Modal Genomics-Proteomics
Joseph Wakim · Vinayak Gupta · Jose Marti · Jonathan Allen · Brian Bartoldson · Bhavya Kailkhura
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
GLM-Prior: A Genomic Language Model for Sequence-Derived Prior Knowledge in GRN Inference
Claudia Skok Gibbs · Angelica Chen · Richard Bonneau · Kyunghyun Cho
Decoding Histone Modification Signatures of Non-Coding RNAs via Foundation Models
Nishant Sharma · Mohammad Atif Quamar · Pengtao Xie
A multi-domain EHR foundation model for predicting Hepatitis B liver disease: a clinical perspective
Caroline Weis · Max Horn · Max Burg · Filippo Grazioli · Adam Kania · Giovanni Visonà · Jonathan Golob · Patrick Schwab
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 · Nick Youngblut · Jure Leskovec · Luke Gilbert · Silvana Konermann · Patrick Hsu · Alexander Dobin · Dave Burke · Hani Goodarzi · Yusuf Roohani
Motif-aware Tokenization of the Genome: Towards Interpretable Modeling of Gene Regulation
Parmida Davarmanesh · Adityanarayanan Radhakrishnan · Ashia Wilson · Ruochi Zhang · Jimin Tan · Joshua Pereira · Bo Xia
Multimodal Survival Analysis with Locally Deployable Large Language Models
Moritz Gögl · Peter Watkinson · Christopher Yau
Token-Level Guided Discrete Diffusion for Membrane Protein Design
Shrey Goel · Peregrine Schray · Yinuo Zhang · Sophia Vincoff · Huong Kratochvil · Pranam Chatterjee
LLMGEN: Evolving Interpretable Surrogate Programs for Genomics with LLMs
Chandana Rajesh · Wilson Ho · Ziqi Tang · Peter Koo · Thomas Pierrot
Multitask Asynchronous Bidirectional Multimodal Agent for Personalized Treatment Companions
Muhamad Iqbal Januadi Putra · Raka Abdurrahman · Vincent Alexander
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
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 · Jeffery 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 Cheng
BioCLIP 2: Emergent Properties from Scaling Hierarchical Contrastive Learning
Jianyang Gu · Sam Stevens · Elizabeth Campolongo · Matthew Thompson · Net Zhang · Jiaman Wu · Andrei Kopanev · Zheda Mai · Alexander White · James Balhoff · Wasila Dahdul · Daniel Rubenstein · Hilmar Lapp · Tanya Berger-Wolf · Wei-Lun (Harry) Chao · Yu Su
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
GRAM-DTI: Adaptive Multimodal Representation Learning for Drug–Target Interaction Prediction
Feng Jiang · Maolaaisha Aminanmu · Hehuan Ma · Tommaso Mansi · Junzhou Huang · Mangal Prakash · Rui Liao