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Workshop Sun, Dec 7, 2025 • 8:00 AM – 5:00 PM PST

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

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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
LLM-Integrated Representative Path Selection for Context-Aware Drug Repurposing on Biomedical Knowledge Graphs
HAERIN SONG ⋅ Dongmin Bang ⋅ Bonil Koo ⋅ Sun Kim ⋅ Sangseon Lee
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
MolVision: Molecular Property Prediction with Vision Language Models
Deepan Adak ⋅ Yogesh Rawat ⋅ Shruti Vyas
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