Journal Article

A vision–language foundation model for precision oncology

Zhang, Xiaoming, Eweje, Feyisope, Diehn, Maximilian, Willens, Sierra, Li, Ruijiang, Li, Yuchen, Wang, Xiyue, Xiang, Jinxi, Yu, Kun-Hsing, Neal, Joel, Yang, Sen, Chen, Yijiang, Kim, Ted, Gopaulchan, Matthew, Nirschl, Jeffrey J., Xi, Yinghua, Bergstrom, Colin, Olguin, Francesca Maria

2025

Overview

Clinical decision-making is driven by multimodal data, including clinical notes and pathological characteristics. Artificial intelligence approaches that can effectively integrate multimodal data hold significant promise in advancing clinical care 1 , 2 . However, the scarcity of well-annotated multimodal datasets in clinical settings has hindered the development of useful models. In this study, we developed the Multimodal transformer with Unified maSKed modeling (MUSK), a vision–language foundation model designed to leverage large-scale, unlabelled, unpaired image and text data. MUSK was pretrained on 50 million pathology images from 11,577 patients and one billion pathology-related text tokens using unified masked modelling. It was further pretrained on one million pathology image–text pairs to efficiently align the vision and language features. With minimal or no further training, MUSK was tested in a wide range of applications and demonstrated superior performance across 23 patch-level and slide-level benchmarks, including image-to-text and text-to-image retrieval, visual question answering, image classification and molecular biomarker prediction. Furthermore, MUSK showed strong performance in outcome prediction, including melanoma relapse prediction, pan-cancer prognosis prediction and immunotherapy response prediction in lung and gastro-oesophageal cancers. MUSK effectively combined complementary information from pathology images and clinical reports and could potentially improve diagnosis and precision in cancer therapy. Trained on unlabelled, unpaired image and text data, the Multimodal transformer with Unified maSKed modeling excelled in outcome prediction, image-to-text retrieval and visual question answering, potentially improving cancer diagnosis and therapy precision.

• Publisher: Nature Publishing Group UK,Nature Publishing Group
• Subject: 631/114/1305 / 692/308/409 / 692/700/139/422 / 692/700/1750 / Artificial Intelligence / Benchmarks / Biomarkers / Cancer / Cancer therapies / Clinical Decision-Making / Datasets / Decision making / Esophageal cancer / Humanities and Social Sciences / Humans / Image classification / Immunotherapy / Language / Lung Neoplasms - diagnosis / Lung Neoplasms - pathology / Medical imaging / Medical Oncology - methods / Medical prognosis / Melanoma / Melanoma - diagnosis / Melanoma - pathology / multidisciplinary / Neoplasms - diagnosis / Neoplasms - pathology / Neoplasms - therapy / Oncology / Pathology / Precision medicine / Precision Medicine - methods / Predictions / Prognosis / Retrieval / Science / Science (multidisciplinary) / Vision