A foundation model for generalizable cancer diagnosis and survival prediction from histopathological images

Zhaochang Yang, Ting Wei, Ying Liang, Xin Yuan, RuiTian Gao, Yujia Xia, Jie Zhou, Yue Zhang () and Zhangsheng Yu ()
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Zhaochang Yang: Shanghai Jiao Tong University
Ting Wei: Shanghai Jiao Tong University
Ying Liang: Shanghai Jiao Tong University
Xin Yuan: Shanghai Jiao Tong University
RuiTian Gao: Shanghai Jiao Tong University
Yujia Xia: Shanghai Jiao Tong University
Jie Zhou: Shanghai Jiao Tong University
Yue Zhang: Shanghai Jiao Tong University
Zhangsheng Yu: Shanghai Jiao Tong University

Nature Communications, 2025, vol. 16, issue 1, 1-16

Abstract: Abstract Computational pathology, utilizing whole slide images (WSIs) for pathological diagnosis, has advanced the development of intelligent healthcare. However, the scarcity of annotated data and histological differences hinder the general application of existing methods. Extensive histopathological data and the robustness of self-supervised models in small-scale data demonstrate promising prospects for developing foundation pathology models. Here we show BEPH (BEiT-based model Pre-training on Histopathological image), a foundation model that leverages self-supervised learning to learn meaningful representations from 11 million unlabeled histopathological images. These representations are then efficiently adapted to various tasks, including patch-level cancer diagnosis, WSI-level cancer classification, and survival prediction for multiple cancer subtypes. By leveraging the masked image modeling (MIM) pre-training approach, BEPH offers an efficient solution to enhance model performance, reduce the reliance on expert annotations, and facilitate the broader application of artificial intelligence in clinical settings. The pre-trained model is available at https://github.com/Zhcyoung/BEPH .

Date: 2025
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DOI: 10.1038/s41467-025-57587-y

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