A whole-slide foundation model for digital pathology from real-world data

A whole-slide foundation model for digital pathology from real-world data

22 May 2024 | Hanwen Xu, Naoto Usuyama, Jaspreet Bagga, Sheng Zhang, Rajesh Rao, Tristan Naumann, Cliff Wong, Zalelame Gero, Javier González, Yu Gu, Yanbo Xu, Mu Wei, Wenhui Wang, Shuming Ma, Furu Wei, Jianwei Yang, Chunyuan Li, Jianfeng Gao, Jaylen Rosemon, Tucker Bower, Sohee Lee, Roshanthi Weerasinghe, Bill J. Wright, Ari Robicsek, Brian Piening, Carlo Bifulco, Sheng Wang, and Hoifung Poon
The article introduces Prov-GigaPath, a whole-slide pathology foundation model designed to address the unique computational challenges of digital pathology. Prov-GigaPath is pre-trained on a large dataset, Prov-Path, which consists of 1.3 billion 256 × 256 pathology image tiles from 171,189 whole slides, covering more than 30,000 patients and 31 major tissue types. The model is trained using GigaPath, a novel vision transformer architecture that adapts the LongNet method to handle the large number of image tiles in gigapixel slides. Prov-GigaPath demonstrates state-of-the-art performance on various digital pathology tasks, including cancer subtyping and pathomics, with significant improvements over existing models. The article also explores the potential of Prov-GigaPath in vision-language pretraining by incorporating pathology reports, showing its capability in zero-shot subtyping and mutation prediction. Overall, Prov-GigaPath is an open-weight foundation model that leverages real-world data and whole-slide modeling to enhance clinical diagnostics and decision support in computational pathology.The article introduces Prov-GigaPath, a whole-slide pathology foundation model designed to address the unique computational challenges of digital pathology. Prov-GigaPath is pre-trained on a large dataset, Prov-Path, which consists of 1.3 billion 256 × 256 pathology image tiles from 171,189 whole slides, covering more than 30,000 patients and 31 major tissue types. The model is trained using GigaPath, a novel vision transformer architecture that adapts the LongNet method to handle the large number of image tiles in gigapixel slides. Prov-GigaPath demonstrates state-of-the-art performance on various digital pathology tasks, including cancer subtyping and pathomics, with significant improvements over existing models. The article also explores the potential of Prov-GigaPath in vision-language pretraining by incorporating pathology reports, showing its capability in zero-shot subtyping and mutation prediction. Overall, Prov-GigaPath is an open-weight foundation model that leverages real-world data and whole-slide modeling to enhance clinical diagnostics and decision support in computational pathology.
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Understanding A whole-slide foundation model for digital pathology from real-world data