Towards A Generalizable Pathology Foundation Model via Unified Knowledge Distillation
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arXiv
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| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Preprint |
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2024
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| _version_ | 1866915239131348992 |
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| author | Ma, Jiabo Guo, Zhengrui Zhou, Fengtao Wang, Yihui Xu, Yingxue Li, Jinbang Yan, Fang Cai, Yu Zhu, Zhengjie Jin, Cheng Lin, Yi Jiang, Xinrui Zhao, Chenglong Li, Danyi Han, Anjia Li, Zhenhui Chan, Ronald Cheong Kin Wang, Jiguang Fei, Peng Cheng, Kwang-Ting Zhang, Shaoting Liang, Li Chen, Hao |
| author_facet | Ma, Jiabo Guo, Zhengrui Zhou, Fengtao Wang, Yihui Xu, Yingxue Li, Jinbang Yan, Fang Cai, Yu Zhu, Zhengjie Jin, Cheng Lin, Yi Jiang, Xinrui Zhao, Chenglong Li, Danyi Han, Anjia Li, Zhenhui Chan, Ronald Cheong Kin Wang, Jiguang Fei, Peng Cheng, Kwang-Ting Zhang, Shaoting Liang, Li Chen, Hao |
| contents | Foundation models pretrained on large-scale datasets are revolutionizing the field of computational pathology (CPath). The generalization ability of foundation models is crucial for the success in various downstream clinical tasks. However, current foundation models have only been evaluated on a limited type and number of tasks, leaving their generalization ability and overall performance unclear. To address this gap, we established a most comprehensive benchmark to evaluate the performance of off-the-shelf foundation models across six distinct clinical task types, encompassing a total of 72 specific tasks, including slide-level classification, survival prediction, ROI-tissue classification, ROI retrieval, visual question answering, and report generation. Our findings reveal that existing foundation models excel at certain task types but struggle to effectively handle the full breadth of clinical tasks. To improve the generalization of pathology foundation models, we propose a unified knowledge distillation framework consisting of both expert and self-knowledge distillation, where the former allows the model to learn from the knowledge of multiple expert models, while the latter leverages self-distillation to enable image representation learning via local-global alignment. Based on this framework, we curated a dataset of 96,000 whole slide images (WSIs) and developed a Generalizable Pathology Foundation Model (GPFM). This advanced model was trained on a substantial dataset comprising 190 million images extracted from approximately 72,000 publicly available slides, encompassing 34 major tissue types. Evaluated on the established benchmark, GPFM achieves an impressive average rank of 1.6, with 42 tasks ranked 1st, while the second-best model, UNI, attains an average rank of 3.7, with only 6 tasks ranked 1st. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2407_18449 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | Towards A Generalizable Pathology Foundation Model via Unified Knowledge Distillation Ma, Jiabo Guo, Zhengrui Zhou, Fengtao Wang, Yihui Xu, Yingxue Li, Jinbang Yan, Fang Cai, Yu Zhu, Zhengjie Jin, Cheng Lin, Yi Jiang, Xinrui Zhao, Chenglong Li, Danyi Han, Anjia Li, Zhenhui Chan, Ronald Cheong Kin Wang, Jiguang Fei, Peng Cheng, Kwang-Ting Zhang, Shaoting Liang, Li Chen, Hao Image and Video Processing Computer Vision and Pattern Recognition Machine Learning Foundation models pretrained on large-scale datasets are revolutionizing the field of computational pathology (CPath). The generalization ability of foundation models is crucial for the success in various downstream clinical tasks. However, current foundation models have only been evaluated on a limited type and number of tasks, leaving their generalization ability and overall performance unclear. To address this gap, we established a most comprehensive benchmark to evaluate the performance of off-the-shelf foundation models across six distinct clinical task types, encompassing a total of 72 specific tasks, including slide-level classification, survival prediction, ROI-tissue classification, ROI retrieval, visual question answering, and report generation. Our findings reveal that existing foundation models excel at certain task types but struggle to effectively handle the full breadth of clinical tasks. To improve the generalization of pathology foundation models, we propose a unified knowledge distillation framework consisting of both expert and self-knowledge distillation, where the former allows the model to learn from the knowledge of multiple expert models, while the latter leverages self-distillation to enable image representation learning via local-global alignment. Based on this framework, we curated a dataset of 96,000 whole slide images (WSIs) and developed a Generalizable Pathology Foundation Model (GPFM). This advanced model was trained on a substantial dataset comprising 190 million images extracted from approximately 72,000 publicly available slides, encompassing 34 major tissue types. Evaluated on the established benchmark, GPFM achieves an impressive average rank of 1.6, with 42 tasks ranked 1st, while the second-best model, UNI, attains an average rank of 3.7, with only 6 tasks ranked 1st. |
| title | Towards A Generalizable Pathology Foundation Model via Unified Knowledge Distillation |
| topic | Image and Video Processing Computer Vision and Pattern Recognition Machine Learning |
| url | https://arxiv.org/abs/2407.18449 |