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| Main Authors: | , , , , |
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| Format: | Preprint |
| Published: |
2025
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| Subjects: | |
| Online Access: | https://arxiv.org/abs/2511.19751 |
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| _version_ | 1866918217464676352 |
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| author | Diab, Abdul Rahman Karn, Emily E. Wu, Renchin Ruiz, Emily S. Lotter, William |
| author_facet | Diab, Abdul Rahman Karn, Emily E. Wu, Renchin Ruiz, Emily S. Lotter, William |
| contents | Despite the promise of computational pathology foundation models, adapting them to specific clinical tasks remains challenging due to the complexity of whole-slide image (WSI) processing, the opacity of learned features, and the wide range of potential adaptation strategies. To address these challenges, we introduce PathFMTools, a lightweight, extensible Python package that enables efficient execution, analysis, and visualization of pathology foundation models. We use this tool to interface with and evaluate two state-of-the-art vision-language foundation models, CONCH and MUSK, on the task of histological grading in cutaneous squamous cell carcinoma (cSCC), a critical criterion that informs cSCC staging and patient management. Using a cohort of 440 cSCC H&E WSIs, we benchmark multiple adaptation strategies, demonstrating trade-offs across prediction approaches and validating the potential of using foundation model embeddings to train small specialist models. These findings underscore the promise of pathology foundation models for real-world clinical applications, with PathFMTools enabling efficient analysis and validation. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2511_19751 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | Leveraging Foundation Models for Histological Grading in Cutaneous Squamous Cell Carcinoma using PathFMTools Diab, Abdul Rahman Karn, Emily E. Wu, Renchin Ruiz, Emily S. Lotter, William Computer Vision and Pattern Recognition Artificial Intelligence Despite the promise of computational pathology foundation models, adapting them to specific clinical tasks remains challenging due to the complexity of whole-slide image (WSI) processing, the opacity of learned features, and the wide range of potential adaptation strategies. To address these challenges, we introduce PathFMTools, a lightweight, extensible Python package that enables efficient execution, analysis, and visualization of pathology foundation models. We use this tool to interface with and evaluate two state-of-the-art vision-language foundation models, CONCH and MUSK, on the task of histological grading in cutaneous squamous cell carcinoma (cSCC), a critical criterion that informs cSCC staging and patient management. Using a cohort of 440 cSCC H&E WSIs, we benchmark multiple adaptation strategies, demonstrating trade-offs across prediction approaches and validating the potential of using foundation model embeddings to train small specialist models. These findings underscore the promise of pathology foundation models for real-world clinical applications, with PathFMTools enabling efficient analysis and validation. |
| title | Leveraging Foundation Models for Histological Grading in Cutaneous Squamous Cell Carcinoma using PathFMTools |
| topic | Computer Vision and Pattern Recognition Artificial Intelligence |
| url | https://arxiv.org/abs/2511.19751 |