A comparative study of explainability methods for whole slide classification of lymph node metastases using vision transformers.
Recent advancements in deep learning have shown promise in enhancing the performance of medical image analysis. In pathology, automated whole slide imaging has transformed clinical workflows by streamlining routine tasks and diagnostic and prognostic support. However, the lack of transparency of dee...
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2025-04-01
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| Series: | PLOS Digital Health |
| Online Access: | https://doi.org/10.1371/journal.pdig.0000792 |
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| author | Jens Rahnfeld Mehdi Naouar Gabriel Kalweit Joschka Boedecker Estelle Dubruc Maria Kalweit |
| author_facet | Jens Rahnfeld Mehdi Naouar Gabriel Kalweit Joschka Boedecker Estelle Dubruc Maria Kalweit |
| author_sort | Jens Rahnfeld |
| collection | DOAJ |
| description | Recent advancements in deep learning have shown promise in enhancing the performance of medical image analysis. In pathology, automated whole slide imaging has transformed clinical workflows by streamlining routine tasks and diagnostic and prognostic support. However, the lack of transparency of deep learning models, often described as black boxes, poses a significant barrier to their clinical adoption. This study evaluates various explainability methods for Vision Transformers, assessing their effectiveness in explaining the rationale behind their classification predictions on histopathological images. Using a Vision Transformer trained on the publicly available CAMELYON16 dataset comprising of 399 whole slide images of lymph node metastases of patients with breast cancer, we conducted a comparative analysis of a diverse range of state-of-the-art techniques for generating explanations through heatmaps, including Attention Rollout, Integrated Gradients, RISE, and ViT-Shapley. Our findings reveal that Attention Rollout and Integrated Gradients are prone to artifacts, while RISE and particularly ViT-Shapley generate more reliable and interpretable heatmaps. ViT-Shapley also demonstrated faster runtime and superior performance in insertion and deletion metrics. These results suggest that integrating ViT-Shapley-based heatmaps into pathology reports could enhance trust and scalability in clinical workflows, facilitating the adoption of explainable artificial intelligence in pathology. |
| format | Article |
| id | doaj-art-34b6bae49c32495eb7dfe08e68afb375 |
| institution | OA Journals |
| issn | 2767-3170 |
| language | English |
| publishDate | 2025-04-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLOS Digital Health |
| spelling | doaj-art-34b6bae49c32495eb7dfe08e68afb3752025-08-20T02:12:36ZengPublic Library of Science (PLoS)PLOS Digital Health2767-31702025-04-0144e000079210.1371/journal.pdig.0000792A comparative study of explainability methods for whole slide classification of lymph node metastases using vision transformers.Jens RahnfeldMehdi NaouarGabriel KalweitJoschka BoedeckerEstelle DubrucMaria KalweitRecent advancements in deep learning have shown promise in enhancing the performance of medical image analysis. In pathology, automated whole slide imaging has transformed clinical workflows by streamlining routine tasks and diagnostic and prognostic support. However, the lack of transparency of deep learning models, often described as black boxes, poses a significant barrier to their clinical adoption. This study evaluates various explainability methods for Vision Transformers, assessing their effectiveness in explaining the rationale behind their classification predictions on histopathological images. Using a Vision Transformer trained on the publicly available CAMELYON16 dataset comprising of 399 whole slide images of lymph node metastases of patients with breast cancer, we conducted a comparative analysis of a diverse range of state-of-the-art techniques for generating explanations through heatmaps, including Attention Rollout, Integrated Gradients, RISE, and ViT-Shapley. Our findings reveal that Attention Rollout and Integrated Gradients are prone to artifacts, while RISE and particularly ViT-Shapley generate more reliable and interpretable heatmaps. ViT-Shapley also demonstrated faster runtime and superior performance in insertion and deletion metrics. These results suggest that integrating ViT-Shapley-based heatmaps into pathology reports could enhance trust and scalability in clinical workflows, facilitating the adoption of explainable artificial intelligence in pathology.https://doi.org/10.1371/journal.pdig.0000792 |
| spellingShingle | Jens Rahnfeld Mehdi Naouar Gabriel Kalweit Joschka Boedecker Estelle Dubruc Maria Kalweit A comparative study of explainability methods for whole slide classification of lymph node metastases using vision transformers. PLOS Digital Health |
| title | A comparative study of explainability methods for whole slide classification of lymph node metastases using vision transformers. |
| title_full | A comparative study of explainability methods for whole slide classification of lymph node metastases using vision transformers. |
| title_fullStr | A comparative study of explainability methods for whole slide classification of lymph node metastases using vision transformers. |
| title_full_unstemmed | A comparative study of explainability methods for whole slide classification of lymph node metastases using vision transformers. |
| title_short | A comparative study of explainability methods for whole slide classification of lymph node metastases using vision transformers. |
| title_sort | comparative study of explainability methods for whole slide classification of lymph node metastases using vision transformers |
| url | https://doi.org/10.1371/journal.pdig.0000792 |
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