Diagnostic classification in toxicologic pathology using attention-guided weak supervision and whole slide image features: a pilot study in rat livers
Abstract The diagnostic classification of digitized tissue images based on histopathologic lesions present in whole slide images (WSI) is a significant task that eludes modern image classification techniques. Even with advanced methods designed for digital histopathology, the domain of toxicologic p...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2025-02-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-025-86615-6 |
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| author | Philip Zehnder Jeffrey Feng Trung Nguyen Philip Shen Ruth Sullivan Reina N. Fuji Fangyao Hu |
| author_facet | Philip Zehnder Jeffrey Feng Trung Nguyen Philip Shen Ruth Sullivan Reina N. Fuji Fangyao Hu |
| author_sort | Philip Zehnder |
| collection | DOAJ |
| description | Abstract The diagnostic classification of digitized tissue images based on histopathologic lesions present in whole slide images (WSI) is a significant task that eludes modern image classification techniques. Even with advanced methods designed for digital histopathology, the domain of toxicologic pathology presents challenges in that histopathologic features may be at times complex, subtle, and/or rare. We propose an innovative weakly supervised learning method that leverages minimal annotations, a state-of-the-art self-supervised vision transformer for embedding extraction, and a novel guided attention mechanism that is better suited for heavily imbalanced datasets typical in toxicologic pathology. Our model demonstrates improvements in diagnostic classification and attention heatmap quality over the previously described clustering-constrained-attention multiple-instance learning method on several lesion classes in rat livers (38% improvement in AUC). We also demonstrate how an ensemble of binary classifiers improves interpretability and allows for multiclass classification and the classification of diagnostic regions of interest in each slide. The improved classification performance and higher contrast heatmaps better support toxicologic pathologists’ histopathology analysis and will enable more efficient workflows as they are further refined and integrated into routine use. |
| format | Article |
| id | doaj-art-ee7163278ecd42ceb6628257c83ca7e2 |
| institution | Kabale University |
| issn | 2045-2322 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj-art-ee7163278ecd42ceb6628257c83ca7e22025-02-09T12:33:20ZengNature PortfolioScientific Reports2045-23222025-02-0115111710.1038/s41598-025-86615-6Diagnostic classification in toxicologic pathology using attention-guided weak supervision and whole slide image features: a pilot study in rat liversPhilip Zehnder0Jeffrey Feng1Trung Nguyen2Philip Shen3Ruth Sullivan4Reina N. Fuji5Fangyao Hu6Department of Safety Assessment, Genentech, Inc.Department of Safety Assessment, Genentech, Inc.Department of Safety Assessment, Genentech, Inc.Department of Safety Assessment, Genentech, Inc.Department of Safety Assessment, Genentech, Inc.Department of Safety Assessment, Genentech, Inc.Department of Safety Assessment, Genentech, Inc.Abstract The diagnostic classification of digitized tissue images based on histopathologic lesions present in whole slide images (WSI) is a significant task that eludes modern image classification techniques. Even with advanced methods designed for digital histopathology, the domain of toxicologic pathology presents challenges in that histopathologic features may be at times complex, subtle, and/or rare. We propose an innovative weakly supervised learning method that leverages minimal annotations, a state-of-the-art self-supervised vision transformer for embedding extraction, and a novel guided attention mechanism that is better suited for heavily imbalanced datasets typical in toxicologic pathology. Our model demonstrates improvements in diagnostic classification and attention heatmap quality over the previously described clustering-constrained-attention multiple-instance learning method on several lesion classes in rat livers (38% improvement in AUC). We also demonstrate how an ensemble of binary classifiers improves interpretability and allows for multiclass classification and the classification of diagnostic regions of interest in each slide. The improved classification performance and higher contrast heatmaps better support toxicologic pathologists’ histopathology analysis and will enable more efficient workflows as they are further refined and integrated into routine use.https://doi.org/10.1038/s41598-025-86615-6 |
| spellingShingle | Philip Zehnder Jeffrey Feng Trung Nguyen Philip Shen Ruth Sullivan Reina N. Fuji Fangyao Hu Diagnostic classification in toxicologic pathology using attention-guided weak supervision and whole slide image features: a pilot study in rat livers Scientific Reports |
| title | Diagnostic classification in toxicologic pathology using attention-guided weak supervision and whole slide image features: a pilot study in rat livers |
| title_full | Diagnostic classification in toxicologic pathology using attention-guided weak supervision and whole slide image features: a pilot study in rat livers |
| title_fullStr | Diagnostic classification in toxicologic pathology using attention-guided weak supervision and whole slide image features: a pilot study in rat livers |
| title_full_unstemmed | Diagnostic classification in toxicologic pathology using attention-guided weak supervision and whole slide image features: a pilot study in rat livers |
| title_short | Diagnostic classification in toxicologic pathology using attention-guided weak supervision and whole slide image features: a pilot study in rat livers |
| title_sort | diagnostic classification in toxicologic pathology using attention guided weak supervision and whole slide image features a pilot study in rat livers |
| url | https://doi.org/10.1038/s41598-025-86615-6 |
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