LymphoML: An interpretable artificial intelligence-based method identifies morphologic features that correlate with lymphoma subtype

• URL: http://arxiv.org/abs/2311.09574v3
• Date: Mon, 20 Nov 2023 02:01:33 GMT
• Title: LymphoML: An interpretable artificial intelligence-based method identifies morphologic features that correlate with lymphoma subtype
• Authors: Vivek Shankar, Xiaoli Yang, Vrishab Krishna, Brent Tan, Oscar Silva, Rebecca Rojansky, Andrew Ng, Fabiola Valvert, Edward Briercheck, David Weinstock, Yasodha Natkunam, Sebastian Fernandez-Pol, Pranav Rajpurkar
• Abstract summary: We present LymphoML - an interpretable machine learning method that identifies morphologic features that correlate with lymphoma subtypes. Our method applies steps to process H&E-stained tissue microarray cores, segment nuclei and cells, compute features encompassing morphology, texture, and architecture, and train gradient-boosted models to make diagnostic predictions.
• Score: 3.144172405010392
• License: http://creativecommons.org/licenses/by/4.0/
• Abstract: The accurate classification of lymphoma subtypes using hematoxylin and eosin (H&E)-stained tissue is complicated by the wide range of morphological features these cancers can exhibit. We present LymphoML - an interpretable machine learning method that identifies morphologic features that correlate with lymphoma subtypes. Our method applies steps to process H&E-stained tissue microarray cores, segment nuclei and cells, compute features encompassing morphology, texture, and architecture, and train gradient-boosted models to make diagnostic predictions. LymphoML's interpretable models, developed on a limited volume of H&E-stained tissue, achieve non-inferior diagnostic accuracy to pathologists using whole-slide images and outperform black box deep-learning on a dataset of 670 cases from Guatemala spanning 8 lymphoma subtypes. Using SHapley Additive exPlanation (SHAP) analysis, we assess the impact of each feature on model prediction and find that nuclear shape features are most discriminative for DLBCL (F1-score: 78.7%) and classical Hodgkin lymphoma (F1-score: 74.5%). Finally, we provide the first demonstration that a model combining features from H&E-stained tissue with features from a standardized panel of 6 immunostains results in a similar diagnostic accuracy (85.3%) to a 46-stain panel (86.1%).

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