Multiple-instance-learning-based detection of coeliac disease in histological whole-slide images.
Denholm, J Schreiber, B A Evans, S C Crook, O M Sharma, A Watson, J L Bancroft, H Langman, G Gilbey, J D Schönlieb, C-B
Denholm, J
Schreiber, B A
Evans, S C
Crook, O M
Sharma, A
Watson, J L
Bancroft, H
Langman, G
Gilbey, J D
Schönlieb, C-B
Abstract
We present a multiple-instance-learning-based scheme for detecting coeliac disease, an autoimmune disorder affecting the intestine, in histological whole-slide images (WSIs) of duodenal biopsies. We train our model to detect 2 distinct classes, normal tissue and coeliac disease, on the patch-level, and in turn leverage slide-level classifications. Using 5-fold cross-validation in a training set of 1841 (1163 normal; 680 coeliac disease) WSIs, our model classifies slides as normal with accuracy (96.7±0.6)%, precision (98.0±1.7)%, and recall (96.8±2.5)%, and as coeliac disease with accuracy (96.7±0.5)%, precision (94.9±3.7)%, and recall (96.5±2.9)% where the error bars are the cross-validation standard deviation. We apply our model to 2 test sets: one containing 191 WSIs (126 normal; 65 coeliac) from the same sources as the training data, and another from a completely independent source, containing 34 WSIs (17 normal; 17 coeliac), obtained with a scanner model not represented in the training data. Using the same-source test data, our model classifies slides as normal with accuracy 96.5%, precision 98.4% and recall 96.1%, and positive for coeliac disease with accuracy 96.5%, precision 93.5%, and recall 97.3%. Using the different-source test data the model classifies slides as normal with accuracy 94.1% (32/34), precision 89.5%, and recall 100%, and as positive for coeliac disease with accuracy 94.1%, precision 100%, and recall 88.2%. We discuss generalising our approach to screen for a range of pathologies.
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Date
2022-10-28
Type
Article
Subject
Clinical pathology
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Citation
Denholm J, Schreiber BA, Evans SC, Crook OM, Sharma A, Watson JL, Bancroft H, Langman G, Gilbey JD, Schönlieb CB, Arends MJ, Soilleux EJ. Multiple-instance-learning-based detection of coeliac disease in histological whole-slide images. J Pathol Inform. 2022 Oct 28;13:100151. doi: 10.1016/j.jpi.2022.100151
Journal / Source Title
Journal of Pathology Informatics
DOI
10.1016/j.jpi.2022.100151
PMID
36605111
Publisher
Elsevier
Publisher’s URL
https://www.sciencedirect.com/journal/journal-of-pathology-informatics