Artificial Intelligence-based Analytics for Diagnosis of Small Bowel Enteropathies and Black Box Feature Detection

Sana Syed*, Lubaina Ehsan, Aman Shrivastava, Saurav Sengupta, Marium Khan, Kamran Kowsari, Shan Guleria, Rasoul Sali, Karan Kant, Sung Jun Kang, Kamran Sadiq, Najeeha T. Iqbal, Lin Cheng, Christopher A. Moskaluk, Paul Kelly, Beatrice C. Amadi, Syed Asad Ali, Sean R. Moore, Donald E. Brown*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

5 Scopus citations


Objectives: Striking histopathological overlap between distinct but related conditions poses a disease diagnostic challenge. There is a major clinical need to develop computational methods enabling clinicians to translate heterogeneous biomedical images into accurate and quantitative diagnostics. This need is particularly salient with small bowel enteropathies; environmental enteropathy (EE) and celiac disease (CD). We built upon our preliminary analysis by developing an artificial intelligence (AI)-based image analysis platform utilizing deep learning convolutional neural networks (CNNs) for these enteropathies. Methods: Data for the secondary analysis was obtained from three primary studies at different sites. The image analysis platform for EE and CD was developed using CNNs including one with multizoom architecture. Gradient-weighted class activation mappings (Grad-CAMs) were used to visualize the models' decision-making process for classifying each disease. A team of medical experts simultaneously reviewed the stain color normalized images done for bias reduction and Grad-CAMs to confirm structural preservation and biomedical relevance, respectively. Results: Four hundred and sixty-one high-resolution biopsy images from 150 children were acquired. Median age (interquartile range) was 37.5 (19.0-121.5) months with a roughly equal sex distribution; 77 males (51.3%). ResNet50 and shallow CNN demonstrated 98% and 96% case-detection accuracy, respectively, which increased to 98.3% with an ensemble. Grad-CAMs demonstrated models' ability to learn different microscopic morphological features for EE, CD, and controls. Conclusions: Our AI-based image analysis platform demonstrated high classification accuracy for small bowel enteropathies which was capable of identifying biologically relevant microscopic features and emulating human pathologist decision-making process. Grad-CAMs illuminated the otherwise "black box"of deep learning in medicine, allowing for increased physician confidence in adopting these new technologies in clinical practice.

Original languageEnglish
Pages (from-to)833-841
Number of pages9
JournalJournal of Pediatric Gastroenterology and Nutrition
Issue number6
StatePublished - 1 Jun 2021
Externally publishedYes


  • biopsy image analysis
  • convolutional neural networks
  • environmental enteropathy
  • global health
  • intestinal structure


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