Explainable nucleus classification using Decision Tree Approximation of Learned Embeddings

Mohamed Amgad, Lamees A. Atteya, Hagar Hussein, Kareem Hosny Mohammed, Ehab Hafiz, Maha A.T. Elsebaie, Pooya Mobadersany, David Manthey, David A. Gutman, Habiba Elfandy, Lee A.D. Cooper*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

3 Scopus citations

Abstract

Motivation: Nucleus detection, segmentation and classification are fundamental to high-resolution mapping of the tumor microenvironment using whole-slide histopathology images. The growing interest in leveraging the power of deep learning to achieve state-of-the-art performance often comes at the cost of explainability, yet there is general consensus that explainability is critical for trustworthiness and widespread clinical adoption. Unfortunately, current explainability paradigms that rely on pixel saliency heatmaps or superpixel importance scores are not well-suited for nucleus classification. Techniques like Grad-CAM or LIME provide explanations that are indirect, qualitative and/or nonintuitive to pathologists. Results: In this article, we present techniques to enable scalable nuclear detection, segmentation and explainable classification. First, we show how modifications to the widely used Mask R-CNN architecture, including decoupling the detection and classification tasks, improves accuracy and enables learning from hybrid annotation datasets like NuCLS, which contain mixtures of bounding boxes and segmentation boundaries. Second, we introduce an explainability method called Decision Tree Approximation of Learned Embeddings (DTALE), which provides explanations for classification model behavior globally, as well as for individual nuclear predictions. DTALE explanations are simple, quantitative, and can flexibly use any measurable morphological features that make sense to practicing pathologists, without sacrificing model accuracy. Together, these techniques present a step toward realizing the promise of computational pathology in computer-aided diagnosis and discovery of morphologic biomarkers.

Original languageEnglish (US)
Pages (from-to)513-519
Number of pages7
JournalBioinformatics
Volume38
Issue number2
DOIs
StatePublished - Jan 15 2022

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

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