Identifying patch-level MSI from histological images of Colorectal Cancer by a Knowledge Distillation Model

Jing Ke, Yiqing Shen, Jason D. Wright, Naifeng Jing, Xiaoyao Liang, Dinggang Shen

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Microsatellite instability (MSI) is the result of a defective DNA mismatch repair (MMR) system, and its presence occurs in a variety of cancers. The determination of MSI in colorectal cancer (CRC) will have a better prognosis and management of cancer patients. As the routine MSI identification via molecular testing is expensive, time-consuming, and region-restricted, novel methods to detect MSI are of great interest. In this work, we propose a multi-stage convolutional neural network (CNN) based framework to identify MSI status in colorectal cancer patients from histopathological images. A mislabel-aware module is designed to deal with the uncertainty problem in global-local labelling. An auto-grading model is proposed to discriminate patches by the degree of their histopathological correlation with recognizable MSI status, and subsequently aggregate the weights to make slide-level predictions. Our proposed methodology outperforms the existing models in the classification accuracy, and explicitly sorts out patches with representative features. The research outcome has the potential to assist in the interpretation of histopathology as a surrogate for MSI testing and also in the study of recognizable morphology of MSI-H/MSS tumors. Furthermore, this approach can be extended and applied to other cancer types.

Original languageEnglish
Title of host publicationProceedings - 2020 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2020
EditorsTaesung Park, Young-Rae Cho, Xiaohua Tony Hu, Illhoi Yoo, Hyun Goo Woo, Jianxin Wang, Julio Facelli, Seungyoon Nam, Mingon Kang
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages1043-1046
Number of pages4
ISBN (Electronic)9781728162157
DOIs
Publication statusPublished - 2020 Dec 16
Event2020 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2020 - Virtual, Seoul, Korea, Republic of
Duration: 2020 Dec 162020 Dec 19

Publication series

NameProceedings - 2020 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2020

Conference

Conference2020 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2020
CountryKorea, Republic of
CityVirtual, Seoul
Period20/12/1620/12/19

Keywords

  • Microsatellite instability
  • convolutional neural network
  • deep learning
  • distillation

ASJC Scopus subject areas

  • Computer Science Applications
  • Information Systems and Management
  • Medicine (miscellaneous)
  • Health Informatics

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