Representation learning of histopathology images using graph neural networks

Mohammed Adnan, Shivam Kalra, Hamid R. Tizhoosh

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

Abstract

Representation learning for Whole Slide Images (WSIs) is pivotal in developing image-based systems to achieve higher precision in diagnostic pathology. We propose a two-stage framework for WSI representation learning. We sample relevant patches using a color-based method and use graph neural networks to learn relations among sampled patches to aggregate the image information into a single vector representation. We introduce attention via graph pooling to automatically infer patches with higher relevance. We demonstrate the performance of our approach for discriminating two sub-types of lung cancers, Lung Adenocarcinoma (LUAD) & Lung Squamous Cell Carcinoma (LUSC). We collected 1, 026 lung cancer WSIs with the 40× magnification from The Cancer Genome Atlas (TCGA) dataset, the largest public repository of histopathology images and achieved state-of-the-art accuracy of 88.8% and AUC of 0.89 on lung cancer sub-type classification by extracting features from a pre-trained DenseNet model.

Original languageEnglish (US)
Title of host publicationProceedings - 2020 IEEE/CVF Conference on Computer Vision and Pattern Recognition Workshops, CVPRW 2020
PublisherIEEE Computer Society
Pages4254-4261
Number of pages8
ISBN (Electronic)9781728193601
DOIs
StatePublished - Jun 2020
Event2020 IEEE/CVF Conference on Computer Vision and Pattern Recognition Workshops, CVPRW 2020 - Virtual, Online, United States
Duration: Jun 14 2020Jun 19 2020

Publication series

NameIEEE Computer Society Conference on Computer Vision and Pattern Recognition Workshops
Volume2020-June
ISSN (Print)2160-7508
ISSN (Electronic)2160-7516

Conference

Conference2020 IEEE/CVF Conference on Computer Vision and Pattern Recognition Workshops, CVPRW 2020
Country/TerritoryUnited States
CityVirtual, Online
Period6/14/206/19/20

ASJC Scopus subject areas

  • Computer Vision and Pattern Recognition
  • Electrical and Electronic Engineering

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