Repository logo

Infoscience

  • English
  • French
Log In
Logo EPFL, École polytechnique fédérale de Lausanne

Infoscience

  • English
  • French
Log In
  1. Home
  2. Academic and Research Output
  3. Journal articles
  4. Weakly supervised joint whole-slide segmentation and classification in prostate cancer
 
research article

Weakly supervised joint whole-slide segmentation and classification in prostate cancer

Pati, Pushpak
•
Jaume, Guillaume
•
Ayadi, Zeineb
Show more
August 24, 2023
Medical Image Analysis

The identification and segmentation of histological regions of interest can provide significant support to pathologists in their diagnostic tasks. However, segmentation methods are constrained by the difficulty in obtaining pixel-level annotations, which are tedious and expensive to collect for whole-slide images (WSI). Though several methods have been developed to exploit image-level weak-supervision for WSI classification, the task of segmentation using WSI-level labels has received very little attention. The research in this direction typically require additional supervision beyond image labels, which are difficult to obtain in real world practice. In this study, we propose WholeSIGHT, a weakly-supervised method that can simultaneously segment and classify WSIs of arbitrary shapes and sizes. Formally, WholeSIGHT first constructs a tissue-graph representation of WSI, where the nodes and edges depict tissue regions and their interactions, respectively. During training, a graph classification head classifies the WSI and produces node-level pseudo-labels via post-hoc feature attribution. These pseudo-labels are then used to train a node classification head for WSI segmentation. During testing, both heads simultaneously render segmentation and class prediction for an input WSI. We evaluate the performance of WholeSIGHT on three public prostate cancer WSI datasets. Our method achieves state-of-the-art weakly-supervised segmentation performance on all datasets while resulting in better or comparable classification with respect to state-of-the-art weakly-supervised WSI classification methods. Additionally, we assess the generalization capability of our method in terms of segmentation and classification performance, uncertainty estimation, and model calibration. Our code is available at: https: //github.com/histocartography/wholesight.

  • Details
  • Metrics
Type
research article
DOI
10.1016/j.media.2023.102915
Web of Science ID

WOS:001066216600001

Author(s)
Pati, Pushpak
Jaume, Guillaume
Ayadi, Zeineb
Thandiackal, Kevin
Bozorgtabar, Behzad  
Gabrani, Maria
Goksel, Orcun
Date Issued

2023-08-24

Publisher

ELSEVIER

Published in
Medical Image Analysis
Volume

89

Article Number

102915

Subjects

Computer Science, Artificial Intelligence

•

Computer Science, Interdisciplinary Applications

•

Engineering, Biomedical

•

Radiology, Nuclear Medicine & Medical Imaging

•

Computer Science

•

Engineering

•

computational pathology

•

whole-slide image segmentation

•

weakly supervised learning

•

weakly supervised classification

•

weakly supervised segmentation

•

gleason pattern 4

•

isup consensus conference

•

international-society

•

urological-pathology

•

percentage

Editorial or Peer reviewed

REVIEWED

Written at

EPFL

EPFL units
LTS5  
Available on Infoscience
October 9, 2023
Use this identifier to reference this record
https://infoscience.epfl.ch/handle/20.500.14299/201510
Logo EPFL, École polytechnique fédérale de Lausanne
  • Contact
  • infoscience@epfl.ch

  • Follow us on Facebook
  • Follow us on Instagram
  • Follow us on LinkedIn
  • Follow us on X
  • Follow us on Youtube
AccessibilityLegal noticePrivacy policyCookie settingsEnd User AgreementGet helpFeedback

Infoscience is a service managed and provided by the Library and IT Services of EPFL. © EPFL, tous droits réservés