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REET : robustness evaluation and enhancement toolbox for computational pathology
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Foote, Alex, Asif, Amina, Rajpoot, Nasir and Minhas, Fayyaz (2022) REET : robustness evaluation and enhancement toolbox for computational pathology. Bioinformatics, 38 (12). pp. 3312-3314. doi:10.1093/bioinformatics/btac315 ISSN 1367-4803.
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Official URL: http://dx.doi.org/10.1093/bioinformatics/btac315
Abstract
Motivation
Digitization of pathology laboratories through digital slide scanners and advances in deep learning approaches for objective histological assessment have resulted in rapid progress in the field of computational pathology (CPath) with wide-ranging applications in medical and pharmaceutical research as well as clinical workflows. However, the estimation of robustness of CPath models to variations in input images is an open problem with a significant impact on the downstream practical applicability, deployment and acceptability of these approaches. Furthermore, development of domain-specific strategies for enhancement of robustness of such models is of prime importance as well.
Results
In this work, we propose the first domain-specific Robustness Evaluation and Enhancement Toolbox (REET) for computational pathology applications. It provides a suite of algorithmic strategies for enabling robustness assessment of predictive models with respect to specialized image transformations such as staining, compression, focusing, blurring, changes in spatial resolution, brightness variations, geometric changes as well as pixel-level adversarial perturbations. Furthermore, REET also enables efficient and robust training of deep learning pipelines in computational pathology. Python implementation of REET is available at https://github.com/alexjfoote/reetoolbox.
Supplementary information
Supplementary data are available at Bioinformatics online.
| Item Type: | Journal Article | ||||||||||
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| Divisions: | Faculty of Science, Engineering and Medicine > Science > Computer Science | ||||||||||
| Journal or Publication Title: | Bioinformatics | ||||||||||
| Publisher: | Oxford University Press | ||||||||||
| ISSN: | 1367-4803 | ||||||||||
| Official Date: | 15 June 2022 | ||||||||||
| Dates: |
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| Volume: | 38 | ||||||||||
| Number: | 12 | ||||||||||
| Page Range: | pp. 3312-3314 | ||||||||||
| DOI: | 10.1093/bioinformatics/btac315 | ||||||||||
| Status: | Peer Reviewed | ||||||||||
| Publication Status: | Published | ||||||||||
| Access rights to Published version: | Restricted or Subscription Access | ||||||||||
| Copyright Holders: | The Author(s). Published by Oxford University Press | ||||||||||
| RIOXX Funder/Project Grant: |
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