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- Title
REET: robustness evaluation and enhancement toolbox for computational pathology.
- Authors
Foote, Alex; Asif, Amina; Rajpoot, Nasir; Minhas, Fayyaz
- 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.
- Subjects
PATHOLOGICAL laboratories; DEEP learning; PATHOLOGY; SPATIAL resolution; LABORATORIES; PREDICTION models
- Publication
Bioinformatics, 2022, Vol 38, Issue 12, p3312
- ISSN
1367-4803
- Publication type
Article
- DOI
10.1093/bioinformatics/btac315