A Good Feature Extractor Is All You Need for Weakly Supervised Pathology Slide Classification

Research output: Contribution to book/Conference proceedings/Anthology/ReportConference contributionContributedpeer-review

Contributors

Abstract

Stain normalisation is thought to be a crucial preprocessing step in computational pathology pipelines. We question this belief in the context of weakly supervised whole slide image classification, motivated by the emergence of powerful feature extractors trained using self-supervised learning on diverse pathology datasets. To this end, we performed the most comprehensive evaluation of publicly available pathology feature extractors to date, involving more than 8,000 training runs across nine tasks, five datasets, three downstream architectures, and various preprocessing setups. Notably, we find that omitting stain normalisation and image augmentations does not compromise downstream slide-level classification performance, while incurring substantial savings in memory and compute. Using a new evaluation metric that facilitates relative downstream performance comparison, we identify the best publicly available extractors, and show that their latent spaces are remarkably robust to variations in stain and augmentations like rotation. Contrary to previous patch-level benchmarking studies, our approach emphasises clinical relevance by focusing on slide-level biomarker prediction tasks in a weakly supervised setting with external validation cohorts. Our findings stand to streamline digital pathology workflows by minimising preprocessing needs and informing the selection of feature extractors. Code and data are available at https://georg.woelflein.eu/good-features.

Details

Original languageEnglish
Title of host publicationComputer Vision – ECCV 2024 Workshops
EditorsAlessio Del Bue, Cristian Canton, Jordi Pont-Tuset, Tatiana Tommasi
PublisherSpringer Science and Business Media B.V.
Pages68-87
Number of pages20
ISBN (electronic)978-3-031-91721-9
ISBN (print)978-3-031-91720-2
Publication statusPublished - 2025
Peer-reviewedYes

Publication series

SeriesLecture notes in computer science
Volume15638 LNCS
ISSN0302-9743

Conference

Title18th European Conference on Computer Vision
Abbreviated titleECCV 2024
Conference number18
Duration29 September - 4 October 2024
Website
LocationMiCo Milano
CityMilan
CountryItaly

External IDs

ORCID /0000-0001-8501-1566/work/188859657
ORCID /0000-0002-3730-5348/work/198594675

Keywords

Keywords

  • pathology, stain normalisation, weakly supervised learning