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

Publikation: Beitrag in Buch/Konferenzbericht/Sammelband/GutachtenBeitrag in KonferenzbandBeigetragenBegutachtung

Beitragende

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

OriginalspracheEnglisch
TitelComputer Vision – ECCV 2024 Workshops
Redakteure/-innenAlessio Del Bue, Cristian Canton, Jordi Pont-Tuset, Tatiana Tommasi
Herausgeber (Verlag)Springer Science and Business Media B.V.
Seiten68-87
Seitenumfang20
ISBN (elektronisch)978-3-031-91721-9
ISBN (Print)978-3-031-91720-2
PublikationsstatusVeröffentlicht - 2025
Peer-Review-StatusJa

Publikationsreihe

ReiheLecture notes in computer science
Band15638 LNCS
ISSN0302-9743

Konferenz

Titel18th European Conference on Computer Vision
KurztitelECCV 2024
Veranstaltungsnummer18
Dauer29 September - 4 Oktober 2024
Webseite
OrtMiCo Milano
StadtMilan
LandItalien

Externe IDs

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

Schlagworte

Schlagwörter

  • pathology, stain normalisation, weakly supervised learning