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Pré-Publication, Document De Travail Année : 2023

Democratizing computational pathology: optimized Whole Slide Image representations for The Cancer Genome Atlas

Tristan Lazard
Marvin Lerousseau
Sophie Gardrat
  • Fonction : Auteur
Anne Vincent-Salomon
Marc-Henri Stern
Manuel Rodrigues
Etienne Decencière
  • Fonction : Auteur

Résumé

Abstract Automatic analysis of hematoxylin and eosin (H&E) stained Whole Slide Images (WSI) bears great promise for computer assisted diagnosis and biomarker discovery. However, scarcity of annotated datasets leads to underperforming models. Furthermore, the size and complexity of the image data limit their integration into bioinformatic workflows and thus their adoption by the bioinformatics community. Here, we present Giga-SSL, a self-supervised method for learning WSI representations without any annotation. We show that applying a simple linear classifier on the Giga-SSL representations improves classification performance over the fully supervised alternative on five benchmarked tasks and across different datasets. Moreover, we observe a substantial performance increase for small datasets (average gain of 7 AUC point) and a doubling of the number of mutations predictable from WSIs in a pan-cancer setting (from 45 to 93). We make the WSI representations available, compressing the TCGA-FFPE images from 12TB to 23MB and enabling fast analysis on a laptop CPU. We hope this resource will facilitate multimodal data integration in order to analyze WSI in their genomic and transcriptomic context.
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Dates et versions

hal-04396311 , version 1 (15-01-2024)

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Tristan Lazard, Marvin Lerousseau, Sophie Gardrat, Anne Vincent-Salomon, Marc-Henri Stern, et al.. Democratizing computational pathology: optimized Whole Slide Image representations for The Cancer Genome Atlas. 2024. ⟨hal-04396311⟩
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