Label-Free Coreset Selection with Foundation Models for Efficient Annotation in Computational Pathology
Computational pathology has the potential to improve clinical outcomes through a demonstrated increase in diagnostic and prognostic accuracy. However, the development and validation of deep learning algorithms still require annotated data, a costly procedure involving expert pathologists who already face critical workforce shortages. Existing coreset selection methods to optimize annotation efforts currently all rely on hyperparameters tuned on natural-image benchmarks that do not transfer to histopathology and are cumbersome to use in clinical practice. In this study, we present GCcore, a novel label-free coreset selection method that embeds every image of a dataset with any pathology foundation model and greedily selects the samples that collectively maximize the global coverage of the embedding space. The proposed method provides a lower-bound guarantee on the global coverage of the returned coreset for any coreset size, while being completely hyperparameter-free and deterministic. We demonstrate GCcore's superior performance over 14 baselines including state-of-the-art methods across 10 tasks and datasets spanning whole slide image classification, tile classification, and tissue segmentation, where it ranks first on six and within the top three on nine, while also demonstrating how existing methods can shift by up to five rank positions depending on their hyperparameter settings. Code is publicly available at https://github.com/OncoAI-ULBHUB/GCcore.