From histology to diagnosis: Leveraging pathology foundation models for glioma classification

The fifth edition of the WHO classification of brain tumors increasingly emphasizes the role of extensive genetic testing in the diagnosis of gliomas. In this context, computational pathology foundation models (FMs) present a promising approach for inferring molecular entities directly from conventional, H&E-stained histological images, potentially reducing the need for genetic analysis. We conducted a robust investigation into the ability of five established FMs to generate effective embeddings for downstream glioma classification using three datasets (TCGA, n=839 samples; EBRAINS, n=786 samples; TUM, n=250 samples) and state-of-the-art augmentation techniques. Our results demonstrate that FM embeddings enable competitive glioma classification performance, even with limited training data, achieving one-vs-rest AUC>0.93 on all three datasets. However, we observed substantial differences between FMs in their downstream performance, susceptibility to perturbations, and consistency across multiple datasets. Dataset diversity and content of central nervous tissue were associated with improved generalization, while model and dataset size were not. Common to all FMs was a propensity to capture dataset-specific features in their embeddings. We examined Macenko normalization and random convolutions as potential solutions to combat dataset-dominated embeddings and show that ensembling FM embeddings over multiple augmented views improves downstream classifier performance. In summary, our findings highlight both the promise and current limitations of computational pathology foundation models for glioma classification, emphasizing the critical roles of training data composition and downstream augmentation to achieve strong task performance.