digital pathology platform developers

Abstract: Automated Gleason grading of prostate whole slide images (WSIs) enables faster and more consistent cancer risk stratification. However, it remains a challenging task due to the subtle morphological differences between grades, the severe class imbalance arising from rare patterns, and the diagnostic features that span multiple spatial scales. Pathology foundation models (FMs) extract strong patch representations but often operate at a single-scale, which limits spatial context and disproportionately affects classes that depend on broader context. The challenge of fusing multiple scales and complementary models, with minimal data and computational resources, remains unresolved. We propose a multi-scale classifier built on state-space models. Our method combines two complementary feature sources: a frozen foundation model, and a lightweight FastVim, pre-trained on ImageNet and distilled from the foundation model, that reads the raw image crops. At each scale, a Mamba model encodes the features from both sources with linear-time spatial context, and a jointly trained head fuses the encoded representations into one prediction. On the PANDA dataset, our method reaches macro F1 of 0.894 and Gleason 5 F1 of 0.802 under 5-fold cross-validation, a 12% and 21% relative improvement over the best single-scale model. A controlled study over 5 foundation models, 5 base classifiers and 3 scales confirms that the gain holds across encoders, with larger improvements observed at smaller scales.

Abstract: Pathologists diagnose diseases by first locating suspicious tissue and then examining it at higher magnification, whereas self-supervised vision transformers (ViTs) allocate the same spatial resolution to every image region despite diagnostic evidence being sparse and spanning multiple biological scales. Recent pathology foundation models have substantially improved representation quality by scaling training data and model capacity, but largely retain uniform tokenization. We instead investigate whether pathology representations can be improved by learning where to allocate spatial resolution during self-supervised learning. To this end, we propose CRAFT (Coarse-to-fine Region-Adaptive Feature Tokenization), a DINO-based framework that learns image-dependent mixed-scale representations by using self-supervised attention to selectively refine informative regions while preserving coarse context, together with a symmetric cross-scale regularization objective that encourages complementary coarse and fine representations. Across CAMELYON16, TCGA-Lung subtype classification, and TCGA-LUAD survival prediction, CRAFT consistently outperforms comparable-scale self-supervised methods while requiring lower inference computation. Despite using only a compact 22M parameter backbone trained on comparatively small pathology datasets, CRAFT remains competitive with, and often surpasses, substantially larger pathology foundation models.