GrapHist: Graph Self-Supervised Learning for Histopathology

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.

Computational pathology requires visual representations that transfer across diverse clinical endpoints and remain robust to variation in magnification, staining, scanner type, slide preparation, and input resolution. We present DaX, a pathology vision foundation model that adapts DINOv3-style self-supervised learning to whole-slide histopathology. DaX is initialized from natural-image DINOv3 weights and incorporates continuous magnification training, cross-scale tissue views, orientation-agnostic and acquisition-robust augmentation, multi-input-size training, and Gram-anchored dense consistency. These designs aim to connect local cellular morphology with global tissue architecture while stabilizing dense token-level representations across input scales. We further construct a WSI-level benchmark comprising 161 clinically meaningful tasks from 44 public datasets, covering 28,182 patients and 34,394 slides across four clinical domains and nine task categories. All models are evaluated under a fixed patient-level cross-validation protocol with fold-level statistical ranking, enabling reproducible comparisons that are less sensitive to split-dependent variation. Across this benchmark, DaX achieves the highest mean performance across tasks and consistently strong task-level ranking scores, with gains spanning diagnostic pathology, biomarker and molecular profiling, tissue/specimen context, and risk, response, and prognosis. These results support DaX as a transferable visual encoder for computational pathology and provide a standardized evaluation framework for future pathology foundation models. Project page: https://alibaba-damo-academy.github.io/DaX/benchboard/.

Histopathology remains the gold standard for cancer diagnosis because it provides detailed cellular-level assessment of tissue morphology. However, manual histopathological examination is time-consuming, labour-intensive, and subject to inter-observer variability, creating a demand for reliable computer-assisted diagnostic tools. Recent advances in deep learning, particularly transformer-based architectures, have shown strong potential for modelling complex spatial dependencies in medical images. In this work, we propose DeepHistoViT, a transformer-based framework for automated classification of histopathological images. The model employs a customized Vision Transformer architecture with an integrated attention mechanism designed to capture fine-grained cellular structures while improving interpretability through attention-based localization of diagnostically relevant regions. The framework is evaluated on three publicly available histopathology datasets covering lung cancer, colon cancer, and acute lymphoblastic leukaemia. Experimental results demonstrate state-of-the-art performance across all datasets, with classification accuracy, precision, recall, F1-score, and ROC-AUC reaching 100 percent on the lung and colon cancer datasets, and 99.85 percent, 99.84 percent, 99.86 percent, 99.85 percent, and 99.99 percent respectively on the acute lymphoblastic leukaemia dataset. All performance metrics are reported with 95 percent confidence intervals. These results highlight the effectiveness of transformer-based architectures for histopathological image analysis and demonstrate the potential of DeepHistoViT as an interpretable computer-assisted diagnostic tool to support pathologists in clinical decision-making.