Learning Where to Focus: Self-Supervised Multi-Scale ViTs for Histopathology

Vision Transformers (ViTs) and their hierarchical variants have achieved strong performance in Computational Pathology (CPath). However, most are pre-trained on single-resolution Whole Slide Images (WSIs), limiting their generalization across arbitrary resolutions. Gigapixel WSIs inherently contain diagnostic patterns at multiple scales, including cellular morphologies, tissue architectures, and global context, mirroring how expert pathologists examine WSIs. We introduce Multi-Resolution Pyramid Transformer (MRPT), a model that hierarchically aggregates multi-resolution information from cellular to tissue and WSI levels. MRPT employs a biologically meaningful Consecutive Cross-Resolution Attention (CCRA) mechanism to capture scale-independent interactions and enforces multi-resolution semantic consistency by aligning embeddings across resolutions, yielding robust and generalizable WSI representations. Pre-trained in a multi-resolution self-supervised manner on 624M patches, 2.4M regions, and 36K WSIs, MRPT learns rich coarse-to-fine histopathology features. Extensive experiments on 34 diverse datasets show that MRPT surpasses recent foundation models and Multimodal Large Language Models (MLLMs) in cancer subtype classification, tissue phenotyping, and Visual Question Answering (VQA) for WSI understanding.

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/.

Self-supervised learning (SSL) has emerged as an effective paradigm for learning transferable representations from large-scale unlabeled whole slide images (WSIs). However, existing SSL methods primarily learn generic visual features and often fail to explicitly capture pathology-specific morphological patterns that are critical for disease characterization. To address this limitation, we propose Tiny Vision Transformer with Pathology-Aware Prototype Distillation (TVT-PAPD). This self-supervised pathology representation learning framework integrates a Tiny Vision Transformer (TVT) with a novel Pathology-Aware Prototype Distillation (PAPD) module. PAPD employs a learnable pathology prototype bank to discover and preserve representative tissue morphology patterns, encouraging semantically similar pathological regions to learn consistent and discriminative representations. The proposed framework enhances pathology-aware feature learning while maintaining computational efficiency with 90M parameters. Experiments on the Cancer Genome Atlas (TCGA) low-grade glioma (LGG)/glioblastoma (GBM) dataset and the Indian Pathology Brain (IPD-Brain) dataset demonstrate that TVT-PAPD achieves weighted F1-scores of 93.02% and 90.23%, respectively, for LGG-GBM classification, while exhibiting strong cross-cohort generalization across independent glioma datasets.