MuViT: Multi-Resolution Vision Transformers for Learning Across Scales in Microscopy

Vision Foundation Models (VFMs) have become the cornerstone of modern computer vision, offering robust representations across a wide array of tasks. While recent advances allow these models to handle varying input sizes during training, inference typically remains restricted to a single, fixed scale. This prevalent single-scale paradigm overlooks a fundamental property of visual perception: varying resolutions offer complementary inductive biases, where low-resolution views excel at global semantic recognition and high-resolution views are essential for fine-grained refinement. In this work, we propose Multi-Resolution Fusion (MuRF), a simple yet universally effective strategy to harness this synergy at inference time. Instead of relying on a single view, MuRF constructs a unified representation by processing an image at multiple resolutions through a frozen VFM and fusing the resulting features. The universality of MuRF is its most compelling attribute. It is not tied to a specific architecture, serving instead as a fundamental, training-free enhancement to visual representation. We empirically validate this by applying MuRF to a broad spectrum of critical computer vision tasks across multiple distinct VFM families - primarily DINOv2, but also demonstrating successful generalization to contrastive models like SigLIP2.

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.

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.