Scaling Vision Transformers to Gigapixel Images via Hierarchical Self-Supervised Learning

Vision Transformers (ViTs) and their multi-scale and hierarchical variations have been successful at capturing image representations but their use has been generally studied for low-resolution images (e.g. - 256x256, 384384). For gigapixel whole-slide imaging (WSI) in computational pathology, WSIs can be as large as 150000x150000 pixels at 20X magnification and exhibit a hierarchical structure of visual tokens across varying resolutions: from 16x16 images capture spatial patterns among cells, to 4096x4096 images characterizing interactions within the tissue microenvironment. We introduce a new ViT architecture called the Hierarchical Image Pyramid Transformer (HIPT), which leverages the natural hierarchical structure inherent in WSIs using two levels of self-supervised learning to learn high-resolution image representations. HIPT is pretrained across 33 cancer types using 10,678 gigapixel WSIs, 408,218 4096x4096 images, and 104M 256x256 images. We benchmark HIPT representations on 9 slide-level tasks, and demonstrate that: 1) HIPT with hierarchical pretraining outperforms current state-of-the-art methods for cancer subtyping and survival prediction, 2) self-supervised ViTs are able to model important inductive biases about the hierarchical structure of phenotypes in the tumor microenvironment.

Fast and Scalable Image Search For Histology

The expanding adoption of digital pathology has enabled the curation of large repositories of histology whole slide images (WSIs), which contain a wealth of information. Similar pathology image search offers the opportunity to comb through large historical repositories of gigapixel WSIs to identify cases with similar morphological features and can be particularly useful for diagnosing rare diseases, identifying similar cases for predicting prognosis, treatment outcomes, and potential clinical trial success. A critical challenge in developing a WSI search and retrieval system is scalability, which is uniquely challenging given the need to search a growing number of slides that each can consist of billions of pixels and are several gigabytes in size. Such systems are typically slow and retrieval speed often scales with the size of the repository they search through, making their clinical adoption tedious and are not feasible for repositories that are constantly growing. Here we present Fast Image Search for Histopathology (FISH), a histology image search pipeline that is infinitely scalable and achieves constant search speed that is independent of the image database size while being interpretable and without requiring detailed annotations. FISH uses self-supervised deep learning to encode meaningful representations from WSIs and a Van Emde Boas tree for fast search, followed by an uncertainty-based ranking algorithm to retrieve similar WSIs. We evaluated FISH on multiple tasks and datasets with over 22,000 patient cases spanning 56 disease subtypes. We additionally demonstrate that FISH can be used to assist with the diagnosis of rare cancer types where sufficient cases may not be available to train traditional supervised deep models. FISH is available as an easy-to-use, open-source software package (https://github.com/mahmoodlab/FISH).

Whole Slide Images are 2D Point Clouds: Context-Aware Survival Prediction using Patch-based Graph Convolutional Networks

Cancer prognostication is a challenging task in computational pathology that requires context-aware representations of histology features to adequately infer patient survival. Despite the advancements made in weakly-supervised deep learning, many approaches are not context-aware and are unable to model important morphological feature interactions between cell identities and tissue types that are prognostic for patient survival. In this work, we present Patch-GCN, a context-aware, spatially-resolved patch-based graph convolutional network that hierarchically aggregates instance-level histology features to model local- and global-level topological structures in the tumor microenvironment. We validate Patch-GCN with 4,370 gigapixel WSIs across five different cancer types from the Cancer Genome Atlas (TCGA), and demonstrate that Patch-GCN outperforms all prior weakly-supervised approaches by 3.58-9.46%. Our code and corresponding models are publicly available at https://github.com/mahmoodlab/Patch-GCN.