A Survey on Graph-Based Deep Learning for Computational Histopathology

With the remarkable success of representation learning for prediction problems, we have witnessed a rapid expansion of the use of machine learning and deep learning for the analysis of digital pathology and biopsy image patches. However, traditional learning over patch-wise features using convolutional neural networks limits the model when attempting to capture global contextual information. The phenotypical and topological distribution of constituent histological entities play a critical role in tissue diagnosis. As such, graph data representations and deep learning have attracted significant attention for encoding tissue representations, and capturing intra- and inter- entity level interactions. In this review, we provide a conceptual grounding of graph-based deep learning and discuss its current success for tumor localization and classification, tumor invasion and staging, image retrieval, and survival prediction. We provide an overview of these methods in a systematic manner organized by the graph representation of the input image including whole slide images and tissue microarrays. We also outline the limitations of existing techniques, and suggest potential future advances in this domain.