CCF-GNN: A Unified Model Aggregating Appearance, Microenvironment, and Topology for Pathology Image Classification

Pathology images contain rich information of cell appearance, microenvironment, and topology features for cancer analysis and diagnosis. Among such features, topology becomes increasingly important in analysis for cancer immunotherapy. By analyzing geometric and hierarchically structured cell distribution topology, oncologists can identify densely-packed and cancer-relevant cell communities (CCs) for making decisions. Compared to commonly-used pixel-level Convolution Neural Network (CNN) features and cell-instance-level Graph Neural Network (GNN) features, CC topology features are at a higher level of granularity and geometry. However, topological features have not been well exploited by recent deep learning (DL) methods for pathology image classification due to lack of effective topological descriptors for cell distribution and gathering patterns. In this paper, inspired by clinical practice, we analyze and classify pathology images by comprehensively learning cell appearance, microenvironment, and topology in a fine-to-coarse manner. To describe and exploit topology, we design Cell Community Forest (CCF), a novel graph that represents the hierarchical formulation process of big-sparse CCs from small-dense CCs. Using CCF as a new geometric topological descriptor of tumor cells in pathology images, we propose CCF-GNN, a GNN model that successively aggregates heterogeneous features (e.g., appearance, microenvironment) from cell-instance-level, cell-community-level, into image-level for pathology image classification. Extensive cross-validation experiments show that our method significantly outperforms alternative methods on H&E-stained and immunofluorescence images for disease grading tasks with multiple cancer types. Our proposed CCF-GNN establishes a new topological data analysis (TDA) based method, which facilitates integrating multi-level heterogeneous features of point clouds (e.g., for cells) into a unified DL framework.