🍩 Database of Original & Non-Theoretical Uses of Topology

(found 2 matches in 0.001609s)

  1. Advancing Precision Medicine: Algebraic Topology and Differential Geometry in Radiology and Computational Pathology (2024)

    Richard M. Levenson, Yashbir Singh, Bastian Rieck, Quincy A. Hathaway, Colleen Farrelly, Jennifer Rozenblit, Prateek Prasanna, Bradley Erickson, Ashok Choudhary, Gunnar Carlsson, Deepa Sarkar

  2. CCF-GNN: A Unified Model Aggregating Appearance, Microenvironment, and Topology for Pathology Image Classification (2023)

    Hongxiao Wang, Gang Huang, Zhuo Zhao, Liang Cheng, Anna Juncker-Jensen, Máté Levente Nagy, Xin Lu, Xiangliang Zhang, Danny Z. Chen
    Abstract 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; 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.