HIEGNet: A Heterogenous Graph Neural Network Including the Immune Environment in Glomeruli Classification

Niklas Kormann, Masoud Ramuz, Zeeshan Nisar, Nadine S. Schaadt, Hendrik Annuth, Benjamin Doerr, Friedrich Feuerhake, Thomas Lampert, Johannes F. Lutzeyer

Keywords: Graph Neural Networks, Digital Histopathology, Glomeruli Classification, Immune Environment, Graph Representation of Whole Slide Images

TL;DR: We propose a novel heterogeneous graph representation and corresponding graph neural network to classify glomerular health under consideration of the immune environment in whole slide images.

Abstract: Graph Neural Networks (GNNs) have recently been found to excel in histopathology. However, an important histopathological task, where GNNs have not been extensively explored, is the classification of glomeruli health as an important indicator in nephropathology. This task presents unique difficulties, particularly for the graph construction, i.e., the identification of nodes, edges, and informative features. In this work, we propose a pipeline composed of different traditional and machine learning-based computer vision techniques to identify nodes, edges, and their corresponding features to form a heterogeneous graph. We then proceed to propose a novel heterogeneous GNN architecture for glomeruli classification, called HIEGNet, that integrates both glomeruli and their surrounding immune cells. Hence, HIEGNet is able to consider the immune environment of each glomerulus in its classification. Our HIEGNet was trained and tested on a dataset of Whole Slide Images from kidney transplant patients. Experimental results demonstrate that HIEGNet outperforms several baseline models and generalises best between patients among all baseline models. Our implementation is publicly available at https://github.com/nklsKrmnn/HIEGNet.git.

Primary Subject Area: Geometric Deep Learning

Secondary Subject Area: Application: Histopathology

Paper Type: Both

Registration Requirement: Yes

Reproducibility: https://github.com/nklsKrmnn/HIEGNet.git

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Submission Number: 163