Niklas Kormann

Niklas Kormann, Masoud Ramuz, Zeeshan Nisar et al.

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.

Niklas Kormann, Benjamin Doerr, Johannes F. Lutzeyer

Over-smoothing and over-squashing have been extensively studied in the literature on Graph Neural Networks (GNNs) over the past years. We challenge this prevailing focus in GNN research, arguing that these phenomena are less critical for practical applications than assumed. We suggest that performance decreases often stem from uninformative receptive fields rather than over-smoothing. We support this position with extensive experiments on several standard benchmark datasets, demonstrating that accuracy and over-smoothing are mostly uncorrelated and that optimal model depths remain small even with mitigation techniques, thus highlighting the negligible role of over-smoothing. Similarly, we challenge that over-squashing is always detrimental in practical applications. Instead, we posit that the distribution of relevant information over the graph frequently factorises and is often localised within a small k-hop neighbourhood, questioning the necessity of jointly observing entire receptive fields or engaging in an extensive search for long-range interactions. The results of our experiments show that architectural interventions designed to mitigate over-squashing fail to yield significant performance gains. This position paper advocates for a paradigm shift in theoretical research, urging a diligent analysis of learning tasks and datasets using statistics that measure the underlying distribution of label-relevant information to better understand their localisation and factorisation.