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When Do Graph Neural Networks Help with Node Classification? Investigating the Impact of Homophily Principle on Node Distinguishability

25 Apr 2023arXiv:2304.14274archive 2025-07-28

Sitao Luan, Chenqing Hua, Minkai Xu, Qincheng Lu, Jiaqi Zhu, Xiao-Wen Chang, Jie Fu, Jure Leskovec, Doina Precup

Homophily principle, i.e., nodes with the same labels are more likely to be connected, has been believed to be the main reason for the performance superiority of Graph Neural Networks (GNNs) over Neural Networks on node classification tasks. Recent research suggests that, even in the absence of homophily, the advantage of GNNs still exists as long as nodes from the same class share similar neighborhood patterns. However, this argument only considers intra-class Node Distinguishability (ND) but neglects inter-class ND, which provides incomplete understanding of homophily on GNNs. In this paper, we first demonstrate such deficiency with examples and argue that an ideal situation for ND is to have smaller intra-class ND than inter-class ND. To formulate this idea and study ND deeply, we propose Contextual Stochastic Block Model for Homophily (CSBM-H) and define two metrics, Probabilistic Bayes Error (PBE) and negative generalized Jeffreys divergence, to quantify ND. With the metrics, we visualize and analyze how graph filters, node degree distributions and class variances influence ND, and investigate the combined effect of intra- and inter-class ND. Besides, we discovered the mid-homophily pitfall, which occurs widely in graph datasets. Furthermore, we verified that, in real-work tasks, the superiority of GNNs is indeed closely related to both intra- and inter-class ND regardless of homophily levels. Grounded in this observation, we propose a new hypothesis-testing based performance metric beyond homophily, which is non-linear, feature-based and can provide statistical threshold value for GNNs' the superiority. Experiments indicate that it is significantly more effective than the existing homophily metrics on revealing the advantage and disadvantage of graph-aware modes on both synthetic and benchmark real-world datasets.

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