HoTS: Homophily-Aware Temperature Scaling for Graph Neural Network Calibration

Abstract:For graph node classification, calibrated class probabilities are needed when confidence scores, usually the maximum predicted class probability, are used to rank predictions, defer uncertain nodes to human review, or control risk. Existing post-hoc calibrators either apply one global temperature or use graph-aware modules without a principled structural form. We study how local graph structure should enter node-level calibration. Our first results show that a logit-only temperature rule is insufficient when nodes with identical logits but different local homophily require different optimal temperatures. We then analyze a population-concentration contextual stochastic block model with Gaussian features and a one-layer linear GCN. Under equidistant class means, the Bayes posterior over class-template scores is a temperature-scaled softmax whose inverse-temperature is governed by a homophily-dependent signal strength. In the positive-signal homophilic regime, the resulting temperature decreases approximately inversely with normalized local homophily. This law motivates Homophily-aware Temperature Scaling (HoTS), a simple post-hoc calibrator that assigns each node a positive scalar temperature from entropy-based logit concentration and estimated local homophily. HoTS has three temperature parameters, preserves the predicted class, and learns the strength of the structural correction from calibration data. Across 18 node-classification benchmarks, two GNN backbones, and eight calibration baselines, HoTS achieves the best mean Expected Calibration Error (ECE) of 4.79%, the best average rank, and the most reliable confidence ranking in selective classification. Code is available at this https URL.

37 pages, 9 figures. Accepted at the 40th Conference on Neural Information Processing Systems (NeurIPS 2026)

Machine Learning (cs.LG)

arXiv:2609.32426 [cs.LG]

(or arXiv:2609.32426v1 [cs.LG] for this version)

https://doi.org/10.48550/arXiv.2609.32426 Focus to learn more arXiv-issued DOI via DataCite (pending registration)

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