Graph Label Alignment: A Diagnostic Atlas for Graph Classification

arXiv:2611.14760v1 Announce Type: new
Abstract: Graph classification benchmarks vary widely in difficulty: some are solved by simple pooled baselines, while others remain challenging for GNNs and graph transformers. We take a data-centric view and ask whether benchmark success is driven by genuine structure–feature reasoning or by label signal already accessible from restricted marginal views. We introduce graph label alignment, a lightweight diagnostic that measures label accessibility through two supervised probes computed without training a graph encoder: structural label alignment (SLA), based on permutation-invariant topological and spectral summaries, and feature label alignment (FLA), based on pooled node features with edges removed. Across real graph classification benchmarks and multiple pooled backbones, the resulting SLA–FLA plane strongly organizes test accuracy, with low-alignment datasets forming a consistent regime where standard pooled pipelines struggle. To probe what lies beyond marginal accessibility, we introduce controlled interaction-dominated stress tests, including heterophilic ego-graphs and synthetic Twins tasks whose structural and feature marginals are matched across classes but whose role–feature couplings differ. These results show that high alignment explains much of easy benchmark performance, while low alignment reveals regimes where success requires preserving structure–feature correspondence beyond standard pooled representations.