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. Submission history Access Paper: View PDF HTML (experimental) TeX Source Additional Features Audio Summary Current browse context: References & Citations Google Scholar Semantic Scholar Bookmark Institution arXivLabs is a framework that allows collaborators to develop and share new arXiv features directly on our website. Both individuals and organizations that work with arXivLabs have embraced and accepted our values of openness, community, excellence, and user data privacy. arXiv is committed to these values and only works with partners that adhere to them. Have an idea for a project that will add value for arXiv's community? Learn more about arXivLabs.
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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.
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