aiqbench analysis
This research reveals that Graph Neural Network performance in heterophilic settings is highly dependent on the specific node representation used, challenging the assumption that architectural robustness is independent of input features. By testing seven architectures across varying embeddings on large benchmarks, the study demonstrates that gains from contextual representations fluctuate significantly by model type, necessitating joint evaluation of architecture and feature encoding. These findings are critical for researchers aiming to generalize GNN results beyond fixed-feature baselines.
Beyond Fixed Features: Architecture-Dependent Sensitivity to Node Representations under Heterophily
arXiv:2609.33764v1 Announce Type: new Abstract: Graph Neural Networks (GNNs) perform well on homophilic graphs but struggle in heterophilic settings, where connected nodes often carry dissimilar labels. Existing evaluations typically compare architectures under a fixed node-feature representation, leaving unclear whether conclusions about heterophily robustness remain stable as the input representation changes. We address this question by constructing parallel feature variants of two large-scale heterophilic benchmarks, Roman-Empire and Amazon-Ratings, pairing each graph with representations ranging from static fastText vectors to contextual Transformer embeddings and evaluating seven GNN architectures across these representations. We find that the effect of representation varies across architectures: on Roman-Empire, the contextual gain ranges from 2.38 percentage points for GCN-sep to 13.67 points for GAT, with H2GCN gaining 8.77 points. On Amazon-Ratings, where node text is limited to short product titles, GAT improves by 6.78 points from fastText to MPNet, while GCN-sep changes by only 0.20 points. These results show that architectural performance is conditional on node representation: the same representation change can produce different magnitudes of performance gain across architectures, so architecture and representation cannot be treated as independent evaluation factors. A rank-correlation analysis on these two benchmarks further shows that the relative ordering of architectures remains highly stable across representations, isolating differential sensitivity, rather than ranking instability, as the primary effect.
Abstract:Graph Neural Networks (GNNs) perform well on homophilic graphs but struggle in heterophilic settings, where connected nodes often carry dissimilar labels. Existing evaluations typically compare architectures under a fixed node-feature representation, leaving unclear whether conclusions about heterophily robustness remain stable as the input representation changes. We address this question by constructing parallel feature variants of two large-scale heterophilic benchmarks, Roman-Empire and Amazon-Ratings, pairing each graph with representations ranging from static fastText vectors to contextual Transformer embeddings and evaluating seven GNN architectures across these representations. We find that the effect of representation varies across architectures: on Roman-Empire, the contextual gain ranges from 2.38 percentage points for GCN-sep to 13.67 points for GAT, with H2GCN gaining 8.77 points. On Amazon-Ratings, where node text is limited to short product titles, GAT improves by 6.78 points from fastText to MPNet, while GCN-sep changes by only 0.20 points. These results show that architectural performance is conditional on node representation: the same representation change can produce different magnitudes of performance gain across architectures, so architecture and representation cannot be treated as independent evaluation factors. A rank-correlation analysis on these two benchmarks further shows that the relative ordering of architectures remains highly stable across representations, isolating differential sensitivity, rather than ranking instability, as the primary effect.
Machine Learning (cs.LG); Artificial Intelligence (cs.AI); Information Retrieval (cs.IR)
arXiv:2609.33764 [cs.LG]
(or arXiv:2609.33764v1 [cs.LG] for this version)
https://doi.org/10.48550/arXiv.2609.33764 Focus to learn more arXiv-issued DOI via DataCite (pending registration)
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Full text under the publisher's open licence · 309 words
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