LLM Features Can Hurt GNNs: Concatenation Interference on Homophilous Graph Benchmarks
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Abstract (arXiv)
Adding LLM-generated node features to graph neural networks (GNNs) is widely reported to improve accuracy on standard benchmarks. We document a contrasting observation: when LLM features are introduced through pure input concatenation (rather than joint training, distillation, or prompt-conditioning), they can systematically degrade accuracy on the same homophilous benchmarks where end-to-end LLM pipelines succeed. With an MLP backbone on the Planetoid public split and bag-of-words original features, concatenating SBERT-encoded GPT-4o-mini TAPE features reduces PubMed test accuracy by -17.0 +/- 0.3 pp and Cora by -4.3 +/- 0.6 pp (CiteSeer -0.6 +/- 0.8 pp, within seed noise). The drop attenuates as we relax each condition (GCN / GCNII / GAT backbones, random splits, smaller encoders) and reverses on medium-homophily WikiCS (+4.4 pp) and ogbn-arxiv (+11.7 pp). To predict when concatenation helps versus hurts, we report a simple measure of LLM-alone discriminability, Delta_sig. Across 9 datasets Delta_sig correlates with the concatenation cost more strongly than homophily at point estimate (r^2 = 0.38 vs. 0.06; N=9, bootstrap CIs overlap). The bootstrap-best change-point is tau = 13.8 pp, and the rule "Delta_sig <= tau predicts non-positive concat cost" classifies 7/9 datasets correctly; since 60% of bootstrap samples place tau in [5, 30] pp, we treat Delta_sig as an interpretive lens rather than a precision filter. A dimension-controlled ablation on PubMed places the LLM-feature drop between same-source PCA (-2.3 pp) and same-dim Gaussian noise (-37.3 pp), ruling out dimensionality and weight-decay artifacts. Nine PubMed configurations fit a power law |Delta_concat| proportional to (sqrt(d_l/n))^1.31 with r^2 = 0.97; the low-Delta_sig, small-n corner is exactly where the headline -17 pp PubMed deficit appears.
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References · 22
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- 2020Simple and Deep Graph Convolutional Networkscited by 860
- 2023NLP Evaluation in trouble: On the Need to Measure LLM Data Contamination for each Benchmarkcited by 348
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- 2021Is Homophily a Necessity for Graph Neural Networks?cited by 182
- 2024LLaGA: Large Language and Graph Assistantcited by 181
- 2022Learning on Large-scale Text-attributed Graphs via Variational Inferencecited by 155
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- 2023Harnessing Explanations: LLM-to-LM Interpreter for Enhanced Text-Attributed Graph Representation Learningcited by 133
- 2022Modality Competition: What Makes Joint Training of Multi-modal Network Fail in Deep Learning? (Provably)cited by 122
- 2021GraphSVX: Shapley Value Explanations for Graph Neural Networkscited by 64
- 2024Text-space Graph Foundation Models: Comprehensive Benchmarks and New Insightscited by 44
- 2024GLBench: A Comprehensive Benchmark for Graph with Large Language Modelscited by 36
- 2025A Closer Look at Multimodal Representation Collapsecited by 28
- 2025When Do LLMs Help With Node Classification? A Comprehensive Analysiscited by 21
- 2025Exact Computation of Any-Order Shapley Interactions for Graph Neural Networkscited by 13
- 2024GL-Fusion: Rethinking the Combination of Graph Neural Network and Large Language modelcited by 8
- 2025When Structure Doesn't Help: LLMs Do Not Read Text-Attributed Graphs as Effectively as We Expectedcited by 3
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