The Impact of Global Structural Information in Graph Neural Networks Applications
Abstract
Graph Neural Networks (GNNs) rely on the graph structure to define an aggregation strategy where each node updates its representation by combining information from its neighbours. A known limitation of GNNs is that, as the number of layers increases, information gets smoothed and squashed and node embeddings become indistinguishable, negatively affecting performance. Therefore, practical GNN models employ few layers and only leverage the graph structure in terms of limited, small neighbourhoods around each node. Inevitably, practical GNNs do not capture information depending on the global structure of the graph. While there have been several works studying the limitations and expressivity of GNNs, the question of whether practical applications on graph structured data require global structural knowledge or not remains unanswered. In this work, we empirically address this question by giving access to global information to several GNN models, and observing the impact it has on downstream performance. Our results show that global information can in fact provide significant benefits for common graph-related tasks. We further identify a novel regularization strategy that leads to an average accuracy improvement of more than 5% on all considered tasks.
Benchmark Results
Tested on 4 datasets 1 baseline value reported too low
Tables show presented results in global context (best 3 papers + GCN + MLP).
Classic
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GraphSAGE+CNA | 0.9418
±0.0033 | |
| 2 | GCN+CNA | 0.9366
±0.0048 | |
| 3 | TransformerConv | 0.9350
±0.0058 | |
| 21 | GCN | 0.9004 best reported | best at pub: SplineCNN: Fast Geometric Deep Learning with Continuous B-Spline Kernels (2017) best today: Understanding Heterophily for Graph Neural Networks (ICML 2024) Difference within reported uncertainty; not counted as underperformance. |
| 39 | SAGE | 0.8911
±0.0012 | |
| 44 | GAT | 0.8897
±0.0014 best reported | best at pub: Topology Adaptive Graph Convolutional Networks (2017) |
| 141 | GraphSAGE | 0.8410
±0.0160 | prev best: Spectral Graph Attention Network with Fast Eigen-approximation (2020) best today: Large Language Model Meets Graph Neural Network in Knowledge Distillation (AAAI 2024) |
| 724 | MLP | 0.7768 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | CNA | 0.9575
±0.0058 | |
| 2 | IS-GIB | 0.9390
±0.0187 | |
| 3 | EERM | 0.9112
±0.0145 | |
| 35 | GAT | 0.8080
±0.0026 best reported | best at pub: Topology Adaptive Graph Convolutional Networks (2017) best today: Feature Expansion for Graph Neural Networks (ICML 2023) |
| 44 | GCN | 0.8033
±0.0088 best reported | best at pub: Graph Neural Ordinary Differential Equations (AAAI 2019) Difference within reported uncertainty; not counted as underperformance. |
| 61 | GraphSAGE | 0.7210
±0.0210 | prev best: Spectral Graph Attention Network with Fast Eigen-approximation (2020) best today: Gophormer: Ego-Graph Transformer for Node Classification (2021) |
| 259 | SAGE | 0.7361
±0.0190 | |
| 350 | MLP | 0.7289
±0.0010 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | LGTL | 0.9518
±0.0011 | |
| 2 | MixHop (LO) | 0.9513
±0.0038 | |
| 3 | GraphSAGE (LO) | 0.9511
±0.0036 | |
| 18 | GCN | 0.9296
±0.0015 best reported | best at pub: Graph Neural Ordinary Differential Equations (AAAI 2019) |
| 20 | GAT | 0.8040
±0.0110 | prev best: Topology Adaptive Graph Convolutional Networks (2017) best today: Adaptive Tokenization: On the Hop-Overpriority Problem in Tokenized Graph Learning Models (2025) Improvement within reported uncertainty; not highlighted. |
| 116 | SAGE | 0.8881
±0.0015 | |
| 125 | GraphSAGE | 0.8070
±0.0160 | prev best: Graph Neural Networks With Convolutional ARMA Filters (2019) best today: Non-backtracking Graph Neural Networks (TMLR 2023) Improvement within reported uncertainty; not highlighted. |
| 210 | MLP | 0.8690
±0.0074 |
TU Dortmund
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GC-GNN (GCN) | 0.9210
±0.0810 | |
| 2 | SUGAR | 0.8403
±0.0133 | |
| 3 | Ortho-g-U-Nets | 0.8387 | |
| 15 | SAGE | 0.8088
±0.0233 | |
| 38 | DiffPool | 0.7930
±0.0220 | This paper |
| 127 | k-GNN | 0.7560
±0.0210 | This paper |
| 129 | GCN | 0.7550
±0.0280 | This paper |
