Discovering the Representation Bottleneck of Graph Neural Networks
Abstract
Graph neural networks (GNNs) rely mainly on the message-passing paradigm to propagate node features and build interactions, and different graph learning problems require different ranges of node interactions. In this work, we explore the capacity of GNNs to capture node interactions under contexts of different complexities. We discover that GNNs usually fail to capture the most informative kinds of interaction styles for diverse graph learning tasks, and thus name this phenomenon GNNs' representation bottleneck. As a response, we demonstrate that the inductive bias introduced by existing graph construction mechanisms can result in this representation bottleneck, i.e., preventing GNNs from learning interactions of the most appropriate complexity. To address that limitation, we propose a novel graph rewiring approach based on interaction patterns learned by GNNs to dynamically adjust each node's receptive fields. Extensive experiments on both real-world and synthetic datasets prove the effectiveness of our algorithm in alleviating the representation bottleneck and its superiority in enhancing the performance of GNNs over state-of-the-art graph rewiring baselines.
Benchmark Results
Tested on 4 datasets 6 baseline values 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) |
| 39 | SAGE | 0.8911
±0.0012 | |
| 68 | NodeFormer | 0.8848
±0.0033 best reported | best today: Efficient Tuning and Inference for Large Language Models on Textual Graphs (IJCAI 2024) |
| 301 | ISGR | 0.8408
±0.0047 | This paper |
| 569 | GEN | 0.8166
±0.0091 | This paper |
| 724 | MLP | 0.7768 | |
| 806 | SLAPS | 0.7229
±0.0101 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | CNA | 0.9575
±0.0058 | |
| 2 | IS-GIB | 0.9390
±0.0187 | |
| 3 | EERM | 0.9112
±0.0145 | |
| 44 | GCN | 0.8033
±0.0088 best reported | best at pub: Gophormer: Ego-Graph Transformer for Node Classification (2021) |
| 61 | GraphSAGE | 0.7923
±0.0053 | |
| 76 | NodeFormer | 0.7856
±0.0009 best reported | |
| 303 | GEN | 0.7321
±0.0062 | This paper |
| 315 | ISGR | 0.7316
±0.0159 | This paper |
| 350 | MLP | 0.7289
±0.0010 | |
| 624 | SLAPS | 0.7000
±0.0129 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | LGTL | 0.9518
±0.0011 | |
| 2 | MixHop (LO) | 0.9513
±0.0038 | |
| 3 | GraphSAGE (LO) | 0.9511
±0.0036 | |
| 7 | NodeFormer | 0.9490
±0.0019 best reported | |
| 18 | GCN | 0.9296
±0.0015 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 116 | SAGE | 0.8881
±0.0015 | |
| 210 | MLP | 0.8690
±0.0074 | |
| 486 | ISGR | 0.7963
±0.0042 | This paper |
| 643 | GEN | 0.7849
±0.0398 | This paper |
| 833 | SLAPS | 0.7096
±0.0099 | This paper |
Heterophilic Graphs
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | Hetero-S (GAT 8-layer) | 0.8693 | |
| 2 | Dir-GNN+CNA | 0.8586
±0.0180 | |
| 3 | GAT | 0.8560 best reported | best at pub: Non-Local Graph Neural Networks (2020) best today: The Heterophilic Snowflake Hypothesis: Training and Empowering GNNs for Heterophilic Graphs (KDD 2024) |
| 52 | GCN | 0.7033 best reported | best at pub: Non-Local Graph Neural Networks (2020) best today: Understanding Heterophily for Graph Neural Networks (ICML 2024) |
| 108 | SAGE | 0.6340
±0.0300 | |
| 115 | GraphSAGE | 0.6215
±0.0042 best reported | best at pub: Simplifying approach to Node Classification in Graph Neural Networks (2021) best today: Hierarchical Graph Transformer with Adaptive Node Sampling (NeurIPS 2022) |
| 169 | MLP | 0.5429 | |
| 183 | GraphSAGE + ISGR | 0.5200
±0.0170 | This paper |
| 186 | GAT + ISGR | 0.5170
±0.0140 | This paper |
| 187 | GIN + ISGR | 0.5160
±0.0190 | This paper |
| 189 | GCN + ISGR | 0.5140
±0.0190 | This paper |
| 192 | GIN + SDRF | 0.5040
±0.0390 | This paper |
| 195 | GCN + SDRF | 0.5030
±0.0360 | This paper |
| 196 | GraphSAGE + SDRF | 0.5030
±0.0380 | This paper |
| 198 | GAT + SDRF | 0.5010
±0.0400 | This paper |
| 210 | GAT + DIGL | 0.4770
±0.0240 | This paper |
| 211 | GraphSage+GPL | 0.4770
±0.0240 | This paper |
| 216 | GIN + FA | 0.4650
±0.0210 | This paper |
| 219 | GIN | 0.4610
±0.0170 | This paper |
| 220 | GIN + DIGL | 0.4610
±0.0180 | This paper |
| 221 | GAT + FA | 0.4600
±0.0200 | This paper |
| 222 | GraphSAGE +AE | 0.4600
±0.0210 | This paper |
| 233 | GCN + FA | 0.4360
±0.0210 | This paper |
| 239 | GCN + DIGL | 0.4300
±0.0300 | This paper |
