Wide & Deep Learning for Node Classification
Abstract
Wide&Deep, a simple yet effective learning architecture for recommendation systems developed by Google, has had a significant impact in both academia and industry due to its combination of the memorization ability of generalized linear models and the generalization ability of deep models. Graph convolutional networks (GCNs) remain dominant in node classification tasks; however, recent studies have highlighted issues such as heterophily and expressiveness, which focus on graph structure while seemingly neglecting the potential role of node features. In this paper, we propose a flexible framework GCNIII, which leverages the Wide&Deep architecture and incorporates three techniques: Intersect memory, Initial residual and Identity mapping. We provide comprehensive empirical evidence showing that GCNIII can more effectively balance the trade-off between over-fitting and over-generalization on various semi- and full- supervised tasks. Additionally, we explore the use of large language models (LLMs) for node feature engineering to enhance the performance of GCNIII in cross-domain node classification tasks. Our implementation is available at https://github.com/CYCUCAS/GCNIII.
Benchmark Results
Tested on 4 datasets 15 baseline values reported too low
Tables show presented results in global context (best 3 papers + GCN + MLP).
Classic
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | CNA | 0.9575
±0.0058 | |
| 2 | IS-GIB | 0.9390
±0.0187 | |
| 3 | EERM | 0.9112
±0.0145 | |
| 20 | APPNP | 0.8142
±0.0026 best reported | best at pub: Feature Expansion for Graph Neural Networks (ICML 2023) |
| 35 | GAT | 0.8080
±0.0026 best reported | best at pub: Feature Expansion for Graph Neural Networks (ICML 2023) |
| 36 | GCNII | 0.8076
±0.0030 best reported | best at pub: Feature Expansion for Graph Neural Networks (ICML 2023) |
| 44 | GCN | 0.8033
±0.0088 best reported | best at pub: NTFormer: A Composite Node Tokenized Graph Transformer for Node Classification (2024) |
| 61 | GraphSAGE | 0.7923
±0.0053 | |
| 330 | GCNIII | 0.7300
±0.0050 | This paper |
| 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 | |
| 17 | APPNP | 0.9355
±0.0060 best reported | best at pub: LOGIN: A Large Language Model Consulted Graph Neural Network Training Framework (2024) |
| 18 | GCN | 0.9296
±0.0015 best reported | best at pub: Node Identifiers: Compact, Discrete Representations for Efficient Graph Learning (ICLR 2024) |
| 20 | GAT | 0.9233
±0.0018 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 58 | GCNII | 0.9030
±0.0043 best reported | best at pub: Feature Transportation Improves Graph Neural Networks (AAAI 2023) |
| 116 | SAGE | 0.8881
±0.0015 | |
| 210 | MLP | 0.8690
±0.0074 | |
| 415 | GCNIII | 0.8040
±0.0040 | This paper |
| # | Model | F1 ↑ | Paper |
|---|---|---|---|
| 1 | GAMLP(JK) | 0.9982
±0.0001 | |
| 2 | GraphCON-GCN | 0.9960 | |
| 3 | GCNII | 0.9953
±0.0001 best reported | best at pub: Graph-Coupled Oscillator Networks (ICML 2022) Difference within reported uncertainty; not counted as underperformance. |
| 5 | GCNIII | 0.9950
±0.0300 | This paper |
| 9 | Cluster-GCN | 0.9940 best reported | best at pub: Graph-Coupled Oscillator Networks (ICML 2022) |
| 21 | GCN | 0.9850 | |
| 42 | VR-GCN | 0.9780 | This paper |
| 57 | GAT | 0.9732
±0.0032 best reported | best at pub: HAT-GAE: Self-Supervised Graph Auto-encoders with Hierarchical Adaptive Masking and Trainable Corruption (2023) Difference within reported uncertainty; not counted as underperformance. |
| 101 | GraphSAGE | 0.7860 best reported | best at pub: Optimization-Induced Graph Implicit Nonlinear Diffusion (ICML 2022) |
| 173 | MLP | 0.4620 |
Heterophilic Graphs
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | P^2GNN | 0.9672
±0.0147 | |
| 2 | DoG | 0.9660
±0.0210 | |
| 3 | GPF-plus | 0.9583
±0.0419 | |
| 34 | MLP | 0.9230
±0.0070 | |
| 46 | APPNP | 0.9131
±0.0197 best reported | best at pub: A Quasi-Wasserstein Loss for Learning Graph Neural Networks (WWW 2023) |
| 53 | GraphSAGE | 0.9000
±0.0365 | |
| 70 | GCNII | 0.8918
±0.0443 best reported | best at pub: Global-Local Graph Neural Networks for Node-Classification (2024) best today: Piecewise Constant Spectral Graph Neural Network (TMLR 2025) |
| 211 | GAT | 0.8162
±0.0645 best reported | best at pub: GrokFormer: Graph Fourier Kolmogorov-Arnold Transformers (ICML 2024) best today: Equivariance Everywhere All At Once: A Recipe for Graph Foundation Models (2025) |
| 247 | GCNIII | 0.7973 | This paper |
| 257 | GCN | 0.7933
±0.0447 best reported | best at pub: Graph Wave Networks (WWW 2025) |
| 348 | Geom-GCN-S | 0.7350 best reported | best at pub: Non-Local Graph Neural Networks (2020) |
| 416 | Geom-GCN-P | 0.6757 | This paper |
| 548 | Geom-GCN-I | 0.5758 | This paper |
