GraphMix: Improved Training of GNNs for Semi-Supervised Learning
Abstract
We present GraphMix, a regularization method for Graph Neural Network based semi-supervised object classification, whereby we propose to train a fully-connected network jointly with the graph neural network via parameter sharing and interpolation-based regularization. Further, we provide a theoretical analysis of how GraphMix improves the generalization bounds of the underlying graph neural network, without making any assumptions about the "aggregation" layer or the depth of the graph neural networks. We experimentally validate this analysis by applying GraphMix to various architectures such as Graph Convolutional Networks, Graph Attention Networks and Graph-U-Net. Despite its simplicity, we demonstrate that GraphMix can consistently improve or closely match state-of-the-art performance using even simpler architectures such as Graph Convolutional Networks, across three established graph benchmarks: Cora, Citeseer and Pubmed citation network datasets, as well as three newly proposed datasets: Cora-Full, Co-author-CS and Co-author-Physics.
Benchmark Results
Tested on 5 datasets 3 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 | |
| 43 | DropEdge* | 0.8900 best reported | best today: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 307 | GraphMix | 0.8394
±0.0057 | This paper |
| 342 | BVAT* | 0.8360
±0.0050 | This paper |
| 426 | GraphSGAN* | 0.8300
±0.0130 | This paper |
| 434 | GAT (self-training) | 0.8295
±0.0023 | This paper |
| 460 | GraphVAT* | 0.8260 | This paper |
| 466 | GraphAT* | 0.8250 | This paper |
| 528 | GCN (self-training) | 0.8203
±0.0043 | This paper |
| 530 | Graph-U-Net (self-training) | 0.8201
±0.0091 | This paper |
| 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 | |
| 24 | DropEdge | 0.8130 best reported | best today: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 44 | GCN | 0.8033
±0.0088 | |
| 230 | BVAT | 0.7400
±0.0060 | This paper |
| 251 | GraphVAT | 0.7370 | This paper |
| 267 | DisenGCN | 0.7360
±0.0080 best reported | best today: Adversarial Graph Disentanglement with Component-specific Aggregation (2021) Difference within reported uncertainty; not counted as underperformance. |
| 279 | GraphAT | 0.7349
±0.0038 best reported | best today: Rethinking Graph Regularization for Graph Neural Networks (AAAI 2020) Difference within reported uncertainty; not counted as underperformance. |
| 290 | GCN (self-training) | 0.7338
±0.0035 | This paper |
| 304 | Graph U-Net | 0.7320 | This paper |
| 317 | GraphSGAN | 0.7310
±0.0180 | This paper |
| 322 | GraphScan | 0.7310
±0.0180 | This paper |
| 350 | MLP | 0.7289
±0.0010 best reported | best at pub: Fast Haar Transforms for Graph Neural Networks (2019) best today: Gumbel-MPNN: Graph Rewiring with Gumbel-Softmax (2025) |
| 351 | GAT (self-training) | 0.7287
±0.0051 | This paper |
| 513 | FCN (self-training) | 0.7150
±0.0080 | This paper |
| 617 | Chebyshev | 0.7010
±0.0080 best reported | best at pub: Graph Neural Networks With Convolutional ARMA Filters (2019) Difference within reported uncertainty; not counted as underperformance. |
| 649 | ICA | 0.6910 | This paper |
| 681 | SemiEmb | 0.6810
±0.0010 best reported | best at pub: Learning Discrete Structures for Graph Neural Networks (ICML 2019) |
| 692 | DeepWalk | 0.6785
±0.0079 best reported | best at pub: Topology Adaptive Graph Convolutional Networks (2017) best today: Decoupled Self-supervised Learning for Non-Homophilou Graphs (2022) |
| 697 | ManiReg | 0.6770
±0.0160 best reported | best at pub: Learning Discrete Structures for Graph Neural Networks (ICML 2019) |
| 782 | Planetoid | 0.6470 | This paper |
| 877 | LP | 0.4530 | 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 | |
| 18 | GCN | 0.9296
±0.0015 best reported | best at pub: Auto-GNN: Neural Architecture Search of Graph Neural Networks (2019) |
| 20 | GAT | 0.9233
±0.0018 best reported | best at pub: Topology Adaptive Graph Convolutional Networks (2017) |
| 116 | SAGE | 0.8881
±0.0015 | |
| 210 | MLP | 0.8690
±0.0074 | |
| 367 | GraphMix | 0.8110
±0.0078 | This paper |
| 406 | DisenGCN | 0.8050 | This paper |
| 462 | BVAT | 0.7990
±0.0040 | This paper |
| 490 | Graph U-Net | 0.7960 | This paper |
| 727 | Planetoid | 0.7720 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GrokFormer | 0.9831
±0.0018 | |
| 2 | PolyFormer | 0.9808
±0.0027 | |
| 3 | SGFormer | 0.9796
±0.0081 | |
| 6 | GAT | 0.9782
±0.0028 best reported | best today: GrokFormer: Graph Fourier Kolmogorov-Arnold Transformers (ICML 2024) |
| 9 | GCN | 0.9774
±0.0035 best reported | best today: GrokFormer: Graph Fourier Kolmogorov-Arnold Transformers (ICML 2024) |
| 17 | SAGE | 0.9739
±0.0018 | |
| 58 | MLP | 0.9597
±0.0007 | |
| 177 | GraphMix | 0.9449
±0.0084 | This paper |
| 241 | GS-mean | 0.9300
±0.0080 | This paper |
| 252 | Graph-U-Net | 0.9257
±0.0081 | This paper |
| 253 | MoNet | 0.9250
±0.0090 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | DoG | 0.9690
±0.0030 | |
| 2 | GWN-fa | 0.9667
±0.0026 | |
| 3 | GWN-sym | 0.9666
±0.0026 | |
| 6 | GraphSAGE | 0.9593
±0.0025 | |
| 12 | GCN | 0.9514
±0.0025 best reported | best today: Graph Wave Networks (WWW 2025) |
| 21 | GAT | 0.9437
±0.0028 best reported | best today: Graph Wave Networks (WWW 2025) |
| 88 | MLP | 0.9280
±0.0020 | |
| 131 | GraphMix | 0.9183
±0.0051 | This paper |
| 141 | GS-mean | 0.9130
±0.0280 | This paper |
| 154 | Graph-U-Net | 0.9089
±0.0043 | This paper |
| 155 | MoNet | 0.9082
±0.0160 best reported | best today: Building Shortcuts between Distant Nodes with Biaffine Mapping for Graph Convolutional Networks (2023) Difference within reported uncertainty; not counted as underperformance. |
