Graph Neural Tangent Kernel: Fusing Graph Neural Networks with Graph Kernels
Abstract
While graph kernels (GKs) are easy to train and enjoy provable theoretical guarantees, their practical performances are limited by their expressive power, as the kernel function often depends on hand-crafted combinatorial features of graphs. Compared to graph kernels, graph neural networks (GNNs) usually achieve better practical performance, as GNNs use multi-layer architectures and non-linear activation functions to extract high-order information of graphs as features. However, due to the large number of hyper-parameters and the non-convex nature of the training procedure, GNNs are harder to train. Theoretical guarantees of GNNs are also not well-understood. Furthermore, the expressive power of GNNs scales with the number of parameters, and thus it is hard to exploit the full power of GNNs when computing resources are limited. The current paper presents a new class of graph kernels, Graph Neural Tangent Kernels (GNTKs), which correspond to infinitely wide multi-layer GNNs trained by gradient descent. GNTKs enjoy the full expressive power of GNNs and inherit advantages of GKs. Theoretically, we show GNTKs provably learn a class of smooth functions on graphs. Empirically, we test GNTKs on graph classification datasets and show they achieve strong performance.
Benchmark Results
Tested on 3 datasets 1 baseline value reported too low
Tables show presented results in global context (best 3 papers + GCN + MLP).
TU Dortmund
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | MSH-GNN | 0.9910
±0.0030 | |
| 2 | ID-GNN+BEC | 0.9830
±0.0360 | |
| 3 | SupCosine | 0.9830
±0.0250 | |
| 39 | GIN | 0.9330
±0.0290 | |
| 63 | GCN | 0.9220
±0.0440 best reported | best at pub: Graph Neural Networks With Convolutional ARMA Filters (2019) best today: Depth-Adaptive Graph Neural Networks via Learnable Bakry-Émery Curvature (KDD 2025) Difference within reported uncertainty; not counted as underperformance. |
| 158 | GraphSAGE | 0.9040
±0.0780 best reported | best at pub: Graph Neural Networks With Convolutional ARMA Filters (2019) best today: Asynchronous Neural Networks for Learning in Graphs (2022) Difference within reported uncertainty; not counted as underperformance. |
| 175 | RetGK | 0.9030
±0.0110 | This paper |
| 191 | GNTK | 0.9000
±0.0850 | This paper |
| 403 | MLP | 0.8660
±0.0495 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | WL-MLP | 0.9954 | |
| 2 | GIN | 0.9934 | |
| 3 | GCN | 0.8020
±0.0200 | prev best: Graph Convolutional Networks with EigenPooling (KDD 2019) best today: 1-WL Expressiveness Is (Almost) All You Need (2022) |
| 9 | WL subtree | 0.8600
±0.0180 | This paper |
| 31 | RetGK | 0.8450
±0.0020 | This paper |
| 36 | GNTK | 0.8420
±0.0150 | This paper |
| 131 | GraphSAGE | 0.7770
±0.0150 | prev best: Graph Convolutional Networks with EigenPooling (KDD 2019) best today: Weisfeiler and Leman Go Infinite: Spectral and Combinatorial Pre-Colorings (TMLR 2022) |
| 289 | PatchySan | 0.7860
±0.0190 | This paper |
| 373 | DGCNN | 0.7650
±0.0190 best reported | best at pub: Deep Learning on Attributed Graphs: A Journey from Graphs to Their Embeddings and Back (2018) best today: GraphCrop: Subgraph Cropping for Graph Classification (2020) |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | WL-MLP | 0.9792 | |
| 2 | MSH-GNN | 0.9640
±0.0070 | |
| 3 | CoCN | 0.8722
±0.0013 | |
| 13 | GNTK | 0.8360
±0.0100 | This paper |
| 23 | GCN | 0.8260
±0.0220 best reported | best at pub: Fast Graph Representation Learning with PyTorch Geometric (ICLR 2019) best today: Scalable Expressiveness through Preprocessed Graph Perturbations (2024) |
| 30 | GIN | 0.8220
±0.0210 | |
| 82 | RetGK | 0.8100
±0.0030 | This paper |
| 151 | MLP | 0.7920
±0.0240 |
