Deformable Graph Transformer
Abstract
Transformer-based models have recently shown success in representation learning on graph-structured data beyond natural language processing and computer vision. However, the success is limited to small-scale graphs due to the drawbacks of full dot-product attention on graphs such as the quadratic complexity with respect to the number of nodes and message aggregation from enormous irrelevant nodes. To address these issues, we propose Deformable Graph Transformer (DGT) that performs sparse attention via dynamically sampled relevant nodes for efficiently handling large-scale graphs with a linear complexity in the number of nodes. Specifically, our framework first constructs multiple node sequences with various criteria to consider both structural and semantic proximity. Then, combining with our learnable Katz Positional Encodings, the sparse attention is applied to the node sequences for learning node representations with a significantly reduced computational cost. Extensive experiments demonstrate that our DGT achieves state-of-the-art performance on 7 graph benchmark datasets with 2.5 $ $ 449 times less computational cost compared to transformer-based graph models with full attention.
Benchmark Results
Tested on 3 datasets 10 baseline values reported too low Non-standard metric on 1 dataset
Tables show presented results in global context (best 3 papers + GCN + MLP).
Classic
Sorted by Accuracy. Highlighted rows are from other papers.
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GAP-EDP | 0.9870
±0.0003 | |
| 2 | NE-ASGCN | 0.9758
±0.0027 | |
| 3 | HSGT | 0.9730
±0.0024 | |
| 6 | JKNet | 0.9702 best reported | best at pub: DropEdge: Towards Deep Graph Convolutional Networks on Node Classification (ICLR 2019) |
| 21 | GraphSAGE | 0.9653
±0.0011 best reported | best at pub: DropEdge: Towards Deep Graph Convolutional Networks on Node Classification (ICLR 2019) best today: Hierarchical Transformer for Scalable Graph Learning (IJCAI 2023) |
| 23 | SAGE | 0.9650
±0.0003 | |
| 26 | GCN | 0.9648 best reported | best at pub: DropEdge: Towards Deep Graph Convolutional Networks on Node Classification (ICLR 2019) |
| 30 | DGT | 0.9632
±0.0002 | This paper |
| 37 | MixHop | 0.9623
±0.0004 | This paper |
| 40 | DGT-light | 0.9614
±0.0005 | This paper |
| 73 | SGC | 0.9490 best reported | best at pub: Revisiting Graph Neural Networks: All We Have is Low-Pass Filters (2019) best today: Dissecting the Diffusion Process in Linear Graph Convolutional Networks (NeurIPS 2021) |
| 147 | MLP | 0.8240
±0.0010 best reported | best at pub: GAP: Differentially Private Graph Neural Networks with Aggregation Perturbation (2022) |
Heterophilic Graphs
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | DiGGR | 0.4535
±0.0353 | |
| 2 | TRIGON | 0.4402
±0.0028 | |
| 3 | DoG | 0.4320
±0.0120 | |
| 42 | MLP | 0.4026
±0.0108 best reported | best at pub: Convolutional Neural Networks on Graphs with Chebyshev Approximation, Revisited (NeurIPS 2022) best today: Heterophily-Aware Graph Attention Network (2023) |
| 51 | Transformer | 0.3995
±0.0064 best reported | best today: GrokFormer: Graph Fourier Kolmogorov-Arnold Transformers (ICML 2024) |
| 68 | GraphSAGE | 0.3524
±0.0049 | prev best: Graph Neural Networks Inspired by Classical Iterative Algorithms (ICML 2021) best today: A Quasi-Wasserstein Loss for Learning Graph Neural Networks (WWW 2023) Improvement within reported uncertainty; not highlighted. |
| 71 | H2GCN | 0.3885
±0.0117 best reported | best at pub: ES-GNN: Generalizing Graph Neural Networks Beyond Homophily with Edge Splitting (2022) best today: $P^2$GNN: Two Prototype Sets to boost GNN Performance (2026) |
| 87 | Geom-GCN | 0.3810 best reported | best at pub: Beyond Low-frequency Information in Graph Convolutional Networks (AAAI 2021) |
| 99 | Graphormer | 0.3785
±0.0029 best reported | best today: Hierarchical Graph Transformer with Adaptive Node Sampling (NeurIPS 2022) |
| 134 | DGT | 0.3693
±0.0039 | This paper |
| 135 | GCN | 0.3690 best reported | best at pub: Beyond Low-frequency Information in Graph Convolutional Networks (AAAI 2021) |
| 138 | DGT-light | 0.3686
±0.0053 | This paper |
| 159 | DeformableGCN | 0.3653
±0.0042 | This paper |
| 162 | MixHop | 0.3579
±0.0033 | prev best: Graph Pointer Neural Networks (AAAI 2021) best today: Towards Deep Attention in Graph Neural Networks: Problems and Remedies (ICML 2023) Improvement within reported uncertainty; not highlighted. |
| 182 | GAT | 0.3605
±0.0035 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) best today: Hierarchical Graph Transformer with Adaptive Node Sampling (NeurIPS 2022) |
| 230 | GATv2 | 0.3510
±0.0020 best reported | best today: What Can We Learn From MIMO Graph Convolutions? (IJCAI 2025) |
| 237 | SGC | 0.3490
±0.0070 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) |
| 244 | GT-sparse | 0.3469
±0.0035 | This paper |
| 249 | GT-full | 0.3453
±0.0038 | This paper |
| 266 | GIN | 0.3410
±0.0030 | |
| 281 | JKNet | 0.3039
±0.0035 | prev best: Bag of Tricks for Training Deeper Graph Neural Networks: A Comprehensive Benchmark Study (2021) best today: Hierarchical Graph Transformer with Adaptive Node Sampling (NeurIPS 2022) |
LINKX Benchmarks
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | DGT | 0.6609
±0.0022 | This paper |
| 2 | ICG_u-NN | 0.6608
±0.0074 | |
| 3 | LINKX | 0.6606
±0.0019 | |
| 6 | MixHop | 0.6564
±0.0027 best reported | best today: Graph Neural Networks with Learnable and Optimal Polynomial Bases (ICML 2023) |
| 7 | DGT-light | 0.6559
±0.0025 | This paper |
| 10 | JKNet | 0.6508
±0.0007 | This paper |
| 14 | GraphSAGE | 0.6473
±0.0011 | This paper |
| 16 | GCN | 0.6434
±0.0012 | prev best: Augmentation-Free Graph Contrastive Learning with Performance Guarantee (2022) |
| 20 | GATv2 | 0.6415
±0.0009 | This paper |
| 24 | GT-sparse | 0.6309
±0.0071 | This paper |
| 25 | GAT | 0.6290
±0.0022 | This paper |
| 30 | GIN | 0.6176
±0.0060 | |
| 33 | MLP | 0.6114
±0.0006 | prev best: Convolutional Neural Networks on Graphs with Chebyshev Approximation, Revisited (NeurIPS 2022) |
| 40 | SGC | 0.6047
±0.0014 | This paper |
