A Scalable and Effective Alternative to Graph Transformers
Abstract
Graph Neural Networks (GNNs) have shown impressive performance in graph representation learning, but they face challenges in capturing long-range dependencies due to their limited expressive power. To address this, Graph Transformers (GTs) were introduced, utilizing self-attention mechanism to effectively model pairwise node relationships. Despite their advantages, GTs suffer from quadratic complexity w.r.t. the number of nodes in the graph, hindering their applicability to large graphs. In this work, we present raph- nhanced ontextual perator (GECO), a scalable and effective alternative to GTs that leverages neighborhood propagation and global convolutions to effectively capture local and global dependencies in quasiliniear time. Our study on synthetic datasets reveals that GECO reaches $169 $ speedup on a graph with 2M nodes w.r.t. optimized attention. Further evaluations on diverse range of benchmarks showcase that GECO scales to large graphs where traditional GTs often face memory and time limitations. Notably, GECO consistently achieves comparable or superior quality compared to baselines, improving the SOTA up to $4.5\ and offering a scalable and effective solution for large-scale graph learning.
Benchmark Results
Tested on 10 datasets 4 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 | |
| 16 | GECO | 0.9665
±0.0005 | This paper |
| 18 | GraphSAINT | 0.9660
±0.0010 best reported | best at pub: ROD: Reception-aware Online Distillation for Sparse Graphs (KDD 2021) best today: PaSca: a Graph Neural Architecture Search System under the Scalable Paradigm (WWW 2022) |
| 21 | GraphSAGE | 0.9653
±0.0011 | |
| 23 | SAGE | 0.9650
±0.0003 | This paper |
| 22 | GAT | 0.9650
±0.0011 | This paper |
| 26 | GCN | 0.9648 best reported | best at pub: DropEdge: Towards Deep Graph Convolutional Networks on Node Classification (ICLR 2019) |
| 38 | Cluster-GCN | 0.9623 best reported | |
| 43 | Exphormer | 0.9590
±0.0015 | This paper |
| 147 | MLP | 0.8240
±0.0010 |
OGB
| # | Model | ROC-AUC ↑ | Paper |
|---|---|---|---|
| 1 | Multi-RF Fusion with Multi-GNN Blending | 0.8476
±0.0002 | |
| 2 | HyperFusion | 0.8475
±0.0003 | |
| 3 | PAS+FPs | 0.8420
±0.0015 | |
| 9 | GatedGCN | 0.8090
±0.0160 | |
| 33 | GECO | 0.7980
±0.0200 | This paper |
| 109 | GIN | 0.7780
±0.0182 |
| # | Model | AP ↑ | Paper |
|---|---|---|---|
| 1 | GRPE-Large | 0.3150
±0.0010 | |
| 2 | Graphormer | 0.3140 | |
| 3 | Graphormer-FLAG | 0.3139
±0.0032 | |
| 15 | GECO | 0.2961
±0.0008 | This paper |
| 31 | GIN | 0.2902
±0.0017 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | A-NLSF | 0.8149
±0.0067 | |
| 2 | differential encoding | 0.8096
±0.0029 | |
| 3 | MPNN + VN + NoPE | 0.8055
±0.0038 | |
| 7 | GECO | 0.7982
±0.0042 | This paper |
| 16 | GatedGCN | 0.7531
±0.0083 | |
| 33 | GIN | 0.7037
±0.0107 |
| # | Model | F1 ↑ | Paper |
|---|---|---|---|
| 1 | GMN | 0.2060
±0.0020 | |
| 2 | DirGraphSSM | 0.2050
±0.0023 | |
| 3 | Graph-Mamba | 0.2030
±0.0023 | |
| 15 | GECO | 0.1915
±0.0020 | This paper |
| 35 | GCN | 0.1510
±0.0020 |
LRGB
| # | Model | MAE ↓ | Paper |
|---|---|---|---|
| 1 | GCN | 0.2421
±0.0016 | |
| 2 | IPR-MPNN | 0.2422
±0.0007 | |
| 3 | TANGO-GPS | 0.2422
±0.0014 | |
| 5 | GIN | 0.2429
±0.0019 | |
| 38 | GECO | 0.2464
±0.0009 | This paper |
| 89 | GPS w/ Transformer | 0.2500
±0.0005 | This paper |
| 201 | MLP | 0.4351
±0.0008 |
| # | Model | AP ↑ | Paper |
|---|---|---|---|
| 1 | S^2GCN | 0.7311
±0.0066 | |
| 2 | S4G | 0.7293
±0.0004 | |
| 3 | BuNN | 0.7276
±0.0065 | |
| 4 | GCN | 0.7261
±0.0011 | |
| 39 | GECO | 0.6975
±0.0025 | This paper |
| 93 | GPS w/ Transformer | 0.6535
±0.0041 | This paper |
| 181 | MLP | 0.4060
±0.0021 |
| # | Model | F1 ↑ | Paper |
|---|---|---|---|
| 1 | NeuralWalker | 0.4912
±0.0042 | |
| 2 | PPGT | 0.4641
±0.0033 | |
| 3 | CRaWl | 0.4588
±0.0079 | |
| 23 | GECO | 0.4210
±0.0080 | This paper |
| 41 | GatedGCN | 0.3880
±0.0040 | |
| 45 | GPS w/ Transformer | 0.3748
±0.0109 | This paper |
| 81 | GCN | 0.2380
±0.0160 | |
| 93 | MLP | 0.1140
±0.0230 |
| # | Model | MRR ↑ | Paper |
|---|---|---|---|
| 1 | FloydNet | 0.6143 | |
| 2 | Exphormer | 0.4737
±0.0024 | |
| 3 | Exphormer + LapPE | 0.4737
±0.0024 | |
| 8 | GatedGCN | 0.4670
±0.0004 | |
| 16 | GIN | 0.4617
±0.0005 | |
| 37 | GECO | 0.3526
±0.0016 | This paper |
| 63 | GPS w/ Transformer | 0.3337
±0.0006 | This paper |
| # | Model | F1 ↑ | Paper |
|---|---|---|---|
| 1 | FloydNet | 0.4901 | |
| 2 | CRaWl | 0.4588
±0.0079 | |
| 3 | GPS | 0.4440
±0.0065 | |
| 10 | Exphormer | 0.3455
±0.0009 | prev best: Where Did the Gap Go? Reassessing the Long-Range Graph Benchmark (TMLR 2023) |
| 16 | GatedGCN | 0.3880
±0.0040 | |
| 29 | GPS w/ Transformer | 0.3412
±0.0044 | This paper |
| 30 | GECO | 0.3320
±0.0032 | This paper |
| 34 | GINE | 0.2718
±0.0054 best reported | best at pub: Where Did the Gap Go? Reassessing the Long-Range Graph Benchmark (TMLR 2023) |
| 36 | Transformer+LapPE | 0.2618
±0.0031 | This paper |
| 38 | GatedGCN+RWSE | 0.2574
±0.0034 | This paper |
| 39 | SAN+RWSE | 0.2434
±0.0156 | This paper |
| 45 | GCN | 0.2078
±0.0031 | |
| 74 | MLP | 0.0310
±0.0160 |
