AAAI 2024

A Scalable and Effective Alternative to Graph Transformers

Kaan Sancak, Zhigang Hua, Jin Fang, Yan Xie, A. Malevich, Bo Long, M. F. Balin, Ümit V. Çatalyürek

Main figure for 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.

Proposed method: GECO

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

Reddit

Global leaderboard →
Non-default metric. This paper reports Accuracy; the dataset default is F1. Values below use Accuracy only.

Sorted by Accuracy. Highlighted rows are from other papers.

#ModelAccuracy ↑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
actual #18 vs paper #50 32 places worse
0.9660 ±0.0010
best reported
actual #18 vs paper #50 32 places worse
paper 0.9558 ±0.0007
paper 0.9558 ±0.0007 Δ at pub 0.0102 Δ today 0.0102
21
GraphSAGE
0.9653 ±0.0011
23
SAGE
0.9650 ±0.0003
This paper
22
GAT
0.9650 ±0.0011
This paper
26
GCN
actual #26 vs paper #97 71 places worse
0.9648
best reported
actual #26 vs paper #97 71 places worse
paper 0.9278 ±0.0011
paper 0.9278 ±0.0011 Δ at pub 0.0370
38
Cluster-GCN
actual #38 vs paper #46 8 places worse
0.9623
best reported
actual #38 vs paper #46 8 places worse
paper 0.9570 ±0.0006
43
Exphormer
0.9590 ±0.0015
This paper
147
MLP
0.8240 ±0.0010

OGB

#ModelROC-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
#ModelAP ↑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
#ModelF1 ↑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

#ModelMAE ↓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
#ModelAP ↑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
#ModelF1 ↑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
#ModelMRR ↑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
#ModelF1 ↑Paper
1
FloydNet
0.4901
2
CRaWl
0.4588 ±0.0079
3
GPS
0.4440 ±0.0065
10
Exphormer
actual #10 vs paper #26 16 places worse
0.3455 ±0.0009
actual #10 vs paper #26 16 places worse
paper 0.3455 ±0.0009
paper 0.3455 ±0.0009 Δ at pub 0.0025 Δ today 0.0505
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
actual #34 vs paper #52 18 places worse
0.2718 ±0.0054
best reported
actual #34 vs paper #52 18 places worse
paper 0.1339 ±0.0044
paper 0.1339 ±0.0044 Δ at pub 0.0786 Δ today 0.1379
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
SOTA performance (not significantly different from the best) Proposed method (this paper) Baseline / comparison (this paper) Global context (other papers) Best at pub — reported result worse than the best known when published (best reported in green) Improved at pub — later paper surpassed this result