Deformable Graph Transformer

Jinyoung Park, Seongjun Yun, Hyeon-ju Park, Jaewoo Kang, Jisu Jeong, KyungHyun Kim, Jung-Woo Ha, Hyunwoo J. Kim

Main figure for 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.

Proposed method: DGT

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

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
6
JKNet
actual #6 vs paper #57 51 places worse
0.9702
best reported
actual #6 vs paper #57 51 places worse
paper 0.9528 ±0.0002
paper 0.9528 ±0.0002 Δ at pub 0.0174
21
GraphSAGE
actual #21 vs paper #32 11 places worse
0.9653 ±0.0011
best reported
actual #21 vs paper #32 11 places worse
paper 0.9627 ±0.0001
paper 0.9627 ±0.0001 Δ at pub 0.0020 Δ today 0.0026
23
SAGE
0.9650 ±0.0003
26
GCN
actual #26 vs paper #67 41 places worse
0.9648
best reported
actual #26 vs paper #67 41 places worse
paper 0.9506 ±0.0003
paper 0.9506 ±0.0003 Δ at pub 0.0142
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
actual #73 vs paper #73
0.9490
best reported
actual #73 vs paper #73
paper 0.9472
paper 0.9472 Δ at pub 0.0018 Δ today 0.0018
147
MLP
actual #147 vs paper #154 7 places worse
0.8240 ±0.0010
best reported
actual #147 vs paper #154 7 places worse
paper 0.7003 ±0.0016
paper 0.7003 ±0.0016 Δ at pub 0.1237

Heterophilic Graphs

#ModelAccuracy ↑Paper
1
DiGGR
0.4535 ±0.0353
2
TRIGON
0.4402 ±0.0028
3
DoG
0.4320 ±0.0120
42
MLP
actual #42 vs paper #234 192 places worse
0.4026 ±0.0108
best reported
actual #42 vs paper #234 192 places worse
paper 0.3505 ±0.0038
paper 0.3505 ±0.0038 Δ at pub 0.0513 Δ today 0.0521
51
Transformer
actual #51 vs paper #155 104 places worse
0.3995 ±0.0064
best reported
actual #51 vs paper #155 104 places worse
paper 0.3661 ±0.0039
paper 0.3661 ±0.0039 Δ today 0.0334
68
GraphSAGE
actual #68 vs paper #223 155 places worse
0.3524 ±0.0049
actual #68 vs paper #223 155 places worse
paper 0.3524 ±0.0049

Improvement within reported uncertainty; not highlighted.

paper 0.3524 ±0.0049 Δ at pub 0.0101 Δ today 0.0375
71
H2GCN
actual #71 vs paper #222 151 places worse
0.3885 ±0.0117
best reported
actual #71 vs paper #222 151 places worse
paper 0.3532 ±0.0034
paper 0.3532 ±0.0034 Δ at pub 0.0308 Δ today 0.0353
87
Geom-GCN
actual #87 vs paper #309 222 places worse
0.3810
best reported
actual #87 vs paper #309 222 places worse
paper 0.3153 ±0.0031
paper 0.3153 ±0.0031 Δ at pub 0.0657
99
Graphormer
actual #99 vs paper #158 59 places worse
0.3785 ±0.0029
best reported
actual #99 vs paper #158 59 places worse
paper 0.3654 ±0.0044
paper 0.3654 ±0.0044 Δ today 0.0131
134
DGT
0.3693 ±0.0039
This paper
135
GCN
actual #135 vs paper #348 213 places worse
0.3690
best reported
actual #135 vs paper #348 213 places worse
paper 0.3013 ±0.0030
paper 0.3013 ±0.0030 Δ at pub 0.0677
138
DGT-light
0.3686 ±0.0053
This paper
159
DeformableGCN
0.3653 ±0.0042
This paper
162
MixHop
actual #162 vs paper #194 32 places worse
0.3579 ±0.0033
actual #162 vs paper #194 32 places worse
paper 0.3579 ±0.0033
prev best: Graph Pointer Neural Networks (AAAI 2021)

Improvement within reported uncertainty; not highlighted.

paper 0.3579 ±0.0033 Δ at pub 0.0357 Δ today 0.0069
182
GAT
actual #182 vs paper #342 160 places worse
0.3605 ±0.0035
best reported
actual #182 vs paper #342 160 places worse
paper 0.3025 ±0.0039
paper 0.3025 ±0.0039 Δ at pub 0.0535 Δ today 0.0580
230
GATv2
actual #230 vs paper #336 106 places worse
0.3510 ±0.0020
best reported
actual #230 vs paper #336 106 places worse
paper 0.3054 ±0.0041
paper 0.3054 ±0.0041 Δ today 0.0456
237
SGC
actual #237 vs paper #362 125 places worse
0.3490 ±0.0070
best reported
actual #237 vs paper #362 125 places worse
paper 0.2943 ±0.0041
paper 0.2943 ±0.0041 Δ at pub 0.0547
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
actual #281 vs paper #339 58 places worse
0.3039 ±0.0035
actual #281 vs paper #339 58 places worse
paper 0.3039 ±0.0035
paper 0.3039 ±0.0035 Δ at pub 0.0159 Δ today 0.0303

LINKX Benchmarks

#ModelAccuracy ↑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
actual #6 vs paper #8 2 places worse
0.6564 ±0.0027
best reported
actual #6 vs paper #8 2 places worse
paper 0.6520 ±0.0012
paper 0.6520 ±0.0012 Δ today 0.0044
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
actual #16 vs paper #16
0.6434 ±0.0012
actual #16 vs paper #16
paper 0.6434 ±0.0012
paper 0.6434 ±0.0012 Δ at pub 0.0160
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
actual #33 vs paper #33
0.6114 ±0.0006
actual #33 vs paper #33
paper 0.6114 ±0.0006
paper 0.6114 ±0.0006 Δ at pub 0.0022
40
SGC
0.6047 ±0.0014
This paper
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) Best at pub — reported value improved over the best known when published Improved at pub — later paper surpassed this result Best today — OK at publication; today's leaderboard best is elsewhere