TMLR 2022

Empowering GNNs via Edge-Aware Weisfeiler-Leman Algorithm

Meng Liu, Haiyang Yu, Shuiwang Ji

Main figure for Empowering GNNs via Edge-Aware Weisfeiler-Leman Algorithm

Abstract

Message passing graph neural networks (GNNs) are known to have their expressiveness upper-bounded by 1-dimensional Weisfeiler-Leman (1-WL) algorithm. To achieve more powerful GNNs, existing attempts either require ad hoc features, or involve operations that incur high time and space complexities. In this work, we propose a general and provably powerful GNN framework that preserves the scalability of the message passing scheme. In particular, we first propose to empower 1-WL for graph isomorphism test by considering edges among neighbors, giving rise to NC-1-WL. The expressiveness of NC-1-WL is shown to be strictly above 1-WL and below 3-WL theoretically. Further, we propose the NC-GNN framework as a differentiable neural version of NC-1-WL. Our simple implementation of NC-GNN is provably as powerful as NC-1-WL. Experiments demonstrate that our NC-GNN performs effectively and efficiently on various benchmarks.

Benchmark Results

Tested on 7 datasets 1 baseline value reported too low

Tables show presented results in global context (best 3 papers + GCN + MLP).

TU Dortmund

#ModelAccuracy ↑Paper
1
MSH-GNN
0.9910 ±0.0030
2
ID-GNN+BEC
0.9830 ±0.0360
3
SupCosine
0.9830 ±0.0250
39
GIN
actual #39 vs paper #237 198 places worse
0.9330 ±0.0290
best reported
actual #39 vs paper #237 198 places worse
paper 0.8940 ±0.0560

Difference within reported uncertainty; not counted as underperformance.

paper 0.8940 ±0.0560 Δ at pub 0.0390
48
NC-GNN
actual #48 vs paper #137 89 places worse
0.9280 ±0.0500
best reported
actual #48 vs paper #137 89 places worse
paper 0.9060 ±0.0560

Difference within reported uncertainty; not counted as underperformance.

paper 0.9060 ±0.0560 Δ today 0.0220
63
GCN
0.9220 ±0.0440
403
MLP
0.8660 ±0.0495
#ModelAccuracy ↑Paper
1
WL-MLP
0.9954
2
GIN
actual #2 vs paper #91 89 places worse
0.9934
best reported
actual #2 vs paper #91 89 places worse
paper 0.8270 ±0.0170
paper 0.8270 ±0.0170 Δ at pub 0.1664
3
GCN
0.9727
108
NC-GNN
0.8250 ±0.0190
This paper
131
GraphSAGE
0.8200 ±0.0100
#ModelAccuracy ↑Paper
1
WL-MLP
0.9792
2
MSH-GNN
0.9640 ±0.0070
3
CoCN
0.8722 ±0.0013
23
GCN
0.8260 ±0.0220
24
Empowering GNNs
0.8250 ±0.0120
This paper
30
GIN
actual #30 vs paper #111 81 places worse
0.8220 ±0.0210
best reported
actual #30 vs paper #111 81 places worse
paper 0.8020 ±0.0190

Difference within reported uncertainty; not counted as underperformance.

paper 0.8020 ±0.0190 Δ today 0.0200
59
CIN
0.8140 ±0.0140
This paper
151
MLP
0.7920 ±0.0240
#ModelAccuracy ↑Paper
1
GraphSNN
0.7790 ±0.0360
This paper
2
SIN
0.7560 ±0.0320
This paper
3
CIN
0.7560 ±0.0370
This paper
4
Empowering GNNs
0.7520 ±0.0450
This paper
5
GIN
actual #5 vs paper #5
0.7510 ±0.0510
actual #5 vs paper #5
paper 0.7510 ±0.0510
prev best: Graph Homomorphism Convolution (ICML 2020)
paper 0.7510 ±0.0510 Δ at pub 0.2280
6
GNN-AK+
0.7500 ±0.0420
This paper
7
PPGN
0.7300 ±0.0580
This paper
38
GCN
0.5190

OGB

#ModelAccuracy ↑Paper
1
A-NLSF
0.8149 ±0.0067
2
differential encoding
0.8096 ±0.0029
3
MPNN + VN + NoPE
0.8055 ±0.0038
16
GatedGCN
0.7531 ±0.0083
26
NC-GNN
0.7194 ±0.0043
This paper
31
GraphSNN
0.7066 ±0.0165
This paper
32
GIN + 3-cycle count feature
0.7058 ±0.0064
This paper
33
GIN
actual #33 vs paper #37 4 places worse
0.7037 ±0.0107
best reported
actual #33 vs paper #37 4 places worse
paper 0.6892 ±0.0100

Difference within reported uncertainty; not counted as underperformance.

paper 0.6892 ±0.0100 Δ today 0.0145
38
GCN
0.6857 ±0.0061

GNNBenchmark

#ModelAccuracy ↑Paper
1
GRPE-Small
0.8159 ±0.0019
2
TANGO-GPS
0.8011 ±0.0014
3
GRIT
0.8003 ±0.0028
54
GatedGCN
0.7608 ±0.0020
69
NC-GNN
0.6933 ±0.0036
This paper
70
GCN
0.6903 ±0.0137
79
GIN
0.6472 ±0.0155
This paper
91
PPGN
0.5713 ±0.0654
This paper
104
RingGNN
0.4242 ±0.2006
This paper
114
MLP
0.2097 ±0.0000
#ModelAccuracy ↑Paper
1
DeepGraph (48)
0.9066 ±0.0006
2
GRIT (our run)
0.9041 ±0.0023
3
GRIT 2-QiQRW
0.9016 ±0.0045
55
NC-GNN
0.8663 ±0.0002
This paper
66
GatedGCN
0.8651 ±0.0008
72
RingGNN
0.8625 ±0.0001
This paper
86
PPGN
0.8566 ±0.0035
This paper
88
GCN
0.8561 ±0.0003
89
GIN
0.8559 ±0.0001
This paper
123
MLP
0.5052
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