NeurIPS 2022

Convolutional Neural Networks on Graphs with Chebyshev Approximation, Revisited

Mingguo He, Zhewei Wei, Ji-rong Wen

Main figure for Convolutional Neural Networks on Graphs with Chebyshev Approximation, Revisited

Abstract

Designing spectral convolutional networks is a challenging problem in graph learning. ChebNet, one of the early attempts, approximates the spectral graph convolutions using Chebyshev polynomials. GCN simplifies ChebNet by utilizing only the first two Chebyshev polynomials while still outperforming it on real-world datasets. GPR-GNN and BernNet demonstrate that the Monomial and Bernstein bases also outperform the Chebyshev basis in terms of learning the spectral graph convolutions. Such conclusions are counter-intuitive in the field of approximation theory, where it is established that the Chebyshev polynomial achieves the optimum convergent rate for approximating a function. In this paper, we revisit the problem of approximating the spectral graph convolutions with Chebyshev polynomials. We show that ChebNet's inferior performance is primarily due to illegal coefficients learnt by ChebNet approximating analytic filter functions, which leads to over-fitting. We then propose ChebNetII, a new GNN model based on Chebyshev interpolation, which enhances the original Chebyshev polynomial approximation while reducing the Runge phenomenon. We conducted an extensive experimental study to demonstrate that ChebNetII can learn arbitrary graph convolutions and achieve superior performance in both full- and semi-supervised node classification tasks. Most notably, we scale ChebNetII to a billion graph ogbn-papers100M, showing that spectral-based GNNs have superior performance. Our code is available at.

Proposed method: ChebNetII

Benchmark Results

Tested on 10 datasets 1 baseline value reported too low

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

Classic

#ModelAccuracy ↑Paper
1
CNA
0.9575 ±0.0058
2
IS-GIB
0.9390 ±0.0187
3
EERM
0.9112 ±0.0145
44
GCN
0.8033 ±0.0088
350
MLP
0.7289 ±0.0010
387
ChebBase/k
0.7252 ±0.0029
This paper
576
ChebBase
0.7076 ±0.0037
This paper
#ModelAccuracy ↑Paper
1
LGTL
0.9518 ±0.0011
2
MixHop (LO)
0.9513 ±0.0038
3
GraphSAGE (LO)
0.9511 ±0.0036
18
GCN
0.9296 ±0.0015
210
MLP
0.8690 ±0.0074
553
ChebBase/k
0.7925 ±0.0031
This paper
673
ChebBase
0.7807 ±0.0032
This paper

OGB

#ModelAccuracy ↑Paper
1
SGC
0.7910
2
GAMLP
0.7036 ±0.0002
3
GLEM-GNN
0.7036 ±0.0002
21
ChebNetII
0.6718 ±0.0032
This paper
35
SAGE
0.6644 ±0.0017
38
SIGN
actual #38 vs paper #53 15 places worse
0.6636 ±0.0005
best reported
actual #38 vs paper #53 15 places worse
paper 0.6568 ±0.0016
50
GPR-GNN
0.6589 ±0.0035
This paper
55
NDLS
actual #55 vs paper #55
0.6561 ±0.0029
actual #55 vs paper #55
paper 0.6561 ±0.0029

Improvement within reported uncertainty; not highlighted.

paper 0.6561 ±0.0029 Δ at pub 0.0001
59
GBP
actual #59 vs paper #59
0.6523 ±0.0031
actual #59 vs paper #59
paper 0.6523 ±0.0031

Improvement within reported uncertainty; not highlighted.

paper 0.6523 ±0.0031 Δ at pub 0.0003
95
MLP
0.4960 ±0.0030

Heterophilic Graphs

#ModelAccuracy ↑Paper
1
P^2GNN
0.9672 ±0.0147
2
DoG
0.9660 ±0.0210
3
GPF-plus
0.9583 ±0.0419
23
ChebNetII
0.9328 ±0.0147
This paper
22
BernNet
actual #22 vs paper #30 8 places worse
0.9328 ±0.0148
best reported
actual #22 vs paper #30 8 places worse
paper 0.9262 ±0.0137

Difference within reported uncertainty; not counted as underperformance.

paper 0.9262 ±0.0137 Δ today 0.0066
25
PDE-GCN
0.9324 ±0.0203
This paper
30
GPR-GNN
actual #30 vs paper #30
0.9291 ±0.0132
actual #30 vs paper #30
paper 0.9291 ±0.0132
paper 0.9291 ±0.0132 Δ at pub 0.0832
34
MLP
actual #34 vs paper #104 70 places worse
0.8681 ±0.0224
actual #34 vs paper #104 70 places worse
paper 0.8681 ±0.0224

Improvement within reported uncertainty; not highlighted.

paper 0.8681 ±0.0224 Δ at pub 0.0351 Δ today 0.0549
46
APPNP
actual #46 vs paper #49 3 places worse
0.9064 ±0.0170
actual #46 vs paper #49 3 places worse
paper 0.9064 ±0.0170

Improvement within reported uncertainty; not highlighted.

paper 0.9064 ±0.0170 Δ at pub 0.0875
47
TWIRLS
actual #47 vs paper #47
0.9131 ±0.0336
actual #47 vs paper #47
paper 0.9131 ±0.0336
paper 0.9131 ±0.0336 Δ at pub 0.0672
53
GraphSAGE
0.9000 ±0.0365
70
GCNII
actual #70 vs paper #237 167 places worse
0.8046 ±0.0591
actual #70 vs paper #237 167 places worse
paper 0.8046 ±0.0591
prev best: Graph-Coupled Oscillator Networks (ICML 2022)

Improvement within reported uncertainty; not highlighted.

paper 0.8046 ±0.0591 Δ at pub 0.0286
110
ChebNet
0.8628 ±0.0262
This paper
170
ARMA
0.8397 ±0.0377
This paper
220
EGNN
0.8134 ±0.0156
This paper
257
GCN
actual #257 vs paper #289 32 places worse
0.7697 ±0.0397
actual #257 vs paper #289 32 places worse
paper 0.7697 ±0.0397
paper 0.7697 ±0.0397 Δ at pub 0.1316
#ModelAccuracy ↑Paper
1
P^2GNN
0.9541 ±0.0272
2
ACM-GCN
0.9480 ±0.0380
3
RF-GCN
0.9429
11
GPR-GNN
actual #11 vs paper #21 10 places worse
0.9157 ±0.0196
actual #11 vs paper #21 10 places worse
paper 0.9157 ±0.0196
paper 0.9157 ±0.0196 Δ at pub 0.1230
16
ChebNetII
0.9230 ±0.0148
This paper
17
BernNet
0.9213 ±0.0164
This paper
21
APPNP
actual #21 vs paper #22 1 place worse
0.9152 ±0.0181
actual #21 vs paper #22 1 place worse
paper 0.9152 ±0.0181
paper 0.9152 ±0.0181 Δ at pub 0.0963
24
MLP
actual #24 vs paper #109 85 places worse
0.9136 ±0.0070
best reported
actual #24 vs paper #109 85 places worse
paper 0.8415 ±0.0305
paper 0.8415 ±0.0305 Δ at pub 0.0071 Δ today 0.0721
27
TWIRLS
actual #27 vs paper #27
0.8983 ±0.0229
actual #27 vs paper #27
paper 0.8983 ±0.0229

Improvement within reported uncertainty; not highlighted.

paper 0.8983 ±0.0229 Δ at pub 0.0307
28
PDE-GCN
0.8973 ±0.0135
This paper
35
GCNII
actual #35 vs paper #109 74 places worse
0.8426 ±0.0213
actual #35 vs paper #109 74 places worse
paper 0.8426 ±0.0213

Improvement within reported uncertainty; not highlighted.

paper 0.8426 ±0.0213 Δ at pub 0.0396
82
ARMA
0.8562 ±0.0213
This paper
85
ChebNet
actual #85 vs paper #115 30 places worse
0.8533 ±0.0104
best reported
actual #85 vs paper #115 30 places worse
paper 0.8391 ±0.0217

Difference within reported uncertainty; not counted as underperformance.

paper 0.8391 ±0.0217 Δ today 0.0142
117
EGNN
actual #117 vs paper #155 38 places worse
0.8380 ±0.0460
best reported
actual #117 vs paper #155 38 places worse
paper 0.8209 ±0.0116

Difference within reported uncertainty; not counted as underperformance.

paper 0.8209 ±0.0116 Δ today 0.0171
138
SAGE
0.8269
170
GCN
actual #170 vs paper #322 152 places worse
0.6578 ±0.0416
actual #170 vs paper #322 152 places worse
paper 0.6578 ±0.0416

Improvement within reported uncertainty; not highlighted.

paper 0.6578 ±0.0416 Δ at pub 0.0281 Δ today 0.1504
#ModelAccuracy ↑Paper
1
DiGGR
0.4535 ±0.0353
2
TRIGON
0.4402 ±0.0028
3
DoG
0.4320 ±0.0120
21
BernNet
actual #21 vs paper #22 1 place worse
0.4179 ±0.0101
best reported
actual #21 vs paper #22 1 place worse
paper 0.4171 ±0.0112

Difference within reported uncertainty; not counted as underperformance.

paper 0.4171 ±0.0112 Δ today 0.0008
22
ChebNetII
0.4175 ±0.0107
This paper
38
GCNII
actual #38 vs paper #136 98 places worse
0.3689 ±0.0095
actual #38 vs paper #136 98 places worse
paper 0.3689 ±0.0095
41
APPNP
actual #41 vs paper #54 13 places worse
0.3976 ±0.0049
actual #41 vs paper #54 13 places worse
paper 0.3976 ±0.0049
42
MLP
actual #42 vs paper #43 1 place worse
0.4018 ±0.0055
actual #42 vs paper #43 1 place worse
paper 0.4018 ±0.0055
paper 0.4018 ±0.0055 Δ at pub 0.0401
53
GPR-GNN
actual #53 vs paper #53
0.3991 ±0.0062
actual #53 vs paper #53
paper 0.3991 ±0.0062
paper 0.3991 ±0.0062 Δ at pub 0.0597
55
PDE-GCN
0.3976 ±0.0074
This paper
68
GraphSAGE
0.3899 ±0.0085
85
TWIRLS
actual #85 vs paper #85
0.3813 ±0.0081
actual #85 vs paper #85
paper 0.3813 ±0.0081

Improvement within reported uncertainty; not highlighted.

paper 0.3813 ±0.0081 Δ at pub 0.0070
88
ChebNet
actual #88 vs paper #114 26 places worse
0.3802 ±0.0023
best reported
actual #88 vs paper #114 26 places worse
paper 0.3742 ±0.0058

Difference within reported uncertainty; not counted as underperformance.

paper 0.3742 ±0.0058 Δ today 0.0060
111
ARMA
0.3767 ±0.0054
This paper
135
GCN
actual #135 vs paper #284 149 places worse
0.3690
best reported
actual #135 vs paper #284 149 places worse
paper 0.3326 ±0.0115
paper 0.3326 ±0.0115 Δ at pub 0.0364
224
EGNN
0.3516 ±0.0064
This paper

LINKX Benchmarks

#ModelAccuracy ↑Paper
1
DC-GNN
0.8669 ±0.0022
2
M2M-GNN
0.8594 ±0.0040
3
GloGNN
0.8574 ±0.0042
7
ChebNetII
0.8486 ±0.0033
This paper
11
LINKX
0.8471 ±0.0052
This paper
20
GPR-GNN
0.8354 ±0.0032
This paper
23
BernNet
0.8326 ±0.0029
This paper
27
GCNII
0.8292 ±0.0059
This paper
29
GIN
0.8268 ±0.0032
30
ChebNet
0.8259 ±0.0031
This paper
31
GCN
0.8247 ±0.0027
This paper
40
LINK
0.8079 ±0.0049
This paper
51
MLP
actual #51 vs paper #57 6 places worse
0.7534 ±0.0064
best reported
actual #51 vs paper #57 6 places worse
paper 0.7361 ±0.0040
paper 0.7361 ±0.0040 Δ today 0.0173
#ModelAccuracy ↑Paper
1
LargeScaleNet
0.6582 ±0.0036
2
S² DirGCN
0.6495 ±0.0033
3
FaberNet
0.6462 ±0.0101
13
LINKX
0.5600 ±0.0134
This paper
17
LINK
0.5397 ±0.0018
This paper
24
ChebNetII
0.4853 ±0.0031
This paper
26
GCNII
actual #26 vs paper #26
0.4721 ±0.0028
actual #26 vs paper #26
paper 0.4721 ±0.0028

Improvement within reported uncertainty; not highlighted.

paper 0.4721 ±0.0028 Δ at pub 0.0001
28
ChebNet
0.4676 ±0.0024
This paper
29
BernNet
0.4634 ±0.0032
This paper
31
GCN
actual #31 vs paper #31
0.4602 ±0.0026
actual #31 vs paper #31
paper 0.4602 ±0.0026

Improvement within reported uncertainty; not highlighted.

paper 0.4602 ±0.0026 Δ at pub 0.0002
32
GPR-GNN
0.4597 ±0.0026
This paper
56
MLP
0.3670 ±0.0021
This paper
#ModelAccuracy ↑Paper
1
SAGE
0.8597 ±0.0021
2
Polynormer
0.8595 ±0.0007
3
NID_SAGE
0.8563 ±0.0031
6
ChebNetII
0.8233 ±0.0028
This paper
7
LINKX
0.8204 ±0.0007
This paper
9
BernNet
0.8167 ±0.0017
This paper
13
GPR-GNN
0.8074 ±0.0022
This paper
14
LINK
0.8054 ±0.0003
This paper
16
GCNII
0.7894 ±0.0011
This paper
23
GCN
actual #23 vs paper #24 1 place worse
0.7601 ±0.0049
best reported
actual #23 vs paper #24 1 place worse
paper 0.7545 ±0.0017
paper 0.7545 ±0.0017 Δ today 0.0056
24
GraphSAGE
0.7576 ±0.0004
27
ChebNet
0.7271 ±0.0066
This paper
31
MLP
actual #31 vs paper #39 8 places worse
0.7048 ±0.0077
best reported
actual #31 vs paper #39 8 places worse
paper 0.6237 ±0.0002
paper 0.6237 ±0.0002 Δ today 0.0811
#ModelAccuracy ↑Paper
1
DGT
0.6609 ±0.0022
2
ICG_u-NN
0.6608 ±0.0074
3
LINKX
0.6606 ±0.0019
This paper
11
ChebNetII
0.6503 ±0.0027
This paper
13
LINK
0.6485 ±0.0021
This paper
14
GraphSAGE
0.6473 ±0.0011
16
GCN
actual #16 vs paper #28 12 places worse
0.6434 ±0.0012
best reported
actual #16 vs paper #28 12 places worse
paper 0.6218 ±0.0026
best today: Deformable Graph Transformer (2022)
paper 0.6218 ±0.0026 Δ today 0.0216
18
BernNet
0.6427 ±0.0031
This paper
23
GCNII
0.6339 ±0.0061
This paper
27
GPR-GNN
0.6259 ±0.0038
This paper
28
ChebNet
0.6231 ±0.0037
This paper
33
MLP
actual #33 vs paper #37 4 places worse
0.6114 ±0.0006
best reported
actual #33 vs paper #37 4 places worse
paper 0.6092 ±0.0007
best today: Deformable Graph Transformer (2022)
paper 0.6092 ±0.0007 Δ today 0.0022
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