Node-oriented Spectral Filtering for Graph Neural Networks

Shuai Zheng, Zhenfeng Zhu, Zhizhe Liu, Youru Li, Yao Zhao

Main figure for Node-oriented Spectral Filtering for Graph Neural Networks

Abstract

Graph neural networks (GNNs) have shown remarkable performance on homophilic graph data while being far less impressive when handling non-homophilic graph data due to the inherent low-pass filtering property of GNNs. In general, since real-world graphs are often complex mixtures of diverse subgraph patterns, learning a universal spectral filter on the graph from the global perspective as in most current works may still suffer from great difficulty in adapting to the variation of local patterns. On the basis of the theoretical analysis of local patterns, we rethink the existing spectral filtering methods and propose the ode-oriented spectral iltering for raph eural etwork (namely NFGNN). By estimating the node-oriented spectral filter for each node, NFGNN is provided with the capability of precise local node positioning via the generalized translated operator, thus discriminating the variations of local homophily patterns adaptively. Meanwhile, the utilization of re-parameterization brings a good trade-off between global consistency and local sensibility for learning the node-oriented spectral filters. Furthermore, we theoretically analyze the localization property of NFGNN, demonstrating that the signal after adaptive filtering is still positioned around the corresponding node. Extensive experimental results demonstrate that the proposed NFGNN achieves more favorable performance.

Proposed method: NFGNN

Benchmark Results

Tested on 6 datasets 9 baseline values reported too low

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

Classic

#ModelAccuracy ↑Paper
1
GraphTARIF
0.9703 ±0.0019
2
GAT
actual #2 vs paper #225 223 places worse
0.9294 ±0.0066
actual #2 vs paper #225 223 places worse
paper 0.9294 ±0.0066

Improvement within reported uncertainty; not highlighted.

paper 0.9294 ±0.0066 Δ at pub 0.0030 Δ today 0.0375
3
GAT+T
0.9660 ±0.0007
7
SAGE
0.9643 ±0.0027
8
GCN
actual #8 vs paper #283 275 places worse
0.9249 ±0.0055
actual #8 vs paper #283 275 places worse
paper 0.9249 ±0.0055

Improvement within reported uncertainty; not highlighted.

paper 0.9249 ±0.0055 Δ at pub 0.0007 Δ today 0.0383
21
APPNP
actual #21 vs paper #399 378 places worse
0.9573 ±0.0012
best reported
actual #21 vs paper #399 378 places worse
paper 0.9111 ±0.0026
33
GPRGNN
actual #33 vs paper #111 78 places worse
0.9387 ±0.0042
actual #33 vs paper #111 78 places worse
paper 0.9387 ±0.0042
66
FAGCN
actual #66 vs paper #127 61 places worse
0.9489 ±0.0048
best reported
actual #66 vs paper #127 61 places worse
paper 0.9367 ±0.0050
paper 0.9367 ±0.0050 Δ today 0.0122
67
NFGNN
0.9485 ±0.0024
This paper
119
ChebNet
actual #119 vs paper #138 19 places worse
0.9358 ±0.0019
actual #119 vs paper #138 19 places worse
paper 0.9358 ±0.0019
prev best: Elastic Graph Neural Networks (ICML 2021)
paper 0.9358 ±0.0019 Δ at pub 0.0318
127
BernNet
actual #127 vs paper #174 47 places worse
0.9368 ±0.0028
best reported
actual #127 vs paper #174 47 places worse
paper 0.9332 ±0.0040

Difference within reported uncertainty; not counted as underperformance.

paper 0.9332 ±0.0040 Δ today 0.0036
390
MLP
actual #390 vs paper #489 99 places worse
0.8817 ±0.0062
actual #390 vs paper #489 99 places worse
paper 0.8817 ±0.0062
paper 0.8817 ±0.0062 Δ at pub 0.0963 Δ today 0.0311
470
LINK
0.8928 ±0.0031
This paper
#ModelAccuracy ↑Paper
1
GraphTARIF
0.9461 ±0.0017
2
GCN
actual #2 vs paper #264 262 places worse
0.9412 ±0.0008
best reported
actual #2 vs paper #264 262 places worse
paper 0.8664 ±0.0104
paper 0.8664 ±0.0104 Δ at pub 0.0121 Δ today 0.0748
3
GAT
actual #3 vs paper #293 290 places worse
0.9398 ±0.0022
best reported
actual #3 vs paper #293 290 places worse
paper 0.8583 ±0.0049
8
SAGE
0.9351 ±0.0006
58
APPNP
actual #58 vs paper #208 150 places worse
0.8804 ±0.0051
actual #58 vs paper #208 150 places worse
paper 0.8804 ±0.0051
72
GPRGNN
actual #72 vs paper #247 175 places worse
0.8720 ±0.0047
actual #72 vs paper #247 175 places worse
paper 0.8720 ±0.0047
81
NFGNN
0.9031 ±0.0042
This paper
126
FAGCN
actual #126 vs paper #126
0.8968 ±0.0097
actual #126 vs paper #126
paper 0.8968 ±0.0097
paper 0.8968 ±0.0097 Δ at pub 0.0752
180
BernNet
0.8861 ±0.0041
This paper
216
ChebNet
actual #216 vs paper #216
0.8782 ±0.0072
actual #216 vs paper #216
paper 0.8782 ±0.0072
prev best: Elastic Graph Neural Networks (ICML 2021)
paper 0.8782 ±0.0072 Δ at pub 0.0682
320
MLP
actual #320 vs paper #408 88 places worse
0.8178 ±0.0076
actual #320 vs paper #408 88 places worse
paper 0.8178 ±0.0076
357
LINK
0.8371 ±0.0032
This paper

OGB

#ModelAccuracy ↑Paper
1
GIANT-XRT
0.7612 ±0.0016
2
GEGCN
0.7576 ±0.0064
3
AGDN
0.7522 ±0.0007
23
GCN
actual #23 vs paper #72 49 places worse
0.7300 ±0.0017
best reported
actual #23 vs paper #72 49 places worse
paper 0.7103 ±0.0038
25
GraphSAGE
0.7277 ±0.0016
37
NFGNN
0.7213 ±0.0033
This paper
49
APPNP
actual #49 vs paper #74 25 places worse
0.7190 ±0.0025
best reported
actual #49 vs paper #74 25 places worse
paper 0.7097 ±0.0071

Difference within reported uncertainty; not counted as underperformance.

paper 0.7097 ±0.0071 Δ today 0.0093
55
GPRGNN
actual #55 vs paper #55
0.7168 ±0.0044
actual #55 vs paper #55
paper 0.7168 ±0.0044
paper 0.7168 ±0.0044 Δ at pub 0.0078
64
BernNet
0.7140 ±0.0037
This paper
107
MLP
0.5765 ±0.0012

Heterophilic Graphs

#ModelAccuracy ↑Paper
1
P^2GNN
0.9672 ±0.0147
2
DoG
0.9660 ±0.0210
3
GPF-plus
0.9583 ±0.0419
14
NFGNN
0.9403 ±0.0082
This paper
22
BernNet
actual #22 vs paper #33 11 places worse
0.9328 ±0.0148
best reported
actual #22 vs paper #33 11 places worse
paper 0.9230 ±0.0123

Difference within reported uncertainty; not counted as underperformance.

paper 0.9230 ±0.0123 Δ at pub 0.0032 Δ today 0.0098
26
BMGCN
0.9300 ±0.0057
This paper
28
GPRGNN
actual #28 vs paper #29 1 place worse
0.9292 ±0.0061
actual #28 vs paper #29 1 place worse
paper 0.9292 ±0.0061
paper 0.9292 ±0.0061 Δ at pub 0.0832
34
MLP
actual #34 vs paper #35 1 place worse
0.9226 ±0.0071
actual #34 vs paper #35 1 place worse
paper 0.9226 ±0.0071
paper 0.9226 ±0.0071 Δ at pub 0.0545
46
APPNP
actual #46 vs paper #47 1 place worse
0.9118 ±0.0070
actual #46 vs paper #47 1 place worse
paper 0.9118 ±0.0070

Improvement within reported uncertainty; not highlighted.

paper 0.9118 ±0.0070 Δ at pub 0.0054
53
GraphSAGE
0.9000 ±0.0365
61
FAGCN
actual #61 vs paper #61
0.8961 ±0.0152
actual #61 vs paper #61
paper 0.8961 ±0.0152
62
LINK
actual #62 vs paper #62
0.8961 ±0.0152
actual #62 vs paper #62
paper 0.8961 ±0.0152
paper 0.8961 ±0.0152 Δ at pub 0.1123
110
ChebNet
actual #110 vs paper #119 9 places worse
0.8628 ±0.0262
best reported
actual #110 vs paper #119 9 places worse
paper 0.8608 ±0.0096

Difference within reported uncertainty; not counted as underperformance.

paper 0.8608 ±0.0096 Δ at pub 0.0020 Δ today 0.0020
211
GAT
actual #211 vs paper #265 54 places worse
0.8162 ±0.0645
best reported
actual #211 vs paper #265 54 places worse
paper 0.7887 ±0.0086

Difference within reported uncertainty; not counted as underperformance.

paper 0.7887 ±0.0086 Δ at pub 0.0093 Δ today 0.0275
257
GCN
actual #257 vs paper #318 61 places worse
0.7933 ±0.0447
best reported
actual #257 vs paper #318 61 places worse
paper 0.7516 ±0.0096
best today: Graph Wave Networks (WWW 2025)

Difference within reported uncertainty; not counted as underperformance.

paper 0.7516 ±0.0096 Δ at pub 0.0324 Δ today 0.0417
#ModelAccuracy ↑Paper
1
P^2GNN
0.9541 ±0.0272
2
ACM-GCN
0.9480 ±0.0380
3
RF-GCN
0.9429
17
BernNet
actual #17 vs paper #18 1 place worse
0.9213 ±0.0164
best reported
actual #17 vs paper #18 1 place worse
paper 0.9196 ±0.0107

Difference within reported uncertainty; not counted as underperformance.

paper 0.9196 ±0.0107 Δ at pub 0.0017 Δ today 0.0017
20
NFGNN
0.9190 ±0.0091
This paper
21
APPNP
actual #21 vs paper #21
0.9180 ±0.0063
actual #21 vs paper #21
paper 0.9180 ±0.0063

Improvement within reported uncertainty; not highlighted.

paper 0.9180 ±0.0063 Δ at pub 0.0028
22
GPRGNN
actual #22 vs paper #23 1 place worse
0.9136 ±0.0070
actual #22 vs paper #23 1 place worse
paper 0.9136 ±0.0070
paper 0.9136 ±0.0070 Δ at pub 0.0758
24
MLP
actual #24 vs paper #24
0.9136 ±0.0070
actual #24 vs paper #24
paper 0.9136 ±0.0070

Improvement within reported uncertainty; not highlighted.

paper 0.9136 ±0.0070 Δ at pub 0.0650
38
FAGCN
actual #38 vs paper #38
0.8852 ±0.0133
actual #38 vs paper #38
paper 0.8852 ±0.0133
85
ChebNet
actual #85 vs paper #85
0.8533 ±0.0104
actual #85 vs paper #85
paper 0.8533 ±0.0104

Improvement within reported uncertainty; not highlighted.

paper 0.8533 ±0.0104 Δ at pub 0.0142
138
SAGE
0.8269
158
GAT
actual #158 vs paper #222 64 places worse
0.8190 ±0.0540
best reported
actual #158 vs paper #222 64 places worse
paper 0.7600 ±0.0101
paper 0.7600 ±0.0101 Δ at pub 0.0590
170
GCN
actual #170 vs paper #314 144 places worse
0.8082 ±0.0360
best reported
actual #170 vs paper #314 144 places worse
paper 0.6672 ±0.0137
paper 0.6672 ±0.0137 Δ at pub 0.1248 Δ today 0.1410
387
LINK
actual #387 vs paper #527 140 places worse
0.5916
best reported
actual #387 vs paper #527 140 places worse
paper 0.4491 ±0.0219
paper 0.4491 ±0.0219 Δ at pub 0.1425
#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 #49 28 places worse
0.4179 ±0.0101
best reported
actual #21 vs paper #49 28 places worse
paper 0.4001 ±0.0042
paper 0.4001 ±0.0042 Δ at pub 0.0170 Δ today 0.0178
39
NFGNN
0.4062 ±0.0038
This paper
41
APPNP
actual #41 vs paper #70 29 places worse
0.4046 ±0.0064
best reported
actual #41 vs paper #70 29 places worse
paper 0.3886 ±0.0024
paper 0.3886 ±0.0024 Δ at pub 0.0090 Δ today 0.0160
42
MLP
actual #42 vs paper #76 34 places worse
0.4026 ±0.0108
best reported
actual #42 vs paper #76 34 places worse
paper 0.3858 ±0.0025
paper 0.3858 ±0.0025 Δ at pub 0.0160 Δ today 0.0168
52
GPRGNN
actual #52 vs paper #61 9 places worse
0.3930 ±0.0027
actual #52 vs paper #61 9 places worse
paper 0.3930 ±0.0027

Improvement within reported uncertainty; not highlighted.

paper 0.3930 ±0.0027 Δ at pub 0.0003
56
FAGCN
actual #56 vs paper #66 10 places worse
0.3970
best reported
actual #56 vs paper #66 10 places worse
paper 0.3908 ±0.0065

Difference within reported uncertainty; not counted as underperformance.

paper 0.3908 ±0.0065 Δ at pub 0.0062
68
GraphSAGE
0.3899 ±0.0085
88
ChebNet
actual #88 vs paper #88
0.3802 ±0.0023
actual #88 vs paper #88
paper 0.3802 ±0.0023

Improvement within reported uncertainty; not highlighted.

paper 0.3802 ±0.0023 Δ at pub 0.0060
135
GCN
actual #135 vs paper #336 201 places worse
0.3690
best reported
actual #135 vs paper #336 201 places worse
paper 0.3059 ±0.0023
paper 0.3059 ±0.0023 Δ at pub 0.0631
182
GAT
actual #182 vs paper #186 4 places worse
0.3605 ±0.0035
best reported
actual #182 vs paper #186 4 places worse
paper 0.3598 ±0.0023

Difference within reported uncertainty; not counted as underperformance.

paper 0.3598 ±0.0023 Δ at pub 0.0007
418
LINK
actual #418 vs paper #418
0.2625 ±0.0143
actual #418 vs paper #418
paper 0.2625 ±0.0143
paper 0.2625 ±0.0143 Δ at pub 0.0222
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