GPNet: Simplifying Graph Neural Networks via Multi-channel Geometric Polynomials

Xun Liu, Alex Hay-Man Ng, Fangyu Lei, Yikuan Zhang, Zhengmin Li

Main figure for GPNet: Simplifying Graph Neural Networks via Multi-channel Geometric Polynomials

Abstract

Graph Neural Networks (GNNs) are a promising deep learning approach for circumventing many real-world problems on graph-structured data. However, these models usually have at least one of four fundamental limitations: over-smoothing, over-fitting, difficult to train, and strong homophily assumption. For example, Simple Graph Convolution (SGC) is known to suffer from the first and fourth limitations. To tackle these limitations, we identify a set of key designs including (D1) dilated convolution, (D2) multi-channel learning, (D3) self-attention score, and (D4) sign factor to boost learning from different types (homophily and heterophily) and scales (small, medium, and large) of networks, and combine them into a graph neural network, GPNet, a simple and efficient one-layer model. We theoretically analyze the model and show that it can approximate various graph filters by adjusting the self-attention score and sign factor. Experiments show that GPNet consistently outperforms baselines in terms of average rank, average accuracy, complexity, and parameters on semi-supervised and full-supervised tasks, and achieves competitive performance compared to state-of-the-art model with inductive learning task.

Proposed method: GPNet

Benchmark Results

Tested on 8 datasets 28 baseline values reported too low

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

Classic

#ModelAccuracy ↑Paper
1
GraphSAGE+CNA
0.9418 ±0.0033
2
GCN+CNA
0.9366 ±0.0048
3
TransformerConv
0.9350 ±0.0058
21
GCN
0.9004
50
FAGCN
actual #50 vs paper #289 239 places worse
0.8885 ±0.0136
best reported
actual #50 vs paper #289 239 places worse
paper 0.8410 ±0.0050
paper 0.8410 ±0.0050 Δ today 0.0475
55
JKNet
actual #55 vs paper #599 544 places worse
0.8870
best reported
actual #55 vs paper #599 544 places worse
paper 0.8110
paper 0.8110 Δ at pub 0.0760
99
JKNet+DropEdge
actual #99 vs paper #389 290 places worse
0.8800
best reported
actual #99 vs paper #389 290 places worse
paper 0.8330
paper 0.8330 Δ at pub 0.0470
373
IncepGCN+DropEdge
0.8350
This paper
384
ARMA
0.8340
This paper
544
MixHop-learn
0.8190 ±0.0040
This paper
724
MLP
0.7768
#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
47
JKNet+DropEdge
actual #47 vs paper #373 326 places worse
0.8020
best reported
actual #47 vs paper #373 326 places worse
paper 0.7260
paper 0.7260 Δ at pub 0.0760
62
JKNet
actual #62 vs paper #630 568 places worse
0.7920
best reported
actual #62 vs paper #630 568 places worse
paper 0.6980
paper 0.6980 Δ at pub 0.0940
350
MLP
0.7289 ±0.0010
371
IncepGCN+DropEdge
0.7270
This paper
390
ARMA
0.7250
This paper
522
MixHop-learn
0.7140 ±0.0080
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
24
JKNet
actual #24 vs paper #668 644 places worse
0.9160
best reported
actual #24 vs paper #668 644 places worse
paper 0.7810
paper 0.7810 Δ at pub 0.1350
25
JKNet+DropEdge
actual #25 vs paper #556 531 places worse
0.9160
best reported
actual #25 vs paper #556 531 places worse
paper 0.7920
paper 0.7920 Δ at pub 0.1240
210
MLP
0.8690 ±0.0074
217
ARMA
actual #217 vs paper #602 385 places worse
0.8678 ±0.0021
best reported
actual #217 vs paper #602 385 places worse
paper 0.7890
391
MixHop-learn
0.8080 ±0.0060
This paper
514
IncepGCN+DropEdge
0.7950
This paper
#ModelF1 ↑Paper
1
EnGCN
0.9714 ±0.0003
2
SAGN+SLE
0.9710
3
GAMLP(JK)
0.9704 ±0.0001
14
GraphSAGE
0.9660
26
GaAN
actual #26 vs paper #26
0.9640
actual #26 vs paper #26
paper 0.9640

Improvement within reported uncertainty; not highlighted.

paper 0.9640 Δ at pub 0.0004
46
GPNet
0.9580
This paper
55
SAGE-LSTM
0.9540
This paper
71
SAGE-mean
0.9500
This paper
73
SGC
0.9490
This paper
82
DGI
actual #82 vs paper #84 2 places worse
0.9414 ±0.0003
best reported
actual #82 vs paper #84 2 places worse
paper 0.9400
paper 0.9400 Δ at pub 0.0014
91
FastGCN
0.9370
This paper
109
SAGE-GCN
0.9300
This paper

Heterophilic Graphs

#ModelAccuracy ↑Paper
1
P^2GNN
0.9672 ±0.0147
2
DoG
0.9660 ±0.0210
3
GPF-plus
0.9583 ±0.0419
28
GPRGNN
actual #28 vs paper #269 241 places worse
0.9295 ±0.0131
best reported
actual #28 vs paper #269 241 places worse
paper 0.7838 ±0.0440
paper 0.7838 ±0.0440 Δ at pub 0.0622 Δ today 0.1457
34
MLP
actual #34 vs paper #230 196 places worse
0.9230 ±0.0070
best reported
actual #34 vs paper #230 196 places worse
paper 0.8081 ±0.0480
39
GGCN
actual #39 vs paper #148 109 places worse
0.9213 ±0.0305
best reported
actual #39 vs paper #148 109 places worse
paper 0.8486 ±0.0460
best today: Graph Wave Networks (WWW 2025)
paper 0.8486 ±0.0460 Δ today 0.0727
40
H2GCN
actual #40 vs paper #148 108 places worse
0.9189 ±0.0393
best reported
actual #40 vs paper #148 108 places worse
paper 0.8486 ±0.0720
best at pub: Graph-Coupled Oscillator Networks (ICML 2022)

Difference within reported uncertainty; not counted as underperformance.

paper 0.8486 ±0.0720 Δ at pub 0.0004 Δ today 0.0703
46
APPNP
actual #46 vs paper #272 226 places worse
0.9131 ±0.0197
best reported
actual #46 vs paper #272 226 places worse
paper 0.7837 ±0.0600
paper 0.7837 ±0.0600 Δ at pub 0.1227 Δ today 0.1294
53
GraphSAGE
0.9000 ±0.0365
61
FAGCN
actual #61 vs paper #273 212 places worse
0.8961 ±0.0152
best reported
actual #61 vs paper #273 212 places worse
paper 0.7811 ±0.0500
paper 0.7811 ±0.0500 Δ at pub 0.0432 Δ today 0.1150
70
GCNII
actual #70 vs paper #280 210 places worse
0.8918 ±0.0443
best reported
actual #70 vs paper #280 210 places worse
paper 0.7757 ±0.0380
paper 0.7757 ±0.0380 Δ at pub 0.0289 Δ today 0.1161
93
GPNet
0.8784
This paper
118
Conn-NSD
0.8616 ±0.0220
This paper
141
GloGNN
actual #141 vs paper #164 23 places worse
0.8524 ±0.0490
best reported
actual #141 vs paper #164 23 places worse
paper 0.8432 ±0.0420

Difference within reported uncertainty; not counted as underperformance.

paper 0.8432 ±0.0420 Δ today 0.0092
160
UDGNN_GCN
0.8460 ±0.0530
This paper
211
GAT
actual #211 vs paper #576 365 places worse
0.8162 ±0.0645
best reported
actual #211 vs paper #576 365 places worse
paper 0.5216 ±0.0660
paper 0.5216 ±0.0660 Δ at pub 0.2764 Δ today 0.2946
257
GCN
actual #257 vs paper #568 311 places worse
0.7933 ±0.0447
best reported
actual #257 vs paper #568 311 places worse
paper 0.5514 ±0.0520
best today: Graph Wave Networks (WWW 2025)
paper 0.5514 ±0.0520 Δ at pub 0.2326 Δ today 0.2419
276
MixHop
0.7784 ±0.0770
This paper
325
LINKX
0.7460 ±0.0840
This paper
330
SGC
actual #330 vs paper #497 167 places worse
0.7440 ±0.0600
best reported
actual #330 vs paper #497 167 places worse
paper 0.6043 ±0.0510
paper 0.6043 ±0.0510 Δ at pub 0.1397
390
DeepGCNs
0.7027 ±0.0710
This paper
415
Geom-GCN
actual #415 vs paper #415
0.6760
best reported
actual #415 vs paper #415
paper 0.6757
paper 0.6757 Δ at pub 0.0003
#ModelAccuracy ↑Paper
1
P^2GNN
0.9541 ±0.0272
2
ACM-GCN
0.9480 ±0.0380
3
RF-GCN
0.9429
15
GGCN
actual #15 vs paper #79 64 places worse
0.9230 ±0.0367
best reported
actual #15 vs paper #79 64 places worse
paper 0.8568 ±0.0660

Difference within reported uncertainty; not counted as underperformance.

paper 0.8568 ±0.0660 Δ today 0.0662
21
APPNP
actual #21 vs paper #216 195 places worse
0.9181 ±0.0196
best reported
actual #21 vs paper #216 195 places worse
paper 0.7702 ±0.0700
paper 0.7702 ±0.0700 Δ at pub 0.1450 Δ today 0.1479
22
GPRGNN
actual #22 vs paper #177 155 places worse
0.9157 ±0.0196
best reported
actual #22 vs paper #177 155 places worse
paper 0.8027 ±0.0810

Difference within reported uncertainty; not counted as underperformance.

paper 0.8027 ±0.0810 Δ at pub 0.0351 Δ today 0.1130
24
MLP
actual #24 vs paper #158 134 places worse
0.9136 ±0.0070
best reported
actual #24 vs paper #158 134 places worse
paper 0.8189 ±0.0640

Difference within reported uncertainty; not counted as underperformance.

paper 0.8189 ±0.0640 Δ at pub 0.0297 Δ today 0.0947
35
GCNII
actual #35 vs paper #203 168 places worse
0.8918 ±0.0396
best reported
actual #35 vs paper #203 168 places worse
paper 0.7786 ±0.0380
paper 0.7786 ±0.0380 Δ at pub 0.0640 Δ today 0.1132
38
FAGCN
actual #38 vs paper #222 184 places worse
0.8852 ±0.0133
best reported
actual #38 vs paper #222 184 places worse
paper 0.7612 ±0.0770
paper 0.7612 ±0.0770 Δ at pub 0.0496 Δ today 0.1240
68
H2GCN
actual #68 vs paper #136 68 places worse
0.8623 ±0.0471
best reported
actual #68 vs paper #136 68 places worse
paper 0.8270 ±0.0530
best at pub: Graph-Coupled Oscillator Networks (ICML 2022)

Difference within reported uncertainty; not counted as underperformance.

paper 0.8270 ±0.0530 Δ today 0.0353
76
Conn-NSD
0.8595 ±0.0770
This paper
74
GloGNN
actual #74 vs paper #74
0.8595 ±0.0510
actual #74 vs paper #74
paper 0.8595 ±0.0510

Improvement within reported uncertainty; not highlighted.

paper 0.8595 ±0.0510 Δ at pub 0.0244
105
UDGNN_GCN
0.8432 ±0.0730
This paper
111
GPNet
0.8410 ±0.0010
This paper
123
LINKX
actual #123 vs paper #203 80 places worse
0.8346 ±0.0061
best reported
actual #123 vs paper #203 80 places worse
paper 0.7784 ±0.0580

Difference within reported uncertainty; not counted as underperformance.

paper 0.7784 ±0.0580 Δ today 0.0562
138
SAGE
0.8269
158
GAT
actual #158 vs paper #358 200 places worse
0.8190 ±0.0540
best reported
actual #158 vs paper #358 200 places worse
paper 0.6189 ±0.0510
paper 0.6189 ±0.0510 Δ at pub 0.2001
170
GCN
actual #170 vs paper #372 202 places worse
0.8082 ±0.0360
best reported
actual #170 vs paper #372 202 places worse
paper 0.6054 ±0.0530
paper 0.6054 ±0.0530 Δ at pub 0.1866 Δ today 0.2028
183
MixHop
actual #183 vs paper #249 66 places worse
0.7950 ±0.0630
best reported
actual #183 vs paper #249 66 places worse
paper 0.7351 ±0.0630

Difference within reported uncertainty; not counted as underperformance.

paper 0.7351 ±0.0630 Δ at pub 0.0599
252
SGC
actual #252 vs paper #392 140 places worse
0.7350 ±0.0430
best reported
actual #252 vs paper #392 140 places worse
paper 0.5868 ±0.0380
paper 0.5868 ±0.0380 Δ at pub 0.1482
296
DeepGCNs
0.6838 ±0.0590
This paper
342
Geom-GCN
actual #342 vs paper #369 27 places worse
0.6412
best reported
actual #342 vs paper #369 27 places worse
paper 0.6081
#ModelAccuracy ↑Paper
1
Hetero-S (GAT 8-layer)
0.8693
2
Dir-GNN+CNA
0.8586 ±0.0180
3
GAT
actual #3 vs paper #134 131 places worse
0.8560
best reported
actual #3 vs paper #134 131 places worse
paper 0.6026 ±0.0250
23
GPNet
0.7861 ±0.0020
This paper
29
UDGNN_GCN
0.7453 ±0.0120
This paper
45
GloGNN
actual #45 vs paper #45
0.7133 ±0.0242
best reported
actual #45 vs paper #45
paper 0.7121 ±0.0180

Difference within reported uncertainty; not counted as underperformance.

paper 0.7121 ±0.0180 Δ today 0.0012
48
GGCN
0.7114 ±0.0180
This paper
52
GCN
actual #52 vs paper #95 43 places worse
0.7033
best reported
actual #52 vs paper #95 43 places worse
paper 0.6482 ±0.0220
paper 0.6482 ±0.0220 Δ at pub 0.0278 Δ today 0.0551
64
LINKX
0.6842 ±0.0140
This paper
72
GPRGNN
actual #72 vs paper #215 143 places worse
0.6748 ±0.0040
best reported
actual #72 vs paper #215 143 places worse
paper 0.4658 ±0.0170
paper 0.4658 ±0.0170 Δ at pub 0.1989 Δ today 0.2090
76
SGC
actual #76 vs paper #269 193 places worse
0.6710 ±0.0290
best reported
actual #76 vs paper #269 193 places worse
paper 0.3370 ±0.0350
paper 0.3370 ±0.0350 Δ at pub 0.3340
79
APPNP
actual #79 vs paper #212 133 places worse
0.6670 ±0.0270
best reported
actual #79 vs paper #212 133 places worse
paper 0.4750 ±0.0180
paper 0.4750 ±0.0180 Δ at pub 0.1920
92
Conn-NSD
0.6521 ±0.0200
This paper
103
GCNII
actual #103 vs paper #103
0.6386 ±0.0300
actual #103 vs paper #103
paper 0.6386 ±0.0300

Improvement within reported uncertainty; not highlighted.

paper 0.6386 ±0.0300 Δ at pub 0.0138
107
FAGCN
actual #107 vs paper #157 50 places worse
0.6344 ±0.0205
best reported
actual #107 vs paper #157 50 places worse
paper 0.5631 ±0.0320
paper 0.5631 ±0.0320 Δ at pub 0.0539 Δ today 0.0713
108
SAGE
0.6340 ±0.0300
124
Geom-GCN
0.6090
This paper
129
MixHop
0.6050 ±0.0250
This paper
133
H2GCN
actual #133 vs paper #136 3 places worse
0.6030 ±0.0231
best reported
actual #133 vs paper #136 3 places worse
paper 0.6011 ±0.0220

Difference within reported uncertainty; not counted as underperformance.

paper 0.6011 ±0.0220 Δ at pub 0.0019
169
MLP
actual #169 vs paper #217 48 places worse
0.5429
best reported
actual #169 vs paper #217 48 places worse
paper 0.4621 ±0.0300
paper 0.4621 ±0.0300 Δ at pub 0.0199 Δ today 0.0808
205
DeepGCNs
0.4875 ±0.0260
This paper
#ModelAccuracy ↑Paper
1
IBG-NN
0.7763 ±0.0179
2
Dir-GNN+CNA
0.7747 ±0.0128
3
DHGNN
0.7684 ±0.0161
18
GPNet
0.7157 ±0.0010
This paper
19
GloGNN
actual #19 vs paper #55 36 places worse
0.7121 ±0.0184
best reported
actual #19 vs paper #55 36 places worse
paper 0.5788 ±0.0180
paper 0.5788 ±0.0180 Δ today 0.1333
24
UDGNN_GCN
0.6813 ±0.0260
This paper
39
H2GCN
actual #39 vs paper #202 163 places worse
0.6190 ±0.0140
best reported
actual #39 vs paper #202 163 places worse
paper 0.3648 ±0.0190
paper 0.3648 ±0.0190 Δ at pub 0.0427 Δ today 0.2542
40
LINKX
0.6181 ±0.0180
This paper
46
GCN
actual #46 vs paper #77 31 places worse
0.6067
best reported
actual #46 vs paper #77 31 places worse
paper 0.5343 ±0.0200
paper 0.5343 ±0.0200 Δ at pub 0.0227 Δ today 0.0724
67
GAT
actual #67 vs paper #157 90 places worse
0.5630 ±0.0220
best reported
actual #67 vs paper #157 90 places worse
paper 0.4072 ±0.0160
paper 0.4072 ±0.0160 Δ at pub 0.1558
68
APPNP
actual #68 vs paper #229 161 places worse
0.5590 ±0.0290
best reported
actual #68 vs paper #229 161 places worse
paper 0.3351 ±0.0200
paper 0.3351 ±0.0200 Δ at pub 0.2239
69
GGCN
actual #69 vs paper #71 2 places worse
0.5567 ±0.0187
best reported
actual #69 vs paper #71 2 places worse
paper 0.5517 ±0.0160

Difference within reported uncertainty; not counted as underperformance.

paper 0.5517 ±0.0160 Δ today 0.0050
76
GPRGNN
actual #76 vs paper #235 159 places worse
0.5435 ±0.0087
best reported
actual #76 vs paper #235 159 places worse
paper 0.3161 ±0.0120
paper 0.3161 ±0.0120 Δ at pub 0.1742 Δ today 0.2274
81
SGC
actual #81 vs paper #102 21 places worse
0.5230 ±0.0230
best reported
actual #81 vs paper #102 21 places worse
paper 0.4690 ±0.0170
paper 0.4690 ±0.0170 Δ at pub 0.0540
117
Conn-NSD
0.4519 ±0.0160
This paper
120
SAGE
0.4460 ±0.0130
127
MixHop
0.4380 ±0.0150
This paper
139
FAGCN
actual #139 vs paper #141 2 places worse
0.4243 ±0.0210
actual #139 vs paper #141 2 places worse
paper 0.4243 ±0.0210

Improvement within reported uncertainty; not highlighted.

paper 0.4243 ±0.0210 Δ at pub 0.0273
172
MLP
actual #172 vs paper #243 71 places worse
0.3930 ±0.0079
best reported
actual #172 vs paper #243 71 places worse
paper 0.2877 ±0.0160
paper 0.2877 ±0.0160 Δ at pub 0.0458 Δ today 0.1053
176
GCNII
actual #176 vs paper #178 2 places worse
0.3847 ±0.0160
actual #176 vs paper #178 2 places worse
paper 0.3847 ±0.0160
paper 0.3847 ±0.0160 Δ at pub 0.0627
179
Geom-GCN
actual #179 vs paper #181 2 places worse
0.3832 ±0.0092
best reported
actual #179 vs paper #181 2 places worse
paper 0.3814

Difference within reported uncertainty; not counted as underperformance.

paper 0.3814 Δ today 0.0018
238
DeepGCNs
0.3123 ±0.0140
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 Best today — OK at publication; today's leaderboard best is elsewhere