Scale-aware Message Passing For Graph Node Classification

Qin Jiang, Chengjia Wang, Michael Lones, Wei Pang

Main figure for Scale-aware Message Passing For Graph Node Classification

Abstract

Most Graph Neural Networks (GNNs) operate at the first-order scale, even though multi-scale representations are known to be crucial in domains such as image classification. In this work, we investigate whether GNNs can similarly benefit from multi-scale learning, rather than being limited to a fixed depth of $k$-hop aggregation. We begin by formalizing scale invariance in graph learning, providing theoretical guarantees and empirical evidence for its effectiveness. Building on this principle, we introduce ScaleNet, a scale-aware message-passing architecture that combines directed multi-scale feature aggregation with an adaptive self-loop mechanism. ScaleNet achieves state-of-the-art performance on six benchmark datasets, covering both homophilic and heterophilic graphs. To handle scalability, we further propose LargeScaleNet, which extends multi-scale learning to large graphs and sets new state-of-the-art results on three large-scale benchmarks. We also show that FaberNet’s strength largely arises from multi-scale feature integration. Together with these state-of-the-art results, our findings suggest that scale invariance may serve as a valuable principle for improving the performance of single-order GNNs. The code for all experiments is available at this link.

Benchmark Results

Tested on 6 datasets 19 baseline values reported too low

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

Classic

#ModelAccuracy ↑Paper
1
GCN
actual #1 vs paper #146 145 places worse
0.9302 ±0.0011
best reported
actual #1 vs paper #146 145 places worse
paper 0.7880 ±0.0040
paper 0.7880 ±0.0040 Δ at pub 0.1422
2
RSE + RGCN (70b)
0.8852 ±0.0019
3
LEMP+T
0.8825
9
SAGE
actual #9 vs paper #118 109 places worse
0.8771
best reported
actual #9 vs paper #118 109 places worse
paper 0.7930 ±0.0040
12
APPNP
actual #12 vs paper #188 176 places worse
0.8754
best reported
actual #12 vs paper #188 176 places worse
paper 0.7760 ±0.0060
54
GIN
0.8303 ±0.0021
57
SGFormer
actual #57 vs paper #243 186 places worse
0.8271 ±0.0056
best reported
actual #57 vs paper #243 186 places worse
paper 0.7370 ±0.0050
paper 0.7370 ±0.0050 Δ at pub 0.0901
90
Polynormer
actual #90 vs paper #183 93 places worse
0.8026 ±0.0092
best reported
actual #90 vs paper #183 93 places worse
paper 0.7780 ±0.0060
109
ScaleNet
0.7960 ±0.0070
This paper
110
MagNet
actual #110 vs paper #236 126 places worse
0.7959 ±0.0039
best reported
actual #110 vs paper #236 126 places worse
paper 0.7470 ±0.0060
120
GraphGPS
actual #120 vs paper #224 104 places worse
0.7926 ±0.0057
best reported
actual #120 vs paper #224 104 places worse
paper 0.7550 ±0.0050
paper 0.7550 ±0.0050 Δ at pub 0.0376
127
1iGi2
0.7920 ±0.0050
This paper
137
LargeScaleNet
0.7900 ±0.0050
This paper
167
DiGib
0.7830 ±0.0070
This paper
195
1iG
0.7740 ±0.0060
This paper
202
Dir-GNN
0.7720 ±0.0080
This paper
207
DiG
0.7710 ±0.0100
This paper
210
ChebNet
0.7690 ±0.0090
This paper
223
1iGu2
0.7560 ±0.0090
This paper
227
1ym
0.7540 ±0.0040
This paper
237
MLP
actual #237 vs paper #245 8 places worse
0.7340 ±0.0060
actual #237 vs paper #245 8 places worse
paper 0.7340 ±0.0060

Improvement within reported uncertainty; not highlighted.

paper 0.7340 ±0.0060 Δ at pub 0.0068
262
SigMaNet
0.7140 ±0.0070
This paper
312
QuaNet
0.5520 ±0.0190
This paper

Heterophilic Graphs

#ModelAccuracy ↑Paper
1
Hetero-S (GAT 8-layer)
0.8693
2
Dir-GNN+CNA
0.8586 ±0.0180
3
GAT
0.8560
7
Dir-GNN
actual #7 vs paper #15 8 places worse
0.8048 ±0.0146
best reported
actual #7 vs paper #15 8 places worse
paper 0.7970 ±0.0130

Difference within reported uncertainty; not counted as underperformance.

paper 0.7970 ±0.0130 Δ today 0.0078
11
ScaleNet
0.8010 ±0.0150
This paper
13
LargeScaleNet
0.7990 ±0.0160
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 0.6480 ±0.0220
paper 0.6480 ±0.0220 Δ at pub 0.0553
53
1iG
0.7020 ±0.0160
This paper
79
APPNP
actual #79 vs paper #260 181 places worse
0.6670 ±0.0270
best reported
actual #79 vs paper #260 181 places worse
paper 0.3870 ±0.0240
paper 0.3870 ±0.0240 Δ at pub 0.2800
108
SAGE
0.6340 ±0.0300
This paper
115
GraphSAGE
0.6215 ±0.0042
132
1iGu2
0.6040 ±0.0240
This paper
138
Polynormer
actual #138 vs paper #138
0.6000 ±0.0180
actual #138 vs paper #138
paper 0.6000 ±0.0180
paper 0.6000 ±0.0180 Δ at pub 0.1818
140
ChebNet
actual #140 vs paper #147 7 places worse
0.5928 ±0.0125
best reported
actual #140 vs paper #147 7 places worse
paper 0.5830 ±0.0240

Difference within reported uncertainty; not counted as underperformance.

paper 0.5830 ±0.0240 Δ at pub 0.0098
146
1iGi2
0.5840 ±0.0250
This paper
147
MagNet
actual #147 vs paper #147
0.5820 ±0.0290
actual #147 vs paper #147
paper 0.5820 ±0.0290
150
Sym
0.5780 ±0.0300
This paper
159
GraphGPS
actual #159 vs paper #159
0.5620 ±0.0380
actual #159 vs paper #159
paper 0.5620 ±0.0380
paper 0.5620 ±0.0380 Δ at pub 0.1516
166
1ym
0.5490 ±0.0270
This paper
169
MLP
actual #169 vs paper #253 84 places worse
0.5429
best reported
actual #169 vs paper #253 84 places worse
paper 0.4030 ±0.0580
paper 0.4030 ±0.0580 Δ at pub 0.1399
180
DiGib
0.5220 ±0.0370
This paper
188
SGFormer
actual #188 vs paper #188
0.5140 ±0.0170
actual #188 vs paper #188
paper 0.5140 ±0.0170
paper 0.5140 ±0.0170 Δ at pub 0.0886
193
DiG
0.5040 ±0.0210
This paper
260
QuaNet
0.3880 ±0.0290
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
5
ScaleNet
0.7600 ±0.0200
This paper
6
LargeScaleNet
0.7590 ±0.0200
This paper
7
Dir-GNN
0.7560 ±0.0190
This paper
46
GCN
actual #46 vs paper #107 61 places worse
0.6067
best reported
actual #46 vs paper #107 61 places worse
paper 0.4630 ±0.0190
paper 0.4630 ±0.0190 Δ at pub 0.1437
61
GraphGPS
actual #61 vs paper #61
0.5690 ±0.0300
actual #61 vs paper #61
paper 0.5690 ±0.0300
paper 0.5690 ±0.0300 Δ at pub 0.2141
68
APPNP
actual #68 vs paper #254 186 places worse
0.5590 ±0.0290
best reported
actual #68 vs paper #254 186 places worse
paper 0.2700 ±0.0150
paper 0.2700 ±0.0150 Δ at pub 0.2890
87
1iG
0.5070 ±0.0580
This paper
120
SAGE
0.4460 ±0.0130
This paper
125
ChebNet
actual #125 vs paper #178 53 places worse
0.4386 ±0.0164
best reported
actual #125 vs paper #178 53 places worse
paper 0.3850 ±0.0140
paper 0.3850 ±0.0140 Δ at pub 0.0536
128
GraphSAGE
0.4378 ±0.0190
136
MagNet
actual #136 vs paper #173 37 places worse
0.4270 ±0.0150
best reported
actual #136 vs paper #173 37 places worse
paper 0.3900 ±0.0190
137
1iGi2
0.4270 ±0.0250
This paper
138
SGFormer
actual #138 vs paper #212 74 places worse
0.4265 ±0.0241
best reported
actual #138 vs paper #212 74 places worse
paper 0.3550 ±0.0170
146
Polynormer
actual #146 vs paper #178 32 places worse
0.4197 ±0.0214
best reported
actual #146 vs paper #178 32 places worse
paper 0.3850 ±0.0140
161
1iGu2
0.4040 ±0.0180
This paper
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 0.2870 ±0.0400
paper 0.2870 ±0.0400 Δ at pub 0.0793 Δ today 0.1060
173
DiG
0.3920 ±0.0180
This paper
183
Sym
0.3810 ±0.0140
This paper
190
DiGib
0.3770 ±0.0150
This paper
213
1ym
0.3550 ±0.0110
This paper

Heterophily Benchmark

#ModelAccuracy ↑Paper
1
Dir-Poly
0.9451 ±0.0022
2
D-CDE
0.9387 ±0.0041
3
LargeScaleNet
0.9358 ±0.0024
This paper
7
Polynormer
actual #7 vs paper #28 21 places worse
0.9266 ±0.0060
best reported
actual #7 vs paper #28 21 places worse
paper 0.9032 ±0.0036
9
FaberNet
actual #9 vs paper #9
0.9232 ±0.0030
actual #9 vs paper #9
paper 0.9232 ±0.0030

Improvement within reported uncertainty; not highlighted.

paper 0.9232 ±0.0030 Δ at pub 0.0008
22
DirGNN
0.9130 ±0.0046
This paper
26
GraphSAGE
0.9106 ±0.0027
47
MagNet
0.8807 ±0.0027
This paper
77
GCN
actual #77 vs paper #113 36 places worse
0.8272 ±0.0082
best reported
actual #77 vs paper #113 36 places worse
paper 0.7369 ±0.0074
paper 0.7369 ±0.0074 Δ at pub 0.0903
78
GraphGPS
actual #78 vs paper #78
0.8272 ±0.0068
actual #78 vs paper #78
paper 0.8272 ±0.0068

Improvement within reported uncertainty; not highlighted.

paper 0.8272 ±0.0068 Δ at pub 0.0072
92
FSGNN
0.7992 ±0.0056
This paper
135
MLP
actual #135 vs paper #144 9 places worse
0.6665 ±0.0047
best reported
actual #135 vs paper #144 9 places worse
paper 0.6494 ±0.0062
paper 0.6494 ±0.0062 Δ at pub 0.0171
144
SGphormer
0.6507 ±0.0051
This paper
184
DiGCN
0.5271 ±0.0032
This paper

LINKX Benchmarks

#ModelAccuracy ↑Paper
1
LargeScaleNet
0.6582 ±0.0036
This paper
2
S² DirGCN
0.6495 ±0.0033
3
FaberNet
0.6462 ±0.0101
This paper
5
DirGNN
0.6397 ±0.0030
This paper
9
MagNet
0.6029 ±0.0027
This paper
18
Polynormer
0.5250 ±0.0077
This paper
20
FSGNN
0.5047 ±0.0021
This paper
31
GCN
0.4602 ±0.0026
This paper
56
MLP
0.3670 ±0.0021
This paper
#ModelAccuracy ↑Paper
1
FaberNet
actual #1 vs paper #2 1 place worse
0.7510 ±0.0003
best reported
actual #1 vs paper #2 1 place worse
paper 0.7455 ±0.0011
paper 0.7455 ±0.0011 Δ at pub 0.0055
2
LargeScaleNet
0.7505 ±0.0005
This paper
3
DirGNN
0.7395 ±0.0005
This paper
9
FSGNN
0.6507 ±0.0003
This paper
16
GCN
actual #16 vs paper #16
0.5102 ±0.0006
actual #16 vs paper #16
paper 0.5102 ±0.0006
paper 0.5102 ±0.0006 Δ at pub 0.0532
32
MLP
actual #32 vs paper #32
0.3150
best reported
actual #32 vs paper #32
paper 0.3134 ±0.0005
paper 0.3134 ±0.0005 Δ at pub 0.0016
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