TMLR 2024

SCNode: Spatial and Contextual Coordinates for Graph Representation Learning

Md Joshem Uddin, Astrit Tola, Varin Sikand, C. Akcora, B. Coskunuzer

Main figure for SCNode: Spatial and Contextual Coordinates for Graph Representation Learning

Abstract

Effective node representation lies at the heart of Graph Neural Networks (GNNs), as it directly impacts their ability to perform downstream tasks such as node classification and link prediction. Most existing GNNs, particularly message passing graph neural networks, rely on neighborhood aggregation to iteratively compute node embeddings. While powerful, this paradigm suffers from well-known limitations of oversquashing, oversmoothing, and underreaching that degrade representation quality. More critically, MPGNNs often assume homophily, where connected nodes share similar features or labels, leading to poor generalization in heterophilic graphs where this assumption breaks down. To address these challenges, we propose SCNode, a Spatial-Contextual Node Embedding framework designed to perform consistently well in both homophilic and heterophilic settings. SCNode integrates spatial and contextual information, yielding node embeddings that are not only more discriminative but also structurally aware. Our approach introduces new homophily matrices for understanding class interactions and tendencies. Extensive experiments on benchmark datasets show that SCNode achieves superior performance over conventional GNN models, demonstrating its robustness and adaptability in diverse graph structures.

Proposed method: SCNode

Benchmark Results

Tested on 11 datasets 18 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
58
SCNode
0.8865 ±0.0125
This paper
724
MLP
0.7768

OGB

#ModelAccuracy ↑Paper
1
GIANT-XRT
0.7612 ±0.0016
2
GEGCN
0.7576 ±0.0064
3
AGDN
0.7522 ±0.0007
8
RevGAT
0.7426
This paper
11
UniMP-v2
0.7392
This paper
14
LEGNN
0.7371
This paper
23
GCN
0.7300 ±0.0017
33
DeepGCN
0.7232
This paper
58
SCNode
0.7156
This paper
61
GSAGE
0.7149
This paper
66
S3GCL
0.7136
This paper
107
MLP
0.5765 ±0.0012
#ModelAccuracy ↑Paper
1
LMSPS+LP+MS
0.5784 ±0.0022
2
SeHGNN+emb+ms
0.5719 ±0.0012
3
SeHGNN+ms
0.5671 ±0.0014
10
LMSPS
0.5483
This paper
23
LEGNN
actual #23 vs paper #23
0.5378
actual #23 vs paper #23
paper 0.5378
33
R-HGNN
0.5204
This paper
42
HGT
actual #42 vs paper #45 3 places worse
0.5023 ±0.0048
best reported
actual #42 vs paper #45 3 places worse
paper 0.4921
43
SCNode
0.5003
This paper
47
GAT
actual #47 vs paper #64 17 places worse
0.4860 ±0.0029
best reported
actual #47 vs paper #64 17 places worse
paper 0.3767
48
RGCN
actual #48 vs paper #48
0.4811 ±0.0048
best reported
actual #48 vs paper #48
paper 0.4796

Difference within reported uncertainty; not counted as underperformance.

paper 0.4796 Δ at pub 0.0015
57
GraphSAGE
0.4646 ±0.0060
60
GCN
actual #60 vs paper #71 11 places worse
0.4290 ±0.0050
best reported
actual #60 vs paper #71 11 places worse
paper 0.3487
68
GSAGE
0.3704
This paper
76
MLP
0.3243

Heterophilic Graphs

#ModelAccuracy ↑Paper
1
P^2GNN
0.9672 ±0.0147
2
DoG
0.9660 ±0.0210
3
GPF-plus
0.9583 ±0.0419
10
SCNode
0.9459 ±0.0525
This paper
34
MLP
0.9230 ±0.0070
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 ±0.0723

Difference within reported uncertainty; not counted as underperformance.

paper 0.8486 ±0.0723 Δ at pub 0.0279 Δ today 0.0703
53
GraphSAGE
0.9000 ±0.0365
211
GAT
actual #211 vs paper #572 361 places worse
0.8162 ±0.0645
best reported
actual #211 vs paper #572 361 places worse
paper 0.5432 ±0.0630
paper 0.5432 ±0.0630 Δ at pub 0.2568 Δ today 0.2730
257
GCN
actual #257 vs paper #558 301 places worse
0.7933 ±0.0447
best reported
actual #257 vs paper #558 301 places worse
paper 0.5622 ±0.0581
best today: Graph Wave Networks (WWW 2025)
paper 0.5622 ±0.0581 Δ at pub 0.2218 Δ today 0.2311
415
Geom-GCN
actual #415 vs paper #425 10 places worse
0.6760
best reported
actual #415 vs paper #425 10 places worse
paper 0.6676 ±0.0272

Difference within reported uncertainty; not counted as underperformance.

paper 0.6676 ±0.0272 Δ at pub 0.0084
#ModelAccuracy ↑Paper
1
P^2GNN
0.9541 ±0.0272
2
ACM-GCN
0.9480 ±0.0380
3
RF-GCN
0.9429
24
MLP
0.9136 ±0.0070
43
SCNode
0.8809 ±0.0191
This paper
138
SAGE
0.8269
#ModelAccuracy ↑Paper
1
Hetero-S (GAT 8-layer)
0.8693
2
Dir-GNN+CNA
0.8586 ±0.0180
3
GAT
actual #3 vs paper #260 257 places worse
0.8560
best reported
actual #3 vs paper #260 257 places worse
paper 0.3879 ±0.0307
paper 0.3879 ±0.0307 Δ at pub 0.4681
4
SCNode
0.8408 ±0.0155
This paper
25
FSGNN
actual #25 vs paper #268 243 places worse
0.7827 ±0.0128
best reported
actual #25 vs paper #268 243 places worse
paper 0.3560 ±0.0297
paper 0.3560 ±0.0297 Δ today 0.4267
45
GloGNN
actual #45 vs paper #282 237 places worse
0.7133 ±0.0242
best reported
actual #45 vs paper #282 237 places worse
paper 0.2590 ±0.0182
paper 0.2590 ±0.0182 Δ at pub 0.4531 Δ today 0.4543
52
GCN
0.7033
72
GPRGNN
actual #72 vs paper #254 182 places worse
0.6748 ±0.0040
best reported
actual #72 vs paper #254 182 places worse
paper 0.3993 ±0.0330
paper 0.3993 ±0.0330 Δ at pub 0.2735 Δ today 0.2755
133
H2GCN
actual #133 vs paper #279 146 places worse
0.6030 ±0.0231
best reported
actual #133 vs paper #279 146 places worse
paper 0.2675 ±0.0364
paper 0.2675 ±0.0364 Δ at pub 0.3355
138
Polynormer
actual #138 vs paper #246 108 places worse
0.6000 ±0.0180
best reported
actual #138 vs paper #246 108 places worse
paper 0.4182 ±0.0345
paper 0.4182 ±0.0345 Δ today 0.1818
159
GraphGPS
actual #159 vs paper #249 90 places worse
0.5620 ±0.0380
best reported
actual #159 vs paper #249 90 places worse
paper 0.4104 ±0.0111
paper 0.4104 ±0.0111 Δ today 0.1516
169
MLP
0.5429
188
SGFormer
actual #188 vs paper #242 54 places worse
0.5140 ±0.0170
best reported
actual #188 vs paper #242 54 places worse
paper 0.4254 ±0.0358
paper 0.4254 ±0.0358 Δ today 0.0886
249
LRGNN
0.4124 ±0.0295
This paper
267
NodeFormer
actual #267 vs paper #268 1 place worse
0.3638 ±0.0385
best reported
actual #267 vs paper #268 1 place worse
paper 0.3478 ±0.0414

Difference within reported uncertainty; not counted as underperformance.

paper 0.3478 ±0.0414 Δ today 0.0160
270
CPGNN
0.3300 ±0.0315
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
11
FSGNN
actual #11 vs paper #205 194 places worse
0.7416
best reported
actual #11 vs paper #205 194 places worse
paper 0.3592 ±0.0132
paper 0.3592 ±0.0132 Δ at pub 0.3824
19
GloGNN
actual #19 vs paper #217 198 places worse
0.7121 ±0.0184
best reported
actual #19 vs paper #217 198 places worse
paper 0.3511 ±0.0124
paper 0.3511 ±0.0124 Δ at pub 0.2277 Δ today 0.3610
39
H2GCN
actual #39 vs paper #217 178 places worse
0.6190 ±0.0140
best reported
actual #39 vs paper #217 178 places worse
paper 0.3510 ±0.0115
46
GCN
actual #46 vs paper #226 180 places worse
0.6067
best reported
actual #46 vs paper #226 180 places worse
paper 0.3450 ±0.0161
paper 0.3450 ±0.0161 Δ at pub 0.2617
61
GraphGPS
actual #61 vs paper #213 152 places worse
0.5690 ±0.0300
best reported
actual #61 vs paper #213 152 places worse
paper 0.3549 ±0.0200
paper 0.3549 ±0.0200 Δ today 0.2141
67
GAT
actual #67 vs paper #227 160 places worse
0.5630 ±0.0220
best reported
actual #67 vs paper #227 160 places worse
paper 0.3441 ±0.0096
paper 0.3441 ±0.0096 Δ at pub 0.2189
111
SCNode
0.4585 ±0.0236
This paper
120
SAGE
0.4460 ±0.0130
138
SGFormer
actual #138 vs paper #208 70 places worse
0.4265 ±0.0241
best reported
actual #138 vs paper #208 70 places worse
paper 0.3581 ±0.0202
170
LRGNN
0.3951 ±0.0212
This paper
172
MLP
0.3930 ±0.0079
175
NodeFormer
actual #175 vs paper #178 3 places worse
0.3889 ±0.0267
best reported
actual #175 vs paper #178 3 places worse
paper 0.3852 ±0.0157

Difference within reported uncertainty; not counted as underperformance.

paper 0.3852 ±0.0157 Δ today 0.0037
241
CPGNN
0.3004 ±0.0203
This paper

Heterophily Benchmark

#ModelROC-AUC ↑Paper
1
Polynormer-r
0.8591 ±0.0074
2
DC-GNN
0.8588 ±0.0081
3
TANGO-GPS
0.8566 ±0.0101
28
GAT
actual #28 vs paper #168 140 places worse
0.8443 ±0.0100
best reported
actual #28 vs paper #168 140 places worse
paper 0.4498 ±0.0196
paper 0.4498 ±0.0196 Δ at pub 0.3945
50
GCN
0.8364 ±0.0067
59
SGFormer
0.8333 ±0.0068
This paper
96
SCNode
0.7999 ±0.0041
This paper
139
MLP
0.7362 ±0.0020
#ModelROC-AUC ↑Paper
1
NID_GAT
0.9703 ±0.0002
2
NID_GCN
0.9685 ±0.0010
3
UniGAP
0.8421 ±0.0080
16
GCN
actual #16 vs paper #131 115 places worse
0.7902 ±0.0060
best reported
actual #16 vs paper #131 115 places worse
paper 0.6304 ±0.0161
26
GAT
actual #26 vs paper #85 59 places worse
0.7835 ±0.0116
best reported
actual #26 vs paper #85 59 places worse
paper 0.7342 ±0.0163
paper 0.7342 ±0.0163 Δ at pub 0.0493
46
GraphSAGE
0.7721 ±0.0130
53
SGFormer
actual #53 vs paper #88 35 places worse
0.7681 ±0.0009
best reported
actual #53 vs paper #88 35 places worse
paper 0.7305 ±0.0116
paper 0.7305 ±0.0116 Δ today 0.0376
63
SCNode
0.7604 ±0.0162
This paper
73
GraphGPS
actual #73 vs paper #88 15 places worse
0.7215 ±0.0116
actual #73 vs paper #88 15 places worse
paper 0.7215 ±0.0116

Improvement within reported uncertainty; not highlighted.

paper 0.7215 ±0.0116 Δ at pub 0.0042 Δ today 0.0333
82
NodeFormer
0.7427 ±0.0114
This paper
96
MLP
0.7082 ±0.0010
121
LRGNN
0.6641 ±0.0175
This paper

Other Graph Benchmarks

#ModelAccuracy ↑Paper
1
MA-GCL
0.8883 ±0.0030
2
CCA-SSG
0.8842 ±0.0030
3
ARIEL
0.8827 ±0.0020
9
GAT
actual #9 vs paper #32 23 places worse
0.8693 ±0.0030
best reported
actual #9 vs paper #32 23 places worse
paper 0.4925 ±0.0073
paper 0.4925 ±0.0073 Δ at pub 0.3768
10
GCN
actual #10 vs paper #35 25 places worse
0.8651 ±0.0050
best reported
actual #10 vs paper #35 25 places worse
paper 0.4794 ±0.0062
paper 0.4794 ±0.0062 Δ at pub 0.3857
22
SGFormer
actual #22 vs paper #34 12 places worse
0.7422 ±0.0036
best reported
actual #22 vs paper #34 12 places worse
paper 0.4818 ±0.0071
paper 0.4818 ±0.0071 Δ at pub 0.2604
24
NodeFormer
actual #24 vs paper #51 27 places worse
0.7156 ±0.0042
best reported
actual #24 vs paper #51 27 places worse
paper 0.4386 ±0.0035
paper 0.4386 ±0.0035 Δ at pub 0.2770
27
Polynormer
0.5481 ±0.0049
This paper
28
FSGNN
0.5274 ±0.0083
This paper
29
SCNode
0.5257 ±0.0042
This paper
33
GIN
0.4916 ±0.0102
47
GraphGPS
0.4494 ±0.0077
This paper
48
GPRGNN
0.4488 ±0.0082
This paper
59
LRGNN
0.4223 ±0.0485
This paper
61
H2GCN
actual #61 vs paper #65 4 places worse
0.4071
best reported
actual #61 vs paper #65 4 places worse
paper 0.3647 ±0.0023
64
CPGNN
0.3979 ±0.0077
This paper
65
GloGNN
0.3689 ±0.0014
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