Breaking the Entanglement of Homophily and Heterophily in Semi-supervised Node Classification

Henan Sun, Xunkai Li, Zhengyu Wu, Daohan Su, Ronghua Li, Guoren Wang

Main figure for Breaking the Entanglement of Homophily and Heterophily in Semi-supervised Node Classification

Abstract

Recently, graph neural networks (GNNs) have shown prominent performance in semi-supervised node classification by leveraging knowledge from the graph database. However, most existing GNNs follow the homophily assumption, where connected nodes are more likely to exhibit similar feature distributions and the same labels, and such an assumption has proven to be vulnerable in a growing number of practical applications. As a supplement, heterophily reflects dissimilarity in connected nodes, which has gained significant attention in graph learning. To this end, data engineers aim to develop a powerful GNN model that can ensure performance under both homophily and heterophily. Despite numerous attempts, most existing GNNs struggle to achieve optimal node representations due to the constraints of undirected graphs. The neglect of directed edges results in sub-optimal graph representations, thereby hindering the capacity of GNNs. To address this issue, we introduce AMUD, which quantifies the relationship between node profiles and topology from a statistical perspective, offering valuable insights for daptively odeling the natural directed graphs as the ndirected or irected graph to maximize the benefits from subsequent graph learning. Furthermore, we propose daptive irected attern ggregation (ADPA) as a new directed graph learning paradigm for AMUD. Empirical studies have demonstrated that AMUD guides efficient graph learning. Meanwhile, extensive experiments on 16 benchmark datasets substantiate the impressive performance of ADPA, outperforming baselines by significant margins of 3.96\

Proposed method: AMUD

Benchmark Results

Tested on 4 datasets 30 baseline values 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
32
GPRGNN
actual #32 vs paper #781 749 places worse
0.8102 ±0.0071
best reported
actual #32 vs paper #781 749 places worse
paper 0.6470 ±0.0070
paper 0.6470 ±0.0070 Δ at pub 0.1387 Δ today 0.1632
36
GCNII
actual #36 vs paper #769 733 places worse
0.8076 ±0.0030
best reported
actual #36 vs paper #769 733 places worse
paper 0.6510 ±0.0040
paper 0.6510 ±0.0040 Δ at pub 0.1566
44
GCN
actual #44 vs paper #766 722 places worse
0.8033 ±0.0088
best reported
actual #44 vs paper #766 722 places worse
paper 0.6530 ±0.0050
paper 0.6530 ±0.0050 Δ at pub 0.1413 Δ today 0.1503
61
GraphSAGE
0.7923 ±0.0053
96
SGC
actual #96 vs paper #808 712 places worse
0.7765 ±0.0012
best reported
actual #96 vs paper #808 712 places worse
paper 0.6280 ±0.0030
102
GloGNN
actual #102 vs paper #800 698 places worse
0.7740 ±0.0170
best reported
actual #102 vs paper #800 698 places worse
paper 0.6350 ±0.0100
paper 0.6350 ±0.0100 Δ at pub 0.1390
122
GRAND
actual #122 vs paper #796 674 places worse
0.7657
best reported
actual #122 vs paper #796 674 places worse
paper 0.6380 ±0.0050
paper 0.6380 ±0.0050 Δ at pub 0.1277
312
LINKX
actual #312 vs paper #802 490 places worse
0.7319 ±0.0099
best reported
actual #312 vs paper #802 490 places worse
paper 0.6330 ±0.0040
350
MLP
0.7289 ±0.0010
375
DGCN
actual #375 vs paper #803 428 places worse
0.7260
best reported
actual #375 vs paper #803 428 places worse
paper 0.6320 ±0.0080
paper 0.6320 ±0.0080 Δ at pub 0.0940
507
DirGNN
actual #507 vs paper #788 281 places worse
0.7150 ±0.0088
best reported
actual #507 vs paper #788 281 places worse
paper 0.6420 ±0.0060
paper 0.6420 ±0.0060 Δ today 0.0730
656
MagNet
actual #656 vs paper #796 140 places worse
0.6890 ±0.0067
best reported
actual #656 vs paper #796 140 places worse
paper 0.6380 ±0.0040
paper 0.6380 ±0.0040 Δ today 0.0510
755
AMUD
0.6600 ±0.0040
This paper
773
NSTE
0.6490 ±0.0070
This paper
774
JacobiConv
0.6480 ±0.0090
This paper
775
DIMPA
0.6480 ±0.0090
This paper
776
A2DUG
0.6480 ±0.0080
This paper
783
DiGCN
0.6470 ±0.0060
This paper
785
BerNet
0.6450 ±0.0060
This paper
806
AERO-GNN
0.6300 ±0.0060
This paper

Heterophilic Graphs

#ModelAccuracy ↑Paper
1
P^2GNN
0.9541 ±0.0272
2
ACM-GCN
0.9480 ±0.0380
3
RF-GCN
0.9429
10
JacobiConv
actual #10 vs paper #186 176 places worse
0.9295 ±0.0246
best reported
actual #10 vs paper #186 176 places worse
paper 0.7900 ±0.0440
paper 0.7900 ±0.0440 Δ at pub 0.1395 Δ today 0.1395
22
GPRGNN
actual #22 vs paper #202 180 places worse
0.9157 ±0.0196
best reported
actual #22 vs paper #202 180 places worse
paper 0.7790 ±0.0310
paper 0.7790 ±0.0310 Δ at pub 0.1347 Δ today 0.1367
24
MLP
0.9136 ±0.0070
35
GCNII
actual #35 vs paper #369 334 places worse
0.8918 ±0.0396
best reported
actual #35 vs paper #369 334 places worse
paper 0.6090 ±0.0390
paper 0.6090 ±0.0390 Δ at pub 0.2336 Δ today 0.2828
74
GloGNN
actual #74 vs paper #182 108 places worse
0.8595 ±0.0510
best reported
actual #74 vs paper #182 108 places worse
paper 0.7960 ±0.0300

Difference within reported uncertainty; not counted as underperformance.

paper 0.7960 ±0.0300 Δ at pub 0.0635 Δ today 0.0635
98
AERO-GNN
actual #98 vs paper #175 77 places worse
0.8480 ±0.0330
best reported
actual #98 vs paper #175 77 places worse
paper 0.8040 ±0.0280

Difference within reported uncertainty; not counted as underperformance.

paper 0.8040 ±0.0280 Δ today 0.0440
106
MagNet
actual #106 vs paper #183 77 places worse
0.8430 ±0.0700
best reported
actual #106 vs paper #183 77 places worse
paper 0.7940 ±0.0350

Difference within reported uncertainty; not counted as underperformance.

paper 0.7940 ±0.0350 Δ today 0.0490
123
LINKX
actual #123 vs paper #216 93 places worse
0.8346 ±0.0061
best reported
actual #123 vs paper #216 93 places worse
paper 0.7680 ±0.0520

Difference within reported uncertainty; not counted as underperformance.

paper 0.7680 ±0.0520 Δ at pub 0.0104 Δ today 0.0666
136
AMUD
0.8290 ±0.0300
This paper
138
SAGE
0.8269
142
GRAND
actual #142 vs paper #396 254 places worse
0.8246 ±0.0709
best reported
actual #142 vs paper #396 254 places worse
paper 0.5840 ±0.0380
paper 0.5840 ±0.0380 Δ at pub 0.2380 Δ today 0.2406
170
GCN
actual #170 vs paper #375 205 places worse
0.8082 ±0.0360
best reported
actual #170 vs paper #375 205 places worse
paper 0.6030 ±0.0420
paper 0.6030 ±0.0420 Δ at pub 0.1890 Δ today 0.2052
173
A2DUG
0.8050 ±0.0430
This paper
180
DirGNN
0.8000 ±0.0360
This paper
185
DIMPA
0.7930 ±0.0310
This paper
190
NSTE
0.7860 ±0.0230
This paper
191
BerNet
0.7850 ±0.0230
This paper
203
DGCN
0.7790 ±0.0310
This paper
205
DiGCN
0.7780 ±0.0490
This paper
252
SGC
actual #252 vs paper #426 174 places worse
0.7350 ±0.0430
best reported
actual #252 vs paper #426 174 places worse
paper 0.5560 ±0.0100
paper 0.5560 ±0.0100 Δ at pub 0.1790
#ModelAccuracy ↑Paper
1
Hetero-S (GAT 8-layer)
0.8693
2
Dir-GNN+CNA
0.8586 ±0.0180
3
GAT
0.8560
15
DirGNN
actual #15 vs paper #227 212 places worse
0.7974 ±0.0140
best reported
actual #15 vs paper #227 212 places worse
paper 0.4460 ±0.0170
paper 0.4460 ±0.0170 Δ today 0.3514
31
JacobiConv
actual #31 vs paper #254 223 places worse
0.7420 ±0.0103
best reported
actual #31 vs paper #254 223 places worse
paper 0.4020 ±0.0240
paper 0.4020 ±0.0240 Δ at pub 0.3400
40
AERO-GNN
actual #40 vs paper #250 210 places worse
0.7158 ±0.0240
best reported
actual #40 vs paper #250 210 places worse
paper 0.4100 ±0.0290
paper 0.4100 ±0.0290 Δ today 0.3058
45
GloGNN
actual #45 vs paper #254 209 places worse
0.7133 ±0.0242
best reported
actual #45 vs paper #254 209 places worse
paper 0.4020 ±0.0260
paper 0.4020 ±0.0260 Δ at pub 0.3101 Δ today 0.3113
52
GCN
actual #52 vs paper #246 194 places worse
0.7033
best reported
actual #52 vs paper #246 194 places worse
paper 0.4190 ±0.0110
paper 0.4190 ±0.0110 Δ at pub 0.2606 Δ today 0.2843
64
LINKX
actual #64 vs paper #259 195 places worse
0.6842 ±0.0132
best reported
actual #64 vs paper #259 195 places worse
paper 0.3890 ±0.0230
paper 0.3890 ±0.0230 Δ at pub 0.2952 Δ today 0.2952
72
GPRGNN
actual #72 vs paper #248 176 places worse
0.6748 ±0.0040
best reported
actual #72 vs paper #248 176 places worse
paper 0.4130 ±0.0150
paper 0.4130 ±0.0150 Δ at pub 0.2598 Δ today 0.2618
76
SGC
actual #76 vs paper #264 188 places worse
0.6710 ±0.0290
best reported
actual #76 vs paper #264 188 places worse
paper 0.3690 ±0.0010
paper 0.3690 ±0.0010 Δ at pub 0.3020
103
GCNII
actual #103 vs paper #243 140 places worse
0.6386 ±0.0304
best reported
actual #103 vs paper #243 140 places worse
paper 0.4220 ±0.0090
paper 0.4220 ±0.0090 Δ at pub 0.2166 Δ today 0.2166
108
SAGE
0.6340 ±0.0300
147
MagNet
actual #147 vs paper #228 81 places worse
0.5832 ±0.0287
best reported
actual #147 vs paper #228 81 places worse
paper 0.4450 ±0.0110
paper 0.4450 ±0.0110 Δ today 0.1382
151
GRAND
actual #151 vs paper #251 100 places worse
0.5772 ±0.0186
best reported
actual #151 vs paper #251 100 places worse
paper 0.4070 ±0.0160
169
MLP
0.5429
218
AMUD
0.4620 ±0.0130
This paper
231
DIMPA
0.4380 ±0.0160
This paper
232
A2DUG
0.4380 ±0.0280
This paper
235
DiGCN
0.4340 ±0.0180
This paper
243
DGCN
0.4230 ±0.0230
This paper
244
NSTE
0.4220 ±0.0260
This paper
262
BerNet
0.3860 ±0.0180
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
9
DirGNN
actual #9 vs paper #140 131 places worse
0.7513 ±0.0195
best reported
actual #9 vs paper #140 131 places worse
paper 0.4250 ±0.0080
paper 0.4250 ±0.0080 Δ today 0.3263
19
GloGNN
actual #19 vs paper #151 132 places worse
0.7121 ±0.0184
best reported
actual #19 vs paper #151 132 places worse
paper 0.4130 ±0.0120
paper 0.4130 ±0.0120 Δ at pub 0.1658 Δ today 0.2991
40
LINKX
actual #40 vs paper #166 126 places worse
0.6181 ±0.0180
best reported
actual #40 vs paper #166 126 places worse
paper 0.3980 ±0.0120
paper 0.3980 ±0.0120 Δ at pub 0.2201 Δ today 0.2201
41
AERO-GNN
actual #41 vs paper #149 108 places worse
0.6176 ±0.0240
best reported
actual #41 vs paper #149 108 places worse
paper 0.4180 ±0.0110
paper 0.4180 ±0.0110 Δ today 0.1996
46
GCN
actual #46 vs paper #225 179 places worse
0.6067
best reported
actual #46 vs paper #225 179 places worse
paper 0.3460 ±0.0090
paper 0.3460 ±0.0090 Δ at pub 0.2110 Δ today 0.2607
60
JacobiConv
actual #60 vs paper #195 135 places worse
0.5738 ±0.0125
best reported
actual #60 vs paper #195 135 places worse
paper 0.3740 ±0.0090
paper 0.3740 ±0.0090 Δ at pub 0.1998 Δ today 0.1998
76
GPRGNN
actual #76 vs paper #197 121 places worse
0.5435 ±0.0087
best reported
actual #76 vs paper #197 121 places worse
paper 0.3700 ±0.0090
paper 0.3700 ±0.0090 Δ at pub 0.1315 Δ today 0.1735
81
SGC
actual #81 vs paper #182 101 places worse
0.5230 ±0.0230
best reported
actual #81 vs paper #182 101 places worse
paper 0.3810 ±0.0010
paper 0.3810 ±0.0010 Δ at pub 0.1420
116
AMUD
0.4520 ±0.0130
This paper
120
SAGE
0.4460 ±0.0130
134
A2DUG
0.4280 ±0.0110
This paper
136
MagNet
0.4270 ±0.0150
This paper
145
DiGCN
0.4200 ±0.0170
This paper
148
NSTE
0.4190 ±0.0090
This paper
153
DIMPA
0.4120 ±0.0100
This paper
158
DGCN
0.4060 ±0.0100
This paper
164
GRAND
actual #164 vs paper #231 67 places worse
0.4005 ±0.0150
best reported
actual #164 vs paper #231 67 places worse
paper 0.3310 ±0.0130
172
MLP
0.3930 ±0.0079
176
GCNII
actual #176 vs paper #228 52 places worse
0.3881 ±0.0197
best reported
actual #176 vs paper #228 52 places worse
paper 0.3420 ±0.0080
paper 0.3420 ±0.0080 Δ at pub 0.0427 Δ today 0.0461
188
BerNet
0.3790 ±0.0080
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 today — OK at publication; today's leaderboard best is elsewhere