ICLR 2021

Is Homophily a Necessity for Graph Neural Networks?

Yao Ma, Xiaorui Liu, Neil Shah, Jiliang Tang

Main figure for Is Homophily a Necessity for Graph Neural Networks?

Abstract

Graph neural networks (GNNs) have shown great prowess in learning representations suitable for numerous graph-based machine learning tasks. When applied to semi-supervised node classification, GNNs are widely believed to work well due to the homophily assumption (``like attracts like''), and fail to generalize to heterophilous graphs where dissimilar nodes connect. Recent works have designed new architectures to overcome such heterophily-related limitations. However, we empirically find that standard graph convolutional networks (GCNs) can actually achieve strong performance on some commonly used heterophilous graphs. This motivates us to reconsider whether homophily is truly necessary for good GNN performance. We find that this claim is not quite accurate, and certain types of ``good'' heterophily exist, under which GCNs can achieve strong performance. Our work carefully characterizes the implications of different heterophily conditions, and provides supporting theoretical understanding and empirical observations. Finally, we examine existing heterophilous graphs benchmarks and reconcile how the GCN (under)performs on them based on this understanding.

Benchmark Results

Tested on 4 datasets

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

Heterophilic Graphs

#ModelAccuracy ↑Paper
1
P^2GNN
0.9672 ±0.0147
2
DoG
0.9660 ±0.0210
3
GPF-plus
0.9583 ±0.0419
30
GPR-GNN
actual #30 vs paper #162 132 places worse
0.9291 ±0.0132
best reported
actual #30 vs paper #162 132 places worse
paper 0.8443 ±0.0410
paper 0.8443 ±0.0410 Δ today 0.0848
34
MLP
actual #34 vs paper #180 146 places worse
0.8330 ±0.0454
actual #34 vs paper #180 146 places worse
paper 0.8330 ±0.0454

Improvement within reported uncertainty; not highlighted.

paper 0.8330 ±0.0454 Δ at pub 0.0141 Δ today 0.0900
53
GraphSAGE
0.9000 ±0.0365
150
H2GCN-1
0.8486 ±0.0677
This paper
176
MLP + GCN
0.8360 ±0.0604
This paper
191
CPGNN-MLP
0.8262 ±0.0688
This paper
203
H2GCN-2
0.8216 ±0.0528
This paper
257
GCN
actual #257 vs paper #451 194 places worse
0.6381 ±0.0527
actual #257 vs paper #451 194 places worse
paper 0.6381 ±0.0527
best today: Graph Wave Networks (WWW 2025)

Improvement within reported uncertainty; not highlighted.

paper 0.6381 ±0.0527 Δ at pub 0.0271 Δ today 0.1552
289
CPGNN-Cheby
actual #289 vs paper #302 13 places worse
0.7703 ±0.0583
best reported
actual #289 vs paper #302 13 places worse
paper 0.7596 ±0.0566

Difference within reported uncertainty; not counted as underperformance.

paper 0.7596 ±0.0566 Δ today 0.0107
#ModelAccuracy ↑Paper
1
P^2GNN
0.9541 ±0.0272
2
ACM-GCN
0.9480 ±0.0380
3
RF-GCN
0.9429
11
GPR-GNN
actual #11 vs paper #185 174 places worse
0.9279 ±0.0312
best reported
actual #11 vs paper #185 174 places worse
paper 0.7927 ±0.0603
paper 0.7927 ±0.0603 Δ today 0.1352
24
MLP
actual #24 vs paper #92 68 places worse
0.8486 ±0.0604
actual #24 vs paper #92 68 places worse
paper 0.8486 ±0.0604

Improvement within reported uncertainty; not highlighted.

paper 0.8486 ±0.0604 Δ at pub 0.0326
97
MLP + GCN
0.8482 ±0.0487
This paper
138
SAGE
0.8269
153
H2GCN-1
0.8216 ±0.0600
This paper
154
H2GCN-2
0.8216 ±0.0600
This paper
170
GCN
actual #170 vs paper #383 213 places worse
0.5935 ±0.0419
actual #170 vs paper #383 213 places worse
paper 0.5935 ±0.0419

Improvement within reported uncertainty; not highlighted.

paper 0.5935 ±0.0419 Δ at pub 0.0232 Δ today 0.2147
182
CPGNN-MLP
0.7993 ±0.0612
This paper
233
CPGNN-Cheby
0.7508 ±0.0751
This paper
#ModelAccuracy ↑Paper
1
DiGGR
0.4535 ±0.0353
2
TRIGON
0.4402 ±0.0028
3
DoG
0.4320 ±0.0120
42
MLP
actual #42 vs paper #179 137 places worse
0.3617 ±0.0109
actual #42 vs paper #179 137 places worse
paper 0.3617 ±0.0109

Improvement within reported uncertainty; not highlighted.

paper 0.3617 ±0.0109 Δ at pub 0.0041 Δ today 0.0409
53
GPR-GNN
actual #53 vs paper #270 217 places worse
0.3992 ±0.0067
best reported
actual #53 vs paper #270 217 places worse
paper 0.3394 ±0.0095
paper 0.3394 ±0.0095 Δ today 0.0598
68
GraphSAGE
0.3899 ±0.0085
135
GCN
actual #135 vs paper #342 207 places worse
0.3690
best reported
actual #135 vs paper #342 207 places worse
paper 0.3031 ±0.0098
paper 0.3031 ±0.0098 Δ at pub 0.0659
175
MLP + GCN
0.3624 ±0.0109
This paper
190
H2GCN-1
actual #190 vs paper #192 2 places worse
0.3594 ±0.0130
best reported
actual #190 vs paper #192 2 places worse
paper 0.3586 ±0.0103

Difference within reported uncertainty; not counted as underperformance.

paper 0.3586 ±0.0103 Δ today 0.0008
196
CPGNN-MLP
0.3576 ±0.0092
This paper
204
H2GCN-2
0.3562 ±0.0130
This paper
258
CPGNN-Cheby
0.3428 ±0.0077
This paper
#ModelAccuracy ↑Paper
1
DMD++
0.9190 ±0.0260
2
F-GREAD-BS
0.9059 ±0.0380
3
APPNP
0.9010 ±0.0350
35
H2GCN-1
0.8667 ±0.0469
This paper
36
MLP + GCN
0.8643 ±0.0400
This paper
37
MLP
actual #37 vs paper #37
0.8629 ±0.0450
actual #37 vs paper #37
paper 0.8629 ±0.0450

Improvement within reported uncertainty; not highlighted.

paper 0.8629 ±0.0450 Δ at pub 0.0139
39
H2GCN-2
0.8588 ±0.0422
This paper
47
CPGNN-MLP
0.8458 ±0.0272
This paper
56
GPR-GNN
actual #56 vs paper #57 1 place worse
0.8412
best reported
actual #56 vs paper #57 1 place worse
paper 0.8373 ±0.0402

Difference within reported uncertainty; not counted as underperformance.

paper 0.8373 ±0.0402 Δ today 0.0039
63
GCN
actual #63 vs paper #161 98 places worse
0.6176 ±0.0615
actual #63 vs paper #161 98 places worse
paper 0.6176 ±0.0615

Improvement within reported uncertainty; not highlighted.

paper 0.6176 ±0.0615 Δ at pub 0.0216 Δ today 0.2134
69
GraphSAGE
0.8118 ±0.0556
83
CPGNN-Cheby
0.7919 ±0.0280
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