Graph Neural Networks for Graphs with Heterophily: A Survey

Xin Zheng, Yixin Liu, Shirui Pan, Miao Zhang, Di Jin, Philip S. Yu

Main figure for Graph Neural Networks for Graphs with Heterophily: A Survey

Abstract

Recent years have witnessed fast developments of graph neural networks (GNNs) that have benefited myriad graph analytic tasks and applications. Most GNNs rely on the homophily assumption that nodes belonging to the same class are more likely to be connected. However, as a ubiquitous graph property in numerous real-world scenarios, heterophily,, nodes with different labels tend to be linked, significantly limits the performance of tailor-made homophilic GNNs. Hence, GNNs for heterophilic graphs are gaining increasing research attention to enhance graph learning with heterophily. In this paper, we provide a comprehensive review of GNNs for heterophilic graphs. Specifically, we propose a systematic taxonomy that governs existing heterophilic GNN models, along with general summaries and detailed analyses. Furthermore, we discuss the relationship between heterophily and various graph research domains, aiming to facilitate the development of more effective GNNs across a spectrum of practical applications and learning tasks in the graph research community. In the end, we point out potential directions to advance and inspire future research and applications on heterophilic graph learning with GNNs.

Benchmark Results

Tested on 5 datasets Non-standard metric on 1 dataset

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

Heterophily Benchmark

#ModelAccuracy ↑Paper
1
Dir-Poly
0.9451 ±0.0022
2
D-CDE
0.9387 ±0.0041
3
LargeScaleNet
0.9358 ±0.0024
26
GraphSAGE
0.9106 ±0.0027
35
PD-GNN
0.8923 ±0.0056
This paper
64
SAGE
0.8574 ±0.0067
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 today 0.0903
83
GAT
actual #83 vs paper #84 1 place worse
0.8145 ±0.0009
best reported
actual #83 vs paper #84 1 place worse
paper 0.8087 ±0.0030
paper 0.8087 ±0.0030 Δ today 0.0058
87
AGS-GNN
0.8049 ±0.0048
This paper
115
ACM-GCN
actual #115 vs paper #118 3 places worse
0.7189 ±0.0061
best reported
actual #115 vs paper #118 3 places worse
paper 0.7142 ±0.0038

Difference within reported uncertainty; not counted as underperformance.

paper 0.7142 ±0.0038 Δ today 0.0047
129
H2GCN
actual #129 vs paper #164 35 places worse
0.6809 ±0.0029
best reported
actual #129 vs paper #164 35 places worse
paper 0.6011 ±0.0052
paper 0.6011 ±0.0052 Δ today 0.0798
135
MLP
0.6665 ±0.0047
154
GloGNN
actual #154 vs paper #167 13 places worse
0.6385 ±0.0049
best reported
actual #154 vs paper #167 13 places worse
paper 0.5963 ±0.0069
paper 0.5963 ±0.0069 Δ today 0.0422
168
LINKX
0.5914 ±0.0045
This paper
#ModelAccuracy ↑Paper
1
UniGAP
0.6375 ±0.0110
2
H2GCN + HalfHop
0.5961 ±0.0100
3
GraphSAGE + HalfHop
0.5897 ±0.0150
7
H2GCN
actual #7 vs paper #196 189 places worse
0.5681 ±0.0090
best reported
actual #7 vs paper #196 189 places worse
paper 0.3647 ±0.0023
12
SAGE
actual #12 vs paper #30 18 places worse
0.5569 ±0.0023
best reported
actual #12 vs paper #30 18 places worse
paper 0.5363 ±0.0039
14
GAT
actual #14 vs paper #105 91 places worse
0.5559 ±0.0027
best reported
actual #14 vs paper #105 91 places worse
paper 0.4909 ±0.0063
15
GraphSAGE
0.5540 ±0.0020
24
GCN
actual #24 vs paper #111 87 places worse
0.5411 ±0.0034
best reported
actual #24 vs paper #111 87 places worse
paper 0.4870 ±0.0063
43
AGS-GNN
0.5321 ±0.0046
This paper
47
ACM-GCN
0.5294 ±0.0023
This paper
53
LINKX
0.5268 ±0.0026
This paper
79
PD-GNN
0.5096 ±0.0043
This paper
84
MLP
0.5058
196
GloGNN
actual #196 vs paper #196
0.3728 ±0.0066
best reported
actual #196 vs paper #196
paper 0.3689 ±0.0014

Difference within reported uncertainty; not counted as underperformance.

paper 0.3689 ±0.0014 Δ today 0.0039
#ModelROC-AUC ↑Paper
1
BuNN
0.9899 ±0.0016
2
DC-GNN
0.9850 ±0.0021
3
Tango -GPS
0.9839 ±0.0054
32
PD-GNN
0.9403 ±0.0045
This paper
36
GAT
actual #36 vs paper #60 24 places worse
0.9391 ±0.0035
best reported
actual #36 vs paper #60 24 places worse
paper 0.9201 ±0.0068
paper 0.9201 ±0.0068 Δ today 0.0190
42
GraphSAGE
0.9358 ±0.0005
46
SAGE
0.9351 ±0.0057
This paper
68
GCN
actual #68 vs paper #88 20 places worse
0.9150 ±0.0006
best reported
actual #68 vs paper #88 20 places worse
paper 0.8975 ±0.0052
paper 0.8975 ±0.0052 Δ today 0.0175
81
ACM-GCN
0.9047 ±0.0057
This paper
85
H2GCN
actual #85 vs paper #88 3 places worse
0.8995 ±0.0038
best reported
actual #85 vs paper #88 3 places worse
paper 0.8971 ±0.0031

Difference within reported uncertainty; not counted as underperformance.

paper 0.8971 ±0.0031 Δ today 0.0024
111
AGS-GNN
0.8556 ±0.0028
This paper
120
LINKX
0.8002 ±0.0003
This paper
148
GloGNN
actual #148 vs paper #155 7 places worse
0.6253 ±0.0134
best reported
actual #148 vs paper #155 7 places worse
paper 0.5108 ±0.0123
paper 0.5108 ±0.0123 Δ today 0.1145
156
MLP
0.5099 ±0.0147
#ModelROC-AUC ↑Paper
1
Polynormer-r
0.8591 ±0.0074
2
DC-GNN
0.8588 ±0.0081
3
TANGO-GPS
0.8566 ±0.0101
15
PD-GNN
0.8483 ±0.0040
This paper
28
GAT
actual #28 vs paper #47 19 places worse
0.8443 ±0.0100
best reported
actual #28 vs paper #47 19 places worse
paper 0.8370 ±0.0047

Difference within reported uncertainty; not counted as underperformance.

paper 0.8370 ±0.0047 Δ today 0.0073
50
GCN
0.8364 ±0.0067
This paper
76
SAGE
0.8243 ±0.0044
This paper
77
GraphSAGE
0.8243 ±0.0044
84
LINKX
actual #84 vs paper #94 10 places worse
0.8115 ±0.0123
best reported
actual #84 vs paper #94 10 places worse
paper 0.8007 ±0.0053

Difference within reported uncertainty; not counted as underperformance.

paper 0.8007 ±0.0053 Δ today 0.0108
91
AGS-GNN
0.8052 ±0.0041
This paper
92
ACM-GCN
0.8045 ±0.0054
This paper
113
H2GCN
actual #113 vs paper #141 28 places worse
0.7815
best reported
actual #113 vs paper #141 28 places worse
paper 0.7335 ±0.0101
139
MLP
0.7362 ±0.0020
140
GloGNN
0.7339 ±0.0117
This paper

Questions

Global leaderboard →
Non-default metric. This paper reports Accuracy; the dataset default is ROC-AUC. Values below use Accuracy only.

Sorted by Accuracy. Highlighted rows are from other papers.

#ModelAccuracy ↑Paper
1
MLP
0.9733 ±0.0006
2
AGS-GNN
0.9727
This paper
3
MeanGNN
0.9716 ±0.0006
4
GCN
actual #4 vs paper #34 30 places worse
0.9715 ±0.0004
best reported
actual #4 vs paper #34 30 places worse
paper 0.7609
5
GAT
actual #5 vs paper #31 26 places worse
0.9713 ±0.0005
best reported
actual #5 vs paper #31 26 places worse
paper 0.7743
8
LINKX
0.9706
This paper
11
ACM-GCN
0.9702
This paper
28
PD-GNN
0.7888
This paper
33
SAGE
0.7644
This paper
50
GloGNN
0.6574
This paper
51
H2GCN
0.6359
This paper
SOTA performance (not significantly different from the best) Baseline / comparison (this paper) Global context (other papers) Best today — OK at publication; today's leaderboard best is elsewhere