KDD 2021

Heterogeneous Graph Benchmarks

Qingsong Lv, Ming Ding, Qiang Liu, Yuxiang Chen, Wenzheng Feng, Siming He, Chang Zhou, Jianguo Jiang, Yuxiao Dong, Jie Tang

Main figure for Heterogeneous Graph Benchmarks

Abstract

Heterogeneous graph neural networks (HGNNs) have been blossoming in recent years, but the unique data processing and evaluation setups used by each work obstruct a full understanding of their advancements. In this work, we present a systematical reproduction of 12 recent HGNNs by using their official codes, datasets, settings, and hyperparameters, revealing surprising findings about the progress of HGNNs. We find that the simple homogeneous GNNs, e.g., GCN and GAT, are largely underestimated due to improper settings. GAT with proper inputs can generally match or outperform all existing HGNNs across various scenarios. To facilitate robust and reproducible HGNN research, we construct the Heterogeneous Graph Benchmark (HGB), and the HGB leaderboard is at linkcolor., consisting of 11 diverse datasets with three tasks. HGB standardizes the process of heterogeneous graph data splits, feature processing, and performance evaluation. Finally, we introduce a simple but very strong baseline Simple-HGN ---which significantly outperforms all previous models on HGB---to accelerate the advancement of HGNNs in the future.

Benchmark Results

Tested on 5 datasets 13 baseline values reported too low

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

TU Dortmund

#ModelAccuracy ↑Paper
1
MSH-GNN
0.9910 ±0.0030
2
ID-GNN+BEC
0.9830 ±0.0360
3
SupCosine
0.9830 ±0.0250
39
GIN
0.9330 ±0.0290
63
GCN
actual #63 vs paper #638 575 places worse
0.9220 ±0.0440
best reported
actual #63 vs paper #638 575 places worse
paper 0.7941
paper 0.7941 Δ at pub 0.0969 Δ today 0.1279
183
GAT
actual #183 vs paper #592 409 places worse
0.9010 ±0.0580
best reported
actual #183 vs paper #592 409 places worse
paper 0.8088
paper 0.8088 Δ at pub 0.0922 Δ today 0.0922
403
MLP
0.8660 ±0.0495
557
HAN
0.8235
This paper
558
GTN
0.8235
This paper
559
RSHN
0.8235
This paper

Heterogeneous Graph Benchmarks

#ModelMicro-F1 ↑Paper
1
LMSPS
0.9566 ±0.0020
2
PSHGCN
0.9561 ±0.0012
3
RpHGNN
0.9555 ±0.0029
21
GCN
actual #21 vs paper #71 50 places worse
0.9460 ±0.0031
best reported
actual #21 vs paper #71 50 places worse
paper 0.9147 ±0.0034
22
MAGNN
actual #22 vs paper #36 14 places worse
0.9456
best reported
actual #22 vs paper #36 14 places worse
paper 0.9376 ±0.0045
paper 0.9376 ±0.0045 Δ at pub 0.0080
23
GAT
actual #23 vs paper #42 19 places worse
0.9339 ±0.0030
actual #23 vs paper #42 19 places worse
paper 0.9339 ±0.0030
24
Simple-HGN
actual #24 vs paper #24
0.9448 ±0.0038
best reported
actual #24 vs paper #24
paper 0.9446 ±0.0022

Difference within reported uncertainty; not counted as underperformance.

paper 0.9446 ±0.0022 Δ today 0.0002
32
GTN
actual #32 vs paper #33 1 place worse
0.9417 ±0.0026
best reported
actual #32 vs paper #33 1 place worse
paper 0.9397 ±0.0054

Difference within reported uncertainty; not counted as underperformance.

paper 0.9397 ±0.0054 Δ today 0.0020
35
RSHN
0.9381 ±0.0055
This paper
37
HAN
actual #37 vs paper #66 29 places worse
0.9369
best reported
actual #37 vs paper #66 29 places worse
paper 0.9205 ±0.0062
39
HGT
actual #39 vs paper #39
0.9365
best reported
actual #39 vs paper #39
paper 0.9349 ±0.0025

Difference within reported uncertainty; not counted as underperformance.

paper 0.9349 ±0.0025 Δ at pub 0.0016
43
HetGNN
actual #43 vs paper #60 17 places worse
0.9336
best reported
actual #43 vs paper #60 17 places worse
paper 0.9233 ±0.0041
paper 0.9233 ±0.0041 Δ at pub 0.0103
46
GraphSAGE
0.9306 ±0.0047
66
RGCN
0.9207 ±0.0050
This paper
132
HetSANN
0.8056 ±0.0150
This paper
176
MLP
0.6447 ±0.0136
#ModelMicro-F1 ↑Paper
1
LMSPS
0.9469 ±0.0036
2
PSHGCN
0.9427 ±0.0023
3
SlotGAT
0.9406 ±0.0022
11
Simple-HGN
0.9335 ±0.0045
This paper
19
GAT
actual #19 vs paper #31 12 places worse
0.9273
best reported
actual #19 vs paper #31 12 places worse
paper 0.9219 ±0.0093

Difference within reported uncertainty; not counted as underperformance.

paper 0.9219 ±0.0093 Δ at pub 0.0054
22
GTN
actual #22 vs paper #46 24 places worse
0.9258
best reported
actual #22 vs paper #46 24 places worse
paper 0.9120 ±0.0071
paper 0.9120 ±0.0071 Δ at pub 0.0138
29
GCN
actual #29 vs paper #33 4 places worse
0.9229
best reported
actual #29 vs paper #33 4 places worse
paper 0.9212 ±0.0023

Difference within reported uncertainty; not counted as underperformance.

paper 0.9212 ±0.0023 Δ at pub 0.0017
41
HGT
actual #41 vs paper #48 7 places worse
0.9160 ±0.0060
best reported
actual #41 vs paper #48 7 places worse
paper 0.9100 ±0.0076

Difference within reported uncertainty; not counted as underperformance.

paper 0.9100 ±0.0076 Δ today 0.0060
43
HAN
actual #43 vs paper #50 7 places worse
0.9079 ±0.0043
actual #43 vs paper #50 7 places worse
paper 0.9079 ±0.0043
prev best: Implicit Graph Neural Networks (NeurIPS 2020)
paper 0.9079 ±0.0043 Δ at pub 0.0289 Δ today 0.0068
44
RGCN
0.9141 ±0.0075
This paper
49
GIN
0.9092
51
MAGNN
0.9077 ±0.0065
This paper
60
RSHN
0.9032 ±0.0154
This paper
63
HetSANN
0.8991 ±0.0037
This paper
92
HetGNN
0.8605 ±0.0025
This paper
109
MLP
0.7102 ±0.0221
#ModelMicro-F1 ↑Paper
1
ELLA
0.7930 ±0.0010
2
MHGCN
0.7820 ±0.0138
3
PSHGCN
0.7446 ±0.0032
13
GTN
actual #13 vs paper #31 18 places worse
0.6827 ±0.0065
best reported
actual #13 vs paper #31 18 places worse
paper 0.6514 ±0.0045
paper 0.6514 ±0.0045 Δ today 0.0313
14
GCN
actual #14 vs paper #32 18 places worse
0.6482 ±0.0064
actual #14 vs paper #32 18 places worse
paper 0.6482 ±0.0064
15
GAT
actual #15 vs paper #32 17 places worse
0.6486 ±0.0043
actual #15 vs paper #32 17 places worse
paper 0.6486 ±0.0043
17
MAGNN
actual #17 vs paper #34 17 places worse
0.6782 ±0.0154
best reported
actual #17 vs paper #34 17 places worse
paper 0.6467 ±0.0167
paper 0.6467 ±0.0167 Δ today 0.0315
18
HAN
actual #18 vs paper #34 16 places worse
0.6463 ±0.0058
actual #18 vs paper #34 16 places worse
paper 0.6463 ±0.0058
22
Simple-HGN
0.6736 ±0.0057
This paper
24
HGT
actual #24 vs paper #24
0.6720 ±0.0057
actual #24 vs paper #24
paper 0.6720 ±0.0057
paper 0.6720 ±0.0057 Δ at pub 0.0355
26
RGCN
actual #26 vs paper #47 21 places worse
0.6651 ±0.0028
best reported
actual #26 vs paper #47 21 places worse
paper 0.6205 ±0.0015
35
RSHN
actual #35 vs paper #35
0.6422 ±0.0103
actual #35 vs paper #35
paper 0.6422 ±0.0103

Improvement within reported uncertainty; not highlighted.

paper 0.6422 ±0.0103 Δ at pub 0.0085
44
GraphSAGE
0.6276
53
HetSANN
actual #53 vs paper #63 10 places worse
0.6069
best reported
actual #53 vs paper #63 10 places worse
paper 0.5768 ±0.0044
paper 0.5768 ±0.0044 Δ at pub 0.0301
74
MLP
0.5514
83
HetGNN
0.5116 ±0.0065
This paper
#ModelMacro-F1 ↑Paper
1
ConCH
0.6475
2
HetGNN
0.6292
3
GC-HGNN
0.6247 ±0.0042
5
HGT
actual #5 vs paper #38 33 places worse
0.6176
best reported
actual #5 vs paper #38 33 places worse
paper 0.2928 ±0.0252
paper 0.2928 ±0.0252 Δ at pub 0.3248
7
GCN
actual #7 vs paper #39 32 places worse
0.6090
best reported
actual #7 vs paper #39 32 places worse
paper 0.2784 ±0.0313
paper 0.2784 ±0.0313 Δ at pub 0.3306
10
HAN
actual #10 vs paper #42 32 places worse
0.6011
best reported
actual #10 vs paper #42 32 places worse
paper 0.2131 ±0.0168
paper 0.2131 ±0.0168 Δ at pub 0.3880
25
GAT
actual #25 vs paper #36 11 places worse
0.5109
best reported
actual #25 vs paper #36 11 places worse
paper 0.4074 ±0.0258
paper 0.4074 ±0.0258 Δ at pub 0.1035
29
Simple-HGN
0.4772 ±0.0148
This paper
32
RGCN
0.4678 ±0.0077
This paper
34
GraphSAGE
0.4417 ±0.0114
SOTA performance (not significantly different from the best) 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 Improved at pub — later paper surpassed this result Best today — OK at publication; today's leaderboard best is elsewhere