Efficient Heterogeneous Graph Learning via Random Projection

Jun Hu, Bryan Hooi, Bingsheng He

Main figure for Efficient Heterogeneous Graph Learning via Random Projection

Abstract

Heterogeneous Graph Neural Networks (HGNNs) are powerful tools for deep learning on heterogeneous graphs. Typical HGNNs require repetitive message passing during training, limiting efficiency for large-scale real-world graphs. Recent pre-computation-based HGNNs use one-time message passing to transform a heterogeneous graph into regular-shaped tensors, enabling efficient mini-batch training. Existing pre-computation-based HGNNs can be mainly categorized into two styles, which differ in how much information loss is allowed and efficiency. We propose a hybrid pre-computation-based HGNN, named Random Projection Heterogeneous Graph Neural Network (RpHGNN), which combines the benefits of one style's efficiency with the low information loss of the other style. To achieve efficiency, the main framework of RpHGNN consists of propagate-then-update iterations, where we introduce a Random Projection Squashing step to ensure that complexity increases only linearly. To achieve low information loss, we introduce a Relation-wise Neighbor Collection component with an Even-odd Propagation Scheme, which aims to collect information from neighbors in a finer-grained way. Experimental results indicate that our approach achieves state-of-the-art results on seven small and large benchmark datasets while also being 230\ Surprisingly, our approach not only surpasses pre-processing-based baselines but also outperforms end-to-end methods..

Proposed method: RpHGNN

Benchmark Results

Tested on 5 datasets 21 baseline values reported too low

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

OGB

#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
19
SeHGNN
actual #19 vs paper #36 17 places worse
0.5399 ±0.0018
best reported
actual #19 vs paper #36 17 places worse
paper 0.5145 ±0.0029
paper 0.5145 ±0.0029 Δ at pub 0.0254
28
NARS
actual #28 vs paper #39 11 places worse
0.5240 ±0.0016
best reported
actual #28 vs paper #39 11 places worse
paper 0.5066 ±0.0022
paper 0.5066 ±0.0022 Δ at pub 0.0174 Δ today 0.0174
32
RpHGNN
0.5207 ±0.0017
This paper
42
HGT
actual #42 vs paper #56 14 places worse
0.5023 ±0.0048
best reported
actual #42 vs paper #56 14 places worse
paper 0.4678 ±0.0042
48
RGCN
actual #48 vs paper #48
0.4811 ±0.0048
actual #48 vs paper #48
paper 0.4811 ±0.0048

Improvement within reported uncertainty; not highlighted.

paper 0.4811 ±0.0048 Δ at pub 0.0015
57
GraphSAGE
actual #57 vs paper #57
0.4646 ±0.0060
actual #57 vs paper #57
paper 0.4646 ±0.0060
paper 0.4646 ±0.0060 Δ at pub 0.0942
60
GCN
0.4290 ±0.0050
76
MLP
0.3243

Heterogeneous Graph Benchmarks

#ModelMicro-F1 ↑Paper
1
LMSPS
0.9566 ±0.0020
2
PSHGCN
0.9561 ±0.0012
3
RpHGNN
0.9555 ±0.0029
This paper
5
SeHGNN
actual #5 vs paper #6 1 place worse
0.9542 ±0.0017
best reported
actual #5 vs paper #6 1 place worse
paper 0.9524 ±0.0013

Difference within reported uncertainty; not counted as underperformance.

paper 0.9524 ±0.0013 Δ at pub 0.0018 Δ today 0.0018
13
HINormer
0.9494 ±0.0021
This paper
20
NARS
0.9461 ±0.0042
This paper
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
0.9448 ±0.0022
best reported
actual #23 vs paper #42 19 places worse
paper 0.9339 ±0.0030
best at pub: Heterogeneous Graph Benchmarks (KDD 2021)
paper 0.9339 ±0.0030 Δ today 0.0109
24
Simple-HGN
actual #24 vs paper #24
0.9448 ±0.0038
best reported
actual #24 vs paper #24
paper 0.9446 ±0.0022
best at pub: Heterogeneous Graph Benchmarks (KDD 2021)

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
best at pub: Heterogeneous Graph Benchmarks (KDD 2021)

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
actual #46 vs paper #46
0.9306 ±0.0047
actual #46 vs paper #46
paper 0.9306 ±0.0047
paper 0.9306 ±0.0047 Δ at pub 0.0833
66
RGCN
0.9207 ±0.0050
This paper
88
GIN
0.8720
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
4
RpHGNN
0.9404 ±0.0059
This paper
5
SeHGNN
actual #5 vs paper #5
0.9398 ±0.0036
best reported
actual #5 vs paper #5
paper 0.9387 ±0.0050

Difference within reported uncertainty; not counted as underperformance.

paper 0.9387 ±0.0050 Δ at pub 0.0011 Δ today 0.0011
7
HINormer
actual #7 vs paper #31 24 places worse
0.9383 ±0.0045
best reported
actual #7 vs paper #31 24 places worse
paper 0.9219 ±0.0040
paper 0.9219 ±0.0040 Δ at pub 0.0164
11
Simple-HGN
0.9335 ±0.0045
This paper
14
NARS
0.9331 ±0.0033
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
best at pub: Heterogeneous Graph Benchmarks (KDD 2021)

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
0.9147 ±0.0022
best reported
actual #43 vs paper #50 7 places worse
paper 0.9079 ±0.0043
best at pub: Heterogeneous Graph Benchmarks (KDD 2021)
paper 0.9079 ±0.0043 Δ today 0.0068
44
RGCN
0.9141 ±0.0075
This paper
49
GIN
0.9092
51
MAGNN
0.9077 ±0.0065
This paper
52
GraphSAGE
actual #52 vs paper #52
0.9063 ±0.0076
actual #52 vs paper #52
paper 0.9063 ±0.0076
paper 0.9063 ±0.0076 Δ at pub 0.5298
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
5
SeHGNN
actual #5 vs paper #13 8 places worse
0.7342 ±0.0047
best reported
actual #5 vs paper #13 8 places worse
paper 0.6821 ±0.0032
paper 0.6821 ±0.0032 Δ at pub 0.0521
7
RpHGNN
0.6977 ±0.0066
This paper
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 at pub 0.0313
14
GCN
actual #14 vs paper #32 18 places worse
0.6813 ±0.0083
best reported
actual #14 vs paper #32 18 places worse
paper 0.6482 ±0.0064
paper 0.6482 ±0.0064 Δ at pub 0.0331
15
GAT
actual #15 vs paper #32 17 places worse
0.6808 ±0.0049
best reported
actual #15 vs paper #32 17 places worse
paper 0.6486 ±0.0043
paper 0.6486 ±0.0043 Δ at pub 0.0322
16
HINormer
0.6783 ±0.0034
This paper
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 at pub 0.0315
18
HAN
actual #18 vs paper #34 16 places worse
0.6769 ±0.0064
best reported
actual #18 vs paper #34 16 places worse
paper 0.6463 ±0.0058
paper 0.6463 ±0.0058 Δ at pub 0.0306
22
Simple-HGN
0.6736 ±0.0057
This paper
24
HGT
0.6720 ±0.0057
This paper
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
paper 0.6205 ±0.0015 Δ at pub 0.0446
28
NARS
0.6618 ±0.0070
This paper
35
RSHN
0.6422 ±0.0103
This paper
44
GraphSAGE
actual #44 vs paper #48 4 places worse
0.6276
best reported
actual #44 vs paper #48 4 places worse
paper 0.6192 ±0.0072

Difference within reported uncertainty; not counted as underperformance.

paper 0.6192 ±0.0072 Δ at pub 0.0084
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
20
RpHGNN
0.5402 ±0.0088
This paper
22
HINormer
actual #22 vs paper #26 4 places worse
0.5218 ±0.0039
best reported
actual #22 vs paper #26 4 places worse
paper 0.4994 ±0.0212

Difference within reported uncertainty; not counted as underperformance.

paper 0.4994 ±0.0212 Δ at pub 0.0224
23
SeHGNN
actual #23 vs paper #25 2 places worse
0.5187 ±0.0086
best reported
actual #23 vs paper #25 2 places worse
paper 0.5071 ±0.0044

Difference within reported uncertainty; not counted as underperformance.

paper 0.5071 ±0.0044 Δ at pub 0.0116
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
26
NARS
0.4998 ±0.0177
This paper
29
Simple-HGN
0.4772 ±0.0148
This paper
32
RGCN
0.4678 ±0.0077
This paper
34
GraphSAGE
0.4417 ±0.0114
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