Link Prediction with Untrained Message Passing Layers

Lisi Qarkaxhija, Anatol E. Wegner, Ingo Scholtes

Main figure for Link Prediction with Untrained Message Passing Layers

Abstract

In this work, we explore the use of untrained message passing layers in graph neural networks for link prediction. The untrained message passing layers we consider are derived from widely used graph neural network architectures by removing trainable parameters and nonlinearities in their respective message passing layers. Experimentally, we find that untrained message passing layers can lead to competitive and even superior link prediction performance compared to fully trained message passing layers while being more efficient, especially in the presence of high-dimensional features. We also provide a theoretical analysis of untrained message passing layers in the context of link prediction and show that the inner product of features produced by untrained message passing layers relate to common neighbour and path-based topological measures which are widely used for link prediction. As such, untrained message passing layers offer a more efficient alternative to trained message passing layers in link prediction tasks, with clearer theoretical links to classical path-based heuristics.

Benchmark Results

Tested on 4 datasets 26 baseline values reported too low

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

OGB

#ModelHits@50 ↑Paper
1
PROXI
0.7650 ±0.0027
2
OGB Leader
0.7129 ±0.0018
3
GIDN
0.7096 ±0.0055
9
GCN
actual #9 vs paper #35 26 places worse
0.6621 ±0.0033
best reported
actual #9 vs paper #35 26 places worse
paper 0.5558 ±0.0384
10
Neo-GNN
actual #10 vs paper #117 107 places worse
0.6613 ±0.0061
best reported
actual #10 vs paper #117 107 places worse
paper 0.0523 ±0.0090
paper 0.0523 ±0.0090 Δ at pub 0.5229 Δ today 0.6090
14
BUDDY
actual #14 vs paper #117 103 places worse
0.6594 ±0.0058
best reported
actual #14 vs paper #117 103 places worse
paper 0.0567 ±0.0036
15
NCNC (GIN)
0.6587 ±0.0074
This paper
17
SNCNC (SGCN)
0.6540 ±0.0046
This paper
19
NCN
actual #19 vs paper #117 98 places worse
0.6476 ±0.0087
best reported
actual #19 vs paper #117 98 places worse
paper 0.0509 ±0.0038
paper 0.0509 ±0.0038 Δ at pub 0.5967
20
SEAL
actual #20 vs paper #115 95 places worse
0.6474 ±0.0043
best reported
actual #20 vs paper #115 95 places worse
paper 0.0643 ±0.0032
23
AA
actual #23 vs paper #117 94 places worse
0.6435
best reported
actual #23 vs paper #117 94 places worse
paper 0.0507
26
RA
actual #26 vs paper #116 90 places worse
0.6400
best reported
actual #26 vs paper #116 90 places worse
paper 0.0629
27
CN
actual #27 vs paper #118 91 places worse
0.6137
best reported
actual #27 vs paper #118 91 places worse
paper 0.0420
28
SAGE
actual #28 vs paper #88 60 places worse
0.5944 ±0.0137
best reported
actual #28 vs paper #88 60 places worse
paper 0.4590 ±0.0867

Difference within reported uncertainty; not counted as underperformance.

paper 0.4590 ±0.0867 Δ at pub 0.0873 Δ today 0.1354
34
GAT
actual #34 vs paper #118 84 places worse
0.5643 ±0.0086
best reported
actual #34 vs paper #118 84 places worse
paper 0.0418 ±0.0033
paper 0.0418 ±0.0033 Δ at pub 0.5225
41
GraphSAGE
0.5463 ±0.0112
45
SGCN
0.5413 ±0.0097
This paper
63
SSAGE
0.4992 ±0.0152
This paper
68
Node2Vec
actual #68 vs paper #118 50 places worse
0.4929 ±0.0064
best reported
actual #68 vs paper #118 50 places worse
paper 0.0468 ±0.0008
paper 0.0468 ±0.0008 Δ at pub 0.4461
94
MLP
actual #94 vs paper #117 23 places worse
0.4438 ±0.0347
best reported
actual #94 vs paper #117 23 places worse
paper 0.0537 ±0.0014
best at pub: GNNBenchmark (JMLR 2023)
paper 0.0537 ±0.0014 Δ at pub 0.1498 Δ today 0.3901
98
MF
actual #98 vs paper #117 19 places worse
0.4181 ±0.0167
best reported
actual #98 vs paper #117 19 places worse
paper 0.0489 ±0.0025
paper 0.0489 ±0.0025 Δ at pub 0.3401 Δ today 0.3692
111
NCNC + SAGE
0.1517 ±0.0215
This paper
112
NCNC + GCN
0.1399 ±0.0144
This paper
113
NCNC + GIN
0.1128 ±0.0256
This paper
115
NCNC + SGCN
0.0672 ±0.0085
This paper
116
Katz
0.0631
This paper
118
PEG
0.0483 ±0.0021
This paper
119
Shortest Path
0.0266
This paper
120
NTGCN + GAE
0.0066
This paper
122
NTSAGE + GAE
0.0000
This paper
123
NTGIN + GAE
0.0000
This paper
#ModelHits@20 ↑Paper
1
ELGNN
0.9777 ±0.0037
2
GIDN
0.9542
3
AGDN
0.9538 ±0.0094
14
NCN
actual #14 vs paper #23 9 places worse
0.8232 ±0.0610
best reported
actual #14 vs paper #23 9 places worse
paper 0.6582 ±0.0266
best today: PageRank Bandits for Link Prediction (NeurIPS 2024)
paper 0.6582 ±0.0266 Δ today 0.1650
16
BUDDY
actual #16 vs paper #31 15 places worse
0.7851 ±0.0136
best reported
actual #16 vs paper #31 15 places worse
paper 0.5871 ±0.0163
paper 0.5871 ±0.0163 Δ at pub 0.1980 Δ today 0.1980
20
SAGE
actual #20 vs paper #20
0.6719 ±0.0118
actual #20 vs paper #20
paper 0.6719 ±0.0118
paper 0.6719 ±0.0118 Δ at pub 0.1329
21
GAT
actual #21 vs paper #21
0.6683 ±0.0223
actual #21 vs paper #21
paper 0.6683 ±0.0223
paper 0.6683 ±0.0223 Δ at pub 0.3732
24
GCN
actual #24 vs paper #24
0.6476 ±0.0145
actual #24 vs paper #24
paper 0.6476 ±0.0145
paper 0.6476 ±0.0145 Δ at pub 0.1486
25
Node2Vec
actual #25 vs paper #25
0.6363 ±0.0205
actual #25 vs paper #25
paper 0.6363 ±0.0205
paper 0.6363 ±0.0205 Δ at pub 0.4033
26
Neo-GNN
actual #26 vs paper #40 14 places worse
0.6357 ±0.0352
best reported
actual #26 vs paper #40 14 places worse
paper 0.5194 ±0.1033

Difference within reported uncertainty; not counted as underperformance.

paper 0.5194 ±0.1033 Δ at pub 0.1163 Δ today 0.1163
31
MF
actual #31 vs paper #31
0.5950 ±0.0168
actual #31 vs paper #31
paper 0.5950 ±0.0168
paper 0.5950 ±0.0168 Δ at pub 0.4580
34
GraphConv + GAE
0.5636 ±0.0045
This paper
36
SNCNC (SGIN)
0.5453 ±0.1102
This paper
37
GIN + GAE
0.5421 ±0.0095
This paper
38
GraphSAGE
0.5390 ±0.0474
42
PEG
0.5012 ±0.0655
This paper
43
SEAL
actual #43 vs paper #43
0.4974 ±0.0239
actual #43 vs paper #43
paper 0.4974 ±0.0239
paper 0.4974 ±0.0239 Δ at pub 0.1918
46
NCNC (GCN)
0.4653 ±0.2924
This paper
47
RA
actual #47 vs paper #47
0.4401
actual #47 vs paper #47
paper 0.4401
paper 0.4401 Δ at pub 0.1641
50
AA
actual #50 vs paper #50
0.3975
actual #50 vs paper #50
paper 0.3975
51
CN
actual #51 vs paper #51
0.3869
actual #51 vs paper #51
paper 0.3869
52
Katz
actual #52 vs paper #52
0.3869
actual #52 vs paper #52
paper 0.3869
paper 0.3869 Δ at pub 0.2096
54
GAE
actual #54 vs paper #78 24 places worse
0.3707 ±0.0507
best reported
actual #54 vs paper #78 24 places worse
paper 0.1781 ±0.0980
56
GCN + GAE
0.3448 ±0.0152
This paper
57
NTGCN + GAE
0.3323
This paper
61
SAGE + GAE
0.2930 ±0.0144
This paper
72
SGCN
0.2214 ±0.0338
This paper
75
SSAGE
0.1944 ±0.1084
This paper
77
SGCN + GAE
0.1821 ±0.1038
This paper
85
SSAGE + GAE
0.1098 ±0.0076
This paper
98
Shortest Path
0.0000
This paper
99
SGIN + GAE
0.0000
This paper
100
NTSAGE + GAE
0.0000
This paper
101
NTGIN + GAE
0.0000
This paper
#ModelHits@100 ↑Paper
1
OGB Leader
0.6524 ±0.0150
2
PRB
0.6347 ±0.0175
3
LPFormer
0.6332 ±0.0063
6
NCNC (GIN)
0.5947 ±0.0160
This paper
14
SAGE
actual #14 vs paper #55 41 places worse
0.5013 ±0.0055
best reported
actual #14 vs paper #55 41 places worse
paper 0.2388 ±0.0163
paper 0.2388 ±0.0163 Δ at pub 0.2625
22
SNCNC (SGCN)
0.4602 ±0.0119
This paper
23
MLP
0.4600
45
GCN
actual #45 vs paper #45
0.3084 ±0.0178
actual #45 vs paper #45
paper 0.3084 ±0.0178

Improvement within reported uncertainty; not highlighted.

paper 0.3084 ±0.0178 Δ at pub 0.0127
63
GraphSAGE
0.1655 ±0.0240
66
SGCN
0.1234 ±0.0195
This paper
69
SSAGE
0.0886 ±0.0080
This paper
#ModelMRR ↑Paper
1
CFG
0.8997 ±0.0015
2
SIEG
0.8987 ±0.0018
3
LPFormer
0.8981 ±0.0013
8
SEAL
actual #8 vs paper #76 68 places worse
0.8767 ±0.0032
best reported
actual #8 vs paper #76 68 places worse
paper 0.2060 ±0.0128
9
BUDDY
actual #9 vs paper #78 69 places worse
0.8756 ±0.0011
best reported
actual #9 vs paper #78 69 places worse
paper 0.1917 ±0.0020
paper 0.1917 ±0.0020 Δ at pub 0.6839 Δ today 0.6839
11
Neo-GNN
actual #11 vs paper #78 67 places worse
0.8726 ±0.0084
best reported
actual #11 vs paper #78 67 places worse
paper 0.1612 ±0.0025
paper 0.1612 ±0.0025 Δ at pub 0.7114 Δ today 0.7114
12
GCN
actual #12 vs paper #77 65 places worse
0.8705 ±0.0004
best reported
actual #12 vs paper #77 65 places worse
paper 0.1998 ±0.0035
paper 0.1998 ±0.0035 Δ at pub 0.6481 Δ today 0.6707
30
SAGE
actual #30 vs paper #73 43 places worse
0.8292 ±0.0022
best reported
actual #30 vs paper #73 43 places worse
paper 0.2205 ±0.0012
paper 0.2205 ±0.0012 Δ at pub 0.6055 Δ today 0.6087
32
GraphSAGE
0.8264 ±0.0001
51
RA
actual #51 vs paper #78 27 places worse
0.7604
best reported
actual #51 vs paper #78 27 places worse
paper 0.1779
52
AA
actual #52 vs paper #78 26 places worse
0.7596
best reported
actual #52 vs paper #78 26 places worse
paper 0.1783
54
CN
actual #54 vs paper #78 24 places worse
0.7430
best reported
actual #54 vs paper #78 24 places worse
paper 0.1711
59
Node2Vec
actual #59 vs paper #78 19 places worse
0.6141 ±0.0011
best reported
actual #59 vs paper #78 19 places worse
paper 0.1467 ±0.0018
best at pub: OGB (NeurIPS 2020)
paper 0.1467 ±0.0018 Δ at pub 0.4674 Δ today 0.4674
62
MF
actual #62 vs paper #79 17 places worse
0.5186 ±0.0443
best reported
actual #62 vs paper #79 17 places worse
paper 0.0872 ±0.0260
71
MLP
actual #71 vs paper #78 7 places worse
0.3917 ±0.0044
best reported
actual #71 vs paper #78 7 places worse
paper 0.1632 ±0.0007
73
NCN
0.2335 ±0.0028
This paper
74
NCNC + GCN
0.2152 ±0.0071
This paper
75
NCNC + GIN
0.2136 ±0.0089
This paper
76
NCNC + SGCN
0.2097 ±0.0086
This paper
77
NCNC + SAGE
0.2055 ±0.0029
This paper
78
NCNC
0.1961 ±0.0054
This paper
79
Katz
0.1410
This paper
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 Best today — OK at publication; today's leaderboard best is elsewhere