Subgraph-level Universal Prompt Tuning

Junhyun Lee, Wooseong Yang, Jaewoo Kang

Main figure for Subgraph-level Universal Prompt Tuning

Abstract

In the evolving landscape of machine learning, the adaptation of pre-trained models through prompt tuning has become increasingly prominent. This trend is particularly observable in the graph domain, where diverse pre-training strategies present unique challenges in developing effective prompt-based tuning methods for graph neural networks. Previous approaches have been limited, focusing on specialized prompting functions tailored to models with edge prediction pre-training tasks. These methods, however, suffer from a lack of generalizability across different pre-training strategies. Recently, a simple prompt tuning method has been designed for any pre-training strategy, functioning within the input graph's feature space. This allows it to theoretically emulate any type of prompting function, thereby significantly increasing its versatility for a range of downstream applications. Nevertheless, the capacity of such simple prompts to fully grasp the complex contexts found in graphs remains an open question, necessitating further investigation. Addressing this challenge, our work introduces the Subgraph-level Universal Prompt Tuning (SUPT) approach, focusing on the detailed context within subgraphs. In SUPT, prompt features are assigned at the subgraph-level, preserving the method's universal capability. This requires extremely fewer tuning parameters than fine-tuning-based methods, outperforming them in 42 out of 45 full-shot scenario experiments with an average improvement of over 2.5\ In few-shot scenarios, it excels in 41 out of 45 experiments, achieving an average performance increase of more than 6.6\

Benchmark Results

Tested on 7 datasets Non-standard metric on 1 dataset

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

Classic

PPI

Global leaderboard →
Non-default metric. This paper reports ROC-AUC; the dataset default is F1. Values below use ROC-AUC only.

Sorted by ROC-AUC. Highlighted rows are from other papers.

#ModelROC-AUC ↑Paper
1
AttrMasking SUPT_soft
0.8191
This paper
2
AttrMasking SUPT_hard
0.8190
This paper
3
AttrMasking GPF
0.8147
This paper
4
AttrMasking GPF-plus
0.8143
This paper
5
ContextPred SUPT_soft
0.8086
This paper
6
ContextPred SUPT_hard
0.8085
This paper
7
ContextPred GPF-plus
0.8028
This paper
8
ContextPred GPF
0.8021
This paper
9
EdgePred SUPT_hard
0.8020
This paper
10
EdgePred SUPT_soft
0.8019
This paper
11
EdgePred GPF
0.7996
This paper
12
EdgePred GPF-plus
0.7988
This paper
13
Infomax SUPT_hard
0.7964
This paper
14
Infomax SUPT_soft
0.7945
This paper
15
Infomax GPF
0.7887
This paper
16
Infomax GPF-plus
0.7885
This paper
17
AttrMasking FT
0.7393
This paper
18
ContextPred FT
0.7210
This paper
19
EdgePred FT
0.7154
This paper
20
Infomax FT
0.7129
This paper
21
GCL SUPT_soft
0.6957
This paper
22
GCL SUPT_hard
0.6859
This paper
23
GCL GPF
0.6791
This paper
24
GCL FT
0.6776
This paper
25
GCL GPF-plus
0.6671
This paper

MoleculeNet

#ModelROC-AUC ↑Paper
1
HIMP
0.8740 ±0.0050
2
GINE w/ VN
0.8720 ±0.0030
3
NaiveGINe+ K=3 w/ VN
0.8700 ±0.0040
14
GCN
0.8400 ±0.0040
43
EdgePred SUPT_soft
0.8090
This paper
44
EdgePred SUPT_hard
0.8076
This paper
53
ContextPred SUPT_soft
0.8012
This paper
56
ContextPred SUPT_hard
0.8000
This paper
59
ContextPred GPF-plus
0.7995
This paper
60
EdgePred GPF-plus
0.7991
This paper
64
ContextPred GPF
0.7990
This paper
68
AttrMasking SUPT_soft
0.7973
This paper
70
EdgePred GPF
0.7969
This paper
74
AttrMasking SUPT_hard
0.7950
This paper
87
Infomax SUPT_hard
0.7914
This paper
92
Infomax SUPT_soft
0.7898
This paper
95
AttrMasking GPF-plus
0.7883
This paper
99
EdgePred FT
0.7867
This paper
100
AttrMasking GPF
0.7866
This paper
101
Infomax FT
0.7857
This paper
105
Infomax GPF-plus
0.7850
This paper
111
ContextPred FT
0.7829
This paper
113
AttrMasking FT
0.7828
This paper
118
Infomax GPF
0.7813
This paper
275
GCL SUPT_hard
0.7344
This paper
277
GCL SUPT_soft
0.7340
This paper
278
GCL FT
0.7335
This paper
282
GCL GPF-plus
0.7306
This paper
290
GCL GPF
0.7215
This paper
#ModelROC-AUC ↑Paper
1
ProtoMol
0.9140 ±0.0030
2
MMSG
0.9080 ±0.0050
3
MemGNN
0.9070
43
GIN
0.8646 ±0.0081
68
ContextPred SUPT_soft
0.8527
This paper
69
AttrMasking SUPT_soft
0.8522
This paper
70
ContextPred SUPT_hard
0.8521
This paper
73
ContextPred GPF
0.8503
This paper
74
AttrMasking GPF-plus
0.8501
This paper
76
AttrMasking SUPT_hard
0.8498
This paper
78
AttrMasking GPF
0.8477
This paper
80
ContextPred FT
0.8466
This paper
84
ContextPred GPF-plus
0.8450
This paper
89
Infomax SUPT_hard
0.8405
This paper
90
Infomax SUPT_soft
0.8401
This paper
103
Infomax GPF
0.8324
This paper
108
Infomax GPF-plus
0.8296
This paper
136
EdgePred SUPT_hard
0.8172
This paper
140
EdgePred SUPT_soft
0.8144
This paper
146
Infomax FT
0.8132
This paper
159
AttrMasking FT
0.8094
This paper
162
EdgePred GPF-plus
0.8091
This paper
163
EdgePred FT
0.8090
This paper
181
EdgePred GPF
0.7976
This paper
198
GCL SUPT_hard
0.7917
This paper
203
GCL SUPT_soft
0.7892
This paper
221
GCL GPF-plus
0.7784
This paper
238
GCL GPF
0.7667
This paper
247
GCL FT
0.7551
This paper
#ModelROC-AUC ↑Paper
1
MAGPrompt+
0.9432 ±0.0238
2
CamS-LLaMA
0.9420
3
SE(3)-I MPPH
0.9400 ±0.0210
34
GIN
0.8875 ±0.0049
143
ContextPred SUPT_hard
0.7018
This paper
147
ContextPred SUPT_soft
0.7006
This paper
154
EdgePred SUPT_soft
0.6993
This paper
157
GCL SUPT_soft
0.6979
This paper
161
GCL SUPT_hard
0.6968
This paper
163
ContextPred FT
0.6965
This paper
166
EdgePred SUPT_hard
0.6951
This paper
167
GCL FT
0.6949
This paper
168
EdgePred GPF
0.6936
This paper
169
EdgePred GPF-plus
0.6931
This paper
178
ContextPred GPF
0.6904
This paper
190
ContextPred GPF-plus
0.6859
This paper
195
AttrMasking SUPT_hard
0.6839
This paper
196
AttrMasking SUPT_soft
0.6837
This paper
199
GCL GPF
0.6811
This paper
209
GCL GPF-plus
0.6777
This paper
215
Infomax SUPT_soft
0.6763
This paper
218
Infomax FT
0.6755
This paper
222
AttrMasking GPF
0.6749
This paper
225
AttrMasking GPF-plus
0.6732
This paper
226
Infomax SUPT_hard
0.6729
This paper
233
Infomax GPF-plus
0.6703
This paper
243
Infomax GPF
0.6658
This paper
244
EdgePred FT
0.6656
This paper
248
AttrMasking FT
0.6633
This paper
#ModelROC-AUC ↑Paper
1
SE(3)-I MPPH
0.9930 ±0.0040
2
KA-GCN
0.9920 ±0.0050
3
KA-GAT
0.9910 ±0.0050
19
GCN
0.9130 ±0.0170
114
AttrMasking SUPT_soft
0.7736
This paper
120
Infomax SUPT_soft
0.7608
This paper
122
Infomax SUPT_hard
0.7565
This paper
124
ContextPred SUPT_soft
0.7555
This paper
126
AttrMasking SUPT_hard
0.7525
This paper
128
GCL FT
0.7517
This paper
132
ContextPred SUPT_hard
0.7490
This paper
136
AttrMasking FT
0.7446
This paper
137
AttrMasking GPF-plus
0.7417
This paper
138
Infomax GPF
0.7414
This paper
142
ContextPred FT
0.7371
This paper
145
Infomax GPF-plus
0.7361
This paper
149
ContextPred GPF
0.7315
This paper
152
ContextPred GPF-plus
0.7273
This paper
153
AttrMasking GPF
0.7272
This paper
168
GCL SUPT_soft
0.7121
This paper
171
EdgePred SUPT_soft
0.7041
This paper
173
Infomax FT
0.7006
This paper
174
EdgePred SUPT_hard
0.6997
This paper
176
EdgePred GPF-plus
0.6958
This paper
178
GCL GPF
0.6948
This paper
179
GCL SUPT_hard
0.6947
This paper
181
EdgePred FT
0.6907
This paper
182
GCL GPF-plus
0.6889
This paper
188
EdgePred GPF
0.6792
This paper
#ModelROC-AUC ↑Paper
1
KA-GAT
0.8470 ±0.0020
2
KA-GCN
0.8420 ±0.0010
3
GraphKAN
0.8370 ±0.0010
9
AttrMasking SUPT_hard
0.6882
This paper
10
AttrMasking SUPT_soft
0.6868
This paper
12
AttrMasking GPF-plus
0.6853
This paper
13
AttrMasking GPF
0.6819
This paper
22
EdgePred SUPT_soft
0.6695
This paper
23
EdgePred SUPT_hard
0.6685
This paper
28
AttrMasking FT
0.6677
This paper
29
EdgePred GPF
0.6671
This paper
30
EdgePred GPF-plus
0.6661
This paper
33
ContextPred SUPT_soft
0.6648
This paper
34
ContextPred SUPT_hard
0.6637
This paper
35
ContextPred GPF-plus
0.6632
This paper
38
Infomax GPF-plus
0.6589
This paper
39
Infomax SUPT_soft
0.6588
This paper
40
Infomax SUPT_hard
0.6578
This paper
41
Infomax GPF
0.6564
This paper
45
ContextPred GPF
0.6531
This paper
59
ContextPred FT
0.6445
This paper
61
EdgePred FT
0.6435
This paper
66
GIN
0.6403 ±0.0104
79
Infomax FT
0.6334
This paper
87
GCL SUPT_soft
0.6284
This paper
96
GCL SUPT_hard
0.6251
This paper
122
GCL GPF-plus
0.6157
This paper
143
GCL GPF
0.6100
This paper
154
GCL FT
0.6063
This paper
#ModelROC-AUC ↑Paper
1
GeomGCL
0.7630
2
LiGhT DeepGPT
0.7570 ±0.0110
3
CoMPT
0.7550
14
GCN
0.7350 ±0.0020
51
ContextPred SUPT_soft
0.6850
This paper
53
ContextPred SUPT_hard
0.6840
This paper
63
ContextPred GPF-plus
0.6772
This paper
65
ContextPred GPF
0.6768
This paper
68
AttrMasking SUPT_soft
0.6702
This paper
71
AttrMasking SUPT_hard
0.6679
This paper
73
EdgePred SUPT_soft
0.6665
This paper
74
Infomax SUPT_soft
0.6653
This paper
75
AttrMasking GPF-plus
0.6653
This paper
78
Infomax SUPT_hard
0.6648
This paper
79
EdgePred SUPT_hard
0.6644
This paper
82
ContextPred FT
0.6639
This paper
85
EdgePred FT
0.6629
This paper
88
AttrMasking GPF
0.6609
This paper
90
Infomax GPF
0.6596
This paper
91
Infomax GPF-plus
0.6583
This paper
95
EdgePred GPF
0.6570
This paper
96
EdgePred GPF-plus
0.6566
This paper
101
AttrMasking FT
0.6534
This paper
106
Infomax FT
0.6516
This paper
141
GCL SUPT_soft
0.6342
This paper
146
GCL SUPT_hard
0.6335
This paper
177
GCL FT
0.6254
This paper
189
GCL GPF-plus
0.6147
This paper
196
GCL GPF
0.6073
This paper
SOTA performance (not significantly different from the best) Proposed method (this paper) Baseline / comparison (this paper) Global context (other papers)