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 →Sorted by ROC-AUC. Highlighted rows are from other papers.
| # | Model | ROC-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
| # | Model | ROC-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 |
| # | Model | ROC-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 |
| # | Model | ROC-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 |
| # | Model | ROC-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 |
| # | Model | ROC-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 |
| # | Model | ROC-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 |
