NeurIPS 2022

Universal Prompt Tuning for Graph Neural Networks

Taoran Fang, Yunchao Zhang, Yang Yang, Chunping Wang, Lei Chen

Main figure for Universal Prompt Tuning for Graph Neural Networks

Abstract

In recent years, prompt tuning has sparked a research surge in adapting pre-trained models. Unlike the unified pre-training strategy employed in the language field, the graph field exhibits diverse pre-training strategies, posing challenges in designing appropriate prompt-based tuning methods for graph neural networks. While some pioneering work has devised specialized prompting functions for models that employ edge prediction as their pre-training tasks, these methods are limited to specific pre-trained GNN models and lack broader applicability. In this paper, we introduce a universal prompt-based tuning method called Graph Prompt Feature (GPF) for pre-trained GNN models under any pre-training strategy. GPF operates on the input graph's feature space and can theoretically achieve an equivalent effect to any form of prompting function. Consequently, we no longer need to illustrate the prompting function corresponding to each pre-training strategy explicitly. Instead, we employ GPF to obtain the prompted graph for the downstream task in an adaptive manner. We provide rigorous derivations to demonstrate the universality of GPF and make guarantee of its effectiveness. The experimental results under various pre-training strategies indicate that our method performs better than fine-tuning, with an average improvement of about $1.4\ Moreover, our method significantly outperforms existing specialized prompt-based tuning methods when applied to models utilizing the pre-training strategy they specialize in. These numerous advantages position our method as a compelling alternative to fine-tuning for downstream adaptations. Our code is available at:.

Proposed method: GPF

Benchmark Results

Tested on 6 datasets

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

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
54
GPF-plus
0.8005 ±0.0046
This paper
58
GPF
0.7999 ±0.0024
This paper
98
FT
0.7867 ±0.0035
This paper
313
GraphPrompt
0.6809 ±0.0019
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
57
GPF-plus
0.8581 ±0.0043
This paper
66
GPF
0.8532 ±0.0041
This paper
79
FT
0.8466 ±0.0084
This paper
276
GPPT
0.7085 ±0.0142
This paper
290
GraphPrompt
0.6770 ±0.0126
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
6
GPF-plus
actual #6 vs paper #96 90 places worse
0.9319 ±0.0206
best reported
actual #6 vs paper #96 90 places worse
paper 0.7218 ±0.0093
paper 0.7218 ±0.0093 Δ today 0.2101
9
GPF
actual #9 vs paper #119 110 places worse
0.9273 ±0.0282
best reported
actual #9 vs paper #119 110 places worse
paper 0.7111 ±0.0120
paper 0.7111 ±0.0120 Δ today 0.2162
34
GIN
0.8875 ±0.0049
162
FT
0.6965 ±0.0087
This paper
171
GraphPrompt
0.6929 ±0.0019
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
119
GPF-plus
0.7617 ±0.0298
This paper
127
FT
0.7517 ±0.0214
This paper
129
GPF
0.7506 ±0.0102
This paper
239
GraphPrompt
actual #239 vs paper #240 1 place worse
0.5567 ±0.0708
best reported
actual #239 vs paper #240 1 place worse
paper 0.5537 ±0.0057

Difference within reported uncertainty; not counted as underperformance.

paper 0.5537 ±0.0057 Δ today 0.0030
#ModelROC-AUC ↑Paper
1
KA-GAT
0.8470 ±0.0020
2
KA-GCN
0.8420 ±0.0010
3
GraphKAN
0.8370 ±0.0010
8
GPF
0.6913 ±0.0116
This paper
11
GPF-plus
0.6865 ±0.0072
This paper
27
FT
0.6677 ±0.0013
This paper
66
GIN
0.6403 ±0.0104
206
GraphPrompt
0.5871 ±0.0013
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
59
GPF
0.6792 ±0.0035
This paper
66
GPF-plus
0.6758 ±0.0054
This paper
81
FT
0.6639 ±0.0057
This paper
197
GraphPrompt
0.6054 ±0.0021
This paper
SOTA performance (not significantly different from the best) Proposed method (this paper) Baseline / comparison (this paper) Global context (other papers) Best today — OK at publication; today's leaderboard best is elsewhere