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:.
Benchmark Results
Tested on 6 datasets
Tables show presented results in global context (best 3 papers + GCN + MLP).
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 | |
| 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 |
| # | 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 | |
| 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 |
| # | Model | ROC-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 | 0.9319
±0.0206 best reported | best today: MAGPrompt: Message-Adaptive Graph Prompt Tuning for Graph Neural Networks (2026) |
| 9 | GPF | 0.9273
±0.0282 best reported | best today: MAGPrompt: Message-Adaptive Graph Prompt Tuning for Graph Neural Networks (2026) |
| 34 | GIN | 0.8875
±0.0049 | |
| 162 | FT | 0.6965
±0.0087 | This paper |
| 171 | GraphPrompt | 0.6929
±0.0019 | 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 | |
| 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 | 0.5567
±0.0708 best reported | best today: MolGA: Molecular Graph Adaptation with Pre-trained 2D Graph Encoder (2025) Difference within reported uncertainty; not counted as underperformance. |
| # | Model | ROC-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 |
| # | 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 | |
| 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 |
