ProG: A Graph Prompt Learning Benchmark
Abstract
Artificial general intelligence on graphs has shown significant advancements across various applications, yet the traditional `Pre-train & Fine-tune' paradigm faces inefficiencies and negative transfer issues, particularly in complex and few-shot settings. Graph prompt learning emerges as a promising alternative, leveraging lightweight prompts to manipulate data and fill the task gap by reformulating downstream tasks to the pretext. However, several critical challenges still remain: how to unify diverse graph prompt models, how to evaluate the quality of graph prompts, and to improve their usability for practical comparisons and selection. In response to these challenges, we introduce the first comprehensive benchmark for graph prompt learning. Our benchmark integrates SIX pre-training methods and FIVE state-of-the-art graph prompt techniques, evaluated across FIFTEEN diverse datasets to assess performance, flexibility, and efficiency. We also present `ProG', an easy-to-use open-source library that streamlines the execution of various graph prompt models, facilitating objective evaluations. Additionally, we propose a unified framework that categorizes existing graph prompt methods into two main approaches: prompts as graphs and prompts as tokens. This framework enhances the applicability and comparison of graph prompt techniques. The code is available at:.
Benchmark Results
Tested on 8 datasets 1 baseline value reported too low
Tables show presented results in global context (best 3 papers + GCN + MLP).
Classic
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GraphSAGE+CNA | 0.9418
±0.0033 | |
| 2 | GCN+CNA | 0.9366
±0.0048 | |
| 3 | TransformerConv | 0.9350
±0.0058 | |
| 21 | GCN | 0.9004 | |
| 724 | MLP | 0.7768 | |
| 884 | GPF | 0.5760
±0.1388 best reported | best today: GCoT: Chain-of-Thought Prompt Learning for Graphs (KDD 2025) Difference within reported uncertainty; not counted as underperformance. |
| 888 | GPrompt | 0.5666
±0.1122 | This paper |
| 889 | GPF-plus | 0.5577
±0.1030 | This paper |
| 890 | EdgePreGprompt + GPF_plus | 0.5577
±0.1030 | This paper |
| 891 | GraphMAE + GPF_plus | 0.5426
±0.0748 | This paper |
| 897 | Pre-train & Fine-tune | 0.5261
±0.0173 | This paper |
| 898 | All-In-One | 0.5239
±0.1017 | This paper |
| 909 | GPPT | 0.4315
±0.0944 | This paper |
| 911 | GCL + GPF_plus | 0.3418
±0.1771 | This paper |
| 914 | EdgePreGPPT + GPF_plus | 0.2849
±0.1873 | This paper |
| 918 | Supervised | 0.2656
±0.0555 | This paper |
| 923 | SimGRACE + GPF_plus | 0.2133
±0.1486 | This paper |
| 926 | DGI + GPF_plus | 0.1729
±0.0618 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | CNA | 0.9575
±0.0058 | |
| 2 | IS-GIB | 0.9390
±0.0187 | |
| 3 | EERM | 0.9112
±0.0145 | |
| 44 | GCN | 0.8033
±0.0088 | |
| 350 | MLP | 0.7289
±0.0010 | |
| 603 | GPPT | 0.7031
±0.0039 best reported | |
| 832 | GPF-plus | 0.5967
±0.1187 | This paper |
| 833 | GraphMAE + GPF_plus | 0.5967
±0.1187 | This paper |
| 861 | GPrompt | 0.5321
±0.1094 | prev best: OpenGraph: Towards Open Graph Foundation Models (2024) |
| 867 | EdgePreGprompt + GPF_plus | 0.4943
±0.0821 | This paper |
| 869 | GPF | 0.3116
±0.0805 | prev best: OpenGraph: Towards Open Graph Foundation Models (2024) best today: MAGPrompt: Message-Adaptive Graph Prompt Tuning for Graph Neural Networks (2026) Improvement within reported uncertainty; not highlighted. |
| 882 | All-In-One | 0.4436
±0.0252 best reported | best today: MAGPrompt: Message-Adaptive Graph Prompt Tuning for Graph Neural Networks (2026) Difference within reported uncertainty; not counted as underperformance. |
| 889 | Pre-train & Fine-tune | 0.3505
±0.0437 | This paper |
| 894 | GCL + GPF_plus | 0.2886
±0.2288 | This paper |
| 895 | EdgePreGPPT + GPF_plus | 0.2804
±0.1431 | This paper |
| 896 | DGI + GPF_plus | 0.2660
±0.1324 | This paper |
| 897 | SimGRACE + GPF_plus | 0.2461
±0.2121 | This paper |
| 900 | Supervised | 0.2178
±0.0732 | This paper |
TU Dortmund
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | MSH-GNN | 0.9910
±0.0030 | |
| 2 | ID-GNN+BEC | 0.9830
±0.0360 | |
| 3 | SupCosine | 0.9830
±0.0250 | |
| 39 | GIN | 0.9330
±0.0290 | |
| 403 | MLP | 0.8660
±0.0495 | |
| 532 | Supervised | 0.8289
±0.0616 best reported | best at pub: Fine-tuning Graph Neural Networks by Preserving Graph Generative Patterns (AAAI 2023) |
| 621 | All-In-One | 0.7987
±0.0534 | This paper |
| 622 | EdgePreGPPT + All-in-one | 0.7987
±0.0534 | This paper |
| 701 | DGI + All-in-one | 0.7573
±0.0775 | This paper |
| 706 | EdgePreGprompt + All-in-one | 0.7547
±0.0500 | This paper |
| 735 | GPrompt | 0.7360
±0.0476 | This paper |
| 749 | GraphMAE + All-in-one | 0.7227
±0.0887 | This paper |
| 759 | GCL + All-in-one | 0.7053
±0.0858 | This paper |
| 765 | GPF | 0.6840
±0.0509 | This paper |
| 776 | Pre-train & Fine-tune | 0.6547
±0.0589 | This paper |
| 777 | SimGRACE + All-in-one | 0.6547
±0.0691 | This paper |
| 780 | GPF-plus | 0.6520
±0.0604 | This paper |
| 787 | GPPT | 0.6040
±0.1543 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | MSH-GNN | 0.9410
±0.0330 | |
| 2 | GRDL | 0.8260
±0.0120 | |
| 3 | GMN | 0.8225 | |
| 32 | GIN | 0.7880
±0.0410 | |
| 149 | MLP | 0.7600
±0.0320 | |
| 477 | All-In-One | 0.6649
±0.0626 | This paper |
| 478 | GraphMAE + All-in-one | 0.6649
±0.0626 | This paper |
| 481 | EdgePreGPPT + All-in-one | 0.6571
±0.0549 | This paper |
| 488 | GCL + All-in-one | 0.6436
±0.0730 | This paper |
| 491 | GPF | 0.6391
±0.0326 | This paper |
| 492 | Supervised | 0.6351
±0.0360 best reported | best at pub: Fine-tuning Graph Neural Networks by Preserving Graph Generative Patterns (AAAI 2023) Difference within reported uncertainty; not counted as underperformance. |
| 493 | Pre-train & Fine-tune | 0.6344
±0.0364 | This paper |
| 495 | GPF-plus | 0.6292
±0.0278 | This paper |
| 497 | DGI + All-in-one | 0.6258
±0.0707 | This paper |
| 498 | EdgePreGprompt + All-in-one | 0.6182
±0.0753 | This paper |
| 506 | SimGRACE + All-in-one | 0.6117
±0.0173 | This paper |
| 508 | GPPT | 0.6092
±0.0247 | This paper |
| 513 | GPrompt | 0.5917
±0.1126 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | WL-MLP | 0.9792 | |
| 2 | MSH-GNN | 0.9640
±0.0070 | |
| 3 | CoCN | 0.8722
±0.0013 | |
| 23 | GCN | 0.8260
±0.0220 | |
| 151 | MLP | 0.7920
±0.0240 | |
| 347 | All-In-One | 0.5166
±0.0026 | This paper |
| 348 | GCL + All-in-one | 0.5166
±0.0260 | This paper |
| 350 | GPrompt | 0.4825
±0.1364 | This paper |
| 351 | Pre-train & Fine-tune | 0.4810
±0.0023 | This paper |
| 352 | SimGRACE + All-in-one | 0.4760
±0.0390 | This paper |
| 353 | GPF | 0.4742
±0.1122 | This paper |
| 354 | GPF-plus | 0.4724
±0.0029 | This paper |
| 355 | Supervised | 0.4723
±0.0061 | This paper |
| 356 | GPPT | 0.4718
±0.0593 | This paper |
| 357 | EdgePreGprompt + All-in-one | 0.4287
±0.0619 | This paper |
| 358 | EdgePreGPPT + All-in-one | 0.4274
±0.0465 | This paper |
| 359 | GraphMAE + All-in-one | 0.4082
±0.1463 | This paper |
| 360 | DGI + All-in-one | 0.3956
±0.0500 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GMN | 0.7866 | |
| 2 | MemGNN | 0.7550 | |
| 3 | TFGW SP | 0.7510
±0.0500 | |
| 17 | GatedGCN | 0.7000
±0.0494 | |
| 26 | GraphSAGE | 0.6817
±0.0545 | |
| 124 | MLP | 0.5583
±0.0352 | |
| 251 | All-In-One | 0.2608
±0.0486 best reported | best today: DAGPrompT: Pushing the Limits of Graph Prompting with a Distribution-aware Graph Prompt Tuning Approach (WWW 2025) Difference within reported uncertainty; not counted as underperformance. |
| 258 | DGI + All-in-one | 0.2396
±0.0145 | This paper |
| 263 | GraphMAE + All-in-one | 0.2321
±0.0172 | This paper |
| 267 | GPF-plus | 0.2292
±0.0164 | This paper |
| 274 | SimGRACE + All-in-one | 0.2250
±0.0156 | This paper |
| 277 | GPrompt | 0.2229
±0.0350 | This paper |
| 278 | Pre-train & Fine-tune | 0.2221
±0.0279 | This paper |
| 280 | GPF | 0.2200
±0.0125 | This paper |
| 281 | EdgePreGprompt + All-in-one | 0.2188
±0.0056 | This paper |
| 288 | GPPT | 0.2129
±0.0379 | This paper |
| 289 | EdgePreGPPT + All-in-one | 0.2092
±0.0204 | This paper |
| 291 | Supervised | 0.2058
±0.0200 | prev best: Fine-tuning Graph Neural Networks by Preserving Graph Generative Patterns (AAAI 2023) Improvement within reported uncertainty; not highlighted. |
| 296 | GCL + All-in-one | 0.1946
±0.0285 | This paper |
Heterophilic Graphs
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | P^2GNN | 0.9672
±0.0147 | |
| 2 | DoG | 0.9660
±0.0210 | |
| 3 | GPF-plus | 0.9583
±0.0419 | This paper |
| 4 | GCL + GPF_plus | 0.9583
±0.0419 | This paper |
| 13 | GraphMAE + GPF_plus | 0.9409
±0.0440 | This paper |
| 34 | MLP | 0.9230
±0.0070 | |
| 38 | EdgePreGPPT + GPF_plus | 0.9214
±0.0546 | This paper |
| 49 | SimGRACE + GPF_plus | 0.9074
±0.0312 | This paper |
| 53 | GraphSAGE | 0.9000
±0.0365 | |
| 94 | EdgePreGprompt + GPF_plus | 0.8770
±0.0377 | This paper |
| 100 | GPF | 0.8740
±0.0340 | This paper |
| 252 | DGI + GPF_plus | 0.7954
±0.0189 | This paper |
| 616 | GPrompt | 0.3325
±0.4011 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | DiGGR | 0.4535
±0.0353 | |
| 2 | TRIGON | 0.4402
±0.0028 | |
| 3 | DoG | 0.4320
±0.0120 | |
| 42 | MLP | 0.4026
±0.0108 | |
| 68 | GraphSAGE | 0.3899
±0.0085 | |
| 363 | GPF-plus | 0.2932
±0.0856 | This paper |
| 364 | EdgePreGPPT + GPF_plus | 0.2932
±0.0856 | This paper |
| 382 | GPF | 0.2870
±0.0335 | This paper |
| 414 | GraphMAE + GPF_plus | 0.2658
±0.0784 | This paper |
| 433 | GPrompt | 0.2526
±0.0110 | This paper |
| 440 | All-In-One | 0.2461
±0.0280 | This paper |
| 460 | GCL + GPF_plus | 0.2282
±0.0499 | This paper |
| 461 | EdgePreGprompt + GPF_plus | 0.2268
±0.0364 | This paper |
| 462 | GPPT | 0.2258
±0.0197 | This paper |
| 463 | DGI + GPF_plus | 0.2242
±0.0966 | This paper |
| 483 | Pre-train & Fine-tune | 0.2074
±0.0412 | This paper |
| 485 | Supervised | 0.2057
±0.0447 | This paper |
| 486 | SimGRACE + GPF_plus | 0.2051
±0.0424 | This paper |
