NeurIPS 2024

ProG: A Graph Prompt Learning Benchmark

Chenyi Zi, Haihong Zhao, Xiangguo Sun, Yiqing Lin, Hong Cheng, Jia Li

Main figure for 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

#ModelAccuracy ↑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
actual #884 vs paper #909 25 places worse
0.5760 ±0.1388
best reported
actual #884 vs paper #909 25 places worse
paper 0.3857 ±0.0541

Difference within reported uncertainty; not counted as underperformance.

paper 0.3857 ±0.0541 Δ today 0.1903
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
#ModelAccuracy ↑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
actual #603 vs paper #887 284 places worse
0.7031 ±0.0039
best reported
actual #603 vs paper #887 284 places worse
paper 0.3726 ±0.0617
832
GPF-plus
0.5967 ±0.1187
This paper
833
GraphMAE + GPF_plus
0.5967 ±0.1187
This paper
861
GPrompt
actual #861 vs paper #861
0.5321 ±0.1094
actual #861 vs paper #861
paper 0.5321 ±0.1094
paper 0.5321 ±0.1094 Δ at pub 0.2521
867
EdgePreGprompt + GPF_plus
0.4943 ±0.0821
This paper
869
GPF
actual #869 vs paper #891 22 places worse
0.3116 ±0.0805
actual #869 vs paper #891 22 places worse
paper 0.3116 ±0.0805

Improvement within reported uncertainty; not highlighted.

paper 0.3116 ±0.0805 Δ at pub 0.0006 Δ today 0.1786
882
All-In-One
actual #882 vs paper #887 5 places worse
0.4436 ±0.0252
best reported
actual #882 vs paper #887 5 places worse
paper 0.4041 ±0.0280

Difference within reported uncertainty; not counted as underperformance.

paper 0.4041 ±0.0280 Δ today 0.0395
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

#ModelAccuracy ↑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
actual #532 vs paper #778 246 places worse
0.8289 ±0.0616
best reported
actual #532 vs paper #778 246 places worse
paper 0.6520 ±0.0670
paper 0.6520 ±0.0670 Δ at pub 0.1769
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
#ModelAccuracy ↑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
actual #492 vs paper #515 23 places worse
0.6351 ±0.0360
best reported
actual #492 vs paper #515 23 places worse
paper 0.5636 ±0.0797

Difference within reported uncertainty; not counted as underperformance.

paper 0.5636 ±0.0797 Δ at pub 0.0715
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
#ModelAccuracy ↑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
#ModelAccuracy ↑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
actual #251 vs paper #257 6 places worse
0.2608 ±0.0486
best reported
actual #251 vs paper #257 6 places worse
paper 0.2396 ±0.0145

Difference within reported uncertainty; not counted as underperformance.

paper 0.2396 ±0.0145 Δ today 0.0212
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
actual #291 vs paper #291
0.2058 ±0.0200
actual #291 vs paper #291
paper 0.2058 ±0.0200

Improvement within reported uncertainty; not highlighted.

paper 0.2058 ±0.0200 Δ at pub 0.0008
296
GCL + All-in-one
0.1946 ±0.0285
This paper

Heterophilic Graphs

#ModelAccuracy ↑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
#ModelAccuracy ↑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
SOTA performance (not significantly different from the best) Baseline / comparison (this paper) Global context (other papers) Best at pub — reported result worse than the best known when published (best reported in green) Best at pub — reported value improved over the best known when published Best today — OK at publication; today's leaderboard best is elsewhere