Bag of Tricks for Training Deeper Graph Neural Networks: A Comprehensive Benchmark Study

Tianlong Chen, Kaixiong Zhou, Keyu Duan, Wenqing Zheng, Peihao Wang, Xia Hu, Zhangyang Wang

Main figure for Bag of Tricks for Training Deeper Graph Neural Networks: A Comprehensive Benchmark Study

Abstract

Training deep graph neural networks (GNNs) is notoriously hard. Besides the standard plights in training deep architectures such as vanishing gradients and overfitting, it also uniquely suffers from over-smoothing, information squashing, and so on, which limits their potential power for encoding the high-order neighbor structure in large-scale graphs. Although numerous efforts are proposed to address these limitations, such as various forms of skip connections, graph normalization, and random dropping, it is difficult to disentangle the advantages brought by a deep GNN architecture from those ``tricks" necessary to train such an architecture. Moreover, the lack of a standardized benchmark with fair and consistent experimental settings poses an almost insurmountable obstacle to gauge the effectiveness of new mechanisms. In view of those, we present the first fair and reproducible benchmark dedicated to assessing the ``tricks" of training deep GNNs. We categorize existing approaches, investigate their hyperparameter sensitivity, and unify the basic configuration. Comprehensive evaluations are then conducted on tens of representative graph datasets including the recent large-scale Open Graph Benchmark, with diverse deep GNN backbones. We demonstrate that an organic combo of initial connection, identity mapping, group and batch normalization attains the new state-of-the-art results for deep GNNs on large datasets. Codes are available:.

Benchmark Results

Tested on 6 datasets 9 baseline values reported too low

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

Classic

#ModelAccuracy ↑Paper
1
GraphTARIF
0.9703 ±0.0019
2
GAT
0.9669 ±0.0014
3
GAT+T
0.9660 ±0.0007
7
SAGE
0.9643 ±0.0027
21
APPNP
actual #21 vs paper #562 541 places worse
0.9573 ±0.0012
best reported
actual #21 vs paper #562 541 places worse
paper 0.5962 ±0.2327

Difference within reported uncertainty; not counted as underperformance.

paper 0.5962 ±0.2327 Δ at pub 0.3234 Δ today 0.3611
33
GPRGNN
actual #33 vs paper #359 326 places worse
0.9549 ±0.0014
best reported
actual #33 vs paper #359 326 places worse
paper 0.9174 ±0.0081
paper 0.9174 ±0.0081 Δ today 0.0375
50
SGC
actual #50 vs paper #571 521 places worse
0.9511 ±0.0009
best reported
actual #50 vs paper #571 521 places worse
paper 0.2660 ±0.0464
paper 0.2660 ±0.0464 Δ at pub 0.6500 Δ today 0.6851
87
GCNII
actual #87 vs paper #561 474 places worse
0.9430 ±0.0020
best reported
actual #87 vs paper #561 474 places worse
paper 0.6295 ±0.0941
paper 0.6295 ±0.0941 Δ at pub 0.2693 Δ today 0.3135
260
DAGNN
actual #260 vs paper #451 191 places worse
0.9269
best reported
actual #260 vs paper #451 191 places worse
paper 0.8996 ±0.0116
paper 0.8996 ±0.0116 Δ at pub 0.0273
364
JKNet
actual #364 vs paper #540 176 places worse
0.9169
best reported
actual #364 vs paper #540 176 places worse
paper 0.7842 ±0.0695
paper 0.7842 ±0.0695 Δ at pub 0.0928 Δ today 0.1327
390
MLP
0.9128 ±0.0063
488
OGB
0.8829 ±0.0173
This paper
576
DGMLP
0.2531
This paper
#ModelAccuracy ↑Paper
1
GraphTARIF
0.9461 ±0.0017
2
GCN
0.9412 ±0.0008
3
GAT
0.9398 ±0.0022
8
SAGE
0.9351 ±0.0006
52
GCNII
actual #52 vs paper #496 444 places worse
0.9104 ±0.0041
best reported
actual #52 vs paper #496 444 places worse
paper 0.3756 ±0.0043
58
APPNP
actual #58 vs paper #493 435 places worse
0.9093 ±0.0018
best reported
actual #58 vs paper #493 435 places worse
paper 0.4302 ±0.1016
72
GPRGNN
actual #72 vs paper #494 422 places worse
0.9050 ±0.0091
best reported
actual #72 vs paper #494 422 places worse
paper 0.4194 ±0.0995
paper 0.4194 ±0.0995 Δ today 0.4856
82
SGC
actual #82 vs paper #496 414 places worse
0.9022 ±0.0021
best reported
actual #82 vs paper #496 414 places worse
paper 0.3753 ±0.0020
230
JKNet
actual #230 vs paper #478 248 places worse
0.8760
best reported
actual #230 vs paper #478 248 places worse
paper 0.6799 ±0.0507
paper 0.6799 ±0.0507 Δ at pub 0.1961
320
MLP
0.8463
324
DAGNN
actual #324 vs paper #431 107 places worse
0.8450 ±0.0120
best reported
actual #324 vs paper #431 107 places worse
paper 0.7973 ±0.0363

Difference within reported uncertainty; not counted as underperformance.

paper 0.7973 ±0.0363 Δ at pub 0.0305 Δ today 0.0477
451
OGB
0.7540 ±0.0188
This paper
501
DGMLP
0.3740
This paper
#ModelAccuracy ↑Paper
1
GrokFormer
0.9831 ±0.0018
2
PolyFormer
0.9808 ±0.0027
3
SGFormer
0.9796 ±0.0081
7
GPRGNN
actual #7 vs paper #218 211 places worse
0.9777 ±0.0015
best reported
actual #7 vs paper #218 211 places worse
paper 0.9349 ±0.0059
paper 0.9349 ±0.0059 Δ today 0.0428
9
GCN
0.9774 ±0.0035
42
APPNP
actual #42 vs paper #206 164 places worse
0.9375 ±0.0061
actual #42 vs paper #206 164 places worse
paper 0.9375 ±0.0061
prev best: Elastic Graph Neural Networks (ICML 2021)

Improvement within reported uncertainty; not highlighted.

paper 0.9375 ±0.0061 Δ at pub 0.0005 Δ today 0.0279
59
GCNII
actual #59 vs paper #232 173 places worse
0.9597 ±0.0011
best reported
actual #59 vs paper #232 173 places worse
paper 0.9315 ±0.0092
paper 0.9315 ±0.0092 Δ today 0.0282
58
MLP
0.9597 ±0.0007
70
SGC
actual #70 vs paper #265 195 places worse
0.9580 ±0.0010
best reported
actual #70 vs paper #265 195 places worse
paper 0.9146 ±0.0048
best at pub: Elastic Graph Neural Networks (ICML 2021)
paper 0.9146 ±0.0048 Δ at pub 0.0164 Δ today 0.0434
192
OGB
0.9412 ±0.0056
This paper
197
DAGNN
actual #197 vs paper #219 22 places worse
0.9401 ±0.0060
best reported
actual #197 vs paper #219 22 places worse
paper 0.9331 ±0.0060

Difference within reported uncertainty; not counted as underperformance.

paper 0.9331 ±0.0060 Δ today 0.0070
227
JKNet
actual #227 vs paper #269 42 places worse
0.9325 ±0.0082
best reported
actual #227 vs paper #269 42 places worse
paper 0.9092 ±0.0161

Difference within reported uncertainty; not counted as underperformance.

paper 0.9092 ±0.0161 Δ today 0.0233
261
DGMLP
0.9207 ±0.0031
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
28
GPRGNN
actual #28 vs paper #470 442 places worse
0.9295 ±0.0131
best reported
actual #28 vs paper #470 442 places worse
paper 0.6227 ±0.0497
paper 0.6227 ±0.0497 Δ today 0.3068
34
MLP
0.9230 ±0.0070
46
APPNP
actual #46 vs paper #493 447 places worse
0.9131 ±0.0197
best reported
actual #46 vs paper #493 447 places worse
paper 0.6068 ±0.0450
paper 0.6068 ±0.0450 Δ today 0.3063
53
GraphSAGE
0.9000 ±0.0365
70
GCNII
actual #70 vs paper #400 330 places worse
0.8918 ±0.0443
best reported
actual #70 vs paper #400 330 places worse
paper 0.6919 ±0.0656
paper 0.6919 ±0.0656 Δ at pub 0.0627 Δ today 0.1999
250
OGB
0.7968 ±0.0377
This paper
330
SGC
actual #330 vs paper #557 227 places worse
0.7440 ±0.0600
best reported
actual #330 vs paper #557 227 places worse
paper 0.5641 ±0.0425
paper 0.5641 ±0.0425 Δ today 0.1799
386
DAGNN
actual #386 vs paper #546 160 places worse
0.7027 ±0.0493
best reported
actual #386 vs paper #546 160 places worse
paper 0.5768 ±0.0507
392
JKNet
actual #392 vs paper #489 97 places worse
0.7000 ±0.0549
best reported
actual #392 vs paper #489 97 places worse
paper 0.6108 ±0.0623

Difference within reported uncertainty; not counted as underperformance.

paper 0.6108 ±0.0623 Δ today 0.0892
441
DGMLP
0.6486
This paper
#ModelAccuracy ↑Paper
1
P^2GNN
0.9541 ±0.0272
2
ACM-GCN
0.9480 ±0.0380
3
RF-GCN
0.9429
21
APPNP
actual #21 vs paper #396 375 places worse
0.9181 ±0.0196
best reported
actual #21 vs paper #396 375 places worse
paper 0.5843 ±0.0374
paper 0.5843 ±0.0374 Δ today 0.3338
22
GPRGNN
actual #22 vs paper #400 378 places worse
0.9157 ±0.0196
best reported
actual #22 vs paper #400 378 places worse
paper 0.5827 ±0.0396
paper 0.5827 ±0.0396 Δ today 0.3330
24
MLP
0.9136 ±0.0070
35
GCNII
actual #35 vs paper #247 212 places worse
0.8918 ±0.0396
best reported
actual #35 vs paper #247 212 places worse
paper 0.7416 ±0.0648
paper 0.7416 ±0.0648 Δ at pub 0.0395 Δ today 0.1502
138
SAGE
0.8269
164
OGB
0.8124 ±0.0577
This paper
241
JKNet
actual #241 vs paper #414 173 places worse
0.7443 ±0.0830
best reported
actual #241 vs paper #414 173 places worse
paper 0.5730 ±0.0495
paper 0.5730 ±0.0495 Δ today 0.1713
250
DAGNN
actual #250 vs paper #396 146 places worse
0.7351 ±0.0718
best reported
actual #250 vs paper #396 146 places worse
paper 0.5843 ±0.0393
252
SGC
actual #252 vs paper #395 143 places worse
0.7350 ±0.0430
best reported
actual #252 vs paper #395 143 places worse
paper 0.5857 ±0.0344
paper 0.5857 ±0.0344 Δ today 0.1493
439
DGMLP
0.5405
This paper
#ModelAccuracy ↑Paper
1
DiGGR
0.4535 ±0.0353
2
TRIGON
0.4402 ±0.0028
3
DoG
0.4320 ±0.0120
38
GCNII
actual #38 vs paper #256 218 places worse
0.3428 ±0.0112
actual #38 vs paper #256 218 places worse
paper 0.3428 ±0.0112

Improvement within reported uncertainty; not highlighted.

paper 0.3428 ±0.0112 Δ at pub 0.0043 Δ today 0.0654
41
APPNP
actual #41 vs paper #382 341 places worse
0.4046 ±0.0064
best reported
actual #41 vs paper #382 341 places worse
paper 0.2865 ±0.0128
paper 0.2865 ±0.0128 Δ today 0.1181
42
MLP
0.4026 ±0.0108
52
GPRGNN
actual #52 vs paper #355 303 places worse
0.3992 ±0.0067
best reported
actual #52 vs paper #355 303 places worse
paper 0.2988 ±0.0182
paper 0.2988 ±0.0182 Δ today 0.1004
68
GraphSAGE
0.3899 ±0.0085
139
OGB
0.3684 ±0.0070
This paper
211
DAGNN
actual #211 vs paper #400 189 places worse
0.3551 ±0.0110
best reported
actual #211 vs paper #400 189 places worse
paper 0.2773 ±0.0108
237
SGC
actual #237 vs paper #419 182 places worse
0.3490 ±0.0070
best reported
actual #237 vs paper #419 182 places worse
paper 0.2617 ±0.0115
paper 0.2617 ±0.0115 Δ today 0.0873
281
JKNet
actual #281 vs paper #377 96 places worse
0.3342 ±0.0028
best reported
actual #281 vs paper #377 96 places worse
paper 0.2880 ±0.0097
paper 0.2880 ±0.0097 Δ today 0.0462
426
DGMLP
0.2545 ±0.0015
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 today — OK at publication; today's leaderboard best is elsewhere