ICML 2023

Graph Ladling: Shockingly Simple Parallel GNN Training without Intermediate Communication

A. Jaiswal, Shiwei Liu, Tianlong Chen, Ying Ding, Zhangyang Wang

Main figure for Graph Ladling: Shockingly Simple Parallel GNN Training without Intermediate Communication

Abstract

Graphs are omnipresent and GNNs are a powerful family of neural networks for learning over graphs. Despite their popularity, scaling GNNs either by deepening or widening suffers from prevalent issues of unhealthy gradients, over-smoothening, information squashing, which often lead to sub-standard performance. In this work, we are interested in exploring a principled way to scale GNNs capacity without deepening or widening, which can improve its performance across multiple small and large graphs. Motivated by the recent intriguing phenomenon of model soups, which suggest that fine-tuned weights of multiple large-language pre-trained models can be merged to a better minima, we argue to exploit the fundamentals of model soups to mitigate the aforementioned issues of memory bottleneck and trainability during GNNs scaling. More specifically, we propose not to deepen or widen current GNNs, but instead present a data-centric perspective of model soups tailored for GNNs, i.e., to build powerful GNNs. By dividing giant graph data, we build multiple independently and parallelly trained weaker GNNs (soup ingredient) without any intermediate communication, and combine their strength using a greedy interpolation soup procedure to achieve state-of-the-art performance. Compared to concurrent distributed GNN training works such as, we train each soup ingredient by sampling different subgraphs per epoch and their respective sub-models are merged only after being fully trained (rather than intermediately so). Moreover, we provide a wide variety of model soup preparation techniques by leveraging state-of-the-art graph sampling and graph partitioning approaches that can handle large graphs. Extensive experiments across many real-world small and large graphs, illustrate the effectiveness of our approach and point towards a promising orthogonal direction for GNN scaling. Codes are available at:.

Proposed method: BTM

Benchmark Results

Tested on 10 datasets 33 baseline values 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
333
APPNP Our Soup
0.8370
This paper
339
APPNP Vanilla
0.8364
This paper
363
GCN Our Soup
0.8352
This paper
380
DAGNN Our Soup
0.8345
This paper
388
DAGNN Vanilla
0.8339
This paper
447
GCNII Our Soup
0.8277
This paper
483
GCN vanilla
0.8239
This paper
514
GCNII Vanilla
0.8219
This paper
649
SGC Our Soup
0.8022
This paper
664
JKNet Our Soup
0.7989
This paper
686
SGC Vanilla
0.7931
This paper
693
JKNet Vanilla
0.7906
This paper
724
MLP
0.7768
#ModelAccuracy ↑Paper
1
CNA
0.9575 ±0.0058
2
IS-GIB
0.9390 ±0.0187
3
EERM
0.9112 ±0.0145
20
APPNP
actual #20 vs paper #445 425 places worse
0.8142 ±0.0026
best reported
actual #20 vs paper #445 425 places worse
paper 0.7213
paper 0.7213 Δ at pub 0.0929
36
GCNII
actual #36 vs paper #334 298 places worse
0.8076 ±0.0030
best reported
actual #36 vs paper #334 298 places worse
paper 0.7297
paper 0.7297 Δ at pub 0.0779
44
GCN
actual #44 vs paper #526 482 places worse
0.8033 ±0.0088
best reported
actual #44 vs paper #526 482 places worse
paper 0.7136
61
GraphSAGE
0.7923 ±0.0053
62
JKNet
actual #62 vs paper #722 660 places worse
0.7920
best reported
actual #62 vs paper #722 660 places worse
paper 0.6698
paper 0.6698 Δ at pub 0.1222
75
DAGNN
actual #75 vs paper #324 249 places worse
0.7860
best reported
actual #75 vs paper #324 249 places worse
paper 0.7305
paper 0.7305 Δ at pub 0.0555
96
SGC
actual #96 vs paper #437 341 places worse
0.7765 ±0.0012
best reported
actual #96 vs paper #437 341 places worse
paper 0.7222
350
MLP
0.7289 ±0.0010
#ModelAccuracy ↑Paper
1
LGTL
0.9518 ±0.0011
2
MixHop (LO)
0.9513 ±0.0038
3
GraphSAGE (LO)
0.9511 ±0.0036
17
APPNP
actual #17 vs paper #418 401 places worse
0.9355 ±0.0060
best reported
actual #17 vs paper #418 401 places worse
paper 0.8030
18
GCN
actual #18 vs paper #501 483 places worse
0.9296 ±0.0015
best reported
actual #18 vs paper #501 483 places worse
paper 0.7956
24
JKNet
actual #24 vs paper #724 700 places worse
0.9160
best reported
actual #24 vs paper #724 700 places worse
paper 0.7724
paper 0.7724 Δ at pub 0.1436
58
GCNII
actual #58 vs paper #673 615 places worse
0.9030 ±0.0043
best reported
actual #58 vs paper #673 615 places worse
paper 0.7806
116
SAGE
0.8881 ±0.0015
141
SGC
actual #141 vs paper #673 532 places worse
0.8832 ±0.0055
best reported
actual #141 vs paper #673 532 places worse
paper 0.7806
210
MLP
0.8690 ±0.0074
226
DAGNN
actual #226 vs paper #400 174 places worse
0.8640
best reported
actual #226 vs paper #400 174 places worse
paper 0.8058
paper 0.8058 Δ at pub 0.0582
377
BTM
0.8092
This paper

Reddit

Global leaderboard →

Default metric is F1. The paper reports 6 values on F1 , 1 value on accuracy (percent, no explicit header; source follows benchmark metrics per L381) and 4 values on accuracy (percent, no explicit header) .

#ModelF1 ↑ defaultaccuracy (percent, no explicit header; source follows benchmark metrics per L381) ↑accuracy (percent, no explicit header) ↑Paper
1
Node Sampled Soup
—
—
0.9728 ± 0.0008
accuracy (percent, no explicit header; source follows benchmark metrics per L381) —
accuracy (percent, no explicit header) 0.9728 ± 0.0008
This paper
1
EnGCN
0.9714 ± 0.0003
——
accuracy (percent, no explicit header; source follows benchmark metrics per L381) —
accuracy (percent, no explicit header) —
2
SAGN+SLE
0.9710 ± 0.0000
——
accuracy (percent, no explicit header; source follows benchmark metrics per L381) —
accuracy (percent, no explicit header) —
3
GAMLP(JK)
0.9704 ± 0.0001
——
accuracy (percent, no explicit header; source follows benchmark metrics per L381) —
accuracy (percent, no explicit header) —
4
GraphSAINT
0.9700
best reported
——
accuracy (percent, no explicit header; source follows benchmark metrics per L381) —
accuracy (percent, no explicit header) —
paper 0.9562 ±0.0005
paper 0.9562 ±0.0005 Δ at pub 0.0138
13
GraphSAGE Ensemble
0.9661
——
accuracy (percent, no explicit header; source follows benchmark metrics per L381) —
accuracy (percent, no explicit header) —
This paper
14
GraphSAGE
0.9660
best reported
——
accuracy (percent, no explicit header; source follows benchmark metrics per L381) —
accuracy (percent, no explicit header) —
paper 0.9650 ±0.0003
paper 0.9650 ±0.0003 Δ at pub 0.0010
22
Our Data Partition Soup
—
—
0.9641 ± 0.0008
accuracy (percent, no explicit header; source follows benchmark metrics per L381) —
accuracy (percent, no explicit header) 0.9641 ± 0.0008
This paper
48
ClusterGCN
0.9570
best reported
——
accuracy (percent, no explicit header; source follows benchmark metrics per L381) —
accuracy (percent, no explicit header) —
paper 0.9568 ±0.0003

Difference within reported uncertainty; not counted as underperformance.

paper 0.9568 ±0.0003 Δ at pub 0.0002
49
ClusterGCN Ensemble
0.9570
——
accuracy (percent, no explicit header; source follows benchmark metrics per L381) —
accuracy (percent, no explicit header) —
This paper
58
GCN
0.9530 ± 0.0010
——
accuracy (percent, no explicit header; source follows benchmark metrics per L381) —
accuracy (percent, no explicit header) —
91
FastGCN
0.9370
best reported
——
accuracy (percent, no explicit header; source follows benchmark metrics per L381) —
accuracy (percent, no explicit header) —
paper 0.7950 ±0.0122
111
Edge Sampled Soup
—
—
0.9266 ± 0.0034
accuracy (percent, no explicit header; source follows benchmark metrics per L381) —
accuracy (percent, no explicit header) 0.9266 ± 0.0034
This paper
119
Layer Sampled Soup
—
—
0.8601 ± 0.0017
accuracy (percent, no explicit header; source follows benchmark metrics per L381) —
accuracy (percent, no explicit header) 0.8601 ± 0.0017
This paper
104
LADIES
—
0.6278 ± 0.0089
—
accuracy (percent, no explicit header; source follows benchmark metrics per L381) 0.6278 ± 0.0089
accuracy (percent, no explicit header) —
This paper

OGB

#ModelAccuracy ↑Paper
1
Jacobi
0.8968
2
GPR
0.8953
3
LEMP4HG
0.8939
4
SAGE
0.8933
64
GraphSAINT
actual #64 vs paper #259 195 places worse
0.8383 ±0.0014
best reported
actual #64 vs paper #259 195 places worse
paper 0.7536 ±0.0034
paper 0.7536 ±0.0034 Δ at pub 0.0847
83
GraphSAGE
actual #83 vs paper #134 51 places worse
0.8287
best reported
actual #83 vs paper #134 51 places worse
paper 0.8061 ±0.0016
114
Node Sampled Soup
0.8134 ±0.0028
This paper
130
GraphSAGE Ensemble
0.8085
This paper
170
Our Data Partition Soup
0.7934 ±0.0028
This paper
190
ClusterGCN
actual #190 vs paper #206 16 places worse
0.7897 ±0.0033
best reported
actual #190 vs paper #206 16 places worse
paper 0.7862 ±0.0061

Difference within reported uncertainty; not counted as underperformance.

paper 0.7862 ±0.0061 Δ at pub 0.0035 Δ today 0.0035
198
ClusterGCN Ensemble
0.7874
This paper
256
Edge Sampled Soup
0.7558 ±0.0045
This paper
262
LADIES
0.7531 ±0.0056
This paper
270
Layer Sampled Soup
0.7495 ±0.0038
This paper
308
FastGCN
0.7346 ±0.0020
This paper
351
MLP
0.6605 ±0.0020

ogbn-arxiv

Global leaderboard →

Default metric is Accuracy. The paper reports 6 values on Accuracy and 5 values on accuracy (percent, no explicit header) .

#ModelAccuracy ↑ defaultaccuracy (percent, no explicit header) ↑Paper
1
GIANT-XRT
0.7612 ± 0.0016
—
2
GEGCN
0.7576 ± 0.0064
—
3
AGDN
0.7522 ± 0.0007
—
23
GCN
0.7300 ± 0.0017
—
25
Node Sampled Soup
—
0.7283 ± 0.0021
accuracy (percent, no explicit header) 0.7283 ± 0.0021
This paper
31
Our Data Partition Soup
0.7235 ± 0.0019
—
accuracy (percent, no explicit header) —
This paper
57
GraphSAGE Ensemble
0.7158
—
accuracy (percent, no explicit header) —
This paper
25
GraphSAGE
—
0.7155 ± 0.0041
accuracy (percent, no explicit header) 0.7155 ± 0.0041
This paper
63
ClusterGCN Ensemble
0.7143
—
accuracy (percent, no explicit header) —
This paper
67
ClusterGCN
0.7129 ± 0.0044
—
accuracy (percent, no explicit header) —
This paper
79
GraphSAINT
0.7055 ± 0.0026
—
accuracy (percent, no explicit header) —
This paper
82
Edge Sampled Soup
—
0.7045 ± 0.0029
accuracy (percent, no explicit header) 0.7045 ± 0.0029
This paper
91
Layer Sampled Soup
0.6830 ± 0.0054
—
accuracy (percent, no explicit header) —
This paper
100
FastGCN
—
0.6610 ± 0.0106
accuracy (percent, no explicit header) 0.6610 ± 0.0106
This paper
105
LADIES
—
0.6278 ± 0.0089
accuracy (percent, no explicit header) 0.6278 ± 0.0089
This paper
107
MLP
0.5765 ± 0.0012
—

Heterophilic Graphs

#ModelAccuracy ↑Paper
1
P^2GNN
0.9672 ±0.0147
2
DoG
0.9660 ±0.0210
3
GPF-plus
0.9583 ±0.0419
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 at pub 0.3050 Δ today 0.3063
53
GraphSAGE
0.9000 ±0.0365
70
GCNII
actual #70 vs paper #448 378 places worse
0.8918 ±0.0443
best reported
actual #70 vs paper #448 378 places worse
paper 0.6428 ±0.0293
paper 0.6428 ±0.0293 Δ at pub 0.1618 Δ today 0.2490
257
GCN
actual #257 vs paper #499 242 places worse
0.7933 ±0.0447
best reported
actual #257 vs paper #499 242 places worse
paper 0.6012 ±0.0422
best today: Graph Wave Networks (WWW 2025)
paper 0.6012 ±0.0422 Δ at pub 0.1828 Δ today 0.1921
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 at pub 0.1799
385
BTM
0.7045 ±0.0277
This paper
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 at pub 0.0270 Δ today 0.0892
401
GradientGCN
0.6919 ±0.0656
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 at pub 0.3338
24
MLP
0.9136 ±0.0070
35
GCNII
actual #35 vs paper #395 360 places worse
0.8918 ±0.0396
best reported
actual #35 vs paper #395 360 places worse
paper 0.5851 ±0.0166
paper 0.5851 ±0.0166 Δ at pub 0.2575 Δ today 0.3067
138
SAGE
0.8269
170
GCN
actual #170 vs paper #438 268 places worse
0.8082 ±0.0360
best reported
actual #170 vs paper #438 268 places worse
paper 0.5405 ±0.0711
paper 0.5405 ±0.0711 Δ at pub 0.2515 Δ today 0.2677
223
BTM
0.7590 ±0.0476
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 at pub 0.0088 Δ today 0.1713
248
GradientGCN
0.7416 ±0.0648
This paper
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 at pub 0.1493
#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 #327 289 places worse
0.4082 ±0.0179
best reported
actual #38 vs paper #327 289 places worse
paper 0.3095 ±0.0104
paper 0.3095 ±0.0104 Δ at pub 0.0766 Δ today 0.0987
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 at pub 0.1125 Δ today 0.1181
42
MLP
0.4026 ±0.0108
68
GraphSAGE
0.3899 ±0.0085
135
GCN
actual #135 vs paper #425 290 places worse
0.3690
best reported
actual #135 vs paper #425 290 places worse
paper 0.2546 ±0.0143
paper 0.2546 ±0.0143 Δ at pub 0.1144
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 at pub 0.0873
243
BTM
0.3469 ±0.0051
This paper
257
GradientGCN
0.3428 ±0.0112
This paper
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 at pub 0.0462
#ModelAccuracy ↑Paper
1
DMD++
0.9190 ±0.0260
2
F-GREAD-BS
0.9059 ±0.0380
3
APPNP
actual #3 vs paper #190 187 places worse
0.9010 ±0.0350
best reported
actual #3 vs paper #190 187 places worse
paper 0.5424 ±0.0594
paper 0.5424 ±0.0594 Δ at pub 0.3006 Δ today 0.3586
37
MLP
0.8629 ±0.0450
63
GCN
actual #63 vs paper #196 133 places worse
0.8310 ±0.0320
best reported
actual #63 vs paper #196 133 places worse
paper 0.5294 ±0.0399
paper 0.5294 ±0.0399 Δ at pub 0.3016
69
GraphSAGE
0.8118 ±0.0556
75
GCNII
actual #75 vs paper #172 97 places worse
0.8039 ±0.0340
best reported
actual #75 vs paper #172 97 places worse
paper 0.5919 ±0.0907
paper 0.5919 ±0.0907 Δ at pub 0.2120 Δ today 0.2120
91
SGC
actual #91 vs paper #206 115 places worse
0.7780 ±0.0470
best reported
actual #91 vs paper #206 115 places worse
paper 0.5129 ±0.0644
paper 0.5129 ±0.0644 Δ at pub 0.2651
118
BTM
0.7201 ±0.0389
This paper
126
GradientGCN
0.7031 ±0.0475
This paper
166
JKNet
actual #166 vs paper #196 30 places worse
0.6098 ±0.0297
best reported
actual #166 vs paper #196 30 places worse
paper 0.5276 ±0.0569

Difference within reported uncertainty; not counted as underperformance.

paper 0.5276 ±0.0569 Δ at pub 0.0822
SOTA performance (not significantly different from the best) Proposed method (this paper) 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