TMLR 2025

Towards Efficient Training of Graph Neural Networks: A Multiscale Approach

Eshed Gal, Moshe Eliasof, C. Schönlieb, Eldad Haber, Eran Treister

Main figure for Towards Efficient Training of Graph Neural Networks: A Multiscale Approach

Abstract

Graph Neural Networks (GNNs) have become powerful tools for learning from graph-structured data, finding applications across diverse domains. However, as graph sizes and connectivity increase, standard GNN training methods face significant computational and memory challenges, limiting their scalability and efficiency. In this paper, we present a novel framework for efficient multiscale training of GNNs. Our approach leverages hierarchical graph representations and subgraphs, enabling the integration of information across multiple scales and resolutions. By utilizing coarser graph abstractions and subgraphs, each with fewer nodes and edges, we significantly reduce computational overhead during training. Building on this framework, we propose a suite of scalable training strategies, including coarse-to-fine learning, subgraph-to-full-graph transfer, and multiscale gradient computation. We also provide some theoretical analysis of our methods and demonstrate their effectiveness across various datasets and learning tasks. Our results show that multiscale training can substantially accelerate GNN training for large-scale problems while maintaining, or even improving, predictive performance.

Benchmark Results

Tested on 6 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
377
GCN Subgraphs(p=1)
0.8350 ±0.0040
This paper
433
GCN Random(p=2)
0.8300 ±0.0050
This paper
438
GCN Fine grid
0.8290 ±0.0110
This paper
465
GCN Rand. & Sub.(p=2)
0.8260 ±0.0050
This paper
626
GAT Subgraphs(p=2)
0.8070 ±0.0120
This paper
646
GAT Random(p=1)
0.8030 ±0.0020
This paper
651
GAT Rand. & Sub.(p=2)
0.8020 ±0.0110
This paper
663
GCN Topk(p=1)
0.7990 ±0.0440
This paper
668
GAT Topk(p=1)
0.7980 ±0.0060
This paper
674
GAT Fine grid
0.7960 ±0.0205
This paper
706
GIN Subgraphs(p=1)
0.7870 ±0.0110
This paper
724
MLP
0.7768
729
GIN Topk(p=1)
0.7760 ±0.0560
This paper
737
GIN Random(p=2)
0.7720 ±0.0060
This paper
740
GIN Rand. & Sub.(p=1)
0.7690 ±0.0100
This paper
754
GIN Fine grid
0.7640 ±0.0160
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
349
GAT Random(p=1)
0.7290 ±0.0150
This paper
350
MLP
0.7289 ±0.0010
546
GCN Subgraphs(p=1)
0.7120 ±0.0040
This paper
547
GAT Rand. & Sub.(p=1)
0.7120 ±0.0080
This paper
568
GCN Rand. & Sub.(p=2)
0.7090 ±0.0020
This paper
599
GCN Random(p=1)
0.7040 ±0.0020
This paper
614
GAT Subgraphs(p=1)
0.7020 ±0.0060
This paper
635
GCN Fine grid
0.6960 ±0.0100
This paper
663
GIN Subgraphs(p=1)
0.6880 ±0.0160
This paper
684
GCN Topk(p=1)
0.6810 ±0.0010
This paper
716
GAT Fine grid
0.6720 ±0.0650
This paper
729
GAT Topk(p=1)
0.6680 ±0.0060
This paper
733
GIN Random(p=1)
0.6650 ±0.0220
This paper
756
GIN Rand. & Sub.(p=2)
0.6600 ±0.0020
This paper
781
GIN Topk(p=1)
0.6480 ±0.0390
This paper
797
GIN Fine grid
0.6380 ±0.0260
This paper
#ModelAccuracy ↑Paper
1
LGTL
0.9518 ±0.0011
2
MixHop (LO)
0.9513 ±0.0038
3
GraphSAGE (LO)
0.9511 ±0.0036
18
GCN
0.9296 ±0.0015
210
MLP
0.8690 ±0.0074
664
GCN Topk(p=1)
0.7820 ±0.0030
This paper
682
GCN Subgraphs(p=1)
0.7800 ±0.0030
This paper
697
GCN Rand. & Sub.(p=1)
0.7780 ±0.0080
This paper
712
GCN Fine grid
0.7750 ±0.0040
This paper
713
GCN Random(p=1)
0.7750 ±0.0060
This paper
714
GAT Random(p=1)
0.7750 ±0.0150
This paper
715
GAT Rand. & Sub.(p=2)
0.7750 ±0.0110
This paper
723
GAT Subgraphs(p=2)
0.7730 ±0.0110
This paper
728
GIN Subgraphs(p=1)
0.7720 ±0.0120
This paper
757
GIN Topk(p=2)
0.7650 ±0.0150
This paper
768
GIN Rand. & Sub.(p=1)
0.7610 ±0.0280
This paper
769
GAT Topk(p=1)
0.7610 ±0.0090
This paper
779
GIN Random(p=1)
0.7570 ±0.0200
This paper
786
GAT Fine grid
0.7550 ±0.0050
This paper
791
GIN Fine grid
0.7540 ±0.0040
This paper

TU Dortmund

#ModelAccuracy ↑Paper
1
WL-MLP
0.9954
2
GIN
0.9934
3
GCN
0.9727
131
GraphSAGE
0.8200 ±0.0100
358
Random
actual #358 vs paper #478 120 places worse
0.7700 ±0.0170
best reported
actual #358 vs paper #478 120 places worse
paper 0.7045 ±0.0214
paper 0.7045 ±0.0214 Δ at pub 0.0655
414
topk
actual #414 vs paper #491 77 places worse
0.7500 ±0.0200
best reported
actual #414 vs paper #491 77 places worse
paper 0.6937 ±0.0083
paper 0.6937 ±0.0083 Δ today 0.0563
488
subgraph
0.6973 ±0.0170
This paper
492
Fine Grid
0.6937 ±0.0042
This paper
503
Rand. & Sub.
0.6856 ±0.0088
This paper

OGB

#ModelAccuracy ↑Paper
1
LMSPS+LP+MS
0.5784 ±0.0022
2
SeHGNN+emb+ms
0.5719 ±0.0012
3
SeHGNN+ms
0.5671 ±0.0014
57
GraphSAGE
0.4646 ±0.0060
67
Random
actual #67 vs paper #67
0.3707 ±0.0020
actual #67 vs paper #67
paper 0.3707 ±0.0020

Improvement within reported uncertainty; not highlighted.

paper 0.3707 ±0.0020 Δ at pub 0.0193
69
multiscale training
0.3573 ±0.0040
This paper
70
topk
0.3546 ±0.0040
This paper
72
Rand. & Sub.
0.3464 ±0.0030
This paper
73
Subgraphs
0.3431 ±0.0040
This paper
76
MLP
0.3243

GNNBenchmark

#ModelAccuracy ↑Paper
1
Schrödinger
0.9913 ±0.0004
2
CNN
0.9907 ±0.0007
3
MPNN
0.9895 ±0.0006
11
GatedGCN
0.9855 ±0.0002
32
GIN
0.9833 ±0.0011
126
MLP
0.9534 ±0.0014
146
Random and Subgraphs (p=3)
0.8604 ±0.0010
This paper
147
Subgraphs (p=3)
0.8603
This paper
148
Topk (p=3)
0.8590 ±0.0010
This paper
149
Random (p=3)
0.8585 ±0.0010
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