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
| # | 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 | |
| 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 |
| # | 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 | |
| 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 |
| # | Model | Accuracy ↑ | 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
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | WL-MLP | 0.9954 | |
| 2 | GIN | 0.9934 | |
| 3 | GCN | 0.9727 | |
| 131 | GraphSAGE | 0.8200
±0.0100 | |
| 358 | Random | 0.7700
±0.0170 best reported | best at pub: Higher-order Clustering and Pooling for Graph Neural Networks (2022) |
| 414 | topk | 0.7500
±0.0200 best reported | |
| 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
| # | Model | Accuracy ↑ | 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 | 0.3707
±0.0020 | prev best: Long-range Meta-path Search on Large-scale Heterogeneous Graphs (NeurIPS 2023) Improvement within reported uncertainty; not highlighted. |
| 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
| # | Model | Accuracy ↑ | 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 |
