How Framelets Enhance Graph Neural Networks
Abstract
This paper presents a new approach for assembling graph neural networks based on framelet transforms. The latter provides a multi-scale representation for graph-structured data. We decompose an input graph into low-pass and high-pass frequencies coefficients for network training, which then defines a framelet-based graph convolution. The framelet decomposition naturally induces a graph pooling strategy by aggregating the graph feature into low-pass and high-pass spectra, which considers both the feature values and geometry of the graph data and conserves the total information. The graph neural networks with the proposed framelet convolution and pooling achieve state-of-the-art performance in many node and graph prediction tasks. Moreover, we propose shrinkage as a new activation for the framelet convolution, which thresholds high-frequency information at different scales. Compared to ReLU, shrinkage activation improves model performance on denoising and signal compression: noises in both node and structure can be significantly reduced by accurately cutting off the high-pass coefficients from framelet decomposition, and the signal can be compressed to less than half its original size with well-preserved prediction performance.
Benchmark Results
Tested on 7 datasets 7 baseline values 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 | |
| 141 | GraphSAGE | 0.8708
±0.0085 best reported | best at pub: The Impact of Global Structural Information in Graph Neural Networks Applications (2020) best today: Large Language Model Meets Graph Neural Network in Knowledge Distillation (AAAI 2024) |
| 157 | DCNN | 0.8680 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 343 | UFGConv-R | 0.8360
±0.0060 | This paper |
| 425 | UFGConv-S | 0.8300
±0.0050 | This paper |
| 675 | LanczosNet | 0.7950
±0.0180 | This paper |
| 715 | MPNN | 0.7800
±0.0110 | This paper |
| 724 | MLP | 0.7768 | |
| 793 | Spectral | 0.7330 | 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 | |
| 61 | GraphSAGE | 0.7923
±0.0053 best reported | best at pub: Learned Low Precision Graph Neural Networks (2020) best today: Gophormer: Ego-Graph Transformer for Node Classification (2021) |
| 350 | MLP | 0.7289
±0.0010 | |
| 367 | UFGConv-R | 0.7270
±0.0060 | This paper |
| 558 | UFGConv-S | 0.7100
±0.0060 | This paper |
| 641 | DCNN | 0.6940
±0.0130 | This paper |
| 747 | LanczosNet | 0.6620
±0.0190 | This paper |
| 793 | MPNN | 0.6400
±0.0190 | This paper |
| 838 | Spectral | 0.5890 | 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 | |
| 78 | DCNN | 0.8980 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 125 | GraphSAGE | 0.8864
±0.0030 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) best today: Non-backtracking Graph Neural Networks (TMLR 2023) |
| 210 | MLP | 0.8690
±0.0074 | |
| 464 | UFGConv-R | 0.7990
±0.0010 | This paper |
| 530 | UFGConv-S | 0.7940
±0.0040 | This paper |
| 657 | LanczosNet | 0.7830
±0.0030 | This paper |
| 781 | MPNN | 0.7560
±0.0100 | This paper |
| 812 | Spectral | 0.7390 | This paper |
TU Dortmund
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | MSH-GNN | 0.9410
±0.0330 | |
| 2 | GRDL | 0.8260
±0.0120 | |
| 3 | GMN | 0.8225 | |
| 32 | GIN | 0.7880
±0.0410 | |
| 53 | UFGPool-Sum | 0.7777
±0.0260 | This paper |
| 58 | TopKPool | 0.7768 best reported | best at pub: Memory-Based Graph Networks (ICLR 2020) |
| 68 | UFGPool-Spectrum | 0.7723
±0.0240 | This paper |
| 149 | MLP | 0.7600
±0.0320 | |
| 154 | SAGPool | 0.7589
±0.0291 | prev best: Multi-grained Semantics-aware Graph Neural Networks (2020) Improvement within reported uncertainty; not highlighted. |
| 181 | Attention | 0.7563
±0.0113 best reported | best today: Embedding Graphs on Grassmann Manifold (2022) Difference within reported uncertainty; not counted as underperformance. |
| 259 | SUM | 0.7491
±0.0408 | This paper |
| 340 | MAX | 0.7357
±0.0394 | This paper |
| 359 | MEAN | 0.7313
±0.0318 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GC-GNN (GCN) | 0.9210
±0.0810 | |
| 2 | SUGAR | 0.8403
±0.0133 | |
| 3 | Ortho-g-U-Nets | 0.8387 | |
| 15 | SAGE | 0.8088
±0.0233 | |
| 56 | SAGPool | 0.7870
±0.0229 best reported | best at pub: Contrastive Self-supervised Learning for Graph Classification (AAAI 2020) |
| 92 | Attention | 0.7748
±0.0265 | This paper |
| 110 | TopKPool | 0.7640
±0.0232 best reported | best today: Embedding Graphs on Grassmann Manifold (2022) Difference within reported uncertainty; not counted as underperformance. |
OGB
ogbg-molhiv
Global leaderboard →Default metric is ROC-AUC. The paper reports 2 values on ROC-AUC and 6 values on ROC-AUC (percentage) .
| # | Model | ROC-AUC ↑ default | ROC-AUC (percentage) ↑ | Paper |
|---|---|---|---|---|
| 1 | Multi-RF Fusion with Multi-GNN Blending | 0.8476
±
0.0002 | — | ROC-AUC (percentage)
— |
| 2 | HyperFusion | 0.8475
±
0.0003 | — | ROC-AUC (percentage)
— |
| 3 | PAS+FPs | 0.8420
±
0.0015 | — | ROC-AUC (percentage)
— |
| 9 | GatedGCN | 0.8090
±
0.0160 | — | ROC-AUC (percentage)
— |
| 73 | UFGPool-Sum | —
| 0.7880
±
0.0056 | ROC-AUC (percentage)
0.7880
±
0.0056 |
| 85 | UFGPool-Spectrum | —
| 0.7836
±
0.0077 | ROC-AUC (percentage)
0.7836
±
0.0077 |
| 91 | MEAN | —
| 0.7821
±
0.0090 | ROC-AUC (percentage)
0.7821
±
0.0090 |
| 94 | MAX | —
| 0.7816
±
0.0133 | ROC-AUC (percentage)
0.7816
±
0.0133 |
| 94 | TopKPool | 0.7814
±
0.0062 | — | ROC-AUC (percentage)
— |
| 109 | GIN | 0.7780
±
0.0182 | — | ROC-AUC (percentage)
— |
| 124 | Attention | 0.7744
±0.0127 best reported | — | ROC-AUC (percentage)
— best today: Embedding Graphs on Grassmann Manifold (2022) |
| 129 | SUM | —
| 0.7741
±
0.0116 | ROC-AUC (percentage)
0.7741
±
0.0116 |
| 229 | SAGPool | —
| 0.7526
±
0.0229 | ROC-AUC (percentage)
0.7526
±
0.0229 |
| # | Model | Accuracy ↑ | 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 | |
| 44 | UFGConv-R | 0.7197
±0.0012 | This paper |
| 43 | GaAN | 0.7197
±0.0018 | This paper |
| 46 | SIGN | 0.7195
±0.0011 | This paper |
| 47 | DeeperGCN | 0.7192
±0.0017 | This paper |
| 69 | P&L + C&S | 0.7126
±0.0001 | This paper |
| 70 | GraphZoom | 0.7118
±0.0018 | This paper |
| 85 | UFGConv-S | 0.7004
±0.0022 | This paper |
| 107 | MLP | 0.5765
±0.0012 best reported |
