Towards Better Graph Representation Learning with Parameterized Decomposition & Filtering
Abstract
Proposing an effective and flexible matrix to represent a graph is a fundamental challenge that has been explored from multiple perspectives, e.g., filtering in Graph Fourier Transforms. In this work, we develop a novel and general framework which unifies many existing GNN models from the view of parameterized decomposition and filtering, and show how it helps to enhance the flexibility of GNNs while alleviating the smoothness and amplification issues of existing models. Essentially, we show that the extensively studied spectral graph convolutions with learnable polynomial filters are constrained variants of this formulation, and releasing these constraints enables our model to express the desired decomposition and filtering simultaneously. Based on this generalized framework, we develop models that are simple in implementation but achieve significant improvements and computational efficiency on a variety of graph learning tasks. Code is available at https://github.com/qslim/PDF.
Benchmark Results
Tested on 7 datasets 1 baseline value reported too low
Tables show presented results in global context (best 3 papers + GCN + MLP).
TU Dortmund
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | MSH-GNN | 0.9910
±0.0030 | |
| 2 | ID-GNN+BEC | 0.9830
±0.0360 | |
| 3 | SupCosine | 0.9830
±0.0250 | |
| 39 | GIN | 0.9330
±0.0290 | |
| 143 | PPGNN | 0.9055
±0.0870 | This paper |
| 200 | GSO | 0.8991
±0.0435 | This paper |
| 301 | CapsGNN | 0.8867
±0.0688 | prev best: Molecular Representation Learning via Heterogeneous Motif Graph Neural Networks (ICML 2022) Improvement within reported uncertainty; not highlighted. |
| 403 | MLP | 0.8660
±0.0495 | |
| 418 | k-GNN | 0.8610 | This paper |
| 492 | IGN | 0.8390
±0.1300 best reported | best at pub: Weisfeiler and Lehman Go Cellular: CW Networks (NeurIPS 2021) best today: Multi-Scale Harmonic Encoding for Feature-Wise Graph Message Passing (2025) Difference within reported uncertainty; not counted as underperformance. |
| 501 | RW | 0.8370
±0.0150 best reported | |
| 506 | GK | 0.8350
±0.0060 best reported | best at pub: Supervised Contrastive Learning with Structure Inference for Graph Classification (2022) Difference within reported uncertainty; not counted as underperformance. |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | WL-MLP | 0.9954 | |
| 2 | GIN | 0.9934 | |
| 3 | GCN | 0.9727 | |
| 17 | GSO | 0.8547
±0.0138 | This paper |
| 68 | PPGNN | 0.8319
±0.0111 | This paper |
| 131 | GraphSAGE | 0.8200
±0.0100 | |
| 428 | IGN | 0.7433
±0.0271 | prev best: Weisfeiler and Lehman Go Topological: Message Passing Simplicial Networks (ICML 2021) Improvement within reported uncertainty; not highlighted. |
| # | 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 | |
| 71 | PPGNN | 0.7720
±0.0473 | This paper |
| 100 | IGN | 0.7660
±0.0550 best reported | best today: Multi-Scale Harmonic Encoding for Feature-Wise Graph Message Passing (2025) Difference within reported uncertainty; not counted as underperformance. |
| 126 | CapsGNN | 0.7630
±0.0360 best reported | best at pub: Wasserstein Embedding for Graph Learning (ICLR 2020) Difference within reported uncertainty; not counted as underperformance. |
| 131 | PDF | 0.7628
±0.0510 | This paper |
| 149 | MLP | 0.7600
±0.0320 | |
| 191 | k-GNN | 0.7550 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GMN | 0.7866 | |
| 2 | MemGNN | 0.7550 | |
| 3 | TFGW SP | 0.7510
±0.0500 | |
| 5 | PDF | 0.7350
±0.0639 | This paper |
| 17 | GatedGCN | 0.7000
±0.0494 | |
| 26 | GraphSAGE | 0.6817
±0.0545 | |
| 124 | MLP | 0.5583
±0.0352 | |
| 304 | PSCN | 0.0000 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | OEPG | 0.9630
±0.0090 | |
| 2 | MSH-GNN | 0.9580
±0.0090 | |
| 3 | GNN-AK+ | 0.9480
±0.0080 | |
| 6 | GSO | 0.9340
±0.0130 | This paper |
| 13 | GIN | 0.9240
±0.0250 | |
| 53 | AWE | 0.8789
±0.0253 | This paper |
| 59 | PSCN | 0.8630
±0.0158 | This paper |
| 76 | GK | 0.7734
±0.0018 | This paper |
| 91 | DCNN | 0.4906
±0.0140 | This paper |
OGB
| # | Model | AP ↑ | Paper |
|---|---|---|---|
| 1 | GRPE-Large | 0.3150
±0.0010 | |
| 2 | Graphormer | 0.3140 | |
| 3 | Graphormer-FLAG | 0.3139
±0.0032 | |
| 7 | GSO | 0.3031
±0.0026 | This paper |
| 11 | GINE-AP | 0.2979
±0.0030 | This paper |
| 18 | PHC-GN | 0.2947
±0.0026 | This paper |
| 31 | GIN | 0.2902
±0.0017 | |
| 35 | DeeperG | 0.2842
±0.0043 | This paper |
| 84 | ExpC | 0.2342
±0.0029 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | A-NLSF | 0.8149
±0.0067 | |
| 2 | differential encoding | 0.8096
±0.0029 | |
| 3 | MPNN + VN + NoPE | 0.8055
±0.0038 | |
| 6 | PDF | 0.8010
±0.0052 | This paper |
| 14 | DeeperG | 0.7712
±0.0071 | This paper |
| 16 | GatedGCN | 0.7531
±0.0083 | |
| 18 | KS-SAT | 0.7522
±0.0056 | This paper |
| 33 | GIN | 0.7037
±0.0107 |
