KDD 2025

Partition-wise Graph Filtering: A Unified Perspective Through the Lens of Graph Coarsening

Guoming Li, Jian Yang, Yifan Chen

Main figure for Partition-wise Graph Filtering: A Unified Perspective Through the Lens of Graph Coarsening

Abstract

Filtering-based graph neural networks (GNNs) constitute a distinct class of GNNs that employ graph filters to handle graph-structured data, achieving notable success in various graph-related tasks. Conventional methods adopt a graph-wise filtering paradigm, imposing a uniform filter across all nodes, yet recent findings suggest that this rigid paradigm struggles with heterophilic graphs. To overcome this, recent works have introduced node-wise filtering, which assigns distinct filters to individual nodes, offering enhanced adaptability. However, a fundamental gap remains: a comprehensive framework unifying these two strategies is still absent, limiting theoretical insights into the filtering paradigms. Moreover, through the lens of Contextual Stochastic Block Model, we reveal that a synthesis of graph-wise and node-wise filtering provides a sufficient solution for classification on graphs exhibiting both homophily and heterophily, suggesting the risk of excessive parameterization and potential overfitting with node-wise filtering. To address the limitations, this paper introduces Coarsening-guided Partition-wise Filtering (CPF). CPF innovates by performing filtering on node partitions. The method begins with partition-wise filtering, which filters node partitions obtained via graph coarsening algorithms, and then performs partition-wise filtering, refining node embeddings via filtering on clusters produced by $k$-means clustering over features. In-depth analysis is conducted for each phase of CPF, showing its superiority over other paradigms. Finally, benchmark node classification experiments, along with a real-world graph anomaly detection application, validate CPF's efficacy and practical utility. Code is available with the Github repository:.

Proposed method: CPF

Benchmark Results

Tested on 3 datasets 11 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
actual #21 vs paper #169 148 places worse
0.9004
best reported
actual #21 vs paper #169 148 places worse
paper 0.8648 ±0.0040
paper 0.8648 ±0.0040 Δ at pub 0.0356
36
CPF
0.8928 ±0.0070
This paper
39
SAGE
0.8911 ±0.0012
45
GCNII
actual #45 vs paper #159 114 places worse
0.8893 ±0.0137
best reported
actual #45 vs paper #159 114 places worse
paper 0.8677 ±0.0020
best at pub: Language is All a Graph Needs (2023)
paper 0.8677 ±0.0020 Δ at pub 0.0216 Δ today 0.0216
51
H2GCN
actual #51 vs paper #128 77 places worse
0.8882 ±0.0011
best reported
actual #51 vs paper #128 77 places worse
paper 0.8733 ±0.0060
64
JacobiConv
0.8853 ±0.0080
This paper
72
OptBasis
0.8835 ±0.0060
This paper
73
UniFilter
0.8831 ±0.0070
This paper
76
NIGCN
0.8829 ±0.0050
This paper
77
GPRGNN
0.8826 ±0.0050
This paper
81
AdaptKry
0.8823 ±0.0070
This paper
85
Specformer
0.8819 ±0.0060
This paper
86
ChebNetII
0.8817 ±0.0040
This paper
88
GloGNN
0.8812 ±0.0040
This paper
91
NFGNN
0.8806 ±0.0040
This paper
120
OrderGNN
0.8755 ±0.0020
This paper
133
ACMGCN
0.8721 ±0.0040
This paper
137
Node-MoE
0.8716 ±0.0080
This paper
139
ChebNet
actual #139 vs paper #153 14 places worse
0.8712 ±0.0060
best reported
actual #139 vs paper #153 14 places worse
paper 0.8683 ±0.0070

Difference within reported uncertainty; not counted as underperformance.

paper 0.8683 ±0.0070 Δ at pub 0.0029
243
LINKX
actual #243 vs paper #251 8 places worse
0.8464 ±0.0113
best reported
actual #243 vs paper #251 8 places worse
paper 0.8451 ±0.0060

Difference within reported uncertainty; not counted as underperformance.

paper 0.8451 ±0.0060 Δ at pub 0.0013 Δ today 0.0013
724
MLP
0.7768
#ModelAccuracy ↑Paper
1
LGTL
0.9518 ±0.0011
2
MixHop (LO)
0.9513 ±0.0038
3
GraphSAGE (LO)
0.9511 ±0.0036
16
H2GCN
actual #16 vs paper #136 120 places worse
0.9361 ±0.0013
best reported
actual #16 vs paper #136 120 places worse
paper 0.8839 ±0.0060
18
GCN
actual #18 vs paper #194 176 places worse
0.9296 ±0.0015
best reported
actual #18 vs paper #194 176 places worse
paper 0.8729 ±0.0020
58
GCNII
actual #58 vs paper #114 56 places worse
0.9030 ±0.0043
best reported
actual #58 vs paper #114 56 places worse
paper 0.8886 ±0.0040
76
CPF
0.8993 ±0.0050
This paper
85
GloGNN
actual #85 vs paper #115 30 places worse
0.8960 ±0.0040
best reported
actual #85 vs paper #115 30 places worse
paper 0.8883 ±0.0020
paper 0.8883 ±0.0020 Δ at pub 0.0077
87
JacobiConv
0.8951 ±0.0020
This paper
89
Specformer
actual #89 vs paper #118 29 places worse
0.8947 ±0.0048
best reported
actual #89 vs paper #118 29 places worse
paper 0.8874 ±0.0020
paper 0.8874 ±0.0020 Δ at pub 0.0073
92
OptBasis
0.8938 ±0.0030
This paper
94
UniFilter
0.8930 ±0.0040
This paper
101
GPRGNN
actual #101 vs paper #115 14 places worse
0.8911 ±0.0008
best reported
actual #101 vs paper #115 14 places worse
paper 0.8881 ±0.0020

Difference within reported uncertainty; not counted as underperformance.

paper 0.8881 ±0.0020 Δ at pub 0.0030
110
ChebNetII
0.8898 ±0.0040
This paper
116
SAGE
0.8881 ±0.0015
123
NIGCN
0.8869 ±0.0030
This paper
128
Node-MoE
0.8854 ±0.0050
This paper
134
NFGNN
0.8843 ±0.0040
This paper
137
AdaptKry
0.8838 ±0.0060
This paper
143
OrderGNN
0.8831 ±0.0030
This paper
162
LINKX
actual #162 vs paper #226 64 places worse
0.8786 ±0.0077
best reported
actual #162 vs paper #226 64 places worse
paper 0.8636 ±0.0060
192
ACMGCN
0.8737 ±0.0040
This paper
199
ChebNet
actual #199 vs paper #233 34 places worse
0.8718 ±0.0029
best reported
actual #199 vs paper #233 34 places worse
paper 0.8592 ±0.0050
paper 0.8592 ±0.0050 Δ at pub 0.0126
210
MLP
0.8690 ±0.0074

OGB

#ModelAccuracy ↑Paper
1
SGC
actual #1 vs paper #69 68 places worse
0.7910
best reported
actual #1 vs paper #69 68 places worse
paper 0.6402 ±0.0020
paper 0.6402 ±0.0020 Δ at pub 0.1508
2
GAMLP
0.7036 ±0.0002
3
GLEM-GNN
0.7036 ±0.0002
6
CPF
0.6887 ±0.0030
This paper
21
ChebNetII
actual #21 vs paper #21
0.6718 ±0.0032
best reported
actual #21 vs paper #21
paper 0.6711 ±0.0020

Difference within reported uncertainty; not counted as underperformance.

paper 0.6711 ±0.0020 Δ at pub 0.0007 Δ today 0.0007
23
AdaptKry
0.6707 ±0.0020
This paper
25
OptBasis
0.6703 ±0.0030
This paper
28
UniFilter
0.6679 ±0.0030
This paper
31
NIGCN
0.6657 ±0.0020
This paper
35
SAGE
0.6644 ±0.0017
37
NFGNN
0.6638 ±0.0020
This paper
44
PCConv
0.6619 ±0.0020
This paper
45
GPRGNN
0.6613 ±0.0020
This paper
46
Node-MoE
0.6612 ±0.0020
This paper
47
BernNet
0.6608 ±0.0020
This paper
56
JacobiConv
0.6545 ±0.0020
This paper
60
FEGNN
0.6519 ±0.0030
This paper
80
APPNP
actual #80 vs paper #80
0.6288 ±0.0010
actual #80 vs paper #80
paper 0.6288 ±0.0010
paper 0.6288 ±0.0010 Δ at pub 0.0198
95
MLP
0.4960 ±0.0030
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 at pub — reported value improved over the best known when published