Simplifying Graph Convolutional Networks with Redundancy-Free Neighbors

Jielong Lu, Zhihao Wu, Zhiling Cai, Yueyang Pi, Shiping Wang

Main figure for Simplifying Graph Convolutional Networks with Redundancy-Free Neighbors

Abstract

In recent years, Graph Convolutional Networks (GCNs) have gained popularity for their exceptional ability to process graph-structured data. Existing GCN-based approaches typically employ a shallow model architecture due to the over-smoothing phenomenon. Current approaches to mitigating over-smoothing primarily involve adding supplementary components to GCN architectures, such as residual connections and random edge-dropping strategies. However, these improvements toward deep GCNs have achieved only limited success. In this work, we analyze the intrinsic message passing mechanism of GCNs and identify a critical issue: messages originating from high-order neighbors must traverse through low-order neighbors to reach the target node. This repeated reliance on low-order neighbors leads to redundant information aggregation, a phenomenon we term over-aggregation. Our analysis demonstrates that over-aggregation not only introduces significant redundancy but also serves as the fundamental cause of over-smoothing in GCNs. Motivated by this discovery, we introduce a novel framework named redundancy-free graph convolutional network, where the neighbors of the graph are hierarchically organized so that the multi-order neighbor sets of a specific node do not intersect. This organizational structure enables high-order neighbors to directly propagate their messages to the target node, thereby effectively avoiding duplicate aggregation. The layer number of the proposed method adapts according to the graph structure, eliminating the need for manual adjustments to capture node information at specific distances. The experimental results on sixteen real-world datasets demonstrate the superior performance of the proposed method on node- and graph-level tasks. Graph convolutional network, over-smoothing, hierarchical aggregation, over-aggregation.

Benchmark Results

Tested on 6 datasets 8 baseline values reported too low Non-standard metric on 1 dataset

Tables show presented results in global context (best 3 papers + GCN + MLP).

TU Dortmund

#ModelAccuracy ↑Paper
1
MSH-GNN
0.9910 ±0.0030
2
ID-GNN+BEC
0.9830 ±0.0360
3
SupCosine
0.9830 ±0.0250
39
GIN
actual #39 vs paper #237 198 places worse
0.9330 ±0.0290
best reported
actual #39 vs paper #237 198 places worse
paper 0.8940 ±0.0560

Difference within reported uncertainty; not counted as underperformance.

paper 0.8940 ±0.0560 Δ at pub 0.0390
54
PatchySan
0.9260 ±0.0420
This paper
63
GCN
actual #63 vs paper #432 369 places worse
0.9220 ±0.0440
best reported
actual #63 vs paper #432 369 places worse
paper 0.8560 ±0.0580

Difference within reported uncertainty; not counted as underperformance.

paper 0.8560 ±0.0580 Δ at pub 0.0660
92
RF-GCN
0.9150 ±0.0490
This paper
158
GraphSAGE
0.9040 ±0.0780
300
GCKM
0.8870 ±0.0760
This paper
337
AWL
0.8790 ±0.0980
This paper
403
MLP
actual #403 vs paper #484 81 places worse
0.8660 ±0.0495
best reported
actual #403 vs paper #484 81 places worse
paper 0.8400 ±0.0610

Difference within reported uncertainty; not counted as underperformance.

paper 0.8400 ±0.0610 Δ at pub 0.0260
425
DGCNN
actual #425 vs paper #425
0.8583 ±0.0116
best reported
actual #425 vs paper #425
paper 0.8580
#ModelAccuracy ↑Paper
1
MSH-GNN
0.9410 ±0.0330
2
GRDL
0.8260 ±0.0120
3
GMN
0.8225
32
GIN
actual #32 vs paper #135 103 places worse
0.7880 ±0.0410
best reported
actual #32 vs paper #135 103 places worse
paper 0.7620 ±0.0320

Difference within reported uncertainty; not counted as underperformance.

paper 0.7620 ±0.0320 Δ at pub 0.0260
37
RF-GCN
0.7860 ±0.0240
This paper
67
SAGE
0.7726 ±0.0228
132
DGCNN
actual #132 vs paper #190 58 places worse
0.7626
best reported
actual #132 vs paper #190 58 places worse
paper 0.7550
best at pub: Orthogonal Graph Neural Networks (AAAI 2021)
paper 0.7550 Δ at pub 0.0076
148
GCN
0.7600 ±0.0320
This paper
149
MLP
actual #149 vs paper #149
0.7600 ±0.0320
actual #149 vs paper #149
paper 0.7600 ±0.0320
prev best: GNNBenchmark (JMLR 2023)

Improvement within reported uncertainty; not highlighted.

paper 0.7600 ±0.0320 Δ at pub 0.0018
156
PatchySan
actual #156 vs paper #156
0.7590 ±0.0280
actual #156 vs paper #156
paper 0.7590 ±0.0280
prev best: Memory-Based Graph Networks (ICLR 2020)

Improvement within reported uncertainty; not highlighted.

paper 0.7590 ±0.0280 Δ at pub 0.0090
155
GraphSAGE
0.7590 ±0.0320
This paper
293
GCKM
0.7450 ±0.0390
This paper
#ModelAccuracy ↑Paper
1
WL-MLP
0.9792
2
MSH-GNN
0.9640 ±0.0070
3
CoCN
0.8722 ±0.0013
23
GCN
actual #23 vs paper #156 133 places worse
0.8260 ±0.0220
best reported
actual #23 vs paper #156 133 places worse
paper 0.7900 ±0.0180
paper 0.7900 ±0.0180 Δ at pub 0.0360
30
GIN
actual #30 vs paper #111 81 places worse
0.8220 ±0.0210
best reported
actual #30 vs paper #111 81 places worse
paper 0.8020 ±0.0190

Difference within reported uncertainty; not counted as underperformance.

paper 0.8020 ±0.0190 Δ at pub 0.0200
43
GCKM
0.8170 ±0.0150
This paper
60
RF-GCN
0.8140 ±0.0150
This paper
136
GraphSAGE
0.7970 ±0.0170
151
MLP
actual #151 vs paper #151
0.7920 ±0.0240
actual #151 vs paper #151
paper 0.7920 ±0.0240
paper 0.7920 ±0.0240 Δ at pub 0.1140
191
DGCNN
actual #191 vs paper #269 78 places worse
0.7759 ±0.0224
best reported
actual #191 vs paper #269 78 places worse
paper 0.7370
paper 0.7370 Δ at pub 0.0375 Δ today 0.0389
268
AWL
0.7390 ±0.0190
This paper
280
PatchySan
0.7260 ±0.0420
This paper

Heterophilic Graphs

#ModelAccuracy ↑Paper
1
P^2GNN
0.9541 ±0.0272
2
ACM-GCN
actual #2 vs paper #78 76 places worse
0.8571
actual #2 vs paper #78 76 places worse
paper 0.8571
best today: Heterophily-informed Message Passing (TMLR 2025)

Improvement within reported uncertainty; not highlighted.

paper 0.8571 Δ at pub 0.0057 Δ today 0.0909
3
RF-GCN
0.9429
This paper
24
MLP
0.9136 ±0.0070
65
LRGNN
0.8648
This paper
123
LINKX
actual #123 vs paper #203 80 places worse
0.8346 ±0.0061
best reported
actual #123 vs paper #203 80 places worse
paper 0.7784
paper 0.7784 Δ at pub 0.0562
138
SAGE
0.8269
272
HOG-GCN
0.7143
This paper
342
Geom-GCN
actual #342 vs paper #509 167 places worse
0.6412
best reported
actual #342 vs paper #509 167 places worse
paper 0.4742
paper 0.4742 Δ at pub 0.1670
582
Homophily
0.0030
This paper
#ModelAccuracy ↑Paper
1
DiGGR
0.4535 ±0.0353
2
TRIGON
0.4402 ±0.0028
3
DoG
0.4320 ±0.0120
16
ACM-GCN
actual #16 vs paper #198 182 places worse
0.4198 ±0.0089
best reported
actual #16 vs paper #198 182 places worse
paper 0.3567
paper 0.3567 Δ at pub 0.0593 Δ today 0.0631
42
MLP
0.4026 ±0.0108
68
GraphSAGE
0.3899 ±0.0085
87
Geom-GCN
actual #87 vs paper #411 324 places worse
0.3810
best reported
actual #87 vs paper #411 324 places worse
paper 0.2688
paper 0.2688 Δ at pub 0.1122
117
LRGNN
actual #117 vs paper #440 323 places worse
0.3734 ±0.0178
best reported
actual #117 vs paper #440 323 places worse
paper 0.2437
paper 0.2437 Δ at pub 0.1297
179
RF-GCN
0.3618
This paper
292
HOG-GCN
0.3276
This paper
470
Homophily
0.2200
This paper

Heterogeneous Graph Benchmarks

ACM

Global leaderboard →
Non-default metric. This paper reports F1; the dataset default is Micro-F1. Values below use F1 only.

Sorted by F1. Highlighted rows are from other papers.

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 Best today — OK at publication; today's leaderboard best is elsewhere