A Unified View on Graph Neural Networks as Graph Signal Denoising

Yao Ma, Xiaorui Liu, Tong Zhao, Yozen Liu, Jiliang Tang, Neil Shah

Main figure for A Unified View on Graph Neural Networks as Graph Signal Denoising

Abstract

Graph Neural Networks (GNNs) have risen to prominence in learning representations for graph structured data. A single GNN layer typically consists of a feature transformation and a feature aggregation operation. The former normally uses feed-forward networks to transform features, while the latter aggregates the transformed features over the graph. Numerous recent works have proposed GNN models with different designs in the aggregation operation. In this work, we establish mathematically that the aggregation processes in a group of representative GNN models including GCN, GAT, PPNP, and APPNP can be regarded as (approximately) solving a graph denoising problem with a smoothness assumption. Such a unified view across GNNs not only provides a new perspective to understand a variety of aggregation operations but also enables us to develop a unified graph neural network framework Ugnn. To demonstrate its promising potential, we instantiate a novel GNN model, Ada-Ugnn, derived from Ugnn, to handle graphs with adaptive smoothness across nodes. Comprehensive experiments show the effectiveness of Ada-Ugnn. The implementation of ADA-UGNN is available at.

Proposed method: ADA-UGNN

Benchmark Results

Tested on 6 datasets 7 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 #558 537 places worse
0.9004
best reported
actual #21 vs paper #558 537 places worse
paper 0.8175 ±0.0080
paper 0.8175 ±0.0080 Δ at pub 0.0542 Δ today 0.0829
39
SAGE
0.8911 ±0.0012
44
GAT
actual #44 vs paper #465 421 places worse
0.8897 ±0.0014
best reported
actual #44 vs paper #465 421 places worse
paper 0.8256 ±0.0080
paper 0.8256 ±0.0080 Δ at pub 0.0634 Δ today 0.0641
724
MLP
0.7768
#ModelAccuracy ↑Paper
1
CNA
0.9575 ±0.0058
2
IS-GIB
0.9390 ±0.0187
3
EERM
0.9112 ±0.0145
35
GAT
actual #35 vs paper #574 539 places worse
0.8080 ±0.0026
best reported
actual #35 vs paper #574 539 places worse
paper 0.7077 ±0.0080
paper 0.7077 ±0.0080 Δ at pub 0.0783 Δ today 0.1003
44
GCN
actual #44 vs paper #614 570 places worse
0.8033 ±0.0088
best reported
actual #44 vs paper #614 570 places worse
paper 0.7013 ±0.0100
61
GraphSAGE
0.7923 ±0.0053
350
MLP
0.7289 ±0.0010
#ModelAccuracy ↑Paper
1
LGTL
0.9518 ±0.0011
2
MixHop (LO)
0.9513 ±0.0038
3
GraphSAGE (LO)
0.9511 ±0.0036
18
GCN
actual #18 vs paper #631 613 places worse
0.9296 ±0.0015
best reported
actual #18 vs paper #631 613 places worse
paper 0.7856 ±0.0050
20
GAT
actual #20 vs paper #608 588 places worse
0.9233 ±0.0018
best reported
actual #20 vs paper #608 588 places worse
paper 0.7888 ±0.0050
116
SAGE
0.8881 ±0.0015
210
MLP
0.8690 ±0.0074
#ModelAccuracy ↑Paper
1
GraphTARIF
0.9703 ±0.0019
2
GAT
actual #2 vs paper #438 436 places worse
0.9033 ±0.0120
actual #2 vs paper #438 436 places worse
paper 0.9033 ±0.0120

Improvement within reported uncertainty; not highlighted.

paper 0.9033 ±0.0120 Δ at pub 0.0033 Δ today 0.0636
3
GAT+T
0.9660 ±0.0007
7
SAGE
0.9643 ±0.0027
8
GCN
actual #8 vs paper #460 452 places worse
0.9632 ±0.0008
best reported
actual #8 vs paper #460 452 places worse
paper 0.8960 ±0.0150
paper 0.8960 ±0.0150 Δ at pub 0.0157 Δ today 0.0672
21
APPNP
actual #21 vs paper #384 363 places worse
0.9573 ±0.0012
best reported
actual #21 vs paper #384 363 places worse
paper 0.9138 ±0.0120
377
ADA-UGNN
0.9144 ±0.0120
This paper
390
MLP
0.9128 ±0.0063
#ModelAccuracy ↑Paper
1
GraphTARIF
0.9461 ±0.0017
2
GCN
actual #2 vs paper #387 385 places worse
0.9412 ±0.0008
best reported
actual #2 vs paper #387 385 places worse
paper 0.8279 ±0.0130
paper 0.8279 ±0.0130 Δ at pub 0.0506 Δ today 0.1133
3
GAT
actual #3 vs paper #382 379 places worse
0.9398 ±0.0022
best reported
actual #3 vs paper #382 379 places worse
paper 0.8301 ±0.0150
paper 0.8301 ±0.0150 Δ at pub 0.0139 Δ today 0.1097
8
SAGE
0.9351 ±0.0006
58
APPNP
actual #58 vs paper #383 325 places worse
0.8299 ±0.0160
actual #58 vs paper #383 325 places worse
paper 0.8299 ±0.0160
paper 0.8299 ±0.0160 Δ at pub 0.0282 Δ today 0.0794
320
MLP
0.8463
375
ADA-UGNN
0.8340 ±0.0130
This paper
#ModelAccuracy ↑Paper
1
DoG
0.9690 ±0.0030
2
GWN-fa
0.9667 ±0.0026
3
GWN-sym
0.9666 ±0.0026
6
GraphSAGE
0.9593 ±0.0025
12
GCN
actual #12 vs paper #59 47 places worse
0.9514 ±0.0025
best reported
actual #12 vs paper #59 47 places worse
paper 0.9323 ±0.0070
best today: Graph Wave Networks (WWW 2025)
paper 0.9323 ±0.0070 Δ at pub 0.0037 Δ today 0.0191
21
GAT
actual #21 vs paper #86 65 places worse
0.9437 ±0.0028
best reported
actual #21 vs paper #86 65 places worse
paper 0.9286 ±0.0070
best today: Graph Wave Networks (WWW 2025)
paper 0.9286 ±0.0070 Δ at pub 0.0094 Δ today 0.0151
25
APPNP
actual #25 vs paper #29 4 places worse
0.9384 ±0.0050
actual #25 vs paper #29 4 places worse
paper 0.9384 ±0.0050
paper 0.9384 ±0.0050 Δ at pub 0.0314
28
ADA-UGNN
0.9392 ±0.0060
This paper
88
MLP
0.9280 ±0.0020
SOTA performance (not significantly different from the best) Proposed method (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 Improved at pub — later paper surpassed this result Best today — OK at publication; today's leaderboard best is elsewhere