Towards Understanding Graph Neural Networks: An Algorithm Unrolling Perspective

Zepeng Zhang, Ziping Zhao

Main figure for Towards Understanding Graph Neural Networks: An Algorithm Unrolling Perspective

Abstract

The graph neural network (GNN) has demonstrated its superior performance in various applications. The working mechanism behind it, however, remains mysterious. GNN models are designed to learn effective representations for graph-structured data, which intrinsically coincides with the principle of graph signal denoising (GSD). Algorithm unrolling, a ``learning to optimize'' technique, has gained increasing attention due to its prospects in building efficient and interpretable neural network architectures. In this paper, we introduce a class of unrolled networks built based on truncated optimization algorithms (e.g., gradient descent and proximal gradient descent) for GSD problems. They are shown to be tightly connected to many popular GNN models in that the forward propagations in these GNNs are in fact unrolled networks serving specific GSDs. Besides, the training process of a GNN model can be seen as solving a bilevel optimization problem with a GSD problem at the lower level. Such a connection brings a fresh view of GNNs, as we could try to understand their practical capabilities from their GSD counterparts, and it can also motivate designing new GNN models. Based on the algorithm unrolling perspective, an expressive model named UGDGNN, i.e., unrolled gradient descent GNN, is further proposed which inherits appealing theoretical properties. Extensive numerical simulations on seven benchmark datasets demonstrate that UGDGNN can achieve superior or competitive performance over the state-of-the-art models.

Proposed method: UGDGNN

Benchmark Results

Tested on 5 datasets 21 baseline values reported too low

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

Classic

#ModelAccuracy ↑Paper
1
CNA
0.9575 ±0.0058
2
IS-GIB
0.9390 ±0.0187
3
EERM
0.9112 ±0.0145
20
APPNP
actual #20 vs paper #503 483 places worse
0.8142 ±0.0026
best reported
actual #20 vs paper #503 483 places worse
paper 0.7153 ±0.0059
paper 0.7153 ±0.0059 Δ at pub 0.0897 Δ today 0.0989
32
GPRGNN
actual #32 vs paper #493 461 places worse
0.7164 ±0.0047
actual #32 vs paper #493 461 places worse
paper 0.7164 ±0.0047
36
GCNII
actual #36 vs paper #425 389 places worse
0.8076 ±0.0030
best reported
actual #36 vs paper #425 389 places worse
paper 0.7232 ±0.0061
paper 0.7232 ±0.0061 Δ at pub 0.0279 Δ today 0.0844
44
GCN
actual #44 vs paper #517 473 places worse
0.8033 ±0.0088
best reported
actual #44 vs paper #517 473 places worse
paper 0.7141 ±0.0063
paper 0.7141 ±0.0063 Δ at pub 0.0802 Δ today 0.0892
61
GraphSAGE
0.7923 ±0.0053
62
JKNet
actual #62 vs paper #671 609 places worse
0.7920
best reported
actual #62 vs paper #671 609 places worse
paper 0.6846 ±0.0137
paper 0.6846 ±0.0137 Δ at pub 0.1074
75
DAGNN
actual #75 vs paper #503 428 places worse
0.7860
best reported
actual #75 vs paper #503 428 places worse
paper 0.7156 ±0.0048
paper 0.7156 ±0.0048 Δ at pub 0.0704
96
SGC
actual #96 vs paper #504 408 places worse
0.7765 ±0.0012
best reported
actual #96 vs paper #504 408 places worse
paper 0.7150 ±0.0025
350
MLP
0.7289 ±0.0010
492
UGDGNN
0.7168 ±0.0070
This paper
#ModelAccuracy ↑Paper
1
LGTL
0.9518 ±0.0011
2
MixHop (LO)
0.9513 ±0.0038
3
GraphSAGE (LO)
0.9511 ±0.0036
17
APPNP
actual #17 vs paper #574 557 places worse
0.9355 ±0.0060
best reported
actual #17 vs paper #574 557 places worse
paper 0.7910 ±0.0029
18
GCN
actual #18 vs paper #574 556 places worse
0.9296 ±0.0015
best reported
actual #18 vs paper #574 556 places worse
paper 0.7910 ±0.0042
24
JKNet
actual #24 vs paper #760 736 places worse
0.9160
best reported
actual #24 vs paper #760 736 places worse
paper 0.7635 ±0.0079
paper 0.7635 ±0.0079 Δ at pub 0.1525
58
GCNII
actual #58 vs paper #501 443 places worse
0.9030 ±0.0043
best reported
actual #58 vs paper #501 443 places worse
paper 0.7956 ±0.0042
101
GPRGNN
actual #101 vs paper #571 470 places worse
0.8911 ±0.0008
best reported
actual #101 vs paper #571 470 places worse
paper 0.7914 ±0.0063
paper 0.7914 ±0.0063 Δ today 0.0997
116
SAGE
0.8881 ±0.0015
141
SGC
actual #141 vs paper #622 481 places worse
0.8832 ±0.0055
best reported
actual #141 vs paper #622 481 places worse
paper 0.7877 ±0.0041
210
MLP
0.8690 ±0.0074
226
DAGNN
actual #226 vs paper #573 347 places worse
0.8640
best reported
actual #226 vs paper #573 347 places worse
paper 0.7911 ±0.0071
paper 0.7911 ±0.0071 Δ at pub 0.0729
556
UGDGNN
0.7922 ±0.0035
This paper
#ModelAccuracy ↑Paper
1
GraphTARIF
0.9703 ±0.0019
2
GAT
0.9669 ±0.0014
3
GAT+T
0.9660 ±0.0007
7
SAGE
0.9643 ±0.0027
8
GCN
actual #8 vs paper #437 429 places worse
0.9632 ±0.0008
best reported
actual #8 vs paper #437 429 places worse
paper 0.9037 ±0.0111
paper 0.9037 ±0.0111 Δ at pub 0.0205 Δ today 0.0595
21
APPNP
actual #21 vs paper #433 412 places worse
0.9573 ±0.0012
best reported
actual #21 vs paper #433 412 places worse
paper 0.9042 ±0.0064
33
GPRGNN
actual #33 vs paper #365 332 places worse
0.9549 ±0.0014
best reported
actual #33 vs paper #365 332 places worse
paper 0.9163 ±0.0095
50
SGC
actual #50 vs paper #472 422 places worse
0.9511 ±0.0009
best reported
actual #50 vs paper #472 422 places worse
paper 0.8916 ±0.0106
paper 0.8916 ±0.0106 Δ at pub 0.0244 Δ today 0.0595
87
GCNII
actual #87 vs paper #530 443 places worse
0.9430 ±0.0020
best reported
actual #87 vs paper #530 443 places worse
paper 0.8001 ±0.0243
paper 0.8001 ±0.0243 Δ at pub 0.0987 Δ today 0.1429
260
DAGNN
actual #260 vs paper #433 173 places worse
0.9269
best reported
actual #260 vs paper #433 173 places worse
paper 0.9042 ±0.0126
paper 0.9042 ±0.0126 Δ at pub 0.0227
364
JKNet
actual #364 vs paper #494 130 places worse
0.9169
best reported
actual #364 vs paper #494 130 places worse
paper 0.8755 ±0.0221
paper 0.8755 ±0.0221 Δ at pub 0.0015 Δ today 0.0414
390
MLP
0.9128 ±0.0063
432
UGDGNN
0.9049 ±0.0085
This paper
#ModelAccuracy ↑Paper
1
GrokFormer
0.9831 ±0.0018
2
PolyFormer
0.9808 ±0.0027
3
SGFormer
0.9796 ±0.0081
7
GPRGNN
actual #7 vs paper #206 199 places worse
0.9375 ±0.0072
actual #7 vs paper #206 199 places worse
paper 0.9375 ±0.0072

Improvement within reported uncertainty; not highlighted.

paper 0.9375 ±0.0072 Δ at pub 0.0026 Δ today 0.0402
9
GCN
actual #9 vs paper #206 197 places worse
0.9774 ±0.0035
best reported
actual #9 vs paper #206 197 places worse
paper 0.9371 ±0.0067
paper 0.9371 ±0.0067 Δ at pub 0.0279 Δ today 0.0403
17
SAGE
0.9739 ±0.0018
42
APPNP
actual #42 vs paper #206 164 places worse
0.9376 ±0.0057
actual #42 vs paper #206 164 places worse
paper 0.9376 ±0.0057

Improvement within reported uncertainty; not highlighted.

paper 0.9376 ±0.0057 Δ at pub 0.0001 Δ today 0.0278
59
GCNII
actual #59 vs paper #205 146 places worse
0.9379 ±0.0065
actual #59 vs paper #205 146 places worse
paper 0.9379 ±0.0065

Improvement within reported uncertainty; not highlighted.

paper 0.9379 ±0.0065 Δ at pub 0.0064 Δ today 0.0218
58
MLP
0.9597 ±0.0007
70
SGC
actual #70 vs paper #206 136 places worse
0.9580 ±0.0010
best reported
actual #70 vs paper #206 136 places worse
paper 0.9367 ±0.0074
paper 0.9367 ±0.0074 Δ at pub 0.0213 Δ today 0.0213
191
UGDGNN
0.9414 ±0.0050
This paper
197
DAGNN
actual #197 vs paper #204 7 places worse
0.9381 ±0.0084
actual #197 vs paper #204 7 places worse
paper 0.9381 ±0.0084

Improvement within reported uncertainty; not highlighted.

paper 0.9381 ±0.0084 Δ at pub 0.0050
227
JKNet
actual #227 vs paper #227
0.9325 ±0.0082
actual #227 vs paper #227
paper 0.9325 ±0.0082

Improvement within reported uncertainty; not highlighted.

paper 0.9325 ±0.0082 Δ at pub 0.0233
#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 #132 120 places worse
0.9514 ±0.0025
best reported
actual #12 vs paper #132 120 places worse
paper 0.9176 ±0.0037
best today: Graph Wave Networks (WWW 2025)
paper 0.9176 ±0.0037 Δ at pub 0.0184 Δ today 0.0338
25
APPNP
actual #25 vs paper #125 100 places worse
0.9400 ±0.0030
best reported
actual #25 vs paper #125 100 places worse
paper 0.9195 ±0.0043
paper 0.9195 ±0.0043 Δ at pub 0.0189 Δ today 0.0205
91
DAGNN
actual #91 vs paper #125 34 places worse
0.9280 ±0.0090
best reported
actual #91 vs paper #125 34 places worse
paper 0.9196 ±0.0040

Difference within reported uncertainty; not counted as underperformance.

paper 0.9196 ±0.0040 Δ today 0.0084
88
MLP
0.9280 ±0.0020
96
SGC
actual #96 vs paper #125 29 places worse
0.9270 ±0.0010
best reported
actual #96 vs paper #125 29 places worse
paper 0.9193 ±0.0038
paper 0.9193 ±0.0038 Δ at pub 0.0077
104
GCNII
actual #104 vs paper #152 48 places worse
0.9241 ±0.0050
best reported
actual #104 vs paper #152 48 places worse
paper 0.9103 ±0.0043
114
UGDGNN
0.9218 ±0.0066
This paper
124
GPRGNN
0.9203 ±0.0061
This paper
150
JKNet
actual #150 vs paper #153 3 places worse
0.9110 ±0.0030
best reported
actual #150 vs paper #153 3 places worse
paper 0.9098 ±0.0072

Difference within reported uncertainty; not counted as underperformance.

paper 0.9098 ±0.0072 Δ today 0.0012
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) Improved at pub — later paper surpassed this result Best today — OK at publication; today's leaderboard best is elsewhere