ICML 2021

Graph Neural Networks Inspired by Classical Iterative Algorithms

Yongyi Yang, Tang Liu, Yangkun Wang, Jinjing Zhou, Quan Gan, Zhewei Wei, Zheng Zhang, Zengfeng Huang, D. Wipf

Main figure for Graph Neural Networks Inspired by Classical Iterative Algorithms

Abstract

Despite the recent success of graph neural networks (GNN), common architectures often exhibit significant limitations, including sensitivity to oversmoothing, long-range dependencies, and spurious edges, e.g., as can occur as a result of graph heterophily or adversarial attacks. To at least partially address these issues within a simple transparent framework, we consider a new family of GNN layers designed to mimic and integrate the update rules of two classical iterative algorithms, namely, proximal gradient descent and iterative reweighted least squares (IRLS). The former defines an extensible base GNN architecture that is immune to oversmoothing while nonetheless capturing long-range dependencies by allowing arbitrary propagation steps. In contrast, the latter produces a novel attention mechanism that is explicitly anchored to an underlying end-to-end energy function, contributing stability with respect to edge uncertainty. When combined we obtain an extremely simple yet robust model that we evaluate across disparate scenarios including standardized benchmarks, adversarially-perturbated graphs, graphs with heterophily, and graphs involving long-range dependencies. In doing so, we compare against SOTA GNN approaches that have been explicitly designed for the respective task, achieving competitive or superior node classification accuracy. Our code is available at https://github.com/FFTYYY/TWIRLS.

Benchmark Results

Tested on 6 datasets 19 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 #573 552 places worse
0.9004
best reported
actual #21 vs paper #573 552 places worse
paper 0.8150
paper 0.8150 Δ at pub 0.0567 Δ today 0.0854
39
SAGE
0.8911 ±0.0012
45
GCNII
actual #45 vs paper #203 158 places worse
0.8550 ±0.0050
actual #45 vs paper #203 158 places worse
paper 0.8550 ±0.0050
55
JKNet
actual #55 vs paper #599 544 places worse
0.8870
best reported
actual #55 vs paper #599 544 places worse
paper 0.8110
paper 0.8110 Δ at pub 0.0760
70
DAGNN
actual #70 vs paper #259 189 places worse
0.8840
best reported
actual #70 vs paper #259 189 places worse
paper 0.8440 ±0.0050
paper 0.8440 ±0.0050 Δ at pub 0.0400
108
APPNP
actual #108 vs paper #389 281 places worse
0.8787
best reported
actual #108 vs paper #389 281 places worse
paper 0.8330
paper 0.8330 Δ at pub 0.0440 Δ today 0.0457
223
SGC
actual #223 vs paper #558 335 places worse
0.8509 ±0.0648
best reported
actual #223 vs paper #558 335 places worse
paper 0.8170 ±0.0010
paper 0.8170 ±0.0010 Δ at pub 0.0020 Δ today 0.0339
295
TWIRLS base
0.8410 ±0.0050
This paper
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
20
APPNP
actual #20 vs paper #474 454 places worse
0.8142 ±0.0026
best reported
actual #20 vs paper #474 454 places worse
paper 0.7180
paper 0.7180 Δ at pub 0.0870 Δ today 0.0962
36
GCNII
actual #36 vs paper #279 243 places worse
0.8076 ±0.0030
best reported
actual #36 vs paper #279 243 places worse
paper 0.7340 ±0.0060
paper 0.7340 ±0.0060 Δ at pub 0.0036 Δ today 0.0736
44
GCN
actual #44 vs paper #550 506 places worse
0.8033 ±0.0088
best reported
actual #44 vs paper #550 506 places worse
paper 0.7110
61
GraphSAGE
0.7923 ±0.0053
62
JKNet
actual #62 vs paper #630 568 places worse
0.7920
best reported
actual #62 vs paper #630 568 places worse
paper 0.6980
paper 0.6980 Δ at pub 0.0940
75
DAGNN
actual #75 vs paper #292 217 places worse
0.7860
best reported
actual #75 vs paper #292 217 places worse
paper 0.7330 ±0.0060
paper 0.7330 ±0.0060 Δ at pub 0.0530
96
SGC
actual #96 vs paper #528 432 places worse
0.7765 ±0.0012
best reported
actual #96 vs paper #528 432 places worse
paper 0.7130 ±0.0020
paper 0.7130 ±0.0020 Δ at pub 0.0060 Δ today 0.0635
223
TWIRLS base
0.7420 ±0.0045
This paper
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
17
APPNP
actual #17 vs paper #439 422 places worse
0.9355 ±0.0060
best reported
actual #17 vs paper #439 422 places worse
paper 0.8010
18
GCN
actual #18 vs paper #585 567 places worse
0.9296 ±0.0015
best reported
actual #18 vs paper #585 567 places worse
paper 0.7900
24
JKNet
actual #24 vs paper #668 644 places worse
0.9160
best reported
actual #24 vs paper #668 644 places worse
paper 0.7810
paper 0.7810 Δ at pub 0.1350
58
GCNII
actual #58 vs paper #418 360 places worse
0.8030 ±0.0040
actual #58 vs paper #418 360 places worse
paper 0.8030 ±0.0040

Improvement within reported uncertainty; not highlighted.

paper 0.8030 ±0.0040 Δ at pub 0.0059 Δ today 0.1000
116
SAGE
0.8881 ±0.0015
141
SGC
actual #141 vs paper #602 461 places worse
0.8832 ±0.0055
best reported
actual #141 vs paper #602 461 places worse
paper 0.7890 ±0.0010
paper 0.7890 ±0.0010 Δ at pub 0.0352 Δ today 0.0942
210
MLP
0.8690 ±0.0074
226
DAGNN
actual #226 vs paper #403 177 places worse
0.8640
best reported
actual #226 vs paper #403 177 places worse
paper 0.8050 ±0.0050
paper 0.8050 ±0.0050 Δ at pub 0.0590
397
TWIRLS
0.8070 ±0.0050
This paper

Heterophilic Graphs

#ModelAccuracy ↑Paper
1
P^2GNN
0.9672 ±0.0147
2
DoG
0.9660 ±0.0210
3
GPF-plus
0.9583 ±0.0419
34
MLP
actual #34 vs paper #207 173 places worse
0.9230 ±0.0070
best reported
actual #34 vs paper #207 173 places worse
paper 0.8189 ±0.0478
40
H2GCN
actual #40 vs paper #148 108 places worse
0.9189 ±0.0393
best reported
actual #40 vs paper #148 108 places worse
paper 0.8486 ±0.0677

Difference within reported uncertainty; not counted as underperformance.

paper 0.8486 ±0.0677 Δ today 0.0703
47
TWIRLS
actual #47 vs paper #160 113 places worse
0.9131 ±0.0336
best reported
actual #47 vs paper #160 113 places worse
paper 0.8459 ±0.0383
paper 0.8459 ±0.0383 Δ today 0.0672
53
GraphSAGE
actual #53 vs paper #193 140 places worse
0.8243 ±0.0614
actual #53 vs paper #193 140 places worse
paper 0.8243 ±0.0614
189
SAGE
0.8269
212
TWIRLS-base
0.8162 ±0.0551
This paper
211
GAT
actual #211 vs paper #533 322 places worse
0.8162 ±0.0645
best reported
actual #211 vs paper #533 322 places worse
paper 0.5838 ±0.0445
best at pub: Heterophilic Graphs (ICLR 2020)
paper 0.5838 ±0.0445 Δ today 0.2324
257
GCN
actual #257 vs paper #513 256 places worse
0.7933 ±0.0447
best reported
actual #257 vs paper #513 256 places worse
paper 0.5946 ±0.0525
best today: Graph Wave Networks (WWW 2025)
paper 0.5946 ±0.0525 Δ at pub 0.0164 Δ today 0.1987
415
Geom-GCN
actual #415 vs paper #415
0.6760
best reported
actual #415 vs paper #415
paper 0.6757
paper 0.6757 Δ at pub 0.0003
#ModelAccuracy ↑Paper
1
P^2GNN
0.9541 ±0.0272
2
ACM-GCN
0.9480 ±0.0380
3
RF-GCN
0.9429
24
MLP
actual #24 vs paper #166 142 places worse
0.9136 ±0.0070
best reported
actual #24 vs paper #166 142 places worse
paper 0.8108 ±0.0637
paper 0.8108 ±0.0637 Δ at pub 0.0052 Δ today 0.1028
27
TWIRLS
actual #27 vs paper #55 28 places worse
0.8983 ±0.0229
best reported
actual #27 vs paper #55 28 places worse
paper 0.8676 ±0.0505

Difference within reported uncertainty; not counted as underperformance.

paper 0.8676 ±0.0505 Δ today 0.0307
68
H2GCN
actual #68 vs paper #151 83 places worse
0.8623 ±0.0471
best reported
actual #68 vs paper #151 83 places worse
paper 0.8216 ±0.0480

Difference within reported uncertainty; not counted as underperformance.

paper 0.8216 ±0.0480 Δ today 0.0407
122
TWIRLS-base
0.8351 ±0.0730
This paper
138
SAGE
0.8269
157
GraphSAGE
actual #157 vs paper #222 65 places worse
0.7595 ±0.0501
actual #157 vs paper #222 65 places worse
paper 0.7595 ±0.0501
158
GAT
actual #158 vs paper #388 230 places worse
0.8190 ±0.0540
best reported
actual #158 vs paper #388 230 places worse
paper 0.5892 ±0.0332
170
GCN
actual #170 vs paper #417 247 places worse
0.8082 ±0.0360
best reported
actual #170 vs paper #417 247 places worse
paper 0.5703 ±0.0467
342
Geom-GCN
actual #342 vs paper #369 27 places worse
0.6081
actual #342 vs paper #369 27 places worse
paper 0.6081
paper 0.6081 Δ at pub 0.0001 Δ today 0.0331
#ModelAccuracy ↑Paper
1
DiGGR
0.4535 ±0.0353
2
TRIGON
0.4402 ±0.0028
3
DoG
0.4320 ±0.0120
42
MLP
actual #42 vs paper #195 153 places worse
0.4026 ±0.0108
best reported
actual #42 vs paper #195 153 places worse
paper 0.3576 ±0.0098
68
GraphSAGE
actual #68 vs paper #258 190 places worse
0.3423 ±0.0099
actual #68 vs paper #258 190 places worse
paper 0.3423 ±0.0099
71
H2GCN
actual #71 vs paper #192 121 places worse
0.3885 ±0.0117
best reported
actual #71 vs paper #192 121 places worse
paper 0.3586 ±0.0103
paper 0.3586 ±0.0103 Δ today 0.0299
85
TWIRLS
actual #85 vs paper #114 29 places worse
0.3813 ±0.0081
best reported
actual #85 vs paper #114 29 places worse
paper 0.3743 ±0.0150

Difference within reported uncertainty; not counted as underperformance.

paper 0.3743 ±0.0150 Δ today 0.0070
87
Geom-GCN
actual #87 vs paper #305 218 places worse
0.3810
best reported
actual #87 vs paper #305 218 places worse
paper 0.3163
paper 0.3163 Δ at pub 0.0647
130
TWIRLS-base
0.3710 ±0.0107
This paper
135
GCN
actual #135 vs paper #342 207 places worse
0.3690
best reported
actual #135 vs paper #342 207 places worse
paper 0.3026 ±0.0079
paper 0.3026 ±0.0079 Δ at pub 0.0664
182
GAT
actual #182 vs paper #417 235 places worse
0.3605 ±0.0035
best reported
actual #182 vs paper #417 235 places worse
paper 0.2628 ±0.0173
paper 0.2628 ±0.0173 Δ at pub 0.0312 Δ today 0.0977
266
GIN
0.3410 ±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 Improved at pub — later paper surpassed this result Best today — OK at publication; today's leaderboard best is elsewhere