Learning on Attribute-Missing Graphs

Xu Chen, Siheng Chen, Jiangchao Yao, Huangjie Zheng, Ya Zhang, I. Tsang

Main figure for Learning on Attribute-Missing Graphs

Abstract

Graphs with complete node attributes have been widely explored recently. While in practice, there is a graph where attributes of only partial nodes could be available and those of the others might be entirely missing. This attribute-missing graph is related to numerous real-world applications and there are limited studies investigating the corresponding learning problems. Existing graph learning methods including the popular GNN cannot provide satisfied learning performance since they are not specified for attribute-missing graphs. Thereby, designing a new GNN for these graphs is a burning issue to the graph learning community. In this paper, we make a shared-latent space assumption on graphs and develop a novel distribution matching based GNN called structure-attribute transformer (SAT) for attribute-missing graphs. SAT leverages structures and attributes in a decoupled scheme and achieves the joint distribution modeling of structures and attributes by distribution matching techniques. It could not only perform the link prediction task but also the newly introduced node attribute completion task. Furthermore, practical measures are introduced to quantify the performance of node attribute completion. Extensive experiments on seven real-world datasets indicate SAT shows better performance than other methods on both link prediction and node attribute completion tasks. Codes and data are available online:

Benchmark Results

Tested on 3 datasets 4 baseline values reported too low

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

Classic

#ModelAccuracy ↑Paper
1
GraphTARIF
0.9703 ±0.0019
2
GAT
actual #2 vs paper #573 571 places worse
0.9669 ±0.0014
best reported
actual #2 vs paper #573 571 places worse
paper 0.2598
paper 0.2598 Δ at pub 0.6402 Δ today 0.7071
3
GAT+T
0.9660 ±0.0007
7
SAGE
0.9643 ±0.0027
8
GCN
actual #8 vs paper #396 388 places worse
0.9117
actual #8 vs paper #396 388 places worse
paper 0.9117

Improvement within reported uncertainty; not highlighted.

paper 0.9117 Δ at pub 0.0057 Δ today 0.0515
56
GraphSAGE
actual #56 vs paper #573 517 places worse
0.9508 ±0.0026
best reported
actual #56 vs paper #573 517 places worse
paper 0.2598
371
True attributes
0.9151
This paper
390
MLP
0.9128 ±0.0063
438
SAT(GraphSage)
0.9035
This paper
464
DeepWalk+MLP
0.8955
This paper
474
Node2Vec+MLP
0.8908
This paper
485
NeighAggre
0.8846
This paper
501
SAT(GCN)-no adver
0.8629
This paper
503
SAT(GCN)-no self
0.8585
This paper
518
GraphRNA
0.8407
This paper
568
ARWMF
0.4675
This paper
572
SAT(GCN)-no cross
0.2613
This paper
574
VAE
0.2598
This paper
575
Hers
0.2598
This paper
#ModelAccuracy ↑Paper
1
GraphTARIF
0.9461 ±0.0017
2
GCN
actual #2 vs paper #213 211 places worse
0.8785
actual #2 vs paper #213 211 places worse
paper 0.8785
paper 0.8785 Δ at pub 0.0595 Δ today 0.0627
3
GAT
actual #3 vs paper #497 494 places worse
0.9398 ±0.0022
best reported
actual #3 vs paper #497 494 places worse
paper 0.3747
8
SAGE
0.9351 ±0.0006
46
GraphSAGE
actual #46 vs paper #497 451 places worse
0.9120 ±0.0029
best reported
actual #46 vs paper #497 451 places worse
paper 0.3747
paper 0.3747 Δ at pub 0.4293 Δ today 0.5373
320
MLP
0.8463
329
DeepWalk+MLP
0.8444
This paper
341
True attributes
0.8423
This paper
344
Node2Vec+MLP
0.8415
This paper
354
SAT(GraphSage)
0.8396
This paper
362
NeighAggre
0.8365
This paper
455
SAT(GCN)-no self
0.7410
This paper
460
SAT(GCN)-no adver
0.7356
This paper
475
GraphRNA
0.6968
This paper
486
ARWMF
0.5608
This paper
497
SAT(GCN)-no cross
0.3748
This paper
498
VAE
0.3747
This paper
499
Hers
0.3747
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
actual #6 vs paper #208 202 places worse
0.9593 ±0.0025
best reported
actual #6 vs paper #208 202 places worse
paper 0.2317
best today: Graph Wave Networks (WWW 2025)
paper 0.2317 Δ at pub 0.6943 Δ today 0.7276
12
GCN
actual #12 vs paper #190 178 places worse
0.9514 ±0.0025
best reported
actual #12 vs paper #190 178 places worse
paper 0.8370
best today: Graph Wave Networks (WWW 2025)
paper 0.8370 Δ at pub 0.0990 Δ today 0.1144
21
GAT
actual #21 vs paper #208 187 places worse
0.9437 ±0.0028
best reported
actual #21 vs paper #208 187 places worse
paper 0.2317
best today: Graph Wave Networks (WWW 2025)
paper 0.2317 Δ at pub 0.7063 Δ today 0.7120
27
True attributes
0.9396
This paper
88
MLP
0.9280 ±0.0020
138
GIN
0.9140 ±0.0020
191
NeighAggre
0.8031
This paper
193
GraphRNA
0.7710
This paper
194
SAT(GAT)
0.7672
This paper
196
DeepWalk+MLP
0.7561
This paper
197
Node2Vec+MLP
0.7554
This paper
198
SAT(GCN)-no self
0.7504
This paper
201
SAT(GCN)-no adver
0.6879
This paper
207
VAE
0.2335
This paper
208
ARWMF
0.2320
This paper
209
Hers
0.2317
This paper
210
SAT(GCN)-no cross
0.2317
This paper
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