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
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GraphTARIF | 0.9703
±0.0019 | |
| 2 | GAT | 0.9669
±0.0014 best reported | best at pub: Directed Graph Convolutional Network (2020) |
| 3 | GAT+T | 0.9660
±0.0007 | |
| 7 | SAGE | 0.9643
±0.0027 | |
| 8 | GCN | 0.9117 | prev best: Measuring and Relieving the Over-smoothing Problem for Graph Neural Networks from the Topological View (AAAI 2019) best today: Graph Transductive Sharpening: Leveraging Unlabeled Predictions in Node Classification (2026) Improvement within reported uncertainty; not highlighted. |
| 56 | GraphSAGE | 0.9508
±0.0026 best reported | best at pub: Measuring and Relieving the Over-smoothing Problem for Graph Neural Networks from the Topological View (AAAI 2019) best today: A Quasi-Wasserstein Loss for Learning Graph Neural Networks (WWW 2023) |
| 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 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GraphTARIF | 0.9461
±0.0017 | |
| 2 | GCN | 0.8785 | prev best: Graph-Revised Convolutional Network (2019) |
| 3 | GAT | 0.9398
±0.0022 best reported | best at pub: Learned Low Precision Graph Neural Networks (2020) |
| 8 | SAGE | 0.9351
±0.0006 | |
| 46 | GraphSAGE | 0.9120
±0.0029 best reported | best at pub: Directed Graph Convolutional Network (2020) best today: Can TabPFN Compete with GNNs for Node Classification via Graph Tabularization? (LoG 2025) |
| 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 |
| # | Model | Accuracy ↑ | 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 best reported | best at pub: Unifying Graph Convolutional Neural Networks and Label Propagation (2020) best today: Graph Wave Networks (WWW 2025) |
| 12 | GCN | 0.9514
±0.0025 best reported | best at pub: Unifying Graph Convolutional Neural Networks and Label Propagation (2020) best today: Graph Wave Networks (WWW 2025) |
| 21 | GAT | 0.9437
±0.0028 best reported | best at pub: Unifying Graph Convolutional Neural Networks and Label Propagation (2020) best today: Graph Wave Networks (WWW 2025) |
| 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 |
