KDD 2023

Variational Graph Autoencoder for Heterogeneous Information Networks with Missing and Inaccurate Attributes

Yige Zhao, Jianxiang Yu, Yao Cheng, Chengcheng Yu, Yiding Liu, Xiang Li, Shuaiqiang Wang

Main figure for Variational Graph Autoencoder for Heterogeneous Information Networks with Missing and Inaccurate Attributes

Abstract

Heterogeneous Information Networks (HINs), which consist of various types of nodes and edges, have recently witnessed excellent performance in graph mining. However, most existing heterogeneous graph neural networks (HGNNs) fail to simultaneously handle the problems of missing attributes, inaccurate attributes and scarce node labels, which limits their expressiveness. In this paper, we propose a generative self-supervised model GraMI\ to address these issues simultaneously. Specifically, GraMI\ first initializes all the nodes in the graph with a low-dimensional representation matrix. After that, based on the variational graph autoencoder framework, GraMI\ learns both node-level and attribute-level embeddings in the encoder, which can provide fine-grained semantic information to construct node attributes. In the decoder, GraMI\ reconstructs both links and attributes. Instead of directly reconstructing raw features for attributed nodes, GraMI\ generates the initial low-dimensional representation matrix for all the nodes, based on which raw features of attributed nodes are further reconstructed. In this way, GraMI\ can not only complete informative features for non-attributed nodes, but rectify inaccurate ones for attributed nodes. Finally, we conduct extensive experiments to show the superiority of GraMI\ in tackling HINs with missing and inaccurate attributes. Our code and data can be found here:.

Proposed method: GraMI

Benchmark Results

Tested on 1 dataset 5 baseline values reported too low

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

Heterogeneous Graph Benchmarks

#ModelMicro-F1 ↑Paper
1
LMSPS
0.9566 ±0.0020
2
PSHGCN
0.9561 ±0.0012
3
RpHGNN
0.9555 ±0.0029
10
GraMI
0.9503
This paper
21
GCN
0.9460 ±0.0031
22
MAGNN
actual #22 vs paper #39 17 places worse
0.9456
best reported
actual #22 vs paper #39 17 places worse
paper 0.9357
23
GAT
actual #23 vs paper #113 90 places worse
0.9448 ±0.0022
best reported
actual #23 vs paper #113 90 places worse
paper 0.8351
paper 0.8351 Δ at pub 0.1097
29
HGCA
0.9434
This paper
37
HAN
actual #37 vs paper #37
0.9369
actual #37 vs paper #37
paper 0.9369

Improvement within reported uncertainty; not highlighted.

paper 0.9369 Δ at pub 0.0042
41
HGMAE
actual #41 vs paper #73 32 places worse
0.9340 ±0.0060
best reported
actual #41 vs paper #73 32 places worse
paper 0.9129
44
DMGI
actual #44 vs paper #44
0.9331
actual #44 vs paper #44
paper 0.9331
paper 0.9331 Δ at pub 0.0171
47
Mp2vec
actual #47 vs paper #50 3 places worse
0.9304
best reported
actual #47 vs paper #50 3 places worse
paper 0.9287
79
DGI
actual #79 vs paper #108 29 places worse
0.9016 ±0.0060
best reported
actual #79 vs paper #108 29 places worse
paper 0.8476
paper 0.8476 Δ at pub 0.0540
93
SEEGERA
0.8664
This paper
176
MLP
0.6447 ±0.0136
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