ProtoMGAE: Prototype-Aware Masked Graph Auto-Encoder for Graph Representation Learning

Abstract

Graph self-supervised representation learning has gained considerable attention and demonstrated remarkable efficacy in extracting meaningful representations from graphs, particularly in the absence of labeled data. Two representative methods in this domain are graph auto-encoding and graph contrastive learning. However, the former methods primarily focus on global structures, potentially overlooking some fine-grained information during reconstruction. The latter methods emphasize node similarity across correlated views in the embedding space, potentially neglecting the inherent global graph information in the original input space. Moreover, handling incomplete graphs in real-world scenarios, where original features are unavailable for certain nodes, poses challenges for both types of methods. To alleviate these limitations, we integrate masked graph auto-encoding and prototype-aware graph contrastive learning into a unified model to learn node representations in graphs. In our method, we begin by masking a portion of node features and utilize a specific decoding strategy to reconstruct the masked information. This process facilitates the recovery of graphs from a global or macro level and enables handling incomplete graphs easily. Moreover, we treat the masked graph and the original one as a pair of contrasting views, enforcing the alignment and uniformity between their corresponding node representations at a local or micro level. Last, to capture cluster structures from a meso level and learn more discriminative representations, we introduce a prototype-aware clustering consistency loss that is jointly optimized with the preceding two complementary objectives. Extensive experiments conducted on several datasets demonstrate that the proposed method achieves significantly better or competitive performance on downstream tasks, especially for graph clustering, compared with the state-of-the-art methods, showcasing its superiority in enhancing graph representation learning.