Boosting GNN-Based Link Prediction via PU-AUC Optimization

Yuren Mao, Yu Hao, Xin Cao, Yunjun Gao, Chang Yao, Xuemin Lin

Abstract: Link prediction, which aims to predict the existence of a link between two nodes in a network, has various applications ranging from friend recommendation to protein interaction prediction. Recently, Graph Neural Network (GNN)-based link prediction has demonstrated its advantages and achieved the state-of-the-art performance. Typically, GNN-based link prediction can be formulated as a binary classification problem. However, in link prediction, we only have positive data (observed links) and unlabeled data (unobserved links), but no negative data. Therefore, Positive Unlabeled (PU) learning naturally fits the link prediction scenario. Unfortunately, the unknown class prior and data imbalance of networks impede the use of PU learning in link prediction. To deal with these issues, this paper proposes a novel model-agnostic PU learning algorithm for GNN-based link prediction by means of Positive-Unlabeled Area Under the Receiver Operating Characteristic Curve (PU-AUC) optimization. The proposed method is free of class prior estimation and able to handle the data imbalance. Moreover, we propose an accelerated method to reduce the operational complexity of PU-AUC optimization from quadratic to approximately linear. Extensive experiments back up our theoretical analysis and validate that the proposed method is capable of boosting the performance of the state-of-the-art GNN-based link prediction models.