Revisiting Graph Neural Networks for Link Prediction

Graph neural networks (GNNs) have achieved great success in recent years. Three most common applications include node classification, link prediction, and graph classification. While there is rich literature on node classification and graph classification, GNNs for link prediction is relatively less studied and less understood. Two representative classes of methods exist: GAE and SEAL. GAE (Graph Autoencoder) first uses a GNN to learn node embeddings for all nodes, and then aggregates the embeddings of the source and target nodes as their link representation. SEAL extracts a subgraph around the source and target nodes, labels the nodes in the subgraph, and then uses a GNN to learn a link representation from the labeled subgraph. In this paper, we thoroughly discuss the differences between these two classes of methods, and conclude that simply aggregating \textit{node} embeddings does not lead to effective \textit{link} representations, while learning from \textit{properly labeled subgraphs} around links provides highly expressive and generalizable link representations. Experiments on the recent large-scale OGB link prediction datasets show that SEAL has up to 195\% performance gains over GAE methods, achieving new state-of-the-art results on 3 out of 4 datasets.