Efficient Link Prediction via GNN Layers Induced by Negative Sampling

• Published in: IEEE transactions on knowledge and data engineering 2025-01, Vol.37 (1), p.253-264
• Main Authors: Wang, Yuxin, Hu, Xiannian, Gan, Quan, Huang, Xuanjing, Qiu, Xipeng, Wipf, David
• Format: Article
• Language: English
• Subjects: Accuracy; Artificial intelligence (AI); Computational modeling; Computer architecture; Convergence; Costs; Decoding; Graph neural networks; graph neural networks (GNN); link prediction; machine learning; Optimization; Predictive models; Training
• ISSN: 1041-4347; 1558-2191
• DOI: 10.1109/TKDE.2024.3481015

Graph neural networks (GNNs) for link prediction can loosely be divided into two broad categories. First, node-wise architectures pre-compute individual embeddings for each node that are later combined by a simple decoder to make predictions. While extremely efficient at inference time, model expressiveness is limited such that isomorphic nodes contributing to candidate edges may not be distinguishable, compromising accuracy. In contrast, edge-wise methods rely on the formation of edge-specific subgraph embeddings to enrich the representation of pair-wise relationships, disambiguating isomorphic nodes to improve accuracy, but with increased model complexity. To better navigate this trade-off, we propose a novel GNN architecture whereby the forward pass explicitly depends on both positive (as is typical) and negative (unique to our approach) edges to inform more flexible, yet still cheap node-wise embeddings. This is achieved by recasting the embeddings themselves as minimizers of a forward-pass-specific energy function that favors separation of positive and negative samples. Notably, this energy is distinct from the actual training loss shared by most existing link prediction models, where contrastive pairs only influence the backward pass . As demonstrated by extensive empirical evaluations, the resulting architecture retains the inference speed of node-wise models, while producing competitive accuracy with edge-wise alternatives.