Entity Alignment (EA) aims to identify equivalent entities across different Knowledge Graphs (KGs), enabling knowledge fusion and integration. In recent years, Graph Neural Networks (GNNs) have emerged as a powerful paradigm for EA by leveraging structural information in KGs. However, most existing studies emphasize novel message passing mechanisms while overlooking other crucial GNN design components. This paper presents a comprehensive and systematic evaluation of GNN-based EA methods, focusing on three key aspects: message passing strategies, the number of GNN layers, and the construction of final entity representations. We benchmark a diverse set of GNN models originally developed for tasks such as node classification and knowledge graph completion, and we assess their adaptability to the EA task. Additionally, we explore the effectiveness of skip connection techniques, activation functions, and relational information integration. Our experiments, conducted on standard EA benchmarks including DBP15K and SRPRS, reveal several counterintuitive findings: (1) message passing is indispensable for EA; (2) many node classification GNNs are highly competitive for EA; (3) one or two GNN layers generally achieve optimal performance; and (4) activation functions have minimal impact, while skip connections significantly enhance results. This study provides a principled framework and empirical foundation for designing more effective GNN-based EA models. Code and datasets are publicly available at https://github.com/kg-bnu/GNN-EA.
Ding et al. (Sun,) studied this question.