Rediscovering alignment relations with Graph Convolutional Networks

Pierre Monnin, Chedy Raïssi, Amedeo Napoli, Adrien Coulet

Published 2020-11-11Version 1

Knowledge graphs are concurrently published and edited in the Web of data. Hence they may overlap, which makes key the task that consists in matching their content. This task encompasses the identification, within and across knowledge graphs, of nodes that are equivalent, more specific, or weakly related. In this article, we propose to match nodes of a knowledge graph by (i) learning node embeddings with Graph Convolutional Networks such that similar nodes have low distances in the embedding space, and (ii) clustering nodes based on their embeddings. We experimented this approach on a biomedical knowledge graph and particularly investigated the interplay between formal semantics and GCN models with the two following main focuses. Firstly, we applied various inference rules associated with domain knowledge, independently or combined, before learning node embeddings, and we measured the improvements in matching results. Secondly, while our GCN model is agnostic to the exact alignment relations (e.g., equivalence, weak similarity), we observed that distances in the embedding space are coherent with the "strength" of these different relations (e.g., smaller distances for equivalences), somehow corresponding to their rediscovery by the model.