Enhancing Embedding Representations of Biomedical Data using Logic Knowledge
This work addresses a bottleneck in biomedical knowledge graph completion by enhancing embeddings with logic rules, offering incremental improvements for domain-specific applications.
The paper tackles the problem of Knowledge Graph Embeddings (KGEs) failing to represent complex relational dependencies like logic rules in biomedical data, specifically on the PharmKG dataset, and shows that using Relational Reasoning Network (R2N) to incorporate logic rules significantly improves state-of-the-art results.
Knowledge Graph Embeddings (KGE) have become a quite popular class of models specifically devised to deal with ontologies and graph structure data, as they can implicitly encode statistical dependencies between entities and relations in a latent space. KGE techniques are particularly effective for the biomedical domain, where it is quite common to deal with large knowledge graphs underlying complex interactions between biological and chemical objects. Recently in the literature, the PharmKG dataset has been proposed as one of the most challenging knowledge graph biomedical benchmark, with hundreds of thousands of relational facts between genes, diseases and chemicals. Despite KGEs can scale to very large relational domains, they generally fail at representing more complex relational dependencies between facts, like logic rules, which may be fundamental in complex experimental settings. In this paper, we exploit logic rules to enhance the embedding representations of KGEs on the PharmKG dataset. To this end, we adopt Relational Reasoning Network (R2N), a recently proposed neural-symbolic approach showing promising results on knowledge graph completion tasks. An R2N uses the available logic rules to build a neural architecture that reasons over KGE latent representations. In the experiments, we show that our approach is able to significantly improve the current state-of-the-art on the PharmKG dataset. Finally, we provide an ablation study to experimentally compare the effect of alternative sets of rules according to different selection criteria and varying the number of considered rules.