Knowledge graph embeddings in the biomedical domain: are they useful? A look at link prediction, rule learning, and downstream polypharmacy tasks

Abstract

Abstract Summary Knowledge graphs (KGs) are powerful tools for representing and organizing complex biomedical data. They empower researchers, physicians, and scientists by facilitating rapid access to biomedical information, enabling the discernment of patterns or insights, and fostering the formulation of decisions and the generation of novel knowledge. To automate these activities, several KG embedding algorithms have been proposed to learn from and complete KGs. However, the efficacy of these embedding algorithms appears limited when applied to biomedical KGs, prompting questions about whether they can be useful in this field. To that end, we explore several widely used KG embedding models and evaluate their performance and applications using a recent biomedical KG, BioKG. We also demonstrate that by using recent best practices for training KG embeddings, it is possible to improve performance over BioKG. Additionally, we address interpretability concerns that naturally arise with such machine learning methods. In particular, we examine rule-based methods that aim to address these concerns by making interpretable predictions using learned rules, achieving comparable performance. Finally, we discuss a realistic use case where a pretrained BioKG embedding is further trained for a specific task, in this case, four polypharmacy scenarios where the goal is to predict missing links or entities in another downstream KGs in four polypharmacy scenarios. We conclude that in the right scenarios, biomedical KG embeddings can be effective and useful. Availability and implementation Our code and data is available at https://github.com/aryopg/biokge.