Clinical trial recommendations using Semantics-Based inductive inference and knowledge graph embeddings

• Published in: Journal of biomedical informatics 2024-06, Vol.154, p.104627, Article 104627
• Main Authors: Devarakonda, Murthy V., Mohanty, Smita, Sunkishala, Raja Rao, Mallampalli, Nag, Liu, Xiong
• Format: Article
• Language: English
• Subjects: Algorithms; Clinical trials; Clinical Trials as Topic; Data Mining - methods; Graph Attention Networks (GATs); Graph embeddings; Graph Neural Networks (GNNs); Humans; Inductive inference; Knowledge graphs; Neural Networks, Computer; Recommendation systems; Research Design; Semantics; Transductive inference
• ISSN: 1532-0464; 1532-0480; 1532-0480
• DOI: 10.1016/j.jbi.2024.104627

[Display omitted] Designing a new clinical trial entails many decisions, such as defining a cohort and setting the study objectives to name a few, and therefore can benefit from recommendations based on exhaustive mining of past clinical trial records. This study proposes an approach based on knowledge graph embeddings and semantics-driven inductive inference for generating such recommendations. The proposed recommendation methodology is based on neural embeddings trained on first-of-its-kind knowledge graph constructed from clinical trials data. The methodology includes design of a knowledge graph for clinical trial data, evaluation of various knowledge graph embedding techniques for it, application of a novel inductive inference method using these embeddings, and generation of recommendations for clinical trial design. The study uses freely available data from clinicaltrials.gov and related sources. The proposed approach for recommendations obtained relevance scores ranging from 70% to 83%. These scores were determined by evaluating the text similarity of recommended elements to actual elements used in clinical trials that are in progress. Furthermore, the most pertinent recommendations were consistently located towards the top of the list, indicating the effectiveness of our method. Our study suggests that inductive inference using node semantics is a viable approach for generating recommendations using graphs neural embeddings, and that there is a potential for improvement in training graph embeddings using node semantics.