Drug-drug interaction predictions via knowledge graph and text embedding: Instrument validation study

Abstract

Background: Minimizing adverse reactions caused by drug-drug interactions (DDIs) has always been a prominent research topic in clinical pharmacology. Detecting all possible interactions through clinical studies before a drug is released to the market is a demanding task. The power of big data is opening up new approaches to discovering various DDIs. However, these data contain a huge amount of noise and provide knowledge bases that are far from being complete or used with reliability. Most existing studies focus on predicting binary DDIs between drug pairs and ignore other interactions. Objective: Leveraging both drug knowledge graphs and biomedical text is a promising pathway for rich and comprehensive DDI prediction, but it is not without issues. Our proposed model seeks to address the following challenges: data noise and incompleteness, data sparsity, and computational complexity. Methods: We propose a novel framework, Predicting Rich DDI, to predict DDIs. The framework uses graph embedding to overcome data incompleteness and sparsity issues to make multiple DDI label predictions. First, a large-scale drug knowledge graph is generated from different sources. The knowledge graph is then embedded with comprehensive biomedical text into a common low-dimensional space. Finally, the learned embeddings are used to efficiently compute rich DDI information through a link prediction process. Results: To validate the effectiveness of the proposed framework, extensive experiments were conducted on real-world data sets. The results demonstrate that our model outperforms several state-of-the-art baseline methods in terms of capability and accuracy. Conclusions: We propose a novel framework, Predicting Rich DDI, to predict DDIs. Using rich DDI information, it can competently predict multiple labels for a pair of drugs across numerous domains, ranging from pharmacological mechanisms to side effects. To the best of our knowledge, this framework is the first to provide a joint translation-based embedding model that learns DDIs by integrating drug knowledge graphs and biomedical text simultaneously in a common low-dimensional space. The model also predicts DDIs using multiple labels rather than single or binary labels. Extensive experiments were conducted on real-world data sets to demonstrate the effectiveness and efficiency of the model. The results show our proposed framework outperforms several state-of-the-art baselines.