Predicting microRNA-disease associations from knowledge graph using tensor decomposition with relational constraints

Motivation: MiRNAs are a kind of small non-coding RNAs that are not translated into proteins, and aberrant expression of miRNAs is associated with human diseases. Since miRNAs have different roles in diseases, the miRNA-disease associations are categorized into multiple types according to their roles. Predicting miRNA-disease associations and types is critical to understand the underlying pathogenesis of human diseases from the molecular level. Results: In this paper, we formulate the problem as a link prediction in knowledge graphs. We use biomedical knowledge bases to build a knowledge graph of entities representing miRNAs and disease and multi-relations, and we propose a tensor decomposition-based model named TDRC to predict miRNA-disease associations and their types from the knowledge graph. We have experimentally evaluated our method and compared it to several baseline methods. The results demonstrate that the proposed method has high-accuracy and high-efficiency performances.