Generative Adversarial Matrix Completion Network based on Multi-Source Data Fusion for miRNA–Disease Associations Prediction

Abstract Numerous biological studies have shown that considering disease-associated micro RNAs (miRNAs) as potential biomarkers or therapeutic targets offers new avenues for the diagnosis of complex diseases. Computational methods have gradually been introduced to reveal disease-related miRNAs. Considering that previous models have not fused sufficiently diverse similarities, that their inappropriate fusion methods may lead to poor quality of the comprehensive similarity network and that their results are often limited by insufficiently known associations, we propose a computational model called Generative Adversarial Matrix Completion Network based on Multi-source Data Fusion (GAMCNMDF) for miRNA–disease association prediction. We create a diverse network connecting miRNAs and diseases, which is then represented using a matrix. The main task of GAMCNMDF is to complete the matrix and obtain the predicted results. The main innovations of GAMCNMDF are reflected in two aspects: GAMCNMDF integrates diverse data sources and employs a nonlinear fusion approach to update the similarity networks of miRNAs and diseases. Also, some additional information is provided to GAMCNMDF in the form of a ‘hint’ so that GAMCNMDF can work successfully even when complete data are not available. Compared with other methods, the outcomes of 10-fold cross-validation on two distinct databases validate the superior performance of GAMCNMDF with statistically significant results. It is worth mentioning that we apply GAMCNMDF in the identification of underlying small molecule-related miRNAs, yielding outstanding performance results in this specific domain. In addition, two case studies about two important neoplasms show that GAMCNMDF is a promising prediction method.