PGCNMDA: Learning node representations along paths with graph convolutional network for predicting miRNA-disease associations

Abstract

Identifying miRNA-disease associations (MDAs) is crucial for improving the diagnosis and treatment of various diseases. However, biological experiments can be time-consuming and expensive. To overcome these challenges, computational approaches have been developed, with Graph Convolutional Network (GCN) showing promising results in MDA prediction. The success of GCN-based methods relies on learning a meaningful spatial operator to extract effective node feature representations. To enhance the inference of MDAs, we propose a novel method called PGCNMDA, which employs graph convolutional networks with a learning graph spatial operator from paths. This approach enables the generation of meaningful spatial convolutions from paths in GCN, leading to improved prediction performance. On HMDD v2.0, PGCNMDA obtains a mean AUC of 0.9229 and an AUPRC of 0.9206 under 5-fold cross-validation (5-CV), and a mean AUC of 0.9235 and an AUPRC of 0.9212 under 10-fold cross-validation (10-CV), respectively. Additionally, the AUC of PGCNMDA also reaches 0.9238 under global leave-one-out cross-validation (GLOOCV). On HMDD v3.2, PGCNMDA obtains a mean AUC of 0.9413 and an AUPRC of 0.9417 under 5-CV, and a mean AUC of 0.9419 and an AUPRC of 0.9425 under 10-CV, respectively. Furthermore, the AUC of PGCNMDA also reaches 0.9415 under GLOOCV. The results show that PGCNMDA is superior to other compared methods. In addition, the case studies on pancreatic neoplasms, thyroid neoplasms and leukemia show that 50, 50 and 48 of the top 50 predicted miRNAs linked to these diseases are confirmed, respectively. It further validates the effectiveness and feasibility of PGCNMDA in practical applications.