DeepWalk based method to predict lncRNA-miRNA associations via lncRNA-miRNA-disease-protein-drug graph

Abstract

Abstract Background Long non-coding RNAs (lncRNAs) play a crucial role in diverse biological processes and have been confirmed to be concerned with various diseases. Largely uncharacterized of the physiological role and functions of lncRNA remains. MicroRNAs (miRNAs), which are usually 20–24 nucleotides, have several critical regulatory parts in cells. LncRNA can be regarded as a sponge to adsorb miRNA and indirectly regulate transcription and translation. Thus, the identification of lncRNA-miRNA associations is essential and valuable. Results In our work, we present DWLMI to infer the potential associations between lncRNAs and miRNAs by representing them as vectors via a lncRNA-miRNA-disease-protein-drug graph. Specifically, DeepWalk can be used to learn the behavior representation of vertices. The methods of fingerprint, k-mer and MeSH descriptors were mainly used to learn the attribute representation of vertices. By combining the above two kinds of information, unknown lncRNA-miRNA associations can be predicted by the random forest classifier. Under the five-fold cross-validation, the proposed DWLMI model obtained an average prediction accuracy of 95.22% with a sensitivity of 94.35% at the AUC of 98.56%. Conclusions The experimental results demonstrated that DWLMI can effectively predict the potential lncRNA-miRNA associated pairs, and the results can provide a new insight for related non-coding RNA researchers in the field of combing biology big data with deep learning.

Keywords

• DeepWalk
• LncRNA
• miRNA
• Random forest