An ensemble of stacking classifiers for improved prediction of miRNA–mRNA interactions

MicroRNAs (miRNAs) are small non-coding RNA molecules that play a crucial role in regulating gene expression at the post-transcriptional level by binding to potential target sites of messenger RNAs (mRNAs), facilitated by the Argonaute family of proteins. Selecting the conservative candidate target sites (CTS) is a challenging step, considering that most of the existing computational algorithms primarily focus on canonical site types, which is a time-consuming and inefficient utilization of miRNA target site interactions. We developed a stacking classifier algorithm that addresses the CTS selection criteria using feature-encoding techniques that generates feature vectors, including k-mer nucleotide composition, dinucleotide composition, pseudo-nucleotide composition, and sequence order coupling. This innovative stacking classifier algorithm surpassed previous state-of-the-art algorithms in predicting functional miRNA targets. We evaluated the performance of the proposed model on 10 independent test datasets and obtained an average accuracy of 79.77%, which is a significant improvement of 7.26 % over previous models. This improvement shows that the proposed method has great potential for distinguishing highly functional miRNA targets and can serve as a valuable tool in biomedical and drug development research.