Empowering prediction of miRNA–mRNA interactions in species with limited training data through transfer learning

Abstract

MicroRNAs (miRNAs) play a crucial role in mRNA regulation. Identifying functionally important mRNA targets of a specific miRNA is essential for uncovering its biological function and assisting miRNA–based drug development. Datasets of high-throughput direct bona fide miRNA–target interactions (MTIs) exist only for a few model organisms, prompting the need for computational prediction. However, the scarcity of data poses a challenge in training accurate machine learning models for MTI prediction. In this study, we explored the potential of transfer learning technique (with ANN and XGB) to address the limited data challenge by leveraging the similarities in interaction rules between species. Furthermore, we introduced a novel approach called TransferSHAP for estimating the feature importance of transfer learning in tabular dataset tasks. We demonstrated that transfer learning improves MTI prediction accuracy for species with limited datasets and identified the specific interaction features the models employed to transfer information across different species.