RPI-SE: A stacking ensemble learning framework for ncRNA-protein interactions prediction using sequence information

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Abstract

Background: The interactions between non-coding RNAs (ncRNA) and proteins play an essential role in many biological processes. Several high-throughput experimental methods have been applied to detect ncRNA-protein interactions. However, these methods are time-consuming and expensive. Accurate and efficient computational methods can assist and accelerate the study of ncRNA-protein interactions. Results: In this work, we develop a stacking ensemble computational framework, RPI-SE, for effectively predicting ncRNA-protein interactions. More specifically, to fully exploit protein and RNA sequence feature, Position Weight Matrix combined with Legendre Moments is applied to obtain protein evolutionary information. Meanwhile, k-mer sparse matrix is employed to extract efficient feature of ncRNA sequences. Finally, an ensemble learning framework integrated different types of base classifier is developed to predict ncRNA-protein interactions using these discriminative features. The accuracy and robustness of RPI-SE was evaluated on three benchmark data sets under five-fold cross-validation and compared with other state-of-the-art methods. Conclusions: The results demonstrate that RPI-SE is competent for ncRNA-protein interactions prediction task with high accuracy and robustness. It's anticipated that this work can provide a computational prediction tool to advance ncRNA-protein interactions related biomedical research.

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Yi, H. C., You, Z. H., Wang, M. N., Guo, Z. H., Wang, Y. B., & Zhou, J. R. (2020). RPI-SE: A stacking ensemble learning framework for ncRNA-protein interactions prediction using sequence information. BMC Bioinformatics, 21(1). https://doi.org/10.1186/s12859-020-3406-0

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