RNAI-FRID: novel feature representation method with information enhancement and dimension reduction for RNA–RNA interaction

Abstract

Abstract Different ribonucleic acids (RNAs) can interact to form regulatory networks that play important role in many life activities. Molecular biology experiments can confirm RNA–RNA interactions to facilitate the exploration of their biological functions, but they are expensive and time-consuming. Machine learning models can predict potential RNA–RNA interactions, which provide candidates for molecular biology experiments to save a lot of time and cost. Using a set of suitable features to represent the sample is crucial for training powerful models, but there is a lack of effective feature representation for RNA–RNA interaction. This study proposes a novel feature representation method with information enhancement and dimension reduction for RNA–RNA interaction (named RNAI-FRID). Diverse base features are first extracted from RNA data to contain more sample information. Then, the extracted base features are used to construct the complex features through an arithmetic-level method. It greatly reduces the feature dimension while keeping the relationship between molecule features. Since the dimension reduction may cause information loss, in the process of complex feature construction, the arithmetic mean strategy is adopted to enhance the sample information further. Finally, three feature ranking methods are integrated for feature selection on constructed complex features. It can adaptively retain important features and remove redundant ones. Extensive experiment results show that RNAI-FRID can provide reliable feature representation for RNA–RNA interaction with higher efficiency and the model trained with generated features obtain better performance than other deep neural network predictors.