mSRFR: a machine learning model using microalgal signature features for ncRNA classification

This work presents mSRFR (microalgae SMOTE Random Forest Relief model), a classification tool for noncoding RNAs (ncRNAs) in microalgae, including green algae, diatoms, golden algae, and cyanobacteria. First, the SMOTE technique was applied to address the challenge of imbalanced data due to the different numbers of microalgae ncRNAs from different species in the EBI RNA-central database. Then the top 20 significant features from a total of 106 features, including sequence-based, secondary structure, base-pair, and triplet sequence-structure features, were selected using the Relief feature selection method. Next, ten-fold cross-validation was applied to choose a classifier algorithm with the highest performance among Support Vector Machine, Random Forest, Decision Tree, Naïve Bayes, K-nearest Neighbor, and Neural Network, based on the receiver operating characteristic (ROC) area. The results showed that the Random Forest classifier achieved the highest ROC area of 0.992. Then, the Random Forest algorithm was selected and compared with other tools, including RNAcon, CPC, CPC2, CNCI, and CPPred. Our model achieved a high accuracy of about 97% and a low false-positive rate of about 2% in predicting the test dataset of microalgae. Furthermore, the top features from Relief revealed that the %GA dinucleotide is a signature feature of microalgal ncRNAs when compared to Escherichia coli, Saccharomyces cerevisiae, Arabidopsis thaliana, and Homo sapiens.