Nucleotide-level Convolutional Neural Networks for Pre-miRNA Classification

Due to the biogenesis difference, miRNAs can be divided into canonical microRNAs and mirtrons. Compared to canonical microRNAs, mirtrons are less conserved and hard to be identified. Except stringent annotations based on experiments, many in silico computational methods have be developed to classify miRNAs. Although several machine learning classifiers delivered high classification performance, all the predictors depended heavily on the selection of calculated features. Here, we introduced nucleotide-level convolutional neural networks (CNNs) for pre-miRNAs classification. By using “one-hot” encoding and padding, pre-miRNAs were converted into matrixes with the same shape. The convolution and max-pooling operations can automatically extract features from pre-miRNAs sequences. Evaluation on test dataset showed that our models had a satisfactory performance. Our investigation showed that it was feasible to apply CNNs to extract features from biological sequences. Since there are many hyperparameters can be tuned in CNNs, we believe that the performance of nucleotide-level convolutional neural networks can be greatly improved in the future.