A Robust and Precise ConvNet for small non-coding RNA classification

Functional or non-coding RNAs are attracting more attention as they are now potentially considered valuable resources in the development of new drugs intended to cure several human diseases. The identification of drugs targeting the regulatory circuits of functional RNAs depends on knowing its family, a task which is known as RNA sequence classification. State-of-the-art small noncoding RNA classification methodologies take secondary structural features as input. However, in such classification, feature extraction approaches only take global characteristics into account and completely oversight co-relative effect of local structures. Furthermore secondary structure based approaches incorporate high dimensional feature space which proves computationally expensive. This paper proposes a novel Robust and Precise ConvNet (RPC-snRC) methodology which classifies small non-coding RNAs sequences into their relevant families by utilizing the primary sequence of RNAs. RPC-snRC methodology learns hierarchical representation of features by utilizing positioning and occurrences information of nucleotides. To avoid exploding and vanishing gradient problems, we use an approach similar to DenseNet in which gradient can flow straight from subsequent layers to previous layers. In order to assess the effectiveness of deeper architectures for small non-coding RNA classification, we also adapted two ResNet architectures having different number of layers. Experimental results on a benchmark small non-coding RNA dataset show that our proposed methodology does not only outperform existing small non-coding RNA classification approaches with a significant performance margin of 10% but it also outshines adapted ResNet architectures.