MSNet-4mC: Learning effective multi-scale representations for identifying DNA N4-methylcytosine sites

Abstract

Motivation: N4-methylcytosine (4mC) is an essential kind of epigenetic modification that regulates a wide range of biological processes. However, experimental methods for detecting 4mC sites are time-consuming and labor-intensive. As an alternative, computational methods that are capable of automatically identifying 4mC with data analysis techniques become a reasonable option. A major challenge is how to develop effective methods to fully exploit the complex interactions within the DNA sequences to improve the predictive capability. Results: In this work, we propose MSNet-4mC, a lightweight neural network building upon convolutional operations with multi-scale receptive fields to perceive cross-element relationships over both short and long ranges of given DNA sequences. With strong imbalances in the number of candidates in different species in mind, we compute and apply class weights in the cross-entropy loss to balance the training process. Extensive benchmarking experiments show that our method achieves a significant performance improvement and outperforms other state-of-the-art methods. Availability and implementation: The source code and models are freely available for download at https://github.com/LIU-CT/MSNet-4mC, implemented in Python and supported on Linux and Windows. Supplementary information: Supplementary data are available at Bioinformatics online.