pysster: Classification Of Biological Sequences By Learning Sequence And Structure Motifs With Convolutional Neural Networks

Abstract

SummaryConvolutional neural networks (CNNs) have been shown to perform exceptionally well in a variety of tasks, including biological sequence classification. Available implementations, however, are usually optimized for a particular task and difficult to reuse. To enable researchers to utilize these networks more easily we implemented pysster, a Python package for training CNNs on biological sequence data. Sequences are classified by learning sequence and structure motifs and the package offers an automated hyper-parameter optimization procedure and options to visualize learned motifs along with information about their positional and class enrichment. The package runs seamlessly on CPU and GPU and provides a simple interface to train and evaluate a network with a handful lines of code. Using an RNA A-to-I editing data set and CLIP-seq binding site sequences we demonstrate that pysster classifies sequences with higher accuracy than other methods and is able to recover known sequence and structure motifs.\n\nAvailabilitypysster is freely available at https://github.com/budach/pysster.\n\nContactbudach@molgen.mpg.de, marsico@molgen.mpg.de