An introduction to deep learning on biological sequence data: Examples and solutions

Motivation: Deep neural network architectures such as convolutional and long short-term memory networks have become increasingly popular as machine learning tools during the recent years. The availability of greater computational resources, more data, new algorithms for training deep models and easy to use libraries for implementation and training of neural networks are the drivers of this development. The use of deep learning has been especially successful in image recognition; and the development of tools, applications and code examples are in most cases centered within this field rather than within biology. Results: Here, we aim to further the development of deep learning methods within biology by providing application examples and ready to apply and adapt code templates. Given such examples, we illustrate how architectures consisting of convolutional and long short-term memory neural networks can relatively easily be designed and trained to state-of-the-art performance on three biological sequence problems: prediction of subcellular localization, protein secondary structure and the binding of peptides to MHC Class II molecules. Availability and implementation: All implementations and datasets are available online to the scientific community at https://github.com/vanessajurtz/lasagne4bio. Supplementary information: Supplementary data are available at Bioinformatics online.Fil: Jurtz, Vanessa Isabell. Technical University of Denmark; DinamarcaFil: Johansen, Alexander Rosenberg. Technical University of Denmark; DinamarcaFil: Nielsen, Morten. Technical University of Denmark; Dinamarca. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús). Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús); ArgentinaFil: Almagro Armenteros, Jose Juan. Technical University of Denmark; DinamarcaFil: Nielsen, Henrik. Technical University of Denmark; DinamarcaFil: Sønderby, Casper Kaae. Universidad de Copenhagen; DinamarcaFil: Winther, Ole. Universidad de Copenhagen; DinamarcaFil: Sønderby, Søren Kaae. Universidad de Copenhagen; Dinamarc