Protein secondary structure prediction with cascaded CNN and RNN

This is an example of the application of deep learning to protein secondary structure prediction. This example is based on [1], but some minor modifications are applied.

See commentary.md for a detailed explanation

Dependency

• Chainer
• NumPy
• six

Usage

Retrieve dataset

bash get_data.sh

Train

PYTHONPATH="." python tools/train.py

Reference

[1] Li, Z., & Yu, Y. (2016). Protein Secondary Structure Prediction Using Cascaded Convolutional and Recurrent Neural Networks. arXiv preprint arXiv:1604.07176.