MUST-CNN: a multilayer shift-and-stitch deep convolutional architecture for sequence-based protein structure prediction

Z Lin, J Lanchantin, Y Qi - Proceedings of the AAAI Conference on …, 2016 - ojs.aaai.org
Proceedings of the AAAI Conference on Artificial Intelligence, 2016ojs.aaai.org
Predicting protein properties such as solvent accessibility and secondary structure from its
primary amino acid sequence is an important task in bioinformatics. Recently, a few deep
learning models have surpassed the traditional window based multilayer perceptron. Taking
inspiration from the image classification domain we propose a deep convolutional neural
network architecture, MUST-CNN, to predict protein properties. This architecture uses a
novel multilayer shift-and-stitch (MUST) technique to generate fully dense per-position …
Abstract
Predicting protein properties such as solvent accessibility and secondary structure from its primary amino acid sequence is an important task in bioinformatics. Recently, a few deep learning models have surpassed the traditional window based multilayer perceptron. Taking inspiration from the image classification domain we propose a deep convolutional neural network architecture, MUST-CNN, to predict protein properties. This architecture uses a novel multilayer shift-and-stitch (MUST) technique to generate fully dense per-position predictions on protein sequences. Our model is significantly simpler than the state-of-the-art, yet achieves better results. By combining MUST and the efficient convolution operation, we can consider far more parameters while retaining very fast prediction speeds. We beat the state-of-the-art performance on two large protein property prediction datasets.
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