Bidirectional segmented-memory recurrent neural network for protein secondary structure prediction

The formation of protein secondary structure especially the regions of β-sheets involves long-range interactions between amino acids. We propose a novel recurrent neural network architecture called segmented-memory recurrent neural network (SMRNN) and present experimental results showing that SMRNN outperforms conventional recurrent neural networks on long-term dependency problems. In order to capture long-term dependencies in protein sequences for secondary structure prediction, we develop a predictor based on bidirectional segmented-memory recurrent neural network (BSMRNN), which is a noncausal generalization of SMRNN. In comparison with the existing predictor based on bidirectional recurrent neural network (BRNN), the BSMRNN predictor can improve prediction performance especially the recognition accuracy of β-sheets.