Deep Recurrent Conditional Random Field Network for Protein Secondary Prediction

Deep learning has become the state-of-the-art method for predicting protein secondary structure from only its amino acid residues and sequence profile. Building upon these results, we propose to combine a bi-directional recurrent neural network (biRNN) with a conditional random field (CRF), which we call the biRNN-CRF. The biRNN-CRF may be seen as an improved alternative to an auto-regressive uni-directional RNN where predictions are performed sequentially conditioning on the prediction in the previous time-step. The CRF is instead nearest neighbor-aware and models for the joint distribution of the labels for all time-steps. We condition the CRF on the output of biRNN, which learns a distributed representation based on the entire sequence. The biRNN-CRF is therefore close to ideally suited for the secondary structure task because a high degree of cross-talk between neighboring elements can be expected. We validate the model on several benchmark datasets. For example, on CB513, a model with 1.7 million parameters, achieves a Q8 accuracy of 69.4 for single model and 70.9 for ensemble, which to our knowledge is state-of-the-art.