Protein Ensemble Learning with Atrous Spatial Pyramid Networks for Secondary Structure Prediction

The secondary structure of proteins is significant for studying the three-dimensional structure and functions of proteins. Several models from image understanding and natural language modeling have been successfully adapted in the protein sequence study area, such as Long Short-term Memory (LSTM) network and Convolutional Neural Network (CNN). Recently, Gated Convolutional Neural Network (GCNN) has been proposed for natural language processing and reduces latency while achieving high levels of sentence scoring. Conditionally Parameterized Convolution (CondConv), which use extra sample-dependant modules to conditionally adjust the convolutional network, have achieved great success in the image processing area. In this paper, we propose a novel Conditionally Parameterized Convolutional network (CondGCNN) which utilize the power of both CondConv and GCNN, and we leverage an ensemble encoder to combine the capabilities of both LSTM and CondGCNN to encode protein sequences to obtain better sequential features from proteins. In addition, due to the similarity between the image segmentation problem and the secondary structure prediction problem, we propose an ASP network (Atrous Spatial Pyramid Pooling (ASPP) based network) as the secondary structure generator in our proposed framework. We have conducted extensive ablation studies over each component in the proposed model to verify its effectiveness. Extensive experiments show that the proposed method can achieve higher performance on protein secondary structure prediction task than existing methods on CB513, Caspll and CASP12 datasets. Our method is expected to be useful for protein structure and further protein functions prediction.