Unified Deep Learning Architecture for Modeling Biology Sequence

Prediction of the spatial structure or function of biological macromolecules based on their sequences remains an important challenge in bioinformatics. When modeling biological sequences using traditional sequencing models, long-range interaction, complicated and variable output of labeled structures, and variable length of biological sequences usually lead to different solutions on a case-by-case basis. This study proposed a unified deep learning architecture based on long short-term memory or a gated recurrent unit to capture long-range interactions. The architecture designs the optional reshape operator to adapt to the diversity of the output labels and implements a training algorithm to support the training of sequence models capable of processing variable-length sequences. The merging and pooling operators enhances the ability of capturing short-range interactions between basic units of biological sequences. The proposed deep-learning architecture and its training algorithm might be capable of solving currently variable biological sequence-modeling problems under a unified framework. We validated the model on one of the most difficult biological sequence-modeling problems, protein residue interaction prediction. The results indicate that the accuracy of obtaining the residue interactions of the model exceeded popular approaches by 10 percent on multiple widely-used benchmarks.