ProLanGO: Protein Function Prediction Using Neural~Machine Translation Based on a Recurrent Neural Network

With the development of next generation sequencing techniques, it is fast and cheap to determine protein sequences but relatively slow and expensive to extract useful information from protein sequences because of limitations of traditional biological experimental techniques. Protein function prediction has been a long standing challenge to fill the gap between the huge amount of protein sequences and the known function. In this paper, we propose a novel method to convert the protein function problem into a language translation problem by the new proposed protein sequence language "ProLan" to the protein function language "GOLan", and build a neural machine translation model based on recurrent neural networks to translate "ProLan" language to "GOLan" language. We blindly tested our method by attending the latest third Critical Assessment of Function Annotation (CAFA 3) in 2016, and also evaluate the performance of our methods on selected proteins whose function was released after CAFA competition. The good performance on the training and testing datasets demonstrates that our new proposed method is a promising direction for protein function prediction. In summary, we first time propose a method which converts the protein function prediction problem to a language translation problem and applies a neural machine translation model for protein function prediction.Comment: 13 pages, 5 figure

Semi-Autoregressive Neural Machine Translation

Existing approaches to neural machine translation are typically autoregressive models. While these models attain state-of-the-art translation quality, they are suffering from low parallelizability and thus slow at decoding long sequences. In this paper, we propose a novel model for fast sequence generation --- the semi-autoregressive Transformer (SAT). The SAT keeps the autoregressive property in global but relieves in local and thus is able to produce multiple successive words in parallel at each time step. Experiments conducted on English-German and Chinese-English translation tasks show that the SAT achieves a good balance between translation quality and decoding speed. On WMT'14 English-German translation, the SAT achieves 5.58$\times$ speedup while maintains 88\% translation quality, significantly better than the previous non-autoregressive methods. When produces two words at each time step, the SAT is almost lossless (only 1\% degeneration in BLEU score).Comment: EMNLP 201