Predicting protein properties such as solvent accessibility and secondary structure from its primary amino acid sequence is an important task in bioinformatics. Recently, a few deep learning models have surpassed the traditional window based multilayer perceptron. Taking inspiration from the image classification domain we propose a deep convolutional neural network architecture, MUST-CNN, to predict protein properties. This architecture uses a novel multilayer shift-and-stitch (MUST) technique to generate fully dense per-position predictions on protein sequences. Our model is significantly simpler than the state-of-the-art, yet achieves better results. By combining MUST and the efficient convolution operation, we can consider far more parameters while retaining very fast prediction speeds. We beat the state-of-the-art performance on two large protein property prediction datasets.
Recently, work has also been done on the model side, particularly in natural language processing and image recognition tasks. @cite_6 created a similar algorithm in the natural language processing domain, where they labeled word properties, such as part of speech or category of a named entity, on text data. If we consider each protein chain to be a sentence and each amino acid to be a word, the techniques transfer easily. @cite_6 used both a windowed approach and a sentence level approach with a convolutional network, though their network was shallow and only outputed predictions for one position at a time. Long-short term memory networks have been used very successfully in sequence learning, machine translation @cite_23 @cite_11 and language modeling @cite_1 . We note that machine translation is a much more general sequence to sequence task where the input and output sizes are not matched. Language modeling tries to guess future words based on past words, while protein sequences has no innate direction.
@cite_1 @cite_23 @cite_6 @cite_11
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Sequence-to-sequence translation methods based on generation with a side-conditioned language model have recently shown promising results in several tasks. In machine translation, models conditioned on source side words have been used to produce target-language text, and in image captioning, models conditioned images have been used to generate caption text. Past work with this approach has focused on large vocabulary tasks, and measured quality in terms of BLEU. In this paper, we explore the applicability of such models to the qualitatively different grapheme-to-phoneme task. Here, the input and output side vocabularies are small, plain n-gram models do well, and credit is only given when the output is exactly correct. We find that the simple side-conditioned generation approach is able to rival the state-of-the-art, and we are able to significantly advance the stat-of-the-art with bi-directional long short-term memory (LSTM) neural networks that use the same alignment information that is used in conventional approaches. A variety of functionally important protein properties, such as secondary structure, transmembrane topology and solvent accessibility, can be encoded as a labeling of amino acids. Indeed, the prediction of such properties from the primary amino acid sequence is one of the core projects of computational biology. Accordingly, a panoply of approaches have been developed for predicting such properties; however, most such approaches focus on solving a single task at a time. Motivated by recent, successful work in natural language processing, we propose to use multitask learning to train a single, joint model that exploits the dependencies among these various labeling tasks. We describe a deep neural network architecture that, given a protein sequence, outputs a host of predicted local properties, including secondary structure, solvent accessibility, transmembrane topology, signal peptides and DNA-binding residues. The network is trained jointly on all these tasks in a supervised fashion, augmented with a novel form of semi-supervised learning in which the model is trained to distinguish between local patterns from natural and synthetic protein sequences. The task-independent architecture of the network obviates the need for task-specific feature engineering. We demonstrate that, for all of the tasks that we considered, our approach leads to statistically significant improvements in performance, relative to a single task neural network approach, and that the resulting model achieves state-of-the-art performance. Attentional sequence-to-sequence models have become the new standard for machine translation, but one challenge of such models is a significant increase in training and decoding cost compared to phrase-based systems. Here, we focus on efficient decoding, with a goal of achieving accuracy close the state-of-the-art in neural machine translation (NMT), while achieving CPU decoding speed throughput close to that of a phrasal decoder. We approach this problem from two angles: First, we describe several techniques for speeding up an NMT beam search decoder, which obtain a 4.4x speedup over a very efficient baseline decoder without changing the decoder output. Second, we propose a simple but powerful network architecture which uses an RNN (GRU LSTM) layer at bottom, followed by a series of stacked fully-connected layers applied at every timestep. This architecture achieves similar accuracy to a deep recurrent model, at a small fraction of the training and decoding cost. By combining these techniques, our best system achieves a very competitive accuracy of 38.3 BLEU on WMT English-French NewsTest2014, while decoding at 100 words sec on single-threaded CPU. We believe this is the best published accuracy speed trade-off of an NMT system. Recurrent sequence generators conditioned on input data through an attention mechanism have recently shown very good performance on a range of tasks including machine translation, handwriting synthesis [1,2] and image caption generation [3]. We extend the attention-mechanism with features needed for speech recognition. We show that while an adaptation of the model used for machine translation in [2] reaches a competitive 18.7 phoneme error rate (PER) on the TIMET phoneme recognition task, it can only be applied to utterances which are roughly as long as the ones it was trained on. We offer a qualitative explanation of this failure and propose a novel and generic method of adding location-awareness to the attention mechanism to alleviate this issue. The new method yields a model that is robust to long inputs and achieves 18 PER in single utterances and 20 in 10-times longer (repeated) utterances. Finally, we propose a change to the attention mechanism that prevents it from concentrating too much on single frames, which further reduces PER to 17.6 level.