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 citing sentence is one that appears in a scientific article and cites previous work. Citing sentences have been studied and used in many applications. For example, they have been used in scientific paper summarization, automatic survey generation, paraphrase identification, and citation function classification. Citing sentences that cite multiple papers are common in scientific writing. This observation should be taken into consideration when using citing sentences in applications. For instance, when a citing sentence is used in a summary of a scientific paper, only the fragments of the sentence that are relevant to the summarized paper should be included in the summary. In this paper, we present and compare three different approaches for identifying the fragments of a citing sentence that are related to a given target reference. Our methods are: word classification, sequence labeling, and segment classification. Our experiments show that segment classification achieves the best results. 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. We introduce a neural machine translation model that views the input and output sentences as sequences of characters rather than words. Since word-level information provides a crucial source of bias, our input model composes representations of character sequences into representations of words (as determined by whitespace boundaries), and then these are translated using a joint attention translation model. In the target language, the translation is modeled as a sequence of word vectors, but each word is generated one character at a time, conditional on the previous character generations in each word. As the representation and generation of words is performed at the character level, our model is capable of interpreting and generating unseen word forms. A secondary benefit of this approach is that it alleviates much of the challenges associated with preprocessing tokenization of the source and target languages. We show that our model can achieve translation results that are on par with conventional word-based models.