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. In neural machine translation, a source sequence of words is encoded into a vector from which a target sequence is generated in the decoding phase. Differently from statistical machine translation, the associations between source words and their possible target counterparts are not explicitly stored. Source and target words are at the two ends of a long information processing procedure, mediated by hidden states at both the source encoding and the target decoding phases. This makes it possible that a source word is incorrectly translated into a target word that is not any of its admissible equivalent counterparts in the target language. In this paper, we seek to somewhat shorten the distance between source and target words in that procedure, and thus strengthen their association, by means of a method we term bridging source and target word embeddings. We experiment with three strategies: (1) a source-side bridging model, where source word embeddings are moved one step closer to the output target sequence; (2) a target-side bridging model, which explores the more relevant source word embeddings for the prediction of the target sequence; and (3) a direct bridging model, which directly connects source and target word embeddings seeking to minimize errors in the translation of ones by the others. Experiments and analysis presented in this paper demonstrate that the proposed bridging models are able to significantly improve quality of both sentence translation, in general, and alignment and translation of individual source words with target words, in particular. We describe a single convolutional neural network architecture that, given a sentence, outputs a host of language processing predictions: part-of-speech tags, chunks, named entity tags, semantic roles, semantically similar words and the likelihood that the sentence makes sense (grammatically and semantically) using a language model. The entire network is trained jointly on all these tasks using weight-sharing, an instance of multitask learning. All the tasks use labeled data except the language model which is learnt from unlabeled text and represents a novel form of semi-supervised learning for the shared tasks. We show how both multitask learning and semi-supervised learning improve the generalization of the shared tasks, resulting in state-of-the-art-performance. Abstract Documents in computer-readable form can be used to provide information about other documents, i.e. those they cite. To do this efficiently requires procedures for computer recognition of citing statements. This is not easy, especially for multi-sentence citing statements. Computer recognition procedures have been developed which are accurate to the following extent: 73 of the words in statements selected by computer procedures as being citing statements are words which are correctly attributable to the corresponding documents. The retrieval effectiveness of computer-recognized citing statements was tested in the following way. First, for eight retrieval requests in inorganiic chemistry, average recall by search of Chemical Abstracts Service indexing and Chemical Abstracts abstract text words was found to be 50 . Words from citing statements referring to the papers to be retrieved were then added to the index terms and abstract words as additional access points, and searching was repeated. Average recall increased to 70 . Only words from citing statements published within a year of the cited papers were used. The retrieval effect of citing statement words alone (published within a year) without index or abstract terms was the following: average recall was 40 . When just the words of the titles of the cited papers were added to those citing statement words, average recall increased to 50 . Abstract : For most people, watching a brief video and describing what happened (inwords) is an easy task. For machines, extracting the meaning from video pixelsand generating a sentence description is a very complex problem. The goal of myresearch is to develop models that can automatically generate natural language(NL) descriptions for events in videos. As a first step, this proposal presentsdeep recurrent neural network models for video to text generation. I build onrecent deep machine learning approaches to develop video description modelsusing a unified deep neural network with both convolutional and recurrentstructure. This technique treats the video domain as another language andtakes a machine translation approach using the deep network to translate videosto text. In my initial approach, I adapt a model that can learn on images andcaptions to transfer knowledge from this auxiliary task to generate descriptionsfor short video clips. Next, I present an end-to-end deep network that can jointlymodel a sequence of video frames and a sequence of words. The second part ofthe proposal outlines a set of models to significantly extend work in this area.Specifically, I propose techniques to integrate linguistic knowledge from plaintext corpora; and attention methods to focus on objects and track their interactionsto generate more diverse and accurate descriptions. To move beyondshort video clips, I also outline models to process multi-activity movie videos,learning to jointly segment and describe coherent event sequences. I proposefurther extensions to take advantage of movie scripts and subtitle informationto generate richer descriptions. Countless learning tasks require dealing with sequential data. Image captioning, speech synthesis, and music generation all require that a model produce outputs that are sequences. In other domains, such as time series prediction, video analysis, and musical information retrieval, a model must learn from inputs that are sequences. Interactive tasks, such as translating natural language, engaging in dialogue, and controlling a robot, often demand both capabilities. Recurrent neural networks (RNNs) are connectionist models that capture the dynamics of sequences via cycles in the network of nodes. Unlike standard feedforward neural networks, recurrent networks retain a state that can represent information from an arbitrarily long context window. Although recurrent neural networks have traditionally been dicult to train, and often contain millions of parameters, recent advances in network architectures, optimization techniques, and parallel computation have enabled successful large-scale learning with them. In recent years, systems based on long short-term memory (LSTM) and bidirectional (BRNN) architectures have demonstrated ground-breaking performance on tasks as varied as image captioning, language translation, and handwriting recognition. In this survey, we review and synthesize the research that over the past three decades rst yielded and then made practical these powerful learning models. When appropriate, we reconcile conicting notation and nomenclature. Our goal is to provide a selfcontained explication of the state of the art together with a historical perspective and references to primary research. Sequence-to-sequence (Seq2Seq) models with attention have excelled at tasks which involve generating natural language sentences such as machine translation, image captioning and speech recognition. Performance has further been improved by leveraging unlabeled data, often in the form of a language model. In this work, we present the Cold Fusion method, which leverages a pre-trained language model during training, and show its effectiveness on the speech recognition task. We show that Seq2Seq models with Cold Fusion are able to better utilize language information enjoying i) faster convergence and better generalization, and ii) almost complete transfer to a new domain while using less than 10 of the labeled training data. Because of their superior ability to preserve sequence information over time, Long Short-Term Memory (LSTM) networks, a type of recurrent neural network with a more complex computational unit, have obtained strong results on a variety of sequence modeling tasks. The only underlying LSTM structure that has been explored so far is a linear chain. However, natural language exhibits syntactic properties that would naturally combine words to phrases. We introduce the Tree-LSTM, a generalization of LSTMs to tree-structured network topologies. Tree-LSTMs outperform all existing systems and strong LSTM baselines on two tasks: predicting the semantic relatedness of two sentences (SemEval 2014, Task 1) and sentiment classification (Stanford Sentiment Treebank). A Long Short-Term Memory (LSTM) network is a type of recurrent neural network architecture which has recently obtained strong results on a variety of sequence modeling tasks. The only underlying LSTM structure that has been explored so far is a linear chain. However, natural language exhibits syntactic properties that would naturally combine words to phrases. We introduce the Tree-LSTM, a generalization of LSTMs to tree-structured network topologies. TreeLSTMs outperform all existing systems and strong LSTM baselines on two tasks: predicting the semantic relatedness of two sentences (SemEval 2014, Task 1) and sentiment classification (Stanford Sentiment Treebank). A fully integrated approach to speech input language translation in limited domain applications is presented. The mapping from the input to the output language is modeled in terms of a finite state translation model which is learned from examples of input output sentences of the task considered. This model is tightly integrated with standard acoustic phonetic models of the input language and the resulting global model directly supplies, through Viterbi search, an optimal output language sentence for each input language utterance. Several extensions to this framework, recently developed to cope with the increasing difficulty of translation tasks, are reviewed. Finally, results for a task in the framework of hotel front desk communication, with a vocabulary of about 700 words, are reported. Neural network based approaches have recently produced record-setting performances in natural language understanding tasks such as word labeling. In the word labeling task, a tagger is used to assign a label to each word in an input sequence. Specifically, simple recurrent neural networks (RNNs) and convolutional neural networks (CNNs) have shown to significantly outperform the previous state-of-the-art - conditional random fields (CRFs). This paper investigates using long short-term memory (LSTM) neural networks, which contain input, output and forgetting gates and are more advanced than simple RNN, for the word labeling task. To explicitly model output-label dependence, we propose a regression model on top of the LSTM un-normalized scores. We also propose to apply deep LSTM to the task. We investigated the relative importance of each gate in the LSTM by setting other gates to a constant and only learning particular gates. Experiments on the ATIS dataset validated the effectiveness of the proposed models. Many researchers have explored the relation between discrete-time recurrent neural networks (DTRNN) and finite-state machines (FSMs) either by showing their computational equivalence or by training them to perform as finite-state recognizers from examples. Most of this work has focused on the simplest class of deterministic state machines, that is deterministic finite automata and Mealy (or Moore) machines. The class of translations these machines can perform is very limited, mainly because these machines output symbols at the same rate as they input symbols, and therefore, the input and the translation have the same length; one may call these translations synchronous. Real-life translations are more complex: word reorderings, deletions, and insertions are common in natural-language translations; or, in speech-to-phoneme conversion, the number of frames corresponding to each phoneme is different and depends on the particular speaker or word. There are, however, simple deterministic, finite-state machines (extensions of Mealy machines) that may perform these classes of "asynchronous" or "time-warped" translations. A simple DTRNN model with input and output control lines inspired on this class of machines is presented and successfully applied to simple asynchronous translation tasks with interesting results regarding generalization. Training of these nets from input-output pairs is complicated by the fact that the time alignment between the target output sequence and the input sequence is unknown and has to be learned: we propose a new error function to tackle this problem. This approach to the induction of asynchronous translators is discussed in connection with other approaches. In order to capture rich language phenomena, neural machine translation models have to use a large vocabulary size, which requires high computing time and large memory usage. In this paper, we alleviate this issue by introducing a sentence-level or batch-level vocabulary, which is only a very small sub-set of the full output vocabulary. For each sentence or batch, we only predict the target words in its sentencelevel or batch-level vocabulary. Thus, we reduce both the computing time and the memory usage. Our method simply takes into account the translation options of each word or phrase in the source sentence, and picks a very small target vocabulary for each sentence based on a wordto-word translation model or a bilingual phrase library learned from a traditional machine translation model. Experimental results on the large-scale English-toFrench task show that our method achieves better translation performance by 1 BLEU point over the large vocabulary neural machine translation system of (2015). This paper investigates the framework of encoder-decoder with attention for sequence labelling based spoken language understanding. We introduce Bidirectional Long Short Term Memory - Long Short Term Memory networks (BLSTM-LSTM) as the encoder-decoder model to fully utilize the power of deep learning. In the sequence labelling task, the input and output sequences are aligned word by word, while the attention mechanism cannot provide the exact alignment. To address this limitation, we propose a novel focus mechanism for encoder-decoder framework. Experiments on the standard ATIS dataset showed that BLSTM-LSTM with focus mechanism defined the new state-of-the-art by outperforming standard BLSTM and attention based encoder-decoder. Further experiments also show that the proposed model is more robust to speech recognition errors. Solving the visual symbol grounding problem has long been a goal of artificial intelligence. The field appears to be advancing closer to this goal with recent breakthroughs in deep learning for natural language grounding in static images. In this paper, we propose to translate videos directly to sentences using a unified deep neural network with both convolutional and recurrent structure. Described video datasets are scarce, and most existing methods have been applied to toy domains with a small vocabulary of possible words. By transferring knowledge from 1.2M+ images with category labels and 100,000+ images with captions, our method is able to create sentence descriptions of open-domain videos with large vocabularies. We compare our approach with recent work using language generation metrics, subject, verb, and object prediction accuracy, and a human evaluation. Linguistic sequence labeling is a general modeling approach that encompasses a variety of problems, such as part-of-speech tagging and named entity recognition. Recent advances in neural networks (NNs) make it possible to build reliable models without handcrafted features. However, in many cases, it is hard to obtain sufficient annotations to train these models. In this study, we develop a novel neural framework to extract abundant knowledge hidden in raw texts to empower the sequence labeling task. Besides word-level knowledge contained in pre-trained word embeddings, character-aware neural language models are incorporated to extract character-level knowledge. Transfer learning techniques are further adopted to mediate different components and guide the language model towards the key knowledge. Comparing to previous methods, these task-specific knowledge allows us to adopt a more concise model and conduct more efficient training. Different from most transfer learning methods, the proposed framework does not rely on any additional supervision. It extracts knowledge from self-contained order information of training sequences. Extensive experiments on benchmark datasets demonstrate the effectiveness of leveraging character-level knowledge and the efficiency of co-training. For example, on the CoNLL03 NER task, model training completes in about 6 hours on a single GPU, reaching F1 score of 91.71 @math 0.10 without using any extra annotation. Natural language inference (NLI) is a fundamentally important task in natural language processing that has many applications. The recently released Stanford Natural Language Inference (SNLI) corpus has made it possible to develop and evaluate learning-centered methods such as deep neural networks for natural language inference (NLI). In this paper, we propose a special long short-term memory (LSTM) architecture for NLI. Our model builds on top of a recently proposed neural attention model for NLI but is based on a significantly different idea. Instead of deriving sentence embeddings for the premise and the hypothesis to be used for classification, our solution uses a match-LSTM to perform word-by-word matching of the hypothesis with the premise. This LSTM is able to place more emphasis on important word-level matching results. In particular, we observe that this LSTM remembers important mismatches that are critical for predicting the contradiction or the neutral relationship label. On the SNLI corpus, our model achieves an accuracy of 86.1 , outperforming the state of the art.