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. We develop a representation suitable for the unconstrained recognition of words in natural images: the general case of no fixed lexicon and unknown length. To this end we propose a convolutional neural network (CNN) based architecture which incorporates a Conditional Random Field (CRF) graphical model, taking the whole word image as a single input. The unaries of the CRF are provided by a CNN that predicts characters at each position of the output, while higher order terms are provided by another CNN that detects the presence of N-grams. We show that this entire model (CRF, character predictor, N-gram predictor) can be jointly optimised by back-propagating the structured output loss, essentially requiring the system to perform multi-task learning, and training uses purely synthetically generated data. The resulting model is a more accurate system on standard real-world text recognition benchmarks than character prediction alone, setting a benchmark for systems that have not been trained on a particular lexicon. In addition, our model achieves state-of-the-art accuracy in lexicon-constrained scenarios, without being specifically modelled for constrained recognition. To test the generalisation of our model, we also perform experiments with random alpha-numeric strings to evaluate the method when no visual language model is applicable. Abstract: We develop a representation suitable for the unconstrained recognition of words in natural images: the general case of no fixed lexicon and unknown length. To this end we propose a convolutional neural network (CNN) based architecture which incorporates a Conditional Random Field (CRF) graphical model, taking the whole word image as a single input. The unaries of the CRF are provided by a CNN that predicts characters at each position of the output, while higher order terms are provided by another CNN that detects the presence of N-grams. We show that this entire model (CRF, character predictor, N-gram predictor) can be jointly optimised by back-propagating the structured output loss, essentially requiring the system to perform multi-task learning, and training uses purely synthetically generated data. The resulting model is a more accurate system on standard real-world text recognition benchmarks than character prediction alone, setting a benchmark for systems that have not been trained on a particular lexicon. In addition, our model achieves state-of-the-art accuracy in lexicon-constrained scenarios, without being specifically modelled for constrained recognition. To test the generalisation of our model, we also perform experiments with random alpha-numeric strings to evaluate the method when no visual language model is applicable. Even though a linguistics-free sequence to sequence model in neural machine translation (NMT) has certain capability of implicitly learning syntactic information of source sentences, this paper shows that source syntax can be explicitly incorporated into NMT effectively to provide further improvements. Specifically, we linearize parse trees of source sentences to obtain structural label sequences. On the basis, we propose three different sorts of encoders to incorporate source syntax into NMT: 1) Parallel RNN encoder that learns word and label annotation vectors parallelly; 2) Hierarchical RNN encoder that learns word and label annotation vectors in a two-level hierarchy; and 3) Mixed RNN encoder that stitchingly learns word and label annotation vectors over sequences where words and labels are mixed. Experimentation on Chinese-to-English translation demonstrates that all the three proposed syntactic encoders are able to improve translation accuracy. It is interesting to note that the simplest RNN encoder, i.e., Mixed RNN encoder yields the best performance with an significant improvement of 1.4 BLEU points. Moreover, an in-depth analysis from several perspectives is provided to reveal how source syntax benefits NMT. Recurrent sequence generators conditioned on input data through an attention mechanism have recently shown very good performance on a range of tasks in- cluding machine translation, handwriting synthesis and image caption gen- eration. 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 reaches a competitive 18.7 phoneme error rate (PER) on the TIMIT 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 at- tention mechanism that prevents it from concentrating too much on single frames, which further reduces PER to 17.6 level. 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. While neural machine translation (NMT) is making good progress in the past two years, tens of millions of bilingual sentence pairs are needed for its training. However, human labeling is very costly. To tackle this training data bottleneck, we develop a dual-learning mechanism, which can enable an NMT system to automatically learn from unlabeled data through a dual-learning game. This mechanism is inspired by the following observation: any machine translation task has a dual task, e.g., English-to-French translation (primal) versus French-to-English translation (dual); the primal and dual tasks can form a closed loop, and generate informative feedback signals to train the translation models, even if without the involvement of a human labeler. In the dual-learning mechanism, we use one agent to represent the model for the primal task and the other agent to represent the model for the dual task, then ask them to teach each other through a reinforcement learning process. Based on the feedback signals generated during this process (e.g., the language-model likelihood of the output of a model, and the reconstruction error of the original sentence after the primal and dual translations), we can iteratively update the two models until convergence (e.g., using the policy gradient methods). We call the corresponding approach to neural machine translation . Experiments show that dual-NMT works very well on English @math French translation; especially, by learning from monolingual data (with 10 bilingual data for warm start), it achieves a comparable accuracy to NMT trained from the full bilingual data for the French-to-English translation task. 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. While neural machine translation (NMT) is making good progress in the past two years, tens of millions of bilingual sentence pairs are needed for its training. However, human labeling is very costly. To tackle this training data bottleneck, we develop a dual-learning mechanism, which can enable an NMT system to automatically learn from unlabeled data through a dual-learning game. This mechanism is inspired by the following observation: any machine translation task has a dual task, e.g., English-to-French translation (primal) versus French-to-English translation (dual); the primal and dual tasks can form a closed loop, and generate informative feedback signals to train the translation models, even if without the involvement of a human labeler. In the dual-learning mechanism, we use one agent to represent the model for the primal task and the other agent to represent the model for the dual task, then ask them to teach each other through a reinforcement learning process. Based on the feedback signals generated during this process (e.g., the language-model likelihood of the output of a model, and the reconstruction error of the original sentence after the primal and dual translations), we can iteratively update the two models until convergence (e.g., using the policy gradient methods). We call the corresponding approach to neural machine translation dual-NMT. Experiments show that dual-NMT works very well on English ↔ French translation; especially, by learning from monolingual data (with 10 bilingual data for warm start), it achieves a comparable accuracy to NMT trained from the full bilingual data for the French-to-English translation task. Machine learning based predictions of protein–protein interactions (PPIs) could provide valuable insights into protein functions, disease occurrence, and therapy design on a large scale. The intensive feature engineering in most of these methods makes the prediction task more tedious and trivial. The emerging deep learning technology enabling automatic feature engineering is gaining great success in various fields. However, the over-fitting and generalization of its models are not yet well investigated in most scenarios. Here, we present a deep neural network framework (DNN-PPI) for predicting PPIs using features learned automatically only from protein primary sequences. Within the framework, the sequences of two interacting proteins are sequentially fed into the encoding, embedding, convolution neural network (CNN), and long short-term memory (LSTM) neural network layers. Then, a concatenated vector of the two outputs from the previous layer is wired as the input of the fully connected neural network. Finally, the Adam optimizer is applied to learn the network weights in a back-propagation fashion. The different types of features, including semantic associations between amino acids, position-related sequence segments (motif), and their long- and short-term dependencies, are captured in the embedding, CNN and LSTM layers, respectively. When the model was trained on Pan’s human PPI dataset, it achieved a prediction accuracy of 98.78 at the Matthew’s correlation coefficient (MCC) of 97.57 . The prediction accuracies for six external datasets ranged from 92.80 to 97.89 , making them superior to those achieved with previous methods. When performed on Escherichia coli, Drosophila, and Caenorhabditis elegans datasets, DNN-PPI obtained prediction accuracies of 95.949 , 98.389 , and 98.669 , respectively. The performances in cross-species testing among the four species above coincided in their evolutionary distances. However, when testing Mus Musculus using the models from those species, they all obtained prediction accuracies of over 92.43 , which is difficult to achieve and worthy of note for further study. These results suggest that DNN-PPI has remarkable generalization and is a promising tool for identifying protein interactions. Transferring representations from large supervised tasks to downstream tasks has shown promising results in AI fields such as Computer Vision and Natural Language Processing (NLP). In parallel, the recent progress in Machine Translation (MT) has enabled one to train multilingual Neural MT (NMT) systems that can translate between multiple languages and are also capable of performing zero-shot translation. However, little attention has been paid to leveraging representations learned by a multilingual NMT system to enable zero-shot multilinguality in other NLP tasks. In this paper, we demonstrate a simple framework, a multilingual Encoder-Classifier, for cross-lingual transfer learning by reusing the encoder from a multilingual NMT system and stitching it with a task-specific classifier component. Our proposed model achieves significant improvements in the English setup on three benchmark tasks - Amazon Reviews, SST and SNLI. Further, our system can perform classification in a new language for which no classification data was seen during training, showing that zero-shot classification is possible and remarkably competitive. In order to understand the underlying factors contributing to this finding, we conducted a series of analyses on the effect of the shared vocabulary, the training data type for NMT, classifier complexity, encoder representation power, and model generalization on zero-shot performance. Our results provide strong evidence that the representations learned from multilingual NMT systems are widely applicable across languages and tasks. Two recent approaches have achieved state-of-the-art results in image captioning. The first uses a pipelined process where a set of candidate words is generated by a convolutional neural network (CNN) trained on images, and then a maximum entropy (ME) language model is used to arrange these words into a coherent sentence. The second uses the penultimate activation layer of the CNN as input to a recurrent neural network (RNN) that then generates the caption sequence. In this paper, we compare the merits of these different language modeling approaches for the first time by using the same state-of-the-art CNN as input. We examine issues in the different approaches, including linguistic irregularities, caption repetition, and data set overlap. By combining key aspects of the ME and RNN methods, we achieve a new record performance over previously published results on the benchmark COCO dataset. However, the gains we see in BLEU do not translate to human judgments. We introduce a novel schema for sequence to sequence learning with a Deep Q-Network (DQN), which decodes the output sequence iteratively. The aim here is to enable the decoder to first tackle easier portions of the sequences, and then turn to cope with difficult parts. Specifically, in each iteration, an encoder-decoder Long Short-Term Memory (LSTM) network is employed to, from the input sequence, automatically create features to represent the internal states of and formulate a list of potential actions for the DQN. Take rephrasing a natural sentence as an example. This list can contain ranked potential words. Next, the DQN learns to make decision on which action (e.g., word) will be selected from the list to modify the current decoded sequence. The newly modified output sequence is subsequently used as the input to the DQN for the next decoding iteration. In each iteration, we also bias the reinforcement learning's attention to explore sequence portions which are previously difficult to be decoded. For evaluation, the proposed strategy was trained to decode ten thousands natural sentences. Our experiments indicate that, when compared to a left-to-right greedy beam search LSTM decoder, the proposed method performed competitively well when decoding sentences from the training set, but significantly outperformed the baseline when decoding unseen sentences, in terms of BLEU score obtained. In this paper, we propose an effective way for biasing the attention mechanism of a sequence-to-sequence neural machine translation (NMT) model towards the well-studied statistical word alignment models. We show that our novel guided alignment training approach improves translation quality on real-life e-commerce texts consisting of product titles and descriptions, overcoming the problems posed by many unknown words and a large type token ratio. We also show that meta-data associated with input texts such as topic or category information can significantly improve translation quality when used as an additional signal to the decoder part of the network. With both novel features, the BLEU score of the NMT system on a product title set improves from 18.6 to 21.3 . Even larger MT quality gains are obtained through domain adaptation of a general domain NMT system to e-commerce data. The developed NMT system also performs well on the IWSLT speech translation task, where an ensemble of four variant systems outperforms the phrase-based baseline by 2.1 BLEU absolute. We improve automatic correction of grammatical, orthographic, and collocation errors in text using a multilayer convolutional encoder-decoder neural network. The network is initialized with embeddings that make use of character N-gram information to better suit this task. When evaluated on common benchmark test data sets (CoNLL-2014 and JFLEG), our model substantially outperforms all prior neural approaches on this task as well as strong statistical machine translation-based systems with neural and task-specific features trained on the same data. Our analysis shows the superiority of convolutional neural networks over recurrent neural networks such as long short-term memory (LSTM) networks in capturing the local context via attention, and thereby improving the coverage in correcting grammatical errors. By ensembling multiple models, and incorporating an N-gram language model and edit features via rescoring, our novel method becomes the first neural approach to outperform the current state-of-the-art statistical machine translation-based approach, both in terms of grammaticality and fluency. Natural language processing (NLP) models often require a massive number of parameters for word embeddings, resulting in a large storage or memory footprint. Deploying neural NLP models to mobile devices requires compressing the word embeddings without any significant sacrifices in performance. For this purpose, we propose to construct the embeddings with few basis vectors. For each word, the composition of basis vectors is determined by a hash code. To maximize the compression rate, we adopt the multi-codebook quantization approach instead of binary coding scheme. Each code is composed of multiple discrete numbers, such as (3, 2, 1, 8), where the value of each component is limited to a fixed range. We propose to directly learn the discrete codes in an end-to-end neural network by applying the Gumbel-softmax trick. Experiments show the compression rate achieves 98 in a sentiment analysis task and 94 99 in machine translation tasks without performance loss. In both tasks, the proposed method can improve the model performance by slightly lowering the compression rate. Compared to other approaches such as character-level segmentation, the proposed method is language-independent and does not require modifications to the network architecture. Many natural language processing applications use language models to generate text. These models are typically trained to predict the next word in a sequence, given the previous words and some context such as an image. However, at test time the model is expected to generate the entire sequence from scratch. This discrepancy makes generation brittle, as errors may accumulate along the way. We address this issue by proposing a novel sequence level training algorithm that directly optimizes the metric used at test time, such as BLEU or ROUGE. On three different tasks, our approach outperforms several strong baselines for greedy generation. The method is also competitive when these baselines employ beam search, while being several times faster.