Abstract Clinical named entity recognition aims to identify and classify clinical terms such as diseases, symptoms, treatments, exams, and body parts in electronic health records, which is a fundamental and crucial task for clinical and translational research. In recent years, deep neural networks have achieved significant success in named entity recognition and many other natural language processing tasks. Most of these algorithms are trained end to end, and can automatically learn features from large scale labeled datasets. However, these data-driven methods typically lack the capability of processing rare or unseen entities. Previous statistical methods and feature engineering practice have demonstrated that human knowledge can provide valuable information for handling rare and unseen cases. In this paper, we propose a new model which combines data-driven deep learning approaches and knowledge-driven dictionary approaches. Specifically, we incorporate dictionaries into deep neural networks. In addition, two different architectures that extend the bi-directional long short-term memory neural network and five different feature representation schemes are also proposed to handle the task. Computational results on the CCKS-2017 Task 2 benchmark dataset show that the proposed method achieves the highly competitive performance compared with the state-of-the-art deep learning methods.
Recently, deep learning approaches @cite_34 , especially the methods based on Bidirectional Recurrent Neural Network (RNN) using CRF as the output interface (Bi-RNN-CRF) @cite_38 , achieve state-of-the-art performance in CNER tasks and outperform the traditional statistical models @cite_29 @cite_2 @cite_31 . RNNs with gated recurrent cells, such as Long-Short Term Memory (LSTM) @cite_10 and Gated Recurrent Units (GRU) @cite_26 , are capable of capturing long dependencies and retrieving rich global information. The sequential CRF on top of the recurrent layers ensures that the optimal sequence of tags over the entire sentence is obtained.
@cite_38 @cite_26 @cite_29 @cite_2 @cite_31 @cite_34 @cite_10
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Recurrent neural networks (RNNs) such as long short-term memory and gated recurrent units are pivotal building blocks across a broad spectrum of sequence modeling problems. This paper proposes a recurrently controlled recurrent network (RCRN) for expressive and powerful sequence encoding. More concretely, the key idea behind our approach is to learn the recurrent gating functions using recurrent networks. Our architecture is split into two components - a controller cell and a listener cell whereby the recurrent controller actively influences the compositionality of the listener cell. We conduct extensive experiments on a myriad of tasks in the NLP domain such as sentiment analysis (SST, IMDb, Amazon reviews, etc.), question classification (TREC), entailment classification (SNLI, SciTail), answer selection (WikiQA, TrecQA) and reading comprehension (NarrativeQA). Across all 26 datasets, our results demonstrate that RCRN not only consistently outperforms BiLSTMs but also stacked BiLSTMs, suggesting that our controller architecture might be a suitable replacement for the widely adopted stacked architecture. Additionally, RCRN achieves state-of-the-art results on several well-established datasets. Recurrent Neural Networks (RNNs) with sophisticated units that implement a gating mechanism have emerged as powerful technique for modeling sequential signals such as speech or electroencephalography (EEG). The latter is the focus on this paper. A significant big data resource, known as the TUH EEG Corpus (TUEEG), has recently become available for EEG research, creating a unique opportunity to evaluate these recurrent units on the task of seizure detection. In this study, we compare two types of recurrent units: long short-term memory units (LSTM) and gated recurrent units (GRU). These are evaluated using a state of the art hybrid architecture that integrates Convolutional Neural Networks (CNNs) with RNNs. We also investigate a variety of initialization methods and show that initialization is crucial since poorly initialized networks cannot be trained. Furthermore, we explore regularization of these convolutional gated recurrent networks to address the problem of overfitting. Our experiments revealed that convolutional LSTM networks can achieve significantly better performance than convolutional GRU networks. The convolutional LSTM architecture with proper initialization and regularization delivers 30 sensitivity at 6 false alarms per 24 hours. Recurrent neural networks (RNNs) have been widely used for processing sequential data. However, RNNs are commonly difficult to train due to the well-known gradient vanishing and exploding problems and hard to learn long-term patterns. Long short-term memory (LSTM) and gated recurrent unit (GRU) were developed to address these problems, but the use of hyperbolic tangent and the sigmoid action functions results in gradient decay over layers. Consequently, construction of an efficiently trainable deep network is challenging. In addition, all the neurons in an RNN layer are entangled together and their behaviour is hard to interpret. To address these problems, a new type of RNN, referred to as independently recurrent neural network (IndRNN), is proposed in this paper, where neurons in the same layer are independent of each other and they are connected across layers. We have shown that an IndRNN can be easily regulated to prevent the gradient exploding and vanishing problems while allowing the network to learn long-term dependencies. Moreover, an IndRNN can work with non-saturated activation functions such as relu (rectified linear unit) and be still trained robustly. Multiple IndRNNs can be stacked to construct a network that is deeper than the existing RNNs. Experimental results have shown that the proposed IndRNN is able to process very long sequences (over 5000 time steps), can be used to construct very deep networks (21 layers used in the experiment) and still be trained robustly. Better performances have been achieved on various tasks by using IndRNNs compared with the traditional RNN and LSTM. Recurrent neural networks (RNNs) have shown clear superiority in sequence modeling, particularly the ones with gated units, such as long short-term memory (LSTM) and gated recurrent unit (GRU). However, the dynamic properties behind the remarkable performance remain unclear in many applications, e.g., automatic speech recognition (ASR). This paper employs visualization techniques to study the behavior of LSTM and GRU when performing speech recognition tasks. Our experiments show some interesting patterns in the gated memory, and some of them have inspired simple yet effective modifications on the network structure. We report two of such modifications: (1) lazy cell update in LSTM, and (2) shortcut connections for residual learning. Both modifications lead to more comprehensible and powerful networks.