Sequence labeling is a widely used method for named entity recognition and information extraction from unstructured natural language data. In clinical domain one major application of sequence labeling involves extraction of medical entities such as medication, indication, and side-effects from Electronic Health Record narratives. Sequence labeling in this domain, presents its own set of challenges and objectives. In this work we experimented with various CRF based structured learning models with Recurrent Neural Networks. We extend the previously studied LSTM-CRF models with explicit modeling of pairwise potentials. We also propose an approximate version of skip-chain CRF inference with RNN potentials. We use these methodologies for structured prediction in order to improve the exact phrase detection of various medical entities.
As mentioned in the previous sections, both Neural Networks and Conditional Random Fields have been widely used for sequence labeling tasks in NLP. Specially, CRFs @cite_0 have a long history of being used for various sequence labeling tasks in general and named entity recognition in particular. Some early notable works include McCallum et. al. , and Sha et. al. . Hammerton et. al. and Chiu et. al. used Long Short Term Memory (LSTM) @cite_6 for named entity recognition.
@cite_0 @cite_6
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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. Conditional random fields (, 2001) are quite effective at sequence labeling tasks like shallow parsing (Sha and Pereira, 2003) and named-entity extraction (McCallum and Li, 2003). CRFs are log-linear, allowing the incorporation of arbitrary features into the model. To train on unlabeled data, we require unsupervised estimation methods for log-linear models; few exist. We describe a novel approach, contrastive estimation. We show that the new technique can be intuitively understood as exploiting implicit negative evidence and is computationally efficient. Applied to a sequence labeling problem---POS tagging given a tagging dictionary and unlabeled text---contrastive estimation outperforms EM (with the same feature set), is more robust to degradations of the dictionary, and can largely recover by modeling additional features. Large amounts of available training data and increasing computing power have led to the recent success of deep convolutional neural networks (CNN) on a large number of applications. In this paper, we propose an effective semantic pixel labelling using CNN features, hand-crafted features and Conditional Random Fields (CRFs). Both CNN and hand-crafted features are applied to dense image patches to produce per-pixel class probabilities. The CRF infers a labelling that smooths regions while respecting the edges present in the imagery. The method is applied to the ISPRS 2D semantic labelling challenge dataset with competitive classification accuracy. In this approach to named entity recognition, a recurrent neural network, known as Long Short-Term Memory, is applied. The network is trained to perform 2 passes on each sentence, outputting its decisions on the second pass. The first pass is used to acquire information for disambiguation during the second pass. SARDNET, a self-organising map for sequences is used to generate representations for the lexical items presented to the LSTM network, whilst orthogonal representations are used to represent the part of speech and chunk tags.