In biomedical literature, it is common for entity boundaries to not align with word boundaries. Therefore, effective identification of entity spans requires approaches capable of considering tokens that are smaller than words. We introduce a novel, subword approach for named entity recognition (NER) that uses byte-pair encodings (BPE) in combination with convolutional and recurrent neural networks to produce byte-level tags of entities. We present experimental results on several standard biomedical datasets, namely the BioCreative VI Bio-ID, JNLPBA, and GENETAG datasets. We demonstrate competitive performance while bypassing the specialized domain expertise needed to create biomedical text tokenization rules.
State-of-the-art neural NER techniques developed in recent years use a combination of neural networks (NN) and Conditional Random Fields (CRFs) to achieve high precision and recall of named entities. These techniques pass word and character embeddings to a bi-directional long short term memory (BLSTM) layer, which may be followed by a CRF layer @cite_2 @cite_15 @cite_5 . These state-of-the-art techniques have also been successfully applied to biomedical datasets @cite_6 @cite_4 . Although these techniques use subword'' features such as character embeddings, these models take as input a sequence of words and output a sequence of word tags, and are thus different from what we refer to as subword models in this paper. We build upon state-of-the-art neural techniques to evaluate models that take subword input features and produce corresponding subword output tags.
@cite_4 @cite_6 @cite_2 @cite_5 @cite_15
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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. Most state-of-the-art named entity recognition (NER) systems rely on handcrafted features and on the output of other NLP tasks such as part-of-speech (POS) tagging and text chunking. In this work we propose a language-independent NER system that uses automatically learned features only. Our approach is based on the CharWNN deep neural network, which uses word-level and character-level representations (embeddings) to perform sequential classification. We perform an extensive number of experiments using two annotated corpora in two different languages: HAREM I corpus, which contains texts in Portuguese; and the SPA CoNLL-2002 corpus, which contains texts in Spanish. Our experimental results shade light on the contribution of neural character embeddings for NER. Moreover, we demonstrate that the same neural network which has been successfully applied to POS tagging can also achieve state-of-the-art results for language-independet NER, using the same hyperparameters, and without any handcrafted features. For the HAREM I corpus, CharWNN outperforms the state-of-the-art system by 7.9 points in the F1-score for the total scenario (ten NE classes), and by 7.2 points in the F1 for the selective scenario (five NE classes). 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. In this paper, we propose a variety of Long Short-Term Memory (LSTM) based models for sequence tagging. These models include LSTM networks, bidirectional LSTM (BI-LSTM) networks, LSTM with a Conditional Random Field (CRF) layer (LSTM-CRF) and bidirectional LSTM with a CRF layer (BI-LSTM-CRF). Our work is the first to apply a bidirectional LSTM CRF (denoted as BI-LSTM-CRF) model to NLP benchmark sequence tagging data sets. We show that the BI-LSTM-CRF model can efficiently use both past and future input features thanks to a bidirectional LSTM component. It can also use sentence level tag information thanks to a CRF layer. The BI-LSTM-CRF model can produce state of the art (or close to) accuracy on POS, chunking and NER data sets. In addition, it is robust and has less dependence on word embedding as compared to previous observations.