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Register a new userClinical Named Entity Recognition using Contextualized Token Representations
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The clinical named entity recognition (CNER) task seeks to locate and classify clinical terminologies into predefined categories, such as diagnostic procedure, disease disorder, severity, medication, medication dosage, and sign symptom. CNER facilitates the study of side-effect on medications including identification of novel phenomena and human-focused information extraction. Existing approaches in extracting the entities of interests focus on using static word embeddings to represent each word. However, one word can have different interpretations that depend on the context of the sentences. Evidently, static word embeddings are insufficient to integrate the diverse interpretation of a word. To overcome this challenge, the technique of contextualized word embedding has been introduced to better capture the semantic meaning of each word based on its context. Two of these language models, ELMo and Flair, have been widely used in the field of Natural Language Processing to generate the contextualized word embeddings on domain-generic documents. However, these embeddings are usually too general to capture the proximity among vocabularies of specific domains. To facilitate various downstream applications using clinical case reports (CCRs), we pre-train two deep contextualized language models, Clinical Embeddings from Language Model (C-ELMo) and Clinical Contextual String Embeddings (C-Flair) using the clinical-related corpus from the PubMed Central. Explicit experiments show that our models gain dramatic improvements compared to both static word embeddings and domain-generic language models.
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Named entity recognition (NER) models are typically based on the architecture of Bi-directional LSTM (BiLSTM). The constraints of sequential nature and the modeling of single input prevent the full utilization of global information from larger scope, not only in the entire sentence, but also in the entire document (dataset). In this paper, we address these two deficiencies and propose a model augmented with hierarchical contextualized representation: sentence-level representation and document-level representation. In sentence-level, we take different contributions of words in a single sentence into consideration to enhance the sentence representation learned from an independent BiLSTM via label embedding attention mechanism. In document-level, the key-value memory network is adopted to record the document-aware information for each unique word which is sensitive to similarity of context information. Our two-level hierarchical contextualized representations are fused with each input token embedding and corresponding hidden state of BiLSTM, respectively. The experimental results on three benchmark NER datasets (CoNLL-2003 and Ontonotes 5.0 English datasets, CoNLL-2002 Spanish dataset) show that we establish new state-of-the-art results.
Fine-Grained Named Entity Recognition (FG-NER) is critical for many NLP applications. While classical named entity recognition (NER) has attracted a substantial amount of research, FG-NER is still an open research domain. The current state-of-the-art (SOTA) model for FG-NER relies heavily on manual efforts for building a dictionary and designing hand-crafted features. The end-to-end framework which achieved the SOTA result for NER did not get the competitive result compared to SOTA model for FG-NER. In this paper, we investigate how effective multi-task learning approaches are in an end-to-end framework for FG-NER in different aspects. Our experiments show that using multi-task learning approaches with contextualized word representation can help an end-to-end neural network model achieve SOTA results without using any additional manual effort for creating data and designing features.
There is a recent interest in investigating few-shot NER, where the low-resource target domain has different label sets compared with a resource-rich source domain. Existing methods use a similarity-based metric. However, they cannot make full use of knowledge transfer in NER model parameters. To address the issue, we propose a template-based method for NER, treating NER as a language model ranking problem in a sequence-to-sequence framework, where original sentences and statement templates filled by candidate named entity span are regarded as the source sequence and the target sequence, respectively. For inference, the model is required to classify each candidate span based on the corresponding template scores. Our experiments demonstrate that the proposed method achieves 92.55% F1 score on the CoNLL03 (rich-resource task), and significantly better than fine-tuning BERT 10.88%, 15.34%, and 11.73% F1 score on the MIT Movie, the MIT Restaurant, and the ATIS (low-resource task), respectively.
This paper presents a novel framework, MGNER, for Multi-Grained Named Entity Recognition where multiple entities or entity mentions in a sentence could be non-overlapping or totally nested. Different from traditional approaches regarding NER as a sequential labeling task and annotate entities consecutively, MGNER detects and recognizes entities on multiple granularities: it is able to recognize named entities without explicitly assuming non-overlapping or totally nested structures. MGNER consists of a Detector that examines all possible word segments and a Classifier that categorizes entities. In addition, contextual information and a self-attention mechanism are utilized throughout the framework to improve the NER performance. Experimental results show that MGNER outperforms current state-of-the-art baselines up to 4.4% in terms of the F1 score among nested/non-overlapping NER tasks.
Named Entity Recognition (NER) is a fundamental task in Natural Language Processing, concerned with identifying spans of text expressing references to entities. NER research is often focused on flat entities only (flat NER), ignoring the fact that entity references can be nested, as in [Bank of [China]] (Finkel and Manning, 2009). In this paper, we use ideas from graph-based dependency parsing to provide our model a global view on the input via a biaffine model (Dozat and Manning, 2017). The biaffine model scores pairs of start and end tokens in a sentence which we use to explore all spans, so that the model is able to predict named entities accurately. We show that the model works well for both nested and flat NER through evaluation on 8 corpora and achieving SoTA performance on all of them, with accuracy gains of up to 2.2 percentage points.
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