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2017 ; 2017
(ä): 1812-1819
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Clinical Named Entity Recognition Using Deep Learning Models
#MMPMID29854252
Wu Y
; Jiang M
; Xu J
; Zhi D
; Xu H
AMIA Annu Symp Proc
2017[]; 2017
(ä): 1812-1819
PMID29854252
show ga
Clinical Named Entity Recognition (NER) is a critical natural language processing
(NLP) task to extract important concepts (named entities) from clinical
narratives. Researchers have extensively investigated machine learning models for
clinical NER. Recently, there have been increasing efforts to apply deep learning
models to improve the performance of current clinical NER systems. This study
examined two popular deep learning architectures, the Convolutional Neural
Network (CNN) and the Recurrent Neural Network (RNN), to extract concepts from
clinical texts. We compared the two deep neural network architectures with three
baseline Conditional Random Fields (CRFs) models and two state-of-the-art
clinical NER systems using the i2b2 2010 clinical concept extraction corpus. The
evaluation results showed that the RNN model trained with the word embeddings
achieved a new state-of-the- art performance (a strict F1 score of 85.94%) for
the defined clinical NER task, outperforming the best-reported system that used
both manually defined and unsupervised learning features. This study demonstrates
the advantage of using deep neural network architectures for clinical concept
extraction, including distributed feature representation, automatic feature
learning, and long-term dependencies capture. This is one of the first studies to
compare the two widely used deep learning models and demonstrate the superior
performance of the RNN model for clinical NER.