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In BMC medical informatics and decision making ; h5-index 38.0

BACKGROUND : To detect attributes of medical concepts in clinical text, a traditional method often consists of two steps: named entity recognition of attributes and then relation classification between medical concepts and attributes. Here we present a novel solution, in which attribute detection of given concepts is converted into a sequence labeling problem, thus attribute entity recognition and relation classification are done simultaneously within one step.

METHODS : A neural architecture combining bidirectional Long Short-Term Memory networks and Conditional Random fields (Bi-LSTMs-CRF) was adopted to detect various medical concept-attribute pairs in an efficient way. We then compared our deep learning-based sequence labeling approach with traditional two-step systems for three different attribute detection tasks: disease-modifier, medication-signature, and lab test-value.

RESULTS : Our results show that the proposed method achieved higher accuracy than the traditional methods for all three medical concept-attribute detection tasks.

CONCLUSIONS : This study demonstrates the efficacy of our sequence labeling approach using Bi-LSTM-CRFs on the attribute detection task, indicating its potential to speed up practical clinical NLP applications.

Xu Jun, Li Zhiheng, Wei Qiang, Wu Yonghui, Xiang Yang, Lee Hee-Jin, Zhang Yaoyun, Wu Stephen, Xu Hua

2019-Dec-05

Clinical notes, Information extraction, Natural language processing