计算机科学
命名实体识别
疾病
人工智能
自然语言处理
医学
病理
工程类
系统工程
任务(项目管理)
作者
Kai Xu,Zhenguo Yang,Peipei Kang,Qi Wang,Liu Wenyin
标识
DOI:10.1016/j.compbiomed.2019.04.002
摘要
Disease named entity recognition (NER) plays an important role in biomedical research. There are a significant number of challenging issues to be addressed; among these, the identification of rare diseases and complex disease names and the problem of tagging inconsistency (i.e., if an entity is tagged differently in a document) are attracting substantial research attention.We propose a new neural network method named Dic-Att-BiLSTM-CRF (DABLC) for disease NER. DABLC applies an efficient exact string matching method to match disease entities with a disease dictionary; here, the dictionary is constructed based on the Disease Ontology. Furthermore, DABLC constructs a dictionary attention layer by incorporating a disease dictionary matching method and document-level attention mechanism. Finally, a bidirectional long short-term memory network and conditional random field (BiLSTM-CRF) with a dictionary attention layer is proposed to combine the disease dictionary to develop disease NER.Extensive experiments are conducted on two widely-used corpora: the NCBI disease corpus and the BioCreative V CDR corpus. We apply each test on 10 executions of each model, with a 95% confidence interval. DABLC achieves the highest F1 scores (NCBI: Precision = 0.883, Recall = 0.89, F1 = 0.886; BioCreative V CDR: Precision = 0.891, Recall = 0.875, F1 = 0.883), outperforming the state-of-the-art methods.DABLC combines the advantages of both external dictionary resources and deep attention neural networks. This aids the identification of rare diseases and complex disease names; moreover, it reduces the impact of tagging inconsistency. Special disease NER and deep learning models addressing long sentences are noteworthy areas for future examination.
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