A novel deep learning approach to extract Chinese clinical entities for lung cancer screening and staging

BMC Medical Informatics and Decision Making

Huanyao Zhang¹  Huilong Duan¹  Xudong Lu¹  Danqing Hu¹  Nan Wu²  Shaolei Li² 

[1] College of Biomedical Engineering and Instrument Science, Zhejiang University, Zheda Road, Hangzhou, China;Key Laboratory for Biomedical Engineering, Ministry of Education, Zheda Road, Hangzhou, China;Department of Thoracic Surgery II, Peking University Cancer Hospital & Institute, Beijing, China;

关键词: Transformer;    BERT;    Pre-training;    CT reports;    Lung cancer screening and staging;    Named entity recognition;   

DOI  :  10.1186/s12911-021-01575-x

来源: Springer

【 摘 要 】

BackgroundComputed tomography (CT) reports record a large volume of valuable information about patients’ conditions and the interpretations of radiology images from radiologists, which can be used for clinical decision-making and further academic study. However, the free-text nature of clinical reports is a critical barrier to use this data more effectively. In this study, we investigate a novel deep learning method to extract entities from Chinese CT reports for lung cancer screening and TNM staging.MethodsThe proposed approach presents a new named entity recognition algorithm, namely the BERT-based-BiLSTM-Transformer network (BERT-BTN) with pre-training, to extract clinical entities for lung cancer screening and staging. Specifically, instead of traditional word embedding methods, BERT is applied to learn the deep semantic representations of characters. Following the long short-term memory layer, a Transformer layer is added to capture the global dependencies between characters. Besides, pre-training technique is employed to alleviate the problem of insufficient labeled data.ResultsWe verify the effectiveness of the proposed approach on a clinical dataset containing 359 CT reports collected from the Department of Thoracic Surgery II of Peking University Cancer Hospital. The experimental results show that the proposed approach achieves an 85.96% macro-F1 score under exact match scheme, which improves the performance by 1.38%, 1.84%, 3.81%,4.29%,5.12%,5.29% and 8.84% compared to BERT-BTN, BERT-LSTM, BERT-fine-tune, BERT-Transformer, FastText-BTN, FastText-BiLSTM and FastText-Transformer, respectively.ConclusionsIn this study, we developed a novel deep learning method, i.e., BERT-BTN with pre-training, to extract the clinical entities from Chinese CT reports. The experimental results indicate that the proposed approach can efficiently recognize various clinical entities about lung cancer screening and staging, which shows the potential for further clinical decision-making and academic research.

【 授权许可】

CC BY