In JMIR medical informatics ; h5-index 23.0
BACKGROUND : Lung cancer is the leading cause of cancer deaths worldwide. Clinical staging of lung cancer plays a crucial role in making treatment decisions and evaluating prognosis. However, in clinical practice, approximately one-half of the clinical stages of lung cancer patients are inconsistent with their pathological stages. As one of the most important diagnostic modalities for staging, chest computed tomography (CT) provides a wealth of information about cancer staging, but the free-text nature of the CT reports obstructs their computerization.
OBJECTIVE : We aimed to automatically extract the staging-related information from CT reports to support accurate clinical staging of lung cancer.
METHODS : In this study, we developed an information extraction (IE) system to extract the staging-related information from CT reports. The system consisted of the following three parts: named entity recognition (NER), relation classification (RC), and postprocessing (PP). We first summarized 22 questions about lung cancer staging based on the TNM staging guideline. Next, three state-of-the-art NER algorithms were implemented to recognize the entities of interest. Next, we designed a novel RC method using the relation sign constraint (RSC) to classify the relations between entities. Finally, a rule-based PP module was established to obtain the formatted answers using the results of NER and RC.
RESULTS : We evaluated the developed IE system on a clinical data set containing 392 chest CT reports collected from the Department of Thoracic Surgery II in the Peking University Cancer Hospital. The experimental results showed that the bidirectional encoder representation from transformers (BERT) model outperformed the iterated dilated convolutional neural networks-conditional random field (ID-CNN-CRF) and bidirectional long short-term memory networks-conditional random field (Bi-LSTM-CRF) for NER tasks with macro-F1 scores of 80.97% and 90.06% under the exact and inexact matching schemes, respectively. For the RC task, the proposed RSC showed better performance than the baseline methods. Further, the BERT-RSC model achieved the best performance with a macro-F1 score of 97.13% and a micro-F1 score of 98.37%. Moreover, the rule-based PP module could correctly obtain the formatted results using the extractions of NER and RC, achieving a macro-F1 score of 94.57% and a micro-F1 score of 96.74% for all the 22 questions.
CONCLUSIONS : We conclude that the developed IE system can effectively and accurately extract information about lung cancer staging from CT reports. Experimental results show that the extracted results have significant potential for further use in stage verification and prediction to facilitate accurate clinical staging.
Hu Danqing, Zhang Huanyao, Li Shaolei, Wang Yuhong, Wu Nan, Lu Xudong
clinical staging, information extraction, lung cancer, named entity recognition, relation classification