Automated extraction of information of lung cancer staging from unstructured reports of PET-CT interpretation: natural language processing with deep-learning

Abstract

Abstract Background Extracting metastatic information from previous radiologic-text reports is important, however, laborious annotations have limited the usability of these texts. We developed a deep-learning model for extracting primary lung cancer sites and metastatic lymph nodes and distant metastasis information from PET-CT reports for determining lung cancer stages. Methods PET-CT reports, fully written in English, were acquired from two cohorts of patients with lung cancer who were diagnosed at a tertiary hospital between January 2004 and March 2020. One cohort of 20,466 PET-CT reports was used for training and the validation set, and the other cohort of 4190 PET-CT reports was used for an additional-test set. A pre-processing model (Lung Cancer Spell Checker) was applied to correct the typographical errors, and pseudo-labelling was used for training the model. The deep-learning model was constructed using the Convolutional-Recurrent Neural Network. The performance metrics for the prediction model were accuracy, precision, sensitivity, micro-AUROC, and AUPRC. Results For the extraction of primary lung cancer location, the model showed a micro-AUROC of 0.913 and 0.946 in the validation set and the additional-test set, respectively. For metastatic lymph nodes, the model showed a sensitivity of 0.827 and a specificity of 0.960. In predicting distant metastasis, the model showed a micro-AUROC of 0.944 and 0.950 in the validation and the additional-test set, respectively. Conclusion Our deep-learning method could be used for extracting lung cancer stage information from PET-CT reports and may facilitate lung cancer studies by alleviating laborious annotation by clinicians.

Keywords

• Natural language processing
• Auto-annotation
• Deep learning
• Lung cancer
• Pseudo-labelling