Identification of patients with carotid stenosis using natural language processing.

Purpose: The highly structured nature of medical reports makes them feasible for automated large-scale patient identification. This study aimed to develop a natural language processing (NLP) model to retrospectively retrieve patients with presence and history of carotid stenosis (CS) using their ultrasound reports.

Methods: Ultrasound reports from our institution between January 2016 and December 2017 were selected. To process the texts, we developed a parser to divide the raw text into fields. For baseline method, we used bag-of-n-grams and term frequency inverse document frequency as the features and used linear classifiers. Logistic regression was performed as the baseline model. Convolution and recurrent neural networks (CNN; RNN) with attention mechanism were applied to the dataset to improve the classification accuracy.

Results: We had 1220 ultrasound reports for training and 307 for testing, totaling to 1527 reports. For predicting history of CS, both CNN and RNN-attention models had a significantly higher specificity than logistic regression. In addition, RNN-attention also had a significantly higher F1 score and accuracy. For predicting presence of carotid stenosis, all models achieved above 93% accuracy. RNN-attention achieved a 95.4% accuracy, although the difference with logistic regression was not statistically significant. RNN-attention had a statistically significant higher specificity than logistic regression.

Conclusions: We developed linear, CNN, and RNN models to predict history and presence of CS from ultrasound reports. We have demonstrated NLP to be an efficient, accurate approach for large-scale retrospective patient identification, with applications in long-term follow-up of patients and clinical research studies.

Key Points: • Natural language processing models using both linear classifiers and neural networks can achieve a good performance, with an overall accuracy above 90% in predicting history and presence of carotid stenosis. • Convolution and recurrent neural networks, especially with additional features including field awareness and attention mechanism, have superior performance than traditional linear classifiers. • NLP is shown to be an efficient approach for large-scale retrospective patient identification, with applications in long-term follow-up of patients and further clinical research studies.