Abstract
BACKGROUND: Clinical notes record the health status, clinical manifestations and other detailed information of each patient. The International Classification of Diseases (ICD) codes are important labels for electronic health records. Automatic medical codes assignment to clinical notes through the deep learning model can not only improve work efficiency and accelerate the development of medical informatization but also facilitate the resolution of many issues related to medical insurance. Recently, neural network-based methods have been proposed for the automatic medical code assignment. However, in the medical field, clinical notes are usually long documents and contain many complex sentences, most of the current methods cannot effective in learning the representation of potential features from document text. METHODS: In this paper, we propose a hybrid capsule network model. Specifically, we use bi-directional LSTM (Bi-LSTM) with forwarding and backward directions to merge the information from both sides of the sequence. The label embedding framework embeds the text and labels together to leverage the label information. We then use a dynamic routing algorithm in the capsule network to extract valuable features for medical code prediction task. RESULTS: We applied our model to the task of automatic medical codes assignment to clinical notes and conducted a series of experiments based on MIMIC-III data. The experimental results show that our method achieves a micro F1-score of 67.5% on MIMIC-III dataset, which outperforms the other state-of-the-art methods. CONCLUSIONS: The proposed model employed the dynamic routing algorithm and label embedding framework can effectively capture the important features across sentences. Both Capsule networks and domain knowledge are helpful for medical code prediction task.