Application of specialized word embeddings and named entity and attribute recognition to the problem of unsupervised automated clinical coding

Abstract

Notes documented by clinicians, such as patient histories, hospital courses, lab reports and others are often annotated with standardized clinical codes by medical coders to facilitate a variety of secondary processing applications such as billing and statistical analyses. Clinical coding, traditionally manual and labor-intensive, has seen a surge in research interest by deep learning researchers pursuing to automate it. However, deep learning methods require large volumes of annotated clinical data for training and offer little to explain why codes were assigned to pieces of text. In this paper, we propose an unsupervised method which does not need annotated clinical text and is fully interpretable, by using Named Entity and Attribute Recognition and word embeddings specialized for the clinical domain. These methods successfully glean important information from large volumes of clinical notes and encode them effectively in order to perform automatic clinical coding.