Topic Segmentation and Medical Named Entities Recognition for Pictorially Visualizing Health Record Summary System

Abstract

Medical Information Visualization makes optimized use of digitized data of medical records, e.g. Electronic Medical Record. This thesis is an extended work of Pictorial Information Visualization System (PIVS) developed by Yongji Jin (Jin, 2016) Jiaren Suo (Suo, 2017) which is a graphical visualization system by picturizing patient’s medical history summary depicting patients’ medical information in order to help patients and doctors to easily capture patients’ past and present conditions. The summary information has been manually entered into the interface where the information can be taken from clinical notes. This study proposes a methodology of automatically extracting medical information from patients’ clinical notes by using the techniques of Natural Language Processing in order to produce medical history summarization from past medical records. We develop a Named Entities Recognition system to extract the information of the medical imaging procedure (performance date, human body location, imaging results and so on) and medications (medication names, frequency and quantities) by applying the model of conditional random fields with three main features and others: word-based, part-of-speech, Metamap semantic features. Adding Metamap semantic features is a novel idea which raised the accuracy compared to previous studies. Our evaluation shows that our model has higher accuracy than others on medication extraction as a case study. For enhancing the accuracy of entities extraction, we also propose a methodology of Topic Segmentation to clinical notes using boundary detection by determining the difference of classification probabilities of subsequence sequences, which is different from the traditional Topic Segmentation approaches such as TextTiling, TopicTiling and Beeferman Statistical Model. With Topic Segmentation combined for Named Entities Extraction, we observed higher accuracy for medication extraction compared to the case without the segmentation. Finally, we also present a prototype of integrating our information extraction system with PIVS by simply building the database of interface coordinates and the terms of human body parts.