Clinical named entity extraction for extracting information from medical data

Abstract

Clinical named entity extraction (NER) based on deep learning gained much attention among researchers and data analysts. This paper proposes a NER approach to extract valuable Parkinson’s disease-related information. To develop an effective NER method and to handle problems in disease data analytics, a unique NER technique applies a “recognize-map-extract (RME)” mechanism and aims to deal with complex relationships present in the data. Due to the fast-growing medical data, there is a challenge in the development of suitable deep-learning methods for NER. Furthermore, the traditional machine learning approaches rely on the time-consuming process of creating corpora and cannot extract information for specific needs and locations in certain situations. This paper presents a clinical NER approach based on a convolutional neural network (CNN) for better use of specific features around medical entities and analyzes the performance of the proposed approach through fine-tuning NER with effective pre-training on the BC5CDR dataset. The proposed method uses annotation of entities for various medical concepts. The second stage develops a clinically NER method. This proposed method shows interesting results on the performance measures achieving a precision of 92.57%, recall of 92.22%, and F1- measure of 91.6%.