Clinical named entity extraction for extracting information from medical data

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%.