ABSTRACT
Objectives@#A substantial portion of the data contained in Electronic Health Records (EHR) is unstructured, often appearing as free text. This format restricts its potential utility in clinical decision-making. Named entity recognition (NER) methods address the challenge of extracting pertinent information from unstructured text. The aim of this study was to outline the current NER methods and trace their evolution from 2011 to 2022. @*Methods@#We conducted a methodological literature review of NER methods, with a focus on distinguishing the classification models, the types of tagging systems, and the languages employed in various corpora. @*Results@#Several methods have been documented for automatically extracting relevant information from EHRs using natural language processing techniques such as NER and relation extraction (RE). These methods can automatically extract concepts, events, attributes, and other data, as well as the relationships between them. Most NER studies conducted thus far have utilized corpora in English or Chinese. Additionally, the bidirectional encoder representation from transformers using the BIO tagging system architecture is the most frequently reported classification scheme. We discovered a limited number of papers on the implementation of NER or RE tasks in EHRs within a specific clinical domain. @*Conclusions@#EHRs play a pivotal role in gathering clinical information and could serve as the primary source for automated clinical decision support systems. However, the creation of new corpora from EHRs in specific clinical domains is essential to facilitate the swift development of NER and RE models applied to EHRs for use in clinical practice.
ABSTRACT
BACKGROUND AND OBJECTIVE: The swallowing is a complex process mediated by the central nervous system, that implies voluntary and involuntary components, including 26 pairs of muscles. Non-invasive strategies, including the surface electromyography (sEMG), have been proposed to evaluate the swallowing. However, such analyses have been mostly descriptive, and the detection of neuromuscular activity has been limited to the visual inspection (VIS). Nonetheless, the VIS lacks reliability since the swallowing related muscles have small size, they are not completely shallow, suffer from cross-talk and have low signal-to-noise ratio (SNR). In this way, we propose a wavelet based method to automatically detect activations in sEMG signals acquired during praxis and swallowing tasks. METHODS: The proposed strategy, namely Scalogram-Energy based Segmentation method, was applied on sEMG signals recorded in masseteric, orbicular, supra- and infrahyoid muscles. The method was trained in a database of 35 healthy subjects by the use of multi-objective genetic algorithms and tested via cross-validation, aiming to maximize the F1 score and minimize the timing error between the automatic and VIS related marks. Furthermore, the proposed method was tested in a database of semi-synthetic signals with variable SNR built from signals collected from 10 individuals. Additionally, the method was compared with a double threshold based algorithm as well as with other based on energy and morphological operators. RESULTS: The algorithm achieved a F1 score of 0.82 and almost 13 ms of error in the estimation of onset and offset. Afterwards, we applied the optimized algorithm to a set with semi-synthetic signals with variable SNR, that achieved F1 score of 0.85 for SNR=6 dB and 0.97 for SNR=8 and 10 dB. The mean of the timing error was smaller than 9 ms for SNR=6,8 and 10 dB. The method was also compared with a double threshold based algorithm as well as with other based on energy and morphological operators. CONCLUSIONS: The proposed method shown to be useful to automatically analyze the electrophysiological activity associated to praxis and swallowing process. Nonetheless, the obtained results could be extended to other sEMG related applications.
