scholarly journals A NLP Pipeline for the Automatic Extraction of Microorganisms Names from Microbiological Notes

2021 ◽  
Author(s):  
Sara Mora ◽  
Jacopo Attene ◽  
Roberta Gazzarata ◽  
Giustino Parruti ◽  
Mauro Giacomini

According to the “Istituto Superiore di Sanita‘” (ISS), hospital infections are the most frequent and serious complication of health care. This constitutes a real health emergency which requires incisive and joint action at all levels of the local and national health organization. Most of the valuable information related to the presence of a specific microorganism in the blood are written into the notes field of the laboratory exams results. The main objective of this work is to build a Natural Language Processing (NLP) pipeline for the automatic extraction of the names of microorganisms present in the clinical texts. A sample of 499 microbiological notes have been analysed with the developed system and all the microorganisms names have been extracted correctly, according to the labels given by the expert.

Author(s):  
Mario Jojoa Acosta ◽  
Gema Castillo-Sánchez ◽  
Begonya Garcia-Zapirain ◽  
Isabel de la Torre Díez ◽  
Manuel Franco-Martín

The use of artificial intelligence in health care has grown quickly. In this sense, we present our work related to the application of Natural Language Processing techniques, as a tool to analyze the sentiment perception of users who answered two questions from the CSQ-8 questionnaires with raw Spanish free-text. Their responses are related to mindfulness, which is a novel technique used to control stress and anxiety caused by different factors in daily life. As such, we proposed an online course where this method was applied in order to improve the quality of life of health care professionals in COVID 19 pandemic times. We also carried out an evaluation of the satisfaction level of the participants involved, with a view to establishing strategies to improve future experiences. To automatically perform this task, we used Natural Language Processing (NLP) models such as swivel embedding, neural networks, and transfer learning, so as to classify the inputs into the following three categories: negative, neutral, and positive. Due to the limited amount of data available—86 registers for the first and 68 for the second—transfer learning techniques were required. The length of the text had no limit from the user’s standpoint, and our approach attained a maximum accuracy of 93.02% and 90.53%, respectively, based on ground truth labeled by three experts. Finally, we proposed a complementary analysis, using computer graphic text representation based on word frequency, to help researchers identify relevant information about the opinions with an objective approach to sentiment. The main conclusion drawn from this work is that the application of NLP techniques in small amounts of data using transfer learning is able to obtain enough accuracy in sentiment analysis and text classification stages.


2016 ◽  
Vol 19 (3) ◽  
pp. A4 ◽  
Author(s):  
E.T. Masters ◽  
J. Mardekian ◽  
A. Ramaprasan ◽  
K. Saunders ◽  
D.E. Gross ◽  
...  

2017 ◽  
Vol 9 (1) ◽  
Author(s):  
Dino P. Rumoro ◽  
Shital C. Shah ◽  
Gillian S. Gibbs ◽  
Marilyn M. Hallock ◽  
Gordon M. Trenholme ◽  
...  

ObjectiveTo explain the utility of using an automated syndromic surveillanceprogram with advanced natural language processing (NLP) to improveclinical quality measures reporting for influenza immunization.IntroductionClinical quality measures (CQMs) are tools that help measure andtrack the quality of health care services. Measuring and reportingCQMs helps to ensure that our health care system is deliveringeffective, safe, efficient, patient-centered, equitable, and timely care.The CQM for influenza immunization measures the percentage ofpatients aged 6 months and older seen for a visit between October1 and March 31 who received (or reports previous receipt of) aninfluenza immunization. Centers for Disease Control and Preventionrecommends that everyone 6 months of age and older receive aninfluenza immunization every season, which can reduce influenza-related morbidity and mortality and hospitalizations.MethodsPatients at a large academic medical center who had a visit toan affiliated outpatient clinic during June 1 - 8, 2016 were initiallyidentified using their electronic medical record (EMR). The 2,543patients who were selected did not have documentation of influenzaimmunization in a discrete field of the EMR. All free text notes forthese patients between August 1, 2015 and March 31, 2016 wereretrieved and analyzed using the sophisticated NLP built withinGeographic Utilization of Artificial Intelligence in Real-Timefor Disease Identification and Alert Notification (GUARDIAN)– a syndromic surveillance program – to identify any mention ofinfluenza immunization. The goal was to identify additional cases thatmet the CQM measure for influenza immunization and to distinguishdocumented exceptions. The patients with influenza immunizationmentioned were further categorized by GUARDIAN NLP intoReceived, Recommended, Refused, Allergic, and Unavailable.If more than one category was applicable for a patient, they wereindependently counted in their respective categories. A descriptiveanalysis was conducted, along with manual review of a sample ofcases per each category.ResultsFor the 2,543 patients who did not have influenza immunizationdocumentation in a discrete field of the EMR, a total of 78,642 freetext notes were processed using GUARDIAN. Four hundred fiftythree (17.8%) patients had some mention of influenza immunizationwithin the notes, which could potentially be utilized to meet the CQMinfluenza immunization requirement. Twenty two percent (n=101)of patients mentioned already having received the immunizationwhile 34.7% (n=157) patients refused it during the study time frame.There were 27 patients with the mention of influenza immunization,who could not be differentiated into a specific category. The numberof patients placed into a single category of influenza immunizationwas 351 (77.5%), while 75 (16.6%) were classified into more thanone category. See Table 1.ConclusionsUsing GUARDIAN’s NLP can identify additional patients whomay meet the CQM measure for influenza immunization or whomay be exempt. This tool can be used to improve CQM reportingand improve overall influenza immunization coverage by using it toalert providers. Next steps involve further refinement of influenzaimmunization categories, automating the process of using the NLPto identify and report additional cases, as well as using the NLP forother CQMs.Table 1. Categorization of influenza immunization documentation within freetext notes of 453 patients using NLP


2020 ◽  
Vol 8 ◽  
Author(s):  
Majed Al-Jefri ◽  
Roger Evans ◽  
Joon Lee ◽  
Pietro Ghezzi

Objective: Many online and printed media publish health news of questionable trustworthiness and it may be difficult for laypersons to determine the information quality of such articles. The purpose of this work was to propose a methodology for the automatic assessment of the quality of health-related news stories using natural language processing and machine learning.Materials and Methods: We used a database from the website HealthNewsReview.org that aims to improve the public dialogue about health care. HealthNewsReview.org developed a set of criteria to critically analyze health care interventions' claims. In this work, we attempt to automate the evaluation process by identifying the indicators of those criteria using natural language processing-based machine learning on a corpus of more than 1,300 news stories. We explored features ranging from simple n-grams to more advanced linguistic features and optimized the feature selection for each task. Additionally, we experimented with the use of pre-trained natural language model BERT.Results: For some criteria, such as mention of costs, benefits, harms, and “disease-mongering,” the evaluation results were promising with an F1 measure reaching 81.94%, while for others the results were less satisfactory due to the dataset size, the need of external knowledge, or the subjectivity in the evaluation process.Conclusion: These used criteria are more challenging than those addressed by previous work, and our aim was to investigate how much more difficult the machine learning task was, and how and why it varied between criteria. For some criteria, the obtained results were promising; however, automated evaluation of the other criteria may not yet replace the manual evaluation process where human experts interpret text senses and make use of external knowledge in their assessment.


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