Dataset Information

Influenza detection from emergency department reports using natural language processing and Bayesian network classifiers.

ABSTRACT: To evaluate factors affecting performance of influenza detection, including accuracy of natural language processing (NLP), discriminative ability of Bayesian network (BN) classifiers, and feature selection.We derived a testing dataset of 124 influenza patients and 87 non-influenza (shigellosis) patients. To assess NLP finding-extraction performance, we measured the overall accuracy, recall, and precision of Topaz and MedLEE parsers for 31 influenza-related findings against a reference standard established by three physician reviewers. To elucidate the relative contribution of NLP and BN classifier to classification performance, we compared the discriminative ability of nine combinations of finding-extraction methods (expert, Topaz, and MedLEE) and classifiers (one human-parameterized BN and two machine-parameterized BNs). To assess the effects of feature selection, we conducted secondary analyses of discriminative ability using the most influential findings defined by their likelihood ratios.The overall accuracy of Topaz was significantly better than MedLEE (with post-processing) (0.78 vs 0.71, p<0.0001). Classifiers using human-annotated findings were superior to classifiers using Topaz/MedLEE-extracted findings (average area under the receiver operating characteristic (AUROC): 0.75 vs 0.68, p=0.0113), and machine-parameterized classifiers were superior to the human-parameterized classifier (average AUROC: 0.73 vs 0.66, p=0.0059). The classifiers using the 17 'most influential' findings were more accurate than classifiers using all 31 subject-matter expert-identified findings (average AUROC: 0.76>0.70, p<0.05).Using a three-component evaluation method we demonstrated how one could elucidate the relative contributions of components under an integrated framework. To improve classification performance, this study encourages researchers to improve NLP accuracy, use a machine-parameterized classifier, and apply feature selection methods.

SUBMITTER: Ye Y

PROVIDER: S-EPMC4147621 | biostudies-literature | 2014 Sep-Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Influenza detection from emergency department reports using natural language processing and Bayesian network classifiers.

Ye Ye Y Tsui Fuchiang Rich FR Wagner Michael M Espino Jeremy U JU Li Qi Q

Journal of the American Medical Informatics Association : JAMIA 20140109 5

<h4>Objectives</h4>To evaluate factors affecting performance of influenza detection, including accuracy of natural language processing (NLP), discriminative ability of Bayesian network (BN) classifiers, and feature selection.<h4>Methods</h4>We derived a testing dataset of 124 influenza patients and 87 non-influenza (shigellosis) patients. To assess NLP finding-extraction performance, we measured the overall accuracy, recall, and precision of Topaz and MedLEE parsers for 31 influenza-related find ...[more]

PMID: 24406261

Similar Datasets

Project description:BackgroundNatural language processing (NLP) has a significant role in advancing healthcare and has been found to be key in extracting structured information from radiology reports. Understanding recent developments in NLP application to radiology is of significance but recent reviews on this are limited. This study systematically assesses and quantifies recent literature in NLP applied to radiology reports.MethodsWe conduct an automated literature search yielding 4836 results using automated filtering, metadata enriching steps and citation search combined with manual review. Our analysis is based on 21 variables including radiology characteristics, NLP methodology, performance, study, and clinical application characteristics.ResultsWe present a comprehensive analysis of the 164 publications retrieved with publications in 2019 almost triple those in 2015. Each publication is categorised into one of 6 clinical application categories. Deep learning use increases in the period but conventional machine learning approaches are still prevalent. Deep learning remains challenged when data is scarce and there is little evidence of adoption into clinical practice. Despite 17% of studies reporting greater than 0.85 F1 scores, it is hard to comparatively evaluate these approaches given that most of them use different datasets. Only 14 studies made their data and 15 their code available with 10 externally validating results.ConclusionsAutomated understanding of clinical narratives of the radiology reports has the potential to enhance the healthcare process and we show that research in this field continues to grow. Reproducibility and explainability of models are important if the domain is to move applications into clinical use. More could be done to share code enabling validation of methods on different institutional data and to reduce heterogeneity in reporting of study properties allowing inter-study comparisons. Our results have significance for researchers in the field providing a systematic synthesis of existing work to build on, identify gaps, opportunities for collaboration and avoid duplication.

Project description:OBJECTIVE:To examine the association between the medical imaging utilization and information related to patients' socioeconomic, demographic and clinical factors during the patients' ED visits; and to develop predictive models using these associated factors including natural language elements to predict the medical imaging utilization at pediatric ED. METHODS:Pediatric patients' data from the 2012-2016 United States National Hospital Ambulatory Medical Care Survey was included to build the models to predict the use of imaging in children presenting to the ED. Multivariable logistic regression models were built with structured variables such as temperature, heart rate, age, and unstructured variables such as reason for visit, free text nursing notes and combined data available at triage. NLP techniques were used to extract information from the unstructured data. RESULTS:Of the 27,665 pediatric ED visits included in the study, 8394 (30.3%) received medical imaging in the ED, including 6922 (25.0%) who had an X-ray and 1367 (4.9%) who had a computed tomography (CT) scan. In the predictive model including only structured variables, the c-statistic was 0.71 (95% CI: 0.70-0.71) for any imaging use, 0.69 (95% CI: 0.68-0.70) for X-ray, and 0.77 (95% CI: 0.76-0.78) for CT. Models including only unstructured information had c-statistics of 0.81 (95% CI: 0.81-0.82) for any imaging use, 0.82 (95% CI: 0.82-0.83) for X-ray, and 0.85 (95% CI: 0.83-0.86) for CT scans. When both structured variables and free text variables were included, the c-statistics reached 0.82 (95% CI: 0.82-0.83) for any imaging use, 0.83 (95% CI: 0.83-0.84) for X-ray, and 0.87 (95% CI: 0.86-0.88) for CT. CONCLUSIONS:Both CT and X-rays are commonly used in the pediatric ED with one third of the visits receiving at least one. Patients' socioeconomic, demographic and clinical factors presented at ED triage period were associated with the medical imaging utilization. Predictive models combining structured and unstructured variables available at triage performed better than models using structured or unstructured variables alone, suggesting the potential for use of NLP in determining resource utilization.

Project description:BackgroundSilent brain infarction (SBI) is defined as the presence of 1 or more brain lesions, presumed to be because of vascular occlusion, found by neuroimaging (magnetic resonance imaging or computed tomography) in patients without clinical manifestations of stroke. It is more common than stroke and can be detected in 20% of healthy elderly people. Early detection of SBI may mitigate the risk of stroke by offering preventative treatment plans. Natural language processing (NLP) techniques offer an opportunity to systematically identify SBI cases from electronic health records (EHRs) by extracting, normalizing, and classifying SBI-related incidental findings interpreted by radiologists from neuroimaging reports.ObjectiveThis study aimed to develop NLP systems to determine individuals with incidentally discovered SBIs from neuroimaging reports at 2 sites: Mayo Clinic and Tufts Medical Center.MethodsBoth rule-based and machine learning approaches were adopted in developing the NLP system. The rule-based system was implemented using the open source NLP pipeline MedTagger, developed by Mayo Clinic. Features for rule-based systems, including significant words and patterns related to SBI, were generated using pointwise mutual information. The machine learning models adopted convolutional neural network (CNN), random forest, support vector machine, and logistic regression. The performance of the NLP algorithm was compared with a manually created gold standard. The gold standard dataset includes 1000 radiology reports randomly retrieved from the 2 study sites (Mayo and Tufts) corresponding to patients with no prior or current diagnosis of stroke or dementia. 400 out of the 1000 reports were randomly sampled and double read to determine interannotator agreements. The gold standard dataset was equally split to 3 subsets for training, developing, and testing.ResultsAmong the 400 reports selected to determine interannotator agreement, 5 reports were removed due to invalid scan types. The interannotator agreements across Mayo and Tufts neuroimaging reports were 0.87 and 0.91, respectively. The rule-based system yielded the best performance of predicting SBI with an accuracy, sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of 0.991, 0.925, 1.000, 1.000, and 0.990, respectively. The CNN achieved the best score on predicting white matter disease (WMD) with an accuracy, sensitivity, specificity, PPV, and NPV of 0.994, 0.994, 0.994, 0.994, and 0.994, respectively.ConclusionsWe adopted a standardized data abstraction and modeling process to developed NLP techniques (rule-based and machine learning) to detect incidental SBIs and WMDs from annotated neuroimaging reports. Validation statistics suggested a high feasibility of detecting SBIs and WMDs from EHRs using NLP.

Dataset Information

Influenza detection from emergency department reports using natural language processing and Bayesian network classifiers.

Publications

Influenza detection from emergency department reports using natural language processing and Bayesian network classifiers.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure