Abstract P259: Using Natural Language Processing and Machine Learning to Identify Incident Stroke From Electronic Health Records

Background: The focus of most existing phenotyping algorithms based on electronic health record (EHR) data has been to accurately identify cases and non-cases of specific diseases. However, a more challenging task is to accurately identify disease incidence, as identifying the first occurrence of disease is more important for efficient and valid clinical and epidemiological research. Moreover, stroke is a challenging phenotype due to diagnosis difficulty and common miscoding. This task generally requires utilization of multiple types of EHR data (e.g., diagnoses and procedure codes, unstructured clinical notes) and a more robust algorithm integrating both natural language processing and machine learning. In this study, we developed and validated an EHR-based classifier to accurately identify stroke incidence among a cohort of atrial fibrillation (AF) patients Methods: We developed a stroke phenotyping algorithm using International Classification of Diseases, Ninth Revision (ICD-9) codes, Current Procedural Terminology (CPT) codes, and expert-provided keywords as model features. Structured data was extracted from Rochester Epidemiology Project (REP) database. Natural Language Processing (NLP) was used to extract and validate keyword occurrence in clinical notes. A window of ±30 days was considered when including/excluding keywords/codes into the input vector. Frequencies of keywords/codes were used as input feature sets for model training. Multiple competing models were trained using various combinations of feature sets and two machine learning algorithms: logistic regression and random forest. Training data were provided by two nurse abstractors and included validated stroke incidences from a previously established atrial fibrillation cohort. Precision, recall, and F-score of the algorithm were calculated to assess and compare model performances. Results: Among 4,914 patients with atrial fibrillation, 1,773 patients were screened. 3,141 patients had no stroke-related codes or keywords and were presumed to be free of stroke during follow-up. Among the screened patients, 740 had validated strokes and 1,033 did not have a stroke based on review of the EHR by trained nurse abstractors. The best performing stroke incidence phenotyping classifier utilized Keywords+ICD-9+CPT features using a random forest classifier, achieving a precision of 0.942, recall of 0.943, and F-score of 0.943. Conclusion: In conclusion, we developed and validated a stroke algorithm that performed well for identifying stroke incidence in an enriched population (AF cohort), which extends beyond the typical binary case/non-case stroke identification problem. Future work will involve testing the generalizability of this algorithm in a general population.

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Natural language processing and machine learning to identify alcohol misuse from the electronic health record in trauma patients: development and internal validation

Journal of the American Medical Informatics Association ◽

10.1093/jamia/ocy166 ◽

2019 ◽

Vol 26 (3) ◽

pp. 254-261 ◽

Cited By ~ 12

Author(s):

Majid Afshar ◽

Andrew Phillips ◽

Niranjan Karnik ◽

Jeanne Mueller ◽

Daniel To ◽

...

Keyword(s):

Machine Learning ◽

Natural Language Processing ◽

Natural Language ◽

Electronic Health Record ◽

Language Processing ◽

Alcohol Misuse ◽

Health Record ◽

Trauma Patients ◽

Clinical Notes ◽

Electronic Health

AbstractObjectiveAlcohol misuse is present in over a quarter of trauma patients. Information in the clinical notes of the electronic health record of trauma patients may be used for phenotyping tasks with natural language processing (NLP) and supervised machine learning. The objective of this study is to train and validate an NLP classifier for identifying patients with alcohol misuse.Materials and MethodsAn observational cohort of 1422 adult patients admitted to a trauma center between April 2013 and November 2016. Linguistic processing of clinical notes was performed using the clinical Text Analysis and Knowledge Extraction System. The primary analysis was the binary classification of alcohol misuse. The Alcohol Use Disorders Identification Test served as the reference standard.ResultsThe data corpus comprised 91 045 electronic health record notes and 16 091 features. In the final machine learning classifier, 16 features were selected from the first 24 hours of notes for identifying alcohol misuse. The classifier’s performance in the validation cohort had an area under the receiver-operating characteristic curve of 0.78 (95% confidence interval [CI], 0.72 to 0.85). Sensitivity and specificity were at 56.0% (95% CI, 44.1% to 68.0%) and 88.9% (95% CI, 84.4% to 92.8%). The Hosmer-Lemeshow goodness-of-fit test demonstrates the classifier fits the data well (P = .17). A simpler rule-based keyword approach had a decrease in sensitivity when compared with the NLP classifier from 56.0% to 18.2%.ConclusionsThe NLP classifier has adequate predictive validity for identifying alcohol misuse in trauma centers. External validation is needed before its application to augment screening.

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Development of algorithm for classification smoking status from unstructured bilingual electronic health records based on natural language processing (Preprint)

10.2196/preprints.26978 ◽

2021 ◽

Author(s):

Ye Seul Bae ◽

Kyung Hwan Kim ◽

Han Kyul Kim ◽

Sae Won Choi ◽

Taehoon Ko ◽

...

Keyword(s):

Natural Language Processing ◽

Electronic Health Records ◽

Natural Language ◽

Language Processing ◽

Smoking Status ◽

Svm Classifier ◽

Keyword Extraction ◽

Health Records ◽

Clinical Notes ◽

Electronic Health

BACKGROUND Smoking is a major risk factor and important variable for clinical research, but there are few studies regarding automatic obtainment of smoking classification from unstructured bilingual electronic health records (EHR). OBJECTIVE We aim to develop an algorithm to classify smoking status based on unstructured EHRs using natural language processing (NLP). METHODS With acronym replacement and Python package Soynlp, we normalize 4,711 bilingual clinical notes. Each EHR notes was classified into 4 categories: current smokers, past smokers, never smokers, and unknown. Subsequently, SPPMI (Shifted Positive Point Mutual Information) is used to vectorize words in the notes. By calculating cosine similarity between these word vectors, keywords denoting the same smoking status are identified. RESULTS Compared to other keyword extraction methods (word co-occurrence-, PMI-, and NPMI-based methods), our proposed approach improves keyword extraction precision by as much as 20.0%. These extracted keywords are used in classifying 4 smoking statuses from our bilingual clinical notes. Given an identical SVM classifier, the extracted keywords improve the F1 score by as much as 1.8% compared to those of the unigram and bigram Bag of Words. CONCLUSIONS Our study shows the potential of SPPMI in classifying smoking status from bilingual, unstructured EHRs. Our current findings show how smoking information can be easily acquired and used for clinical practice and research.

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Semantic computational analysis of anticoagulation use in atrial fibrillation from real world data

10.1101/19011643 ◽

2019 ◽

Author(s):

Daniel M. Bean ◽

James Teo ◽

Honghan Wu ◽

Ricardo Oliveira ◽

Raj Patel ◽

...

Keyword(s):

Atrial Fibrillation ◽

Natural Language Processing ◽

Natural Language ◽

Electronic Health Record ◽

Open Source ◽

Language Processing ◽

Risk Scores ◽

Free Text ◽

Health Record ◽

Electronic Health

AbstractAtrial fibrillation (AF) is the most common arrhythmia and significantly increases stroke risk. This risk is effectively managed by oral anticoagulation. Recent studies using national registry data indicate increased use of anticoagulation resulting from changes in guidelines and the availability of newer drugs.The aim of this study is to develop and validate an open source risk scoring pipeline for free-text electronic health record data using natural language processing.AF patients discharged from 1st January 2011 to 1st October 2017 were identified from discharge summaries (N=10,030, 64.6% male, average age 75.3 ± 12.3 years). A natural language processing pipeline was developed to identify risk factors in clinical text and calculate risk for ischaemic stroke (CHA2DS2-VASc) and bleeding (HAS-BLED). Scores were validated vs two independent experts for 40 patients.Automatic risk scores were in strong agreement with the two independent experts for CHA2DS2-VASc (average kappa 0.78 vs experts, compared to 0.85 between experts). Agreement was lower for HAS-BLED (average kappa 0.54 vs experts, compared to 0.74 between experts).In high-risk patients (CHA2DS2-VASc ≥2) OAC use has increased significantly over the last 7 years, driven by the availability of DOACs and the transitioning of patients from AP medication alone to OAC. Factors independently associated with OAC use included components of the CHA2DS2-VASc and HAS-BLED scores as well as discharging specialty and frailty. OAC use was highest in patients discharged under cardiology (69%).Electronic health record text can be used for automatic calculation of clinical risk scores at scale. Open source tools are available today for this task but require further validation. Analysis of routinely-collected EHR data can replicate findings from large-scale curated registries.

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Sentiment Analysis on Twitter Data of World Cup Soccer Tournament Using Machine Learning

IoT ◽

10.3390/iot1020014 ◽

2020 ◽

Vol 1 (2) ◽

pp. 218-239 ◽

Cited By ~ 2

Author(s):

Ravikumar Patel ◽

Kalpdrum Passi

Keyword(s):

Machine Learning ◽

Natural Language Processing ◽

Random Forest ◽

Natural Language ◽

Language Processing ◽

Machine Learning Algorithms ◽

World Cup ◽

Part Of Speech ◽

Twitter Data ◽

Processing Techniques

In the derived approach, an analysis is performed on Twitter data for World Cup soccer 2014 held in Brazil to detect the sentiment of the people throughout the world using machine learning techniques. By filtering and analyzing the data using natural language processing techniques, sentiment polarity was calculated based on the emotion words detected in the user tweets. The dataset is normalized to be used by machine learning algorithms and prepared using natural language processing techniques like word tokenization, stemming and lemmatization, part-of-speech (POS) tagger, name entity recognition (NER), and parser to extract emotions for the textual data from each tweet. This approach is implemented using Python programming language and Natural Language Toolkit (NLTK). A derived algorithm extracts emotional words using WordNet with its POS (part-of-speech) for the word in a sentence that has a meaning in the current context, and is assigned sentiment polarity using the SentiWordNet dictionary or using a lexicon-based method. The resultant polarity assigned is further analyzed using naïve Bayes, support vector machine (SVM), K-nearest neighbor (KNN), and random forest machine learning algorithms and visualized on the Weka platform. Naïve Bayes gives the best accuracy of 88.17% whereas random forest gives the best area under the receiver operating characteristics curve (AUC) of 0.97.

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