AI/ML

Clinical Annotation Research Kit (CLARK): Computable Phenotyping Using Machine Learning.




Icon for JMIR Publications Icon for PubMed Central Related Articles

Clinical Annotation Research Kit (CLARK): Computable Phenotyping Using Machine Learning.

JMIR Med Inform. 2020 Jan 24;8(1):e16042

Authors: Pfaff ER, Crosskey M, Morton K, Krishnamurthy A

Abstract
Computable phenotypes are algorithms that translate clinical features into code that can be run against electronic health record (EHR) data to define patient cohorts. However, computable phenotypes that only make use of structured EHR data do not capture the full richness of a patient's medical record. While natural language processing (NLP) methods have shown success in extracting clinical features from text, the use of such tools has generally been limited to research groups with substantial NLP expertise. Our goal was to develop an open-source phenotyping software, Clinical Annotation Research Kit (CLARK), that would enable clinical and translational researchers to use machine learning-based NLP for computable phenotyping without requiring deep informatics expertise. CLARK enables nonexpert users to mine text using machine learning classifiers by specifying features for the software to match in clinical notes. Once the features are defined, the user-friendly CLARK interface allows the user to choose from a variety of standard machine learning algorithms (linear support vector machine, Gaussian Naïve Bayes, decision tree, and random forest), cross-validation methods, and the number of folds (cross-validation splits) to be used in evaluation of the classifier. Example phenotypes where CLARK has been applied include pediatric diabetes (sensitivity=0.91; specificity=0.98), symptomatic uterine fibroids (positive predictive value=0.81; negative predictive value=0.54), nonalcoholic fatty liver disease (sensitivity=0.90; specificity=0.94), and primary ciliary dyskinesia (sensitivity=0.88; specificity=1.0). In each of these use cases, CLARK allowed investigators to incorporate variables into their phenotype algorithm that would not be available as structured data. Moreover, the fact that nonexpert users can get started with machine learning-based NLP with limited informatics involvement is a significant improvement over the status quo. We hope to disseminate CLARK to other organizations that may not have NLP or machine learning specialists available, enabling wider use of these methods.

PMID: 32012059 [PubMed]

Source link







WordPress database error: [Error writing file '/tmp/MYga01Ug' (Errcode: 28 - No space left on device)]
SELECT SQL_CALC_FOUND_ROWS wp_posts.ID FROM wp_posts LEFT JOIN wp_term_relationships ON (wp_posts.ID = wp_term_relationships.object_id) WHERE 1=1 AND wp_posts.ID NOT IN (350936) AND ( wp_term_relationships.term_taxonomy_id IN (313) ) AND wp_posts.post_type = 'post' AND (wp_posts.post_status = 'publish') GROUP BY wp_posts.ID ORDER BY RAND() LIMIT 0, 3

This website uses cookies to improve your experience. We'll assume you're ok with this, but you can opt-out if you wish. Accept Read More

Privacy & Cookies Policy