title: A machine learning-based framework to identify type 2 diabetes through electronic health records.
abstract: To discover diverse genotype-phenotype associations affiliated with Type 2 Diabetes Mellitus (T2DM) via genome-wide association study (GWAS) and phenome-wide association study (PheWAS), more cases (T2DM subjects) and controls (subjects without T2DM) are required to be identified (e.g., via Electronic Health Records (EHR)). However, existing expert based identification algorithms often suffer in a low recall rate and could miss a large number of valuable samples under conservative filtering standards. The goal of this work is to develop a semi-automated framework based on machine learning as a pilot study to liberalize filtering criteria to improve recall rate with a keeping of low false positive rate.
  
  
  
  We propose a data informed framework for identifying subjects with and without T2DM from EHR via feature engineering and machine learning. We evaluate and contrast the identification performance of widely-used machine learning models within our framework, including k-Nearest-Neighbors, Naïve Bayes, Decision Tree, Random Forest, Support Vector Machine and Logistic Regression. Our framework was conducted on 300 patient samples (161 cases, 60 controls and 79 unconfirmed subjects), randomly selected from 23,281 diabetes related cohort retrieved from a regional distributed EHR repository ranging from 2012 to 2014.
  
  
  
  We apply top-performing machine learning algorithms on the engineered features. We benchmark and contrast the accuracy, precision, AUC, sensitivity and specificity of classification models against the state-of-the-art expert algorithm for identification of T2DM subjects. Our results indicate that the framework achieved high identification performances (∼0.98 in average AUC), which are much higher than the state-of-the-art algorithm (0.71 in AUC).
  
  
  
  Expert algorithm-based identification of T2DM subjects from EHR is often hampered by the high missing rates due to their conservative selection criteria. Our framework leverages machine learning and feature engineering to loosen such selection criteria to achieve a high identification rate of cases and controls.
  
  
  
  Our proposed framework demonstrates a more accurate and efficient approach for identifying subjects with and without T2DM from EHR.
authors.affiliation: Institute of Image Communication and Networking, Shanghai Jiao Tong University, Shanghai, China; Tongren Hospital Shanghai Jiao Tong University, Shanghai, China.
authors.forename: Tao
authors.initials: T
authors.lastname: Zheng
authors.affiliation: Department of Electrical Engineering & Computer Science, Vanderbilt University, Nashville, TN, USA.
authors.forename: Wei
authors.initials: W
authors.lastname: Xie
authors.affiliation: Tongren Hospital Shanghai Jiao Tong University, Shanghai, China.
authors.forename: Liling
authors.initials: L
authors.lastname: Xu
authors.affiliation: Department of Endocrinology, the First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China.
authors.forename: Xiaoying
authors.initials: X
authors.lastname: He
authors.affiliation: Institute of Image Communication and Networking, Shanghai Jiao Tong University, Shanghai, China.
authors.forename: Ya
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Division of Epidemiology, Vanderbilt University, Nashville, TN, USA.
authors.forename: Mingrong
authors.initials: M
authors.lastname: You
authors.affiliation: Division of Epidemiology, Vanderbilt University, Nashville, TN, USA.
authors.forename: Gong
authors.initials: G
authors.lastname: Yang
authors.affiliation: Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, USA. Electronic address: you.chen@vanderbilt.edu.
authors.forename: You
authors.initials: Y
authors.lastname: Chen
mesh_terms: D000465:Algorithms; D001499:Bayes Theorem; D003924:Diabetes Mellitus, Type 2 / Q000175:diagnosis*; D057286:Electronic Health Records; D055106:Genome-Wide Association Study; D006801:Humans; D016015:Logistic Models; D000069550:Machine Learning; D010865:Pilot Projects; D060388:Support Vector Machine
keywords: Data mining; Electronic health records; Feature engineering; Machine learning; Type 2 diabetes