title: Surrogate-assisted feature extraction for high-throughput phenotyping.
abstract: OBJECTIVE
  Phenotyping algorithms are capable of accurately identifying patients with specific phenotypes from within electronic medical records systems. However, developing phenotyping algorithms in a scalable way remains a challenge due to the extensive human resources required. This paper introduces a high-throughput unsupervised feature selection method, which improves the robustness and scalability of electronic medical record phenotyping without compromising its accuracy.
  
  
  METHODS
  The proposed Surrogate-Assisted Feature Extraction (SAFE) method selects candidate features from a pool of comprehensive medical concepts found in publicly available knowledge sources. The target phenotype's International Classification of Diseases, Ninth Revision and natural language processing counts, acting as noisy surrogates to the gold-standard labels, are used to create silver-standard labels. Candidate features highly predictive of the silver-standard labels are selected as the final features.
  
  
  RESULTS
  Algorithms were trained to identify patients with coronary artery disease, rheumatoid arthritis, Crohn's disease, and ulcerative colitis using various numbers of labels to compare the performance of features selected by SAFE, a previously published automated feature extraction for phenotyping procedure, and domain experts. The out-of-sample area under the receiver operating characteristic curve and F -score from SAFE algorithms were remarkably higher than those from the other two, especially at small label sizes.
  
  
  CONCLUSIONS
  SAFE advances high-throughput phenotyping methods by automatically selecting a succinct set of informative features for algorithm training, which in turn reduces overfitting and the needed number of gold-standard labels. SAFE also potentially identifies important features missed by automated feature extraction for phenotyping or experts.
authors.affiliation: Center for Statistical Science, Tsinghua University, Beijing, China.|Department of Industrial Engineering, Tsinghua University, Beijing, China.
authors.forename: Sheng
authors.initials: S
authors.lastname: Yu
authors.affiliation: Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA.
authors.forename: Abhishek
authors.initials: A
authors.lastname: Chakrabortty
authors.affiliation: Division of Rheumatology, Brigham and Women's Hospital, Boston, Massachusetts, USA.
authors.forename: Katherine P
authors.initials: KP
authors.lastname: Liao
authors.affiliation: Department of Radiology, Brigham and Women's Hospital, Boston, Massachusetts, USA.
authors.forename: Tianrun
authors.initials: T
authors.lastname: Cai
authors.affiliation: Division of Gastroenterology, Massachusetts General Hospital, Boston, Massachusetts, USA.
authors.forename: Ashwin N
authors.initials: AN
authors.lastname: Ananthakrishnan
authors.affiliation: Research IS and Computing, Partners HealthCare, Charlestown, Massachusetts, USA.
authors.forename: Vivian S
authors.initials: VS
authors.lastname: Gainer
authors.affiliation: Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA.
authors.forename: Susanne E
authors.initials: SE
authors.lastname: Churchill
authors.affiliation: Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
authors.forename: Peter
authors.initials: P
authors.lastname: Szolovits
authors.affiliation: Research IS and Computing, Partners HealthCare, Charlestown, Massachusetts, USA.|Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA.
authors.forename: Shawn N
authors.initials: SN
authors.lastname: Murphy
authors.affiliation: Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA.
authors.forename: Isaac S
authors.initials: IS
authors.lastname: Kohane
authors.affiliation: Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA.
authors.forename: Tianxi
authors.initials: T
authors.lastname: Cai
mesh_terms: D000465:Algorithms; D057225:Data Mining; D057286:Electronic Health Records; D006801:Humans; D000069550:Machine Learning; D009323:Natural Language Processing; D010641:Phenotype
keywords: data mining; electronic medical records; machine learning; phenotyping