Surrogate-assisted feature extraction for high-throughput phenotyping

Author:

Yu Sheng12,Chakrabortty Abhishek3,Liao Katherine P4,Cai Tianrun5,Ananthakrishnan Ashwin N6,Gainer Vivian S7,Churchill Susanne E8,Szolovits Peter9,Murphy Shawn N710,Kohane Isaac S8,Cai Tianxi3

Affiliation:

1. Center for Statistical Science, Tsinghua University, Beijing, China

2. Department of Industrial Engineering, Tsinghua University, Beijing, China

3. Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA

4. Division of Rheumatology, Brigham and Women’s Hospital, Boston, Massachusetts, USA

5. Department of Radiology, Brigham and Women’s Hospital, Boston, Massachusetts, USA

6. Division of Gastroenterology, Massachusetts General Hospital, Boston, Massachusetts, USA

7. Research IS and Computing, Partners HealthCare, Charlestown, Massachusetts, USA

8. Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA

9. Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA

10. Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA

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. Conclusion: 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.

Funder

National Institutes of Health grants

Publisher

Oxford University Press (OUP)

Subject

Health Informatics

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