Enabling EHR for Research

• Automated feature exactions

• Natural language processing

• High throughout phenotyping

Research Team

Cai, Tianxi

Yu, Sheng

Liao, Katherine

Cai, Tianrun

Hong, Chuan

Ahujia, Yuri

He, Zeling

Cho, Kelly

Selected Publications

• Yichi Zhang*, Tianrun Cai*, Sheng Yu*, Kelly Cho, Chuan Hong, Jiehuan Sun, Jie Huang, Yuk-Lam Ho, Ashwin Ananthakrishnan, Zongqi Xia, Stanley Shaw, Vivian Gainer, Victor Castro, Nicholas Link, Jacqueline Honerlaw, Selena Huang, David Gagnon, Elizabeth Karlson, Robert Plenge, Peter Szolovits, Guergana Savova, Susanne Churchill, Christopher O’Donnell, Shawn Murphy, J Michael Gaziano, Isaac Kohane, Tianxi Cai*, and Katherine Liao*. Methods for High-throughput Phenotyping with Electronic Medical Record Data Using a Common Semi-supervised Approach (PheCAP). Nature Protocols (2019). *contributed equally.

• Katherine P. Liao, Jiehuan Sun, Tianrun A. Cai, Nicholas Link, Chuan Hong, Jie Huang, Jennifer E. Huffman, Jessica Gronsbell, Yichi Zhang, Yuk-Lam Ho, Victor Castro, Vivian Gainer, Shawn N. Murphy, Christopher J. O’Donnell, J. Michael Gaziano, Kelly Cho, Peter Szolovits, Isaac S. Kohane, Sheng Yu, Tianxi Cai, with the VA Million Veteran Program (2019). High-throughput Multimodal Automated Phenotyping (MAP) with Application to PheWAS. https://doi.org/10.1101/587436

• J. Gronsbell, J. Minnier, S. Yu, K. Liao, and T. Cai, 2019 “Automated Feature Selection of Predictors in Electronic Medical Records Data.” Biometrics, doi: 10.1111/biom.12987.

• C. Hong, K. Liao and T. Cai, 2019 “Semi-supervised Validation of Multiple Surrogate Outcomes with Application to Electronic Medical Records Phenotyping.” Biometrics, doi: 10.1111/biom.12971.

• Sheng Yu*, Yumeng Ma, Jessica Gronsbell, Tianrun Cai, Ashwin N. Ananthakrishnan, Vivian S. Gainer, Susanne E. Churchill, Peter Szolovits, Shawn N. Murphy, Isaac S. Kohane, Katherine P. Liao, Tianxi Cai. Enabling Phenotypic Big Data with PheNorm; Journal of the American Medical Informatics Association (2018), 25(1, special issue featuring data science):54-60; https://doi.org/10.1093/jamia/ocx111

• Sheng Yu*, Abhishek Chakrabortty, Katherine P. Liao, Tianrun Cai, Ashwin N. Ananthakrishnan, Vivian S. Gainer, Susanne E. Churchill, Peter Szolovits, Shawn N. Murphy, Isaac S. Kohane, Tianxi Cai. Surrogate-assisted Feature Extraction for High-throughput Phenotyping; Journal of the American Medical Informatics Association (2017), 24 (e1): e143-e149; https://doi.org/10.1093/jamia/ocw135

• Sheng Yu*, Katherine P. Liao, Stanley Y. Shaw, Vivian S. Gainer, Susanne E. Churchill, Peter Szolovits, Shawn N. Murphy, Isaac Kohane, and Tianxi Cai. Toward High-throughput Phenotyping: Unbiased Automated Feature Extraction and Selection from Knowledge Sources; Journal of the American Medical Informatics Association (2015), 22(5):993-1000; https://doi.org/10.1093/jamia/ocv034