Text Mining

• Medical natural language processing

• High-throughput phenotyping

• Language-agnostic term identification

Research Team

Cai, Tianxi

Yu, Sheng

Liao, Katherine

Sinnott, Jennifer

Zhang, Yichi

Cai, Tianrun

Selected Publications

• Sheng Yu*, Tianrun Cai, Tianxi Cai. NILE: Fast Natural Language Processing for Electronic Health Records. arXiv:1311.6063

• 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).

• 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, MD, Sheng Yu*, Tianxi Cai*. High-throughput Multimodal Automated Phenotyping (MAP) with Application to PheWAS. Journal of the American Medical Informatics Association (2019). #contributed equally, *contributed equally.

• Wenxin Ning, Stephanie Chan, Andrew Beam, Ming Yu, Alon Geva, Katherine P Liao, Mary Mullen, Kenneth D Mandl, Isaac S Kohane, Tianxi Cai, Sheng Yu*. Feature Extraction for Phenotyping from Semantic and Knowledge Resources. Journal of Biomedical Informatics (2019), 91:103122.

• Jennifer A. Sinnott*, Fiona Cai, Sheng Yu, Boris P. Hejblum, Chuan Hong, Isaac S. Kohane, Katherine P. Liao. PheProb: Probabilistic Phenotyping Using Diagnosis Codes to Improve Power for Genetic Association Studies. Journal of the American Medical Informatics Association (2018), 25(10):1359–1365.

• Thomas H. McCoy#, Sheng Yu#, Kamber L. Hart, Victor M. Castro, Hannah E. Brown, James N. Rosenquist, Alysa E. Doyle, Pieter J. Vuijk, Tianxi Cai*, Roy H. Perlis*. High Throughput Phenotyping for Dimensional Psychopathology in Electronic Health Records. Biological Psychiatry (2018), 83(12), 997-1004. #contributed equally.

• 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):54-60.

• 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; doi: 10.1093/jamia/ocw135.

• Tianrun Cai, Andreas A. Giannopoulos, Sheng Yu, Tatiana Kelil, Beth Ripley, Kanako K. Kumamaru, Frank J. Rybicki, and Dimitrios Mitsouras*. Natural Language Processing Technologies in Radiology Research and Clinical Applications. RadioGraphics, 36, no. 1 (2016): 176-191.

• 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.

• Yuanhao Liu and Sheng Yu*. Word segmentation as graph partition. arXiv:1804.01778.