Gregory Cooper, MD, PhD

Research Interests: 
  • Application of decision theory, probability theory, Bayesian statistics, and artificial intelligence to biomedical informatics research problems 
  • Causal modeling and discovery from clinical and high-throughput molecular data
  • Computer-aided medical diagnosis and prediction
  • Machine-learning approaches to improving patient safety
  • Biosurveillance of disease outbreaks
Professor, Department of Biomedical Informatics and of Intelligent Systems
Vice Chairman, Department of Biomedical Informatics
University of Pittsburgh School of Medicine
Publications: 

Aronis JM, Millett NE, Wagner MM, Tsui F, Ye Y, Ferraro JP, Haug PJ, Gesteland PH, Cooper GF. A Bayesian system to detect and characterize overlapping outbreaks. J Biomed Inform. 2017 Sep;73:171-181. doi: 10.1016/j.jbi.2017.08.003. Epub 2017 Aug 7. PMID: 28797710. PMC5604259.

King AJ, Hochheiser H, Visweswaran S, Clermont G, Cooper GF. Eye-tracking for Clinical Decision Support: A Method to Capture Automatically What Physicians Are Viewing in the EMR. AMIA Jt Summits Transl Sci Proc. 2017 Jul 26;2017:512-521. eCollection 2017. PMID: 28815151. PMCID: PMC5543363.

Ferraro JP, Ye Y, Gesteland PH, Haug PJ, Tsui F-C, Cooper GF, Van Bree R, Ginter T, Nowalk AJ, Wagner MM. The effects of natural language processing on cross-institutional portability of influenza case detection for disease surveillance. Appl Clin Inform. 2017 May 31;8(2):560-580. doi:10.4338/ACI-2016-12-RA-0211. PubMed PMID: 28561130.

Ye Y, Wagner MM, Cooper GF, Ferraro JP, Su H, Gesteland PH, Haug PJ, Millett NE, Aronis JM, Nowalk AJ, Ruiz VM, López Pineda A, Shi L, Van Bree R, Ginter T, Tsui F. A study of the transferability of influenza case detection systems between two large healthcare systems. PLoS One. 2017 Apr 5;12(4):e0174970. doi: 10.1371/journal.pone.0174970. eCollection 2017. PMID: 28380048 PMCID: PMC5381795

Ding MQ, Chen L, Cooper GF, Young JD, Lu X. Precision Oncology Beyond Targeted Therapy: Combining Omics Data with Machine Learning Matches the Majority of Cencer Cells to Effective Therapeutics. Mol Cancer Res. 2017 Nov 13. pii: molcanres.0378.2017. doi: 10.1158/1541-7786.MCR-17-0378. [Epub ahead of print] PMID: 29133589

Tsui F, Ye Y, Ruiz V, Cooper GF, Wagner MM. Automated influenza case detection for public health surveillance and clinical diagnosis using dynamic influenza prevalence method. J Public Health (Oxf). 2017 Oct 20:1-8. doi: 10.1093/pubmed/fdx141. [Epub ahead of print]. PMID: 29059331.

Naeini Pakdaman M, Cooper GF. Binary classifier calibration using an ensemble of linear trend estimation. In: Proceedings of the 2016 SIAM International Conference on Data Mining (2016) May;2016:261-269. doi: 10:1137/1.9781611974348.30.  PMID: 28357159 PMCID: PMC5367639

Hill SM, et al. Inferring causal molecular networks: Empirical assessment through a community-based effort. Nature Methods (2016) Apr; 13(4):310-318. doi: 10.1038/nmeth.3773. PMID: 26901648 PMCID: PMC4854847

Naeini Pakdaman M, Cooper GF. Binary classifier calibration using an ensemble of near isotonic regression models. In: Proceedings of the IEEE International Conference on Data Mining (2016) Dec;2016:360-369.  doi: 10.1109/ICDM.2016.0047  PMID: 28316511 PMCID: PMC5351887

Hauskrecht M, Batal I, Hong C, Nguyen Q, Cooper GF, Visweswaran S, Clermont G. Outlier-based detection of unusual patient-management actions: An ICU study. Journal of Biomedical Informatics (2016) Oct 5  pii: S1532-0464(16)30135-6. doi: http://dx.doi.org/10.1016/j.jbi.2016.10.002 PMID: 27720983

Cooper GF, Bahar I, Becich MJ, Benos PV, Berg J, Espino JU, Jacobson RC, Kienholz M, Lee AV, Lu X, Scheines R, Center for Causal Discovery team. The Center for causal discovery of biomedical knowledge from Big Data. Journal of the American Medical Informatics Association 2015 Jul 2. pii: ocv059. doi: 10.1093/jamia/ocv059. [Epub ahead of print]  PMID: 26138794

Visweswaran S, Ferreira A, Cooper GF. Personalized modeling for prediction with decision-path models. PLoS One. 2015 Jun 22;10(6):e0131022 PMID: 26098570 PMCID: PMC4476684

Cooper, G. F., Villamarin, R., Tsui, F.-C. (Rich), Millett, N., Espino, J. U., & Wagner, M. M. (2015). A Method for Detecting and Characterizing Outbreaks of Infectious Disease from Clinical Reports. Journal of Biomedical Informatics, 53, 15–26. http://doi.org/10.1016/j.jbi.2014.08.011 PMID: 25181466 PMCID: PMC4441330

Sverchkov Y, Cooper GF. A Bayesian approach for identifying multivariate differences between groups. In: Proceedings of the International Symposium on Intelligent Data Analysis (2015). Adv Intell Data Anal. 2015 Oct;9385:275-285. Epub 2015 Nov 22.  PMCID: 27069983 PMCID: PMC4825814

King AJ, Cooper GF, Hochheiser H, Clermont G. Development and preliminary evaluation of a prototype of a learning electronic medical record system. In: Proceedings of the Symposium of the American Medical Informatics Association, (2015) Nov 5;2015:1967-75 PMID: 26958296 PMCID: PMC4765593

Cooper GF, Villamarin R, Tsui FC, Millett N, Espino J, Wagner MM. A method for detecting and characterizing outbreaks of infectious disease from clinical reports. Journal of Biomedical Informatics (2014).   Aug 30. pii: S1532-0464(14)00192-0. doi: 10.1016/j.jbi.2014.08.011. [Epub ahead of print] PMID:25181466 PMC4441330

Jiang X, Cai B, Xue D, Lu X, Cooper GF, Neapolitan RE. A comparative analysis of methods for predicting clinical outcomes using high-dimensional genomic datasets. Journal of the American Medical Informatics Association (2014). Oct;21(e2):e312-9. doi: 10.1136/amiajnl-2013-002358. Epub 2014 Apr 15.  PMID: 24737607 PMC4173174

Villamarín R, Cooper G, Wagner M, Tsui FC, Espino JU. A method for estimating from thermometer sales the incidence of diseases that are symptomatically similar to influenza. Journal of Biomedical Informatics. 2013 Jun;46(3):444-57. PMID: 23501015 PMCID: PMC4609543

Pineda, A. L., Tsui, F.-C., Visweswaran, S., & Cooper, G. F. (2013). Detection of Patients with Influenza Syndrome Using Machine-Learning Models Learned from Emergency Department Reports. Online Journal of Public Health Informatics, 5(1), e41.

David J. Montefusco, Lujia Chen, Nabil Matmati, Songjian Lu, Benjamin Newcomb, Gregory F. Cooper, Yusuf A. Hannun, and Xinghua Lu.  Science Signaling, 6(299): p. rs14 [DOI: 10.1126/scisignal.2004515] http://stke.sciencemag.org/cgi/content/full/sigtrans;6/299/rs14

Sverchkov Y, Visweswaran S, Clermont G, Hauskrecht M, Cooper GF. A multivariate probabilistic method for comparing two clinical datasets. In: Proceedings of the ACM International Health Informatics Symposium (2012) 795-800.

Jiang X, Neapolitan RE, Barmada M, Visweswaran S, Cooper GF.   A fast algorithm for learning epistatic genomic relationships.  In: Proceedings of the Annual Symposium of the American Medical Informatics Association (2010) 341-345. PMID: 21346997 PMC3041370

Jiang X, Cooper GF. Modeling the Temporal Trend of the Daily Severity of an Outbreak using Bayesian Networks. In: Holmes DE, Jain LC, editors. Innovations in Bayesian Networks of Studies in Computational Intelligence. NY: Springer-Verlag, 2008.

Cooper GF.  A diagnostic method that uses causal knowledge and linear programming in the application of Bayes' formula. Computer Methods and Programs in Biomedicine 22 (1986) 223–237. PMID: 3519071

 

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