Publications for Gregory Cooper, MD, PhD

2020

Young JD, Andrews B, Cooper GF, Lu X. Learning Latent Causal Structures with a Redundant Input Neural Network. arXiv:2003.13135v1 29 Mar 2020.

King AJ, Cooper GF, Clermont G, Hochheiser H, Hauskrecht M, Sittig DF, Visweswaran S. Leveraging Eye Tracking to Prioritize Relevant Medical Record Data: Comparative Machine Learning Study J Med Internet Res 2020;22(4):e15876 
Aronis JM, Ferraro JP, Gesteland PH, Tsui F, Ye Y, Wagner MM, Cooper GF. A Bayesian approach for detecting a disease that is not being modeled. PLOSOne. 2020 Feb 28;15(2):e0229658. doi: 10.1371
Andrews B, Spirtes P, Cooper GF.  On the Completeness of Causal Discovery in the Presence of Latent Confounding with Tiered Background Knowledge.  Proceedings of Machine Learning Research JMLR:108.

Fattaneh Jabbari, Lisa C. Villaruz, Mike Davis, Gregory F. Cooper.  Lung Cancer Survival Prediction Using Instance-Specific Bayesian Networks. In: Michalowski M., Moskovitch R. (eds) Artificial Intelligence in Medicine. AIME 2020. Lecture Notes in Computer Science, vol 12299. Springer, Cham. https://doi.org/10.1007/978-3-030-59137-3_14.

Sofia Triantafillou, Gregory F. Cooper. Learning Adjustment Sets from Observational and Limited Experimental Data. 2020 . arXiv preprint arXiv:2005.08749, 2020

Liu J, Ma X, Cooper G, Lu X. Explicit representation of protein activity states significantly improves causal discovery of protein phosphorylation networks. BMC Bioinformatics. (2020) Sep 17;21(Suppl 13):379. doi: 10.1186/s12859-020-03676-2. PMID: 32938361 PMCID: PMC7496209
Jabbari F, Cooper GF. An instance-specific algorithm for learning the structure of causal Bayesian networks containing latent variables. In: Proceedings of the SIAM International Conference on Data Minin (2020) 433-441.

2019

Andrews B, Ramsey J, Cooper GF.  Learning high-dimensional directed acyclic graphs with mixed data-types. Proceedings of Machine Learning Research 2019 Aug; 104: 4-21. PMID: 31453569 PMCID: PMC6709674

 

Cai C, Cooper GF, Lu KN, Ma X, Xu S, Zhao Z, Chen X, Xue Y, Lee AV, Clark N, Chen V, Lu S, Chen L, Yu L, Hochheiser HS, Jiang X, Wang JQ, Lu X. Systematic discovery of the functional impact of somatic genome alterations in individual tumors through tumor-specific causal inference. PLOS Comput Biol, 2019 Jul 15(7):e1007088. doi: 10.1371/journal.pcbi.1007088. [Epub ahead of print] PMID: 31276486; PMCID: PMC6650088.

Seymour CW, Kennedy JN, Wang S, Chang CH, Elliott CF, Xu Z, Berry S, Clermont G, Cooper G, Gomez H, Huang DT, Kellum JA, Mi Q, Opal SM, Talisa V, van der Poll T, Visweswaran S, Vodovotz Y, Weiss JC, Yealy DM, Yende S, Angus DC. Derivation, Validation, and Potential Treatment Implications of Novel Clinical Phenotypes for Sepsis. Journal of the American Medical Association ( 2019). doi:10.1001/jama.2019.5791. PMID: 31104070 PMCID: PMC6537818

Cai C, Cooper GF, Lu KN, Ma X, Xu S, Zhao Z, Chen X, Xue Y, Lee AV, Clark N, Chen V, Lu S, Chen L, Hochheiser HS, Jiang X, Wang QJ, Lu X.  Systematic discovery of the functional impact of somatic genome alterations in individual tumors through tumor-specific causal inference. PLoS Computational Biology. Published online July 5, 2019. doi: 10.137/journal,pcbi.1007088.  PMID: 31276486

King A, Cooper GF, Clermont G, Hochheiser H, Hauskrecht M, Sittig DF, Visweswaran S. Using machine learning to selectively highlight patient information. Journal of Biomedical Informatics.  2019; Oct 29;100:103327. DOI: 1016/j.jbi.2019.103329. PMID: 31676461; PMCID: PMC6932869 [Available on 2020-12-01].

2018

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 Cancer Cells to Effective Therapeutics. Mol Cancer Res. 2018 Feb;16(2):269-278. doi: 10.1158/1541-7786.MCR-17-0378. Epub 2017 Nov 13. PMID: 29133589. PMCID: PMC5821274.

Andrews B, Ramsey J, Cooper GF. Scoring Bayesian networks of mixed variables. International Journal of Data Science and Analytics (2018) 1-16. First Online 11 January 2018.

Jabbari F, Viswewaran S, Cooper GF. Instance-Specific Bayesian Network Structure Learning. Proceedings of the International Conference on Probabilistic Graphical Models (2018) Sep;72:169-180.  PMID: 30775723. PMCID: PMC6376975.

Millett NE, Aronis JM, Wagner MM, Tsui F, Ye Y, Ferrar JP, Huag PJ, Gesteland PH, Cooper GF. The design and evaluation of a Bayesian System for detecting and characterizing outbreaks of influenza. Online Journal of Public Health Informatics, 11(2) (2019). Doi: https://doi.org/10.1101/435727.

King AJ, Cooper GF, Hochheiser H, Clermont G, Hausrecht M, Visweswaran S. Using Machine Learning to Predict the Information Seeking Behavior of Clinicians Using an Electronic Medical Record System. AMIA Annual Symp Proc. 2018 Dec 5;2018:673-682. eCollection 2018. PubMed PMID: 30815109. PMCID: PMC6371238.

2017

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.

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.

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.

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.

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. Journal of Biomedical Informatics 2017 Sep;73:171-181. doi: 10.1016/j.jbi.2017.08.003. Epub 2017 Aug 7. PMID: 28797710. PMCID: PMC5604259.

Naeini MP, Cooper GF. Binary classifier calibration using an ensemble of regression models. Journal of Knowledge and Information System 2018 Jan;54(1); 151-170. Doi:10.1007/s10115-017-1133-2. Epub 2017 Nov 17. PMID: 29606784. PMCID: PMC5875942.

Jabbari F, Ramsey J, Spirtes P, Cooper GF. Discovery of causal models that contain latent variables through Bayesian scoring of independence constraints. In: Proceeding of the European Conference on Machine Learning (2017).

Kummerfeld E, Cooper GF. A new method for estimating causal model learning accuracy. In: Workshop on Data Mining for Medical Informatics (DMMI) – Causal Inference for Health Data Analytics (2017).

Naeini Pakdaman M, Jabbari F, Cooper GF. An assessment of the calibration of causal relationships learned using RFCI and bootstrapping. In: AMIA Workshop on Data Mining for Medical Informatics (DMMI) – Causal Inference for Health Data Analytics (2017).

Cooper G, Cai C, Lu X. Tumor-specific Causal Inference (TCI): A Bayesian Method for Identifying Causative Genome Alterations within Individual Tumors. bioRxiv (2017). Doi: https://doi.org/10.1101/225631.

Jabbari F, Naeini MP, Cooper GF. Obtaining Accurate Probabilistic Causal Inference by Post-Processing Calibration. arXiv (2017). https://arxiv.org/pdf/1712.08626v1.

2016

Lu S, Cai C, Yan G, Zhou Z, Wan Y, Chen V, Chen L, Cooper GF, Obeid LM, Hannun YA, Lee AV, Lu X. Signal-Oriented Pathway Analyses Reveal a Signaling Complex as a Synthetic Lethal Target for p53 Mutations. Cancer Res. 206 Dec 1:76(23):6785-6794. doi: 10.1158/0008-5472.CAN-16-1740. Epub 2016 Oct 10. PMID: 27758891. PMCID: PMC5165695.

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

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. PMCID: PMC5207478.

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

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

2015

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. J Am Med Inform Assoc. 2015 Nov;22(6): 1132-6. doi: 10.1093/jamia/ocv059. Epub 2015 Jul 2.  PMID: 26138794. PMCID: PMC5009908.

Cooper GF, Villamarin R, Rich Tsui FC, Millett N, Espino JU, Wagner MM. A method for detecting and characterizing outbreaks of infectious disease from clinical reports. J Biomed Inform. 2015 Feb; 53:15-26.  doi: 10.1016/j.jbi.2014.08.011. Epub 2014 Aug 30.  PMID: 25181466. PMCID: PMC4441330.

Batal I, Cooper G, Fradkin D, Harrison J, Moerchen F, Hauskrecht M. An efficient pattern mining approach for event detection in multivariate temporal data. The Journal of Knowledge and Information Systems (2015) 1-36 [PubMed – in progress].

Naeini MP, Cooper GF, Hauskrecht M. Obtaining well calibrated probabilities using Bayesian binning. In: Proceedings of the Conference of the Association for the Advancement of Artificial Intelligence (2015) Jan;2015:2901-2907. PMID: 25927013 PMC4410090.

López Pineda A, Ye Y, Visweswaran S, Cooper GF, Wagner MM, Tsui FR. Comparison of Machine Learning Classifiers for Influenza Detection from Emergency Department Free-text Reports. J Biomed Inform. 2015 Dec;58:60-69. doi: 10.1016/j.jbi.2015.08.019. Epub 2015 Sep 16. PMID: 26385375. PMCID: PMC4684714.

Naeini MP, Cooper GF, Hauskrecht M. Binary classifier calibration using a Bayesian non-parametric approach. In: Proceedings of the SIAM International Conference on Data Mining (2015).

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. AMIA Annu Symp Proc. 2015 Nov 5;2015:1967-75. eCollection 2015. PMID: 26958296 PMCID: PMC4765593.

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.

2014

Balasubramanian JB, Cooper GF, Visweswaran S, Gopalakrishnan V. Selective Model Averaging with Bayesian Rule Learning for Predictive Biomedicine. Proceedings of the AMIA 2014 Joint Summits in Translational Science (In Press); April 2014; San Francisco, CA, USA2014.

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. J Am Med Inform Assoc. 2014 Oct;21(e2):e312-9. doi: 10.1136/amiajnl-2013-002358. Epub 2014 Apr 15. PMID: 24737607. PMCID: PMC4173174.

Avali VR, Cooper GF, Gopalakrishnan V. Application of Bayesian logistic regression to mining biomedical data. In: Proceedings of the Fall Symposium of the American Medical Informatics Association (2014) Nov 14;2014:266-73. PMID: 25954328 PMC4419893

2013

Batal I, Valizadegan H, Cooper GF, Hauskrecht M. A temporal pattern mining approach for classifying electronic health record data. ACM Transactions on Intelligent Systems and Technology 4 (2013). PMID: 25309815 PMC4192602

Hauskrecht M, Batal I, Valko M, Visweswaran S, Cooper GF, Clermont G. Outlier-detection for patient monitoring and alerting. Journal of Biomedical Informatics 46 (2013) 47-55. PMID: 22944172. PMCID: PMC3567774

Pineda AL, Tsui FC, Visweswaran S, Cooper GF. (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.

Villamarin 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. J Biomed Inform. 2013 Jun; 46(3):444-57. doi: 10.1016/j.jbi.2013.02.003. Epub 2013 Mar 14. PMID: 23501015. PMCID: PMC4609543.

Montefusco DJ, Chen L, Matmati N, Lu S, Newcomb B, Cooper GF, Hannun YA, Lu X. Distinct signaling roles of ceramide species in yeast revealed through systematic perturbation and systems biology analyses. Sci Signal. 2013 Oct 29;6(299): rs14. doi: 10.1126/scisignal.2004515. PMID: 24170935. PMC3974757.

Hauskrecht M, Visweswaran S, Cooper GF, Clermont G.  Data-driven identification of unusual clinical actions in the ICU.   In: Proceedings of the Annual Symposium of the American Medical Informatics Association (2013).

Ferreira A, Cooper GF, Visweswaran S.  Decision path models for patient-specific modeling of patient outcomes.  In: Proceedings of the Annual Symposium of the American Medical Informatics Association (2013) 413-21. PMID: 24551347. PMCID: PMC3900188

2012

M. Wagner, Cooper G, Tsui F, Espino JU, Harkema H, Levander J, Villamarin R, Millett N, Brown ST, Gallaggher A "A Decision-Theoretic Model of Disease Surveillance and Control and a Prototype Implementation for the Disease Influenza," Data Engineering Workshops (ICDEW), 2012 IEEE 28th International Conference on, Arlington, VA, 2012, pp. 49-54.
doi: 10.1109/ICDEW.2012.32

Sverchkov Y, Jiang X, Cooper GF.  Spatial cluster detection using dynamic programming. BMC Medical Informatics & Decision Making 12:22(2012).  Doi:10.1186/1472-6947-12-22.  PMID: 22443103. PMC: PMC3403878.

Batal I, Cooper G, Hauskrecht M. A Bayesian scoring technique for mining predictive and non-spurious rules. Machine Learning and Knowledge Discovery in Databases 7524 (2012) 260-276.  PMID: 25938136 PMC4416489

Hennings-Yeomans PH, Cooper GF. Improving the prediction of clinical outcomes from genomic data using multiresolution analysis. IEEE/ACM Transactions on Computational Biology and Bioinformatics 9 (2012) 1442 - 1450. PMID: 22641708

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.

2011

Wei W, Visweswaran S, Cooper GF. The application of naive Bayes model averaging to predict Alzheimer’s disease from genome-wide data. Journal of the American Medical Informatics Association (2011) Jul 1; 18(4): 370-5.  PMID: 21672907 PMCID: PMC3128400.

Wagner M, Tsui F, Cooper G, Espino JU, Harkema H, Levander J, Villamarin R, Voorhees R, Millett N, Keane C, Dey A, Razdan M, Hu Y, Tsai M, Brown S, Lee BY, Gallagher A, Potter M. Probabilistic, Decision-theoretic Disease Surveillance and Control. Online J Public Health Inform. 2011;3(3) doi: 10.5210/ojphi.v3i3.3798. Epub 2011 Dec 22.  PubMed PMID:  23569617.  PMCID: PMC3615794.

Jiang X, Barmada MM, Cooper GF, Becich MJ. A Bayesian method for evaluating and discovering disease loci associations. PLoS ONE. 2011;6(8):e22075. doi: 101371/journal.pone.0022075. Epub 2011 Aug 10. PMID: 21853025. PMCID: PMC3154195.

Lustgarten JL, Visweswaran S, Gopalakrishnan V, Cooper GF. Application of an efficient Bayesian  discretization method to biomedical data. BMC Bioinformatics 12 (2011) 309 http://www.biomedcentral.com/1471-2105/12/309.   PMID: 21798039 PMC3162539

Tsui F-C, Wagner MM, Cooper G, Que J, Harkema H, Dowling J, Sriburadej T, Li Q, Espino JU, Voorhees R. Probabilistic case detection for disease surveillance using data in electronic medical records.  Online J Public Health Inform.  2011 Dec;3(3) Epub 2011 Dec 22.  PubMed PMID: 23569615.  PMCID:PMC3615792.

Valko M, Kveton B, Valizadegan H,  Cooper GF, Hauskrecht M. Conditional anomaly detection with soft harmonic functions. In: Proceedings of the International Conference on Data Mining (2011) 735-743.

Batal I, Valizadegan H, Cooper GF, Hauskrecht M. A pattern mining approach for classifying multivariate temporal data. In: Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (2011) 358-365. PMCID: PMC3261774. PMID: 22267987.

2010

Jiang X, Cooper G. Joint SNP analysis using a breast cancer GWAS data set. In: Proceedings of Cancer Informatics Workshop. Cancer Informatics Workshop; 2010; Cambridge UK 2010.

Jiang X, Neill DB, Cooper GF.  A Bayesian network model for spatial event surveillance. International Journal of Approximate Reasoning (2010) 51:224-239.  doi: ttp://dx.doi.org/10.1016/j.ijar.2009.01.001.

Shen Y, Cooper GF. A new prior for Bayesian anomaly detection – Application to biosurveillance. Methods of Information in Medicine 49 (2010) 44-53. PMID: 20027381.

Neill DB, Cooper GF.  A multivariate Bayesian scan statistic for early event detection and characterization.  Machine Learning 79 (2010) 261-282.  Publication not directly supported by NIH

Jiang X, Cooper GF.  A real-time temporal Bayesian architecture for event surveillance and its application to patient-specific multiple disease outbreak detection. Data Mining and Knowledge Discovery (2010). DOI: 10.1007/s10618-009-0151-4.  

Gopalakrishnan V, Lustgarten JL, Visweswaran S, Cooper GF. Bayesian rule learning for biomedical data mining. Bioinformatics 26 (2010) 668-675. Doi:10.1093/bioinformatics/btq005.  PMID: 20080512.  PMC2852212.

Jiang X, Cooper GF. A Bayesian spatio-temporal method for disease outbreak detection. Journal of the American Medical Informatics Association 17 (2010) 462-471. PMID: 20595315.  PMC2995651.

Visweswaran S, Angus DC, Hsieh M, Weissfeld L, Yealy D, Cooper GF.  Learning patient-specific predictive models from clinical data.  Journal of Biomedical Informatics 43 (2010) 669-685.  PMID: 20450985 PMCID: PMC2933959.

Visweswaran S, Cooper GF.  Learning instance-specific predictive models. Journal of Machine Learning Research (2010) Dec; 11:3333-3369.  PMID; 25045325 PMC4102007 http://jmlr.csail.mit.edu/papers/volume11/visweswaran10a/visweswaran10a.pdf  

Shen Y, Cooper GF. Multivariate Bayesian modeling of known and unknown causes of events – An application to biosurveillance.  Journal of Computer Methods and Programs in Biomedicine 107 (2010) 436-446. doi:10.1016/j.cmpb.2010.11.015  PMID: 21195503. Publication not directly supported by NIH.

Cooper GF, Hennings-Yeomans P, Visweswaran S, Barmada M. An efficient Bayesian method for predicting clinical outcomes from genome-wide data. In: Proceedings of the Annual Symposium of the American Medical Informatics Association (2010) 127-131. PMID: 21346951 PMC3041321

Visweswaran S, Mezger J, Clermont G, Hauskrecht M, Cooper GF. Identifying deviations from usual medical care using a statistical approach. In: Proceedings of the Annual Symposium of the American Medical Informatics Association (2010) 827-831. PMID: 21347094 PMC3041340

Hauskrecht M, Valko M, Batal I, Clermont G, Visweswaran S, Cooper GF. Conditional outlier detection for clinical alerting. In: Proceedings of the Annual Symposium of the American Medical Informatics Association (2010) 286-290. PMID: 21346986 PMC3041310

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, Neill DB, Cooper GF. On the robustness of Bayesian network based spatial event surveillance. International Journal of Approximate Reasoning, 51 (2010) p 224-239.  http://dx.doi.org/10.1016/j.ijar.2009.01.001.

2009

Neill DB, Cooper GF, Das K, Jiang X, Schneider J. Bayesian Networks Scan Statistics for Multivariate Pattern Detection. In: Glaz J, Pozdnyakov V, Wallenstein S, editors. Scan Statistics - Methods and Applications. Birkhauser, 2009.

Jiang X, Wallstrom G, Cooper GF, Wagner MM. Bayesian prediction of an epidemic curve. J Biomed Inform. 2009 Feb; 42(1):90-9. doi: 10.1016/j.jbi.2008.05.013. Epub 2008 Jun 13.  PMID: 18593605.  

Jiang X, Neill DB, Cooper GF.  Generalized AMOC curves for evaluation and improvement of event surveillance. In: Proceedings of the Annual Symposium of the American Medical Informatics Association (2009) 281-285. PMID: 20351865. PMC2815453.

Shen Y, Cooper GF.  Bayesian modeling of unknown disease for biosurveillance. In: Proceedings of the Annual Symposium of the American Medical Informatics Association (2009) 589-593.  PMID: 20351923 PMC2815446.

Shen Y, Cooper GF.  A New Prior for Bayesian Anomaly Detection—Application to Biosurveillance.  Accepted by Methods of Information in Medicine July 2009 (to appear).

2008

Jiang X, Cooper GF. A temporal method for outbreak detection using a Bayesian networks. In: Proceedings of the International Symposium on Disease Surveillance. 5(2) 105, 2008.

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.

Shen Y, Adamou C, Dowling JN, Cooper GF. Estimating the joint disease outbreak-detection time when an automated biosurveillance system is augmenting traditional clinical case finding. Journal of Biomedical Informatics 41 (2008) :224-231.  PMID:  18194876. Publication not directly supported by NIH.

Dara J, Dowling JN, Travers D, Cooper GF, Chapman WW. Evaluation of preprocessing techniques for chief complaint classification. Journal of Biomedical Informatics 41 (2008) 612-623.  PMID: 18166502

Sutovsky P, Cooper GF. Hierarchical explanation of inference in Bayesian networks that represent a population of independent agents. In: Proceedings of the European Conference on Artificial Intelligence (2008) 214-218.

Valko M, Cooper G, Seybert A, Visweswaran S, Hauskrecht M.  Conditional anomaly detection methods for patient-management alert systems.  In: Proceedings of the Workshop on Machine Learning in Health Care Applications of the 25th International Conference on Machine Learning (2008).

Wadhwa R, Fridsma DS, Saul MI, Penrod LE, Visweswaran S, Cooper GF, Chapman W. Analysis of a failed clinical decision support system for management of congestive heart failure. In: Proceedings of the Annual Symposium of the American Medical Informatics Association (2008) 773-777. PMID:18999183 PMC2655961

Wadhwa R, Fridsma DB, Saul MI, Penrod LE, Visweswaran S, Cooper GF, Chapman W. Analysis of a failed clinical decision support system for management of congestive heart failure. In: Proceedings of the Fall Symposium of the American Medical Informatics Association (Nov 2008) 773-7. PMID: 18999183. PMCID: PMC2655961.

2007

Hogan WR, Cooper GF, Wallstrom GL, Wagner MM, Depinay JM. The Bayesian aerosol release detector: an algorithm for detecting and characterizing outbreaks caused by an atmospheric release of Bacillus anthracis. Stat Med. 2007 Dec 20;26(29):5225-52. PMID: 17948918.

Rolka H, Burkom H, Cooper GF, Kulldorff M, Madigan D, Wong WK. Issues in applied statistics for public health bioterrorism surveillance using multiple data streams: Research needs.
Statistics in Medicine 26 (2007) 1834-1856. PMID: 17221940

Shen Y, Cooper GF. A Bayesian Biosurveillance Method that Models Unknown Outbreak Diseases. Proceedings of the Conference on Intelligence and Security Informatics: Biosurveillance, (2007) 209-215.

Hauskrecht M, Valko M, Kveton B, Visweswaran S, Cooper GF. Evidence-based anomaly detection in clinical domains. In: Proceedings of the Fall Symposium of the American Medical Informatics Association (2007) 319-232.  PMID:  18693850. PMC2655918

Jiang X, Cooper GF. A recursive algorithm for spatial cluster detection. In: Proceedings of the Fall Symposium of the American Medical Informatics Association (2007) 369-373. PMID:  18693860. PMC2655859.

2006

Yoo C, Cooper GF, Schmidt M. A controlled study to evaluate a computer-based microarray experiment-design-recommendation system for gene-regulation pathway discovery. Journal of Biomedical Informatics 39 (2006) 126-146.  PMCD: 16203178

Mani S, Cooper GF, Spirtes P. A theoretical study of Y structures for causal discovery. In: Proceedings of the Conference on Uncertainty in Artificial Intelligence (2006).

2005

Visweswaran S, Cooper GF. Instance-specific Bayesian model averaging for classification. In: Proceedings of the Neural Information Processing Systems Conference (NIPS) (2005) 1449-1456.

Middleton B, Hammond WE, Brennan PF, Cooper GF. Accelerating U.S. EHR adoption: How to get there from here. Journal of the American Medical Informatics Association 12 (2005):13-19.  PMID: 15492028  PMC543821

Auble TE, Hsieh M, Gardner W, Cooper GF, Stone RA, McCausland JB, Yealy DM. A prediction rule to identify low-risk patients with heart failure. Academic Emergency Medicine 12 (2005) 514-521.  PMID: 15930402

Cooper GF, Abraham V, Aliferis CF, Aronis JM, Buchanan BG, Caruana R, Fine MJ, Janosky JE, Livingston G, Mitchell T, Monti S, Spirtes P. Predicting dire outcomes of patients with community acquired pneumonia. Journal of Biomedical Informatics 38 (2005) 347-366.  PMID:  16198995

Wong WK, Cooper GF, Dash DH, Levander JD, Dowling J, Hogan WR, Wagner MM. Bayesian biosurveillance using multiple data streams. Morbidity and Mortality Weekly Report 54 (2005) 63-69.  PMID: 16177695

Wong WK, Moore A, Cooper GF, Wagner MW. What's Strange About Recent Events (WSARE): An algorithm for the early detection of disease outbreaks. Journal of Machine Learning Research 6 (2005) 1961-1998.  PMID: 12791781

Neill DB, Moore AW, Cooper GF. A Bayesian spatial scan statistic. In: Proceedings the Neural Information Processing Systems Conference (NIPS) (2005).

Cooper GF, Visweswaran S. Deriving the expected utility of a predictive model when the utilities are uncertain. In: Proceedings of the Annual Symposium of the American Medical Informatics Association (2005) 161-165.  PMID:  16779022

2004

Yoo C, Cooper GF. An evaluation of a system that recommends microarray experiments to perform to discover gene-regulation pathways. Artificial Intelligence in Medicine 31 (2004) 169-182.  PMID:  1529293

Dash D, Cooper GF. Model averaging for prediction with discrete Bayesian networks. Journal of Machine Learning Research (2004) 1177-1203. 

Cooper GF, Dash DH, Levander JD, Wong WK, Hogan WR, Wagner MM.  Bayesian biosurveillance of disease outbreaks.  In:  Proceedings of the Conference on Uncertainty in Artificial Intelligence (2004) 94-103.

Mani S, Cooper GF.  Causal discovery using a Bayesian local causal discovery algorithm.  In:  Proceedings of the World Congress on Medical Informatics (2004) 731-735.  PMID:  15360909

2003

Chapman WW, Cooper GF, Hanbury P, Chapman BE, Harrison LH, Wagner MM. Creating a text classifier to detect radiology reports describing mediastinal findings associated with inhalational anthrax and other disorders. Journal of the American Medical Informatics Association 10 (2003) 494-503.  PMID: 12807805  PMC212787

Wong WK, Moore A, Cooper G, Wagner M. WSARE: What's Strange About Recent Events? Journal of Urban Health 80 (2003) 66-75.  PMID: 12791781 

Wong WK, Moore A, Cooper GF, Wagner MM., Bayesian network anomaly pattern detection for disease outbreaks. In: Proceedings of the International Conference on Machine Learning (ICML) (2003).

Visweswaran S, Hanbury P, Saul M, Cooper GF. Detecting adverse drug events in discharge summaries using variations on the simple Bayes model. In: Proceedings of the Annual Symposium of the American Medical Informatics Association (2003) 689-693. PMID: 14728261.

Yoo C, Cooper GF. A computer-based microarray experiment design-system for gene-regulation pathway discovery. In: Proceedings of the Annual Symposium of the American Medical Informatics Association (2003) 733-737.  PMID:  14728270

2002

Chapman WW, Bridewell W, Hanbury P, Cooper GF, Buchanan BG. A simple algorithm for identifying negated findings and diseases in discharge summaries. Journal of Biomedical Informatics 34 (2002) 301-310.  PMID: 12123149

Yoo C, Thorsson V, Cooper GF.  Discovery of causal relationships in a gene-regulation pathway from a mixture of experimental and observational DNA microarray data. In: Proceedings of the Pacific Symposium in Biocomputing (2002) 498-509.  PMID:  11928502

Wong WK, Moore AM, Cooper GF, Wagner MM.  Rule-based anomaly pattern detection for detecting disease outbreaks.  In: Proceedings of National Conference on Artificial Intelligence (AAAI) (2002) 217-223.

Kayaalp M, Cooper GF.  A Bayesian network scoring metric that is based on globally uniform parameter priors.  In: Proceedings of the Conference on Uncertainty in Artificial Intelligence (2002), 251-258.

Dash D, Cooper GF. Exact model averaging with naive Bayesian classifiers. In: Proceedings of the International Conference on Machine Learning (2002) 91-98.

Yoo C, Cooper GF.  Discovery of gene-regulation pathways using local causal search.  In: Proceedings of the Annual Symposium of the American Medical Informatics Association (2002) 914-918.  PMID:  12463958

2001

Mani S, Cooper GF.  A simulation study of three related causal data mining algorithms. In: Proceedings of the International Workshop on Artificial Intelligence and Statistics (2001) 73-80.

Kayaalp M, Cooper GF, Clermont G.  Predicting with variables constructed from temporal sequences. In: Proceedings of the International Workshop on Artificial Intelligence and Statistics (2001) 220-225.

Scheines R, Cooper GF, Yoo C, Chu T.  Piecewise linear instrumental variable estimation of causal influence.  In: Proceedings of the International Workshop on Artificial Intelligence and Statistics (2001) 286-291.

Chapman WW, Bridewell W, Hanbury P, Cooper GF, Buchanan BG.  Evaluation of negation phrases in narrative clinical reports. In: Proceedings of the Annual Symposium of the American Medical Informatics Association (2001) 105-109.   PMID:  11825163

2000

Arora A, Cooper GF, Krishnan R, Padman R. IBIZA: E-market infrastructure for custom-built information products. Information Systems Frontiers (2000) 65-84.  

Cooper GF. A Bayesian method for causal modeling and discovery under selection. In: Proceedings of the Conference on Uncertainty in Artificial Intelligence (2000) 98-106.

Mani S, Cooper GF. Causal discovery from medical textual data. In: Proceedings of the Annual Symposium of the American Medical Informatics Association (2000) 542-546.  PMID:  11079942

Kayaalp MM, Cooper GF, Clermont G. Predicting ICU motality: A comparison of stationary and nonstationary temporal models. In: Proceedings of the Annual Symposium of the American Medical Informatics Association (2000) 418-422.   PMID:  11079917

1999

Glymour C, Cooper GF. (Eds.). Computation, Causation, and Discovery (MIT Press, Cambridge, MA, 1999). Note: This is an edited book and was not peer reviewed. [cited over 350 times]

Monti S, Cooper GF. A Bayesian network classifier that combines a finite mixture model and a naïve Bayes model. In: Proceedings of the Conference on Uncertainty in Artificial Intelligence (1999) 447-456

Cooper GF, Yoo C.  Causal discovery from a mixture of experimental and observational data. In: Proceedings of the Conference on Uncertainty in Artificial Intelligence (1999) 116-125.   PMID:  12463958

Mani S, Cooper GF.  A study in causal discovery from population-based infant birth and death records. In: Proceedings of the Annual Symposium of the American Medical Informatics Association (1999) 315-319.  PMID: 10566372

Spirtes P, Cooper GF. An experiment in causal discovery using a pneumonia database. In: Proceedings of International Workshop in Artificial Intelligence and Statistics (1999) 162-168.

Aronis J, Cooper GF, Kayaalp M, Buchanan BG. Identifying patient subgroups with simple Bayes. In: Proceedings of the Annual Symposium of the American Medical Informatics Association (1999) 658-662.  PMID:  10566441

Monti S, Cooper GF. A latent variable model for multivariate discretization. Proceedings of International Workshop in Artificial Intelligence and Statistics (1999) 249-254

1998

Cooper GF, Miller RA. An experiment comparing lexical and statistical methods for extracting MeSH terms from clinical free text. Journal of the American Medical Informatics Association 5 (1998) 62-75.  PMID: 9452986  PMC61276

Monti S, Cooper GF. A multivariate discretization method for learning Bayesian networks from mixed data. In: Proceedings of the Conference on Uncertainty in Artificial Intelligence (1998) 404-413.

Aliferis CF, Cooper GF. Temporal representation design principles: An assessment in the domain of liver transplantation. In: Proceedings of the Annual Symposium of the American Medical Informatics Association (1998) 170-174.  PMID:  9929204

Monti S, Cooper GF. The impact of modeling the dependencies among patient findings on classification accuracy and calibration. In: Proceedings of the Annual Symposium of the American Medical Informatics Association (1998) 592-596.  PMID:  9929288

Cooper GF, Buchanan BG, Kayaalp M, Saul M, Vries JK. Using computer modeling to help identify patient subgroups in clinical data repositories. In: Proceedings of the Annual Symposium of the American Medical Informatics Association (1998) 180-184.  PMID:  9929206

1997

Citro G, Banks G, Cooper G. INKBLOT: A neurological diagnostic decision support system integrating causal and anatomical knowledge. Artificial Intelligence in Medicine 10 (1997) 257-267.  PMID:  9232188

Cooper GF. A simple algorithm for efficiently mining observational databases for causal relationships. Journal of Data Mining and Knowledge Discovery 1 (1997) 203-224.

Cooper GF, Aliferis CF, Ambrosino R, Aronis J, Buchanan BG, Caruana R, Fine MJ, Glymour C, Gordon G, Hanusa BH, Janosky J, Meek C, Mitchell T, Richardson T, Spirtes, P. An evaluation of machine-learning methods for predicting pneumonia mortality. Artificial Intelligence in Medicine 9 (1997) 107-138.  PMID: 9040894

Aliferis CF, Cooper GF, Pollack ME, Buchanan BG, Wagner MM. Representing and developing temporally abstracted knowledge as a means towards facilitating time modeling in medical decision support systems. Computers in Biology and Medicine 27 (1997) 411-434.  PMID:  9397342

1996

Aliferis CF, Cooper GF, Miller RA, Buchanan BG, Bankowitz R, Giuse N. A temporal analysis of QMR. Journal of the American Medical Informatics Association 3 (1996) 79–91.  PMID: 8750392

Monti S, Cooper GF. Bounded recursive decomposition: A search-based method for belief-network inference under limited resources. International Journal of Approximate Reasoning 15 (1996) 49-75.

Aliferis CF, Cooper GF. A structurally and temporally extended Bayesian belief network model: Definitions, properties, and modeling techniques. In: Proceedings of Conference on Uncertainty in Artificial Intelligence (1996) 28-39.

Hashem AI, Cooper GF. Human causal discovery from observational data. In: Proceedings of the Annual Symposium of the American Medical Informatics Association (1996) 27-31.  PMID:  894721

Wagner MM, Overhage JM, Rodriguez E, Cooper GF. Representing CARE rules in a decision-theoretic formalism. In: Proceedings of the Annual Conference of the American Medical Informatics Association (1996) 582-586.  PMID:  8947733

Monti S, Cooper GF. Learning Bayesian belief networks with neural network estimators. In: Proceedings of the Conference on Neural Information Processing Systems (1996).

1995

Cooper GF. A method for learning belief networks that contain hidden variables. Journal of Intelligent Information Systems 4 (1995) 1–18.

Lowe HJ, Buchanan BG, Cooper GF, Vries JK. Building a medical multimedia database to integrate clinical information: An application of high-performance computing and communications technology. Bulletin of the Medical Library Association 83 (1995) 57-64.  PMID: 7703940  PMC225998

Aliferis CF, Cooper GF, Buchanan BG, Miller RA, Bankowitz R, Giuse N. Temporal reasoning abstractions in QMR. In: Proceedings of MEDINFO (1995) 847–857. PMID:  8591343

Aliferis CF, Cooper GF. A new formalism for temporal modeling in medical decision-support systems. In:   Proceedings of the Symposium on Computer Applications in Medical Care (1995) 213–217.  PMID;  8563270

Ambrosino R, Buchanan BG, Cooper GF, Fine MJ. The use of misclassification costs to learn rule-based decision support models for cost-effective hospital admission strategies. In: Proceedings of the Symposium on Computer Applications in Medical Care (1995) 304–308.  PMID:  8563290

Cooper GF.  Causal discovery from data in the presence of selection bias. In: Proceedings of the Workshop on Artificial Intelligence and Statistics (1995) 140–150.

Lowe HJ, Buchanan BG, Cooper GF, Kaplan B, Vries JK. Image Engine: An integrated multimedia clinical information system. In: Proceedings of MEDINFO (1995) 421-425.  PMID:  8591216

Wagner MM, Cooper GF. Evaluation of a belief-network-based reminder system that learns from utility feedback. In: Proceedings of the Symposium on Computer Applications to Medical Care (1995) 666–672.  PMID:  8563370

1994

Aliferis CF, Cooper GF. An evaluation of an algorithm for inductive learning of Bayesian belief networks using simulated data sets. In: Proceedings of the Conference on Uncertainty in Artificial Intelligence (1994) 8–14.   PMID:  7950017

Aliferis CF, Cooper GF, Bankowitz R. A temporal analysis of QMR: Abstracted temporal representation and reasoning and initial assessment of diagnostic performance trade-offs. In: Proceedings of the Symposium on Computer Applications in Medical Care (1994) 709–716.

1993

Suermondt HJ, Cooper GF. An evaluation of explanations of probabilistic inference. Computers and Biomedical Research 26 (1993) 242–254.  PMID: 8325004

Aliferis CF, Chao E, Cooper GF. Data Explorer: A prototype expert system for statistical analysis. In: Proceedings of the Symposium on Computer Applications in Medical Care (1993) 389–393.  PMID: 8130501

Cooper GF. A Bayesian method for learning belief networks that contain hidden variables. Proceedings of the Workshop on Knowledge Discovery in Databases (1993) 112–124

Cooper GF, Owens G. Patient simulation using seamless digital video. In: Proceedings of the Symposium on Computer Applications in Medical Care (1993) 796-800.  PMID: 8130587

Wagner MM, Cooper GF. Decision-theoretic information pretrieval: A generalization of reminding. In: Proceedings of the Symposium on Computer Applications in Medical Care (1993) 512–516.  PMID:  8130526.

1992

Cooper GF, Herskovits EH. A Bayesian method for the induction of probabilistic networks from data. Machine Learning 9 (1992) 309–347.

Wagner MM, Cooper GF. Evaluation of a Meta-1-based automatic indexing method for medical documents. Computers and Biomedical Research 25 (1992) 336–350.  PMID: 1511595

Miller RA, Gieszczykiewicz FM, Vries JK, Cooper GF. CHARTLINE: Providing bibliographic references relevant to patient charts using the UMLS Metathesaurus knowledge sources. In: Proceedings of the Symposium on Computer Applications in Medical Care (1992) 86–90.  PMID: 1483014

1991

Middleton B, Shwe MA, Heckerman DE, Henrion M, Horvitz EJ, Lehmann H, Cooper GF. Probabilistic diagnosis using a reformulation of the INTERNIST-1/QMR knowledge base — Evaluation of diagnostic performance. Methods of Information in Medicine 30 (1991) 256–267.   PMID: 1762579

Shiffman S, Wu AW, Poon AD, Lane CD, Middleton BF, Miller RA, Masarie Jr FE, Cooper GF, Shortliffe, EH, Fagan LM. Building a speech interface to a medical diagnostic system. IEEE Expert 6 (1991) 41–49.

Shwe MA, Cooper GF. An empirical analysis of likelihood-weighting simulation on a large, multiply-connected belief network. Computers and Biomedical Research 24 (1991) 453–475.  PMID: 1743005

Suermondt HJ, Cooper GF. Initialization for the method of conditioning in Bayesian belief networks. Artificial Intelligence 50 (1991) 83–94.

Suermondt HJ, Cooper GF. A combination of exact algorithms for inference on Bayesian belief networks. International Journal of Approximate Reasoning 5 (1991) 521–542.

Cooper GF, Herskovits EH. A Bayesian method for constructing Bayesian belief networks from databases. In: Proceedings of the Conference on Uncertainty in Artificial Intelligence (1991) 86–94.

Herskovits EH, Cooper GF. Algorithms for Bayesian belief-network precomputation. Methods of Information in Medicine 30 (1991) 81–89.  PMID:  1857253

Shwe MA, Middleton B, Heckerman DE, Henrion M, Horvitz EJ, Lehmann H, Cooper GF. Probabilistic diagnosis using a reformulation of the INTERNIST-1/QMR knowledge base - The probabilistic model and inference algorithms. Methods of Information in Medicine 30 (1991) 241–255.  PMID: 1762578

1990

Chavez RM, Cooper GF. Hypermedia and randomized algorithms for medical expert systems.  Computer Methods and Programs in Biomedicine 32 (1990) 5–16.  PMID: 2205445

Cooper GF. The computational complexity of probabilistic inference using Bayesian belief networks. Artificial Intelligence 42 (1990) 393–405.

Suermondt HJ, Cooper GF. Probabilistic inference in multiply connected belief networks using loop cutsets. International Journal of Approximate Reasoning 4 (1990) 283–306.

Chavez RM, Cooper GF. A randomized approximation algorithm for probabilistic inference on Bayesian belief networks. Networks 20 (1990) 661–685.

Chavez RM, Cooper GF. KNET: Integrating hypermedia and normative Bayesian modeling. In: Uncertainty in Artificial Intelligence 4 (North-Holland, Amsterdam, 1990) 339–349.

Herskovits EH, Cooper GF. Kutató: An entropy-driven system for the construction of probabilistic expert systems from databases. In: Proceedings of the Conference on Uncertainty in Artificial Intelligence (1990) 54–62.

Shwe MA, Cooper GF. An empirical analysis of likelihood-weighting simulation on a large, multiply-connected belief network. In: Proceedings of the Conference on Uncertainty in Artificial Intelligence (1990) 498–508.

Shwe MA, Middleton B, Heckerman DE, Henrion M, Horvitz EJ, Lehmann H, Cooper GF. A probabilistic reformulation of the Quick Medical Reference System. In: Symposium on Computer Applications in Medical Care  (1990) 790–794. PMID: 1762578

Suermondt HJ, Cooper GF, Heckerman DE. A combination of cutset conditioning and clique-tree propagation in the Pathfinder system. In: Proceedings of the Conference on Uncertainty in Artificial Intelligence (1990) 86–90.

1989

Chin HL, Cooper GF. Case-based tutoring from a medical knowledge base. Computer Methods and Programs in Biomedicine 30 (1989) 185–198.  PMID: 2684491

Beinlich IA, Suermondt HJ, Chavez RM, Cooper GF. The ALARM monitoring system: A case study with two probabilistic inference techniques for belief networks. In: Proceedings of the Conference on Artificial Intelligence in Medical Care, 1989.

Chavez RM, Cooper GF. An empirical evaluation of a randomized algorithm for probabilistic inference. In: Proceedings of the Workshop on Uncertainty in Artificial Intelligence (1989) 60–70.

Chin HL, Cooper GF. Stochastic simulation of causal Bayesian models. In: Uncertainty in Artificial Intelligence 3 (North-Holland, Amsterdam, 1989) 129–147.

Cooper GF. An algorithm for computing probabilistic propositions. In: Uncertainty in Artificial Intelligence 3 (North-Holland, Amsterdam, 1989) 1–14.

Horvitz EJ, Suermondt HJ, Cooper GF. Bounded conditioning: Flexible inference for decisions under scarce resources. In: Proceedings of the Workshop on Uncertainty in Artificial Intelligence (1989) 181–193.

Horvitz EJ, Cooper GF, Heckerman DE. Reflection and action under scarce resources: Theoretical principles and empirical study. In: Proceedings of the International Joint Conference on Artificial Intelligence (1989) 1121–1127.

1988

Cooper GF. A method for using belief networks as influence diagrams. In: Proceedings of the Workshop on Uncertainty in Artificial Intelligence (1988) 55–63.

1986

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

1984

Cooper GF. NESTOR: A Computer-Based Medical Diagnostic Aid that Integrates Causal and Probabilistic Knowledge (doctoral dissertation, Stanford University, 1984). [cited over 260 times, according to Google Scholar]
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