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United States

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Papers

Aronis JM, Ye Y, Espino J, Michaels MG, Hochheiser H, Cooper GF. (2026). An evaluation of a Bayesian method to track outbreaks of known and novel influenza-like illnesses. Scientific reports

Sun Y, Yu R, Bao R, Xie Y, Ye Y, Jia X. Domain-Adaptive Continual Meta-Learning for Modeling Dynamical Systems: An Application in Environmental Ecosystems. Proceedings of the ... SIAM International Conference on Data Mining. SIAM International Conference on Data Mining, (2025)

Gao Y, Bao R, Ji Y, Sun Y, Song C, Ferraro JP, Ye Y. (2025). Transfer Learning with Clinical Concept Embeddings from Large Language. AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science, (2025)

Aronis JM, Ye Y, Espino J, Hochheiser H, Michaels MG, Cooper GF. (2024). A Bayesian System to Detect and Track Outbreaks of Influenza-Like Illnesses Including Novel Diseases. JMIR public health and surveillance

Sun Y, Gao Y, Bao R, Cooper GF, Espino J, Hochheiser H, Michaels MG, Aronis JM, Song C, Ye Y. (2024). Online Transfer Learning for RSV Case Detection. Proceedings. IEEE International Conference on Healthcare Informatics, (2024)

Gao Y, Mazurek JM, Li Y, Blackley D, Weissman DN, Burton SV, Amin W, Landsittel D, Becich MJ, Ye Y. (2023). Industry, occupation, and exposure history of mesothelioma patients in the U.S. National Mesothelioma Virtual Bank, 2006-2022. Environmental research, (230)

Ji Y, Gao Y, Bao R, Li Q, Liu D, Sun Y, Ye Y. (2023). Prediction of COVID-19 Patients' Emergency Room Revisit using Multi-Source Transfer Learning. IEEE International Conference on Healthcare Informatics. IEEE International Conference on Healthcare Informatics, (2023)

Bernstam EV, Shireman PK, Meric-Bernstam F, N Zozus M, Jiang X, Brimhall BB, Windham AK, Schmidt S, Visweswaran S, Ye Y, Goodrum H, Ling Y, Barapatre S, Becich MJ. (2021). Artificial intelligence in clinical and translational science: Successes, challenges and opportunities. Clinical and translational science

Jackson BR, Ye Y, Crawford JM, Becich MJ, Roy S, Botkin JR, de Baca ME, Pantanowitz L. (2021). The Ethics of Artificial Intelligence in Pathology and Laboratory Medicine: Principles and Practice. Academic pathology, (8)

Ye Y, Barapatre S, Davis MK, Elliston KO, Davatzikos C, Fedorov A, Fillion-Robin JC, Foster I, Gilbertson JR, Lasso A, Miller JV, Morgan M, Pieper S, Raumann BE, Sarachan BD, Savova G, Silverstein JC, Taylor DP, Zelnis JB, Zhang GQ, Cuticchia J, Becich MJ. (2021). Open-source Software Sustainability Models: Initial White Paper From the Informatics Technology for Cancer Research Sustainability and Industry Partnership Working Group. Journal of medical Internet research, 23(12)

Aronis JM, Ferraro JP, Gesteland PH, Tsui F, Ye Y, Wagner MM, Cooper GF. (2020). A Bayesian approach for detecting a disease that is not being modeled. PLOS ONE, 15(2)

Y Ye, RD Boyce, MK Davis, K Elliston, C Davatzikos, A Fedorov, JC Fillion-Robin, I Foster, J Gilbertson, M Heiskanen, J Klemm, A Lasso, JV Miller, M Morgan, S Pieper, B Raumann, B Sarachan, G Savova, JC Silverstein, D Taylor, J Zelnis, GQ Zhang, MJ Becich. (2019). Open Source Software Sustainability Models: Initial White Paper from the Information Technology for Cancer Research Sustainability and Industry Partnership Work Group. arXiv

Millett NE, Aronis JM, Wagner MM, Tsui F, Ye Y, Ferraro JP, Haug PJ, Gesteland PH, Cooper GF. (2019). The design and evaluation of a Bayesian system for detecting and characterizing outbreaks of influenza. Online journal of public health informatics, 11(2)

Jeffrey P. Ferraro, Ye Ye, Per H. Gesteland, Peter J. Haug, Fuchiang Tsui, Gregory F. Cooper, Rudy Van Bree, Thomas Ginter, Andrew J. Nowalk, Michael Wagner. (2017). The effects of natural language processing on cross-institutional portability of influenza case detection for disease surveillance. Applied Clinical Informatics, 8(2)

John M Aronis, Nicholas E Millett, Michael M Wagner, Fuchiang Tsui, Ye Ye, Jeffrey Ferraro, Peter J Haug, Gregory F Cooper. (2017). Detecting Overlapping Outbreaks of Influenza. Online Journal of Public Health Informatics, 9(1)

Tsui F, Ye Y, Ruiz V, Cooper GF, Wagner MM. (2018). Automated influenza case detection for public health surveillance and clinical diagnosis using dynamic influenza prevalence method. Journal of public health (Oxford, England), 40(4)

Aronis JM, Millett NE, Wagner MM, Tsui F, Ye Y, Ferraro JP, Haug PJ, Gesteland PH, Cooper GF. (2017). A Bayesian system to detect and characterize overlapping outbreaks. Journal of biomedical informatics, (73)

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. (2017). A study of the transferability of influenza case detection systems between two large healthcare systems. PloS one, 12(4)

John Aronis, Nicholas Millett, Michael Wagner, Fuchiang (Rich) Tsui, Ye Ye, Gregory Cooper. (2016). A Method for Detecting and Characterizing Multiple Outbreaks of Infectious Diseases. Online Journal of Public Health Informatics

Ruhsary Rexit, Fuchiang Rich Tsui, Jeremy Espino, Panos K Chrysanthis, Sahawut Wesaratchakit, Ye Ye. (2015). An analytics appliance for identifying (near) optimal over-the-counter medicine products as health indicators for influenza surveillance. Information Systems, (48)

López Pineda A, Ye Y, Visweswaran S, Cooper GF, Wagner MM, Tsui FR. (2015). Comparison of machine learning classifiers for influenza detection from emergency department free-text reports. Journal of Biomedical Informatics, (58)

Ye Y, Tsui FR, Wagner M, Espino JU, Li Q. (2014). Influenza detection from emergency department reports using natural language processing and Bayesian network classifiers. Journal of the American Medical Informatics Association : JAMIA, 21(5)

Tang L, Lyles RH, Ye Y, Lo Y, King CC. (2013). Extended Matrix and Inverse Matrix Methods Utilizing Internal Validation Data When Both Disease and Exposure Status Are Misclassified. Epidemiologic Methods, 2(1)

Sisi Lu, Ye Ye, Rich Tsui, Howard Su, Ruhsary Rexit, Sahawut Wesaratchakit, Xiaochu Liu, Rebecca Hwa. (2013). Domain ontology-based feature reduction for high dimensional drug data and its application to 30-day heart failure readmission prediction. 9th IEEE International Conference on Collaborative Computing: Networking, Applications and Worksharing

R. Rexit, F. Tsui, J. Espino, S. Wesaratchakit, Ye Ye and P. K. Chrysanthis. (2012). Using a distributed search engine to identify optimal product sets for use in an outbreak detection system. 8th International Conference on Collaborative Computing: Networking, Applications and Worksharing (CollaborateCom)

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