Abstract
Predictive modeling is the application of supervised machine learning methods to risk assessment and stratification, diagnosis, prognosis and therapeutics. With increasing availability of big biomedical data, predictive modeling is increasingly applied to leverage the data for clinical medicine, public health, and biomedical research. This chapter will describe key methods and application examples in the development, validation, dissemination and deployment of clinical predictive models.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Moons KGM, Altman DG, Vergouwe Y, Royston P. Prognosis and prognostic research: application and impact of prognostic models in clinical practice. Br Med J. 2009;338:b606.
Wilson PWF, D’Agostino RB, Levy D, Belanger AM, Silbershatz H, Kannel WB. Prediction of coronary heart disease using risk factor categories. Circulation. 1998;97:1837–47.
Jessen MK, Mackenhauer J, Hvass AMSW, Ellermann-Eriksen S, Skibsted S, Kirkegaard H, et al. Prediction of bacteremia in the emergency department: an external validation of a clinical decision rule. Eur J Emerg Med. 2016;23:44–9.
Shapiro NI, Wolfe RE, Wright SB, Moore R, Bates DW. Who needs a blood culture? A prospectively derived and validated prediction rule. J Emerg Med. 2008;35:255–64.
LaHaye SA, Gibbens SL, Ball DGA, Day AG, Olesen JB, Skanes AC. A clinical decision aid for the selection of antithrombotic therapy for the prevention of stroke due to atrial fibrillation. Eur Heart J. 2012;33:2163–71.
Brownstein JS, Freifeld CC, Chan EH, Keller M, Sonricker AL, Mekaru SR, et al. Information technology and global surveillance of cases of 2009 H1N1 influenza. N Engl J Med. 2010;362:1731–5.
Steyerberg EW. Clinical prediction models: a practical approach to development, validation, and updating. New York: Springer; 2008.
Clark GM, Zborowski DM, Culbertson JL, Whitehead M, Savoie M, Seymour L, et al. Clinical utility of epidermal growth factor receptor expression for selecting patients with advanced non-small cell lung cancer for treatment with erlotinib. J Thorac Oncol. 2006;1:837–46.
Sechidis K, Papangelou K, Metcalfe PD, Svensson D, Weatherall J, Brown G. Distinguishing prognostic and predictive biomarkers: an information theoretic approach. Bioinformatics. 2018;1:12.
Labarère J, Bertrand R, Fine MJ. How to derive and validate clinical prediction models for use in intensive care medicine. Intensive Care Med. 2014;40:513–27.
Hendriksen JMT, Geersing GJ, Moons KGM, De Groot JAH. Diagnostic and prognostic prediction models. J Thromb Haemost. 2013;11:129–41.
Alba AC, Agoritsas T, Walsh M, Hanna S, Iorio A, Devereaux PJ, et al. Discrimination and calibration of clinical prediction models: users’ guides to the medical literature. J Am Med Assoc. 2017;318:1377–84.
Collart F, Feier H, Kerbaul F, Mouly-Bandini A, Riberi A, Mesana TG, et al. Valvular surgery in octogenarians: operative risks factors, evaluation of Euroscore and long term results. Eur J Cardio Thoracic Surg. 2005;27:276–80.
Nashef SAM, Roques F, Sharples LD, Nilsson J, Smith C, Goldstone AR, et al. Euroscore II. Eur J Cardio Thoracic Surg. 2012;41:734–45.
Guyon I, Elisseeff A. An introduction to variable and feature selection. J Mach Learn Res. 2003;3:1157–82.
Zeng Y, Luo J, Lin S. Classification using Markov blanket for feature selection. IEEE International Conference on Granular Computing. 2009. p. 743–7.
Aliferis CF, Statnikov A, Tsamardinos I, Mani S, Koutsoukos XD. Local causal and Markov blanket induction for causal discovery and feature selection for classification part I: algorithms and empirical evaluation. J Mach Learn Res. 2010;11:171–234.
Aliferis CF, Statnikov A, Tsamardinos I, Mani S, Koutsoukos XD. Local causal and Markov blanket induction for causal discovery and feature selection for classification part II: analysis and extensions. J Mach Learn Res. 2010;11:235–84.
Margaritis D, Thrun S. Bayesian network induction via local neighborhoods. Proc Adv Neural Inf Process Syst. 2000:505–11.
Tsamardinos I, Aliferis CF, Statnikov AR, Statnikov E. Algorithms for large scale Markov blanket discovery. Proc Florida Artif Intell Res Soc. 2003:376–80.
Aliferis CF, Tsamardinos I, Statnikov A. HITON: a novel Markov blanket algorithm for optimal variable selection. AMIA Annu Symp Proc. 2003;2003:21–5.
Tsamardinos I, Brown LE, Aliferis CF. The max-min hill-climbing Bayesian network structure learning algorithm. Mach Learn. 2006;65:31–78.
Strobl EV, Visweswaran S. Markov blanket ranking using kernel-based conditional dependence measures. arXiv Prepr arXiv14020108. 2014.
Hoeting JA, Madigan D, Raftery AE, Volinsky CT. Bayesian model averaging: a tutorial. Stat Sci. 1999;14:382–401.
Madigan D, Raftery AE. Model selection and accounting for model uncertainty in graphical models using Occam’s window. J Am Stat Assoc. 1994;89:1535–46.
Yeung KY, Bumgarner RE, Raftery AE. Bayesian model averaging: development of an improved multi-class, gene selection and classification tool for microarray data. Bioinformatics. 2005;21:2394–402.
Wei W, Visweswaran S, Cooper GF. The application of naive Bayes model averaging to predict Alzheimer’s disease from genome-wide data. J Am Med Inform Assoc. 2011;18:370–5.
Fragoso TM, Bertoli W, Louzada F. Bayesian model averaging: a systematic review and conceptual classification. Int Stat Rev. 2018;86:1–28.
Dash D, Cooper GF. Exact model averaging with naive Bayesian classifiers. Proc Int Conf Int Conf Mach Learn. 2002:91–8.
Collins FS, Varmus H. A new initiative on precision medicine. N Engl J Med. 2015;372:793–5. https://doi.org/10.1056/NEJMp1500523.
Visweswaran S, Angus DC, Hsieh M, Weissfeld L, Yealy D, Cooper GF. Learning patient-specific predictive models from clinical data. J Biomed Inform. 2010;43:669–85.
Visweswaran S, Cooper GF. Learning instance-specific predictive models. J Mach Learn Res. 2010;11:3333–69.
Visweswaran S, Ferreira A, Ribeiro GA, Oliveira AC, Cooper GF. Personalized modeling for prediction with decision-path models. PLoS One. 2015;10:e0131022.
Visweswaran S, Cooper GF. Patient-specific models for predicting the outcomes of patients with community acquired pneumonia. AMIA Annu Symp Proc. 2005;2005:759–63.
Suermondt HJ, Cooper GF. An evaluation of explanations of probabilistic inference. Comput Biomed Res. 1993;26:242–54.
Caruana R, Lou Y, Gehrke J, Koch P, Sturm M, Elhadad N. Intelligible models for healthcare: predicting pneumonia risk and hospital 30-day readmission. Proceedings of the 21th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, ACM; 2015. p. 1721–30.
Ribeiro MT, Singh S, Guestrin C. Why should I trust you?: explaining the predictions of any classifier. Proceedings of the ACM SIGKDD International Conference on Knowledge Discovery and Data Mining 2016. p. 1135–44.
Moons KGM, Altman DG, Reitsma JB, Ioannidis JPA, Macaskill P, Steyerberg EW, et al. Transparent reporting of a multivariable prediction model for individual prognosis or diagnosis (TRIPOD): explanation and elaboration. Ann Intern Med. 2015;162:W1–73.
Heus P, Damen JAAG, Pajouheshnia R, Scholten RJPM, Reitsma JB, Collins GS, et al. Poor reporting of multivariable prediction model studies: towards a targeted implementation strategy of the TRIPOD statement. BMC Med. 2018;16:120.
Wilkinson MD, Dumontier M, Aalbersberg IJ, Appleton G, Axton M, Baak A, et al. The FAIR guiding principles for scientific data management and stewardship. Sci Data. 2016;3:160018.
Flynn AJ, Friedman CP, Boisvert P, Landis-Lewis Z, Lagoze C. The knowledge object reference ontology (KORO): a formalism to support management and sharing of computable biomedical knowledge for learning health systems. Learn Heal Syst. 2018;2:e10054.
Collins FS, Hudson KL, Briggs JP, Lauer MS. PCORnet: turning a dream into reality. J Am Med Inform Assoc. 2014;21:576–7.
Visweswaran S, Becich MJ, D’Itri VS, Sendro ER, MacFadden D, Anderson NR, et al. Accrual to clinical trials (ACT): a clinical and translational science award consortium network. JAMIA Open. 2018;1:147–52. https://doi.org/10.1093/jamiaopen/ooy033.
Hripcsak G, Duke JD, Shah NH, Reich CG, Huser V, Schuemie MJ, et al. Observational health data sciences and informatics (OHDSI): opportunities for observational researchers. Stud Health Technol Inform. 2015;216:574.
Reps JM, Schuemie MJ, Suchard MA, Ryan PB, Rijnbeek PR. Design and implementation of a standardized framework to generate and evaluate patient-level prediction models using observational healthcare data. J Am Med Inform Assoc. 2018;25:969–75.
Cohen IG, Amarasingham R, Shah A, Xie B, Lo B. The legal and ethical concerns that arise from using complex predictive analytics in health care. Health Aff. 2014;33:1139–47.
National Institutes of Health. NIH strategic plan for data science [Internet]. [cited 2018 Oct 21]. p. 1–26. https://grants.nih.gov/grants/rfi/NIH-Strategic-Plan-for-Data-Science.pdf.
Brennan PF. Models: the third leg in data-driven discovery – NLM musings from the mezzanine [internet]. 2017 [cited 2018 Oct 21]. https://nlmdirector.nlm.nih.gov/2017/12/12/models-the-third-leg-in-data-driven-discovery/.
Ravi D, Wong C, Deligianni F, Berthelot M, Andreu-Perez J, Lo B, et al. Deep learning for health informatics. IEEE J Biomed Heal Informat. 2017;21:4–21. http://ieeexplore.ieee.org/document/7801947/.
Voigt P, von dem Bussche A. The EU General Data Protection Regulation (GDPR): a practical guide. Cham: Springer; 2017.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2020 Springer Nature Switzerland AG
About this chapter
Cite this chapter
Visweswaran, S., Cooper, G.F. (2020). Risk Stratification and Prognosis Using Predictive Modelling and Big Data Approaches. In: Adam, T., Aliferis, C. (eds) Personalized and Precision Medicine Informatics. Health Informatics. Springer, Cham. https://doi.org/10.1007/978-3-030-18626-5_7
Download citation
DOI: https://doi.org/10.1007/978-3-030-18626-5_7
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-030-18625-8
Online ISBN: 978-3-030-18626-5
eBook Packages: MedicineMedicine (R0)