IDEAS home Printed from https://ideas.repec.org/a/spr/stabio/v8y2016i1d10.1007_s12561-015-9131-y.html
   My bibliography  Save this article

Hybrid Mixture Model for Subpopulation Identification

Author

Listed:
  • Hung-Chia Chen

    (U.S. Food and Drug Administration)

  • James J. Chen

    (U.S. Food and Drug Administration)

Abstract

Personalized medicine aims to identify those patients who have good or poor prognosis for overall disease outcomes or therapeutic efficacy for a specific treatment. A well-established approach is to identify a set of biomarkers using statistical methods with a classification algorithm to identify patient subgroups for treatment selection. However, there are potential false positives and false negatives in classification resulting in incorrect patient treatment assignment. In this paper, we propose a hybrid mixture model taking uncertainty in class labels into consideration, where the class labels are modeled by a Bernoulli random variable. An EM algorithm was developed to estimate the model parameters, and a parametric bootstrap method was used to test the significance of the predictive variables that were associated with subgroup memberships. Simulation experiments showed that the proposed method averagely had higher accuracy in identifying the subpopulations than the Naïve Bayes classifier and logistic regression. A breast cancer dataset was analyzed to illustrate the proposed hybrid mixture model.

Suggested Citation

  • Hung-Chia Chen & James J. Chen, 2016. "Hybrid Mixture Model for Subpopulation Identification," Statistics in Biosciences, Springer;International Chinese Statistical Association, vol. 8(1), pages 28-42, June.
  • Handle: RePEc:spr:stabio:v:8:y:2016:i:1:d:10.1007_s12561-015-9131-y
    DOI: 10.1007/s12561-015-9131-y
    as

    Download full text from publisher

    File URL: http://link.springer.com/10.1007/s12561-015-9131-y
    File Function: Abstract
    Download Restriction: Access to the full text of the articles in this series is restricted.

    File URL: https://libkey.io/10.1007/s12561-015-9131-y?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    References listed on IDEAS

    as
    1. Hanfeng Chen & Jiahua Chen & John D. Kalbfleisch, 2004. "Testing for a finite mixture model with two components," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 66(1), pages 95-115, February.
    2. Xin Liu & Cristian Pasarica & Yongzhao Shao, 2003. "Testing Homogeneity in Gamma Mixture Models," Scandinavian Journal of Statistics, Danish Society for Theoretical Statistics;Finnish Statistical Society;Norwegian Statistical Association;Swedish Statistical Association, vol. 30(1), pages 227-239, March.
    3. Lin-An Chen & Dung-Tsa Chen & Wenyaw Chan, 2010. "The distribution-based p-value for the outlier sum in differential gene expression analysis," Biometrika, Biometrika Trust, vol. 97(1), pages 246-253.
    4. Lo, Yungtai, 2005. "Likelihood ratio tests of the number of components in a normal mixture with unequal variances," Statistics & Probability Letters, Elsevier, vol. 71(3), pages 225-235, March.
    5. Chen, Hanfeng & Chen, Jiahua, 2001. "Large sample distribution of the likelihood ratio test for normal mixtures," Statistics & Probability Letters, Elsevier, vol. 52(2), pages 125-133, April.
    6. Chen-An Tsai & Huey-miin Hsueh & James J. Chen, 2003. "Estimation of False Discovery Rates in Multiple Testing: Application to Gene Microarray Data," Biometrics, The International Biometric Society, vol. 59(4), pages 1071-1081, December.
    7. G. J. McLachlan, 1987. "On Bootstrapping the Likelihood Ratio Test Statistic for the Number of Components in a Normal Mixture," Journal of the Royal Statistical Society Series C, Royal Statistical Society, vol. 36(3), pages 318-324, November.
    8. John D. Storey, 2002. "A direct approach to false discovery rates," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 64(3), pages 479-498, August.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Robert R. Delongchamp & John F. Bowyer & James J. Chen & Ralph L. Kodell, 2004. "Multiple-Testing Strategy for Analyzing cDNA Array Data on Gene Expression," Biometrics, The International Biometric Society, vol. 60(3), pages 774-782, September.
    2. Lo, Yungtai, 2011. "Bias from misspecification of the component variances in a normal mixture," Computational Statistics & Data Analysis, Elsevier, vol. 55(9), pages 2739-2747, September.
    3. Yongqiang Tang & Subhashis Ghosal & Anindya Roy, 2007. "Nonparametric Bayesian Estimation of Positive False Discovery Rates," Biometrics, The International Biometric Society, vol. 63(4), pages 1126-1134, December.
    4. Kenneth Rice & David Spiegelhalter, 2006. "A Simple Diagnostic Plot Connecting Robust Estimation, Outlier Detection, and False Discovery Rates," Journal of Applied Statistics, Taylor & Francis Journals, vol. 33(10), pages 1131-1147.
    5. Hunt, Daniel L. & Cheng, Cheng & Pounds, Stanley, 2009. "The beta-binomial distribution for estimating the number of false rejections in microarray gene expression studies," Computational Statistics & Data Analysis, Elsevier, vol. 53(5), pages 1688-1700, March.
    6. Pittau, Maria Grazia & Zelli, Roberto & Johnson, Paul, "undated". "Mixture Models and Convergence Clubs," Vassar College Department of Economics Working Paper Series 91, Vassar College Department of Economics.
    7. Maciejowska, Katarzyna, 2013. "Assessing the number of components in a normal mixture: an alternative approach," MPRA Paper 50303, University Library of Munich, Germany.
    8. Garel, Bernard, 2007. "Recent asymptotic results in testing for mixtures," Computational Statistics & Data Analysis, Elsevier, vol. 51(11), pages 5295-5304, July.
    9. Wong, Tony Siu Tung & Li, Wai Keung, 2014. "Test for homogeneity in gamma mixture models using likelihood ratio," Computational Statistics & Data Analysis, Elsevier, vol. 70(C), pages 127-137.
    10. Ramesh Gupta & Hui Tao, 2010. "A generalized correlated binomial distribution with application in multiple testing problems," Metrika: International Journal for Theoretical and Applied Statistics, Springer, vol. 71(1), pages 59-77, January.
    11. Maria Grazia Pittau & Roberto Zelli & Paul A. Johnson, 2010. "Mixture Models, Convergence Clubs, And Polarization," Review of Income and Wealth, International Association for Research in Income and Wealth, vol. 56(1), pages 102-122, March.
    12. József Bukszár & Edwin J. C. G. van den Oord, 2006. "Optimization of Two-Stage Genetic Designs Where Data Are Combined Using an Accurate and Efficient Approximation for Pearson's Statistic," Biometrics, The International Biometric Society, vol. 62(4), pages 1132-1137, December.
    13. Youngchao Ge & Sandrine Dudoit & Terence Speed, 2003. "Resampling-based multiple testing for microarray data analysis," TEST: An Official Journal of the Spanish Society of Statistics and Operations Research, Springer;Sociedad de Estadística e Investigación Operativa, vol. 12(1), pages 1-77, June.
    14. Fetene B. Tekle & Dereje W. Gudicha & Jeroen K. Vermunt, 2016. "Power analysis for the bootstrap likelihood ratio test for the number of classes in latent class models," Advances in Data Analysis and Classification, Springer;German Classification Society - Gesellschaft für Klassifikation (GfKl);Japanese Classification Society (JCS);Classification and Data Analysis Group of the Italian Statistical Society (CLADAG);International Federation of Classification Societies (IFCS), vol. 10(2), pages 209-224, June.
    15. Bajgrowicz, Pierre & Scaillet, Olivier, 2012. "Technical trading revisited: False discoveries, persistence tests, and transaction costs," Journal of Financial Economics, Elsevier, vol. 106(3), pages 473-491.
    16. Wen Shi & Xi Chen & Jennifer Shang, 2019. "An Efficient Morris Method-Based Framework for Simulation Factor Screening," INFORMS Journal on Computing, INFORMS, vol. 31(4), pages 745-770, October.
    17. Dørum Guro & Snipen Lars & Solheim Margrete & Saebo Solve, 2011. "Smoothing Gene Expression Data with Network Information Improves Consistency of Regulated Genes," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 10(1), pages 1-26, August.
    18. Jianqing Fan & Xu Han, 2017. "Estimation of the false discovery proportion with unknown dependence," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 79(4), pages 1143-1164, September.
    19. A Bottle & P Aylin, 2011. "Predicting the false alarm rate in multi-institution mortality monitoring," Journal of the Operational Research Society, Palgrave Macmillan;The OR Society, vol. 62(9), pages 1711-1718, September.
    20. Van Hanh Nguyen & Catherine Matias, 2014. "On Efficient Estimators of the Proportion of True Null Hypotheses in a Multiple Testing Setup," Scandinavian Journal of Statistics, Danish Society for Theoretical Statistics;Finnish Statistical Society;Norwegian Statistical Association;Swedish Statistical Association, vol. 41(4), pages 1167-1194, December.

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:spr:stabio:v:8:y:2016:i:1:d:10.1007_s12561-015-9131-y. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.springer.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.