IDEAS home Printed from https://ideas.repec.org/a/plo/pone00/0212108.html
   My bibliography  Save this article

Drug sensitivity prediction with high-dimensional mixture regression

Author

Listed:
  • Qianyun Li
  • Runmin Shi
  • Faming Liang

Abstract

This paper proposes a mixture regression model-based method for drug sensitivity prediction. The proposed method explicitly addresses two fundamental issues in drug sensitivity prediction, namely, population heterogeneity and feature selection pertaining to each of the subpopulations. The mixture regression model is estimated using the imputation-conditional consistency algorithm, and the resulting estimator is consistent. This paper also proposes an average-BIC criterion for determining the number of components for the mixture regression model. The proposed method is applied to the CCLE dataset, and the numerical results indicate that the proposed method can make a drastic improvement over the existing ones, such as random forest, support vector regression, and regularized linear regression, in both drug sensitivity prediction and feature selection. The p-values for the comparisons in drug sensitivity prediction can reach the order O(10−8) or lower for the drugs with heterogeneous populations.

Suggested Citation

  • Qianyun Li & Runmin Shi & Faming Liang, 2019. "Drug sensitivity prediction with high-dimensional mixture regression," PLOS ONE, Public Library of Science, vol. 14(2), pages 1-18, February.
  • Handle: RePEc:plo:pone00:0212108
    DOI: 10.1371/journal.pone.0212108
    as

    Download full text from publisher

    File URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0212108
    Download Restriction: no

    File URL: https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0212108&type=printable
    Download Restriction: no

    File URL: https://libkey.io/10.1371/journal.pone.0212108?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
    ---><---

    References listed on IDEAS

    as
    1. Fan J. & Li R., 2001. "Variable Selection via Nonconcave Penalized Likelihood and its Oracle Properties," Journal of the American Statistical Association, American Statistical Association, vol. 96, pages 1348-1360, December.
    2. Hui Zou & Trevor Hastie, 2005. "Addendum: Regularization and variable selection via the elastic net," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 67(5), pages 768-768, November.
    3. Hui Zou & Trevor Hastie, 2005. "Regularization and variable selection via the elastic net," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 67(2), pages 301-320, April.
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. You, Na & Dai, Hongsheng & Wang, Xueqin & Yu, Qingyun, 2024. "Sequential estimation for mixture of regression models for heterogeneous population," Computational Statistics & Data Analysis, Elsevier, vol. 194(C).

    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. Tutz, Gerhard & Pößnecker, Wolfgang & Uhlmann, Lorenz, 2015. "Variable selection in general multinomial logit models," Computational Statistics & Data Analysis, Elsevier, vol. 82(C), pages 207-222.
    2. Margherita Giuzio, 2017. "Genetic algorithm versus classical methods in sparse index tracking," Decisions in Economics and Finance, Springer;Associazione per la Matematica, vol. 40(1), pages 243-256, November.
    3. Shuichi Kawano, 2014. "Selection of tuning parameters in bridge regression models via Bayesian information criterion," Statistical Papers, Springer, vol. 55(4), pages 1207-1223, November.
    4. Yize Zhao & Matthias Chung & Brent A. Johnson & Carlos S. Moreno & Qi Long, 2016. "Hierarchical Feature Selection Incorporating Known and Novel Biological Information: Identifying Genomic Features Related to Prostate Cancer Recurrence," Journal of the American Statistical Association, Taylor & Francis Journals, vol. 111(516), pages 1427-1439, October.
    5. Changrong Yan & Dixin Zhang, 2013. "Sparse dimension reduction for survival data," Computational Statistics, Springer, vol. 28(4), pages 1835-1852, August.
    6. Gareth M. James & Peter Radchenko & Jinchi Lv, 2009. "DASSO: connections between the Dantzig selector and lasso," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 71(1), pages 127-142, January.
    7. Soave, David & Lawless, Jerald F., 2023. "Regularized regression for two phase failure time studies," Computational Statistics & Data Analysis, Elsevier, vol. 182(C).
    8. Zemin Zheng & Jie Zhang & Yang Li, 2022. "L 0 -Regularized Learning for High-Dimensional Additive Hazards Regression," INFORMS Journal on Computing, INFORMS, vol. 34(5), pages 2762-2775, September.
    9. Alexander Chudik & George Kapetanios & M. Hashem Pesaran, 2016. "Big Data Analytics: A New Perspective," CESifo Working Paper Series 5824, CESifo.
    10. Umberto Amato & Anestis Antoniadis & Italia De Feis & Irene Gijbels, 2021. "Penalised robust estimators for sparse and high-dimensional linear models," Statistical Methods & Applications, Springer;Società Italiana di Statistica, vol. 30(1), pages 1-48, March.
    11. Xiao Ni & Daowen Zhang & Hao Helen Zhang, 2010. "Variable Selection for Semiparametric Mixed Models in Longitudinal Studies," Biometrics, The International Biometric Society, vol. 66(1), pages 79-88, March.
    12. Camila Epprecht & Dominique Guegan & Álvaro Veiga & Joel Correa da Rosa, 2017. "Variable selection and forecasting via automated methods for linear models: LASSO/adaLASSO and Autometrics," Post-Print halshs-00917797, HAL.
    13. Zichen Zhang & Ye Eun Bae & Jonathan R. Bradley & Lang Wu & Chong Wu, 2022. "SUMMIT: An integrative approach for better transcriptomic data imputation improves causal gene identification," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    14. Wang, Christina Dan & Chen, Zhao & Lian, Yimin & Chen, Min, 2022. "Asset selection based on high frequency Sharpe ratio," Journal of Econometrics, Elsevier, vol. 227(1), pages 168-188.
    15. Bartosz Uniejewski, 2024. "Regularization for electricity price forecasting," Papers 2404.03968, arXiv.org.
    16. Peter Bühlmann & Jacopo Mandozzi, 2014. "High-dimensional variable screening and bias in subsequent inference, with an empirical comparison," Computational Statistics, Springer, vol. 29(3), pages 407-430, June.
    17. Peter Martey Addo & Dominique Guegan & Bertrand Hassani, 2018. "Credit Risk Analysis Using Machine and Deep Learning Models," Risks, MDPI, vol. 6(2), pages 1-20, April.
    18. Capanu, Marinela & Giurcanu, Mihai & Begg, Colin B. & Gönen, Mithat, 2023. "Subsampling based variable selection for generalized linear models," Computational Statistics & Data Analysis, Elsevier, vol. 184(C).
    19. Weng, Jiaying, 2022. "Fourier transform sparse inverse regression estimators for sufficient variable selection," Computational Statistics & Data Analysis, Elsevier, vol. 168(C).
    20. Ander Wilson & Brian J. Reich, 2014. "Confounder selection via penalized credible regions," Biometrics, The International Biometric Society, vol. 70(4), pages 852-861, December.

    More about this item

    Statistics

    Access and download statistics

    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:plo:pone00:0212108. 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: plosone (email available below). General contact details of provider: https://journals.plos.org/plosone/ .

    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.