IDEAS home Printed from https://ideas.repec.org/a/plo/pone00/0245376.html
   My bibliography  Save this article

Ridge regression and its applications in genetic studies

Author

Listed:
  • M Arashi
  • M Roozbeh
  • N A Hamzah
  • M Gasparini

Abstract

With the advancement of technology, analysis of large-scale data of gene expression is feasible and has become very popular in the era of machine learning. This paper develops an improved ridge approach for the genome regression modeling. When multicollinearity exists in the data set with outliers, we consider a robust ridge estimator, namely the rank ridge regression estimator, for parameter estimation and prediction. On the other hand, the efficiency of the rank ridge regression estimator is highly dependent on the ridge parameter. In general, it is difficult to provide a satisfactory answer about the selection for the ridge parameter. Because of the good properties of generalized cross validation (GCV) and its simplicity, we use it to choose the optimum value of the ridge parameter. The GCV function creates a balance between the precision of the estimators and the bias caused by the ridge estimation. It behaves like an improved estimator of risk and can be used when the number of explanatory variables is larger than the sample size in high-dimensional problems. Finally, some numerical illustrations are given to support our findings.

Suggested Citation

  • M Arashi & M Roozbeh & N A Hamzah & M Gasparini, 2021. "Ridge regression and its applications in genetic studies," PLOS ONE, Public Library of Science, vol. 16(4), pages 1-17, April.
    • Handle: RePEc:plo:pone00:0245376
    DOI: 10.1371/journal.pone.0245376
    as

    Download full text from publisher

    File URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0245376
    Download Restriction: no
    File URL: https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0245376&type=printable
    Download Restriction: no
    File URL: https://libkey.io/10.1371/journal.pone.0245376?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. Roozbeh, Mahdi, 2018. "Optimal QR-based estimation in partially linear regression models with correlated errors using GCV criterion," Computational Statistics & Data Analysis, Elsevier, vol. 117(C), pages 45-61.
    3. Roozbeh, Mahdi, 2016. "Robust ridge estimator in restricted semiparametric regression models," Journal of Multivariate Analysis, Elsevier, vol. 147(C), pages 127-144.
    4. Amini, Morteza & Roozbeh, Mahdi, 2015. "Optimal partial ridge estimation in restricted semiparametric regression models," Journal of Multivariate Analysis, Elsevier, vol. 136(C), pages 26-40.
    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. Supareuk Tarapituxwong & Namchok Chimprang & Woraphon Yamaka & Piangtawan Polard, 2023. "A Lasso and Ridge-Cox Proportional Hazard Model Analysis of Thai Tourism Businesses’ Resilience and Survival in the COVID-19 Crisis," Sustainability, MDPI, vol. 15(18), pages 1-22, September.

    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. Guoping Zeng & Sha Tao, 2023. "A Generalized Linear Transformation and Its Effects on Logistic Regression," Mathematics, MDPI, vol. 11(2), pages 1-19, January.
    2. Roozbeh, Mahdi, 2018. "Optimal QR-based estimation in partially linear regression models with correlated errors using GCV criterion," Computational Statistics & Data Analysis, Elsevier, vol. 117(C), pages 45-61.
    3. M. Nooi Asl & H. Bevrani & R. Arabi Belaghi & K. Mansson, 2021. "Ridge-type shrinkage estimators in generalized linear models with an application to prostate cancer data," Statistical Papers, Springer, vol. 62(2), pages 1043-1085, April.
    4. Lei Qiao & Bing Wang, 2024. "Kernel-Based Multivariate Nonparametric CUSUM Multi-Chart for Detection of Abrupt Changes," Mathematics, MDPI, vol. 12(10), pages 1-12, May.
    5. Morteza Amini & Mahdi Roozbeh, 2019. "Improving the prediction performance of the LASSO by subtracting the additive structural noises," Computational Statistics, Springer, vol. 34(1), pages 415-432, March.
    6. 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.
    7. Xu, Yang & Zhao, Shishun & Hu, Tao & Sun, Jianguo, 2021. "Variable selection for generalized odds rate mixture cure models with interval-censored failure time data," Computational Statistics & Data Analysis, Elsevier, vol. 156(C).
    8. Emmanouil Androulakis & Christos Koukouvinos & Kalliopi Mylona & Filia Vonta, 2010. "A real survival analysis application via variable selection methods for Cox's proportional hazards model," Journal of Applied Statistics, Taylor & Francis Journals, vol. 37(8), pages 1399-1406.
    9. Singh, Rakhi & Stufken, John, 2024. "Factor selection in screening experiments by aggregation over random models," Computational Statistics & Data Analysis, Elsevier, vol. 194(C).
    10. Koki Momoki & Takuma Yoshida, 2024. "Hypothesis testing for varying coefficient models in tail index regression," Statistical Papers, Springer, vol. 65(6), pages 3821-3852, August.
    11. Lili Pan & Ziyan Luo & Naihua Xiu, 2017. "Restricted Robinson Constraint Qualification and Optimality for Cardinality-Constrained Cone Programming," Journal of Optimization Theory and Applications, Springer, vol. 175(1), pages 104-118, October.
    12. Gerhard Tutz & Moritz Berger, 2018. "Tree-structured modelling of categorical predictors in generalized additive regression," 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. 12(3), pages 737-758, September.
    13. Chenchuan (Mark) Li & Ulrich K. Müller, 2021. "Linear regression with many controls of limited explanatory power," Quantitative Economics, Econometric Society, vol. 12(2), pages 405-442, May.
    14. 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.
    15. Hang Yu & Yuanjia Wang & Donglin Zeng, 2023. "A general framework of nonparametric feature selection in high‐dimensional data," Biometrics, The International Biometric Society, vol. 79(2), pages 951-963, June.
    16. 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.
    17. Shuang Zhang & Xingdong Feng, 2022. "Distributed identification of heterogeneous treatment effects," Computational Statistics, Springer, vol. 37(1), pages 57-89, March.
    18. Jun Zhu & Hsin‐Cheng Huang & Perla E. Reyes, 2010. "On selection of spatial linear models for lattice data," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 72(3), pages 389-402, June.
    19. Zak-Szatkowska, Malgorzata & Bogdan, Malgorzata, 2011. "Modified versions of the Bayesian Information Criterion for sparse Generalized Linear Models," Computational Statistics & Data Analysis, Elsevier, vol. 55(11), pages 2908-2924, November.
    20. Lam, Clifford, 2008. "Estimation of large precision matrices through block penalization," LSE Research Online Documents on Economics 31543, London School of Economics and Political Science, LSE Library.

    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:pone00:0245376. 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.