IDEAS home Printed from https://ideas.repec.org/a/eee/csdana/v182y2023ics0167947323000142.html
   My bibliography  Save this article

Regularized regression for two phase failure time studies

Author

Listed:
  • Soave, David
  • Lawless, Jerald F.

Abstract

Two-phase study designs are ideal for focused sub-studies based on large prospective cohorts when the outcome of interest is an event that is rare in the full cohort, and additional covariates are expensive or difficult to measure. Researchers often wish to examine large numbers of covariates for association with outcomes of interest. In the context of cancer, hundreds to millions of genetic markers may be considered, along with environmental exposures. A computationally efficient variable selection method is proposed for two-phase failure time studies with stratified sampling under the Cox proportional hazards model. The penalized estimator is obtained from a penalized (weighted) Cox log partial likelihood using a pathwise cyclical coordinate descent algorithm which is scalable for high dimensional datasets where the number of features is much larger than the sample size (p≫n). A detailed simulation study to examine the performance of the proposed methodology is described. The variable selection and estimation procedure is then used to obtain a model for predicting acute myeloid leukaemia using somatic stem cell mutation profiles derived from blood samples, based on a two-phase sample from the European Prospective Investigation into Cancer and Nutrition (EPIC) study.

Suggested Citation

  • Soave, David & Lawless, Jerald F., 2023. "Regularized regression for two phase failure time studies," Computational Statistics & Data Analysis, Elsevier, vol. 182(C).
    • Handle: RePEc:eee:csdana:v:182:y:2023:i:c:s0167947323000142
    DOI: 10.1016/j.csda.2023.107703
    as

    Download full text from publisher

    File URL: http://www.sciencedirect.com/science/article/pii/S0167947323000142
    Download Restriction: Full text for ScienceDirect subscribers only.
    File URL: https://libkey.io/10.1016/j.csda.2023.107703?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. J. F. Lawless, 2018. "Two-phase outcome-dependent studies for failure times and testing for effects of expensive covariates," Lifetime Data Analysis: An International Journal Devoted to Statistical Methods and Applications for Time-to-Event Data, Springer, vol. 24(1), pages 28-44, January.
    2. Ai Ni & Jianwen Cai & Donglin Zeng, 2016. "Variable selection for case-cohort studies with failure time outcome," Biometrika, Biometrika Trust, vol. 103(3), pages 547-562.
    3. Simon, Noah & Friedman, Jerome H. & Hastie, Trevor & Tibshirani, Rob, 2011. "Regularization Paths for Cox's Proportional Hazards Model via Coordinate Descent," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 39(i05).
    4. 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.
    5. Sagi Abelson & Grace Collord & Stanley W. K. Ng & Omer Weissbrod & Netta Mendelson Cohen & Elisabeth Niemeyer & Noam Barda & Philip C. Zuzarte & Lawrence Heisler & Yogi Sundaravadanam & Robert Luben &, 2018. "Prediction of acute myeloid leukaemia risk in healthy individuals," Nature, Nature, vol. 559(7714), pages 400-404, July.
    6. Sven Ove Samuelsen & Hallvard Ånestad & Anders Skrondal, 2007. "Stratified Case‐Cohort Analysis of General Cohort Sampling Designs," Scandinavian Journal of Statistics, Danish Society for Theoretical Statistics;Finnish Statistical Society;Norwegian Statistical Association;Swedish Statistical Association, vol. 34(1), pages 103-119, March.
    7. Dandan Liu & Tianxi Cai & Yingye Zheng, 2012. "Evaluating the Predictive Value of Biomarkers with Stratified Case-Cohort Design," Biometrics, The International Biometric Society, vol. 68(4), pages 1219-1227, December.
    8. 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.
    9. 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)

    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. 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.
    2. Takumi Saegusa & Tianzhou Ma & Gang Li & Ying Qing Chen & Mei-Ling Ting Lee, 2020. "Variable Selection in Threshold Regression Model with Applications to HIV Drug Adherence Data," Statistics in Biosciences, Springer;International Chinese Statistical Association, vol. 12(3), pages 376-398, December.
    3. Yoonsuh Jung, 2018. "Multiple predicting K-fold cross-validation for model selection," Journal of Nonparametric Statistics, Taylor & Francis Journals, vol. 30(1), pages 197-215, January.
    4. Zhixuan Fu & Chirag R. Parikh & Bingqing Zhou, 2017. "Penalized variable selection in competing risks regression," Lifetime Data Analysis: An International Journal Devoted to Statistical Methods and Applications for Time-to-Event Data, Springer, vol. 23(3), pages 353-376, July.
    5. Rafael Blanquero & Emilio Carrizosa & Pepa Ramírez-Cobo & M. Remedios Sillero-Denamiel, 2021. "A cost-sensitive constrained Lasso," 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. 15(1), pages 121-158, 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. 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.
    8. 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.
    9. 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.
    10. 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.
    11. Changrong Yan & Dixin Zhang, 2013. "Sparse dimension reduction for survival data," Computational Statistics, Springer, vol. 28(4), pages 1835-1852, August.
    12. 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.
    13. Alexander Chudik & George Kapetanios & M. Hashem Pesaran, 2016. "Big Data Analytics: A New Perspective," CESifo Working Paper Series 5824, CESifo.
    14. 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.
    15. 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.
    16. 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.
    17. 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.
    18. 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.
    19. 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.
    20. 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.

    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:eee:csdana:v:182:y:2023:i:c:s0167947323000142. 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: Catherine Liu (email available below). General contact details of provider: http://www.elsevier.com/locate/csda .

    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.