IDEAS home Printed from https://ideas.repec.org/a/spr/stabio/v9y2017i1d10.1007_s12561-016-9169-5.html
   My bibliography  Save this article

Prediction-Oriented Marker Selection (PROMISE): With Application to High-Dimensional Regression

Author

Listed:
  • Soyeon Kim

    () (Rice University
    The University of Texas MD Anderson Cancer Center)

  • Veerabhadran Baladandayuthapani

    () (The University of Texas MD Anderson Cancer Center)

  • J. Jack Lee

    () (The University of Texas MD Anderson Cancer Center)

Abstract

Abstract In personalized medicine, biomarkers are used to select therapies with the highest likelihood of success based on an individual patient’s biomarker/genomic profile. Two goals are to choose important biomarkers that accurately predict treatment outcomes and to cull unimportant biomarkers to reduce the cost of biological and clinical verifications. These goals are challenging due to the high dimensionality of genomic data. Variable selection methods based on penalized regression (e.g., the lasso and elastic net) have yielded promising results. However, selecting the right amount of penalization is critical to simultaneously achieving these two goals. Standard approaches based on cross-validation (CV) typically provide high prediction accuracy with high true positive rates (TPRs) but at the cost of too many false positives. Alternatively, stability selection (SS) controls the number of false positives, but at the cost of yielding too few true positives. To circumvent these issues, we propose prediction-oriented marker selection (PROMISE), which combines SS with CV to conflate the advantages of both methods. Our application of PROMISE with the lasso and elastic net in data analysis shows that, compared to CV, PROMISE produces sparse solutions, few false positives, and small type I + type II error, and maintains good prediction accuracy, with a marginal decrease in the TPRs. Compared to SS, PROMISE offers better prediction accuracy and TPRs. In summary, PROMISE can be applied in many fields to select regularization parameters when the goals are to minimize false positives and maximize prediction accuracy.

Suggested Citation

  • Soyeon Kim & Veerabhadran Baladandayuthapani & J. Jack Lee, 2017. "Prediction-Oriented Marker Selection (PROMISE): With Application to High-Dimensional Regression," Statistics in Biosciences, Springer;International Chinese Statistical Association, vol. 9(1), pages 217-245, June.
  • Handle: RePEc:spr:stabio:v:9:y:2017:i:1:d:10.1007_s12561-016-9169-5
    DOI: 10.1007/s12561-016-9169-5
    as

    Download full text from publisher

    File URL: http://link.springer.com/10.1007/s12561-016-9169-5
    File Function: Abstract
    Download Restriction: Access to the full text of the articles in this series is restricted.

    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. Nicolai Meinshausen & Peter Bühlmann, 2010. "Stability selection," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 72(4), pages 417-473.
    2. Friedman, Jerome H. & Hastie, Trevor & Tibshirani, Rob, 2010. "Regularization Paths for Generalized Linear Models via Coordinate Descent," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 33(i01).
    3. Jianqing Fan & Jinchi Lv, 2008. "Sure independence screening for ultrahigh dimensional feature space," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 70(5), pages 849-911.
    4. 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.
    5. 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.
    Full references (including those not matched with items on IDEAS)

    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:9:y:2017:i:1:d:10.1007_s12561-016-9169-5. See general information about how to correct material in RePEc.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: (Sonal Shukla) or (Rebekah McClure). General contact details of provider: http://www.springer.com .

    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 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.

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

    IDEAS is a RePEc service hosted by the Research Division of the Federal Reserve Bank of St. Louis . RePEc uses bibliographic data supplied by the respective publishers.