Kernel based methods for accelerated failure time model with ultra-high dimensional data View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2010-12

AUTHORS

Zhenqiu Liu, Dechang Chen, Ming Tan, Feng Jiang, Ronald B Gartenhaus

ABSTRACT

BACKGROUND: Most genomic data have ultra-high dimensions with more than 10,000 genes (probes). Regularization methods with L₁ and L(p) penalty have been extensively studied in survival analysis with high-dimensional genomic data. However, when the sample size n << m (the number of genes), directly identifying a small subset of genes from ultra-high (m > 10, 000) dimensional data is time-consuming and not computationally efficient. In current microarray analysis, what people really do is select a couple of thousands (or hundreds) of genes using univariate analysis or statistical tests, and then apply the LASSO-type penalty to further reduce the number of disease associated genes. This two-step procedure may introduce bias and inaccuracy and lead us to miss biologically important genes. RESULTS: The accelerated failure time (AFT) model is a linear regression model and a useful alternative to the Cox model for survival analysis. In this paper, we propose a nonlinear kernel based AFT model and an efficient variable selection method with adaptive kernel ridge regression. Our proposed variable selection method is based on the kernel matrix and dual problem with a much smaller n x n matrix. It is very efficient when the number of unknown variables (genes) is much larger than the number of samples. Moreover, the primal variables are explicitly updated and the sparsity in the solution is exploited. CONCLUSIONS: Our proposed methods can simultaneously identify survival associated prognostic factors and predict survival outcomes with ultra-high dimensional genomic data. We have demonstrated the performance of our methods with both simulation and real data. The proposed method performs superbly with limited computational studies. More... »

PAGES

606

References to SciGraph publications

  • 2007-12. Additive risk survival model with microarray data in BMC BIOINFORMATICS
  • Identifiers

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    http://scigraph.springernature.com/pub.10.1186/1471-2105-11-606

    DOI

    http://dx.doi.org/10.1186/1471-2105-11-606

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1008623646

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/21176134


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