Biostatistics - Advance Access

Rank-based estimation in the {ell}1-regularized partly linear model for censored outcomes with application to integrated analyses of clinical predictors and gene expression data

Johnson, B. A. — 2009-06-24

We consider estimation and variable selection in the partial linear model for censored data. The partial linear model for censored data is a direct extension of the accelerated failure time model, the latter of which is a very important alternative model to the proportional hazards model. We extend rank-based lasso-type estimators to a model that may contain nonlinear effects. Variable selection in such partial linear model has direct application to high-dimensional survival analyses that attempt to adjust for clinical predictors. In the microarray setting, previous methods can adjust for other clinical predictors by assuming that clinical and gene expression data enter the model linearly in the same fashion. Here, we select important variables after adjusting for prognostic clinical variables but the clinical effects are assumed nonlinear. Our estimator is based on stratification and can be extended naturally to account for multiple nonlinear effects. We illustrate the utility of our method through simulation studies and application to the Wisconsin prognostic breast cancer data set.

A semiparametric 2-part mixed-effects heteroscedastic transformation model for correlated right-skewed semicontinuous data

Lin, H., Zhou, X.-H. — 2009-06-22

In longitudinal or hierarchical structure studies, we often encounter a semicontinuous variable that has a certain proportion of a single value and a continuous and skewed distribution among the rest of values. In this paper, we propose a new semiparametric 2-part mixed-effects transformation model to fit correlated skewed semicontinuous data. In our model, we allow the transformation to be nonparametric. Fitting the proposed model faces computational challenges due to intractable numerical integrations. We derive the estimates for the parameter and the transformation function based on an approximate likelihood, which has high-order accuracy but less computational burden. We also propose an estimator for the expected value of the semicontinuous outcome on the original scale. Finally, we apply the proposed methods to a clinical study on effectiveness of a collaborative care treatment on late-life depression on health care costs.

Variable selection and dependency networks for genomewide data

Dobra, A. — 2009-06-11

We describe a new stochastic search algorithm for linear regression models called the bounded mode stochastic search (BMSS). We make use of BMSS to perform variable selection and classification as well as to construct sparse dependency networks. Furthermore, we show how to determine genetic networks from genomewide data that involve any combination of continuous and discrete variables. We illustrate our methodology with several real-world data sets.

Estimation and inference for case-control studies with multiple non-gold standard exposure assessments: with an occupational health application

Chu, H., Cole, S. R., Wei, Y., Ibrahim, J. G. — 2009-06-09

In occupational case–control studies, work-related exposure assessments are often fallible measures of the true underlying exposure. In lieu of a gold standard, often more than 2 imperfect measurements (e.g. triads) are used to assess exposure. While methods exist to assess the diagnostic accuracy in the absence of a gold standard, these methods are infrequently used to correct for measurement error in exposure–disease associations in occupational case–control studies. Here, we present a likelihood-based approach that (a) provides evidence regarding whether the misclassification of tests is differential or nondifferential; (b) provides evidence whether the misclassification of tests is independent or dependent conditional on latent exposure status, and (c) estimates the measurement error–corrected exposure–disease association. These approaches use information from all imperfect assessments simultaneously in a unified manner, which in turn can provide a more accurate estimate of exposure–disease association than that based on individual assessments. The performance of this method is investigated through simulation studies and applied to the National Occupational Hazard Survey, a case–control study assessing the association between asbestos exposure and mesothelioma.

A novel approach to cancer staging: application to esophageal cancer

Ishwaran, H., Blackstone, E. H., Apperson-Hansen, C., Rice, T. W. — 2009-06-05

A novel 3-step random forests methodology involving survival data (survival forests), ordinal data (multiclass forests), and continuous data (regression forests) is introduced for cancer staging. The methodology is illustrated for esophageal cancer using worldwide esophageal cancer collaboration data involving 4627 patients.