Efficient regularized isotonic regression with application to gene--gene interaction search

Isotonic regression is a nonparametric approach for fitting monotonic models to data that has been widely studied from both theoretical and practical perspectives. However, this approach encounters computational and statistical overfitting issues in higher dimensions. To address both concerns, we present an algorithm, which we term Isotonic Recursive Partitioning (IRP), for isotonic regression based on recursively partitioning the covariate space through solution of progressively smaller "best cut" subproblems. This creates a regularized sequence of isotonic models of increasing model complexity that converges to the global isotonic regression solution. The models along the sequence are often more accurate than the unregularized isotonic regression model because of the complexity control they offer. We quantify this complexity control through estimation of degrees of freedom along the path. Success of the regularized models in prediction and IRPs favorable computational properties are demonstrated through a series of simulated and real data experiments. We discuss application of IRP to the problem of searching for gene--gene interactions and epistasis, and demonstrate it on data from genome-wide association studies of three common diseases.Comment: Published in at http://dx.doi.org/10.1214/11-AOAS504 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Online Isotonic Regression

We consider the online version of the isotonic regression problem. Given a set of linearly ordered points (e.g., on the real line), the learner must predict labels sequentially at adversarially chosen positions and is evaluated by her total squared loss compared against the best isotonic (non-decreasing) function in hindsight. We survey several standard online learning algorithms and show that none of them achieve the optimal regret exponent; in fact, most of them (including Online Gradient Descent, Follow the Leader and Exponential Weights) incur linear regret. We then prove that the Exponential Weights algorithm played over a covering net of isotonic functions has a regret bounded by $O\big(T^{1/3} \log^{2/3}(T)\big)$ and present a matching $\Omega(T^{1/3})$ lower bound on regret. We provide a computationally efficient version of this algorithm. We also analyze the noise-free case, in which the revealed labels are isotonic, and show that the bound can be improved to $O(\log T)$ or even to $O(1)$ (when the labels are revealed in isotonic order). Finally, we extend the analysis beyond squared loss and give bounds for entropic loss and absolute loss.Comment: 25 page

Extension of CART using multiple splits under order restrictions

CART was introduced by Breiman et al. (1984) as a classification tool. It divides the whole sample recursively in two subpopulations by finding the best possible split with respect to a optimisation criterion. This method, restricted up to date to binary splits, is extended in this paper for allowing also multiple splits. The main problem with this extension is related to the optimal number of splits and the location of the corresponding cutpoints. In order to reduce the computational effort and enhance parsimony, the reduced isotonic regression was used in order to solve this problem. The extended CART method was tested in a simulation study and was compared with the classical approach in an epidemiological study. In both studies the extended CART turned out to be a useful and reliable alternative