On Degrees of Freedom of Projection Estimators with Applications to Multivariate Nonparametric Regression

In this paper, we consider the nonparametric regression problem with multivariate predictors. We provide a characterization of the degrees of freedom and divergence for estimators of the unknown regression function, which are obtained as outputs of linearly constrained quadratic optimization procedures, namely, minimizers of the least squares criterion with linear constraints and/or quadratic penalties. As special cases of our results, we derive explicit expressions for the degrees of freedom in many nonparametric regression problems, e.g., bounded isotonic regression, multivariate (penalized) convex regression, and additive total variation regularization. Our theory also yields, as special cases, known results on the degrees of freedom of many well-studied estimators in the statistics literature, such as ridge regression, Lasso and generalized Lasso. Our results can be readily used to choose the tuning parameter(s) involved in the estimation procedure by minimizing the Stein's unbiased risk estimate. As a by-product of our analysis we derive an interesting connection between bounded isotonic regression and isotonic regression on a general partially ordered set, which is of independent interest.Comment: 72 pages, 7 figures, Journal of the American Statistical Association (Theory and Methods), 201

The asymptotic distribution of the isotonic regression estimator over a general countable pre-ordered set

We study the isotonic regression estimator over a general countable pre-ordered set. We obtain the limiting distribution of the estimator and study its properties. It is proved that, under some general assumptions, the limiting distribution of the isotonized estimator is given by the concatenation of the separate isotonic regressions of the certain subvectors of an unrestrecred estimator's asymptotic distribution. Also, we show that the isotonization preserves the rate of convergence of the underlying estimator. We apply these results to the problems of estimation of a bimonotone regression function and estimation of a bimonotone probability mass function

A dynamic programming approach for generalized nearly isotonic optimization

Shape restricted statistical estimation problems have been extensively studied, with many important practical applications in signal processing, bioinformatics, and machine learning. In this paper, we propose and study a generalized nearly isotonic optimization (GNIO) model, which recovers, as special cases, many classic problems in shape constrained statistical regression, such as isotonic regression, nearly isotonic regression and unimodal regression problems. We develop an efficient and easy-to-implement dynamic programming algorithm for solving the proposed model whose recursion nature is carefully uncovered and exploited. For special $\ell_2$-GNIO problems, implementation details and the optimal ${\cal O}(n)$ running time analysis of our algorithm are discussed. Numerical experiments, including the comparison between our approach and the powerful commercial solver Gurobi for solving $\ell_1$-GNIO and $\ell_2$-GNIO problems, on both simulated and real data sets are presented to demonstrate the high efficiency and robustness of our proposed algorithm in solving large scale GNIO problems

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

Binary Classifier Calibration using an Ensemble of Near Isotonic Regression Models

Learning accurate probabilistic models from data is crucial in many practical tasks in data mining. In this paper we present a new non-parametric calibration method called \textit{ensemble of near isotonic regression} (ENIR). The method can be considered as an extension of BBQ, a recently proposed calibration method, as well as the commonly used calibration method based on isotonic regression. ENIR is designed to address the key limitation of isotonic regression which is the monotonicity assumption of the predictions. Similar to BBQ, the method post-processes the output of a binary classifier to obtain calibrated probabilities. Thus it can be combined with many existing classification models. We demonstrate the performance of ENIR on synthetic and real datasets for the commonly used binary classification models. Experimental results show that the method outperforms several common binary classifier calibration methods. In particular on the real data, ENIR commonly performs statistically significantly better than the other methods, and never worse. It is able to improve the calibration power of classifiers, while retaining their discrimination power. The method is also computationally tractable for large scale datasets, as it is $O(N \log N)$ time, where $N$ is the number of samples