This paper considers the computer model calibration problem and provides a general frequentist solution. Under the proposed framework, the data model is semi-parametric with a nonparametric discrepancy function which accounts for any discrepancy between the physical reality and the computer model. In an attempt to solve a fundamentally important (but often ignored) identifiability issue between the computer model parameters and the discrepancy function, this paper proposes a new and identifiable parametrization of the calibration problem.It also develops a two-step procedure for estimating all the relevant quantities under the new parameterization. This estimation procedure is shown to enjoy excellent rates of convergence and can be straightforwardly implemented with existing software. For uncertainty quantification, bootstrapping is adopted to construct confidence regions for the quantities of interest. The practical performance of the proposed methodology is illustrated through simulation examples and an application to a computational fluid dynamics model.

Covariate balance is often advocated for objective causal inference since it mimics randomization in observational data. Unlike methods that balance specific moments of covariates, our proposal attains uniform approximate balance for covariate functions in a reproducing-kernel Hilbert space. The corresponding infinite-dimensional optimization problem is shown to have a finite-dimensional representation in terms of an eigenvalue optimization problem. Large-sample results are studied, and numerical examples show that the proposed method achieves better balance with smaller sampling variability than existing methods.

Description This package provides robust estimation for generalized additive models. It implements a fast and stable algorithm in Wong, Yao and Lee (2013). The implementation also contains three automatic selection methods for smoothing parameter. They are designed to be robust to outliers. For more details, see Wong, Yao and Lee (2013). License GPL (>= 2) Depends Rcpp (>= 0.9.13), RcppArmadillo (>= 0.3.4.4) , mgcv (>= 1.7-20), robustbase (>= 0.9-3) LinkingTo Rcpp, RcppArmadillo NeedsCompilation yes Repository CRAN Date/Publication 2014-01-02 19:18:27 cplot.robustgam robustgam-package Robust Estimation for Generalized Additive Models Description This package provides robust estimation for generalized additive models. It implements a fast and stable algorithm in Wong, Yao and Lee (2013). The implementation also contains three automatic selection methods for smoothing parameter. They are designed to be robust to outliers. For more details, see Wong, Yao and Lee (2013).

We investigate a class of partially linear functional additive models (PLFAM) that predicts a scalar response by both parametric effects of a multivariate predictor and nonparametric effects of a multivariate functional predictor. We jointly model multiple functional predictors that are cross-correlated using multivariate functional principal component analysis (mFPCA), and model the nonparametric effects of the principal component scores as additive components in the PLFAM. To address the high dimensional nature of functional data, we let the number of mFPCA components diverge to infinity with the sample size, and adopt the COmponent Selection and Smoothing Operator (COSSO) penalty to select relevant components and regularize the fitting. A fundamental difference between our framework and the existing high dimensional additive models is that the mFPCA scores are estimated with error, and the magnitude of measurement error increases with the order of mFPCA. We establish the asymptotic convergence rate for our estimator, while allowing the number of components diverge. When the number of additive components is fixed, we also establish the asymptotic distribution for the partially linear coefficients. The practical performance of the proposed methods is illustrated via simulation studies and a crop yield prediction application.

In functional data analysis (FDA), covariance function is fundamental not only as a critical quantity for understanding elementary aspects of functional data but also as an indispensable ingredient for many advanced FDA methods. This paper develops a new class of nonparametric covariance function estimators in terms of various spectral regularizations of an operator associated with a reproducing kernel Hilbert space. Despite their nonparametric nature, the covariance estimators are automatically positive semi-definite without any additional modification steps. An unconventional representer theorem is established to provide a finite dimensional representation for this class of covariance estimators, which leads to a closed-form expression of the corresponding L 2 eigen-decomposition. Trace-norm regularization is particularly studied to further achieve a low-rank representation, another desirable property which leads to dimension reduction and is often needed in advanced FDA approaches. An efficient algorithm is developed based on the accelerated proximal gradient method. This resulted estimator is shown to enjoy an excellent rate of convergence under both fixed and random designs. The outstanding practical performance of the trace-norm-regularized covariance estimator is demonstrated by a simulation study and the analysis of a traffic dataset.

Diffusion magnetic resonance imaging is an imaging technology designed to probe anatomical architectures of biological samples in an in vivo and noninvasive manner through measuring water diffusion. The contribution of this paper is threefold. First, it proposes a new method to identify and estimate multiple diffusion directions within a voxel through a new and identifiable parametrization of the widely used multi-tensor model. Unlike many existing methods, this method focuses on the estimation of diffusion directions rather than the diffusion tensors. Second, this paper proposes a novel direction smoothing method which greatly improves direction estimation in regions with crossing fibers. This smoothing method is shown to have excellent theoretical and empirical properties. Last, this paper develops a fiber tracking algorithm that can handle multiple directions within a voxel. The overall methodology is illustrated with simulated data and a data set collected for the study of Alzheimer’s disease by the Alzheimer’s Disease Neuroimaging Initiative (ADNI).

Boolean networks are a simple but efficient model for describing gene regulatory systems. A number of algorithms have been proposed to infer Boolean networks. However, these methods do not take full consideration of the effects of noise and model uncertainty. In this paper, we propose a full Bayesian approach to infer Boolean genetic networks. Markov chain Monte Carlo algorithms are used to obtain the posterior samples of both the network structure and the related parameters. In addition to regular link addition and removal moves, which can guarantee the irreducibility of the Markov chain for traversing the whole network space, carefully constructed mixture proposals are used to improve the Markov chain Monte Carlo convergence. Both simulations and a real application on cell-cycle data show that our method is more powerful than existing methods for the inference of both the topology and logic relations of the Boolean network from observed data.

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