We propose a new method named calibrated multivariate regression (CMR) for fitting high dimensional multivariate regression models. Compared to existing methods, CMR calibrates the regularization for each regression task with respect to its noise level so that it is simultaneously tuning insensitive and achieves an improved finite-sample performance. Computationally, we develop an efficient smoothed proximal gradient algorithm which has a worst-case iteration complexity $O(1/\epsilon)$, where $\epsilon$ is a pre-specified numerical accuracy. Theoretically, we prove that CMR achieves the optimal rate of convergence in parameter estimation. We illustrate the usefulness of CMR by thorough numerical simulations and show that CMR consistently outperforms other high dimensional multivariate regression methods. We also apply CMR on a brain activity prediction problem and find that CMR is as competitive as the handcrafted model created by human experts.

Model selection is indispensable to high-dimensional sparse modeling in selecting the best set of covariates among a sequence of candidate models. Most existing work assumes implicitly that the model is correctly specified or of fixed dimensions. Yet model misspecification and high dimensionality are common in real applications. In this paper, we investigate two classical Kullback-Leibler divergence and Bayesian principles of model selection in the setting of high-dimensional misspecified models. Asymptotic expansions of these principles reveal that the effect of model misspecification is crucial and should be taken into account, leading to the generalized AIC and generalized BIC in high dimensions. With a natural choice of prior probabilities, we suggest the generalized BIC with prior probability which involves a logarithmic factor of the dimensionality in penalizing model complexity. We further establish the consistency of the covariance contrast matrix estimator in a general setting. Our results and new method are supported by numerical studies.

Several new estimation methods have been recently proposed for the linear regression model with observation error in the design. Different assumptions on the data generating process have motivated different estimators and analysis. In particular, the literature considered (1) observation errors in the design uniformly bounded by some $\bar \delta$, and (2) zero mean independent observation errors. Under the first assumption, the rates of convergence of the proposed estimators depend explicitly on $\bar \delta$, while the second assumption has been applied when an estimator for the second moment of the observational error is available. This work proposes and studies two new estimators which, compared to other procedures for regression models with errors in the design, exploit an additional $l_{\infty}$-norm regularization. The first estimator is applicable when both (1) and (2) hold but does not require an estimator for the second moment of the observational error. The second estimator is applicable under (2) and requires an estimator for the second moment of the observation error. Importantly, we impose no assumption on the accuracy of this pilot estimator, in contrast to the previously known procedures. As the recent proposals, we allow the number of covariates to be much larger than the sample size. We establish the rates of convergence of the estimators and compare them with the bounds obtained for related estimators in the literature. These comparisons show interesting insights on the interplay of the assumptions and the achievable rates of convergence.

We demonstrate that the primal-dual witness proof method may be used to establish variable selection consistency and $\ell_\infty$-bounds for sparse regression problems, even when the loss function and/or regularizer are nonconvex. Using this method, we derive two theorems concerning support recovery and $\ell_\infty$-guarantees for the regression estimator in a general setting. Our results provide rigorous theoretical justification for the use of nonconvex regularization: For certain nonconvex regularizers with vanishing derivative away from the origin, support recovery consistency may be guaranteed without requiring the typical incoherence conditions present in $\ell_1$-based methods. We then derive several corollaries that illustrate the wide applicability of our method to analyzing composite objective functions involving losses such as least squares, nonconvex modified least squares for errors-in variables linear regression, the negative log likelihood for generalized linear models, and the graphical Lasso. We conclude with empirical studies to corroborate our theoretical predictions.

In this paper we study the consistency of an empirical minimum error entropy (MEE) algorithm in a regression setting. We introduce two types of consistency. The error entropy consistency, which requires the error entropy of the learned function to approximate the minimum error entropy, is shown to be always true if the bandwidth parameter tends to 0 at an appropriate rate. The regression consistency, which requires the learned function to approximate the regression function, however, is a complicated issue. We prove that the error entropy consistency implies the regression consistency for homoskedastic models where the noise is independent of the input variable. But for heteroskedastic models, a counterexample is used to show that the two types of consistency do not coincide. A surprising result is that the regression consistency is always true, provided that the bandwidth parameter tends to infinity at an appropriate rate. Regression consistency of two classes of special models is shown to hold with fixed bandwidth parameter, which further illustrates the complexity of regression consistency of MEE. Fourier transform plays crucial roles in our analysis.

We propose the supervised hierarchical Dirichlet process (sHDP), a nonparametric generative model for the joint distribution of a group of observations and a response variable directly associated with that whole group. We compare the sHDP with another leading method for regression on grouped data, the supervised latent Dirichlet allocation (sLDA) model. We evaluate our method on two real-world classification problems and two real-world regression problems. Bayesian nonparametric regression models based on the Dirichlet process, such as the Dirichlet process-generalised linear models (DP-GLM) have previously been explored; these models allow flexibility in modelling nonlinear relationships. However, until now, Hierarchical Dirichlet Process (HDP) mixtures have not seen significant use in supervised problems with grouped data since a straightforward application of the HDP on the grouped data results in learnt clusters that are not predictive of the responses. The sHDP solves this problem by allowing for clusters to be learnt jointly from the group structure and from the label assigned to each group.

This paper introduces Kernel-based Information Criterion (KIC) for model selection in regression analysis. The novel kernel-based complexity measure in KIC efficiently computes the interdependency between parameters of the model using a variable-wise variance and yields selection of better, more robust regressors. Experimental results show superior performance on both simulated and real data sets compared to Leave-One-Out Cross-Validation (LOOCV), kernel-based Information Complexity (ICOMP), and maximum log of marginal likelihood in Gaussian Process Regression (GPR).

Factor analysis provides linear factors that describe relationships between individual variables of a data set. We extend this classical formulation into linear factors that describe relationships between groups of variables, where each group represents either a set of related variables or a data set. The model also naturally extends canonical correlation analysis to more than two sets, in a way that is more flexible than previous extensions. Our solution is formulated as variational inference of a latent variable model with structural sparsity, and it consists of two hierarchical levels: The higher level models the relationships between the groups, whereas the lower models the observed variables given the higher level. We show that the resulting solution solves the group factor analysis problem accurately, outperforming alternative factor analysis based solutions as well as more straightforward implementations of group factor analysis. The method is demonstrated on two life science data sets, one on brain activation and the other on systems biology, illustrating its applicability to the analysis of different types of high-dimensional data sources.

We propose a new algorithm called PLUTO for building logistic regression trees to binary response data. PLUTO can capture the nonlinear and interaction patterns in messy data by recursively partitioning the sample space. It fits a simple or a multiple linear logistic regression model in each partition. PLUTO employs the cyclical coordinate descent method for estimation of multiple linear logistic regression models with elastic net penalties, which allows it to deal with high-dimensional data efficiently. The tree structure comprises a graphical description of the data. Together with the logistic regression models, it provides an accurate classifier as well as a piecewise smooth estimate of the probability of "success". PLUTO controls selection bias by: (1) separating split variable selection from split point selection; (2) applying an adjusted chi-squared test to find the split variable instead of exhaustive search. A bootstrap calibration technique is employed to further correct selection bias. Comparison on real datasets shows that on average, the multiple linear PLUTO models predict more accurately than other algorithms.

Ensemble-of-trees methods have become popular choices for forecasting in both regression and classification problems. Algorithms such as random forests (Breiman 2001) and stochastic gradient boosting (Friedman 2002) are two well-established and widely employed procedures. Recent advances in ensemble methods include dynamic trees (Taddy, Gramacy, and Polson 2011) and Bayesian additive regression trees (BART, Chipman, George, and McCulloch 2010), which depart from predecessors in that they rely on an underlying Bayesian probability model rather than a pure algorithm. BART has demonstrated substantial promise in a wide variety of simulations and real world applications such as predicting avalanches on mountain roads (Blattenberger and Fowles 2014), predicting how transcription factors interact with DNA (Zhou and Liu 2008) and predicting movie box office revenues (Eliashberg 2010). This paper introduces bartMachine, a new R (R Core Team 2014) package available from the Comprehensive R Archive Network at http://CRAN.R-project.org/package