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We consider the sparse inverse covariance regularization problem or graphical lasso with regularization parameter λ. Suppose the sample covariance graph formed by thresholding the entries of the sample covariance matrix at λ is decomposed into connected components. We show that the vertex-partition induced by the connected components of the thresholded sample covariance graph (at λ) is exactly equal to that induced by the connected components of the estimated concentration graph, obtained by solving the graphical lasso problem for the same λ. This characterizes a very interesting property of a path of graphical lasso solutions. Furthermore, this simple rule, when used as a wrapper around existing algorithms for the graphical lasso, leads to enormous performance gains. For a range of values of λ, our proposal splits a large graphical lasso problem into smaller tractable problems, making it possible to solve an otherwise infeasible large-scale problem. We illustrate the graceful scalability of our proposal via synthetic and real-life microarray examples. [ABSTRACT FROM AUTHOR]

In ecological modeling of the habitat of a species, it can be prohibitively expensive to determine species absence. Presence-only data consist of a sample of locations with observed presences and a separate group of locations sampled from the full landscape, with unknown presences. We propose an expectation–maximization algorithm to estimate the underlying presence–absence logistic model for presence-only data. This algorithm can be used with any off-the-shelf logistic model. For models with stepwise fitting procedures, such as boosted trees, the fitting process can be accelerated by interleaving expectation steps within the procedure. Preliminary analyses based on sampling from presence–absence records of fish in New Zealand rivers illustrate that this new procedure can reduce both deviance and the shrinkage of marginal effect estimates that occur in the naive model often used in practice. Finally, it is shown that the population prevalence of a species is only identifiable when there is some unrealistic constraint on the structure of the logistic model. In practice, it is strongly recommended that an estimate of population prevalence be provided. [ABSTRACT FROM AUTHOR]

The authors comment on the article "Evidence Contrary to Statistical View of Boosting," by David Mease and Abraham Wyner that was published within the issue. The three important properties that contribute to the success of boosting methods are mentioned. The authors claim that the paper attributes consequences of statistical view that are not the case, including the requirement that test error have a unique minimum as a function of the number of included terms.

We propose a method for the classification of more than two classes, from high-dimensional features. Our approach is to build a binary decision tree in a top-down manner, using the optimal margin classifier at each split. We implement an exact greedy algorithm for this task, and compare its performance to less greedy procedures based on clustering of the matrix of pairwise margins. We compare the performance of the "margin tree" to the closely related "all-pairs" (one versus one) support vector machine, and nearest centroids on a number of cancer microarray data sets. We also develop a simple method for feature selection. We find that the margin tree has accuracy that is competitive with other methods and offers additional interpretability in its putative grouping of the classes. [ABSTRACT FROM AUTHOR]

Principal component analysis (PCA) is widely used in data processing and dimensionality reduction. However, PCA suffers from the fact that each principal component is a linear combination of all the original variables, thus it is often difficult to interpret the results. We introduce a new method called sparse principal component analysis (SPCA) using the lasso (elastic net) to produce modified principal components with sparse loadings. We first show that PCA can be formulated as a regression-type optimization problem; sparse loadings are then obtained by imposing the lasso (elastic net) constraint on the regression coefficients. Efficient algorithms are proposed to fit our SPCA models for both regular multivariate data and gene expression arrays. We also give a new formula to compute the total variance of modified principal components. As illustrations, SPCA is applied to real and simulated data with encouraging results. [ABSTRACT FROM AUTHOR]

Discusses an alternative algorithm in which the smooth functions are estimated using smoothing spline. The generalized cross-validation (GSV) based techniques used to select the smoothing parameters and number of terms; Structure of the automatic smoothing spline projection pursuit (ASP) algorithm; Examples comparing ASP with the standard supersmoother-based PPR algorithm of Friedman.

Principal curves are smooth one-dimensional curves that pass through the middle of a p-dimensional data set, providing a nonlinear summary of the data. They are nonparametric, and their shape is suggested by the data. The algorithm for constructing principal curves starts with some prior summary, such as the usual principal-component line. The curve in each successive iteration is a smooth or local average of the p-dimensional points, where the definition of local is based on the distance in arc length of the projections of the points onto the curve found in the previous iteration. In this article principal curves are defined, an algorithm for their construction is given, some theoretical results arc presented, and the procedure is compared to other generalizations of principal components. Two applications illustrate the use of principal curves. The first describes how the principal-curve procedure was used to align the magnets of the Stanford linear collider. The collider uses about 950 magnets in a roughly circular arrangement to bend electron and positron beams and bring them to collision. After construction, it was found that some of the magnets had ended up significantly out of place. As a result, the beams had to be bent too sharply and could not be focused. The engineers realized that the magnets did not have to be moved to their originally planned locations, but rather to a sufficiently smooth are through the middle of the existing positions. This arc was found using the principal curve procedure. In the second application, two different assays for gold content in several samples of computer chip waste appear to show some systematic differences that are blurred by measurement error. The classical approach using linear errors in variables regression can detect systematic linear differences but is not able to account for nonlinearities. When the first linear principal component is replaced with a... [ABSTRACT FROM AUTHOR]

Generalized additive models have the form eta (x) = alpha + SIGMA f[sub j](x[sub j]), where eta might be the regression function in a multiple regression or the logistic transformation of the posterior probability Pr(y = 1 | x) in a logistic regression. In fact, these models generalize the whole family of generalized linear models eta(x) = beta'x, where eta(x) = g(mu(x)) is some transformation of the regression function. We use the local scoring algorithm to estimate the functions f[sub j](x[sub j]) nonparametrically, using a scatterplot smoother as a building block. We demonstrate the models in two different analyses: a nonparametric analysis of covariance and a logistic regression. The procedure can be used as a diagnostic tool for identifying parametric transformations of the covariates in a standard linear analysis. A variety of inferential tools have been developed to aid the analyst in assessing the relevance and significance of the estimated functions: these include confidence curves, degrees of freedom estimates, and approximate hypothesis tests. The local scoring algorithm is analogous to the iterative reweighted least squares algorithm for solving likelihood and nonlinear regression equations. At each iteration, an adjusted dependent variable is formed and an additive regression model is fit using the backfitting algorithm. The backfitting algorithm cycles through the variables and estimates each coordinated function by smoothing the partial residuals. [ABSTRACT FROM AUTHOR]

Unmeasured or latent variables are often the cause of correlations between multivariate measurements, which are studied in a variety of fields such as psychology, ecology, and medicine. For Gaussian measurements, there are classical tools such as factor analysis or principal component analysis with a well-established theory and fast algorithms. Generalized Linear Latent Variable models (GLLVMs) generalize such factor models to non-Gaussian responses. However, current algorithms for estimating model parameters in GLLVMs require intensive computation and do not scale to large data sets with thousands of observational units or responses. In this article, we propose a new approach for fitting GLLVMs to high-dimensional data sets, based on approximating the model using penalized quasi-likelihood and then using a Newton method and Fisher scoring to learn the model parameters. Computationally, our method is noticeably faster and more stable, enabling GLLVM fits to much larger matrices than previously possible. We apply our method on a data set of 48,000 observational units with over 2,000 observed species in each unit and find that most of the variability can be explained with a handful of factors. We publish an easy-to-use implementation of our proposed fitting algorithms. [ABSTRACT FROM AUTHOR]