To better understand the spatial structure of large panels of economic and financial time series and provide a guideline for constructing semiparametric models, this paper first considers estimating a large spatial covariance matrix of the generalized $m$-dependent and $\beta$-mixing time series (with $J$ variables and $T$ observations) by hard thresholding regularization as long as ${{\log J \, \cx^*(\ct)}}/{T} = \Co(1)$ (the former scheme with some time dependence measure $\cx^*(\ct)$) or $\log J /{T} = \Co(1)$ (the latter scheme with some upper bounded mixing coefficient). We quantify the interplay between the estimators' consistency rate and the time dependence level, discuss an intuitive resampling scheme for threshold selection, and also prove a general cross-validation result justifying this. Given a consistently estimated covariance (correlation) matrix, by utilizing its natural links with graphical models and semiparametrics, after "screening" the (explanatory) variables, we implement a novel forward (and backward) label permutation procedure to cluster the "relevant" variables and construct the corresponding semiparametric model, which is further estimated by the groupwise dimension reduction method with sign constraints. We call this the SCE (screen - cluster - estimate) approach for modeling high dimensional data with complex spatial structure. Finally we apply this method to study the spatial structure of large panels of economic and financial time series and find the proper semiparametric structure for estimating the consumer price index (CPI) to illustrate its superiority over the linear models.

Divergence estimators based on direct approximation of density-ratios without going through separate approximation of numerator and denominator densities have been successfully applied to machine learning tasks that involve distribution comparison such as outlier detection, transfer learning, and two-sample homogeneity test. However, since density-ratio functions often possess high fluctuation, divergence estimation is still a challenging task in practice. In this paper, we propose to use relative divergences for distribution comparison, which involves approximation of relative density-ratios. Since relative density-ratios are always smoother than corresponding ordinary density-ratios, our proposed method is favorable in terms of the non-parametric convergence speed. Furthermore, we show that the proposed divergence estimator has asymptotic variance independent of the model complexity under a parametric setup, implying that the proposed estimator hardly overfits even with complex models. Through experiments, we demonstrate the usefulness of the proposed approach.

We propose an active set selection framework for Gaussian process classification for cases when the dataset is large enough to render its inference prohibitive. Our scheme consists of a two step alternating procedure of active set update rules and hyperparameter optimization based upon marginal likelihood maximization. The active set update rules rely on the ability of the predictive distributions of a Gaussian process classifier to estimate the relative contribution of a datapoint when being either included or removed from the model. This means that we can use it to include points with potentially high impact to the classifier decision process while removing those that are less relevant. We introduce two active set rules based on different criteria, the first one prefers a model with interpretable active set parameters whereas the second puts computational complexity first, thus a model with active set parameters that directly control its complexity. We also provide both theoretical and empirical support for our active set selection strategy being a good approximation of a full Gaussian process classifier. Our extensive experiments show that our approach can compete with state-of-the-art classification techniques with reasonable time complexity. Source code publicly available at http://cogsys.imm.dtu.dk/passgp.

Motivation: Biomarker discovery from high-dimensional data is a crucial problem with enormous applications in biology and medicine. It is also extremely challenging from a statistical viewpoint, but surprisingly few studies have investigated the relative strengths and weaknesses of the plethora of existing feature selection methods. Methods: We compare 32 feature selection methods on 4 public gene expression datasets for breast cancer prognosis, in terms of predictive performance, stability and functional interpretability of the signatures they produce. Results: We observe that the feature selection method has a significant influence on the accuracy, stability and interpretability of signatures. Simple filter methods generally outperform more complex embedded or wrapper methods, and ensemble feature selection has generally no positive effect. Overall a simple Student's t-test seems to provide the best results. Availability: Code and data are publicly available at http://cbio.ensmp.fr/~ahaury/.

Undirected graphs are often used to describe high dimensional distributions. Under sparsity conditions, the graph can be estimated using $\ell_1$-penalization methods. We propose and study the following method. We combine a multiple regression approach with ideas of thresholding and refitting: first we infer a sparse undirected graphical model structure via thresholding of each among many $\ell_1$-norm penalized regression functions; we then estimate the covariance matrix and its inverse using the maximum likelihood estimator. We show that under suitable conditions, this approach yields consistent estimation in terms of graphical structure and fast convergence rates with respect to the operator and Frobenius norm for the covariance matrix and its inverse. We also derive an explicit bound for the Kullback Leibler divergence.

This paper considers the robust and efficient implementation of Gaussian process regression with a Student-t observation model. The challenge with the Student-t model is the analytically intractable inference which is why several approximative methods have been proposed. The expectation propagation (EP) has been found to be a very accurate method in many empirical studies but the convergence of the EP is known to be problematic with models containing non-log-concave site functions such as the Student-t distribution. In this paper we illustrate the situations where the standard EP fails to converge and review different modifications and alternative algorithms for improving the convergence. We demonstrate that convergence problems may occur during the type-II maximum a posteriori (MAP) estimation of the hyperparameters and show that the standard EP may not converge in the MAP values in some difficult cases. We present a robust implementation which relies primarily on parallel EP updates and utilizes a moment-matching-based double-loop algorithm with adaptively selected step size in difficult cases. The predictive performance of the EP is compared to the Laplace, variational Bayes, and Markov chain Monte Carlo approximations.

We develop, analyze, and evaluate a novel, supervised, specific-to-general learner for a simple temporal logic and use the resulting algorithm to learn visual event definitions from video sequences. First, we introduce a simple, propositional, temporal, event-description language called AMA that is sufficiently expressive to represent many events yet sufficiently restrictive to support learning. We then give algorithms, along with lower and upper complexity bounds, for the subsumption and generalization problems for AMA formulas. We present a positive-examples--only specific-to-general learning method based on these algorithms. We also present a polynomial-time--computable ``syntactic'' subsumption test that implies semantic subsumption without being equivalent to it. A generalization algorithm based on syntactic subsumption can be used in place of semantic generalization to improve the asymptotic complexity of the resulting learning algorithm. Finally, we apply this algorithm to the task of learning relational event definitions from video and show that it yields definitions that are competitive with hand-coded ones.

Finding the place (or time) where most or all of a set of one-dimensional signals (or profiles) jointly change in some specific way is an important question in several fields. A common situation is when we want to find change-points in a multidimensional signal, e.g., in audio and image processing [1, 2], to detect intrusion in computer networks [3, 4], or in financial and economics time series analysis [5]. Another important situation is when we are confronted with several 1-dimensional signals which we believe share common changepoints, e.g., genomic profiles of a set of patients. The latter application is increasingly important in biology and medicine, in particular for the detection of copy-number variation along the genome [6], or the analysis of microarray and genetic linkage studies [7]. The common thread in biological applications is the search for data patterns shared by a set of individuals, such as cancer patients, at precise places on the genome; in particular, sudden changes in measured values. As opposed to the segmentation of multidimensional signals such as speech, where the dimension is fixed and collecting more data means having longer profiles, the length of signals in genomic studies (i.e., the number of probes measured along the genome) is fixed for a given technology while the number of signals (i.e., the number of individuals) can increase when we collect data about more patients. From a statistical point of view, it is therefore of interest to develop methods that identify multiple change-points shared by several signals that can benefit from increasing the number of signals. There exists a vast literature on the change-point detection problem [8, 9]. Here we focus on computationally efficient methods to segment a multidimensional signal by approximating it with a piecewiseconstant one, using quadratic error criteria.

Probabilistic principal component analysis (PPCA) seeks a low dimensional representation of a data set in the presence of independent spherical Gaussian noise, Sigma = (sigma^2)*I. The maximum likelihood solution for the model is an eigenvalue problem on the sample covariance matrix. In this paper we consider the situation where the data variance is already partially explained by other factors, e.g. covariates of interest, or temporal correlations leaving some residual variance. We decompose the residual variance into its components through a generalized eigenvalue problem, which we call residual component analysis (RCA). We show that canonical covariates analysis (CCA) is a special case of our algorithm and explore a range of new algorithms that arise from the framework. We illustrate the ideas on a gene expression time series data set and the recovery of human pose from silhouette.

One popular approach for nonstructural economic and financial forecasting is to include a large number of economic and financial variables, which has been shown to lead to significant improvements for forecasting, for example, by the dynamic factor models. A challenging issue is to determine which variables and (their) lags are relevant, especially when there is a mixture of serial correlation (temporal dynamics), high dimensional (spatial) dependence structure and moderate sample size (relative to dimensionality and lags). To this end, an \textit{integrated} solution that addresses these three challenges simultaneously is appealing. We study the large vector auto regressions here with three types of estimates. We treat each variable's own lags different from other variables' lags, distinguish various lags over time, and is able to select the variables and lags simultaneously. We first show the consequences of using Lasso type estimate directly for time series without considering the temporal dependence. In contrast, our proposed method can still produce an estimate as efficient as an \textit{oracle} under such scenarios. The tuning parameters are chosen via a data driven "rolling scheme" method to optimize the forecasting performance. A macroeconomic and financial forecasting problem is considered to illustrate its superiority over existing estimators.