稳健高效的高维成分数据近似零值插补方法及应用

随着计算机技术的迅猛发展,高维成分数据不断涌现并伴有大量近似零值和缺失,数据的高维特性不仅给传统统计方法带来了巨大的挑战,其厚尾特征、复杂的协方差结构也使得理论分析难上加难。于是如何对高维成分数据的近似零值进行稳健的插补,挖掘潜在的内蕴结构成为当今学者研究的焦点。对此,本文结合修正的EM算法,提出基于R型聚类的Lasso-分位回归插补法(SubLQR)对高维成分数据的近似零值问题予以解决。与现有高维近似零值插补方法相比,本文所提出的SubLQR具有如下优势。①稳健全面性:利用Lasso-分位回归方法,不仅可以有效地探测到响应变量的整个条件分布,还能提供更加真实的高维稀疏模式;②有效准确性:采用基于R型聚类的思想进行插补,可以降低计算复杂度,极大提高插补的精度。模拟研究证实,本文提出的SubLQR高效灵活准确,特别在零值、异常值较多的情形更具优势。最后将SubLQR方法应用于罕见病代谢组学研究中,进一步表明本文所提出的方法具有广泛的适用性。     

Least squares variogram fitting by spatial subsampling

Summary. Least squares methods are popular for fitting valid variogram models to spatial data. The paper proposes a new least squares method based on spatial subsampling for variogram model fitting. We show that the method proposed is statistically efficient among a class of least squares methods, including the generalized least squares method. Further, it is computationally much simpler than the generalized least squares method. The method produces valid variogram estimators under very mild regularity conditions on the underlying random field and may be applied with different choices of the generic variogram estimator without analytical calculation. An extension of the method proposed to a class of spatial regression models is illustrated with a real data example. Results from a simulation study on finite sample properties of the method are also reported.     

Regression methods for high dimensional multicollinear data

To compare their performance on high dimensional data, several regression methods are applied to data sets in which the number of exploratory variables greatly exceeds the sample sizes. The methods are stepwise regression, principal components regression, two forms of latent root regression, partial least squares, and a new method developed here. The data are four sample sets for which near infrared reflectance spectra have been determined and the regression methods use the spectra to estimate the concentration of various chemical constituents, the latter having been determined by standard chemical analysis. Thirty-two regression equations are estimated using each method and their performances are evaluated using validation data sets. Although it is the most widely used, stepwise regression was decidedly poorer than the other methods considered. Differences between the latter were small with partial least squares performing slightly better than other methods under all criteria examined, albeit not by a statistically significant amount.     

Fitting linear regression models to censored data by least squares and maximum likelihood methods

Several approaches have been suggested for fitting linear regression models to censored data. These include Cox's propor­tional hazard models based on quasi-likelihoods. Methods of fitting based on least squares and maximum likelihoods have also been proposed. The methods proposed so far all require special purpose optimization routines. We describe an approach here which requires only a modified standard least squares routine.

We present methods for fitting a linear regression model to censored data by least squares and method of maximum likelihood. In the least squares method, the censored values are replaced by their expectations, and the residual sum of squares is minimized. Several variants are suggested in the ways in which the expect­ation is calculated. A parametric (assuming a normal error model) and two non-parametric approaches are described. We also present a method for solving the maximum likelihood equations in the estimation of the regression parameters in the censored regression situation. It is shown that the solutions can be obtained by a recursive algorithm which needs only a least squares routine for optimization. The suggested procesures gain considerably in computational officiency. The Stanford Heart Transplant data is used to illustrate the various methods.     

Partial least squares Cox regression for genome-wide data

Most methods for survival prediction from high-dimensional genomic data combine the Cox proportional hazards model with some technique of dimension reduction, such as partial least squares regression (PLS). Applying PLS to the Cox model is not entirely straightforward, and multiple approaches have been proposed. The method of Park et al. (Bioinformatics 18(Suppl. 1):S120–S127, 2002) uses a reformulation of the Cox likelihood to a Poisson type likelihood, thereby enabling estimation by iteratively reweighted partial least squares for generalized linear models. We propose a modification of the method of park et al. (2002) such that estimates of the baseline hazard and the gene effects are obtained in separate steps. The resulting method has several advantages over the method of park et al. (2002) and other existing Cox PLS approaches, as it allows for estimation of survival probabilities for new patients, enables a less memory-demanding estimation procedure, and allows for incorporation of lower-dimensional non-genomic variables like disease grade and tumor thickness. We also propose to combine our Cox PLS method with an initial gene selection step in which genes are ordered by their Cox score and only the highest-ranking k% of the genes are retained, obtaining a so-called supervised partial least squares regression method. In simulations, both the unsupervised and the supervised version outperform other Cox PLS methods.     

Dimensionality reduction approach to multivariate prediction

The authors consider dimensionality reduction methods used for prediction, such as reduced rank regression, principal component regression and partial least squares. They show how it is possible to obtain intermediate solutions by estimating simultaneously the latent variables for the predictors and for the responses. They obtain a continuum of solutions that goes from reduced rank regression to principal component regression via maximum likelihood and least squares estimation. Different solutions are compared using simulated and real data.     

Heteroskedastic linear regression model with compositional response and covariates

Compositional data are known as a sort of complex multidimensional data with the feature that reflect the relative information rather than absolute information. There are a variety of models for regression analysis with compositional variables. Similar to the traditional regression analysis, the heteroskedasticity still exists in these models. However, the existing heteroskedastic regression analysis methods cannot apply in these models with compositional error term. In this paper, we mainly study the heteroskedastic linear regression model with compositional response and covariates. The parameter estimator is obtained through weighted least squares method. For the hypothesis test of parameter, the test statistic is based on the original least squares estimator and corresponding heteroskedasticity-consistent covariance matrix estimator. When the proposed method is applied to both simulation and real example, we use the original least squares method as a comparison during the whole process. The results implicate the model's practicality and effectiveness in regression analysis with heteroskedasticity.     

Diagnostics for non-linear regression

Sensitivity analysis in regression is concerned with assessing the sensitivity of the results of a regression model (e.g., the objective function, the regression parameters, and the fitted values) to changes in the data. Sensitivity analysis in least squares linear regression has seen a great surge of research activities over the last three decades. By contrast, sensitivity analysis in non-linear regression has received very little attention. This paper deals with the problem of local sensitivity analysis in non-linear regression. Closed-form general formulas are provided for the sensitivities of three standard methods for the estimation of the parameters of a non-linear regression model based on a set of data. These methods are the least squares, the minimax, and the least absolute value methods. The effectiveness of the proposed measures is illustrated by application to several non-linear models including the ultrasonic data and the onion yield data. The proposed sensitivity measures are shown to deal effectively with the detection of influential observations in non-linear regression models.     

A Bayesian hierarchical approach to dual response surface modelling

In modern quality engineering, dual response surface methodology is a powerful tool to model an industrial process by using both the mean and the standard deviation of the measurements as the responses. The least squares method in regression is often used to estimate the coefficients in the mean and standard deviation models, and various decision criteria are proposed by researchers to find the optimal conditions. Based on the inherent hierarchical structure of the dual response problems, we propose a Bayesian hierarchical approach to model dual response surfaces. Such an approach is compared with two frequentist least squares methods by using two real data sets and simulated data.     

Sparse partial least squares regression for simultaneous dimension reduction and variable selection

Summary.  Partial least squares regression has been an alternative to ordinary least squares for handling multicollinearity in several areas of scientific research since the 1960s. It has recently gained much attention in the analysis of high dimensional genomic data. We show that known asymptotic consistency of the partial least squares estimator for a univariate response does not hold with the very large p and small n paradigm. We derive a similar result for a multivariate response regression with partial least squares. We then propose a sparse partial least squares formulation which aims simultaneously to achieve good predictive performance and variable selection by producing sparse linear combinations of the original predictors. We provide an efficient implementation of sparse partial least squares regression and compare it with well-known variable selection and dimension reduction approaches via simulation experiments. We illustrate the practical utility of sparse partial least squares regression in a joint analysis of gene expression and genomewide binding data.     

Krylov Sequences as a Tool for Analysing Iterated Regression Algorithms

Abstract.  We use Krylov sequences to analyse a class of regression methods based on successive identification of latent factors. Some results already proved for partial least squares regression (PLSR) are shown to hold for other methods also. We prove that the well-known peculiar pattern of alternating shrinkage and inflation of the principal components is not unique for PLSR. We also show that for any method in the class under study, the coefficient of determination is always at least as high as for principal components regression with the same number of factors.     

The peculiar shrinkage properties of partial least squares regression

Partial least squares regression has been widely adopted within some areas as a useful alternative to ordinary least squares regression in the manner of other shrinkage methods such as principal components regression and ridge regression. In this paper we examine the nature of this shrinkage and demonstrate that partial least squares regression exhibits some undesirable properties.     

Dimension Reduction in the Linear Model for Right-Censored Data: Predicting the Change of HIV-I RNA Levels using Clinical and Protease Gene Mutation Data

With rapid development in the technology of measuring disease characteristics at molecular or genetic level, it is possible to collect a large amount of data on various potential predictors of the clinical outcome of interest in medical research. It is often of interest to effectively use the information on a large number of predictors to make prediction of the interested outcome. Various statistical tools were developed to overcome the difficulties caused by the high-dimensionality of the covariate space in the setting of a linear regression model. This paper focuses on the situation, where the interested outcomes are subjected to right censoring. We implemented the extended partial least squares method along with other commonly used approaches for analyzing the high-dimensional covariates to the ACTG333 data set. Especially, we compared the prediction performance of different approaches with extensive cross-validation studies. The results show that the Buckley–James based partial least squares, stepwise subset model selection and principal components regression have similar promising predictive power and the partial least square method has several advantages in terms of interpretability and numerical computation.     

The regression dilemma

A substantial fraction of the statistical analyses and in particular statistical computing is done under the heading of multiple linear regression. That is the fitting of equations to multivariate data using the least squares technique for estimating parameters The optimality properties of these estimates are described in an ideal setting which is not often realized in practice.

Frequently, we do not have "good" data in the sense that the errors are non-normal or the variance is non-homogeneous. The data may contain outliers or extremes which are not easily detectable but variables in the proper functional, and we. may have the linearity

Prior to the mid-sixties regression programs provided just the basic least squares computations plus possibly a step-wise algorithm for variable selection. The increased interest in regression prompted by dramatic improvements in computers has led to a vast amount of literatur describing alternatives to least squares improved variable selection methods and extensive diagnostic procedures

The purpose of this paper is to summarize and illustrate some of these recent developments. In particular we shall review some of the potential problems with regression data discuss the statistics and techniques used to detect these problems and consider some of the proposed solutions. An example is presented to illustrate the effectiveness of these diagnostic methods in revealing such problems and the potential consequences of employing the proposed methods.     

Forecasting functional time series

We propose forecasting functional time series using weighted functional principal component regression and weighted functional partial least squares regression. These approaches allow for smooth functions, assign higher weights to more recent data, and provide a modeling scheme that is easily adapted to allow for constraints and other information. We illustrate our approaches using age-specific French female mortality rates from 1816 to 2006 and age-specific Australian fertility rates from 1921 to 2006, and show that these weighted methods improve forecast accuracy in comparison to their unweighted counterparts. We also propose two new bootstrap methods to construct prediction intervals, and evaluate and compare their empirical coverage probabilities.     

Robust Estimation of Multi-response Surfaces Considering Correlation Structure

Response surfaces express the behavior of responses and can be used for both single and multi-response problems. A common approach to estimate a response surface using experimental results is the ordinary least squares (OLS) method. Since OLS is very sensitive to outliers, some robust approaches have been discussed in the literature. Although there are many methods available in the literature for multiple response optimizations, there are a few studies in model building especially robust models. Assuming correlated responses, in this paper, a robust coefficient estimation method is proposed for multi response problem based on M-estimators. In order to illustrate the performance of the proposed procedure, a contaminated experimental design using a numerical example available in the literature with some modifications is used. Both the classical multivariate least squares method and the proposed robust multivariate approach are used to estimate regression coefficients of multi-response surfaces based on this example. Moreover, a comparison of the proposed robust multi response surface (RMRS) approach with separate robust estimation of single response show that the proposed approach is more efficient.     

Markov regression models for count time series with excess zeros: A partial likelihood approach

Count data with excess zeros are common in many biomedical and public health applications. The zero-inflated Poisson (ZIP) regression model has been widely used in practice to analyze such data. In this paper, we extend the classical ZIP regression framework to model count time series with excess zeros. A Markov regression model is presented and developed, and the partial likelihood is employed for statistical inference. Partial likelihood inference has been successfully applied in modeling time series where the conditional distribution of the response lies within the exponential family. Extending this approach to ZIP time series poses methodological and theoretical challenges, since the ZIP distribution is a mixture and therefore lies outside the exponential family. In the partial likelihood framework, we develop an EM algorithm to compute the maximum partial likelihood estimator (MPLE). We establish the asymptotic theory of the MPLE under mild regularity conditions and investigate its finite sample behavior in a simulation study. The performances of different partial-likelihood based model selection criteria are compared in the presence of model misspecification. Finally, we present an epidemiological application to illustrate the proposed methodology.     

SNP selection for predicting a quantitative trait

Molecular markers combined with powerful statistical tools have made it possible to detect and analyze multiple loci on the genome that are responsible for the phenotypic variation in quantitative traits. The objectives of the study presented in this paper are to identify a subset of single nucleotide polymorphism (SNP) markers that are associated with a particular trait and to construct a model that can best predict the value of the trait given the genotypic information of the SNPs using a three-step strategy. In the first step, a genome-wide association test is performed to screen SNPs that are associated with the quantitative trait of interest. SNPs with p-values of less than 5% are then analyzed in the second step. In the second step, a large number of randomly selected models, each consisting of a fixed number of randomly selected SNPs, are analyzed using the least angle regression method. This step will further remove redundant SNPs due to the complicated association among SNPs. A subset of SNPs that are shown to have a significant effect on the response trait more often than by chance are considered for the third step. In the third step, two alternative methods are considered: the least angle shrinkage and selection operation and sparse partial least squares regression. For both methods, the predictive ability of the fitted model is evaluated by an independent test set. The performance of the proposed method is illustrated by the analysis of a real data set on Canadian Holstein cattle.     

Classification trees aided mixed regression model

This paper introduces a novel hybrid regression method (MixReg) combining two linear regression methods, ordinary least square (OLS) and least squares ratio (LSR) regression. LSR regression is a method to find the regression coefficients minimizing the sum of squared error rate while OLS minimizes the sum of squared error itself. The goal of this study is to combine two methods in a way that the proposed method superior both OLS and LSR regression methods in terms of R² statistics and relative error rate. Applications of MixReg, on both simulated and real data, show that MixReg method outperforms both OLS and LSR regression.     

Comparison of prediction methods for multicollinear data

In this paper we discuss the partial least squares (PLS) prediction method. The method is compared to the predictor based on principal component regression (PCR). Both theoretical considerations and computations on artificial and real data are presented.