B样条copula函数由归一化B样条基元的线性组合定义。我们提出了一种改进的EM算法，用于最大化惩罚伪似然函数，其中惩罚项采用平滑剪切绝对偏差（SCAD）惩罚函数。我们开展了模拟研究，验证了所提数值过程的稳定性，结果表明当真实参数矩阵具有稀疏性时，惩罚项能得到均方误差更小的估计，并给出了调优参数确定与模型选择的方法。我们以“Our World in Data”网站上可获取的237个国家的出生率与死亡率数据集为例进行分析，估计了两类比率的边际密度与分布函数，以及我们的B-spline copula模型的所有参数。
英文摘要：
The B-spline copula function is defined by a linear combination of elements of the normalized B-spline basis. We develop a modified EM algorithm, to maximize the penalized pseudo-likelihood function, wherein we use the smoothly clipped absolute deviation (SCAD) penalty function for the penalization term. We conduct simulation studies to demonstrate the stability of the proposed numerical procedure, show that penalization yields estimates with smaller mean-square errors when the true parameter matrix is sparse, and provide methods for determining tuning parameters and for model selection. We analyze as an example a data set consisting of birth and death rates from 237 countries, available at the website, ''Our World in Data,'' and we estimate the marginal density and distribution functions of those rates together with all parameters of our B-spline copula model.
In this article, we consider the problem of reconstructing networks for continuous, binary, count and discrete ordinal variables by estimating sparse precision matrix in Gaussian copula graphical models. We propose two approaches: $\ell_1$ penalized extended rank likelihood with Monte Carlo Expectation-Maximization algorithm (copula EM glasso) and copula skeptic with pair-wise copula estimation for copula Gaussian graphical models. The proposed approaches help to infer networks arising from nonnormal and mixed variables. We demonstrate the performance of our methods through simulation studies …
Penalized spline smoothing is a popular and flexible method of obtaining estimates in nonparametric regression but the classical least-squares criterion is highly susceptible to model deviations and atypical observations. Penalized spline estimation with a resistant loss function is a natural remedy, yet to this day the asymptotic properties of M-type penalized spline estimators have not been studied. We show in this paper that M-type penalized spline estimators achieve the same rates of convergence as their least-squares counterparts, even with auxiliary scale estimation. We further find theo…
Regression spline is a useful tool in nonparametric regression. However, finding the optimal knot locations is a known difficult problem. In this article, we introduce the Non-concave Penalized Regression Spline. This proposal method not only produces smoothing spline with optimal convergence rate, but also can adaptively select optimal knots simultaneously. It is insensitive to the number of origin knots. The method's performance in a simulation has been studied to compare the other methods. The problem of how to choose smoothing parameters, i.e. penalty parameters in the non-concave regressi…
The paper motivates high dimensional smoothing with penalized splines and its numerical calculation in an efficient way. If smoothing is carried out over three or more covariates the classical tensor product spline bases explode in their dimension bringing the estimation to its numerical limits. A recent approach by Siebenborn and Wagner(2019) circumvents storage expensive implementations by proposing matrix-free calculations which allows to smooth over several covariates. We extend their approach here by linking penalized smoothing and its Bayesian formulation as mixed model which provides a …
Vine copulas (or pair-copula constructions) have become an important tool for high-dimensional dependence modeling. Typically, so called simplified vine copula models are estimated where bivariate conditional copulas are approximated by bivariate unconditional copulas. We present the first non-parametric estimator of a non-simplified vine copula that allows for varying conditional copulas using penalized hierarchical B-splines. Throughout the vine copula, we test for the simplifying assumption in each edge, establishing a data-driven non-simplified vine copula estimator. To overcome the curse …
We propose a flexible copula model to describe changes with a covariate in the dependence structure of (conditionally exchangeable) random variables. The starting point is a spline approximation to the generator of an Archimedean copula. Changes in the dependence structure with a covariate $x$ are modelled by flexible regression of the spline coefficients on $x$. The performances and properties of the spline estimate of the reference generator and the abilities of these conditional models to approximate conditional copulas are studied through simulations. Inference is made using Bayesian argum…
The selection of smoothing parameter is central to the estimation of penalized splines. The best value of the smoothing parameter is often the one that optimizes a smoothness selection criterion, such as generalized cross-validation error (GCV) and restricted likelihood (REML). To correctly identify the global optimum rather than being trapped in an undesired local optimum, grid search is recommended for optimization. Unfortunately, the grid search method requires a pre-specified search interval that contains the unknown global optimum, yet no guideline is available for providing this interval…
Data analysed here derive from experiments conducted to study neurons' activity in the visual cortex of behaving monkeys. We consider a spatio-temporal adaptive penalized spline (P-spline) approach for modelling the firing rate of visual neurons. To the best of our knowledge, this is the first attempt in the statistical literature for locally adaptive smoothing in three dimensions. Estimation is based on the Separation of Overlapping Penalties (SOP) algorithm, which provides the stability and speed we look for.
Bayesian P-splines assume an intrinsic Gaussian Markov random field prior on the spline coefficients, conditional on a precision hyper-parameter $τ$. Prior elicitation of $τ$ is difficult. To overcome this issue we aim to building priors on an interpretable property of the model, indicating the complexity of the smooth function to be estimated. Following this idea, we propose Penalized Complexity (PC) priors for the number of effective degrees of freedom. We present the general ideas behind the construction of these new PC priors, describe their properties and show how to implement them in P-s…
Penalized spline estimation with discrete difference penalties (P-splines) is a popular estimation method for semiparametric models, but the classical least-squares estimator is highly sensitive to deviations from its ideal model assumptions. To remedy this deficiency, a broad class of P-spline estimators based on general loss functions is introduced and studied. Robust estimators are obtained by well-chosen loss functions, such as the Huber or Tukey loss function. A preliminary scale estimator can also be included in the loss function. It is shown that this class of P-spline estimators enjoys…
Penalized spline regression is a popular method for scatterplot smoothing, but there has long been a debate on how to construct confidence intervals for penalized spline fits. Due to the penalty, the fitted smooth curve is a biased estimate of the target function. Many methods, including Bayesian intervals and the simple-shift bias-reduction, have been proposed to upgrade the coverage of the confidence intervals, but these methods usually fail to adequately improve the situation at predictor values where the function is sharply curved. In this paper, we develop a novel approach to improving th…
In the past decades, the growing amount of network data has lead to many novel statistical models. In this paper we consider so called geometric networks. Typical examples are road networks or other infrastructure networks. But also the neurons or the blood vessels in a human body can be interpreted as a geometric network embedded in a three-dimensional space. In all these applications a network specific metric rather than the Euclidean metric is usually used, which makes the analyses on network data challenging. We consider network based point processes and our task is to estimate the intensi…
In the presence of unmeasured spatial confounding, spatial models may actually increase (rather than decrease) bias, leading to uncertainty as to how they should be applied in practice. We evaluated spatial modeling approaches through simulation and application to a big data electronic health record study. Whereas the risk of bias was high for purely spatial exposures (e.g., built environment), we found very limited potential for increased bias for individual-level exposures that cluster spatially (e.g., smoking status). We also proposed a novel exposure-penalized spline approach that selects …
Despite their widespread use in practice, the asymptotic properties of Bayesian penalized splines have not been investigated so far. We close this gap and study posterior concentration rates for Bayesian penalized splines in a Gaussian nonparametric regression model. A key feature of the approach is the hyperprior on the smoothing variance, which allows for adaptive smoothing in practice but complicates the theoretical analysis considerably as it destroys conjugacy and precludes analytic expressions for the posterior moments. To derive our theoretical results, we rely on several new concepts i…
Nonparametric Density Estimation for Data Scattered on Irregular Spatial Domains: A Likelihood-Based Approach Using Bivariate Penalized Spline Smoothing
Stochastic volatility (SV) models mimic many of the stylized facts attributed to time series of asset returns, while maintaining conceptual simplicity. The commonly made assumption of conditionally normally distributed or Student-t-distributed returns, given the volatility, has however been questioned. In this manuscript, we introduce a novel maximum penalized likelihood approach for estimating the conditional distribution in an SV model in a nonparametric way, thus avoiding any potentially critical assumptions on the shape. The considered framework exploits the strengths both of the powerful …
Generalized additive models (GAMs) are a well-established statistical tool for modeling complex nonlinear relationships between covariates and a response assumed to have a conditional distribution in the exponential family. In this article, P-splines and the Laplace approximation are coupled for flexible and fast approximate Bayesian inference in GAMs. The proposed Laplace-P-spline model contributes to the development of a new methodology to explore the posterior penalty space by considering a deterministic grid-based strategy or a Markov chain sampler, depending on the number of smooth additi…
P-splines are penalized B-splines, in which finite order differences in coefficients are typically penalized with an $\ell_2$ norm. P-splines can be used for semiparametric regression and can include random effects to account for within-subject variability. In addition to $\ell_2$ penalties, $\ell_1$-type penalties have been used in nonparametric and semiparametric regression to achieve greater flexibility, such as in locally adaptive regression splines, $\ell_1$ trend filtering, and the fused lasso additive model. However, there has been less focus on using $\ell_1$ penalties in P-splines, pa…
For multivariate nonparametric regression, functional analysis-of-variance (ANOVA) modeling aims to capture the relationship between a response and covariates by decomposing the unknown function into various components, representing main effects, two-way interactions, etc. Such an approach has been pursued explicitly in smoothing spline ANOVA modeling and implicitly in various greedy methods such as MARS. We develop a new method for functional ANOVA modeling, based on doubly penalized estimation using total-variation and empirical-norm penalties, to achieve sparse selection of component functi…
We propose a fast penalized spline method for bivariate smoothing. Univariate P-spline smoothers (Eilers and Marx, 1996) are applied simultaneously along both coordinates. The new smoother has a sandwich form which suggested the name "sandwich smoother" to a referee. The sandwich smoother has a tensor product structure that simplifies an asymptotic analysis and it can be fast computed. We derive a local central limit theorem for the sandwich smoother, with simple expressions for the asymptotic bias and variance, by showing that the sandwich smoother is asymptotically equivalent to a bivariate …
Spatial Capture-Recapture With Penalized Regression Splines to Flexibly Model Wildlife Density and Distribution
Utrecht University（乌得勒支大学）；University of Glasgow（格拉斯哥大学）；University of St Andrews（圣安德鲁斯大学）；World Wide Fund for Nature（世界自然基金会）；University of Auckland（奥克兰大学）
In the last decade, simplified vine copula models have been an active area of research. They build a high dimensional probability density from the product of marginals densities and bivariate copula densities. Besides parametric models, several approaches to nonparametric estimation of vine copulas have been proposed. In this article, we extend these approaches and compare them in an extensive simulation study and a real data application. We identify several factors driving the relative performance of the estimators. The most important one is the strength of dependence. No method was found to …
The functional linear model is a popular tool to investigate the relationship between a scalar/functional response variable and a scalar/functional covariate. We generalize this model to a functional linear mixed-effects model when repeated measurements are available on multiple subjects. Each subject has an individual intercept and slope function, while shares common population intercept and slope function. This model is flexible in the sense of allowing the slope random effects to change with the time. We propose a penalized spline smoothing method to estimate the population and random slope…
We consider efficient estimation of flexible transformation models with interval-censored data. To reduce the dimension of semi-parametric models, the unknown monotone transformation function is approximated via monotone splines. A penalization technique is used to provide more computationally efficient estimation of all parameters. To accomplish model fitting, a computationally efficient nested iterative expectation-maximization (EM) based algorithm is developed for estimation, and an easily implemented variance-covariance approach is proposed for inference on regression parameters. Theoretic…
Handling Overlapping Asymmetric Datasets -- A Twice Penalized P-Spline Approach
Newcastle University（纽卡斯尔大学）；School of Computing（计算机学院）；School of Mathematics, Statistics and Physics（数学、统计与物理学院）；Translational & Clinical Research Institute（转化与临床研究院）
Covariance estimation is essential yet underdeveloped for analyzing multivariate functional data. We propose a fast covariance estimation method for multivariate sparse functional data using bivariate penalized splines. The tensor-product B-spline formulation of the proposed method enables a simple spectral decomposition of the associated covariance operator and explicit expressions of the resulting eigenfunctions as linear combinations of B-spline bases, thereby dramatically facilitating subsequent principal component analysis. We derive a fast algorithm for selecting the smoothing parameters…
In many psychometric applications, the relationship between the mean of an outcome and a quantitative covariate is too complex to be described by simple parametric functions; instead, flexible nonlinear relationships can be incorporated using penalized splines. Penalized splines can be conveniently represented as a linear mixed effects model (LMM), where the coefficients of the spline basis functions are random effects. The LMM representation of penalized splines makes the extension to multivariate outcomes relatively straightforward. In the LMM, no effect of the quantitative covariate on the …
Dynamic Contrast-enhanced Magnetic Resonance Imaging (DCE-MRI) is an important tool for detecting subtle kinetic changes in cancerous tissue. Quantitative analysis of DCE-MRI typically involves the convolution of an arterial input function (AIF) with a nonlinear pharmacokinetic model of the contrast agent concentration. Parameters of the kinetic model are biologically meaningful, but the optimization of the non-linear model has significant computational issues. In practice, convergence of the optimization algorithm is not guaranteed and the accuracy of the model fitting may be compromised. To …
Extreme-value copulas arise as the limiting dependence structure of component-wise maxima. Defined in terms of a functional parameter, they are one of the most widespread copula families due to their flexibility and ability to capture asymmetry. Despite this, meeting the complex analytical properties of this parameter in an unconstrained setting remains a challenge, restricting most uses to models with very few parameters or nonparametric models. Focusing on the bivariate case, we propose a novel semiparametric approach. Our procedure relies on a series of transformations, including Williamson…
Rigby & Stasinopoulos (2005) introduced generalized additive models for location, scale and shape (GAMLSS) where the response distribution is not restricted to belong to the exponential family and its parameters can be specified as functions of additive predictors that allows for several types of covariate effects (e.g., linear, non-linear, random and spatial effects). In many empirical situations, however, modeling simultaneously two or more responses conditional on some covariates can be of considerable relevance. In this article, we extend the scope of GAMLSS by introducing a bivariate copu…
Spatial data collected worldwide at a huge number of locations are frequently used in environmental and climate studies. Spatial modelling for this type of data presents both methodological and computational challenges. In this work we illustrate a computationally efficient non parametric framework to model and estimate the spatial field while accounting for geodesic distances between locations. The spatial field is modelled via penalized splines (P-splines) using intrinsic Gaussian Markov Random Field (GMRF) priors for the spline coefficients. The key idea is to use the sphere as a surrogate …
We consider estimation and inference in a single index regression model with an unknown but smooth link function. In contrast to the standard approach of using kernels or regression splines, we use smoothing splines to estimate the smooth link function. We develop a method to compute the penalized least squares estimators (PLSEs) of the parametric and the nonparametric components given independent and identically distributed (i.i.d.)~data. We prove the consistency and find the rates of convergence of the estimators. We establish asymptotic normality under under mild assumption and prove asympt…
In this paper we introduce a new methodology to determine an optimal coefficient of penalized functional regression. We assume the dependent, independent variables and the regression coefficients are functions of time and error dynamics follow a stochastic differential equation. First we construct our objective function as a time dependent residual sum of square and then minimize it with respect to regression coefficients subject to different error dynamics such as LASSO, group LASSO, fused LASSO and cubic smoothing spline. Then we use Feynman-type path integral approach to determine a Schrödi…
Regression models with functional responses and covariates constitute a powerful and increasingly important model class. However, regression with functional data poses well known and challenging problems of non-identifiability. This non-identifiability can manifest itself in arbitrarily large errors for coefficient surface estimates despite accurate predictions of the responses, thus invalidating substantial interpretations of the fitted models. We offer an accessible rephrasing of these identifiability issues in realistic applications of penalized linear function-on-function-regression and de…
A theorem of McCann shows that for any two absolutely continuous probability measures on R^d there exists a monotone transformation sending one probability measure to the other. A consequence of this theorem, relevant to statistics, is that density estimation can be recast in terms of transformations. In particular, one can fix any absolutely continuous probability measure, call it P, and then reparameterize the whole class of absolutely continuous probability measures as monotone transformations from P. In this paper we utilize this reparameterization of densities, as monotone transformations…
Smoothing of noisy sample covariances is an important component in functional data analysis. We propose a novel covariance smoothing method based on penalized splines and associated software. The proposed method is a bivariate spline smoother that is designed for covariance smoothing and can be used for sparse functional or longitudinal data. We propose a fast algorithm for covariance smoothing using leave-one-subject-out cross validation. Our simulations show that the proposed method compares favorably against several commonly used methods. The method is applied to a study of child growth led…
Similar to variable selection in the linear regression model, selecting significant components in the popular additive regression model is of great interest. However, such components are unknown smooth functions of independent variables, which are unobservable. As such, some approximation is needed. In this paper, we suggest a combination of penalized regression spline approximation and group variable selection, called the lasso-type spline method (LSM), to handle this component selection problem with a diverging number of strongly correlated variables in each group. It is shown that the propo…
Recombinant Inbred Lines derived from divergent parental lines can display extensive segregation distortion and long-range linkage disequilibrium (LD) between distant loci. These genomic signatures are consistent with epistatic selection during inbreeding. Epistatic interactions affect growth and fertility traits or even cause complete lethality. Detecting epistasis is challenging as multiple testing approaches are under-powered and true long-range LD is difficult to distinguish from drift. Here we develop a method for reconstructing an underlying network of genomic signatures of high-dimensio…
We discuss the semiparametric modeling of mark-recapture-recovery data where the temporal and/or individual variation of model parameters is explained via covariates. Typically, in such analyses a fixed (or mixed) effects parametric model is specified for the relationship between the model parameters and the covariates of interest. In this paper, we discuss the modeling of the relationship via the use of penalized splines, to allow for considerably more flexible functional forms. Corresponding models can be fitted via numerical maximum penalized likelihood estimation, employing cross-validatio…
A novel generalized additive scalar-on-function regression model for partially observed multidimensional functional data: An application to air quality classification
