Bayesian penalized B-spline estimation approach for epidemic models

Ordinary differential equations (ODEs) are normally used to model dynamic processes in applied sciences such as biology, engineering, physics, and many other areas. In these models, the parameters are usually unknown, and thus they are often specified artificially or empirically. Alternatively, a feasible method is to estimate the parameters based on observed data. In this study, we propose a Bayesian penalized B-spline approach to estimate the parameters and initial values for ODEs used in epidemiology. We evaluated the efficiency of the proposed method based on simulations using the Markov chain Monte Carlo algorithm for the Kermack–McKendrick model. The proposed approach is also illustrated based on a real application to the transmission dynamics of hepatitis C virus in mainland China.     

Estimation of parameters in incomplete data models defined by dynamical systems

Parametric incomplete data models defined by ordinary differential equations (ODEs) are widely used in biostatistics to describe biological processes accurately. Their parameters are estimated on approximate models, whose regression functions are evaluated by a numerical integration method. Accurate and efficient estimations of these parameters are critical issues. This paper proposes parameter estimation methods involving either a stochastic approximation EM algorithm (SAEM) in the maximum likelihood estimation, or a Gibbs sampler in the Bayesian approach. Both algorithms involve the simulation of non-observed data with conditional distributions using Hastings–Metropolis (H–M) algorithms. A modified H–M algorithm, including an original local linearization scheme to solve the ODEs, is proposed to reduce the computational time significantly. The convergence on the approximate model of all these algorithms is proved. The errors induced by the numerical solving method on the conditional distribution, the likelihood and the posterior distribution are bounded. The Bayesian and maximum likelihood estimation methods are illustrated on a simulated pharmacokinetic nonlinear mixed-effects model defined by an ODE. Simulation results illustrate the ability of these algorithms to provide accurate estimates.     

Estimating mixed-effects differential equation models

Ordinary differential equations (ODEs) are popular tools for modeling complicated dynamic systems in many areas. When multiple replicates of measurements are available for the dynamic process, it is of great interest to estimate mixed-effects in the ODE model for the process. We propose a semiparametric method to estimate mixed-effects ODE models. Rather than using the ODE numeric solution directly, which requires providing initial conditions, this method estimates a spline function to approximate the dynamic process using smoothing splines. A roughness penalty term is defined using the ODEs, which measures the fidelity of the spline function to the ODEs. The smoothing parameter, which controls the trade-off between fitting the data and maintaining fidelity to the ODEs, can be specified by users or selected objectively by generalized cross validation. The spline coefficients, the ODE random effects, and the ODE fixed effects are estimated in three nested levels of optimization. Two simulation studies show that the proposed method obtains good estimates for mixed-effects ODE models. The semiparametric method is demonstrated with an application of a pharmacokinetic model in a study of HIV combination therapy.     

Adaptive estimation in partially linear autoregressive models

The authors consider a partially linear autoregressive model and construct kernel‐based estimates for both the parametric and nonparametric components. They propose an estimation procedure for the model and illustrate it through simulated and real data. Their work shows that the proposed estimation procedure not only has good asymptotic properties but also works well numerically. It also suggests that a partially linear autoregression is more appropriate than a completely nonparametric autoregression for some sets of data.     

A comparison of some robust, adaptive, and partially adaptive estimators of regression models

Numerous estimation techniques for regression models have been proposed. These procedures differ in how sample information is used in the estimation procedure. The efficiency of least squares (OLS) estimators implicity assumes normally distributed residuals and is very sensitive to departures from normality, particularly to "outliers" and thick-tailed distributions. Lead absolute deviation (LAD) estimators are less sensitive to outliers and are optimal for laplace random disturbances, but not for normal errors. This paper reports monte carlo comparisons of OLS,LAD, two robust estimators discussed by huber, three partially adaptiveestimators, newey's generalized method of moments estimator, and an adaptive maximum likelihood estimator based on a normal kernal studied by manski. This paper is the first to compare the relative performance of some adaptive robust estimators (partially adaptive and adaptive procedures) with some common nonadaptive robust estimators. The partially adaptive estimators are based on three flxible parametric distributions for the errors. These include the power exponential (Box-Tiao) and generalized t distributions, as well as a distribution for the errors, which is not necessarily symmetric. The adaptive procedures are "fully iterative" rather than one step estimators. The adaptive estimators have desirable large sample properties, but these properties do not necessarily carry over to the small sample case.

The monte carlo comparisons of the alternative estimators are based on four different specifications for the error distribution: a normal, a mixture of normals (or variance-contaminated normal), a bimodal mixture of normals, and a lognormal. Five hundred samples of 50 are used. The adaptive and partially adaptive estimators perform very well relative to the other estimation procedures considered, and preliminary results suggest that in some important cases they can perform much better than OLS with 50 to 80% reductions in standard errors.     

Random time step probabilistic methods for uncertainty quantification in chaotic and geometric numerical integration

A novel probabilistic numerical method for quantifying the uncertainty induced by the time integration of ordinary differential equations (ODEs) is introduced. Departing from the classical strategy to randomise ODE solvers by adding a random forcing term, we show that a probability measure over the numerical solution of ODEs can be obtained by introducing suitable random time steps in a classical time integrator. This intrinsic randomisation allows for the conservation of geometric properties of the underlying deterministic integrator such as mass conservation, symplecticity or conservation of first integrals. Weak and mean square convergence analysis is derived. We also analyse the convergence of the Monte Carlo estimator for the proposed random time step method and show that the measure obtained with repeated sampling converges in the mean square sense independently of the number of samples. Numerical examples including chaotic Hamiltonian systems, chemical reactions and Bayesian inferential problems illustrate the accuracy, robustness and versatility of our probabilistic numerical method.     

A comparison of some robust,adaptive, and partially adaptive estimators of regression models

Numerous estimation techniques for regression models have been proposed. These procedures differ in how sample information is used in the estimation procedure. The efficiency of least squares (OLS) estimators implicity assumes normally distributed residuals and is very sensitive to departures from normality, particularly to "outliers" and thick-tailed distributions. Lead absolute deviation (LAD) estimators are less sensitive to outliers and are optimal for laplace random disturbances, but not for normal errors. This paper reports monte carlo comparisons of OLS,LAD, two robust estimators discussed by huber, three partially adaptiveestimators, newey's generalized method of moments estimator, and an adaptive maximum likelihood estimator based on a normal kernal studied by manski. This paper is the first to compare the relative performance of some adaptive robust estimators (partially adaptive and adaptive procedures) with some common nonadaptive robust estimators. The partially adaptive estimators are based on three flxible parametric distributions for the errors. These include the power exponential (Box-Tiao) and generalized t distributions, as well as a distribution for the errors, which is not necessarily symmetric. The adaptive procedures are "fully iterative" rather than one step estimators. The adaptive estimators have desirable large sample properties, but these properties do not necessarily carry over to the small sample case.

The monte carlo comparisons of the alternative estimators are based on four different specifications for the error distribution: a normal, a mixture of normals (or variance-contaminated normal), a bimodal mixture of normals, and a lognormal. Five hundred samples of 50 are used. The adaptive and partially adaptive estimators perform very well relative to the other estimation procedures considered, and preliminary results suggest that in some important cases they can perform much better than OLS with 50 to 80% reductions in standard errors.

     

Quantile regression estimation of partially linear additive models

In this paper, we consider the estimation of partially linear additive quantile regression models where the conditional quantile function comprises a linear parametric component and a nonparametric additive component. We propose a two-step estimation approach: in the first step, we approximate the conditional quantile function using a series estimation method. In the second step, the nonparametric additive component is recovered using either a local polynomial estimator or a weighted Nadaraya–Watson estimator. Both consistency and asymptotic normality of the proposed estimators are established. Particularly, we show that the first-stage estimator for the finite-dimensional parameters attains the semiparametric efficiency bound under homoskedasticity, and that the second-stage estimators for the nonparametric additive component have an oracle efficiency property. Monte Carlo experiments are conducted to assess the finite sample performance of the proposed estimators. An application to a real data set is also illustrated.     

Semiparametric estimation of multivariate partially linear models

Inspired by a primary hypertension study was conducted by Chinese government in the Inner Mongolia Autonomous Region, we introduce partially linear models with multivariate responses to evaluate the simultaneous effects of modifiable risk factors on both the systolic and the diastolic blood pressures. We propose a class of weighted profile least-squares approaches to estimate both the parametric and the nonparametric components of the multivariate partially linear models. We also investigate how the weight matrix affects the resultant estimation efficiency. We illustrate our proposals through simulations and an analysis of the primary hypertension data. Our analysis provides strong evidence that the obesity is indeed an important risk factor predisposing to primary hypertension even after adjusting for the ageing effect.     

Estimation and inference for varying coefficient partially nonlinear models

In this paper, we extend the varying coefficient partially linear model to the varying coefficient partially nonlinear model in which the linear part of the varying coefficient partially linear model is replaced by a nonlinear function of the covariates. A profile nonlinear least squares estimation procedure for the parameter vector and the coefficient function vector of the varying coefficient partially nonlinear model is proposed and the asymptotic properties of the resulting estimators are established. We further propose a generalized likelihood ratio (GLR) test to check whether or not the varying coefficients in the model are constant. The asymptotic null distribution of the GLR statistic is derived and a residual-based bootstrap procedure is also suggested to derive the p-value of the GLR test. Some simulations are conducted to assess the performance of the proposed estimating and testing procedures and the results show that both the procedures perform well in finite samples. Furthermore, a real data example is given to demonstrate the application of the proposed model and its estimating and testing procedures.     

A refined parameter estimating approach for HIV dynamic model

HIV dynamic models, a set of ordinary differential equations (ODEs), have provided new understanding of the pathogenesis of HIV infection and the treatment effects of antiviral therapies. However, to estimate parameters for ODEs is very challenging due to the complexity of this nonlinear system. In this article, we propose a comprehensive procedure to deal with this issue. In the proposed procedure, a series of cutting-edge statistical methods and techniques are employed, including nonparametric mixed-effects smoothing-based methods for ODE models and stochastic approximation expectation–maximization (EM) approach for mixed-effects ODE models. A simulation study is performed to validate the proposed approach. An application example from a real HIV clinical trial study is used to illustrate the usefulness of the proposed method.     

Asymptotic properties of MLE for partially observed fractional diffusion system with dependent noises

The paper studies long time asymptotic properties of the maximum likelihood estimator (MLE) for the signal drift parameter in a partially observed fractional diffusion system with dependent noise. Using the method of weak convergence of likelihoods due to Ibragimov and Khasminskii [1981. Statistics of Random Processes. Springer, New-York], consistency, asymptotic normality and convergence of the moments are established for MLE. The proof is based on Laplace transform computations which was introduced in Brouste and Kleptsyna [2008. Asymptotic properties of MLE for partially observed fractional diffusion system, preprint].     

Statistical Inference on Partially Linear Additive Models with Missing Response Variables and Error-prone Covariates

This paper considers statistical inference for the partially linear additive models, which are useful extensions of additive models and partially linear models. We focus on the case where some covariates are measured with additive errors, and the response variable is sometimes missing. We propose a profile least-squares estimator for the parametric component and show that the resulting estimator is asymptotically normal. To construct a confidence region for the parametric component, we also propose an empirical-likelihood-based statistic, which is shown to have a chi-squared distribution asymptotically. Furthermore, a simulation study is conducted to illustrate the performance of the proposed methods.     

Mixture Model Analysis of Partially Rank‐Ordered Set Samples: Age Groups of Fish from Length‐Frequency Data

We present a novel methodology for estimating the parameters of a finite mixture model (FMM) based on partially rank‐ordered set (PROS) sampling and use it in a fishery application. A PROS sampling design first selects a simple random sample of fish and creates partially rank‐ordered judgement subsets by dividing units into subsets of prespecified sizes. The final measurements are then obtained from these partially ordered judgement subsets. The traditional expectation–maximization algorithm is not directly applicable for these observations. We propose a suitable expectation–maximization algorithm to estimate the parameters of the FMMs based on PROS samples. We also study the problem of classification of the PROS sample into the components of the FMM. We show that the maximum likelihood estimators based on PROS samples perform substantially better than their simple random sample counterparts even with small samples. The results are used to classify a fish population using the length‐frequency data.     

Estimating the Pareto parameters under progressive censoring data for constant-partially accelerated life tests

Accelerated life testing is widely used in product life testing experiments since it provides significant reduction in time and cost of testing. In this paper, assuming that the lifetime of items under use condition follow the two-parameter Pareto distribution of the second kind, partially accelerated life tests based on progressively Type-II censored samples are considered. The likelihood equations of the model parameters and the acceleration factor are reduced to a single nonlinear equation to be solved numerically to obtain the maximum-likelihood estimates (MLEs). Based on normal approximation to the asymptotic distribution of MLEs, the approximate confidence intervals (ACIs) for the parameters are derived. Two bootstrap CIs are also proposed. The classical Bayes estimates cannot be obtained in explicit form, so we propose to apply Markov chain Monte Carlo method to tackle this problem, which allows us to construct the credible interval of the involved parameters. Analysis of a simulated data set has also been presented for illustrative purposes. Finally, a Monte Carlo simulation study is carried out to investigate the precision of the Bayes estimates with MLEs and to compare the performance of different corresponding CIs considered.     

Semiparametric Estimation of Stochastic Production Frontier Models

This article extends the linear stochastic frontier model proposed by Aigner, Lovell, and Schmidt to a semiparametric frontier model in which the functional form of the production frontier is unspecified and the distributions of the composite error terms are of known form. Pseudolikelihood estimators of the parameters characterizing the two error terms of the model are constructed based on kernel estimation of the conditional mean function. The Monte Carlo results show that the proposed estimators perform well in finite samples. An empirical application is presented. Extensions to a partially linear frontier function and to more flexible one-sided error distributions than the half-normal are discussed     

Estimating partially linear panel data models with one-way error components

We consider the problem of estimating a partially linear panel data model whenthe error follows an one-way error components structure. We propose a feasiblesemiparametric generalized least squares (GLS) type estimator for estimating the coefficient of the linear component and show that it is asymptotically more efficient than a semiparametric ordinary least squares (OLS) type estimator. We also discussed the case when the regressor of the parametric component is correlated with the error, and propose an instrumental variable GLS-type semiparametric estimator.     

Partially Accelerated Life Tests for the Weibull Distribution Under Multiply Censored Data

This article aims to estimate the parameters of the Weibull distribution in step-stress partially accelerated life tests under multiply censored data. The step partially acceleration life test is that all test units are first run simultaneously under normal conditions for a pre-specified time, and the surviving units are then run under accelerated conditions until a predetermined censoring time. The maximum likelihood estimates are used to obtaining the parameters of the Weibull distribution and the acceleration factor under multiply censored data. Additionally, the confidence intervals for the estimators are obtained. Simulation results show that the maximum likelihood estimates perform well in most cases in terms of the mean bias, errors in the root mean square and the coverage rate. An example is used to illustrate the performance of the proposed approach.     

Empirical likelihood inferences for varying coefficient partially nonlinear models

In this article, empirical likelihood inferences for the varying coefficient partially nonlinear models are investigated. An empirical log-likelihood ratio function for the unknown parameter vector in the nonlinear function part and a residual-adjusted empirical log-likelihood ratio function for the nonparametric component are proposed. The corresponding Wilks phenomena are proved and the confidence regions for parametric component and nonparametric component are constructed. Simulation studies indicate that, in terms of coverage probabilities and average areas of the confidence regions, the empirical likelihood method performs better than the normal approximation-based method. Furthermore, a real data set application is also provided to illustrate the proposed empirical likelihood estimation technique.     

部分线性模型非参数部分的多项式类关系的检验

对于部分线性模型中非参数部分是否为多项式函数的检验问题,应该先确定其是否为多项式函数类。通过对部分线性模型的拟合残差进行再光滑,基于其变化的趋势性构造统计量以检验其是否为多项式函数类,给出了计算检验P-值的精确算法和三阶矩χ2逼近方法,模拟例子与实际例子充分显示了本方法的有效性。