Bayesian curve fitting and clustering with Dirichlet process mixture models for microarray data

In the field of molecular biology, it is often of interest to analyze microarray data for clustering genes based on similar profiles of gene expression to identify genes that are differentially expressed under multiple biological conditions. One of the notable characteristics of a gene expression profile is that it shows a cyclic curve over a course of time. To group sequences of similar molecular functions, we propose a Bayesian Dirichlet process mixture of linear regression models with a Fourier series for the regression coefficients, for each of which a spike and slab prior is assumed. A full Gibbs-sampling algorithm is developed for an efficient Markov chain Monte Carlo (MCMC) posterior computation. Due to the so-called “label-switching” problem and different numbers of clusters during the MCMC computation, a post-process approach of Fritsch and Ickstadt (2009) is additionally applied to MCMC samples for an optimal single clustering estimate by maximizing the posterior expected adjusted Rand index with the posterior probabilities of two observations being clustered together. The proposed method is illustrated with two simulated data and one real data of the physiological response of fibroblasts to serum of Iyer et al. (1999).     

Path analysis and determining the distribution of indirect effects via simulation

The difference between a path analysis and the other multivariate analyses is that the path analysis has the ability to compute the indirect effects apart from the direct effects. The aim of this study is to investigate the distribution of indirect effects that is one of the components of path analysis via generated data. To realize this, a simulation study has been conducted with four different sample sizes, three different numbers of explanatory variables and with three different correlation matrices. A replication of 1000 has been applied for every single combination. According to the results obtained, it is found that irrespective of the sample size path coefficients tend to be stable. Moreover, path coefficients are not affected by correlation types either. Since the replication number is 1000, which is fairly large, the indirect effects from the path models have been treated as normal and their confidence intervals have been presented as well. It is also found that the path analysis should not be used with three explanatory variables. We think that this study would help scientists who are working in both natural and social sciences to determine sample size and different number of variables in the path analysis.     

Non-parametric Estimation for the Location of a Change-point in an Otherwise Smooth Hazard Function under Random Censoring

A non-parametric wavelet based estimator is proposed for the location of a change-point in an otherwise smooth hazard function under non-informative random right censoring. The proposed estimator is based on wavelet coefficients differences via an appropriate parametrization of the time-frequency plane. The study of the estimator is facilitated by the strong representation theorem for the Kaplan–Meier estimator established by Lo and Singh (1986). The performance of the estimator is checked via simulations and two real examples conclude the paper.     

Simulation-based diagnostics in random-coefficient models

Commonly applied diagnostic procedures in random-coefficient (multilevel) analysis are based on an inspection of the residuals, motivated by established procedures for ordinary regression. The deficiencies of such procedures are discussed and an alternative based on simulation from the fitted model (parametric bootstrap) is proposed. Although computationally intensive, the method proposed requires little programming effort additional to implementing the model fitting procedure. It can be tailored for specific kinds of outliers. Some computationally less demanding alternatives are described.     

Sampling Adjusted Analysis of Dynamic Additive Regression Models for Longitudinal Data

We consider a modelling approach to longitudinal data that aims at estimating flexible covariate effects in a model where the sampling probabilities are modelled explicitly. The joint modelling yields simple estimators that are easy to compute and analyse, even if the sampling of the longitudinal responses interacts with the response level. An incorrect model for the sampling probabilities results in biased estimates. Non-representative sampling occurs, for example, if patients with an extreme development (based on extreme values of the response) are called in for additional examinations and measurements. We allow covariate effects to be time-varying or time-constant. Estimates of covariate effects are obtained by solving martingale equations locally for the cumulative regression functions. Using Aalen's additive model for the sampling probabilities, we obtain simple expressions for the estimators and their asymptotic variances. The asymptotic distributions for the estimators of the non-parametric components as well as the parametric components of the model are derived drawing on general martingale results. Two applications are presented. We consider the growth of cystic fibrosis patients and the prothrombin index for liver cirrhosis patients. The conclusion about the growth of the cystic fibrosis patients is not altered when adjusting for a possible non-representativeness in the sampling, whereas we reach substantively different conclusions about the treatment effect for the liver cirrhosis patients.     

Eyes on the Block: Measuring Urban Physical Disorder Through In-Person Observation

In this paper, we present results from measuring physical disorder in Los Angeles neighborhoods. Disorder measures came from structured observations conducted by trained field interviewers. We examine inter-rater reliability of disorder measures in depth. We assess the effects of observation conditions on the reliability of reporting. Finally, we examine the relationships between disorder, other indicators of neighborhood status, and selected individual outcomes.Our results indicate that there is considerable variation in the level of agreement among independent observations across items, although overall agreement is moderate to high. Durable indicators of disorder provide the most reliable measures of neighborhood conditions. Circumstances of observation have statistically significant effects on the observers’ perceived level of disorder. Physical disorder is significantly related to other indicators of neighborhood status, and to children’s reading and behavior development.This result suggests a need for further research into the effects of neighborhood disorder on children.     

关键词拍卖中最优保留价的研究

研究了近年来在搜索引擎上广泛采用的一种广告形式——关键词拍卖.在关键词拍卖中如何设定每个关键词的保留价是搜索引擎在实践中向理论界提出的一个难题.通过建立一个可分单物品的拍卖模型来描述这种广告服务的销售机制,进而利用最优机制理论推导出每个关键词最优保留价所满足的方程.这一结果是对Riley和Samuelson关于最优机制研究中一个经典结论的推广,并可直接用于实践.     

Improving the Numerical Performance of Static and Dynamic Aggregate Discrete Choice Random Coefficients Demand Estimation

The widely used estimator of Berry, Levinsohn, and Pakes (1995) produces estimates of consumer preferences from a discrete‐choice demand model with random coefficients, market‐level demand shocks, and endogenous prices. We derive numerical theory results characterizing the properties of the nested fixed point algorithm used to evaluate the objective function of BLP's estimator. We discuss problems with typical implementations, including cases that can lead to incorrect parameter estimates. As a solution, we recast estimation as a mathematical program with equilibrium constraints, which can be faster and which avoids the numerical issues associated with nested inner loops. The advantages are even more pronounced for forward‐looking demand models where the Bellman equation must also be solved repeatedly. Several Monte Carlo and real‐data experiments support our numerical concerns about the nested fixed point approach and the advantages of constrained optimization. For static BLP, the constrained optimization approach can be as much as ten to forty times faster for large‐dimensional problems with many markets.     

实正弦信号的快速相位差分频率估计方法

基于最小均方误差相位差分频率估计原理,提出了能够直接处理实正弦信号的相位差分频率估计算法。新的修改算法利用零交越或FFT变换,能快速有效地在时域或频域上得到实正弦信号的相位信息,改善了频率估计的SNR阈值,且便于工程实现。     

Simulation of stationary Gaussian vector fields

In earlier work we described a circulant embedding approach for simulating scalar-valued stationary Gaussian random fields on a finite rectangular grid, with the covariance function prescribed. Here, we explain how the circulant embedding approach can be used to simulate Gaussian vector fields. As in the scalar case, the simulation procedure is theoretically exact if a certain non-negativity condition is satisfied. In the vector setting, this exactness condition takes the form of a nonnegative definiteness condition on a certain set of Hermitian matrices. The main computational tool used is the Fast Fourier Transform. Consequently, when implemented appropriately, the procedure is highly efficient, in terms of both CPU time and storage.