When portfolio selection is implemented by using the past sample values, parameter uncertainty may lead to suboptimal portfolios. Previous studies of portfolio selection demonstrate that classical approach based on the simple mean estimator is less reliable cause of inherent estimation error. In this paper, we investigate a shrinkage estimator based on Stein’s idea in measuring the expected returns. We apply the research of Jorion (1985) to Taiwan Stock market, present the effects of estimation error on the portfolio selection and demonstrate that the shrinkage estimator is robust and dominates the classical estimator on the MSE criterion. In addition, we also examine the effect of different shrinkage target on the performance of the Bayes-Stein estimator and find that this estimator still has lower risk than the classical sample mean.

Specifying a prior distribution for the large number of parameters in the linear statistical model is a difficult step in the Bayesian approach to the design and analysis of experiments. Here we address this difficulty by proposing the use of functional priors and then by working out important details for three and higher level experiments. One of the challenges presented by higher level experiments is that a factor can be either qualitative or quantitative. We propose appropriate correlation functions and coding schemes so that the prior distribution is simple and the results easily interpretable. The prior incorporates well known experimental design principles such as effect hierarchy and effect heredity, which helps to automatically resolve the aliasing problems experienced in fractional designs. The second part of the thesis focuses on the analysis of optimization experiments. Not uncommon are designed experiments with their primary purpose being to determine optimal settings for all of the factors in some predetermined set. Here we distinguish between the two concepts of statistical significance and practical significance. We perform estimation via an empirical Bayes data analysis methodology that has been detailed in the recent literature. But then propose an alternative to the usual next step in determining optimal factor level settings. Instead of implementing variable or model selection techniques, we propose an objective function that assists in our goal of finding the ideal settings for all factors over which we experimented. The usefulness of the new approach is illustrated through the analysis of some real experiments as well as simulation.

The shrinkage estimation has proven to be very useful when dealing with a large number of mean parameters. In this dissertation, we consider the problem of simultaneous estimation of multiple variances and construct a shrinkage type, non-parametric estimator. We take the non-parametric empirical Bayes approach by starting with an arbitrary prior on the variances. Under an invariant loss function, the resultant Bayes estimator relies on the marginal cumulative distribution function of the sample variances. Replacing the marginal cdf by the empirical distribution function, we obtain a Non-parametric Empirical Bayes estimator for multiple Variances (NEBV). The proposed estimator converges to the corresponding Bayes version uniformly over a large set. Consequently, the NEBV works well in a post-selection setting. We then apply the NEBV to construct condence intervals for mean parameters in a post-selection setting. It is shown that the intervals based on the NEBV are shortest among all the intervals which guarantee a desired coverage probability. Through real data analysis, we have further shown that the NEBV based intervals lead to the smallest number of discordances, a desirable property when we are faced with the current "replication crisis". / Statistics

Mass spectrometry (MS) is widely used for proteomic and metabolomic profiling of biological samples. Data obtained by MS are often zero-inflated. Those zero values are called point mass values (PMVs). Zero values can be further grouped into biological PMVs and technical PMVs. The former type is caused by the absence of components and the latter type is caused by detection limit. There is no simple solution to separate those two types of PMVs. Mixture models were developed to separate the two types of zeros apart and to perform the differential abundance analysis. However, we notice that the mixture model can be unstable when the number of non-zero values is small. In this dissertation, we propose a new differential abundance (DA) analysis method, DASEV, which applies an empirical Bayes shrinkage estimation on variance. We hypothesized that performance on variance estimation could be more robust and thus enhance the accuracy of differential abundance analysis. Disregarding the issue the mixture models have, the method has shown promising strategies to separate two types of PMVs. We adapted the mixture distribution proposed in the original mixture model design and assumed that the variances for all components follow a certain distribution. We proposed to calculate the estimated variances by borrowing information from other components via applying the assumed distribution of variance, and then re-estimate other parameters using the estimated variances. We obtained better and more stable estimations on variance, means abundances, and proportions of biological PMVs, especially where the proportion of zeros is large. Therefore, the proposed method achieved obvious improvements in DA analysis. We also propose to extend the method for clustering analysis. To our knowledge, commonly used cluster methods for MS omics data are only K-means and Hierarchical. Both methods have their own limitations while being applied to the zero-inflated data. Model-based clustering methods are widely used by researchers for various data types including zero-inflated data. We propose to use the extension (DASEV.C) as a model-based cluster method. We compared the clustering performance of DASEV.C with K-means and Hierarchical. Under certain scenarios, the proposed method returned more accurate clusters than the standard methods. We also develop an R package dasev for the proposed methods presented in this dissertation. The major functions DASEV.DA and DASEV.C in this R package aim to implement the Bayes shrinkage estimation on variance then conduct the differential abundance and cluster analysis. We designed the functions to allow the flexibility for researchers to specify certain input options.

High-dimensional data are becoming increasingly available as data collection technology advances. Over the last decade, significant developments have been taking place in high-dimensional data analysis, driven primarily by a wide range of applications in many fields such as genomics, signal processing, and environmental studies. Statistical techniques such as dimension reduction and variable selection play important roles in high dimensional data analysis. Sufficient dimension reduction provides a way to find the reduced space of the original space without a parametric model. This method has been widely applied in many scientific fields such as genetics, brain imaging analysis, econometrics, environmental sciences, etc. in recent years. In this dissertation, we worked on three projects. The first one combines local modal regression and Minimum Average Variance Estimation (MAVE) to introduce a robust dimension reduction approach. In addition to being robust to outliers or heavy-tailed distribution, our proposed method has the same convergence rate as the original MAVE. Furthermore, we combine local modal base MAVE with a $L_1$ penalty to select informative covariates in a regression setting. This new approach can exhaustively estimate directions in the regression mean function and select informative covariates simultaneously, while being robust to the existence of possible outliers in the dependent variable. The second project develops sparse adaptive MAVE (saMAVE). SaMAVE has advantages over adaptive LASSO because it extends adaptive LASSO to multi-dimensional and nonlinear settings, without any model assumption, and has advantages over sparse inverse dimension reduction methods in that it does not require any particular probability distribution on \textbf{X}. In addition, saMAVE can exhaustively estimate the dimensions in the conditional mean function. The third project extends the envelope method to multivariate spatial data. The envelope technique is a new version of the classical multivariate linear model. The estimator from envelope asymptotically has less variation compare to the Maximum Likelihood Estimator (MLE). The current envelope methodology is for independent observations. While the assumption of independence is convenient, this does not address the additional complication associated with a spatial correlation. This work extends the idea of the envelope method to cases where independence is an unreasonable assumption, specifically multivariate data from spatially correlated process. This novel approach provides estimates for the parameters of interest with smaller variance compared to maximum likelihood estimator while still being able to capture the spatial structure in the data.