Recent advances in technology for brain imaging and high-throughput genotyping have motivated studies examining the influence of genetic variation on brain structure. In this setting, high-dimensional regression for multi-SNP association analysis is challenging as the brain imaging phenotypes are multivariate and there is a desire to incorporate a biological group structure among SNPs based on their belonging genes. Wang et al. (Bioinformatics, 2012) have recently developed an approach for simultaneous estimation and SNP selection based on penalized regression with regularization based on a novel group l_{2,1}-norm penalty, which encourages sparsity at the gene level. A problem with the proposed approach is that it only provides a point estimate. We solve this problem by developing a corresponding Bayesian formulation based on a three-level hierarchical model that allows for full posterior inference using Gibbs sampling. For the selection of tuning parameters, we consider techniques based on: (i) a fully Bayes approach with hyperpriors, (ii) empirical Bayes with implementation based on a Monte Carlo EM algorithm, and (iii) cross-validation (CV). When the number of SNPs is greater than the number of observations we find that both the fully Bayes and empirical Bayes approaches overestimate the tuning parameters, leading to overshrinkage of regression coefficients. To understand this problem we derive an approximation to the marginal likelihood and investigate its shape under different settings. Our investigation sheds some light on the problem and suggests the use of cross-validation or its approximation with WAIC (Watanabe, 2010) when the number of SNPs is relatively large. Properties of our Gibbs-WAIC approach are investigated using a simulation study and we apply the methodology to a large dataset collected as part of the Alzheimer's Disease Neuroimaging Initiative. / Graduate

There has been extensive research done in the area of Semiparametric Regression. These techniques deliver substantial improvements over previously developed methods, such as Ordinary Least Squares and Kernel Regression. Two of these hybrid techniques: Model Robust Regression 1 (MRR1) and Model Robust Regression 2 (MRR2) require the choice of an appropriate bandwidth for smoothing and a mixing parameter that allows a portion of a nonparametric fit to be used in fitting a model that may be misspecifed by other regression methods. The current method of choosing the bandwidth and mixing parameter does not guarantee the optimal choices in either case. The immediate objective of the current work is to address this process of choosing the optimal bandwidth and mixing parameter and to examine the behavior of these estimates using 3D plots. The 3D plots allow us to examine how the semiparametric techniques: MRR1 and MRR2, behave for the optimal (AVEMSE) selection process when compared to data-driven selectors, such as PRESS* and PRESS**. It was found that the structure of MRR2 behaved consistently under all conditions. MRR2 displayed a wider range of "acceptable" values for the choice of bandwidth as opposed to a much more limited choice when using MRR1. These results provide general support for earlier fndings by Mays et al. (2000).

No description available.

This thesis is a contribution to the research area concerned with selection of smoothing parameters in the framework of nonparametric and semiparametric regression. Selection of smoothing parameters is one of the most important issues in this framework and the choice can heavily influence subsequent results. A nonparametric or semiparametric approach is often desirable when large datasets are available since this allow us to make fewer and weaker assumptions as opposed to what is needed in a parametric approach. In the first paper we consider smoothing parameter selection in nonparametric regression when the purpose is to accurately predict future or unobserved data. We study the use of accumulated prediction errors and make comparisons to leave-one-out cross-validation which is widely used by practitioners. In the second paper a general semiparametric additive model is considered and the focus is on selection of smoothing parameters when optimal estimation of some specific parameter is of interest. We introduce a double smoothing estimator of a mean squared error and propose to select smoothing parameters by minimizing this estimator. Our approach is compared with existing methods.The third paper is concerned with the selection of smoothing parameters optimal for estimating average treatment effects defined within the potential outcome framework. For this estimation problem we propose double smoothing methods similar to the method proposed in the second paper. Theoretical properties of the proposed methods are derived and comparisons with existing methods are made by simulations.In the last paper we apply our results from the third paper by using a double smoothing method for selecting smoothing parameters when estimating average treatment effects on the treated. We estimate the effect on BMI of divorcing in middle age. Rich data on socioeconomic conditions, health and lifestyle from Swedish longitudinal registers is used.

No description available.

京都大学 / 0048 / 新制・課程博士 / 博士(工学) / 甲第22757号 / 工博第4756号 / 新制||工||1744(附属図書館) / 京都大学大学院工学研究科都市社会工学専攻 / (主査)教授 五十嵐 晃, 教授 高橋 良和, 准教授 古川 愛子 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DFAM

No description available.

This study intends to build up new techniques for how to obtain completely data-driven choices of the smoothing parameter in functional estimation, within the confines of minimal assumptions. The focus of the study will be within the framework of the estimation of the distribution function, the density function and their multivariable extensions along with some of their functionals such as the location and the integrated squared derivatives.

The estimation of the ratio of two probability densities is an important statistical tool in supervised machine learning. In this work, we introduce new methods of density ratio estimation based on the solution of a multidimensional integral equation involving cumulative distribution functions. The resulting methods use the novel V -matrix, a concept that does not appear in previous density ratio estimation methods. Experiments demonstrate the good potential of this new approach against previous methods. Mutual Information - MI - estimation is a key component in feature selection and essentially depends on density ratio estimation. Using one of the methods of density ratio estimation proposed in this work, we derive a new estimator - VMI - and compare it experimentally to previously proposed MI estimators. Experiments conducted solely on mutual information estimation show that VMI compares favorably to previous estimators. Experiments applying MI estimation to feature selection in classification tasks evidence that better MI estimation leads to better feature selection performance. Parameter selection greatly impacts the classification accuracy of the kernel-based Support Vector Machines - SVM. However, this step is often overlooked in experimental comparisons, for it is time consuming and requires familiarity with the inner workings of SVM. In this work, we propose procedures for SVM parameter selection which are economic in their running time. In addition, we propose the use of a non-linear kernel function - the min kernel - that can be applied to both low- and high-dimensional cases without adding another parameter to the selection process. The combination of the proposed parameter selection procedures and the min kernel yields a convenient way of economically extracting good classification performance from SVM. The Regularized Least Squares - RLS - regression method is another kernel method that depends on proper selection of its parameters. When training data is scarce, traditional parameter selection often leads to poor regression estimation. In order to mitigate this issue, we explore a kernel that is less susceptible to overfitting - the additive INK-splines kernel. Then, we consider alternative parameter selection methods to cross-validation that have been shown to perform well for other regression methods. Experiments conducted on real-world datasets show that the additive INK-splines kernel outperforms both the RBF and the previously proposed multiplicative INK-splines kernel. They also show that the alternative parameter selection procedures fail to consistently improve performance. Still, we find that the Finite Prediction Error method with the additive INK-splines kernel performs comparably to cross-validation. / A estimação da razão entre duas densidades de probabilidade é uma importante ferramenta no aprendizado de máquina supervisionado. Neste trabalho, novos métodos de estimação da razão de densidades são propostos baseados na solução de uma equação integral multidimensional. Os métodos resultantes usam o conceito de matriz-V , o qual não aparece em métodos anteriores de estimação da razão de densidades. Experimentos demonstram o bom potencial da nova abordagem com relação a métodos anteriores. A estimação da Informação Mútua - IM - é um componente importante em seleção de atributos e depende essencialmente da estimação da razão de densidades. Usando o método de estimação da razão de densidades proposto neste trabalho, um novo estimador - VMI - é proposto e comparado experimentalmente a estimadores de IM anteriores. Experimentos conduzidos na estimação de IM mostram que VMI atinge melhor desempenho na estimação do que métodos anteriores. Experimentos que aplicam estimação de IM em seleção de atributos para classificação evidenciam que uma melhor estimação de IM leva as melhorias na seleção de atributos. A tarefa de seleção de parâmetros impacta fortemente o classificador baseado em kernel Support Vector Machines - SVM. Contudo, esse passo é frequentemente deixado de lado em avaliações experimentais, pois costuma consumir tempo computacional e requerer familiaridade com as engrenagens de SVM. Neste trabalho, procedimentos de seleção de parâmetros para SVM são propostos de tal forma a serem econômicos em gasto de tempo computacional. Além disso, o uso de um kernel não linear - o chamado kernel min - é proposto de tal forma que possa ser aplicado a casos de baixa e alta dimensionalidade e sem adicionar um outro parâmetro a ser selecionado. A combinação dos procedimentos de seleção de parâmetros propostos com o kernel min produz uma maneira conveniente de se extrair economicamente um classificador SVM com boa performance. O método de regressão Regularized Least Squares - RLS - é um outro método baseado em kernel que depende de uma seleção de parâmetros adequada. Quando dados de treinamento são escassos, uma seleção de parâmetros tradicional em RLS frequentemente leva a uma estimação ruim da função de regressão. Para aliviar esse problema, é explorado neste trabalho um kernel menos suscetível a superajuste - o kernel INK-splines aditivo. Após, são explorados métodos de seleção de parâmetros alternativos à validação cruzada e que obtiveram bom desempenho em outros métodos de regressão. Experimentos conduzidos em conjuntos de dados reais mostram que o kernel INK-splines aditivo tem desempenho superior ao kernel RBF e ao kernel INK-splines multiplicativo previamente proposto. Os experimentos também mostram que os procedimentos alternativos de seleção de parâmetros considerados não melhoram consistentemente o desempenho. Ainda assim, o método Finite Prediction Error com o kernel INK-splines aditivo possui desempenho comparável à validação cruzada.

The estimation of the ratio of two probability densities is an important statistical tool in supervised machine learning. In this work, we introduce new methods of density ratio estimation based on the solution of a multidimensional integral equation involving cumulative distribution functions. The resulting methods use the novel V -matrix, a concept that does not appear in previous density ratio estimation methods. Experiments demonstrate the good potential of this new approach against previous methods. Mutual Information - MI - estimation is a key component in feature selection and essentially depends on density ratio estimation. Using one of the methods of density ratio estimation proposed in this work, we derive a new estimator - VMI - and compare it experimentally to previously proposed MI estimators. Experiments conducted solely on mutual information estimation show that VMI compares favorably to previous estimators. Experiments applying MI estimation to feature selection in classification tasks evidence that better MI estimation leads to better feature selection performance. Parameter selection greatly impacts the classification accuracy of the kernel-based Support Vector Machines - SVM. However, this step is often overlooked in experimental comparisons, for it is time consuming and requires familiarity with the inner workings of SVM. In this work, we propose procedures for SVM parameter selection which are economic in their running time. In addition, we propose the use of a non-linear kernel function - the min kernel - that can be applied to both low- and high-dimensional cases without adding another parameter to the selection process. The combination of the proposed parameter selection procedures and the min kernel yields a convenient way of economically extracting good classification performance from SVM. The Regularized Least Squares - RLS - regression method is another kernel method that depends on proper selection of its parameters. When training data is scarce, traditional parameter selection often leads to poor regression estimation. In order to mitigate this issue, we explore a kernel that is less susceptible to overfitting - the additive INK-splines kernel. Then, we consider alternative parameter selection methods to cross-validation that have been shown to perform well for other regression methods. Experiments conducted on real-world datasets show that the additive INK-splines kernel outperforms both the RBF and the previously proposed multiplicative INK-splines kernel. They also show that the alternative parameter selection procedures fail to consistently improve performance. Still, we find that the Finite Prediction Error method with the additive INK-splines kernel performs comparably to cross-validation. / A estimação da razão entre duas densidades de probabilidade é uma importante ferramenta no aprendizado de máquina supervisionado. Neste trabalho, novos métodos de estimação da razão de densidades são propostos baseados na solução de uma equação integral multidimensional. Os métodos resultantes usam o conceito de matriz-V , o qual não aparece em métodos anteriores de estimação da razão de densidades. Experimentos demonstram o bom potencial da nova abordagem com relação a métodos anteriores. A estimação da Informação Mútua - IM - é um componente importante em seleção de atributos e depende essencialmente da estimação da razão de densidades. Usando o método de estimação da razão de densidades proposto neste trabalho, um novo estimador - VMI - é proposto e comparado experimentalmente a estimadores de IM anteriores. Experimentos conduzidos na estimação de IM mostram que VMI atinge melhor desempenho na estimação do que métodos anteriores. Experimentos que aplicam estimação de IM em seleção de atributos para classificação evidenciam que uma melhor estimação de IM leva as melhorias na seleção de atributos. A tarefa de seleção de parâmetros impacta fortemente o classificador baseado em kernel Support Vector Machines - SVM. Contudo, esse passo é frequentemente deixado de lado em avaliações experimentais, pois costuma consumir tempo computacional e requerer familiaridade com as engrenagens de SVM. Neste trabalho, procedimentos de seleção de parâmetros para SVM são propostos de tal forma a serem econômicos em gasto de tempo computacional. Além disso, o uso de um kernel não linear - o chamado kernel min - é proposto de tal forma que possa ser aplicado a casos de baixa e alta dimensionalidade e sem adicionar um outro parâmetro a ser selecionado. A combinação dos procedimentos de seleção de parâmetros propostos com o kernel min produz uma maneira conveniente de se extrair economicamente um classificador SVM com boa performance. O método de regressão Regularized Least Squares - RLS - é um outro método baseado em kernel que depende de uma seleção de parâmetros adequada. Quando dados de treinamento são escassos, uma seleção de parâmetros tradicional em RLS frequentemente leva a uma estimação ruim da função de regressão. Para aliviar esse problema, é explorado neste trabalho um kernel menos suscetível a superajuste - o kernel INK-splines aditivo. Após, são explorados métodos de seleção de parâmetros alternativos à validação cruzada e que obtiveram bom desempenho em outros métodos de regressão. Experimentos conduzidos em conjuntos de dados reais mostram que o kernel INK-splines aditivo tem desempenho superior ao kernel RBF e ao kernel INK-splines multiplicativo previamente proposto. Os experimentos também mostram que os procedimentos alternativos de seleção de parâmetros considerados não melhoram consistentemente o desempenho. Ainda assim, o método Finite Prediction Error com o kernel INK-splines aditivo possui desempenho comparável à validação cruzada.