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Neste trabalho estudam-se alguns novos métodos de seleção de variáveis no contexto da regressão linear que surgiram nos últimos 15 anos, especificamente o LARS - Least Angle Regression, o NAMS - Noise Addition Model Selection, a Razão de Falsa Seleção - RFS (FSR em inglês), o LASSO Bayesiano e o Spike-and-Slab LASSO. A metodologia foi a análise e comparação dos métodos estudados e aplicações. Após esse estudo, realizam-se aplicações em bases de dados reais e um estudo de simulação, em que todos os métodos se mostraram promissores, com os métodos Bayesianos apresentando os melhores resultados. / In this work, some new variable selection methods that have appeared in the last 15 years in the context of linear regression are studied, specifically the LARS - Least Angle Regression, the NAMS - Noise Addition Model Selection, the False Selection Rate - FSR, the Bayesian LASSO and the Spike-and-Slab LASSO. The methodology was the analysis and comparison of the studied methods. After this study, applications to real data bases are made, as well as a simulation study, in which all methods are shown to be promising, with the Bayesian methods showing the best results.

Neste trabalho estudam-se alguns novos métodos de seleção de variáveis no contexto da regressão linear que surgiram nos últimos 15 anos, especificamente o LARS - Least Angle Regression, o NAMS - Noise Addition Model Selection, a Razão de Falsa Seleção - RFS (FSR em inglês), o LASSO Bayesiano e o Spike-and-Slab LASSO. A metodologia foi a análise e comparação dos métodos estudados e aplicações. Após esse estudo, realizam-se aplicações em bases de dados reais e um estudo de simulação, em que todos os métodos se mostraram promissores, com os métodos Bayesianos apresentando os melhores resultados. / In this work, some new variable selection methods that have appeared in the last 15 years in the context of linear regression are studied, specifically the LARS - Least Angle Regression, the NAMS - Noise Addition Model Selection, the False Selection Rate - FSR, the Bayesian LASSO and the Spike-and-Slab LASSO. The methodology was the analysis and comparison of the studied methods. After this study, applications to real data bases are made, as well as a simulation study, in which all methods are shown to be promising, with the Bayesian methods showing the best results.

We develop statistical methods for tackling two important problems in genetic association studies. First, we propose a Bayesian approach to overcome the winner's curse in genetic studies. Second, we consider a Bayesian latent variable model for analyzing longitudinal family data with pleiotropic phenotypes. Winner's curse in genetic association studies refers to the estimation bias of the reported odds ratios (OR) for an associated genetic variant from the initial discovery samples. It is a consequence of the sequential procedure in which the estimated effect of an associated genetic marker must first pass a stringent significance threshold. We propose a hierarchical Bayes method in which a spike-and-slab prior is used to account for the possibility that the significant test result may be due to chance. We examine the robustness of the method using different priors corresponding to different degrees of confidence in the testing results and propose a Bayesian model averaging procedure to combine estimates produced by different models. The Bayesian estimators yield smaller variance compared to the conditional likelihood estimator and outperform the latter in the low power studies. We investigate the performance of the method with simulations and applications to four real data examples. Pleiotropy occurs when a single genetic factor influences multiple quantitative or qualitative phenotypes, and it is present in many genetic studies of complex human traits. The longitudinal family studies combine the features of longitudinal studies in individuals and cross-sectional studies in families. Therefore, they provide more information about the genetic and environmental factors associated with the trait of interest. We propose a Bayesian latent variable modeling approach to model multiple phenotypes simultaneously in order to detect the pleiotropic effect and allow for longitudinal and/or family data. An efficient MCMC algorithm is developed to obtain the posterior samples by using hierarchical centering and parameter expansion techniques. We apply spike and slab prior methods to test whether the phenotypes are significantly associated with the latent disease status. We compute Bayes factors using path sampling and discuss their application in testing the significance of factor loadings and the indirect fixed effects. We examine the performance of our methods via extensive simulations and apply them to the blood pressure data from a genetic study of type 1 diabetes (T1D) complications.

We develop statistical methods for tackling two important problems in genetic association studies. First, we propose a Bayesian approach to overcome the winner's curse in genetic studies. Second, we consider a Bayesian latent variable model for analyzing longitudinal family data with pleiotropic phenotypes. Winner's curse in genetic association studies refers to the estimation bias of the reported odds ratios (OR) for an associated genetic variant from the initial discovery samples. It is a consequence of the sequential procedure in which the estimated effect of an associated genetic marker must first pass a stringent significance threshold. We propose a hierarchical Bayes method in which a spike-and-slab prior is used to account for the possibility that the significant test result may be due to chance. We examine the robustness of the method using different priors corresponding to different degrees of confidence in the testing results and propose a Bayesian model averaging procedure to combine estimates produced by different models. The Bayesian estimators yield smaller variance compared to the conditional likelihood estimator and outperform the latter in the low power studies. We investigate the performance of the method with simulations and applications to four real data examples. Pleiotropy occurs when a single genetic factor influences multiple quantitative or qualitative phenotypes, and it is present in many genetic studies of complex human traits. The longitudinal family studies combine the features of longitudinal studies in individuals and cross-sectional studies in families. Therefore, they provide more information about the genetic and environmental factors associated with the trait of interest. We propose a Bayesian latent variable modeling approach to model multiple phenotypes simultaneously in order to detect the pleiotropic effect and allow for longitudinal and/or family data. An efficient MCMC algorithm is developed to obtain the posterior samples by using hierarchical centering and parameter expansion techniques. We apply spike and slab prior methods to test whether the phenotypes are significantly associated with the latent disease status. We compute Bayes factors using path sampling and discuss their application in testing the significance of factor loadings and the indirect fixed effects. We examine the performance of our methods via extensive simulations and apply them to the blood pressure data from a genetic study of type 1 diabetes (T1D) complications.

We study how to perform effective Bayesian inference in high-dimensional sparse Factor Analysis models with a zero-norm, sparsity-inducing prior on the model parameters. Such priors represent a methodological ideal, but Bayesian inference in such models is usually regarded as impractical. We test this view. After empirically characterising the properties of existing algorithmic approaches, we use techniques from statistical mechanics to derive a theory of optimal learning in the restricted setting of sparse PCA with a single factor. Finally, we describe a novel `Dense Message Passing' algorithm (DMP) which achieves near-optimal performance on synthetic data generated from this model.DMP exploits properties of high-dimensional problems to operate successfully on a densely connected graphical model. Similar algorithms have been developed in the statistical physics community and previously applied to inference problems in coding and sparse classification. We demonstrate that DMP out-performs both a newly proposed variational hybrid algorithm and two other recently published algorithms (SPCA and emPCA) on synthetic data while it explains at least the same amount of variance, for a given level of sparsity, in two gene expression datasets used in previous studies of sparse PCA.A significant potential advantage of DMP is that it provides an estimate of the marginal likelihood which can be used for hyperparameter optimisation. We show that, for the single factor case, this estimate exhibits good qualitative agreement both with theoretical predictions and with the hyperparameter posterior inferred by a collapsed Gibbs sampler. Preliminary work on an extension to inference of multiple factors indicates its potential for selecting an optimal model from amongst candidates which differ both in numbers of factors and their levels of sparsity.