Simultaneous analysis of gene expression data and genetic variants is highly of interest, especially when the number of gene expressions and genetic variants are both greater than the sample size. Association of both causal genes and effective SNPs makes the use of sparse modeling of such genetic data sets, highly important. The high-dimensional sparse instrumental variables models are one of such useful association models, which models the simultaneous relation of the gene expressions and genetic variants with complex traits. From a Bayesian viewpoint, the sparsity can be favored using sparsity-enforcing priors such as spike-and-slab priors. A two-stage modification of the expectation propagation (EP) algorithm is proposed and examined for approximate inference in high-dimensional sparse instrumental variables models with spike-and-slab priors. This method is an adoption of the classical two-stage least squares method, to be used with the Bayes context. A simulation study is performed to examine the performance of the methods. The proposed method is applied to analysis of the mouse obesity data.
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Unsupervised learning is often used to uncover clusters in data. However, different kinds of noise may impede the discovery of useful patterns from real-world time-series data. In this work, we focus on mitigating the interference of interval censoring in the task of clustering for disease phenotyping. We develop a deep generative, continuous-time model of time-series data that clusters time-series while correcting for censorship time. We provide conditions under which clusters and the amount of delayed entry may be identified from data under a noiseless model.
We present a numerical stability analysis of the immersed boundary(IB) method for a special case which is constructed so that Fourier analysis is applicable. We examine the stability of the immersed boundary method with the discrete Fourier transforms defined differently on the fluid grid and the boundary grid. This approach gives accurate theoretical results about the stability boundary since it takes the effects of the spreading kernel of the immersed boundary method on the numerical stability into account. In this paper, the spreading kernel is the standard 4-point IB delta function. A three-dimensional incompressible viscous flow and a no-slip planar boundary are considered. The case of a planar elastic membrane is also analyzed using the same analysis framework and it serves as an example of many possible generalizations of our theory. We present some numerical results and show that the observed stability behaviors are consistent with what are predicted by our theory.
Physical simulation-based optimization is a common task in science and engineering. Many such simulations produce image- or tensor-based outputs where the desired objective is a function of those outputs, and optimization is performed over a high-dimensional parameter space. We develop a Bayesian optimization method leveraging tensor-based Gaussian process surrogates and trust region Bayesian optimization to effectively model the image outputs and to efficiently optimize these types of simulations, including a radio-frequency tower configuration problem and an optical design problem.
In this work, we focus on the high-dimensional trace regression model with a low-rank coefficient matrix. We establish a nearly optimal in-sample prediction risk bound for the rank-constrained least-squares estimator under no assumptions on the design matrix. Lying at the heart of the proof is a covering number bound for the family of projection operators corresponding to the subspaces spanned by the design. By leveraging this complexity result, we perform a power analysis for a permutation test on the existence of a low-rank signal under the high-dimensional trace regression model. Finally, we use alternating minimization to approximately solve the rank-constrained least-squares problem to evaluate its empirical in-sample prediction risk and power of the resulting permutation test in our numerical study.
Beta regression model is useful in the analysis of bounded continuous outcomes such as proportions. It is well known that for any regression model, the presence of multicollinearity leads to poor performance of the maximum likelihood estimators. The ridge type estimators have been proposed to alleviate the adverse effects of the multicollinearity. Furthermore, when some of the predictors have insignificant or weak effects on the outcomes, it is desired to recover as much information as possible from these predictors instead of discarding them all together. In this paper we proposed ridge type shrinkage estimators for the low and high dimensional beta regression model, which address the above two issues simultaneously. We compute the biases and variances of the proposed estimators in closed forms and use Monte Carlo simulations to evaluate their performances. The results show that, both in low and high dimensional data, the performance of the proposed estimators are superior to ridge estimators that discard weak or insignificant predictors. We conclude this paper by applying the proposed methods for two real data from econometric and medicine.
Feature selection is an extensively studied technique in the machine learning literature where the main objective is to identify the subset of features that provides the highest predictive power. However, in causal inference, our goal is to identify the set of variables that are associated with both the treatment variable and outcome (i.e., the confounders). While controlling for the confounding variables helps us to achieve an unbiased estimate of causal effect, recent research shows that controlling for purely outcome predictors along with the confounders can reduce the variance of the estimate. In this paper, we propose an Outcome Adaptive Elastic-Net (OAENet) method specifically designed for causal inference to select the confounders and outcome predictors for inclusion in the propensity score model or in the matching mechanism. OAENet provides two major advantages over existing methods: it performs superiorly on correlated data, and it can be applied to any matching method and any estimates. In addition, OAENet is computationally efficient compared to state-of-the-art methods.
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We prove the RLWE/PLWE equivalence for the maximal totally real subextension of the $2^rpq$-th cyclotomic field and discuss some of its applications to cryptoanalysis.
The past decade has witnessed a surge of endeavors in statistical inference for high-dimensional sparse regression, particularly via de-biasing or relaxed orthogonalization. Nevertheless, these techniques typically require a more stringent sparsity condition than needed for estimation consistency, which seriously limits their practical applicability. To alleviate such constraint, we propose to exploit the identifiable features to residualize the design matrix before performing debiasing-based inference over the parameters of interest. This leads to a hybrid orthogonalization (HOT) technique that performs strict orthogonalization against the identifiable features but relaxed orthogonalization against the others. Under an approximately sparse model with a mixture of identifiable and unidentifiable signals, we establish the asymptotic normality of the HOT test statistic while accommodating as many identifiable signals as consistent estimation allows. The efficacy of the proposed test is also demonstrated through simulation and analysis of a stock market dataset.
We consider the Bayesian approach to the linear Gaussian inference problem of inferring the initial condition of a linear dynamical system from noisy output measurements taken after the initial time. In practical applications, the large dimension of the dynamical system state poses a computational obstacle to computing the exact posterior distribution. Model reduction offers a variety of computational tools that seek to reduce this computational burden. In particular, balanced truncation is a system-theoretic approach to model reduction which obtains an efficient reduced-dimension dynamical system by projecting the system operators onto state directions which trade off the reachability and observability of state directions as expressed through the associated Gramians. We introduce Gramian definitions relevant to the inference setting and propose a balanced truncation approach based on these inference Gramians that yield a reduced dynamical system that can be used to cheaply approximate the posterior mean and covariance. Our definitions exploit natural connections between (i) the reachability Gramian and the prior covariance and (ii) the observability Gramian and the Fisher information. The resulting reduced model then inherits stability properties and error bounds from system theoretic considerations, and in some settings yields an optimal posterior covariance approximation. Numerical demonstrations on two benchmark problems in model reduction show that our method can yield near-optimal posterior covariance approximations with order-of-magnitude state dimension reduction.
Arsenic (As) and other toxic elements contamination of groundwater in Bangladesh poses a major threat to millions of people on a daily basis. Understanding complex relationships between arsenic and other elements can provide useful insights for mitigating arsenic poisoning in drinking water and requires multivariate modeling of the elements. However, environmental monitoring of such contaminants often involves a substantial proportion of left-censored observations falling below a minimum detection limit (MDL). This problem motivates us to propose a multivariate spatial Bayesian model for left-censored data for investigating the abundance of arsenic in Bangladesh groundwater and for creating spatial maps of the contaminants. Inference about the model parameters is drawn using an adaptive Markov Chain Monte Carlo (MCMC) sampling. The computation time for the proposed model is of the same order as a multivariate Gaussian process model that does not impute the censored values. The proposed method is applied to the arsenic contamination dataset made available by the Bangladesh Water Development Board (BWDB). Spatial maps of arsenic, barium (Ba), and calcium (Ca) concentrations in groundwater are prepared using the posterior predictive means calculated on a fine lattice over Bangladesh. Our results indicate that Chittagong and Dhaka divisions suffer from excessive concentrations of arsenic and only the divisions of Rajshahi and Rangpur have safe drinking water based on recommendations by the World Health Organization (WHO).
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