Miracle-dz/UniFAR-FTUs huggingface dataset:
Graphs for Margins of Bayesian Networks

Directed acyclic graph (DAG) models—also called Bayesian networks—are widely used in probabilistic reasoning, machine learning and causal inference. If latent variables are present, then the set of possible marginal distributions over the remaining (observed) variables is generally not represented by any DAG. Larger classes of mixed graphical models have been introduced to overcome this; however, as we show, these classes are not sufficiently rich to capture all the marginal models that can arise. We introduce a new class of hyper‐graphs, called mDAGs, and a latent projection operation to obtain an mDAG from the margin of a DAG. We show that each distinct marginal of a DAG model is represented by at least one mDAG and provide graphical results towards characterizing equivalence of these models. Finally, we show that mDAGs correctly capture the marginal structure of causally interpreted DAGs under interventions on the observed variables.
Bayesian meta-analysis of correlation coefficients through power prior

ABSTRACT This article proposes a Bayesian approach for meta-analysis of correlation coefficients through power prior. The primary purpose of this method is to allow meta-analytic researchers to evaluate the contribution and influence of each individual study to the estimated overall effect size though power prior. We use the relationship between high-performance work systems and financial performance as an example to illustrate how to apply this method. We also introduce free online software that can be used to conduct Bayesian meta-analysis proposed in this study. Implications and future directions are also discussed in this article.
A Factor-Adjusted Multiple Testing Procedure With Application to Mutual Fund Selection

In this article, we propose a factor-adjusted multiple testing (FAT) procedure based on factor-adjusted p-values in a linear factor model involving some observable and unobservable factors, for the purpose of selecting skilled funds in empirical finance. The factor-adjusted p-values were obtained after extracting the latent common factors by the principal component method. Under some mild conditions, the false discovery proportion can be consistently estimated even if the idiosyncratic errors are allowed to be weakly correlated across units. Furthermore, by appropriately setting a sequence of threshold values approaching zero, the proposed FAT procedure enjoys model selection consistency. Extensive simulation studies and a real data analysis for selecting skilled funds in the U.S. financial market are presented to illustrate the practical utility of the proposed method. Supplementary materials for this article are available online.
Regression Trees for Longitudinal Data

While studying response trajectory, often the population of interest may be diverse enough to exist distinct subgroups within it and the longitudinal change in response may not be uniform in these subgroups. That is, the timeslope and/or influence of covariates in longitudinal profile may vary among these different subgroups. For example, Raudenbush (2001) used depression as an example to argue that it is incorrect to assume that all the people in a given population would be experiencing either increasing or decreasing levels of depression. In such cases, traditional linear mixed effects model (assuming common parametric form for covariates and time) is not directly applicable for the entire population as a group-averaged trajectory can mask important subgroup differences. Our aim is to identify and characterize longitudinally homogeneous subgroups based on the combination of baseline covariates in the most parsimonious way. This goal can be achieved via constructing regression tree for longitudinal data using baseline covariates as partitioning variables. We have proposed LongCART algorithm to construct regression tree for the longitudinal data. In each node, the proposed LongCART algorithm determines the need for further splitting (i.e. whether parameter(s) of longitudinal profile is influenced by any baseline attributes) via parameter instability tests and thus the decision of further splitting is type-I error controlled. We have obtained the asymptotic results for the proposed instability test and examined finite sample behavior of the whole algorithm through simulation studies. Finally, we have applied the LongCART algorithm to study the longitudinal changes in choline level among HIV patients.
Rates of convergence in conditional covariance matrix with nonparametric entries estimation

Abstract Given and two random variables, assume the model where is an unknown function and ε is a random error. We estimate the conditional covariance matrix applying a plug-in kernel-based algorithm to its entries. Next, we investigate the estimators rate of convergence under smoothness hypotheses on the density function of In a high-dimensional context, we improve the consistency the whole matrix estimator by providing a decreasing structure over the entries. We illustrate a sliced inverse regression setting with a simulation study.
Generalizations related to hypothesis testing with the Posterior distribution of the Likelihood Ratio

The Posterior distribution of the Likelihood Ratio (PLR) is proposed by Dempster in 1974 for significance testing in the simple vs composite hypotheses case. In this hypotheses test case, classical frequentist and Bayesian hypotheses tests are irreconcilable, as emphasized by Lindley's paradox, Berger & Selke in 1987 and many others. However, Dempster shows that the PLR (with inner threshold 1) is equal to the frequentist p-value in the simple Gaussian case. In 1997, Aitkin extends this result by adding a nuisance parameter and showing its asymptotic validity under more general distributions. Here we extend the reconciliation between the PLR and a frequentist p-value for a finite sample, through a framework analogous to the Stein's theorem frame in which a credible (Bayesian) domain is equal to a confidence (frequentist) domain. This general reconciliation result only concerns simple vs composite hypotheses testing. The measures proposed by Aitkin in 2010 and Evans in 1997 have interesting properties and extend Dempster's PLR but only by adding a nuisance parameter. Here we propose two extensions of the PLR concept to the general composite vs composite hypotheses test. The first extension can be defined for improper priors as soon as the posterior is proper. The second extension appears from a new Bayesian-type Neyman-Pearson lemma and emphasizes, from a Bayesian perspective, the role of the LR as a discrepancy variable for hypothesis testing.
Quantile Regression for Location‐Scale Time Series Models with Conditional Heteroscedasticity

This paper considers quantile regression for a wide class of time series models including autoregressive and moving average (ARMA) models with asymmetric generalized autoregressive conditional heteroscedasticity errors. The classical mean‐variance models are reinterpreted as conditional location‐scale models so that the quantile regression method can be naturally geared into the considered models. The consistency and asymptotic normality of the quantile regression estimator is established in location‐scale time series models under mild conditions. In the application of this result to ARMA‐generalized autoregressive conditional heteroscedasticity models, more primitive conditions are deduced to obtain the asymptotic properties. For illustration, a simulation study and a real data analysis are provided.
Adaptive LASSO model selection in a multiphase quantile regression

We propose a general adaptive LASSO method for a quantile regression model. Our method is very interesting when we know nothing about the first two moments of the model error. We first prove that the obtained estimators satisfy the oracle properties, which involves the relevant variable selection without using hypothesis test. Next, we study the proposed method when the (multiphase) model changes to unknown observations called change-points. Convergence rates of the change-points and of the regression parameter estimators in each phase are found. The sparsity of the adaptive LASSO quantile estimators of the regression parameters is not affected by the change-points estimation. If the number of phases is unknown, a consistent criterion is proposed. Numerical studies by Monte Carlo simulations show the performance of the proposed method, compared to other existing methods in the literature, for models with a single phase or for multiphase models. The adaptive LASSO quantile method performs better than known variable selection methods, as the least squared method with adaptive LASSO penalty, -method with LASSO-type penalty and quantile method with SCAD penalty.
Higher criticism: $p$-values and criticism

This paper compares the higher criticism statistic (Donoho and Jin [Ann. Statist. 32 (2004) 962-994]), a modification of the higher criticism statistic also suggested by Donoho and Jin, and two statistics of the Berk-Jones [Z. Wahrsch. Verw. Gebiete 47 (1979) 47-59] type. New approximations to the significance levels of the statistics are derived, and their accuracy is studied by simulations. By numerical examples it is shown that over a broad range of sample sizes the Berk-Jones statistics have a better power function than the higher criticism statistics to detect sparse mixtures. The applications suggested by Meinshausen and Rice [Ann. Statist. 34 (2006) 373-393], to find lower confidence bounds for the number of false hypotheses, and by Jeng, Cai and Li [Biometrika 100 (2013) 157-172], to detect copy number variants, are also studied.
The Efficiency of Density Deconvolution

The density deconvolution problem involves recovering a target density g from a sample that has been corrupted by noise. From the perspective of Le Cam's local asymptotic normality theory, we show that non-parametric density deconvolution with Gaussian noise behaves similarly to a low-dimensional parametric problem that can easily be solved by maximum likelihood. This framework allows us to give a simple account of the statistical efficiency of density deconvolution and to concisely describe the effect of Gaussian noise on our ability to estimate g, all while relying on classical maximum likelihood theory instead of the kernel estimators typically used to study density deconvolution.
Estimating the turning point location in shifted exponential model of time series

ABSTRACT We consider the distribution of the turning point location of time series modeled as the sum of deterministic trend plus random noise. If the variables are modeled by shifted exponentials, whose location parameters define the trend, we provide a formula for computing the distribution of the turning point location and consequently to estimate a confidence interval for the location. We test this formula in simulated data series having a trend with asymmetric minimum, investigating the coverage rate as a function of a bandwidth parameter. The method is applied to estimate the confidence interval of the minimum location of two types of real-time series: the RT intervals extracted from the electrocardiogram recorded during the exercise test and an economic indicator, the current account balance. We discuss the connection with stochastic ordering.
A fully Bayesian strategy for high-dimensional hierarchical modeling using massively parallel computing

Markov chain Monte Carlo (MCMC) is the predominant tool used in Bayesian parameter estimation for hierarchical models. When the model expands due to an increasing number of hierarchical levels, number of groups at a particular level, or number of observations in each group, a fully Bayesian analysis via MCMC can easily become computationally demanding, even intractable. We illustrate how the steps in an MCMC for hierarchical models are predominantly one of two types: conditionally independent draws or low-dimensional draws based on summary statistics of parameters at higher levels of the hierarchy. Parallel computing can increase efficiency by performing embarrassingly parallel computations for conditionally independent draws and calculating the summary statistics using parallel reductions. During the MCMC algorithm, we record running means and means of squared parameter values to allow convergence diagnosis and posterior inference while avoiding the costly memory transfer bottleneck. We demonstrate the effectiveness of the algorithm on a model motivated by next generation sequencing data, and we release our implementation in R packages fbseq and fbseqCUDA.
Analysis of Non‐Stationary Modulated Time Series with Applications to Oceanographic Surface Flow Measurements

We propose a new class of univariate non‐stationary time series models, using the framework of modulated time series, which is appropriate for the analysis of rapidly evolving time series as well as time series observations with missing data. We extend our techniques to a class of bivariate time series that are isotropic. Exact inference is often not computationally viable for time series analysis, and so we propose an estimation method based on the Whittle likelihood, a commonly adopted pseudo‐likelihood. Our inference procedure is shown to be consistent under standard assumptions, as well as having considerably lower computational cost than exact likelihood in general. We show the utility of this framework for the analysis of drifting instruments, an analysis that is key to characterizing global ocean circulation and therefore also for decadal to century‐scale climate understanding.
The regularized tau estimator: A robust and efficient solution to ill-posed linear inverse problems

Linear inverse problems are ubiquitous. Often the measurements do not follow a Gaussian distribution. Additionally, a model matrix with a large condition number can complicate the problem further by making it ill-posed. In this case, the performance of popular estimators may deteriorate significantly. We have developed a new estimator that is both nearly optimal in the presence of Gaussian errors while being also robust against outliers. Furthermore, it obtains meaningful estimates when the problem is ill-posed through the inclusion of $\ell_1$ and $\ell_2$ regularizations. The computation of our estimate involves minimizing a non-convex objective function. Hence, we are not guaranteed to find the global minimum in a reasonable amount of time. Thus, we propose two algorithms that converge to a good local minimum in a reasonable (and adjustable) amount of time, as an approximation of the global minimum. We also analyze how the introduction of the regularization term affects the statistical properties of our estimator. We confirm high robustness against outliers and asymptotic efficiency for Gaussian distributions by deriving measures of robustness such as the influence function, sensitivity curve, bias, asymptotic variance, and mean square error. We verify the theoretical results using numerical experiments and show that the proposed estimator outperforms recently proposed methods, especially for increasing amounts of outlier contamination. Python code for all of the algorithms are available online in the spirit of reproducible research.
High Dimensional Linear Regression via the R2-D2 Shrinkage Prior

We propose a new class of priors for linear regression, the R-square induced Dirichlet Decomposition (R2-D2) prior. The prior is induced by a Beta prior on the coefficient of determination, and then the total prior variance of the regression coefficients is decomposed through a Dirichlet prior. We demonstrate both theoretically and empirically the advantages of the R2-D2 prior over a number of common shrink- age priors, including the Horseshoe, Horseshoe+, and Dirichlet-Laplace priors. The R2-D2 prior possesses the fastest concentration rate around zero and heaviest tails among these common shrinkage priors, which is established based on its marginal density, a Meijer G-function. We show that its Bayes estimator converges to the truth at a Kullback-Leibler super-efficient rate, attaining a sharper information theoretic bound than existing common shrinkage priors. We also demonstrate that the R2-D2 prior yields a consistent posterior. The R2-D2 prior permits straightforward Gibbs sampling and thus enjoys computational tractability. The proposed prior is further investigated in a mouse gene expression application.
Tensor Graphical Model: Non-Convex Optimization and Statistical Inference

We consider the estimation and inference of graphical models that characterize the dependency structure of high-dimensional tensor-valued data. To facilitate the estimation of the precision matrix corresponding to each way of the tensor, we assume the data follow a tensor normal distribution whose covariance has a Kronecker product structure. A critical challenge in the estimation and inference of this model is the fact that its penalized maximum likelihood estimation involves minimizing a non-convex objective function. To address it, this paper makes two contributions: (i) In spite of the non-convexity of this estimation problem, we prove that an alternating minimization algorithm, which iteratively estimates each sparse precision matrix while fixing the others, attains an estimator with an optimal statistical rate of convergence. (ii) We propose a de-biased statistical inference procedure for testing hypotheses on the true support of the sparse precision matrices, and employ it for testing a growing number of hypothesis with false discovery rate (FDR) control. The asymptotic normality of our test statistic and the consistency of FDR control procedure are established. Our theoretical results are backed up by thorough numerical studies and our real applications on neuroimaging studies of Autism spectrum disorder and users’ advertising click analysis bring new scientific findings and business insights. The proposed methods are encoded into a publicly available R package Tlasso.
Identifying Outliers using Influence Function of Multiple Kernel Canonical Correlation Analysis

Imaging genetic research has essentially focused on discovering unique and co-association effects, but typically ignoring to identify outliers or atypical objects in genetic as well as non-genetics variables. Identifying significant outliers is an essential and challenging issue for imaging genetics and multiple sources data analysis. Therefore, we need to examine for transcription errors of identified outliers. First, we address the influence function (IF) of kernel mean element, kernel covariance operator, kernel cross-covariance operator, kernel canonical correlation analysis (kernel CCA) and multiple kernel CCA. Second, we propose an IF of multiple kernel CCA, which can be applied for more than two datasets. Third, we propose a visualization method to detect influential observations of multiple sources of data based on the IF of kernel CCA and multiple kernel CCA. Finally, the proposed methods are capable of analyzing outliers of subjects usually found in biomedical applications, in which the number of dimension is large. To examine the outliers, we use the stem-and-leaf display. Experiments on both synthesized and imaging genetics data (e.g., SNP, fMRI, and DNA methylation) demonstrate that the proposed visualization can be applied effectively.
Iterative Ensemble Smoother as an Approximate Solution to a Regularized Minimum-Average-Cost Problem: Theory and Applications

The focus of this work is on an alternative implementation of the iterative ensemble smoother (iES). We show that iteration formulae similar to those used in \cite{chen2013-levenberg,emerick2012ensemble} can be derived by adopting a regularized Levenberg-Marquardt (RLM) algorithm \cite{jin2010regularized} to approximately solve a minimum-average-cost (MAC) problem. This not only leads to an alternative theoretical tool in understanding and analyzing the behaviour of the aforementioned iES, but also provides insights and guidelines for further developments of the smoothing algorithms. For illustration, we compare the performance of an implementation of the RLM-MAC algorithm to that of the approximate iES used in \cite{chen2013-levenberg} in three numerical examples: an initial condition estimation problem in a strongly nonlinear system, a facies estimation problem in a 2D reservoir and the history matching problem in the Brugge field case. In these three specific cases, the RLM-MAC algorithm exhibits comparable or even better performance, especially in the strongly nonlinear system.
A test for second‐order stationarity of time series based on unsystematic sub‐samples

In this paper, we introduce a new method for testing the stationarity of time series, where the test statistic is obtained from measuring and maximizing the difference in the second‐order structure over pairs of randomly drawn intervals. The asymptotic normality of the test statistic is established for both Gaussian and a range of non‐Gaussian time series, and a bootstrap procedure is proposed for estimating the variance of the main statistics. Further, we show the consistency of our test under local alternatives. Because of the flexibility inherent in the random, unsystematic sub‐samples used for test statistic construction, the proposed method is able to identify the intervals of significant departure from the stationarity without any dyadic constraints, which is an advantage over other tests employing systematic designs. We demonstrate its good finite sample performance on both simulated and real data, particularly in detecting localized departure from the stationarity. Copyright © 2016 John Wiley & Sons, Ltd.
Exact Clustering of Weighted Graphs via Semidefinite Programming

As a model problem for clustering, we consider the densest k-disjoint-clique problem of partitioning a weighted complete graph into k disjoint subgraphs such that the sum of the densities of these subgraphs is maximized. We establish that such subgraphs can be recovered from the solution of a particular semidefinite relaxation with high probability if the input graph is sampled from a distribution of clusterable graphs. Specifically, the semidefinite relaxation is exact if the graph consists of k large disjoint subgraphs, corresponding to clusters, with weight concentrated within these subgraphs, plus a moderate number of outliers. Further, we establish that if noise is weakly obscuring these clusters, i.e, the between-cluster edges are assigned very small weights, then we can recover significantly smaller clusters. For example, we show that in approximately sparse graphs, where the between-cluster weights tend to zero as the size n of the graph tends to infinity, we can recover clusters of size polylogarithmic in n. Empirical evidence from numerical simulations is also provided to support these theoretical phase transitions to perfect recovery of the cluster structure.
Minimum disparity estimation in controlled branching processes

Minimum disparity estimation in controlled branching processes is dealt with by assuming that the offspring law belongs to a general parametric family. Under some regularity conditions it is proved that the minimum disparity estimators proposed -based on the nonparametric maximum likelihood estimator of the offspring law when the entire family tree is observed- are consistent and asymptotic normally distributed. Moreover, it is discussed the robustness of the estimators proposed. Through a simulated example, focussing on the minimum Hellinger and negative exponential disparity estimators, it is shown that both are robust against outliers, being the negative exponential one also robust against inliers.