cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5885179
title: Graphical Model Selection for Gaussian Conditional Random Fields in the Presence of Latent Variables

description: We consider the problem of learning a conditional Gaussian graphical model in the presence of latent variables. Building on recent advances in this field, we suggest a method that decomposes the parameters of a conditional Markov random field into the sum of a sparse and a low-rank matrix. We derive convergence bounds for this estimator and show that it is well-behaved in the high-dimensional regime as well as “sparsistent” (i.e., capable of recovering the graph structure). We then show how proximal gradient algorithms and semi-definite programming techniques can be employed to fit the model to thousands of variables. Through extensive simulations, we illustrate the conditions required for identifiability and show that there is a wide range of situations in which this model performs significantly better than its counterparts, for example, by accommodating more latent variables. Finally, the suggested method is applied to two datasets comprising individual level data on genetic variants and metabolites levels. We show our results replicate better than alternative approaches and show enriched biological signal. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.6075764
title: Probabilistic Community Detection With Unknown Number of Communities

description: A fundamental problem in network analysis is clustering the nodes into groups which share a similar connectivity pattern. Existing algorithms for community detection assume the knowledge of the number of clusters or estimate it a priori using various selection criteria and subsequently estimate the community structure. Ignoring the uncertainty in the first stage may lead to erroneous clustering, particularly when the community structure is vague. We instead propose a coherent probabilistic framework for simultaneous estimation of the number of communities and the community structure, adapting recently developed Bayesian nonparametric techniques to network models. An efficient Markov chain Monte Carlo (MCMC) algorithm is proposed which obviates the need to perform reversible jump MCMC on the number of clusters. The methodology is shown to outperform recently developed community detection algorithms in a variety of synthetic data examples and in benchmark real-datasets. Using an appropriate metric on the space of all configurations, we develop nonasymptotic Bayes risk bounds even when the number of clusters is unknown. Enroute, we develop concentration properties of nonlinear functions of Bernoulli random variables, which may be of independent interest in analysis of related models. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.6075764.v2
title: Probabilistic Community Detection With Unknown Number of Communities

description: A fundamental problem in network analysis is clustering the nodes into groups which share a similar connectivity pattern. Existing algorithms for community detection assume the knowledge of the number of clusters or estimate it a priori using various selection criteria and subsequently estimate the community structure. Ignoring the uncertainty in the first stage may lead to erroneous clustering, particularly when the community structure is vague. We instead propose a coherent probabilistic framework for simultaneous estimation of the number of communities and the community structure, adapting recently developed Bayesian nonparametric techniques to network models. An efficient Markov chain Monte Carlo (MCMC) algorithm is proposed which obviates the need to perform reversible jump MCMC on the number of clusters. The methodology is shown to outperform recently developed community detection algorithms in a variety of synthetic data examples and in benchmark real-datasets. Using an appropriate metric on the space of all configurations, we develop nonasymptotic Bayes risk bounds even when the number of clusters is unknown. Enroute, we develop concentration properties of nonlinear functions of Bernoulli random variables, which may be of independent interest in analysis of related models. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.6826949
title: Functional Data Analysis of Dynamic PET Data

description: One application of positron emission tomography (PET), a nuclear imaging technique, in neuroscience involves in vivo estimation of the density of various proteins (often, neuroreceptors) in the brain. PET scanning begins with the injection of a radiolabeled tracer that binds preferentially to the target protein; tracer molecules are then continuously delivered to the brain via the bloodstream. By detecting the radioactive decay of the tracer over time, dynamic PET data are constructed to reflect the concentration of the target protein in the brain at each time. The fundamental problem in the analysis of dynamic PET data involves estimating the impulse response function (IRF), which is necessary for describing the binding behavior of the injected radiotracer. Virtually all existing methods have three common aspects: summarizing the entire IRF with a single scalar measure; modeling each subject separately; and the imposition of parametric restrictions on the IRF. In contrast, we propose a functional data analytic approach that regards each subject’s IRF as the basic analysis unit, models multiple subjects simultaneously, and estimates the IRF nonparametrically. We pose our model as a linear mixed effect model in which population level fixed effects and subject-specific random effects are expanded using a <i>B</i>-spline basis. Shrinkage and roughness penalties are incorporated in the model to enforce identifiability and smoothness of the estimated curves, respectively, while monotonicity and nonnegativity constraints impose biological information on estimates. We illustrate this approach by applying it to clinical PET data with subjects belonging to three diagnosic groups. We explore differences among groups by means of pointwise confidence intervals of the estimated mean curves based on bootstrap samples. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.5985043.v3
title: <b>cmenet</b>: A New Method for Bi-Level Variable Selection of Conditional Main Effects

description: This article introduces a novel method for selecting main effects and a set of reparameterized effects called conditional main effects (CMEs), which capture the conditional effect of a factor at a fixed level of another factor. CMEs represent interpretable, domain-specific phenomena for a wide range of applications in engineering, social sciences, and genomics. The key challenge is in incorporating the implicit grouped structure of CMEs within the variable selection procedure itself. We propose a new method, cmenet, which employs two principles called CME coupling and CME reduction to effectively navigate the selection algorithm. Simulation studies demonstrate the improved CME selection performance of cmenet over more generic selection methods. Applied to a gene association study on fly wing shape, cmenet not only yields more parsimonious models and improved predictive performance over standard two-factor interaction analysis methods, but also reveals important insights on gene activation behavior, which can be used to guide further experiments. Efficient implementations of our algorithms are available in the R package cmenet in CRAN. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.5985043
title: <b>cmenet</b>: A New Method for Bi-Level Variable Selection of Conditional Main Effects

description: This article introduces a novel method for selecting main effects and a set of reparameterized effects called conditional main effects (CMEs), which capture the conditional effect of a factor at a fixed level of another factor. CMEs represent interpretable, domain-specific phenomena for a wide range of applications in engineering, social sciences, and genomics. The key challenge is in incorporating the implicit grouped structure of CMEs within the variable selection procedure itself. We propose a new method, cmenet, which employs two principles called CME coupling and CME reduction to effectively navigate the selection algorithm. Simulation studies demonstrate the improved CME selection performance of cmenet over more generic selection methods. Applied to a gene association study on fly wing shape, cmenet not only yields more parsimonious models and improved predictive performance over standard two-factor interaction analysis methods, but also reveals important insights on gene activation behavior, which can be used to guide further experiments. Efficient implementations of our algorithms are available in the R package cmenet in CRAN. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.6826949.v3
title: Functional Data Analysis of Dynamic PET Data

description: One application of positron emission tomography (PET), a nuclear imaging technique, in neuroscience involves in vivo estimation of the density of various proteins (often, neuroreceptors) in the brain. PET scanning begins with the injection of a radiolabeled tracer that binds preferentially to the target protein; tracer molecules are then continuously delivered to the brain via the bloodstream. By detecting the radioactive decay of the tracer over time, dynamic PET data are constructed to reflect the concentration of the target protein in the brain at each time. The fundamental problem in the analysis of dynamic PET data involves estimating the impulse response function (IRF), which is necessary for describing the binding behavior of the injected radiotracer. Virtually all existing methods have three common aspects: summarizing the entire IRF with a single scalar measure; modeling each subject separately; and the imposition of parametric restrictions on the IRF. In contrast, we propose a functional data analytic approach that regards each subject’s IRF as the basic analysis unit, models multiple subjects simultaneously, and estimates the IRF nonparametrically. We pose our model as a linear mixed effect model in which population level fixed effects and subject-specific random effects are expanded using a <i>B</i>-spline basis. Shrinkage and roughness penalties are incorporated in the model to enforce identifiability and smoothness of the estimated curves, respectively, while monotonicity and nonnegativity constraints impose biological information on estimates. We illustrate this approach by applying it to clinical PET data with subjects belonging to three diagnosic groups. We explore differences among groups by means of pointwise confidence intervals of the estimated mean curves based on bootstrap samples. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.6938537
title: Joint Indirect Standardization When Only Marginal Distributions are Observed in the Index Population

description: It is a common interest in medicine to determine whether a hospital meets a benchmark created from an aggregate reference population, after accounting for differences in distributions of multiple covariates. Due to the difficulties of collecting individual-level data, however, it is often the case that only marginal distributions of the covariates are available, making covariate-adjusted comparison challenging. We propose and evaluate a novel approach for conducting indirect standardization when only marginal covariate distributions of the studied hospital are known, but complete information is available for the reference hospitals. We do this with the aid of two existing methods: iterative proportional fit, which estimates the cells of a contingency table when only marginal sums are known, and synthetic control methods, which create a counterfactual control group using a weighted combination of potential control groups. The proper application of these existing methods for indirect standardization would require accounting for the statistical uncertainties induced by a situation where no individual-level data are collected from the studied population. We address this need with a novel method which uses a random Dirichlet parameterization of the synthetic control weights to estimate uncertainty intervals for the standard incidence ratio. We demonstrate our novel methods by estimating hospital-level standardized incidence ratios for comparing the adjusted probability of computed tomography examinations with high radiations doses, relative to a reference standard and we evaluate out methods in a simulation study. Supplementary materials for this article, including a standardized description of the materials available for reproducing the work, are available as an online supplement.
DOI: 10.6084/m9.figshare.6938537.v3
title: Joint Indirect Standardization When Only Marginal Distributions are Observed in the Index Population

description: It is a common interest in medicine to determine whether a hospital meets a benchmark created from an aggregate reference population, after accounting for differences in distributions of multiple covariates. Due to the difficulties of collecting individual-level data, however, it is often the case that only marginal distributions of the covariates are available, making covariate-adjusted comparison challenging. We propose and evaluate a novel approach for conducting indirect standardization when only marginal covariate distributions of the studied hospital are known, but complete information is available for the reference hospitals. We do this with the aid of two existing methods: iterative proportional fit, which estimates the cells of a contingency table when only marginal sums are known, and synthetic control methods, which create a counterfactual control group using a weighted combination of potential control groups. The proper application of these existing methods for indirect standardization would require accounting for the statistical uncertainties induced by a situation where no individual-level data are collected from the studied population. We address this need with a novel method which uses a random Dirichlet parameterization of the synthetic control weights to estimate uncertainty intervals for the standard incidence ratio. We demonstrate our novel methods by estimating hospital-level standardized incidence ratios for comparing the adjusted probability of computed tomography examinations with high radiations doses, relative to a reference standard and we evaluate out methods in a simulation study. Supplementary materials for this article, including a standardized description of the materials available for reproducing the work, are available as an online supplement.
DOI: 10.6084/m9.figshare.6406043
title: Causal Interaction in Factorial Experiments: Application to Conjoint Analysis

description: We study causal interaction in factorial experiments, in which several factors, each with multiple levels, are randomized to form a large number of possible treatment combinations. Examples of such experiments include conjoint analysis, which is often used by social scientists to analyze multidimensional preferences in a population. To characterize the structure of causal interaction in factorial experiments, we propose a new causal interaction effect, called the <i>average marginal interaction effect</i> (AMIE). Unlike the conventional interaction effect, the relative magnitude of the AMIE does not depend on the choice of baseline conditions, making its interpretation intuitive even for higher-order interactions. We show that the AMIE can be nonparametrically estimated using ANOVA regression with weighted zero-sum constraints. Because the AMIEs are invariant to the choice of baseline conditions, we directly regularize them by collapsing levels and selecting factors within a penalized ANOVA framework. This regularized estimation procedure reduces false discovery rate and further facilitates interpretation. Finally, we apply the proposed methodology to the conjoint analysis of ethnic voting behavior in Africa and find clear patterns of causal interaction between politicians’ ethnicity and their prior records. The proposed methodology is implemented in an open source software package. Supplementary materials for this article, including a standardized description of the materials available for reproducing the work, are available as an online supplement.
DOI: 10.6084/m9.figshare.6826949.v2
title: Functional Data Analysis of Dynamic PET Data

description: One application of positron emission tomography (PET), a nuclear imaging technique, in neuroscience involves in vivo estimation of the density of various proteins (often, neuroreceptors) in the brain. PET scanning begins with the injection of a radiolabeled tracer that binds preferentially to the target protein; tracer molecules are then continuously delivered to the brain via the bloodstream. By detecting the radioactive decay of the tracer over time, dynamic PET data are constructed to reflect the concentration of the target protein in the brain at each time. The fundamental problem in the analysis of dynamic PET data involves estimating the impulse response function (IRF), which is necessary for describing the binding behavior of the injected radiotracer. Virtually all existing methods have three common aspects: summarizing the entire IRF with a single scalar measure; modeling each subject separately; and the imposition of parametric restrictions on the IRF. In contrast, we propose a functional data analytic approach that regards each subject’s IRF as the basic analysis unit, models multiple subjects simultaneously, and estimates the IRF nonparametrically. We pose our model as a linear mixed effect model in which population level fixed effects and subject-specific random effects are expanded using a <i>B</i>-spline basis. Shrinkage and roughness penalties are incorporated in the model to enforce identifiability and smoothness of the estimated curves, respectively, while monotonicity and nonnegativity constraints impose biological information on estimates. We illustrate this approach by applying it to clinical PET data with subjects belonging to three diagnosic groups. We explore differences among groups by means of pointwise confidence intervals of the estimated mean curves based on bootstrap samples. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.6938537.v2
title: Joint Indirect Standardization When Only Marginal Distributions are Observed in the Index Population

description: It is a common interest in medicine to determine whether a hospital meets a benchmark created from an aggregate reference population, after accounting for differences in distributions of multiple covariates. Due to the difficulties of collecting individual-level data, however, it is often the case that only marginal distributions of the covariates are available, making covariate-adjusted comparison challenging. We propose and evaluate a novel approach for conducting indirect standardization when only marginal covariate distributions of the studied hospital are known, but complete information is available for the reference hospitals. We do this with the aid of two existing methods: iterative proportional fit, which estimates the cells of a contingency table when only marginal sums are known, and synthetic control methods, which create a counterfactual control group using a weighted combination of potential control groups. The proper application of these existing methods for indirect standardization would require accounting for the statistical uncertainties induced by a situation where no individual-level data are collected from the studied population. We address this need with a novel method which uses a random Dirichlet parameterization of the synthetic control weights to estimate uncertainty intervals for the standard incidence ratio. We demonstrate our novel methods by estimating hospital-level standardized incidence ratios for comparing the adjusted probability of computed tomography examinations with high radiations doses, relative to a reference standard and we evaluate out methods in a simulation study. Supplementary materials for this article, including a standardized description of the materials available for reproducing the work, are available as an online supplement.
DOI: 10.6084/m9.figshare.6287705
title: A Mallows-Type Model Averaging Estimator for the Varying-Coefficient Partially Linear Model

description: In the last decade, significant theoretical advances have been made in the area of frequentist model averaging (FMA); however, the majority of this work has emphasized parametric model setups. This article considers FMA for the semiparametric varying-coefficient partially linear model (VCPLM), which has gained prominence to become an extensively used modeling tool in recent years. Within this context, we develop a Mallows-type criterion for assigning model weights and prove its asymptotic optimality. A simulation study and a real data analysis demonstrate that the FMA estimator that arises from this criterion is vastly preferred to information criterion score-based model selection and averaging estimators. Our analysis is complicated by the fact that the VCPLM is subject to uncertainty arising not only from the choice of covariates, but also whether the covariate should enter the parametric or nonparametric parts of the model. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.6406043.v1
title: Causal Interaction in Factorial Experiments: Application to Conjoint Analysis

description: We study causal interaction in factorial experiments, in which several factors, each with multiple levels, are randomized to form a large number of possible treatment combinations. Examples of such experiments include conjoint analysis, which is often used by social scientists to analyze multidimensional preferences in a population. To characterize the structure of causal interaction in factorial experiments, we propose a new causal interaction effect, called the <i>average marginal interaction effect</i> (AMIE). Unlike the conventional interaction effect, the relative magnitude of the AMIE does not depend on the choice of baseline conditions, making its interpretation intuitive even for higher-order interactions. We show that the AMIE can be nonparametrically estimated using ANOVA regression with weighted zero-sum constraints. Because the AMIEs are invariant to the choice of baseline conditions, we directly regularize them by collapsing levels and selecting factors within a penalized ANOVA framework. This regularized estimation procedure reduces false discovery rate and further facilitates interpretation. Finally, we apply the proposed methodology to the conjoint analysis of ethnic voting behavior in Africa and find clear patterns of causal interaction between politicians' ethnicity and their prior records. The proposed methodology is implemented in an open source software package.