arXiv subjects

Yanyuan Ma

Publications and source records attributed to Yanyuan Ma.

53 records · Page 3Linked to original sources

arXiv2020

Inference in High-Dimensional Linear Measurement Error Models

For a high-dimensional linear model with a finite number of covariates measured with error, we study statistical inference on the parameters associated with the error-prone covariates, and propose a new corrected decorrelated score test and the corresponding one-step estimator. We further establish asymptotic properties of the newly proposed test statistic and the one-step estimator. Under local alternatives, we show that the limiting distribution of our corrected decorrelated score test statistic is non-central normal. The finite-sample performance of the proposed inference procedure is examined through simulation studies. We further illustrate the proposed procedure via an empirical analysis of a real data example.

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arXiv2020

Optimal subsampling for quantile regression in big data

We investigate optimal subsampling for quantile regression. We derive the asymptotic distribution of a general subsampling estimator and then derive two versions of optimal subsampling probabilities. One version minimizes the trace of the asymptotic variance-covariance matrix for a linearly transformed parameter estimator and the other minimizes that of the original parameter estimator. The former does not depend on the densities of the responses given covariates and is easy to implement. Algorithms based on optimal subsampling probabilities are proposed and asymptotic distributions and asymptotic optimality of the resulting estimators are established. Furthermore, we propose an iterative subsampling procedure based on the optimal subsampling probabilities in the linearly transformed parameter estimation which has great scalability to utilize available computational resources. In addition, this procedure yields standard errors for parameter estimators without estimating the densities of the responses given the covariates. We provide numerical examples based on both simulated and real data to illustrate the proposed method.

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arXiv2019

A spline-assisted semiparametric approach to non-parametric measurement error models

It is well known that the minimax rates of convergence of nonparametric density and regression function estimation of a random variable measured with error is much slower than the rate in the error free case. Surprisingly, we show that if one is willing to impose a relatively mild assumption in requiring that the error-prone variable has a compact support, then the results can be greatly improved. We describe new and constructive methods to take full advantage of the compact support assumption via spline-assisted semiparametric methods. We further prove that the new estimator achieves the usual nonparametric rate in estimating both the density and regression functions as if there were no measurement error. The proof involves linear and bilinear operator theories, semiparametric theory, asymptotic analysis regarding Bsplines, as well as integral equation treatments. The performance of the new methods is demonstrated through several simulations and a data example.

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arXiv2019

A Versatile Estimation Procedure without Estimating the Nonignorable Missingness Mechanism

We consider the estimation problem in a regression setting where the outcome variable is subject to nonignorable missingness and identifiability is ensured by the shadow variable approach. We propose a versatile estimation procedure where modeling of missingness mechanism is completely bypassed. We show that our estimator is easy to implement and we derive the asymptotic theory of the proposed estimator. We also investigate some alternative estimators under different scenarios. Comprehensive simulation studies are conducted to demonstrate the finite sample performance of the method. We apply the estimator to a children's mental health study to illustrate its usefulness.

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arXiv2019

Electronic Health Record Phenotyping with Internally Assessable Performance (PhIAP) using Anchor-Positive and Unlabeled Patients

Building phenotype models using electronic health record (EHR) data conventionally requires manually labeled cases and controls. Assigning labels is labor intensive and, for some phenotypes, identifying gold-standard controls is prohibitive. To facilitate comprehensive clinical decision support and research, we sought to develop an accurate EHR phenotyping approach that assesses its performance without a validation set. Our framework relies on specifying a random subset of cases, potentially using an anchor variable that has excellent positive predictive value and sensitivity that is independent of predictors. We developed a novel maximum likelihood approach that efficiently leverages data from anchor-positive and unlabeled patients to develop logistic regression phenotyping models. Additionally, we described novel statistical methods for estimating phenotyping prevalence and assessing model calibration and predictive performance measures. Theoretical and simulation studies indicated our method generates accurate predicted probabilities, leading to excellent discrimination and calibration, and consistent estimates of phenotype prevalence and anchor sensitivity. The method appeared robust to minor lack-of-fit and the proposed calibration assessment detected major lack-of-fit. We applied our method to EHR data to develop a preliminary model for identifying patients with primary aldosteronism, which achieved an AUC of 0.99 and PPV of 0.8. We developed novel statistical methods for accurate model development and validation with minimal manual labeling, facilitating development of scalable, transferable, semi-automated case labeling and practice-specific models. Our EHR phenotyping approach decreases labor-intensive manual phenotyping and annotation, which should enable broader model development and dissemination for EHR clinical decision support and research.

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arXiv2018

Sufficient Dimension Reduction for Feasible and Robust Estimation of Average Causal Effect

When estimating the treatment effect in an observational study, we use a semiparametric locally efficient dimension reduction approach to assess both the treatment assignment mechanism and the average responses in both treated and nontreated groups. We then integrate all results through imputation, inverse probability weighting and doubly robust augmentation estimators. Doubly robust estimators are locally efficient while imputation estimators are super-efficient when the response models are correct. To take advantage of both procedures, we introduce a shrinkage estimator to automatically combine the two, which retains the double robustness property while improving on the variance when the response model is correct. We demonstrate the performance of these estimators through simulated experiments and a real dataset concerning the effect of maternal smoking on baby birth weight. Key words and phrases: Average Treatment Effect, Doubly Robust Estimator, Efficiency, Inverse Probability Weighting, Shrinkage Estimator.

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arXiv2018

Semiparametric Mixture Regression with Unspecified Error Distributions

In fitting a mixture of linear regression models, normal assumption is traditionally used to model the error and then regression parameters are estimated by the maximum likelihood estimators (MLE). This procedure is not valid if the normal assumption is violated. To relax the normal assumption on the error distribution hence reduce the modeling bias, we propose semiparametric mixture of linear regression models with unspecified error distributions. We establish a more general identifiability result under weaker conditions than existing results, construct a class of new estimators, and establish their asymptotic properties. These asymptotic results also apply to many existing semiparametric mixture regression estimators whose asymptotic properties have remained unknown due to the inherent difficulties in obtaining them. Using simulation studies, we demonstrate the superiority of the proposed estimators over the MLE when the normal error assumption is violated and the comparability when the error is normal. Analysis of a newly collected Equine Infectious Anemia Virus data in 2017 is employed to illustrate the usefulness of the new estimator.

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arXiv2017

Efficient Estimation for Dimension Reduction with Censored Data

We propose a general index model for survival data, which generalizes many commonly used semiparametric survival models and belongs to the framework of dimension reduction. Using a combination of geometric approach in semiparametrics and martingale treatment in survival data analysis, we devise estimation procedures that are feasible and do not require covariate-independent censoring as assumed in many dimension reduction methods for censored survival data. We establish the root-$n$ consistency and asymptotic normality of the proposed estimators and derive the most efficient estimator in this class for the general index model. Numerical experiments are carried out to demonstrate the empirical performance of the proposed estimators and an application to an AIDS data further illustrates the usefulness of the work.

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arXiv2015

A Paradigmatic Regression Algorithm for Gene Selection Problems

Motivation: Gene selection has become a common task in most gene expression studies. The objective of such research is often to identify the smallest possible set of genes that can still achieve good predictive performance. The problem of assigning tumours to a known class is a particularly important example that has received considerable attention in the last ten years. Many of the classification methods proposed recently require some form of dimension-reduction of the problem. These methods provide a single model as an output and, in most cases, rely on the likelihood function in order to achieve variable selection. Results: We propose a prediction-based objective function that can be tailored to the requirements of practitioners and can be used to assess and interpret a given problem. The direct optimization of such a function can be very difficult because the problem is potentially discontinuous and nonconvex. We therefore propose a general procedure for variable selection that resembles importance sampling to explore the feature space. Our proposal compares favorably with competing alternatives when applied to two cancer data sets in that smaller models are obtained for better or at least comparable classification errors. Furthermore by providing a set of selected models instead of a single one, we construct a network of possible models for a target prediction accuracy level.

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arXiv2015

Fused kernel-spline smoothing for repeatedly measured outcomes in a generalized partially linear model with functional single index

We propose a generalized partially linear functional single index risk score model for repeatedly measured outcomes where the index itself is a function of time. We fuse the nonparametric kernel method and regression spline method, and modify the generalized estimating equation to facilitate estimation and inference. We use local smoothing kernel to estimate the unspecified coefficient functions of time, and use B-splines to estimate the unspecified function of the single index component. The covariance structure is taken into account via a working model, which provides valid estimation and inference procedure whether or not it captures the true covariance. The estimation method is applicable to both continuous and discrete outcomes. We derive large sample properties of the estimation procedure and show a different convergence rate for each component of the model. The asymptotic properties when the kernel and regression spline methods are combined in a nested fashion has not been studied prior to this work, even in the independent data case.

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arXiv2015

Functional Inverse Regression in an Enlarged Dimension Reduction Space

We consider an enlarged dimension reduction space in functional inverse regression. Our operator and functional analysis based approach facilitates a compact and rigorous formulation of the functional inverse regression problem. It also enables us to expand the possible space where the dimension reduction functions belong. Our formulation provides a unified framework so that the classical notions, such as covariance standardization, Mahalanobis distance, SIR and linear discriminant analysis, can be naturally and smoothly carried out in our enlarged space. This enlarged dimension reduction space also links to the linear discriminant space of Gaussian measures on a separable Hilbert space.

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arXiv2014

Combining isotonic regression and EM algorithm to predict genetic risk under monotonicity constraint

In certain genetic studies, clinicians and genetic counselors are interested in estimating the cumulative risk of a disease for individuals with and without a rare deleterious mutation. Estimating the cumulative risk is difficult, however, when the estimates are based on family history data. Often, the genetic mutation status in many family members is unknown; instead, only estimated probabilities of a patient having a certain mutation status are available. Also, ages of disease-onset are subject to right censoring. Existing methods to estimate the cumulative risk using such family-based data only provide estimation at individual time points, and are not guaranteed to be monotonic or nonnegative. In this paper, we develop a novel method that combines Expectation-Maximization and isotonic regression to estimate the cumulative risk across the entire support. Our estimator is monotonic, satisfies self-consistent estimating equations and has high power in detecting differences between the cumulative risks of different populations. Application of our estimator to a Parkinson's disease (PD) study provides the age-at-onset distribution of PD in PARK2 mutation carriers and noncarriers, and reveals a significant difference between the distribution in compound heterozygous carriers compared to noncarriers, but not between heterozygous carriers and noncarriers.

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arXiv2013

Optimal variance estimation without estimating the mean function

We study the least squares estimator in the residual variance estimation context. We show that the mean squared differences of paired observations are asymptotically normally distributed. We further establish that, by regressing the mean squared differences of these paired observations on the squared distances between paired covariates via a simple least squares procedure, the resulting variance estimator is not only asymptotically normal and root-$n$ consistent, but also reaches the optimal bound in terms of estimation variance. We also demonstrate the advantage of the least squares estimator in comparison with existing methods in terms of the second order asymptotic properties.

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arXiv2013

Efficient estimation in sufficient dimension reduction

We develop an efficient estimation procedure for identifying and estimating the central subspace. Using a new way of parameterization, we convert the problem of identifying the central subspace to the problem of estimating a finite dimensional parameter in a semiparametric model. This conversion allows us to derive an efficient estimator which reaches the optimal semiparametric efficiency bound. The resulting efficient estimator can exhaustively estimate the central subspace without imposing any distributional assumptions. Our proposed efficient estimation also provides a possibility for making inference of parameters that uniquely identify the central subspace. We conduct simulation studies and a real data analysis to demonstrate the finite sample performance in comparison with several existing methods.

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arXiv2010

A semiparametric efficient estimator in case-control studies

We construct a semiparametric estimator in case-control studies where the gene and the environment are assumed to be independent. A discrete or continuous parametric distribution of the genes is assumed in the model. A discrete distribution of the genes can be used to model the mutation or presence of certain group of genes. A continuous distribution allows the distribution of the gene effects to be in a finite-dimensional parametric family and can hence be used to model the gene expression levels. We leave the distribution of the environment totally unspecified. The estimator is derived through calculating the efficiency score function in a hypothetical setting where a close approximation to the samples is random. The resulting estimator is proved to be efficient in the hypothetical situation. The efficiency of the estimator is further demonstrated to hold in the case-control setting as well.

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arXiv2010

Variable selection in measurement error models

Measurement error data or errors-in-variable data have been collected in many studies. Natural criterion functions are often unavailable for general functional measurement error models due to the lack of information on the distribution of the unobservable covariates. Typically, the parameter estimation is via solving estimating equations. In addition, the construction of such estimating equations routinely requires solving integral equations, hence the computation is often much more intensive compared with ordinary regression models. Because of these difficulties, traditional best subset variable selection procedures are not applicable, and in the measurement error model context, variable selection remains an unsolved issue. In this paper, we develop a framework for variable selection in measurement error models via penalized estimating equations. We first propose a class of selection procedures for general parametric measurement error models and for general semi-parametric measurement error models, and study the asymptotic properties of the proposed procedures. Then, under certain regularity conditions and with a properly chosen regularization parameter, we demonstrate that the proposed procedure performs as well as an oracle procedure. We assess the finite sample performance via Monte Carlo simulation studies and illustrate the proposed methodology through the empirical analysis of a familiar data set.

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arXiv2008

Testing the suitability of polynomial models in errors-in-variables problems

A low-degree polynomial model for a response curve is used commonly in practice. It generally incorporates a linear or quadratic function of the covariate. In this paper we suggest methods for testing the goodness of fit of a general polynomial model when there are errors in the covariates. There, the true covariates are not directly observed, and conventional bootstrap methods for testing are not applicable. We develop a new approach, in which deconvolution methods are used to estimate the distribution of the covariates under the null hypothesis, and a ``wild'' or moment-matching bootstrap argument is employed to estimate the distribution of the experimental errors (distinct from the distribution of the errors in covariates). Most of our attention is directed at the case where the distribution of the errors in covariates is known, although we also discuss methods for estimation and testing when the covariate error distribution is estimated. No assumptions are made about the distribution of experimental error, and, in particular, we depart substantially from conventional parametric models for errors-in-variables problems.

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