arXiv subjects

Runze Li

Publications and source records attributed to Runze Li.

At least 145 records · Page 8Linked to original sources

arXiv2020

Estimation and Inference for the Mediation Effect in a Time-varying Mediation Model

Traditional mediation analysis typically examines the relations among an intervention, a time-invariant mediator, and a time-invariant outcome variable. Although there may be a direct effect of the intervention on the outcome, there is a need to understand the process by which the intervention affects the outcome (i.e. the indirect effect through the mediator). This indirect effect is frequently assumed to be time-invariant. With improvements in data collection technology, it is possible to obtain repeated assessments over time resulting in intensive longitudinal data. This calls for an extension of traditional mediation analysis to incorporate time-varying variables as well as time-varying effects. In this paper, we focus on estimation and inference for the time-varying mediation model, which allows mediation effects to vary as a function of time. We propose a two-step approach to estimate the time-varying mediation effect. Moreover, we use a simulation based approach to derive the corresponding point-wise confidence band for the time-varying mediation effect. Simulation studies show that the proposed procedures perform well when comparing the confidence band and the true underlying model. We further apply the proposed model and the statistical inference procedure to real-world data collected from a smoking cessation study.

stat.AP↗

arXiv2020

A Robust Consistent Information Criterion for Model Selection based on Empirical Likelihood

Conventional likelihood-based information criteria for model selection rely on the distribution assumption of data. However, for complex data that are increasingly available in many scientific fields, the specification of their underlying distribution turns out to be challenging, and the existing criteria may be limited and are not general enough to handle a variety of model selection problems. Here, we propose a robust and consistent model selection criterion based upon the empirical likelihood function which is data-driven. In particular, this framework adopts plug-in estimators that can be achieved by solving external estimating equations, not limited to the empirical likelihood, which avoids potential computational convergence issues and allows versatile applications, such as generalized linear models, generalized estimating equations, penalized regressions and so on. The formulation of our proposed criterion is initially derived from the asymptotic expansion of the marginal likelihood under variable selection framework, but more importantly, the consistent model selection property is established under a general context. Extensive simulation studies confirm the out-performance of the proposal compared to traditional model selection criteria. Finally, an application to the Atherosclerosis Risk in Communities Study illustrates the practical value of this proposed framework.

stat.ME↗

arXiv2020

Towards Visually Explaining Variational Autoencoders

Recent advances in Convolutional Neural Network (CNN) model interpretability have led to impressive progress in visualizing and understanding model predictions. In particular, gradient-based visual attention methods have driven much recent effort in using visual attention maps as a means for visual explanations. A key problem, however, is these methods are designed for classification and categorization tasks, and their extension to explaining generative models, e.g. variational autoencoders (VAE) is not trivial. In this work, we take a step towards bridging this crucial gap, proposing the first technique to visually explain VAEs by means of gradient-based attention. We present methods to generate visual attention from the learned latent space, and also demonstrate such attention explanations serve more than just explaining VAE predictions. We show how these attention maps can be used to localize anomalies in images, demonstrating state-of-the-art performance on the MVTec-AD dataset. We also show how they can be infused into model training, helping bootstrap the VAE into learning improved latent space disentanglement, demonstrated on the Dsprites dataset.

cs.CV↗

arXiv2020

A New Procedure for Controlling False Discovery Rate in Large-Scale t-tests

This paper is concerned with false discovery rate (FDR) control in large-scale multiple testing problems. We first propose a new data-driven testing procedure for controlling the FDR in large-scale t-tests for one-sample mean problem. The proposed procedure achieves exact FDR control in finite sample settings when the populations are symmetric no matter the number of tests or sample sizes. Comparing with the existing bootstrap method for FDR control, the proposed procedure is computationally efficient. We show that the proposed method can control the FDR asymptotically for asymmetric populations even when the test statistics are not independent. We further show that the proposed procedure with a simple correction is as accurate as the bootstrap method to the second-order degree, and could be much more effective than the existing normal calibration. We extend the proposed procedure to two-sample mean problem. Empirical results show that the proposed procedures have better FDR control than existing ones when the proportion of true alternative hypotheses is not too low, while maintaining reasonably good detection ability.

math.ST↗

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.

stat.ME↗

arXiv2019

Central Limit Theorem for Linear Spectral Statistics of Large Dimensional Kendall's Rank Correlation Matrices and its Applications

This paper is concerned with the limiting spectral behaviors of large dimensional Kendall's rank correlation matrices generated by samples with independent and continuous components. We do not require the components to be identically distributed, and do not need any moment conditions, which is very different from the assumptions imposed in the literature of random matrix theory. The statistical setting in this paper covers a wide range of highly skewed and heavy-tailed distributions. We establish the central limit theorem (CLT) for the linear spectral statistics of the Kendall's rank correlation matrices under the Marchenko-Pastur asymptotic regime, in which the dimension diverges to infinity proportionally with the sample size. We further propose three nonparametric procedures for high dimensional independent test and their limiting null distributions are derived by implementing this CLT. Our numerical comparisons demonstrate the robustness and superiority of our proposed test statistics under various mixed and heavy-tailed cases.

math.ST↗

arXiv2019

Retrieval of non-sparse object through scattering media beyond the memory effect

Optical imaging through scattering media is a commonly confronted with the problem of reconstruction of complex objects and optical memory effect. To solve the problem, here, we propose a novel configuration based on the combination of ptychography and shower-curtain effect, which enables the retrieval of non-sparse samples through scattering media beyond the memory effect. Furthermore, by virtue of the shower-curtain effect, the proposed imaging system is insensitive to dynamic scattering media. Results from the retrieval of hair follicle section demonstrate the effectiveness and feasibility of the proposed method. The field of view is improved to 2.64mm. This present technique will be a potential approach for imaging through deep biological tissue.

eess.IV↗

arXiv2019

Distributed Feature Screening via Componentwise Debiasing

Feature screening is a powerful tool in the analysis of high dimensional data. When the sample size $N$ and the number of features $p$ are both large, the implementation of classic screening methods can be numerically challenging. In this paper, we propose a distributed screening framework for big data setup. In the spirit of "divide-and-conquer", the proposed framework expresses a correlation measure as a function of several component parameters, each of which can be distributively estimated using a natural U-statistic from data segments. With the component estimates aggregated, we obtain a final correlation estimate that can be readily used for screening features. This framework enables distributed storage and parallel computing and thus is computationally attractive. Due to the unbiased distributive estimation of the component parameters, the final aggregated estimate achieves a high accuracy that is insensitive to the number of data segments $m$ specified by the problem itself or to be chosen by users. Under mild conditions, we show that the aggregated correlation estimator is as efficient as the classic centralized estimator in terms of the probability convergence bound; the corresponding screening procedure enjoys sure screening property for a wide range of correlation measures. The promising performances of the new method are supported by extensive numerical examples.

stat.ME↗

arXiv2018

Ultrafast lattice deformations studied by means of time-resolved electron and x-ray diffraction

Ultrafast lattice deformation of tens to hundreds of nanometer thick metallic crystals, after femtosecond laser excitation, was measured directly using 8.04 keV subpicosecond x-ray and 59 keV femtosecond electron pulses. Coherent phonons were generated in both single crystal and polycrystalline films. Lattice compression was observed within the first few picoseconds after laser irradiation in single crystal aluminum, which was attributed to the generation of a blast force and the propagation of elastic waves. The different time scale of lattice heating for tens and hundreds nanometer thick films are clearly distinguished by electron and x-ray pulse diffraction. The electron and lattice heating due to ultrafast deposition of photon energy was numerically simulated using the two-temperature model (TTM) and the results agreed with experimental observations. The ultrafast heating described by TTM was also discussed from an electrical circuit perspective, which may provide new insights on the possible connection between thermal and electrical processes. This study demonstrates that the combination of two complimentary ultrafast time-resolved methods, ultrafast x-ray and electron diffraction will provide a panoramic picture of the transient atomic motions and structure in crystals.

cond-mat.mtrl-sci↗

arXiv2017

Direct observation of ultrafast thermal and non-thermal lattice deformation of polycrystalline Aluminum film

The dynamics of thermal and non-thermal lattice deformation of nanometer thick polycrystalline aluminum film has been studied by means of femtosecond (fs) time-resolved electron diffraction. We utilized two different pump wavelengths: 800 nm, the fundamental of Ti: sapphire laser and 1250 nm generated by a home-made optical parametric amplifier(OPA). Our data show that, although coherent phonons were generated under both conditions, the diffraction intensity decayed with the characteristic time of 0.9+/-0.3 ps and 1.7+/-0.3 ps under 800 nm and 1250 nm excitation, respectively. Because the 800 nm laser excitation corresponds to the strong interband transition of aluminum due to the 1.55 eV parallel band structure, our experimental data indicate the presence of non-thermal lattice deformation under 800 nm excitation, which occurs on a time-scale that is shorter than the thermal processes dominated by electron-phonon coupling under 1250 nm excitation.

cond-mat.mtrl-sci↗

arXiv2016

Femtosecond laser induced structural dynamics and melting of Cu (111) single crystal. An ultrafast time-resolved x-ray diffraction study

Femtosecond, 8.04 KeV x-ray pulses are used to probe the lattice dynamics of 150 nm Cu (111) single crystal on mica substrate irradiated with 400 nm, 100 fs laser pulses. For pump fluencies below the damage and melting threshold, we observed lattice contraction due to the formation of a blast force, and coherent acoustic phonons with a period of ~69 ps. At larger pump fluence, solid to liquid phase transition, annealing, and recrystallization were measured in real time by monitoring the intensity evolution of the probing fs x-ray rocking curves and agreed with theoretical simulation results. The experimental data suggest the melting process is a purely thermal phase transition. This study provides, in real time, an ultrafast time-resolved detailed description of the significant processes that occurs as a result of a femtosecond light-pulse interacts with the Cu (111) crystal surface.

cond-mat.mtrl-sci↗

arXiv2016

Carrier emission of n-type Gallium Nitride illuminated by femtosecond laser pulses

The carrier emission efficiency of light emitting diodes is of fundamental importance for many technological applications, including the performance of GaN and other semiconductor photocathodes. We have measured the evolution of the emitted carriers and the associated transient electric field after femtosecond laser excitation of n-type GaN single crystals. These processes were studied using subpicosecond, ultrashort, electron pulses and explained by means of a three-layer analytical model. We find that for pump laser intensities on the order of 10^11 W/cm^2, the electrons that escaped from the crystal surface have a charge of about 2.7 pc and a velocity of about 1.8 um/ps. The associated transient electrical field evolves at intervals ranging from picoseconds to nanoseconds. These results provide a dynamic perspective on the photoemission properties of semiconductor photocathodes.

cond-mat.mtrl-sci↗

arXiv2016

Global solutions to folded concave penalized nonconvex learning

This paper is concerned with solving nonconvex learning problems with folded concave penalty. Despite that their global solutions entail desirable statistical properties, they lack optimization techniques that guarantee global optimality in a general setting. In this paper, we show that a class of nonconvex learning problems are equivalent to general quadratic programs. This equivalence facilitates us in developing mixed integer linear programming reformulations, which admit finite algorithms that find a provably global optimal solution. We refer to this reformulation-based technique as the mixed integer programming-based global optimization (MIPGO). To our knowledge, this is the first global optimization scheme with a theoretical guarantee for folded concave penalized nonconvex learning with the SCAD penalty [J. Amer. Statist. Assoc. 96 (2001) 1348-1360] and the MCP penalty [Ann. Statist. 38 (2001) 894-942]. Numerical results indicate a significant outperformance of MIPGO over the state-of-the-art solution scheme, local linear approximation and other alternative solution techniques in literature in terms of solution quality.

math.ST↗

arXiv2015

Bayesian group Lasso for nonparametric varying-coefficient models with application to functional genome-wide association studies

Although genome-wide association studies (GWAS) have proven powerful for comprehending the genetic architecture of complex traits, they are challenged by a high dimension of single-nucleotide polymorphisms (SNPs) as predictors, the presence of complex environmental factors, and longitudinal or functional natures of many complex traits or diseases. To address these challenges, we propose a high-dimensional varying-coefficient model for incorporating functional aspects of phenotypic traits into GWAS to formulate a so-called functional GWAS or fGWAS. The Bayesian group lasso and the associated MCMC algorithms are developed to identify significant SNPs and estimate how they affect longitudinal traits through time-varying genetic actions. The model is generalized to analyze the genetic control of complex traits using subject-specific sparse longitudinal data. The statistical properties of the new model are investigated through simulation studies. We use the new model to analyze a real GWAS data set from the Framingham Heart Study, leading to the identification of several significant SNPs associated with age-specific changes of body mass index. The fGWAS model, equipped with the Bayesian group lasso, will provide a useful tool for genetic and developmental analysis of complex traits or diseases.

stat.AP↗

arXiv2015

On the Feasibility of Distributed Kernel Regression for Big Data

In modern scientific research, massive datasets with huge numbers of observations are frequently encountered. To facilitate the computational process, a divide-and-conquer scheme is often used for the analysis of big data. In such a strategy, a full dataset is first split into several manageable segments; the final output is then averaged from the individual outputs of the segments. Despite its popularity in practice, it remains largely unknown that whether such a distributive strategy provides valid theoretical inferences to the original data. In this paper, we address this fundamental issue for the distributed kernel regression (DKR), where the algorithmic feasibility is measured by the generalization performance of the resulting estimator. To justify DKR, a uniform convergence rate is needed for bounding the generalization error over the individual outputs, which brings new and challenging issues in the big data setup. Under mild conditions, we show that, with a proper number of segments, DKR leads to an estimator that is generalization consistent to the unknown regression function. The obtained results justify the method of DKR and shed light on the feasibility of using other distributed algorithms for processing big data. The promising preference of the method is supported by both simulation and real data examples.

stat.ML↗

arXiv2015

A fast algorithm for detecting gene-gene interactions in genome-wide association studies

With the recent advent of high-throughput genotyping techniques, genetic data for genome-wide association studies (GWAS) have become increasingly available, which entails the development of efficient and effective statistical approaches. Although many such approaches have been developed and used to identify single-nucleotide polymorphisms (SNPs) that are associated with complex traits or diseases, few are able to detect gene-gene interactions among different SNPs. Genetic interactions, also known as epistasis, have been recognized to play a pivotal role in contributing to the genetic variation of phenotypic traits. However, because of an extremely large number of SNP-SNP combinations in GWAS, the model dimensionality can quickly become so overwhelming that no prevailing variable selection methods are capable of handling this problem. In this paper, we present a statistical framework for characterizing main genetic effects and epistatic interactions in a GWAS study. Specifically, we first propose a two-stage sure independence screening (TS-SIS) procedure and generate a pool of candidate SNPs and interactions, which serve as predictors to explain and predict the phenotypes of a complex trait. We also propose a rates adjusted thresholding estimation (RATE) approach to determine the size of the reduced model selected by an independence screening. Regularization regression methods, such as LASSO or SCAD, are then applied to further identify important genetic effects. Simulation studies show that the TS-SIS procedure is computationally efficient and has an outstanding finite sample performance in selecting potential SNPs as well as gene-gene interactions. We apply the proposed framework to analyze an ultrahigh-dimensional GWAS data set from the Framingham Heart Study, and select 23 active SNPs and 24 active epistatic interactions for the body mass index variation. It shows the capability of our procedure to resolve the complexity of genetic control.

stat.AP↗

arXiv2013

Calibrating nonconvex penalized regression in ultra-high dimension

We investigate high-dimensional nonconvex penalized regression, where the number of covariates may grow at an exponential rate. Although recent asymptotic theory established that there exists a local minimum possessing the oracle property under general conditions, it is still largely an open problem how to identify the oracle estimator among potentially multiple local minima. There are two main obstacles: (1) due to the presence of multiple minima, the solution path is nonunique and is not guaranteed to contain the oracle estimator; (2) even if a solution path is known to contain the oracle estimator, the optimal tuning parameter depends on many unknown factors and is hard to estimate. To address these two challenging issues, we first prove that an easy-to-calculate calibrated CCCP algorithm produces a consistent solution path which contains the oracle estimator with probability approaching one. Furthermore, we propose a high-dimensional BIC criterion and show that it can be applied to the solution path to select the optimal tuning parameter which asymptotically identifies the oracle estimator. The theory for a general class of nonconvex penalties in the ultra-high dimensional setup is established when the random errors follow the sub-Gaussian distribution. Monte Carlo studies confirm that the calibrated CCCP algorithm combined with the proposed high-dimensional BIC has desirable performance in identifying the underlying sparsity pattern for high-dimensional data analysis.

math.ST↗

arXiv2013

Multivariate varying coefficient model for functional responses

Motivated by recent work studying massive imaging data in the neuroimaging literature, we propose multivariate varying coefficient models (MVCM) for modeling the relation between multiple functional responses and a set of covariates. We develop several statistical inference procedures for MVCM and systematically study their theoretical properties. We first establish the weak convergence of the local linear estimate of coefficient functions, as well as its asymptotic bias and variance, and then we derive asymptotic bias and mean integrated squared error of smoothed individual functions and their uniform convergence rate. We establish the uniform convergence rate of the estimated covariance function of the individual functions and its associated eigenvalue and eigenfunctions. We propose a global test for linear hypotheses of varying coefficient functions, and derive its asymptotic distribution under the null hypothesis. We also propose a simultaneous confidence band for each individual effect curve. We conduct Monte Carlo simulation to examine the finite-sample performance of the proposed procedures. We apply MVCM to investigate the development of white matter diffusivities along the genu tract of the corpus callosum in a clinical study of neurodevelopment.

math.ST↗