arXiv subjects

Wenguang Sun

Publications and source records attributed to Wenguang Sun.

28 records · Page 2Linked to original sources

arXiv2022

ZAP: $Z$-value Adaptive Procedures for False Discovery Rate Control with Side Information

Adaptive multiple testing with covariates is an important research direction that has gained major attention in recent years. It has been widely recognized that leveraging side information provided by auxiliary covariates can improve the power of false discovery rate (FDR) procedures. Currently, most such procedures are devised with $p$-values as their main statistics. However, for two-sided hypotheses, the usual data processing step that transforms the primary statistics, known as $z$-values, into $p$-values not only leads to a loss of information carried by the main statistics, but can also undermine the ability of the covariates to assist with the FDR inference. We develop a $z$-value based covariate-adaptive (ZAP) methodology that operates on the intact structural information encoded jointly by the $z$-values and covariates. It seeks to emulate the oracle $z$-value procedure via a working model, and its rejection regions significantly depart from those of the $p$-value adaptive testing approaches. The key strength of ZAP is that the FDR control is guaranteed with minimal assumptions, even when the working model is misspecified. We demonstrate the state-of-the-art performance of ZAP using both simulated and real data, which shows that the efficiency gain can be substantial in comparison with $p$-value based methods. Our methodology is implemented in the $\texttt{R}$ package $\texttt{zap}$.

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arXiv2022

Integrative conformal p-values for powerful out-of-distribution testing with labeled outliers

This paper develops novel conformal methods to test whether a new observation was sampled from the same distribution as a reference set. Blending inductive and transductive conformal inference in an innovative way, the described methods can re-weight standard conformal p-values based on dependent side information from known out-of-distribution data in a principled way, and can automatically take advantage of the most powerful model from any collection of one-class and binary classifiers. The solution can be implemented either through sample splitting or via a novel transductive cross-validation+ scheme which may also be useful in other applications of conformal inference, due to tighter guarantees compared to existing cross-validation approaches. After studying false discovery rate control and power within a multiple testing framework with several possible outliers, the proposed solution is shown to outperform standard conformal p-values through simulations as well as applications to image recognition and tabular data.

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arXiv2021

False Discovery Rate Control Under General Dependence By Symmetrized Data Aggregation

We develop a new class of distribution--free multiple testing rules for false discovery rate (FDR) control under general dependence. A key element in our proposal is a symmetrized data aggregation (SDA) approach to incorporating the dependence structure via sample splitting, data screening and information pooling. The proposed SDA filter first constructs a sequence of ranking statistics that fulfill global symmetry properties, and then chooses a data--driven threshold along the ranking to control the FDR. The SDA filter substantially outperforms the knockoff method in power under moderate to strong dependence, and is more robust than existing methods based on asymptotic $p$-values. We first develop finite--sample theory to provide an upper bound for the actual FDR under general dependence, and then establish the asymptotic validity of SDA for both the FDR and false discovery proportion (FDP) control under mild regularity conditions. The procedure is implemented in the R package \texttt{SDA}. Numerical results confirm the effectiveness and robustness of SDA in FDR control and show that it achieves substantial power gain over existing methods in many settings.

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arXiv2020

Large-Scale Shrinkage Estimation under Markovian Dependence

We consider the problem of simultaneous estimation of a sequence of dependent parameters that are generated from a hidden Markov model. Based on observing a noise contaminated vector of observations from such a sequence model, we consider simultaneous estimation of all the parameters irrespective of their hidden states under square error loss. We study the roles of statistical shrinkage for improved estimation of these dependent parameters. Being completely agnostic on the distributional properties of the unknown underlying Hidden Markov model, we develop a novel non-parametric shrinkage algorithm. Our proposed method elegantly combines \textit{Tweedie}-based non-parametric shrinkage ideas with efficient estimation of the hidden states under Markovian dependence. Based on extensive numerical experiments, we establish superior performance our our proposed algorithm compared to non-shrinkage based state-of-the-art parametric as well as non-parametric algorithms used in hidden Markov models. We provide decision theoretic properties of our methodology and exhibit its enhanced efficacy over popular shrinkage methods built under independence. We demonstrate the application of our methodology on real-world datasets for analyzing of temporally dependent social and economic indicators such as search trends and unemployment rates as well as estimating spatially dependent Copy Number Variations.

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arXiv2020

Heterocedasticity-Adjusted Ranking and Thresholding for Large-Scale Multiple Testing

Standardization has been a widely adopted practice in multiple testing, for it takes into account the variability in sampling and makes the test statistics comparable across different study units. However, despite conventional wisdom to the contrary, we show that there can be a significant loss in information from basing hypothesis tests on standardized statistics rather than the full data. We develop a new class of heteroscedasticity--adjusted ranking and thresholding (HART) rules that aim to improve existing methods by simultaneously exploiting commonalities and adjusting heterogeneities among the study units. The main idea of HART is to bypass standardization by directly incorporating both the summary statistic and its variance into the testing procedure. A key message is that the variance structure of the alternative distribution, which is subsumed under standardized statistics, is highly informative and can be exploited to achieve higher power. The proposed HART procedure is shown to be asymptotically valid and optimal for false discovery rate (FDR) control. Our simulation results demonstrate that HART achieves substantial power gain over existing methods at the same FDR level. We illustrate the implementation through a microarray analysis of myeloma.

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arXiv2020

Structure-Adaptive Sequential Testing for Online False Discovery Rate Control

Consider the online testing of a stream of hypotheses where a real--time decision must be made before the next data point arrives. The error rate is required to be controlled at {all} decision points. Conventional \emph{simultaneous testing rules} are no longer applicable due to the more stringent error constraints and absence of future data. Moreover, the online decision--making process may come to a halt when the total error budget, or alpha--wealth, is exhausted. This work develops a new class of structure--adaptive sequential testing (SAST) rules for online false discover rate (FDR) control. A key element in our proposal is a new alpha--investment algorithm that precisely characterizes the gains and losses in sequential decision making. SAST captures time varying structures of the data stream, learns the optimal threshold adaptively in an ongoing manner and optimizes the alpha-wealth allocation across different time periods. We present theory and numerical results to show that the proposed method is valid for online FDR control and achieves substantial power gain over existing online testing rules.

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arXiv2019

A General Framework for Empirical Bayes Estimation in Discrete Linear Exponential Family

We develop a Nonparametric Empirical Bayes (NEB) framework for compound estimation in the discrete linear exponential family, which includes a wide class of discrete distributions frequently arising from modern big data applications. We propose to directly estimate the Bayes shrinkage factor in the generalized Robbins' formula via solving a scalable convex program, which is carefully developed based on a RKHS representation of the Stein's discrepancy measure. The new NEB estimation framework is flexible for incorporating various structural constraints into the data driven rule, and provides a unified approach to compound estimation with both regular and scaled squared error losses. We develop theory to show that the class of NEB estimators enjoys strong asymptotic properties. Comprehensive simulation studies as well as analyses of real data examples are carried out to demonstrate the superiority of the NEB estimator over competing methods.

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arXiv2019

Adaptive Sparse Estimation with Side Information

The article considers the problem of estimating a high-dimensional sparse parameter in the presence of side information that encodes the sparsity structure. We develop a general framework that involves first using an auxiliary sequence to capture the side information, and then incorporating the auxiliary sequence in inference to reduce the estimation risk. The proposed method, which carries out adaptive SURE-thresholding using side information (ASUS), is shown to have robust performance and enjoy optimality properties. We develop new theories to characterize regimes in which ASUS far outperforms competitive shrinkage estimators, and establish precise conditions under which ASUS is asymptotically optimal. Simulation studies are conducted to show that ASUS substantially improves the performance of existing methods in many settings. The methodology is applied for analysis of data from single cell virology studies and microarray time course experiments.

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arXiv2017

Optimal design for high-throughput screening via false discovery rate control

High-throughput screening (HTS) is a large-scale hierarchical process in which a large number of chemicals are tested in multiple stages. Conventional statistical analyses of HTS studies often suffer from high testing error rates and soaring costs in large-scale settings. This article develops new methodologies for false discovery rate control and optimal design in HTS studies. We propose a two-stage procedure that determines the optimal numbers of replicates at different screening stages while simultaneously controlling the false discovery rate in the confirmatory stage subject to a constraint on the total budget. The merits of the proposed methods are illustrated using both simulated and real data. We show that the proposed screening procedure effectively controls the error rate and the design leads to improved detection power. This is achieved at the expense of a limited budget.

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arXiv2017

Weighted False Discovery Rate Control in Large-Scale Multiple Testing

The use of weights provides an effective strategy to incorporate prior domain knowledge in large-scale inference. This paper studies weighted multiple testing in a decision-theoretic framework. We develop oracle and data-driven procedures that aim to maximize the expected number of true positives subject to a constraint on the weighted false discovery rate. The asymptotic validity and optimality of the proposed methods are established. The results demonstrate that incorporating informative domain knowledge enhances the interpretability of results and precision of inference. Simulation studies show that the proposed method controls the error rate at the nominal level, and the gain in power over existing methods is substantial in many settings. An application to genome-wide association study is discussed.

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