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Register a new userSemi-Penalized Inference with Direct False Discovery Rate Control in High-Dimensions
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Jian Huang
Publication date
2013
fields
Mathematical Statistics
and research's language is
English
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We propose a new method, semi-penalized inference with direct false discovery rate control (SPIDR), for variable selection and confidence interval construction in high-dimensional linear regression. SPIDR first uses a semi-penalized approach to constructing estimators of the regression coefficients. We show that the SPIDR estimator is ideal in the sense that it equals an ideal least squares estimator with high probability under a sparsity and other suitable conditions. Consequently, the SPIDR estimator is asymptotically normal. Based on this distributional result, SPIDR determines the selection rule by directly controlling false discovery rate. This provides an explicit assessment of the selection error. This also naturally leads to confidence intervals for the selected coefficients with a proper confidence statement. We conduct simulation studies to evaluate its finite sample performance and demonstrate its application on a breast cancer gene expression data set. Our simulation studies and data example suggest that SPIDR is a useful method for high-dimensional statistical inference in practice.
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Variable selection on the large-scale networks has been extensively studied in the literature. While most of the existing methods are limited to the local functionals especially the graph edges, this paper focuses on selecting the discrete hub structures of the networks. Specifically, we propose an inferential method, called StarTrek filter, to select the hub nodes with degrees larger than a certain thresholding level in the high dimensional graphical models and control the false discovery rate (FDR). Discovering hub nodes in the networks is challenging: there is no straightforward statistic for testing the degree of a node due to the combinatorial structures; complicated dependence in the multiple testing problem is hard to characterize and control. In methodology, the StarTrek filter overcomes this by constructing p-values based on the maximum test statistics via the Gaussian multiplier bootstrap. In theory, we show that the StarTrek filter can control the FDR by providing accurate bounds on the approximation errors of the quantile estimation and addressing the dependence structures among the maximal statistics. To this end, we establish novel Cramer-type comparison bounds for the high dimensional Gaussian random vectors. Comparing to the Gaussian comparison bound via the Kolmogorov distance established by citet{chernozhukov2014anti}, our Cramer-type comparison bounds establish the relative difference between the distribution functions of two high dimensional Gaussian random vectors. We illustrate the validity of the StarTrek filter in a series of numerical experiments and apply it to the genotype-tissue expression dataset to discover central regulator genes.
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.
The highly influential two-group model in testing a large number of statistical hypotheses assumes that the test statistics are drawn independently from a mixture of a high probability null distribution and a low probability alternative. Optimal control of the marginal false discovery rate (mFDR), in the sense that it provides maximal power (expected true discoveries) subject to mFDR control, is known to be achieved by thresholding the local false discovery rate (locFDR), i.e., the probability of the hypothesis being null given the set of test statistics, with a fixed threshold. We address the challenge of controlling optimally the popular false discovery rate (FDR) or positive FDR (pFDR) rather than mFDR in the general two-group model, which also allows for dependence between the test statistics. These criteria are less conservative than the mFDR criterion, so they make more rejections in expectation. We derive their optimal multiple testing (OMT) policies, which turn out to be thresholding the locFDR with a threshold that is a function of the entire set of statistics. We develop an efficient algorithm for finding these policies, and use it for problems with thousands of hypotheses. We illustrate these procedures on gene expression studies.
Selecting relevant features associated with a given response variable is an important issue in many scientific fields. Quantifying quality and uncertainty of a selection result via false discovery rate (FDR) control has been of recent interest. This paper introduces a way of using data-splitting strategies to asymptotically control the FDR while maintaining a high power. For each feature, the method constructs a test statistic by estimating two independent regression coefficients via data splitting. FDR control is achieved by taking advantage of the statistics property that, for any null feature, its sampling distribution is symmetric about zero. Furthermore, we propose Multiple Data Splitting (MDS) to stabilize the selection result and boost the power. Interestingly and surprisingly, with the FDR still under control, MDS not only helps overcome the power loss caused by sample splitting, but also results in a lower variance of the false discovery proportion (FDP) compared with all other methods in consideration. We prove that the proposed data-splitting methods can asymptotically control the FDR at any designated level for linear and Gaussian graphical models in both low and high dimensions. Through intensive simulation studies and a real-data application, we show that the proposed methods are robust to the unknown distribution of features, easy to implement and computationally efficient, and are often the most powerful ones amongst competitors especially when the signals are weak and the correlations or partial correlations are high among features.
Multiple hypothesis testing, a situation when we wish to consider many hypotheses, is a core problem in statistical inference that arises in almost every scientific field. In this setting, controlling the false discovery rate (FDR), which is the expected proportion of type I error, is an important challenge for making meaningful inferences. In this paper, we consider the problem of controlling FDR in an online manner. Concretely, we consider an ordered, possibly infinite, sequence of hypotheses, arriving one at each timestep, and for each hypothesis we observe a p-value along with a set of features specific to that hypothesis. The decision whether or not to reject the current hypothesis must be made immediately at each timestep, before the next hypothesis is observed. The model of multi-dimensional feature set provides a very general way of leveraging the auxiliary information in the data which helps in maximizing the number of discoveries. We propose a new class of powerful online testing procedures, where the rejections thresholds (significance levels) are learnt sequentially by incorporating contextual information and previous results. We prove that any rule in this class controls online FDR under some standard assumptions. We then focus on a subclass of these procedures, based on weighting significance levels, to derive a practical algorithm that learns a parametric weight function in an online fashion to gain more discoveries. We also theoretically prove, in a stylized setting, that our proposed procedures would lead to an increase in the achieved statistical power over a popular online testing procedure proposed by Javanmard & Montanari (2018). Finally, we demonstrate the favorable performance of our procedure, by comparing it to state-of-the-art online multiple testing procedures, on both synthetic data and real data generated from different applications.
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