Robust inference with knockoffs

DOI10.1214/19-AOS1852MaRDI QIDQ2196226zbMATH OpenOpenAlexFDO

Authors Rina Foygel Barber, Emmanuel J. Candès, Richard Samworth

Publication date 28 August 2020

Published in The Annals of Statistics (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1801.03896, https://projecteuclid.org/euclid.aos/1594972823

zbMATH Keywords

variable selectionfalse discovery ratehigh-dimensional regressionrobustnessknockoffs

Mathematics Subject Classification ID

Parametric hypothesis testing (62F03) Nonparametric hypothesis testing (62G10) Nonparametric robustness (62G35) Robustness and adaptive procedures (parametric inference) (62F35)

Abstract: We consider the variable selection problem, which seeks to identify important variables influencing a response $Y$ out of many candidate features $X_1,ldots,X_p$. We wish to do so while offering finite-sample guarantees about the fraction of false positives - selected variables $X_j$ that in fact have no effect on $Y$ after the other features are known. When the number of features $p$ is large (perhaps even larger than the sample size $n$), and we have no prior knowledge regarding the type of dependence between $Y$ and $X$, the model-X knockoffs framework nonetheless allows us to select a model with a guaranteed bound on the false discovery rate, as long as the distribution of the feature vector $X=(X_1,dots,X_p)$ is exactly known. This model selection procedure operates by constructing "knockoff copies'" of each of the $p$ features, which are then used as a control group to ensure that the model selection algorithm is not choosing too many irrelevant features. In this work, we study the practical setting where the distribution of $X$ could only be estimated, rather than known exactly, and the knockoff copies of the $X_j$'s are therefore constructed somewhat incorrectly. Our results, which are free of any modeling assumption whatsoever, show that the resulting model selection procedure incurs an inflation of the false discovery rate that is proportional to our errors in estimating the distribution of each feature $X_j$ conditional on the remaining features $X_k:keqj$. The model-X knockoff framework is therefore robust to errors in the underlying assumptions on the distribution of $X$, making it an effective method for many practical applications, such as genome-wide association studies, where the underlying distribution on the features $X_1,dots,X_p$ is estimated accurately but not known exactly.

Recommendations

• Relaxing the assumptions of knockoffs by conditioning
• Panning for Gold: ‘Model-X’ Knockoffs for High Dimensional Controlled Variable Selection
• Controlling the false discovery rate via knockoffs
• Derandomizing Knockoffs
• Powerful knockoffs via minimizing reconstructability
• A pseudo knockoff filter for correlated features
• Adjusting the Benjamini–Hochberg method for controlling the false discovery rate in knockoff-assisted variable selection
• Metropolized Knockoff Sampling
• Gene hunting with hidden Markov model knockoffs
• A high-dimensional power analysis of the conditional randomization test and knockoffs

Cites work

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Cited in

(43)

• Robust AIC with high breakdown scale estimate
• Identifying important predictors in large data bases -- multiple testing and model selection
• False Discovery Rate Control via Data Splitting
• A Scale-Free Approach for False Discovery Rate Control in Generalized Linear Models
• Local false discovery rate estimation with competition-based procedures for variable selection
• Relaxing the assumptions of knockoffs by conditioning
• Controlling the false discovery rate by a latent Gaussian copula knockoff procedure
• Familywise error rate control via knockoffs
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