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CDfdr: A Comparison Density Approach to Local False Discovery Rate Estimation

arXiv.org Machine Learning

Efron et al. (2001) proposed empirical Bayes formulation of the frequentist Benjamini and Hochbergs False Discovery Rate method (Benjamini and Hochberg,1995). This article attempts to unify the `two cultures' using concepts of comparison density and distribution function. We have also shown how almost all of the existing local fdr methods can be viewed as proposing various model specification for comparison density - unifies the vast literature of false discovery methods under one concept and notation.


On The Problem of Relevance in Statistical Inference

arXiv.org Machine Learning

How many statistical inference tools we have for inference from massive data? A huge number, but only when we are ready to assume the given database is homogenous, consisting of a large cohort of "similar" cases. Why we need the homogeneity assumption? To make `learning from the experience of others' or `borrowing strength' possible. But, what if, we are dealing with a massive database of heterogeneous cases (which is a norm in almost all modern data-science applications including neuroscience, genomics, healthcare, and astronomy)? How many methods we have in this situation? Not much, if not ZERO. Why? It's not obvious how to go about gathering strength when each piece of information is fuzzy. The danger is that, if we include irrelevant cases, borrowing information might heavily damage the quality of the inference! This raises some fundamental questions for big data inference: When (not) to borrow? Whom (not) to borrow? How (not) to borrow? These questions are at the heart of the "Problem of Relevance" in statistical inference -- a puzzle that has remained too little addressed since its inception nearly half a century ago. Here we offer the first practical theory of relevance with precisely describable statistical formulation and algorithm. Through examples, we demonstrate how our new statistical perspective answers previously unanswerable questions in a realistic and feasible way.


Inference with Transposable Data: Modeling the Effects of Row and Column Correlations

arXiv.org Machine Learning

We consider the problem of large-scale inference on the row or column variables of data in the form of a matrix. Often this data is transposable, meaning that both the row variables and column variables are of potential interest. An example of this scenario is detecting significant genes in microarrays when the samples or arrays may be dependent due to underlying relationships. We study the effect of both row and column correlations on commonly used test-statistics, null distributions, and multiple testing procedures, by explicitly modeling the covariances with the matrix-variate normal distribution. Using this model, we give both theoretical and simulation results revealing the problems associated with using standard statistical methodology on transposable data. We solve these problems by estimating the row and column covariances simultaneously, with transposable regularized covariance models, and de-correlating or sphering the data as a pre-processing step. Under reasonable assumptions, our method gives test statistics that follow the scaled theoretical null distribution and are approximately independent. Simulations based on various models with structured and observed covariances from real microarray data reveal that our method offers substantial improvements in two areas: 1) increased statistical power and 2) correct estimation of false discovery rates.


Feature selection in omics prediction problems using cat scores and false nondiscovery rate control

arXiv.org Machine Learning

We revisit the problem of feature selection in linear discriminant analysis (LDA), that is, when features are correlated. First, we introduce a pooled centroids formulation of the multiclass LDA predictor function, in which the relative weights of Mahalanobis-transformed predictors are given by correlation-adjusted $t$-scores (cat scores). Second, for feature selection we propose thresholding cat scores by controlling false nondiscovery rates (FNDR). Third, training of the classifier is based on James--Stein shrinkage estimates of correlations and variances, where regularization parameters are chosen analytically without resampling. Overall, this results in an effective and computationally inexpensive framework for high-dimensional prediction with natural feature selection. The proposed shrinkage discriminant procedures are implemented in the R package ``sda'' available from the R repository CRAN.


On Estimating Many Means, Selection Bias, and the Bootstrap

arXiv.org Machine Learning

With recent advances in high throughput technology, researchers often find themselves running a large number of hypothesis tests (thousands+) and esti- mating a large number of effect-sizes. Generally there is particular interest in those effects estimated to be most extreme. Unfortunately naive estimates of these effect-sizes (even after potentially accounting for multiplicity in a testing procedure) can be severely biased. In this manuscript we explore this bias from a frequentist perspective: we give a formal definition, and show that an oracle estimator using this bias dominates the naive maximum likelihood estimate. We give a resampling estimator to approximate this oracle, and show that it works well on simulated data. We also connect this to ideas in empirical Bayes.