Annals of Applied Statistics最新文献

We tackle the problem of selecting from among a large number of variables those that are "important" for an outcome. We consider situations where groups of variables are also of interest. For example, each variable might be a genetic polymorphism, and we might want to study how a trait depends on variability in genes, segments of DNA that typically contain multiple such polymorphisms. In this context, to discover that a variable is relevant for the outcome implies discovering that the larger entity it represents is also important. To guarantee meaningful results with high chance of replicability, we suggest controlling the rate of false discoveries for findings at the level of individual variables and at the level of groups. Building on the knockoff construction of Barber and Candès [Ann. Statist. 43 (2015) 2055-2085] and the multilayer testing framework of Barber and Ramdas [J. Roy. Statist. Soc. Ser. B 79 (2017) 1247-1268], we introduce the multilayer knockoff filter (MKF). We prove that MKF simultaneously controls the FDR at each resolution and use simulations to show that it incurs little power loss compared to methods that provide guarantees only for the discoveries of individual variables. We apply MKF to analyze a genetic dataset and find that it successfully reduces the number of false gene discoveries without a significant reduction in power.

Early infancy from at-birth to 3 years is critical for cognitive, emotional and social development of infants. During this period, infant's developmental tempo and outcomes are potentially impacted by in utero exposure to endocrine disrupting compounds (EDCs), such as bisphenol A (BPA) and phthalates. We investigate effects of ten ubiquitous EDCs on the infant growth dynamics of body mass index (BMI) in a birth cohort study.Modeling growth acceleration is proposed to understand the "force of growth" through a class of semiparametric stochastic velocity models. The great flexibility of such a dynamic model enables us to capture subject-specific dynamics of growth trajectories and to assess effects of the EDCs on potential delay of growth. We adopted a Bayesian method with the Ornstein-Uhlenbeck process as the prior for the growth rate function, in which the World Health Organization global infant's growth curves were integrated into our analysis. We found that BPA and most of phthalates exposed during the first trimester of pregnancy were inversely associated with BMI growth acceleration, resulting in a delayed achievement of infant BMI peak. Such early growth deficiency has been reported as a profound impact on health outcomes in puberty (e.g., timing of sexual maturation) and adulthood.

In recent years new technologies in neuroscience have made it possible to measure the activities of large numbers of neurons simultaneously in behaving animals. For each neuron a fluorescence trace is measured; this can be seen as a first-order approximation of the neuron's activity over time. Determining the exact time at which a neuron spikes on the basis of its fluorescence trace is an important open problem in the field of computational neuroscience. Recently, a convex optimization problem involving an ℓ₁ penalty was proposed for this task. In this paper we slightly modify that recent proposal by replacing the ℓ₁ penalty with an ℓ₀ penalty. In stark contrast to the conventional wisdom that ℓ₀ optimization problems are computationally intractable, we show that the resulting optimization problem can be efficiently solved for the global optimum using an extremely simple and efficient dynamic programming algorithm. Our R-language implementation of the proposed algorithm runs in a few minutes on fluorescence traces of 100,000 timesteps. Furthermore, our proposal leads to substantial improvements over the previous ℓ₁ proposal, in simulations as well as on two calcium imaging datasets. R-language software for our proposal is available on CRAN in the package LZeroSpikeInference. Instructions for running this software in python can be found at https://github.com/jewellsean/LZeroSpikeInference.

We propose a novel multivariate model for analyzing hybrid traits and identifying genetic factors for comorbid conditions. Comorbidity is a common phenomenon in mental health in which an individual suffers from multiple disorders simultaneously. For example, in the Study of Addiction: Genetics and Environment (SAGE), alcohol and nicotine addiction were recorded through multiple assessments that we refer to as hybrid traits. Statistical inference for studying the genetic basis of hybrid traits has not been well-developed. Recent rank-based methods have been utilized for conducting association analyses of hybrid traits but do not inform the strength or direction of effects. To overcome this limitation, a parametric modeling framework is imperative. Although such parametric frameworks have been proposed in theory, they are neither well-developed nor extensively used in practice due to their reliance on complicated likelihood functions that have high computational complexity. Many existing parametric frameworks tend to instead use pseudo-likelihoods to reduce computational burdens. Here, we develop a model fitting algorithm for the full likelihood. Our extensive simulation studies demonstrate that inference based on the full likelihood can control the type-I error rate, and gains power and improves the effect size estimation when compared with several existing methods for hybrid models. These advantages remain even if the distribution of the latent variables is misspecified. After analyzing the SAGE data, we identify three genetic variants (rs7672861, rs958331, rs879330) that are significantly associated with the comorbidity of alcohol and nicotine addiction at the chromosome-wide level. Moreover, our approach has greater power in this analysis than several existing methods for hybrid traits.Although the analysis of the SAGE data motivated us to develop the model, it can be broadly applied to analyze any hybrid responses.

Respondent-driven sampling (RDS) is a method for sampling from a target population by leveraging social connections. RDS is invaluable to the study of hard-to-reach populations. However, RDS is costly and can be infeasible. RDS is infeasible when RDS point estimators have small effective sample sizes (large design effects) or when RDS interval estimators have large confidence intervals relative to estimates obtained in previous studies or poor coverage. As a result, researchers need tools to assess whether or not estimation of certain characteristics of interest for specific populations is feasible in advance. In this paper, we develop a simulation-based framework for using pilot data-in the form of a convenience sample of aggregated, egocentric data and estimates of subpopulation sizes within the target population-to assess whether or not RDS is feasible for estimating characteristics of a target population. in doing so, we assume that more is known about egos than alters in the pilot data, which is often the case with aggregated, egocentric data in practice. We build on existing methods for estimating the structure of social networks from aggregated, egocentric sample data and estimates of subpopulation sizes within the target population. We apply this framework to assess the feasibility of estimating the proportion male, proportion bisexual, proportion depressed and proportion infected with HIV/AIDS within three spatially distinct target populations of older lesbian, gay and bisexual adults using pilot data from the caring and Aging with Pride Study and the Gallup Daily Tracking Survey. We conclude that using an RDS sample of 300 subjects is infeasible for estimating the proportion male, but feasible for estimating the proportion bisexual, proportion depressed and proportion infected with HIV/AIDS in all three target populations.