Motivated by inferring cellular signaling networks using noisy flow cytometry data, we develop procedures to draw inference for Bayesian networks based on error-prone data. Two methods for inferring causal relationships between nodes in a network are proposed based on penalized estimation methods that account for measurement error and encourage sparsity. We discuss consistency of the proposed network estimators and develop an approach for selecting the tuning parameter in the penalized estimation methods. Empirical studies are carried out to compare the proposed methods and a naive method that ignores measurement error with applications to synthetic data and to single cell flow cytometry data.
Numerous studies have examined the associations between long-term exposure to fine particulate matter (PM2.5) and adverse health outcomes. Recently, many of these studies have begun to employ high-resolution predicted PM2.5 concentrations, which are subject to measurement error. Previous approaches for exposure measurement error correction have either been applied in non-causal settings or have only considered a categorical exposure. Moreover, most procedures have failed to account for uncertainty induced by error correction when fitting an exposure-response function (ERF). To remedy these def…
Patra and Sen (2016) consider a two-component mixture model, where one component plays the role of background while the other plays the role of signal, and propose to estimate the background component by simply "maximizing" its weight. While in their work the background component is a completely known distribution, we extend their approach here to three emblematic settings: when the background distribution is symmetric; when it is monotonic; and when it is log-concave. In each setting, we derive estimators for the background component, establish consistency, and provide a confidence band. Whil…
Estimating the number of communities is one of the fundamental problems in community detection. We re-examine the Bayesian paradigm for stochastic block models and propose a "corrected Bayesian information criterion",to determine the number of communities and show that the proposed estimator is consistent under mild conditions. The proposed criterion improves those used in Wang and Bickel (2016) and Saldana et al. (2017) which tend to underestimate and overestimate the number of communities, respectively. Along the way, we establish the Wilks theorem for stochastic block models. Moreover, we s…
In the context of regressing a response $Y$ on a predictor $X$, we consider estimating the local modes of the distribution of $Y$ given $X=x$ when $X$ is prone to measurement error. We propose two nonparametric estimation methods, with one based on estimating the joint density of $(X, Y)$ in the presence of measurement error, and the other built upon estimating the conditional density of $Y$ given $X=x$ using error-prone data. We study the asymptotic properties of each proposed mode estimator, and provide implementation details including the mean-shift algorithm for mode seeking and bandwidth …
In this paper, we present a generalized estimating equations based estimation approach and a variable selection procedure for single-index models when the observed data are clustered. Unlike the case of independent observations, bias-correction is necessary when general working correlation matrices are used in the estimating equations. Our variable selection procedure based on smooth-threshold estimating equations \citep{Ueki-2009} can automatically eliminate irrelevant parameters by setting them as zeros and is computationally simpler than alternative approaches based on shrinkage penalty. Th…
Propensity score methods are an important tool to help reduce confounding in non-experimental studies. Most propensity score methods assume that covariates are measured without error. However, covariates are often measured with error, which leads to biased causal effect estimates if the true underlying covariates are the actual confounders. Although some studies have investigated the impact of a single mismeasured covariate on estimating a causal effect and proposed methods for handling the measurement error, almost no work exists investigating the case where multiple covariates are mismeasure…
A new method for estimating structural equation models (SEM) is proposed and evaluated. In contrast to most other methods, it is based directly on the data, not on the covariance matrix of the data. The new approach is flexible enough to handle non-linear and non-smooth models and allows to model various constraints. Principle strengths and weaknesses of this approach are discussed and simulation studies are performed to reveal problems and potentials of this approach.
For a high-dimensional linear model with a finite number of covariates measured with error, we study statistical inference on the parameters associated with the error-prone covariates, and propose a new corrected decorrelated score test and the corresponding one-step estimator. We further establish asymptotic properties of the newly proposed test statistic and the one-step estimator. Under local alternatives, we show that the limiting distribution of our corrected decorrelated score test statistic is non-central normal. The finite-sample performance of the proposed inference procedure is exami…
In this paper, we consider the partially linear single-index models with longitudinal data. To deal with the variable selection problem in this context, we propose a penalized procedure combined with two bias correction methods, resulting in the bias-corrected generalized estimating equation (GEE) and the bias-corrected quadratic inference function (QIF), which can take into account the correlations. Asymptotic properties of these methods are demonstrated. We also evaluate the finite sample performance of the proposed methods via Monte Carlo simulation studies and a real data analysis.
Histogram-based empirical Bayes methods developed for analyzing data for large numbers of genes, SNPs, or other biological features tend to have large biases when applied to data with a smaller number of features such as genes with expression measured conventionally, proteins, and metabolites. To analyze such small-scale and medium-scale data in an empirical Bayes framework, we introduce corrections of maximum likelihood estimators (MLE) of the local false discovery rate (LFDR). In this context, the MLE estimates the LFDR, which is a posterior probability of null hypothesis truth, by estimatin…
We propose a new approach for estimating causal effects when the exposure is measured with error and confounding adjustment is performed via a generalized propensity score (GPS). Using validation data, we propose a regression calibration (RC)-based adjustment for a continuous error-prone exposure combined with GPS to adjust for confounding (RC-GPS). The outcome analysis is conducted after transforming the corrected continuous exposure into a categorical exposure. We consider confounding adjustment in the context of GPS subclassification, inverse probability treatment weighting (IPTW) and match…
Joint models for longitudinal and survival data have gained a lot of attention in recent years, with the development of myriad extensions to the basic model, including those which allow for multivariate longitudinal data, competing risks and recurrent events. Several software packages are now also available for their implementation. Although mathematically straightforward, the inclusion of multiple longitudinal outcomes in the joint model remains computationally difficult due to the large number of random effects required, which hampers the practical application of this extension. We present a…
Measurement Error-Robust Causal Inference via Constructed Instrumental Variables
Columbia Mailman School of Public Health（哥伦比亚大学麦金农公共卫生学院）；Department of Biostatistics, Columbia University（哥伦比亚大学生物统计系）；Harvard T.H. Chan School of Public Health（哈佛大学陈曾熙公共卫生学院）
Models of the spatial distribution of animals provide useful tools to help ecologists quantify species-environment relationships, and they are increasingly being used to help determine the impacts of climate and habitat changes on species. While high-quality survey-style data with known effort are sometimes available, often researchers have multiple datasets of varying quality and type. In particular, collections of sightings made by citizen scientists are becoming increasingly common, with no information typically provided on their observer effort. Many standard modelling approaches ignore ob…
Estimating Interventional Distributions with Uncertain Causal Graphs through Meta-Learning
Imperial College London（伦敦帝国学院）；University of Cambridge（剑桥大学）；University of Toronto（多伦多大学）；Vector Institute（向量研究所）；Alan Turing Institute（艾伦·图灵研究所）；University of Oxford（牛津大学）
This paper deals with the estimation of exogeneous peer effects for partially observed networks under the new inferential paradigm of design identification, which characterizes the missing data challenge arising with sampled networks with the central idea that two full data versions which are topologically compatible with the observed data may give rise to two different probability distributions. We show that peer effects cannot be identified by design when network links between sampled and unsampled units are not observed. Under realistic modeling conditions, and under the assumption that sam…
