Browse
Submit Data
Databases
API
Help

Dataset Information

23 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

General Control Functions for Causal Effect Estimation from Instrumental Variables.

ABSTRACT: Causal effect estimation relies on separating the variation in the outcome into parts due to the treatment and due to the confounders. To achieve this separation, practitioners often use external sources of randomness that only influence the treatment called instrumental variables (IVs). We study variables constructed from treatment and IV that help estimate effects, called control functions. We characterize general control functions for effect estimation in a meta-identification result. Then, we show that structural assumptions on the treatment process allow the construction of general control functions, thereby guaranteeing identification. To construct general control functions and estimate effects, we develop the general control function method (GCFN). GCFN's first stage called variational decoupling (VDE) constructs general control functions by recovering the residual variation in the treatment given the IV. Using VDE's control function, GCFN's second stage estimates effects via regression. Further, we develop semi-supervised GCFN to construct general control functions using subsets of data that have both IV and confounders observed as supervision; this needs no structural treatment process assumptions. We evaluate GCFN on low and high dimensional simulated data and on recovering the causal effect of slave export on modern community trust [30].

SUBMITTER: Puli A

PROVIDER: S-EPMC8096518 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Designs combining instrumental variables with case-control: estimating principal strata causal effects.

Project description:The instrumental variables framework is commonly used for the estimation of causal effects from cohort samples. However, the combination of instrumental variables with more efficient designs such as case-control sampling requires new methodological consideration. For example, as the use of Mendelian randomization studies is increasing and the cost of genotyping and gene expression data can be high, the analysis of data gathered from more cost-effective sampling designs is of prime interest. We show that the standard instrumental variables analysis does not appropriately estimate the causal effects of interest when the instrumental variables design is combined with the case-control design. We also propose a method that can estimate the causal effects in such combined designs. We illustrate the method with a study in oncology.

| S-EPMC3608098 | biostudies-literature

Causal Genetic Inference Using Haplotypes as Instrumental Variables.

Project description:In genomic studies with both genotypes and gene or protein expression profile available, causal effects of gene or protein on clinical outcomes can be inferred through using genetic variants as instrumental variables (IVs). The goal of introducing IV is to remove the effects of unobserved factors that may confound the relationship between the biomarkers and the outcome. A valid inference under the IV framework requires pairwise associations and pathway exclusivity. Among these assumptions, the IV expression association needs to be strong for the casual effect estimates to be unbiased. However, a small number of single nucleotide polymorphisms (SNPs) often provide limited explanation of the variability in the gene or protein expression and can only serve as weak IVs. In this study, we propose to replace SNPs with haplotypes as IVs to increase the variant-expression association and thus improve the casual effect inference of the expression. In the classical two-stage procedure, we developed a haplotype regression model combined with a model selection procedure to identify optimal instruments. The performance of the new method was evaluated through simulations and compared with the IV approaches using observed multiple SNPs. Our results showed the gain of power to detect a causal effect of gene or protein on the outcome using haplotypes compared with using only observed SNPs, under either complete or missing genotype scenarios. We applied our proposed method to a study of the effect of interleukin-1 beta (IL-1?) protein expression on the 90-day survival following sepsis and found that overly expressed IL-1? is likely to increase mortality.

| S-EPMC5625343 | biostudies-literature

Causal Proportional Hazards Estimation with a Binary Instrumental Variable.

Project description:Instrumental variables (IV) are a useful tool for estimating causal effects in the presence of unmeasured confounding. IV methods are well developed for uncensored outcomes, particularly for structural linear equation models, where simple two-stage estimation schemes are available. The extension of these methods to survival settings is challenging, partly because of the nonlinearity of the popular survival regression models and partly because of the complications associated with right censoring or other survival features. Motivated by the Prostate, Lung, Colorectal and Ovarian (PLCO) Cancer screening trial, we develop a simple causal hazard ratio estimator in a proportional hazards model with right censored data. The method exploits a special characterization of IV which enables the use of an intuitive inverse weighting scheme that is generally applicable to more complex survival settings with left truncation, competing risks, or recurrent events. We rigorously establish the asymptotic properties of the estimators, and provide plug-in variance estimators. The proposed method can be implemented in standard software, and is evaluated through extensive simulation studies. We apply the proposed IV method to a data set from the Prostate, Lung, Colorectal and Ovarian cancer screening trial to delineate the causal effect of flexible sigmoidoscopy screening on colorectal cancer survival which may be confounded by informative noncompliance with the assigned screening regimen.

| S-EPMC8716008 | biostudies-literature

Estimation of the Heteroskedastic Canonical Contagion Model with Instrumental Variables.

Project description:Knowledge of contagion among economies is a relevant issue in economics. The canonical model of contagion is an alternative in this case. Given the existence of endogenous variables in the model, instrumental variables can be used to decrease the bias of the OLS estimator. In the presence of heteroskedastic disturbances this paper proposes the use of conditional volatilities as instruments. Simulation is used to show that the homoscedastic and heteroskedastic estimators which use them as instruments have small bias. These estimators are preferable in comparison with the OLS estimator and their asymptotic distribution can be used to construct confidence intervals.

| S-EPMC5193442 | biostudies-literature

Instrumental variables as bias amplifiers with general outcome and confounding.

Project description:Drawing causal inference with observational studies is the central pillar of many disciplines. One sufficient condition for identifying the causal effect is that the treatment-outcome relationship is unconfounded conditional on the observed covariates. It is often believed that the more covariates we condition on, the more plausible this unconfoundedness assumption is. This belief has had a huge impact on practical causal inference, suggesting that we should adjust for all pretreatment covariates. However, when there is unmeasured confounding between the treatment and outcome, estimators adjusting for some pretreatment covariate might have greater bias than estimators without adjusting for this covariate. This kind of covariate is called a bias amplifier, and includes instrumental variables that are independent of the confounder, and affect the outcome only through the treatment. Previously, theoretical results for this phenomenon have been established only for linear models. We fill in this gap in the literature by providing a general theory, showing that this phenomenon happens under a wide class of models satisfying certain monotonicity assumptions. We further show that when the treatment follows an additive or multiplicative model conditional on the instrumental variable and the confounder, these monotonicity assumptions can be interpreted as the signs of the arrows of the causal diagrams.

| S-EPMC5636691 | biostudies-literature

Robust best linear estimation for regression analysis using surrogate and instrumental variables.

Project description:We investigate methods for regression analysis when covariates are measured with errors. In a subset of the whole cohort, a surrogate variable is available for the true unobserved exposure variable. The surrogate variable satisfies the classical measurement error model, but it may not have repeated measurements. In addition to the surrogate variables that are available among the subjects in the calibration sample, we assume that there is an instrumental variable (IV) that is available for all study subjects. An IV is correlated with the unobserved true exposure variable and hence can be useful in the estimation of the regression coefficients. We propose a robust best linear estimator that uses all the available data, which is the most efficient among a class of consistent estimators. The proposed estimator is shown to be consistent and asymptotically normal under very weak distributional assumptions. For Poisson or linear regression, the proposed estimator is consistent even if the measurement error from the surrogate or IV is heteroscedastic. Finite-sample performance of the proposed estimator is examined and compared with other estimators via intensive simulation studies. The proposed method and other methods are applied to a bladder cancer case-control study.

| S-EPMC3413079 | biostudies-literature

Bayesian methods for meta-analysis of causal relationships estimated using genetic instrumental variables.

Project description:Genetic markers can be used as instrumental variables, in an analogous way to randomization in a clinical trial, to estimate the causal relationship between a phenotype and an outcome variable. Our purpose is to extend the existing methods for such Mendelian randomization studies to the context of multiple genetic markers measured in multiple studies, based on the analysis of individual participant data. First, for a single genetic marker in one study, we show that the usual ratio of coefficients approach can be reformulated as a regression with heterogeneous error in the explanatory variable. This can be implemented using a Bayesian approach, which is next extended to include multiple genetic markers. We then propose a hierarchical model for undertaking a meta-analysis of multiple studies, in which it is not necessary that the same genetic markers are measured in each study. This provides an overall estimate of the causal relationship between the phenotype and the outcome, and an assessment of its heterogeneity across studies. As an example, we estimate the causal relationship of blood concentrations of C-reactive protein on fibrinogen levels using data from 11 studies. These methods provide a flexible framework for efficient estimation of causal relationships derived from multiple studies. Issues discussed include weak instrument bias, analysis of binary outcome data such as disease risk, missing genetic data, and the use of haplotypes.

| S-EPMC3648673 | biostudies-literature

Bounded, efficient and multiply robust estimation of average treatment effects using instrumental variables.

Project description:Instrumental variables (IVs) are widely used for estimating causal effects in the presence of unmeasured confounding. Under the standard IV model, however, the average treatment effect (ATE) is only partially identifiable. To address this, we propose novel assumptions that allow for identification of the ATE. Our identification assumptions are clearly separated from model assumptions needed for estimation, so that researchers are not required to commit to a specific observed data model in establishing identification. We then construct multiple estimators that are consistent under three different observed data models, and multiply robust estimators that are consistent in the union of these observed data models. We pay special attention to the case of binary outcomes, for which we obtain bounded estimators of the ATE that are guaranteed to lie between -1 and 1. Our approaches are illustrated with simulations and a data analysis evaluating the causal effect of education on earnings.

| S-EPMC6051728 | biostudies-literature

Instrumental variable estimation of causal odds ratios using structural nested mean models.

Project description:We consider estimating causal odds ratios using an instrumental variable under a logistic structural nested mean model (LSNMM). Current methods for LSNMMs either rely heavily on possible "uncongenial" modeling assumptions or involve intricate numerical challenges, which have impeded their use. In this article, we present an alternative method that ensures a congenial parametrization, circumvents computational complexity of existing methods, and is easy to implement. We illustrate the proposed method to (1) estimate the causal effect of years of education on earnings using data from the NLSYM and (2) assess the impact of moving families from high to low-poverty neighborhoods had on lifetime major depressive disorder among adolescents in the "Moving to Opportunity (MTO) for Fair Housing Demonstration Project" from the Department of Housing and Urban Development.

| S-EPMC5862265 | biostudies-literature

On the Use of the Lasso for Instrumental Variables Estimation with Some Invalid Instruments.

Project description:We investigate the behavior of the Lasso for selecting invalid instruments in linear instrumental variables models for estimating causal effects of exposures on outcomes, as proposed recently by Kang et al. Invalid instruments are such that they fail the exclusion restriction and enter the model as explanatory variables. We show that for this setup, the Lasso may not consistently select the invalid instruments if these are relatively strong. We propose a median estimator that is consistent when less than 50% of the instruments are invalid, and its consistency does not depend on the relative strength of the instruments, or their correlation structure. We show that this estimator can be used for adaptive Lasso estimation, with the resulting estimator having oracle properties. The methods are applied to a Mendelian randomization study to estimate the causal effect of body mass index (BMI) on diastolic blood pressure, using data on individuals from the UK Biobank, with 96 single nucleotide polymorphisms as potential instruments for BMI. Supplementary materials for this article are available online.

| S-EPMC6817329 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data