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Motivated by empirical arguments that are well-known from the genome-wide association studies (GWAS) literature, we study the statistical properties of linear mixed models (LMMs) applied to GWAS. First, we study the sensitivity of LMMs to…

Quantitative Methods · Quantitative Biology 2021-11-09 Haohan Wang , Bryon Aragam , Eric Xing

Traditional GWAS has advanced our understanding of complex diseases but often misses nonlinear genetic interactions. Deep learning offers new opportunities to capture complex genomic patterns, yet existing methods mostly depend on feature…

Machine Learning · Computer Science 2025-07-08 Iqra Farooq , Sara Atito , Ayse Demirkan , Inga Prokopenko , Muhammad Rana

The fundamental challenge of drawing causal inference is that counterfactual outcomes are not fully observed for any unit. Furthermore, in observational studies, treatment assignment is likely to be confounded. Many statistical methods have…

Methodology · Statistics 2022-08-01 Harsh Parikh , Carlos Varjao , Louise Xu , Eric Tchetgen Tchetgen

Mediation analysis in causal inference typically concentrates on one binary exposure, using deterministic interventions to split the average treatment effect into direct and indirect effects through a single mediator. Yet, real-world…

Methodology · Statistics 2023-07-07 David B. McCoy , Alan E. Hubbard , Mark van der Laan , Alejandro Schuler

The incorporation of causal inference in mediation analysis has led to theoretical and methodological advancements -- effect definitions with causal interpretation, clarification of assumptions required for effect identification, and an…

Methodology · Statistics 2022-10-31 Trang Quynh Nguyen , Ian Schmid , Elizabeth A. Stuart

The mainstream of data-driven abstractive summarization models tends to explore the correlations rather than the causal relationships. Among such correlations, there can be spurious ones which suffer from the language prior learned from the…

Computation and Language · Computer Science 2023-08-25 Lu Chen , Ruqing Zhang , Wei Huang , Wei Chen , Jiafeng Guo , Xueqi Cheng

The machine learning community has recently devoted much attention to the problem of inferring causal relationships from statistical data. Most of this work has focused on uncovering connections among scalar random variables. We generalize…

Machine Learning · Statistics 2012-07-10 Doris Entner , Patrik O. Hoyer

Causal mediation analysis is routinely conducted by applied researchers in a variety of disciplines. The goal of such an analysis is to investigate alternative causal mechanisms by examining the roles of intermediate variables that lie in…

Methodology · Statistics 2010-11-05 Kosuke Imai , Luke Keele , Teppei Yamamoto

Causal decomposition analysis provides a way to identify mediators that contribute to health disparities between marginalized and non-marginalized groups. In particular, the degree to which a disparity would be reduced or remain after…

Methodology · Statistics 2021-09-16 Soojin Park , Suyeon Kang , Chioun Lee

This article presents a novel method for causal discovery with generalized structural equation models suited for analyzing diverse types of outcomes, including discrete, continuous, and mixed data. Causal discovery often faces challenges…

Methodology · Statistics 2023-10-26 Minjie Wang , Xiaotong Shen , Wei Pan

Genome-wide association studies (GWAS) are used to identify relationships between genetic variations and specific traits. When applied to high-dimensional medical imaging data, a key step is to extract lower-dimensional, yet informative…

Quantitative Methods · Quantitative Biology 2023-09-28 Yaochen Xie , Ziqian Xie , Sheikh Muhammad Saiful Islam , Degui Zhi , Shuiwang Ji

Causal graph recovery is traditionally done using statistical estimation-based methods or based on individual's knowledge about variables of interests. They often suffer from data collection biases and limitations of individuals' knowledge.…

Computation and Language · Computer Science 2024-06-19 Yuzhe Zhang , Yipeng Zhang , Yidong Gan , Lina Yao , Chen Wang

Despite the accelerating presence of exploratory causal analysis in modern science and medicine, the available non-experimental methods for validating causal models are not well characterized. One of the most popular methods is to evaluate…

Methodology · Statistics 2025-03-20 Ritwick Banerjee , Bryan Andrews , Erich Kummerfeld

Mediation analysis in causal inference has traditionally focused on binary exposures and deterministic interventions, and a decomposition of the average treatment effect in terms of direct and indirect effects. In this paper we present an…

Methodology · Statistics 2020-11-17 Iván Díaz , Nima Hejazi

Genome-wide Association Studies (GWASes) identify genomic variations that are statistically associated with a trait, such as a disease, in a group of individuals. Unfortunately, careless sharing of GWAS statistics might give rise to privacy…

Genomics · Quantitative Biology 2022-09-21 Túlio Pascoal , Jérémie Decouchant , Antoine Boutet , Marcus Völp

Causal mediation analysis is increasingly abundant in biology, psychology, and epidemiology studies, etc. In particular, with the advent of the big data era, the issue of high-dimensional mediators is becoming more prevalent. In…

Methodology · Statistics 2023-07-10 Minghao Chen , Yingchun Zhou

The identification of latent mediator variables is typically conducted using standard structural equation models (SEMs). When SEM is applied to mediation analysis with a causal interpretation, valid inference relies on the strong assumption…

Methodology · Statistics 2025-10-02 Sofia Morelli , Roberto Faleh , Holger Brandt

Simulation methods are among the most ubiquitous methodological tools in statistical science. In particular, statisticians often is simulation to explore properties of statistical functionals in models for which developed statistical theory…

Methodology · Statistics 2023-08-22 Tyrel Stokes , Ian Shrier , Russell Steele

In epidemiological research, causal models incorporating potential mediators along a pathway are crucial for understanding how exposures influence health outcomes. This work is motivated by integrated epidemiological and blood biomarker…

Methodology · Statistics 2024-11-28 Youngho Bae , Chanmin Kim , Fenglei Wang , Qi Sun , Kyu Ha Lee

Gene regulatory networks play a crucial role in controlling an organism's biological processes, which is why there is significant interest in developing computational methods that are able to extract their structure from high-throughput…

Machine Learning · Statistics 2018-09-19 Ioan Gabriel Bucur , Tom van Bussel , Tom Claassen , Tom Heskes
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