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Improved inference in mediation analysis: Introducing the model-based constrained optimization procedure.

ABSTRACT: Mediation analysis is an important approach for investigating causal pathways. One approach used in mediation analysis is the test of an indirect effect, which seeks to measure how the effect of an independent variable impacts an outcome variable through 1 or more mediators. However, in many situations the proposed tests of indirect effects, including popular confidence interval-based methods, tend to produce poor Type I error rates when mediation does not occur and, more generally, only allow dichotomous decisions of "not significant" or "significant" with regards to the statistical conclusion. To remedy these issues, we propose a new method, a likelihood ratio test (LRT), that uses nonlinear constraints in what we term the model-based constrained optimization (MBCO) procedure. The MBCO procedure (a) offers a more robust Type I error rate than existing methods; (b) provides a p value, which serves as a continuous measure of compatibility of data with the hypothesized null model (not just a dichotomous reject or fail-to-reject decision rule); (c) allows simple and complex hypotheses about mediation (i.e., 1 or more mediators; different mediational pathways); and (d) allows the mediation model to use observed or latent variables. The MBCO procedure is based on a structural equation modeling framework (even if latent variables are not specified) with specialized fitting routines, namely with the use of nonlinear constraints. We advocate using the MBCO procedure to test hypotheses about an indirect effect in addition to reporting a confidence interval to capture uncertainty about the indirect effect because this combination transcends existing methods. (PsycInfo Database Record (c) 2020 APA, all rights reserved).

SUBMITTER: Tofighi D

PROVIDER: S-EPMC7877448 | biostudies-literature | 2020 Aug

REPOSITORIES: biostudies-literature

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Improved inference in mediation analysis: Introducing the model-based constrained optimization procedure.

Tofighi Davood D Kelley Ken K

Psychological methods 20200319 4

Mediation analysis is an important approach for investigating causal pathways. One approach used in mediation analysis is the test of an indirect effect, which seeks to measure how the effect of an independent variable impacts an outcome variable through 1 or more mediators. However, in many situations the proposed tests of indirect effects, including popular confidence interval-based methods, tend to produce poor Type I error rates when mediation does not occur and, more generally, only allow d ...[more]

PMID: 32191106

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Project description:BackgroundRecent advances in bioimaging and automated analysis methods have enabled the large-scale systematic analysis of cellular dynamics during the embryonic development of Caenorhabditis elegans. Most of these analyses have focused on cell lineage tracing rather than cell shape dynamics. Cell shape analysis requires cell membrane segmentation, which is challenging because of insufficient resolution and image quality. This problem is currently solved by complicated segmentation methods requiring laborious and time consuming parameter adjustments.ResultsOur new framework BCOMS (Biologically Constrained Optimization based cell Membrane Segmentation) automates the extraction of the cell shape of C. elegans embryos. Both the segmentation and evaluation processes are automated. To automate the evaluation, we solve an optimization problem under biological constraints. The performance of BCOMS was validated against a manually created ground truth of the 24-cell stage embryo. The average deviation of 25 cell shape features was 5.6%. The deviation was mainly caused by membranes parallel to the focal planes, which either contact the surfaces of adjacent cells or make no contact with other cells. Because segmentation of these membranes was difficult even by manual inspection, the automated segmentation was sufficiently accurate for cell shape analysis. As the number of manually created ground truths is necessarily limited, we compared the segmentation results between two adjacent time points. Across all cells and all cell cycles, the average deviation of the 25 cell shape features was 4.3%, smaller than that between the automated segmentation result and ground truth.ConclusionsBCOMS automated the accurate extraction of cell shapes in developing C. elegans embryos. By replacing image processing parameters with easily adjustable biological constraints, BCOMS provides a user-friendly framework. The framework is also applicable to other model organisms. Creating the biological constraints is a critical step requiring collaboration between an experimentalist and a software developer.

Dataset Information

Improved inference in mediation analysis: Introducing the model-based constrained optimization procedure.

Publications

Improved inference in mediation analysis: Introducing the model-based constrained optimization procedure.

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