Dataset Information

Two-Level Dynamic Structural Equation Models with Small Samples.

ABSTRACT: Advances in data collection have made intensive longitudinal data easier to collect, unlocking potential for methodological innovations to model such data. Dynamic structural equation modeling (DSEM) is one such methodology but recent studies have suggested that its small N performance is poor. This is problematic because small N data are omnipresent in empirical applications due to logistical and financial concerns associated with gathering many measurements on many people. In this paper, we discuss how previous studies considering small samples have focused on Bayesian methods with diffuse priors. The small sample literature has shown that diffuse priors may cause problems because they become unintentionally informative. Instead, we outline how researchers can create weakly informative admissible-range-restricted priors, even in the absence of previous studies. A simulation study shows that metrics like relative bias and non-null detection rates with these admissible-range-restricted priors improve small N properties of DSEM compared to diffuse priors.

SUBMITTER: McNeish D

PROVIDER: S-EPMC7451754 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Two-Level Dynamic Structural Equation Models with Small Samples.

McNeish Daniel D

Structural equation modeling : a multidisciplinary journal 20190328 6

Advances in data collection have made intensive longitudinal data easier to collect, unlocking potential for methodological innovations to model such data. Dynamic structural equation modeling (DSEM) is one such methodology but recent studies have suggested that its small N performance is poor. This is problematic because small N data are omnipresent in empirical applications due to logistical and financial concerns associated with gathering many measurements on many people. In this paper, we di ...[more]

PMID: 32863699

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Project description:MotivationWith the exponential growth of expression and protein-protein interaction (PPI) data, the identification of functional modules in PPI networks that show striking changes in molecular activity or phenotypic signatures becomes of particular interest to reveal process-specific information that is correlated with cellular or disease states. This requires both the identification of network nodes with reliability scores and the availability of an efficient technique to locate the network regions with the highest scores. In the literature, a number of heuristic methods have been suggested. We propose SEMtree(), a set of tree-based structure discovery algorithms, combining graph and statistically interpretable parameters together with a user-friendly R package based on structural equation models framework.ResultsCondition-specific changes from differential expression and gene-gene co-expression are recovered with statistical testing of node, directed edge, and directed path difference between groups. In the end, from a list of seed (i.e. disease) genes or gene P-values, the perturbed modules with undirected edges are generated with five state-of-the-art active subnetwork detection methods. The latter are supplied to causal additive trees based on Chu-Liu-Edmonds' algorithm (Chow and Liu, Approximating discrete probability distributions with dependence trees. IEEE Trans Inform Theory 1968;14:462-7) in SEMtree() to be converted in directed trees. This conversion allows to compare the methods in terms of directed active subnetworks. We applied SEMtree() to both Coronavirus disease (COVID-19) RNA-seq dataset (GEO accession: GSE172114) and simulated datasets with various differential expression patterns. Compared to existing methods, SEMtree() is able to capture biologically relevant subnetworks with simple visualization of directed paths, good perturbation extraction, and classifier performance.Availability and implementationSEMtree() function is implemented in the R package SEMgraph, easily available at https://CRAN.R-project.org/package=SEMgraph.

Dataset Information

Two-Level Dynamic Structural Equation Models with Small Samples.

Publications

Two-Level Dynamic Structural Equation Models with Small Samples.

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