Next steps in Bayesian structural equation models: Comments on, variations of, and extensions to Muthén and Asparouhov (2012)

Muthén and Asparouhov (2012) made a strong case for the advantages of Bayesian methodology in factor analysis and structural equation models. I show additional extensions and adaptations of their methods and show how non-Bayesians can take advantage of many (though not all) of these advantages by using interval restrictions on parameters. By keeping parameters restricted to intervals (such as loadings between -.3 and .3 to produce small loadings), frequentists using standard structural equation modeling software can do something similar to what a Bayesian does by putting prior distributions on these parameters. (PsycINFO Database Record (c) 2012 APA, all rights reserved).     

贝叶斯多组比较——渐近测量不变性

在行为科学研究领域中,检验测量工具的测量不变性是进行群体差异比较的前提。目前,多组验证性因子分析(多组CFA)方法被广泛用于检验测量不变性,但是它对跨组等值的限制过于严格,在实际应用中常常存在大量局限。贝叶斯渐近测量不变性方法基于贝叶斯思想的优良特性,放宽了传统多组CFA方法对跨组差异的严格限制,避免了传统方法的问题,具有较高的应用价值。文章详细介绍了贝叶斯渐近测量不变性方法的原理及优势,同时通过实例展示了渐近测量不变性方法在Mplus软件中的具体分析过程。     

Mixed-effects logistic regression for estimating transitional probabilities in sequentially coded observational data

This article demonstrates the use of mixed-effects logistic regression (MLR) for conducting sequential analyses of binary observational data. MLR is a special case of the mixed-effects logit modeling framework, which may be applied to multicategorical observational data. The MLR approach is motivated in part by G. A. Dagne, G. W. Howe, C. H. Brown, & B. O. Muthén (2002) advances in general linear mixed models for sequential analyses of observational data in the form of contingency table frequency counts. The advantage of the MLR approach is that it circumvents obstacles in the estimation of random sampling error encountered using Dagne and colleagues' approach. This article demonstrates the MLR model in an analysis of observed sequences of communication in a sample of young adult same-sex peer dyads. The results obtained using MLR are compared with those of a parallel analysis using Dagne and colleagues' linear mixed model for binary observational data in the form of log odds ratios. Similarities and differences between the results of the 2 approaches are discussed. Implications for the use of linear mixed models versus mixed-effects logit models for sequential analyses are considered.     

Bayesian Factor Analysis as a Variable-Selection Problem: Alternative Priors and Consequences

Factor analysis is a popular statistical technique for multivariate data analysis. Developments in the structural equation modeling framework have enabled the use of hybrid confirmatory/exploratory approaches in which factor-loading structures can be explored relatively flexibly within a confirmatory factor analysis (CFA) framework. Recently, Muthén & Asparouhov proposed a Bayesian structural equation modeling (BSEM) approach to explore the presence of cross loadings in CFA models. We show that the issue of determining factor-loading patterns may be formulated as a Bayesian variable selection problem in which Muthén and Asparouhov's approach can be regarded as a BSEM approach with ridge regression prior (BSEM-RP). We propose another Bayesian approach, denoted herein as the Bayesian structural equation modeling with spike-and-slab prior (BSEM-SSP), which serves as a one-stage alternative to the BSEM-RP. We review the theoretical advantages and disadvantages of both approaches and compare their empirical performance relative to two modification indices-based approaches and exploratory factor analysis with target rotation. A teacher stress scale data set is used to demonstrate our approach.     

Bayesian structural equation modeling: A more flexible representation of substantive theory

This article proposes a new approach to factor analysis and structural equation modeling using Bayesian analysis. The new approach replaces parameter specifications of exact zeros with approximate zeros based on informative, small-variance priors. It is argued that this produces an analysis that better reflects substantive theories. The proposed Bayesian approach is particularly beneficial in applications where parameters are added to a conventional model such that a nonidentified model is obtained if maximum-likelihood estimation is applied. This approach is useful for measurement aspects of latent variable modeling, such as with confirmatory factor analysis, and the measurement part of structural equation modeling. Two application areas are studied, cross-loadings and residual correlations in confirmatory factor analysis. An example using a full structural equation model is also presented, showing an efficient way to find model misspecification. The approach encompasses 3 elements: model testing using posterior predictive checking, model estimation, and model modification. Monte Carlo simulations and real data are analyzed using Mplus. The real-data analyses use data from Holzinger and Swineford's (1939) classic mental abilities study, Big Five personality factor data from a British survey, and science achievement data from the National Educational Longitudinal Study of 1988. (PsycINFO Database Record (c) 2012 APA, all rights reserved).     

Brain lesion and memory functioning: Short-term memory deficit is independent of lesion location

We analyzed the effects of patterns of brain lesions from penetrating head injuries on memory performance in participants of the Vietnam Head Injury Study (Grafman et al., 1988). Classes of lesion patterns were determined by mixture modeling (L. K. Muthén & B. O. Muthén, 1998-2004). Memory performance was assessed for short-term memory (STM), semantic memory, verbal episodic memory, and visual episodic memory. The striking finding was that large STM deficits were observed in all classes of brain-injured individuals, regardless of lesion location pattern. These effects persist despite frequent concomitant effects of depressive symptomatology and substance dependence. Smaller deficits in semantic memory, verbal episodic memory, and visual episodic memory depended on lesion location, in a manner roughly consistent with the existing neuropsychological literature. The theoretical and clinical implications of the striking, seemingly permanent STM deficits in individuals with penetrating head injuries are discussed.     

A Comparison of ML,WLSMV, and Bayesian Methods for Multilevel Structural Equation Models in Small Samples: A Simulation Study

Multilevel structural equation models are increasingly applied in psychological research. With increasing model complexity, estimation becomes computationally demanding, and small sample sizes pose further challenges on estimation methods relying on asymptotic theory. Recent developments of Bayesian estimation techniques may help to overcome the shortcomings of classical estimation techniques. The use of potentially inaccurate prior information may, however, have detrimental effects, especially in small samples. The present Monte Carlo simulation study compares the statistical performance of classical estimation techniques with Bayesian estimation using different prior specifications for a two-level SEM with either continuous or ordinal indicators. Using two software programs (Mplus and Stan), differential effects of between- and within-level sample sizes on estimation accuracy were investigated. Moreover, it was tested to which extent inaccurate priors may have detrimental effects on parameter estimates in categorical indicator models. For continuous indicators, Bayesian estimation did not show performance advantages over ML. For categorical indicators, Bayesian estimation outperformed WLSMV solely in case of strongly informative accurate priors. Weakly informative inaccurate priors did not deteriorate performance of the Bayesian approach, while strong informative inaccurate priors led to severely biased estimates even with large sample sizes. With diffuse priors, Stan yielded better results than Mplus in terms of parameter estimates.     

贝叶斯结构方程模型及其研究现状

在心理学研究中结构方程模型(Structural Equation Modeling, SEM)被广泛用于检验潜变量间的因果效应, 其估计方法有频率学方法(如, 极大似然估计)和贝叶斯方法两类。近年来由于贝叶斯统计的流行及其在结构方程建模中易于处理小样本、缺失数据及复杂模型等方面的优势, 贝叶斯结构方程模型发展迅速, 但其在国内心理学领域的应用不足。主要介绍了贝叶斯结构方程模型的方法基础和优良特性, 及几类常用的贝叶斯结构方程模型及其应用现状, 旨在为应用研究者介绍新的研究工具。     

Bayesian Analysis of Structural Equation Models With Nonlinear Covariates and Latent Variables

In this article, we formulate a nonlinear structural equation model (SEM) that can accommodate covariates in the measurement equation and nonlinear terms of covariates and exogenous latent variables in the structural equation. The covariates can come from continuous or discrete distributions. A Bayesian approach is developed to analyze the proposed model. Markov chain Monte Carlo methods for obtaining Bayesian estimates and their standard error estimates, highest posterior density intervals, and a PP p value are developed. Results obtained from two simulation studies are reported to respectively reveal the empirical performance of the proposed Bayesian estimation in analyzing complex nonlinear SEMs, and in analyzing nonlinear SEMs with the normal assumption of the exogenous latent variables violated. The proposed methodology is further illustrated by a real example. Detailed interpretation about the interaction terms is presented.     

An overview of Bayesian reasoning in the analysis of delay‐discounting data

Statistical inference (including interval estimation and model selection) is increasingly used in the analysis of behavioral data. As with many other fields, statistical approaches for these analyses traditionally use classical (i.e., frequentist) methods. Interpreting classical intervals and p‐values correctly can be burdensome and counterintuitive. By contrast, Bayesian methods treat data, parameters, and hypotheses as random quantities and use rules of conditional probability to produce direct probabilistic statements about models and parameters given observed study data. In this work, we reanalyze two data sets using Bayesian procedures. We precede the analyses with an overview of the Bayesian paradigm. The first study reanalyzes data from a recent study of controls, heavy smokers, and individuals with alcohol and/or cocaine substance use disorder, and focuses on Bayesian hypothesis testing for covariates and interval estimation for discounting rates among various substance use disorder profiles. The second example analyzes hypothetical environmental delay‐discounting data. This example focuses on using historical data to establish prior distributions for parameters while allowing subjective expert opinion to govern the prior distribution on model preference. We review the subjective nature of specifying Bayesian prior distributions but also review established methods to standardize the generation of priors and remove subjective influence while still taking advantage of the interpretive advantages of Bayesian analyses. We present the Bayesian approach as an alternative paradigm for statistical inference and discuss its strengths and weaknesses.     

Coherent psychometric modelling with Bayesian nonparametrics

In this paper we argue that model selection, as commonly practised in psychometrics, violates certain principles of coherence. On the other hand, we show that Bayesian nonparametrics provides a coherent basis for model selection, through the use of a ‘nonparametric’ prior distribution that has a large support on the space of sampling distributions. We illustrate model selection under the Bayesian nonparametric approach, through the analysis of real questionnaire data. Also, we present ways to use the Bayesian nonparametric framework to define very flexible psychometric models, through the specification of a nonparametric prior distribution that supports all distribution functions for the inverse link, including the standard logistic distribution functions. The Bayesian nonparametric approach provides a coherent method for model selection that can be applied to any statistical model, including psychometric models. Moreover, under a ‘non‐informative’ choice of nonparametric prior, the Bayesian nonparametric approach is easy to apply, and selects the model that maximizes the log likelihood. Thus, under this choice of prior, the approach can be extended to non‐Bayesian settings where the parameters of the competing models are estimated by likelihood maximization, and it can be used with any psychometric software package that routinely reports the model log likelihood.     

A generalized,likelihood-free method for posterior estimation

Recent advancements in Bayesian modeling have allowed for likelihood-free posterior estimation. Such estimation techniques are crucial to the understanding of simulation-based models, whose likelihood functions may be difficult or even impossible to derive. However, current approaches are limited by their dependence on sufficient statistics and/or tolerance thresholds. In this article, we provide a new approach that requires no summary statistics, error terms, or thresholds and is generalizable to all models in psychology that can be simulated. We use our algorithm to fit a variety of cognitive models with known likelihood functions to ensure the accuracy of our approach. We then apply our method to two real-world examples to illustrate the types of complex problems our method solves. In the first example, we fit an error-correcting criterion model of signal detection, whose criterion dynamically adjusts after every trial. We then fit two models of choice response time to experimental data: the linear ballistic accumulator model, which has a known likelihood, and the leaky competing accumulator model, whose likelihood is intractable. The estimated posterior distributions of the two models allow for direct parameter interpretation and model comparison by means of conventional Bayesian statistics—a feat that was not previously possible.     

Hierarchical Approximate Bayesian Computation

Approximate Bayesian computation (ABC) is a powerful technique for estimating the posterior distribution of a model’s parameters. It is especially important when the model to be fit has no explicit likelihood function, which happens for computational (or simulation-based) models such as those that are popular in cognitive neuroscience and other areas in psychology. However, ABC is usually applied only to models with few parameters. Extending ABC to hierarchical models has been difficult because high-dimensional hierarchical models add computational complexity that conventional ABC cannot accommodate. In this paper, we summarize some current approaches for performing hierarchical ABC and introduce a new algorithm called Gibbs ABC. This new algorithm incorporates well-known Bayesian techniques to improve the accuracy and efficiency of the ABC approach for estimation of hierarchical models. We then use the Gibbs ABC algorithm to estimate the parameters of two models of signal detection, one with and one without a tractable likelihood function.     

A Bayesian Model For The Estimation Of Latent Interaction And Quadratic Effects When Latent Variables Are Non-Normally Distributed

Structural equation models with interaction and quadratic effects have become a standard tool for testing nonlinear hypotheses in the social sciences. Most of the current approaches assume normally distributed latent predictor variables. In this article, we present a Bayesian model for the estimation of latent nonlinear effects when the latent predictor variables are nonnormally distributed. The nonnormal predictor distribution is approximated by a finite mixture distribution. We conduct a simulation study that demonstrates the advantages of the proposed Bayesian model over contemporary approaches (Latent Moderated Structural Equations [LMS], Quasi-Maximum-Likelihood [QML], and the extended unconstrained approach) when the latent predictor variables follow a nonnormal distribution. The conventional approaches show biased estimates of the nonlinear effects; the proposed Bayesian model provides unbiased estimates. We present an empirical example from work and stress research and provide syntax for substantive researchers. Advantages and limitations of the new model are discussed.     

Marginal distributions for the estimation of proportions inm groups

A Bayesian Model II approach to the estimation of proportions inm groups (discussed by Novick, Lewis, and Jackson) is extended to obtain posterior marginal distributions for the proportions. It is anticipated that these will be useful in applications (such as Individually Prescribed Instruction) where decisions are to be made separately for each proportion, rather than jointly for the set of proportions. In addition, the approach is extended to allow greater use of prior information than previously and the specification of this prior information is discussed.We are grateful to a reviewer for suggestions that made possible a more concise and complete presentation of our work.     

Structural Equation Modeling With AMOS,EQS, and LISREL: Comparative Approaches to Testing for the Factorial Validity of a Measuring Instrument

Using a confirmatory factor analytic (CFA) model as a paradigmatic basis for all comparisons, this article reviews and contrasts important features related to 3 of the most widely-used structural equation modeling (SEM) computer programs: AMOS 4.0 (Arbuckle, 1999), EQS 6 (Bentler, 2000), and LISREL 8 (Joreskog & Sorbom, 1996b). Comparisons focus on (a) key aspects of the programs that bear on the specification and testing of CFA models-preliminary analysis of data, and model specification, estimation, assessment, and misspecification; and (b) other important issues that include treatment of incomplete, nonnormally-distributed, or categorically-scaled data. It is expected that this comparative review will provide readers with at least a flavor of the approach taken by each program with respect to both the application of SEM within the framework of a CFA model, and the critically important issues, previously noted, related to data under study.     

A generative joint model for spike trains and saccades during perceptual decision-making

Theory development in both psychology and neuroscience can benefit by consideration of both behavioral and neural data sets. However, the development of appropriate methods for linking these data sets is a difficult statistical and conceptual problem. Over the past decades, different linking approaches have been employed in the study of perceptual decision-making, beginning with rudimentary linking of the data sets at a qualitative, structural level, culminating in sophisticated statistical approaches with quantitative links. We outline a new approach, in which a single model is developed that jointly addresses neural and behavioral data. This approach allows for specification and testing of quantitative links between neural and behavioral aspects of the model. Estimating the model in a Bayesian framework allows both data sets to equally inform the estimation of all model parameters. The use of a hierarchical model architecture allows for a model, which accounts for and measures the variability between neurons. We demonstrate the approach by re-analysis of a classic data set containing behavioral recordings of decision-making with accompanying single-cell neural recordings. The joint model is able to capture most aspects of both data sets, and also supports the analysis of interesting questions about prediction, including predicting the times at which responses are made, and the corresponding neural firing rates.     

Using priors to formalize theory: Optimal attention and the generalized context model

Formal models in psychology are used to make theoretical ideas precise and allow them to be evaluated quantitatively against data. We focus on one important??but under-used and incorrectly maligned??method for building theoretical assumptions into formal models, offered by the Bayesian statistical approach. This method involves capturing theoretical assumptions about the psychological variables in models by placing informative prior distributions on the parameters representing those variables. We demonstrate this approach of casting basic theoretical assumptions in an informative prior by considering a case study that involves the generalized context model (GCM) of category learning. We capture existing theorizing about the optimal allocation of attention in an informative prior distribution to yield a model that is higher in psychological content and lower in complexity than the standard implementation. We also highlight that formalizing psychological theory within an informative prior distribution allows standard Bayesian model selection methods to be applied without concerns about the sensitivity of results to the prior. We then use Bayesian model selection to test the theoretical assumptions about optimal allocation formalized in the prior. We argue that the general approach of using psychological theory to guide the specification of informative prior distributions is widely applicable and should be routinely used in psychological modeling.     

Introduction to the special section on structural equation modeling

Structural equation modeling (SEM) is a frequently used data-analytic technique in psychopathology research. This popularity is due to the unique capabilities and broad applicability of SEM and to recent advances in model and software development. Unfortunately, the popularity and accessibility of SEM is matched by its complexities and ambiguities. Thus, users are often faced with difficult decisions regarding a variety of issues. This special section is designed to increase the effective use of SEM by reviewing recently developed modeling capabilities, identifying common problems in application, and recommending appropriate strategies for analysis and evaluation.     

A tutorial on approximate Bayesian computation

This tutorial explains the foundation of approximate Bayesian computation (ABC), an approach to Bayesian inference that does not require the specification of a likelihood function, and hence that can be used to estimate posterior distributions of parameters for simulation-based models. We discuss briefly the philosophy of Bayesian inference and then present several algorithms for ABC. We then apply these algorithms in a number of examples. For most of these examples, the posterior distributions are known, and so we can compare the estimated posteriors derived from ABC to the true posteriors and verify that the algorithms recover the true posteriors accurately. We also consider a popular simulation-based model of recognition memory (REM) for which the true posteriors are unknown. We conclude with a number of recommendations for applying ABC methods to solve real-world problems.