Exploration and analysis of a generalized one-parameter item response model with flexible link functions.

This paper primarily analyzes the one-parameter generalized logistic (1PGlogit) model, which is a generalized model containing other one-parameter item response theory (IRT) models. The essence of the 1PGlogit model is the introduction of a generalized link function that includes the probit, logit, and complementary log-log functions. By transforming different parameters, the 1PGlogit model can flexibly adjust the speed at which the item characteristic curve (ICC) approaches the upper and lower asymptote, breaking the previous constraints in one-parameter IRT models where the ICC curves were either all symmetric or all asymmetric. This allows for a more flexible way to fit data and achieve better fitting performance. We present three simulation studies, specifically designed to validate the accuracy of parameter estimation for a variety of one-parameter IRT models using the Stan program, illustrate the advantages of the 1PGlogit model over other one-parameter IRT models from a model fitting perspective, and demonstrate the effective fit of the 1PGlogit model with the three-parameter logistic (3PL) and four-parameter logistic (4PL) models. Finally, we demonstrate the good fitting performance of the 1PGlogit model through an analysis of real data.

A Mixture Response Time Process Model for Aberrant Behaviors and Item Nonresponses.

In high-stakes, large-scale, standardized tests with certain time limits, examinees are likely to engage in either one of the three types of behavior (e.g., van der Linden & Guo, 2008; Wang & Xu, 2015): solution behavior, rapid guessing behavior, and cheating behavior. Oftentimes examinees do not always solve all items due to various reasons such as time limit or test-taking strategy. Item nonresponses may happen due to intentionally omitting some items (omitted responses) or due to lack of time (not-reached responses). Both types are related to latent abilities and hence the missingness is nonignorable. In this article, we proposed an innovative mixture response time process model (1) to detect two most common aberrant behaviors: rapid guessing behavior and cheating behavior, and (2) to account for two types of item nonresponses: not-reached items and omitted items. The new model combines the two-stage approach of Wang et al. (2018) with Lu and Wang (2020) model. It also contains two steps: (1) a mixture response time process model is first fitted to the responses and response times data to distinguish normal and aberrant behaviors and to account for the missing data mechanism; and (2) a Bayesian residual index is used to further distinguish rapid guessing and cheating behaviors. Simulation results show that the two-stage method yields accurate item and person parameter estimates, as well as high detection of aberrant behaviors. A real data analysis was conducted to illustrate the potential application of the proposed method.

Full-information item bifactor model for mathematical ability assessment in Chinese compulsory education quality monitoring.

This study focuses on the measurement of mathematical ability in the Chinese Compulsory Education Qualification Monitoring (CCEQM) framework using bifactor theory. First, we propose a full-information item bifactor (FIBF) model for the measurement of mathematical ability. Second, the performance of the FIBF model is empirically studied using a data set from three representative provinces were selected from CCEQM 2015-2017. Finally, Monte Carlo simulations are conducted to demonstrate the accuracy of the model evaluation indices and parameter estimation methods used in the empirical study. The obtained results are as follows: (1) The results for the four used model selection indices (AIC, SABIC, HQ, BIC) consistently showed that the fit of the FIBF model is better than that of the UIRT; (2) All of the estimated general and domain-specific abilities of the FIBF model have reasonable interpretations; (3) The model evaluation indices and parameter estimation methods exhibit excellent accuracy, indicating that the application of the FIBF model is technically feasible in large-scale testing projects.

A stochastic approximation expectation maximization algorithm for estimating Ramsay-curve three-parameter normal ogive model with non-normal latent trait distributions.

In the estimation of item response models, the normality of latent traits is frequently assumed. However, this assumption may be untenable in real testing. In contrast to the conventional three-parameter normal ogive (3PNO) model, a 3PNO model incorporating Ramsay-curve item response theory (RC-IRT), denoted as the RC-3PNO model, allows for flexible latent trait distributions. We propose a stochastic approximation expectation maximization (SAEM) algorithm to estimate the RC-3PNO model with non-normal latent trait distributions. The simulation studies of this work reveal that the SAEM algorithm produces more accurate item parameters for the RC-3PNO model than those of the 3PNO model, especially when the latent density is not normal, such as in the cases of a skewed or bimodal distribution. Three model selection criteria are used to select the optimal number of knots and the degree of the B-spline functions in the RC-3PNO model. A real data set from the PISA 2018 test is used to demonstrate the application of the proposed algorithm.

Modeling Not-Reached Items in Cognitive Diagnostic Assessments.

In cognitive diagnostic assessments with time limits, not-reached items (i.e., continuous nonresponses at the end of tests) frequently occur because examinees drop out of the test due to insufficient time. Oftentimes, the not-reached items are related to examinees' specific cognitive attributes or knowledge structures. Thus, the underlying missing data mechanism of not-reached items is non-ignorable. In this study, a missing data model for not-reached items in cognitive diagnosis assessments was proposed. A sequential model with linear restrictions on item parameters for missing indicators was adopted; meanwhile, the deterministic inputs, noisy "and" gate model was used to model the responses. The higher-order structure was used to capture the correlation between higher-order ability parameters and dropping-out propensity parameters. A Bayesian Markov chain Monte Carlo method was used to estimate the model parameters. The simulation results showed that the proposed model improved diagnostic feedback results and produced accurate item parameters when the missing data mechanism was non-ignorable. The applicability of our model was demonstrated using a dataset from the Program for International Student Assessment 2018 computer-based mathematics cognitive test.

Sequential Gibbs Sampling Algorithm for Cognitive Diagnosis Models with Many Attributes.

Cognitive diagnosis models (CDMs) are useful statistical tools to provide rich information relevant for intervention and learning. As a popular approach to estimate and make inference of CDMs, the Markov chain Monte Carlo (MCMC) algorithm is widely used in practice. However, when the number of attributes, K, is large, the existing MCMC algorithm may become time-consuming, due to the fact that O(2K) calculations are usually needed in the process of MCMC sampling to get the conditional distribution for each attribute profile. To overcome this computational issue, motivated by Culpepper and Hudson's earlier work in 2018, we propose a computationally efficient sequential Gibbs sampling method, which needs O(K) calculations to sample each attribute profile. We use simulation and real data examples to show the good finite-sample performance of the proposed sequential Gibbs sampling, and its advantage over existing methods.

A Gibbs sampler for the multidimensional four-parameter logistic item response model via a data augmentation scheme.

The four-parameter logistic (4PL) item response model, which includes an upper asymptote for the correct response probability, has drawn increasing interest due to its suitability for many practical scenarios. This paper proposes a new Gibbs sampling algorithm for estimation of the multidimensional 4PL model based on an efficient data augmentation scheme (DAGS). With the introduction of three continuous latent variables, the full conditional distributions are tractable, allowing easy implementation of a Gibbs sampler. Simulation studies are conducted to evaluate the proposed method and several popular alternatives. An empirical data set was analysed using the 4PL model to show its improved performance over the three-parameter and two-parameter logistic models. The proposed estimation scheme is easily accessible to practitioners through the open-source IRTlogit package.

Estimating CDMs Using the Slice-Within-Gibbs Sampler.

In this paper, the slice-within-Gibbs sampler has been introduced as a method for estimating cognitive diagnosis models (CDMs). Compared with other Bayesian methods, the slice-within-Gibbs sampler can employ a wide-range of prior specifications; moreover, it can also be applied to complex CDMs with the aid of auxiliary variables, especially when applying different identifiability constraints. To evaluate its performances, two simulation studies were conducted. The first study confirmed the viability of the slice-within-Gibbs sampler in estimating CDMs, mainly including G-DINA and DINA models. The second study compared the slice-within-Gibbs sampler with other commonly used Markov Chain Monte Carlo algorithms, and the results showed that the slice-within-Gibbs sampler converged much faster than the Metropolis-Hastings algorithm and more flexible than the Gibbs sampling in choosing the distributions of priors. Finally, a fraction subtraction dataset was analyzed to illustrate the use of the slice-within-Gibbs sampler in the context of CDMs.

Stratified Item Selection Methods in Cognitive Diagnosis Computerized Adaptive Testing.

Cognitive diagnostic computerized adaptive testing (CD-CAT) aims to obtain more useful diagnostic information by taking advantages of computerized adaptive testing (CAT). Cognitive diagnosis models (CDMs) have been developed to classify examinees into the correct proficiency classes so as to get more efficient remediation, whereas CAT tailors optimal items to the examinee's mastery profile. The item selection method is the key factor of the CD-CAT procedure. In recent years, a large number of parametric/nonparametric item selection methods have been proposed. In this article, the authors proposed a series of stratified item selection methods in CD-CAT, which are combined with posterior-weighted Kullback-Leibler (PWKL), nonparametric item selection (NPS), and weighted nonparametric item selection (WNPS) methods, and named S-PWKL, S-NPS, and S-WNPS, respectively. Two different types of stratification indices were used: original versus novel. The performances of the proposed item selection methods were evaluated via simulation studies and compared with the PWKL, NPS, and WNPS methods without stratification. Manipulated conditions included calibration sample size, item quality, number of attributes, number of strata, and data generation models. Results indicated that the S-WNPS and S-NPS methods performed similarly, and both outperformed the S-PWKL method. And item selection methods with novel stratification indices performed slightly better than the ones with original stratification indices, and those without stratification performed the worst.

A General Three-Parameter Logistic Model With Time Effect.

Within the framework of item response theory, a new and flexible general three-parameter logistic model with response time (G3PLT) is proposed. The advantage of this model is that it can combine time effect, ability, and item difficulty to influence the correct-response probability. In contrast to the traditional response time models used in educational psychology, the new model incorporates the influence of the time effect on the correct-response probability directly, rather than linking them through a hierarchical method via latent and speed parameters as in van der Linden's model. In addition, the Metropolis-Hastings within Gibbs sampling algorithm is employed to estimate the model parameters. Based on Markov chain Monte Carlo output, two Bayesian model assessment methods are used to assess the goodness of fit between models. Finally, two simulation studies and a real data analysis are performed to further illustrate the advantages of the new model over the traditional three-parameter logistic model.

The extraction of LRP via functional data analysis techniques.

A new strategy based on functional data analysis (FDA) techniques is proposed to extract the lateralized readiness potential (LRP), which treats electroencephalographic data as functional data. This FDA-based method combines longitudinal information from each trial (time series data) with cross-sectional information from all trials at a fixed time point (cross-sectional data). The comparison results show that the FDA-based LRP is closer to the assumed true LRP and is more robust against a reduction in the number of trials than the traditional average-based LRP. Furthermore, the results indicate that the onset of an FDA-based LRP is more accurate than that of an average-based LRP under several measuring criteria.

Efficient semiparametric mean-association estimation for longitudinal binary responses.

Semiparametric methods for longitudinal data with association within subjects have recently received considerable attention. However, existing methods for semiparametric longitudinal binary regression modeling (i) mainly concern mean structures with association parameters treated as nuisance; (ii) generally require a correct specification of the covariance structure for misspecified covariance structure may lead to inefficient mean parameter estimates; and (iii) usually run into computation and estimation problems when the time points are irregularly and possibly subject specific. In this article, we propose a semiparametric logistic regression model, which simultaneously takes into account both the mean and response-association structures (via conditional log-odds ratio) for multivariate longitudinal binary outcomes. Our main interest lies in efficient estimation of both the marginal and association parameters. The estimators of the parameters are obtained via the profile kernel approach. We evaluate the proposed methodology through simulation studies and apply it to a real dataset. Both theoretical and empirical results demonstrate that the proposed method yields highly efficient estimators and performs satisfactorily.

Analyzing Longitudinal Item Response Data via the Pairwise Fitting Method.

Multidimensional item response theory (MIRT) models can be applied to longitudinal educational surveys where a group of individuals are administered different tests over time with some common items. However, computational problems typically arise as the dimension of the latent variables increases. This is especially true when the latent variable distribution cannot be integrated out analytically, as with MIRT models for binary data. In this article, based on the pseudolikelihood theory, we propose a pairwise modeling strategy to estimate item and population parameters in longitudinal studies. Our pairwise method effectively reduces the dimensionality of the problem and hence is applicable to longitudinal IRT data with high-dimensional latent variables, which are challenging for classical methods. And in the low-dimensional case, our simulation study shows that it performs comparably with the classical methods. We further illustrate the implementation of the pairwise method using a development study of mathematics levels of junior high school students in which the response data are collected from 65 classes of 8 schools from 4 different school districts in China.

Sieve Maximum Likelihood Estimation for Doubly Semiparametric Zero-Inflated Poisson Models.

For nonnegative measurements such as income or sick days, zero counts often have special status. Furthermore, the incidence of zero counts is often greater than expected for the Poisson model. This article considers a doubly semiparametric zero-inflated Poisson model to fit data of this type, which assumes two partially linear link functions in both the mean of the Poisson component and the probability of zero. We study a sieve maximum likelihood estimator for both the regression parameters and the nonparametric functions. We show, under routine conditions, that the estimators are strongly consistent. Moreover, the parameter estimators are asymptotically normal and first-order efficient, while the nonparametric components achieve the optimal convergence rates. Simulation studies suggest that the extra flexibility inherent from the doubly semiparametric model is gained with little loss in statistical efficiency. We also illustrate our approach with a dataset from a public health study.

Information criterion-based clustering with order-restricted candidate profiles in short time-course microarray experiments.

BACKGROUND: Time-course microarray experiments produce vector gene expression profiles across a series of time points. Clustering genes based on these profiles is important in discovering functional related and co-regulated genes. Early developed clustering algorithms do not take advantage of the ordering in a time-course study, explicit use of which should allow more sensitive detection of genes that display a consistent pattern over time. Peddada et al. 1 proposed a clustering algorithm that can incorporate the temporal ordering using order-restricted statistical inference. This algorithm is, however, very time-consuming and hence inapplicable to most microarray experiments that contain a large number of genes. Its computational burden also imposes difficulty to assess the clustering reliability, which is a very important measure when clustering noisy microarray data. RESULTS: We propose a computationally efficient information criterion-based clustering algorithm, called ORICC, that also takes account of the ordering in time-course microarray experiments by embedding the order-restricted inference into a model selection framework. Genes are assigned to the profile which they best match determined by a newly proposed information criterion for order-restricted inference. In addition, we also developed a bootstrap procedure to assess ORICC's clustering reliability for every gene. Simulation studies show that the ORICC method is robust, always gives better clustering accuracy than Peddada's method and saves hundreds of times computational time. Under some scenarios, its accuracy is also better than some other existing clustering methods for short time-course microarray data, such as STEM 2 and Wang et al. 3. It is also computationally much faster than Wang et al. 3. CONCLUSION: Our ORICC algorithm, which takes advantage of the temporal ordering in time-course microarray experiments, provides good clustering accuracy and is meanwhile much faster than Peddada's method. Moreover, the clustering reliability for each gene can also be assessed, which is unavailable in Peddada's method. In a real data example, the ORICC algorithm identifies new and interesting genes that previous analyses failed to reveal.

Maximum likelihood estimates of two-locus recombination fractions under some natural inequality restrictions.

BACKGROUND: The goal of linkage analysis is to determine the chromosomal location of the gene(s) for a trait of interest such as a common disease. Three-locus linkage analysis is an important case of multi-locus problems. Solutions can be found analytically for the case of triple backcross mating. However, in the present study of linkage analysis and gene mapping some natural inequality restrictions on parameters have not been considered sufficiently, when the maximum likelihood estimates (MLEs) of the two-locus recombination fractions are calculated. RESULTS: In this paper, we present a study of estimating the two-locus recombination fractions for the phase-unknown triple backcross with two offspring in each family in the framework of some natural and necessary parameter restrictions. A restricted expectation-maximization (EM) algorithm, called REM is developed. We also consider some extensions in which the proposed REM can be taken as a unified method. CONCLUSION: Our simulation work suggests that the REM performs well in the estimation of recombination fractions and outperforms current method. We apply the proposed method to a published data set of mouse backcross families.

On the formula for admixture linkage disequilibrium.

Admixture linkage disequilibrium (ALD), a phenomenon created by gene flow between genetically distinct populations, has for some time been used as a tool in gene mapping. It is therefore important to analyze the pattern of ALD over generations. In this study we explore two models of admixture: the gradual admixture (GA) model, in which admixture occurs at a variable rate in every generation; and the immediate admixture (IA) model, a special case of the GA model, in which admixture occurs in a single generation. In the case of ALD, the well-known formula of linkage disequilibrium (Delta(t)=(1-r)t Delta(0)) is not applicable under these two models. We note the effect of a random mating population (RMP) to the gametic frequencies from the parental population to the offspring population, and provide the correct formula for ALD.

On the use of historical control information for trend test in carcinogenesis.

In this article a new non-model-based significance test for detecting dose-response relationship with the incorporation of historical control data is proposed. This non-model-based test is considered simpler from a regulatory perspective because it does not require validating any modeling assumptions. Moreover, our test is especially appropriate to those studies in which the intravenous doses for the investigational chemical are labeled as, e.g., low, medium and high or the dose labels do not suggest any obvious choices of dose scores. This test can be easily adopted for detecting general dose-response shape, such as an umbrella pattern. Simple adjustments will be proposed for better control of the actual Type I error. Data sets from two carcinogenesis studies will be used to illustrate our method. We also evaluate the performance of the proposed test and the famous model-based Tarone's trend test with respect to size and power.