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There is a great deal of evidence that method bias is really sure influences item validities, measurement error, correlation and covariance between latent constructs and thus leading the researchers to erroneous conclusion due to inflation or deflation during hypothesis testing. To remedy this, the study provides a guideline to minimize the method bias in the context of structural equation modeling employing the covariance method (CB-SEM) using medical tourism model. A practical approach is illustrated for the identification of method bias based on the new construct namely common latent factor. Using this latent construct, we managed to identify which item has potential to permeate more variance from common latent factor. Nevertheless, we figure out that the method bias is do not exist in our developed model. Therefore, this measurement model is appropriate for structural model in order to achieve the research hypotheses. We hope that this discussion will help the researchers anticipate which items are likely exposed on method bias before proceed to advance modeling.

Adaptation to local environments often occurs through natural selection acting on a large number of loci, each having a weak phenotypic effect. One way to detect these loci is to identify genetic polymorphisms that exhibit high correlation with environmental variables used as proxies for ecological pressures. Here, we propose new algorithms based on population genetics, ecological modeling, and statistical learning techniques to screen genomes for signatures of local adaptation. Implemented in the computer program “latent factor mixed model” (LFMM), these algorithms employ an approach in which population structure is introduced using unobserved variables. These fast and computationally efficient algorithms detect correlations between environmental and genetic variation while simultaneously inferring background levels of population structure. Comparing these new algorithms with related methods provides evidence that LFMM can efficiently estimate random effects due to population history and isolation-by-distance patterns when computing gene-environment correlations, and decrease the number of false-positive associations in genome scans. We then apply these models to plant and human genetic data, identifying several genes with functions related to development that exhibit strong correlations with climatic gradients.

Background According to current classification systems, patients with major depressive disorder (MDD) may have very different combinations of symptoms. This symptomatic diversity hinders the progress of research into the causal mechanisms and treatment allocation. Theoretically founded subtypes of depression such as atypical, psychotic, and melancholic depression have limited clinical applicability. Data-driven analyses of symptom dimensions or subtypes of depression are scarce. In this systematic review, we examine the evidence for the existence of data-driven symptomatic subtypes of depression. Methods We undertook a systematic literature search of MEDLINE, PsycINFO and Embase in May 2012. We included studies analyzing the depression criteria of the Diagnostic and Statistical Manual of Mental Disorders , fourth edition (DSM-IV) of adults with MDD in latent variable analyses. Results In total, 1176 articles were retrieved, of which 20 satisfied the inclusion criteria. These reports described a total of 34 latent variable analyses: 6 confirmatory factor analyses, 6 exploratory factor analyses, 12 principal component analyses, and 10 latent class analyses. The latent class techniques distinguished 2 to 5 classes, which mainly reflected subgroups with different overall severity: 62 of 71 significant differences on symptom level were congruent with a latent class solution reflecting severity. The latent class techniques did not consistently identify specific symptom clusters. Latent factor techniques mostly found a factor explaining the variance in the symptoms depressed mood and interest loss (11 of 13 analyses), often complemented by psychomotor retardation or fatigue (8 of 11 analyses). However, differences in found factors and classes were substantial. Conclusions The studies performed to date do not provide conclusive evidence for the existence of depressive symptom dimensions or symptomatic subtypes. The wide diversity of identified factors and classes might result either from the absence of patterns to be found, or from the theoretical and modeling choices preceding analysis.

Robust cross-subject emotion recognition based on multichannel EEG has always been hard work. In this work, we hypothesize that there exist default brain variables across subjects in emotional processes. Hence, the states of the latent variables that relate to emotional processing must contribute to building robust recognition models. Specifically, we propose to utilize an unsupervised deep generative model (e.g., variational autoencoder) to determine the latent factors from the multichannel EEG. Through a sequence modeling method, we examine the emotion recognition performance based on the learnt latent factors. The performance of the proposed methodology is verified on two public datasets (DEAP and SEED) and compared with traditional matrix factorization-based (ICA) and autoencoder-based approaches. Experimental results demonstrate that autoencoder-like neural networks are suitable for unsupervised EEG modeling, and our proposed emotion recognition framework achieves an inspiring performance. As far as we know, it is the first work that introduces variational autoencoder into multichannel EEG decoding for emotion recognition. We think the approach proposed in this work is not only feasible in emotion recognition but also promising in diagnosing depression, Alzheimer's disease, mild cognitive impairment, etc., whose specific latent processes may be altered or aberrant compared with the normal healthy control.

In large-scale panel data models with latent factors the number of factors and their loadings may change over time. Treating the break date as unknown, this article proposes an adaptive group-LASSO estimator that consistently determines the numbers of pre- and post-break factors and the stability of factor loadings if the number of factors is constant. We develop a cross-validation procedure to fine-tune the data-dependent LASSO penalties and show that after the number of factors has been determined, a conventional least-squares approach can be used to estimate the break date consistently. The method performs well in Monte Carlo simulations. In an empirical application, we study the change in factor loadings and the emergence of new factors in a panel of U.S. macroeconomic and financial time series during the Great Recession.

The ongoing global change and the increased interest in macroecological processes call for the analysis of spatially extensive data on species communities to understand and forecast distributional changes of biodiversity. Recently developed joint species distribution models can deal with numerous species efficiently, while explicitly accounting for spatial structure in the data. However, their applicability is generally limited to relatively small spatial data sets because of their severe computational scaling as the number of spatial locations increases. In this work, we propose a practical alleviation of this scalability constraint for joint species modeling by exploiting two spatial-statistics techniques that facilitate the analysis of large spatial data sets: Gaussian predictive process and nearest-neighbor Gaussian process. We devised an efficient Gibbs posterior sampling algorithm for Bayesian model fitting that allows us to analyze community data sets consisting of hundreds of species sampled from up to hundreds of thousands of spatial units. The performance of these methods is demonstrated using an extensive plant data set of 30,955 spatial units as a case study. We provide an implementation of the presented methods as an extension to the hierarchical modeling of species communities framework.

This paper proposes a Bayesian alternative to the synthetic control method for comparative case studies with a single or multiple treated units. We adopt a Bayesian posterior predictive approach to Rubin’s causal model, which allows researchers to make inferences about both individual and average treatment effects on treated observations based on the empirical posterior distributions of their counterfactuals. The prediction model we develop is a dynamic multilevel model with a latent factor term to correct biases induced by unit-specific time trends. It also considers heterogeneous and dynamic relationships between covariates and the outcome, thus improving precision of the causal estimates. To reduce model dependency, we adopt a Bayesian shrinkage method for model searching and factor selection. Monte Carlo exercises demonstrate that our method produces more precise causal estimates than existing approaches and achieves correct frequentist coverage rates even when sample sizes are small and rich heterogeneities are present in data. We illustrate the method with two empirical examples from political economy.

High-throughput DNA sequencing enables detection of copy number variations (CNVs) on the genome-wide scale with finer resolution compared to array-based methods but suffers from biases and artifacts that lead to false discoveries and low sensitivity. We describe CODEX2, as a statistical framework for full-spectrum CNV profiling that is sensitive for variants with both common and rare population frequencies and that is applicable to study designs with and without negative control samples. We demonstrate and evaluate CODEX2 on whole-exome and targeted sequencing data, where biases are the most prominent. CODEX2 outperforms existing methods and, in particular, significantly improves sensitivity for common CNVs.

Background Microbiome sequencing data are often collected from several body sites and exhibit dependencies. Our objective is to develop a model that enables joint analysis of data from different sites by capturing the underlying cross-site dependencies. The proposed model incorporates (i) latent factors shared across sites to explain common subject effects and to serve as the source of correlation between the sites and (ii) mixtures of latent factors to allow heterogeneity among the subjects in cross-site associations. Results Our simulation studies demonstrate that stronger associations between two sites lead to greater efficiency loss in regression analysis when such dependence is ignored in modeling. In a case study involving samples collected from a study on the female urogenital microbiome with aging, our model leads to the detection of covariate associations of the vaginal and urine microbiomes that are otherwise not statistically significant under a similar regression model applied to the two sites separately. Conclusions We propose a latent factor model for microbiome sequencing data collected from multiple sites. It captures the presumptive underlying cross-site associations without compromising estimation accuracy or inference efficiency in the absence of such associations. In addition, our proposed model improves predictive performance by enabling the prediction of microbial abundance at one site based on observations from another. We also provide an extended framework that allows for clustering of subjects (samples) and cluster-specific levels of paired association. Under this extended framework, clusters can be classified according to their association strengths.

Link recommendation, which suggests links to connect currently unlinked users, is a key functionality offered by major online social networks. Salient examples of link recommendation include “People You May Know” on Facebook and LinkedIn as well as “You May Know” on Google+. The main stakeholders of an online social network include users (e.g., Facebook users) who use the network to socialize with other users and an operator (e.g., Facebook Inc.) that establishes and operates the network for its own benefit (e.g., revenue). Existing link recommendation methods recommend links that are likely to be established by users but overlook the benefit a recommended link could bring to an operator. To address this gap, we define the utility of recommending a link and formulate a new research problem—the utility-based link recommendation problem. We then propose a novel utility-based link recommendation method that recommends links based on the value, cost, and linkage likelihood of a link, in contrast to existing link recommendation methods that focus solely on linkage likelihood. Specifically, our method models the dependency relationship between the value, cost, linkage likelihood, and utility-based link recommendation decision using a Bayesian network; predicts the probability of recommending a link with the Bayesian network; and recommends links with the highest probabilities. Using data obtained from a major U.S. online social network, we demonstrate significant performance improvement achieved by our method compared with prevalent link recommendation methods from representative prior research. This paper was accepted by Anandhi Bharadwaj, information systems .