如何利用开源工具分析fMRI数据：基于多体素模式的有监督机器学习算法介绍

摘要：目前,多体素模式分析（MVPA）日渐普遍地应用于脑影像研究。近些年,机器学习的模式分类等算法在MVPA方法中被广泛应用,因其具有能够抽取高维数据模式,提高数据利用率的优点。其中一种典型的应用是利用解码的思想来解决神经表征问题,本文主要介绍了利用基于Python语言的工具库中有监督学习算法分析数据的过程。除介绍Nilearn结合Scikit-learn分析数据的步骤外,还比较不同算法的效率,为算法的选择及参数设备提供具体参考。     

Association rule learning in neuropsychological data analysis for Alzheimer’s disease

Efficient methods of analysis readily available for clinicians continue to be limited within neuropsychological assessment at the raw data level. Here, a novel approach for generating predictive response patterns and analysing neuropsychological raw data is offered. In order to assess the usefulness of association rule learning as an analysis tool for neuropsychological raw data, Frequent Pattern Growth (FP-Growth) was used to mine patterns from the Consortium to Establish a Registry for Alzheimer’s Disease Neuropsychological Battery (CERAD-NB) database. Complete assessment data for 84 post-mortem confirmed Alzheimer’s disease (AD) cases and 294 age, race, and education matched controls were analysed across baseline and one-year follow-up using FP-Growth, for the purpose of assessing the clinical utility of a finer analysis at the raw data level and the feasibility of predicting response patterns for clinical/control groups. Output from FP-Growth, in terms of the number of frequent itemsets retained across both evaluation timepoints, was discernable between controls, mild, and moderate to severe Alzheimer’s disease cases (p < .001, and η² = .488). Patterns within raw data scores, both in terms of frequent itemsets and predictive association rules, appear to be differentiable across groups within neuropsychological analysis, which indicates that FP-Growth is applicable as a supplementary analysis tool for neuropsychological assessment by means of offering an additional level of data analysis, predictive item response capabilities, and aiding in clinical decision making.     

Trade‐off ranking method for multi‐criteria decision analysis

Multi‐criteria decision analysis presumes trade‐off between different criteria. As a result, the optimal solution is not unique and can be represented by the Pareto frontier in the objective space. Each Pareto solution is a compromise between different objectives. Despite a limited number of Pareto optimal solutions, the decision‐maker eventually has to choose only one option. Such a choice has to be made with the use of additional preferences not included in the original formulation of the optimization problem. The paper represents a new approach to an automatic ranking that can help the decision‐maker. In contrast to the other methodologies, the proposed method is based on the minimization of trade‐off between different Pareto solutions. To be realized, the approach presumes the existence of a well‐distributed Pareto set representing the entire Pareto frontier. In the paper, such a set is generated with the use of the directed search domain algorithm. The method is applied to a number of test cases and compared against two existing alternative approaches.     

Methodology to select solutions for multiobjective optimization problems: Weighted stress function method

The weighted stress function method is proposed here as a new way of identifying the best solution from a set of nondominated solutions according to the decision maker's preferences, expressed in terms of weights. The method was tested using several benchmark problems from the literature, and the results obtained were compared with those of other methods, namely, the reference point evolutionary multiobjective optimization (EMO), the weighted Tchebycheff metric, and a goal programming method. The weighted stress function method can be seen to exhibit a more direct correspondence between the weights set by the decision maker and the final solutions obtained than the other methods tested.     

改进的MCMC算法及其在估计IRT模型参数中的应用

本文首先简要的阐述了MCMC算法的思想及在IRT参数估计中的操作过程;其次,针对该算法存在的一些问题,提出相应的改进建议;然后,分别运用传统的和改进型的MCMC算法进行模拟数据分析和比较,结果显示新的方法表现更好;最后总结新方法的优点所在,并指出下一步的研究方向。     

Bayesian Analysis of Nonlinear Structural Equation Models with Nonignorable Missing Data

A Bayesian approach is developed for analyzing nonlinear structural equation models with nonignorable missing data. The nonignorable missingness mechanism is specified by a logistic regression model. A hybrid algorithm that combines the Gibbs sampler and the Metropolis–Hastings algorithm is used to produce the joint Bayesian estimates of structural parameters, latent variables, parameters in the nonignorable missing model, as well as their standard errors estimates. A goodness-of-fit statistic for assessing the plausibility of the posited nonlinear structural equation model is introduced, and a procedure for computing the Bayes factor for model comparison is developed via path sampling. Results obtained with respect to different missing data models, and different prior inputs are compared via simulation studies. In particular, it is shown that in the presence of nonignorable missing data, results obtained by the proposed method with a nonignorable missing data model are significantly better than those that are obtained under the missing at random assumption. A real example is presented to illustrate the newly developed Bayesian methodologies. This research is fully supported by a grant (CUHK 4243/03H) from the Research Grant Council of the Hong Kong Special Administration Region. The authors are thankful to the editor and reviewers for valuable comments for improving the paper, and also to ICPSR and the relevant funding agency for allowing the use of the data. Requests for reprints should be sent to Professor S.Y. Lee, Department of Statistics, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong.     

Bayesian adaptive estimation: The next dimension

We propose a new psychometric model for two-dimensional stimuli, such as color differences, based on parameterizing the threshold of a one-dimensional psychometric function as an ellipse. The Ψ Bayesian adaptive estimation method applied to this model yields trials that vary in multiple stimulus dimensions simultaneously. Simulations indicate that this new procedure can be much more efficient than the more conventional procedure of estimating the psychometric function on one-dimensional lines independently, requiring only one-fourth or less the number of trials for equivalent performance in typical situations. In a real psychophysical experiment with a yes-no task, as few as 22 trials per estimated threshold ellipse were enough to consistently demonstrate certain color appearance phenomena. We discuss the practical implications of the multidimensional adaptation. In order to make the application of the model practical, we present two significantly faster algorithms for running the Ψ method: a discretized algorithm utilizing the Fast Fourier Transform for better scaling with the sampling rates and a Monte Carlo particle filter algorithm that should be able to scale into even more dimensions.     

To Weight or Not to Weight? Balancing Influence of Initial Items in Adaptive Testing

It has been widely reported that in computerized adaptive testing some examinees may get much lower scores than they would normally if an alternative paper-and-pencil version were given. The main purpose of this investigation is to quantitatively reveal the cause for the underestimation phenomenon. The logistic models, including the 1PL, 2PL, and 3PL models, are used to demonstrate our assertions. Our analytical derivation shows that, under the maximum information item selection strategy, if an examinee failed a few items at the beginning of the test, easy but more discriminating items are likely to be administered. Such items are ineffective to move the estimate close to the true θ, unless the test is sufficiently long or a variable-length test is used. Our results also indicate that a certain weighting mechanism is necessary to make the algorithm rely less on the items administered at the beginning of the test. This research was partially supported by the NSF Grants SES0241020 and SES0613025. The authors thank the Editor, Associate Editor and two anonymous reviewers for their comments and suggestions. Send further information to Hua-Hua Chang, Department of Psychology, 603 E. Daniel Street, M/C 716, Champaign, IL 61820.     

Building an identifiable latent class model with covariate effects on underlying and measured variables

In recent years, latent class models have proven useful for analyzing relationships between measured multiple indicators and covariates of interest. Such models summarize shared features of the multiple indicators as an underlying categorical variable, and the indicators' substantive associations with predictors are built directly and indirectly in unique model parameters. In this paper, we provide a detailed study on the theory and application of building models that allow mediated relationships between primary predictors and latent class membership, but that also allow direct effects of secondary covariates on the indicators themselves. Theory for model identification is developed. We detail an Expectation-Maximization algorithm for parameter estimation, standard error calculation, and convergent properties. Comparison of the proposed model with models underlying existing latent class modeling software is provided. A detailed analysis of how visual impairments affect older persons' functioning requiring distance vision is used for illustration.This work was supported by National Institute on Aging (NIA) Program Project P01-AG-10184-03 and National Institutes of Mental Health grant R01-MH-56639-01A1. Dr. Bandeen-Roche is a Brookdale National Fellow. The authors wish to thank Drs. Gary Rubin and Sheila West for kindly making the Salisbury Eye Evaluation data available. We also thank the Editor, the Associate Editor, and three referees for their valuable comments.