The guide to available mathematical software problem classification system1

A vast collection of reusable mathematical and statistical software is now available for use by scientists and engineers in their modeling efforts. This software represents a significant source of mathematical expertise, created and maintained at considerable expense. Unfortunately, the collection is so heterogeneous that it is a tedious and error-prone task simply to determine what software is available to solve a given problem. In mathematical problem solving environments of the future such questions will be fielded by expert software advisory systems. One way for such systems to systematically associate available software with the problems they solve is to use a problem classification system. In this paper we describe a detailed tree-structured problem-oriented classification system appropriate for such use.     

Efficient heterogeneous sampling for stochastic simulation with an illustration in health care applications

In modeling disease transmission, contacts are assumed to have different infection rates. A proper simulation must model the heterogeneity in the transmission rates. In this article, we present a computationally efficient algorithm that can be applied to a population with heterogeneous transmission rates. We conducted a simulation study to show that the algorithm is more efficient than other algorithms for sampling the disease transmission in a subset of the heterogeneous population. We use a valid stochastic model of pandemic influenza to illustrate the algorithm and to estimate the overall infection attack rates of influenza A (H1N1) in a Canadian city.     

Factor Multivariate Stochastic Volatility via Wishart Processes

This paper proposes a high dimensional factor multivariate stochastic volatility (MSV) model in which factor covariance matrices are driven by Wishart random processes. The framework allows for unrestricted specification of intertemporal sensitivities, which can capture the persistence in volatilities, kurtosis in returns, and correlation breakdowns and contagion effects in volatilities. The factor structure allows addressing high dimensional setups used in portfolio analysis and risk management, as well as modeling conditional means and conditional variances within the model framework. Owing to the complexity of the model, we perform inference using Markov chain Monte Carlo simulation from the posterior distribution. A simulation study is carried out to demonstrate the efficiency of the estimation algorithm. We illustrate our model on a data set that includes 88 individual equity returns and the two Fama–French size and value factors. With this application, we demonstrate the ability of the model to address high dimensional applications suitable for asset allocation, risk management, and asset pricing.     

Ridge Estimation under the Stochastic Restriction

In linear programming and modeling of an economic system, there may occur some linear stochastic artificial or unnatural manners, which may need serious attentions. These stochastic unusual uncertainty, say stochastic constraints, definitely cause some changes in the estimators under work and their behaviors. In this approach, we are basically concerned with the problem of multicollinearity, when it is suspected that the parameter space may be restricted to some stochastic restrictions. We develop the estimation strategy form unbiasedness to some improved biased adjustment. In this regard, we study the performance of shrinkage estimators under the assumption of elliptically contoured errors and derive the region of optimality of each one. Lastly, a numerical example is taken to determine the adequate ridge parameter for each given estimator.     

Factor Multivariate Stochastic Volatility via Wishart Processes

This paper proposes a high dimensional factor multivariate stochastic volatility (MSV) model in which factor covariance matrices are driven by Wishart random processes. The framework allows for unrestricted specification of intertemporal sensitivities, which can capture the persistence in volatilities, kurtosis in returns, and correlation breakdowns and contagion effects in volatilities. The factor structure allows addressing high dimensional setups used in portfolio analysis and risk management, as well as modeling conditional means and conditional variances within the model framework. Owing to the complexity of the model, we perform inference using Markov chain Monte Carlo simulation from the posterior distribution. A simulation study is carried out to demonstrate the efficiency of the estimation algorithm. We illustrate our model on a data set that includes 88 individual equity returns and the two Fama-French size and value factors. With this application, we demonstrate the ability of the model to address high dimensional applications suitable for asset allocation, risk management, and asset pricing.     

Investigate Data Dependency for Dynamic Gene Regulatory Network Identification through High-dimensional Differential Equation Approach

Gene regulation plays a fundamental role in biological activities. The gene regulation network (GRN) is a high-dimensional complex system, which can be represented by various mathematical or statistical models. The ordinary differential equation (ODE) model is one of the popular dynamic GRN models. We proposed a comprehensive statistical procedure for ODE model to identify the dynamic GRN. In this article, we applied this model to different segments of time course gene expression data from a simulation experiment and a yeast cell cycle study. We found that the two cell cycle and one cell cycle data provided consistent results, but half cell cycle data produced biased estimation. Therefore, we may conclude that the proposed model can quantify both two cell cycle and one cell cycle gene expression dynamics, but not for half cycle dynamics. The findings suggest that the model can identify the dynamic GRN correctly if the time course gene expression data are sufficient enough to capture the overall dynamics of underlying biological mechanism.     

Uncertainty Analysis for Functional Computer Output: A Simulation Study in Inverse Problems

Computer models with functional output are omnipresent throughout science and engineering. Most often the computer model is treated as a black-box and information about the underlying mathematical model is not exploited in statistical analyses. Consequently, general-purpose bases such as wavelets are typically used to describe the main characteristics of the functional output. In this article we advocate for using information about the underlying mathematical model in order to choose a better basis for the functional output. To validate this choice, a simulation study is presented in the context of uncertainty analysis for a computer model from inverse Sturm-Liouville problems.     

High-Dimensional Sparse Factor Modeling: Applications in Gene Expression Genomics

We describe studies in molecular profiling and biological pathway analysis that use sparse latent factor and regression models for microarray gene expression data. We discuss breast cancer applications and key aspects of the modeling and computational methodology. Our case studies aim to investigate and characterize heterogeneity of structure related to specific oncogenic pathways, as well as links between aggregate patterns in gene expression profiles and clinical biomarkers. Based on the metaphor of statistically derived "factors" as representing biological "subpathway" structure, we explore the decomposition of fitted sparse factor models into pathway subcomponents and investigate how these components overlay multiple aspects of known biological activity. Our methodology is based on sparsity modeling of multivariate regression, ANOVA, and latent factor models, as well as a class of models that combines all components. Hierarchical sparsity priors address questions of dimension reduction and multiple comparisons, as well as scalability of the methodology. The models include practically relevant non-Gaussian/nonparametric components for latent structure, underlying often quite complex non-Gaussianity in multivariate expression patterns. Model search and fitting are addressed through stochastic simulation and evolutionary stochastic search methods that are exemplified in the oncogenic pathway studies. Supplementary supporting material provides more details of the applications, as well as examples of the use of freely available software tools for implementing the methodology.     

Regression analysis of zero-inflated time-series counts: application to air pollution related emergency room visit data

Time-series count data with excessive zeros frequently occur in environmental, medical and biological studies. These data have been traditionally handled by conditional and marginal modeling approaches separately in the literature. The conditional modeling approaches are computationally much simpler, whereas marginal modeling approaches can link the overall mean with covariates directly. In this paper, we propose new models that can have conditional and marginal modeling interpretations for zero-inflated time-series counts using compound Poisson distributed random effects. We also develop a computationally efficient estimation method for our models using a quasi-likelihood approach. The proposed method is illustrated with an application to air pollution-related emergency room visits. We also evaluate the performance of our method through simulation studies.     

What Your Future Doctor Should Know About Statistics: Must-Include Topics for Introductory Undergraduate Biostatistics

The increased emphasis on evidence-based medicine creates a greater need for educating future physicians in the general domain of quantitative reasoning, probability, and statistics. Reflecting this trend, more medical schools now require applicants to have taken an undergraduate course in introductory statistics. Given the breadth of statistical applications, we should cover in that course certain essential topics that may not be covered in the more general introductory statistics course. In selecting and presenting such topics, we should bear in mind that doctors also need to communicate probabilistic concepts of risks and benefits to patients who are increasingly expected to be active participants in their own health care choices despite having no training in medicine or statistics. It is also important that interesting and relevant examples accompany the presentation, because the examples (rather than the details) are what students tend to retain years later. Here, we present a list of topics we cover in the introductory biostatistics course that may not be covered in the general introductory course. We also provide some of our favorite examples for discussing these topics.     

Correlation,Regression Lines,and Moments of Inertia

The R language, a freely available environment for statistical computing and graphics is widely used in many fields. This “expert-friendly” system has a powerful command language and programming environment, combined with an active user community. We discuss how R is ideal as a platform to support experimentation in mathematical statistics, both at the undergraduate and graduate levels. Using a series of case studies and activities, we describe how R can be used in a mathematical statistics course as a toolbox for experimentation. Examples include the calculation of a running average, maximization of a nonlinear function, resampling of a statistic, simple Bayesian modeling, sampling from multivariate normal, and estimation of power. These activities, often requiring only a few dozen lines of code, offer students the opportunity to explore statistical concepts and experiment. In addition, they provide an introduction to the framework and idioms available in this rich environment.     

Implementation of Kolmogorov–Smirnov P-value computation in Visual Basic®: implication for Microsoft Excel® library function

This paper investigates methodologies for evaluating the probabilistic value (P-value) of the Kolmogorov–Smirnov (K–S) goodness-of-fit test using algorithmic program development implemented in Microsoft® Visual Basic® (VB). Six methods were examined for the one-sided one-sample and two methods for the two-sided one-sample cumulative sampling distributions in the investigative software implementation that was based on machine-precision arithmetic. For sample sizes n≤2000 considered, results from the Smirnov iterative method found optimal accuracy for K–S P-values≥0.02, while those from the SmirnovD were more accurate for lower P-values for the one-sided one-sample distribution statistics. Also, the Durbin matrix method sustained better P-value results than the Durbin recursion method for the two-sided one-sample tests up to n≤700 sample sizes. Based on these results, an algorithm for Microsoft Excel® function was proposed from which a model function was developed and its implementation was used to test the performance of engineering students in a general engineering course across seven departments.     

Non-parametric Estimation for NHPP Software Reliability Models

The non-homogeneous Poisson process (NHPP) model is a very important class of software reliability models and is widely used in software reliability engineering. NHPPs are characterized by their intensity functions. In the literature it is usually assumed that the functional forms of the intensity functions are known and only some parameters in intensity functions are unknown. The parametric statistical methods can then be applied to estimate or to test the unknown reliability models. However, in realistic situations it is often the case that the functional form of the failure intensity is not very well known or is completely unknown. In this case we have to use functional (non-parametric) estimation methods. The non-parametric techniques do not require any preliminary assumption on the software models and then can reduce the parameter modeling bias. The existing non-parametric methods in the statistical methods are usually not applicable to software reliability data. In this paper we construct some non-parametric methods to estimate the failure intensity function of the NHPP model, taking the particularities of the software failure data into consideration.     

Probabilistic sensitivity measures applied to numerical models of flow and transport

First- and second-order reliability algorithms (FORM AND SORM) have been adapted for use in modeling uncertainty and sensitivity related to flow in porous media. They are called reliability algorithms because they were developed originally for analysis of reliability of structures. FORM and SORM utilize a general joint probability model, the Nataf model, as a basis for transforming the original problem formulation into uncorrelated standard normal space, where a first-order or second-order estimate of the probability related to some failure criterion can easily be made. Sensitivity measures that incorporate the probabilistic nature of the uncertain variables in the problem are also evaluated, and are quite useful in indicating which uncertain variables contribute the most to the probabilistic outcome. In this paper the reliability approach is reviewed and the advantages and disadvantages compared to other typical probabilistic techniques used for modeling flow and transport. Some example applications of FORM and SORM from recent research by the authors and others are reviewed. FORM and SORM have been shown to provide an attractive alternative to other probabilistic modeling techniques in some situations.     

Clustering microarray data using model-based double K-means

The microarray technology allows the measurement of expression levels of thousands of genes simultaneously. The dimension and complexity of gene expression data obtained by microarrays create challenging data analysis and management problems ranging from the analysis of images produced by microarray experiments to biological interpretation of results. Therefore, statistical and computational approaches are beginning to assume a substantial position within the molecular biology area. We consider the problem of simultaneously clustering genes and tissue samples (in general conditions) of a microarray data set. This can be useful for revealing groups of genes involved in the same molecular process as well as groups of conditions where this process takes place. The need of finding a subset of genes and tissue samples defining a homogeneous block had led to the application of double clustering techniques on gene expression data. Here, we focus on an extension of standard K-means to simultaneously cluster observations and features of a data matrix, namely double K-means introduced by Vichi (2000). We introduce this model in a probabilistic framework and discuss the advantages of using this approach. We also develop a coordinate ascent algorithm and test its performance via simulation studies and real data set. Finally, we validate the results obtained on the real data set by building resampling confidence intervals for block centroids.     

Inverse Gaussian Distribution for Modeling Conditional Durations in Finance

The durations between market activities such as trades and quotes provide useful information on the underlying assets while analyzing financial time series. In this article, we propose a stochastic conditional duration model based on the inverse Gaussian distribution. The non-monotonic nature of the failure rate of the inverse Gaussian distribution makes it suitable for modeling the durations in financial time series. The parameters of the proposed model are estimated by an efficient importance sampling method. A simulation experiment is conducted to check the performance of the estimators. These estimates are used to compute estimated hazard functions and to compare with the empirical hazard functions. Finally, a real data analysis is provided to illustrate the practical utility of the models.     

Modeling lactation curves: classical parametric models re-examined and modified

A large number of methods for modeling lactation curves have been proposed – parametric and nonparametric, mathematically or biologically oriented. The most popular of these are methods that express the milk yield in terms of time via a parametric nonlinear functional equation. This is intuitive and allows for relatively easy mathematical and biological interpretations of the parameters involved. Interestingly, as far as we are aware, all such models generate nonzero milk yields on the whole positive time half-line, even though real lactation curves always have finite range, with spans of approximately 300 days for dairy cows. For this reason, we re-examine a number of existing parametric models, and modify them to produce finite-range lactation curves that fit remarkably well to data of milk yields from New Zealand cows. The use of daily or weekly yields rather than the monthly yields normally considered reveals considerable variation that is usually suppressed. Both individual and herd lactation curves are examined in the present paper, and median-based procedures explored as alternatives to the usual average-based methods. These suggestions offer further insights into the existing literature on modeling lactation curves.     

A semiparametric Bayesian approach for joint modeling of longitudinal trait and event time

Inference on the whole biological system is the recent focus in bioscience. Different biomarkers, although seem to function separately, can actually control some event(s) of interest simultaneously. This fundamental biological principle has motivated the researchers for developing joint models which can explain the biological system efficiently. Because of the advanced biotechnology, huge amount of biological information can be easily obtained in current years. Hence dimension reduction is one of the major issues in current biological research. In this article, we propose a Bayesian semiparametric approach of jointly modeling observed longitudinal trait and event-time data. A sure independence screening procedure based on the distance correlation and a modified version of Bayesian Lasso are used for dimension reduction. Traditional Cox proportional hazards model is used for modeling the event-time. Our proposed model is used for detecting marker genes controlling the biomass and first flowering time of soybean plants. Simulation studies are performed for assessing the practical usefulness of the proposed model. Proposed model can be used for the joint analysis of traits and diseases for humans, animals and plants.     

Modified linear projection for large spatial datasets

Recent developments in engineering techniques for spatial data collection such as geographic information systems have resulted in an increasing need for methods to analyze large spatial datasets. These sorts of datasets can be found in various fields of the natural and social sciences. However, model fitting and spatial prediction using these large spatial datasets are impractically time-consuming, because of the necessary matrix inversions. Various methods have been developed to deal with this problem, including a reduced rank approach and a sparse matrix approximation. In this article, we propose a modification to an existing reduced rank approach to capture both the large- and small-scale spatial variations effectively. We have used simulated examples and an empirical data analysis to demonstrate that our proposed approach consistently performs well when compared with other methods. In particular, the performance of our new method does not depend on the dependence properties of the spatial covariance functions.     

Smooth functional tempering for nonlinear differential equation models

Differential equations are used in modeling diverse system behaviors in a wide variety of sciences. Methods for estimating the differential equation parameters traditionally depend on the inclusion of initial system states and numerically solving the equations. This paper presents Smooth Functional Tempering, a new population Markov Chain Monte Carlo approach for posterior estimation of parameters. The proposed method borrows insights from parallel tempering and model based smoothing to define a sequence of approximations to the posterior. The tempered approximations depend on relaxations of the solution to the differential equation model, reducing the need for estimating the initial system states and obtaining a numerical differential equation solution. Rather than tempering via approximations to the posterior that are more heavily rooted in the prior, this new method tempers towards data features. Using our proposed approach, we observed faster convergence and robustness to both initial values and prior distributions that do not reflect the features of the data. Two variations of the method are proposed and their performance is examined through simulation studies and a real application to the chemical reaction dynamics of producing nylon.