Dataset Information

Application of density estimation algorithms in analyzing co-morbidities of migraine.

ABSTRACT: In this study, we will propose a density estimation based data analysis procedure to investigate the co-morbid associations between migraine and the suspected diseases. The primary objective of this study has aimed to develop a novel analysis procedure that can discover insightful knowledge from large medical databases. The entire analysis procedure consists of two stages. During the first stage, a kernel density estimation algorithm named relaxed variable kernel density estimation (RVKDE) is invoked to identify the samples of interest. Then, in the second stage, a density estimation algorithm based on generalized Gaussian components and named G(2)DE is invoked to provide a summarized description of the distribution. The results obtained by applying the proposed two-staged procedure to analyze co-morbidities of migraine revealed that the proposed procedure could effectively identify a number of clusters of samples with distinctive characteristics. The results further revealed that the distinctive characteristics of the clusters extracted by the proposed procedure were in conformity with the observations reported in recently published articles. Accordingly, it is conceivable that the proposed analysis procedure can be exploited to provide valuable clues of pathogenesis and facilitate development of proper treatment strategies.

SUBMITTER: Yang MH

PROVIDER: S-EPMC3873085 | biostudies-other | 2013

REPOSITORIES: biostudies-other

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Application of density estimation algorithms in analyzing co-morbidities of migraine.

Yang Meng-Han MH Yang Fu-Yi FY Oyang Yen-Jen YJ

Network modeling and analysis in health informatics and bioinformatics 20130212

In this study, we will propose a density estimation based data analysis procedure to investigate the co-morbid associations between migraine and the suspected diseases. The primary objective of this study has aimed to develop a novel analysis procedure that can discover insightful knowledge from large medical databases. The entire analysis procedure consists of two stages. During the first stage, a kernel density estimation algorithm named relaxed variable kernel density estimation (RVKDE) is in ...[more]

PMID: 24392299

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Project description:BackgroundSustained research on the problem of determining which genes are differentially expressed on the basis of microarray data has yielded a plethora of statistical algorithms, each justified by theory, simulation, or ad hoc validation and yet differing in practical results from equally justified algorithms. Recently, a concordance method that measures agreement among gene lists have been introduced to assess various aspects of differential gene expression detection. This method has the advantage of basing its assessment solely on the results of real data analyses, but as it requires examining gene lists of given sizes, it may be unstable.ResultsTwo methodologies for assessing predictive error are described: a cross-validation method and a posterior predictive method. As a nonparametric method of estimating prediction error from observed expression levels, cross validation provides an empirical approach to assessing algorithms for detecting differential gene expression that is fully justified for large numbers of biological replicates. Because it leverages the knowledge that only a small portion of genes are differentially expressed, the posterior predictive method is expected to provide more reliable estimates of algorithm performance, allaying concerns about limited biological replication. In practice, the posterior predictive method can assess when its approximations are valid and when they are inaccurate. Under conditions in which its approximations are valid, it corroborates the results of cross validation. Both comparison methodologies are applicable to both single-channel and dual-channel microarrays. For the data sets considered, estimating prediction error by cross validation demonstrates that empirical Bayes methods based on hierarchical models tend to outperform algorithms based on selecting genes by their fold changes or by non-hierarchical model-selection criteria. (The latter two approaches have comparable performance.) The posterior predictive assessment corroborates these findings.ConclusionsAlgorithms for detecting differential gene expression may be compared by estimating each algorithm's error in predicting expression ratios, whether such ratios are defined across microarray channels or between two independent groups.According to two distinct estimators of prediction error, algorithms using hierarchical models outperform the other algorithms of the study. The fact that fold-change shrinkage performed as well as conventional model selection criteria calls for investigating algorithms that combine the strengths of significance testing and fold-change estimation.

Project description:Network representations are becoming increasingly popular for analyzing kinetic data from techniques like Milestoning, Markov State Models, and Transition Path Theory. Mapping continuous phase space trajectories into a relatively small number of discrete states helps in visualization of the data and in dissecting complex dynamics to concrete mechanisms. However, not only are molecular networks derived from molecular dynamics simulations growing in number, they are also getting increasingly complex, owing partly to the growth in computer power that allows us to generate longer and better converged trajectories. The increased complexity of the networks makes simple interpretation and qualitative insight of the molecular systems more difficult to achieve. In this paper, we focus on various network representations of kinetic data and algorithms to identify important edges and pathways in these networks. The kinetic data can be local and partial (such as the value of rate coefficients between states) or an exact solution to kinetic equations for the entire system (such as the stationary flux between vertices). In particular, we focus on the Milestoning method that provides fluxes as the main output. We proposed Global Maximum Weight Pathways as a useful tool for analyzing molecular mechanism in Milestoning networks. A closely related definition was made in the context of Transition Path Theory. We consider three algorithms to find Global Maximum Weight Pathways: Recursive Dijkstra's, Edge-Elimination, and Edge-List Bisection. The asymptotic efficiency of the algorithms is analyzed and numerical tests on finite networks show that Edge-List Bisection and Recursive Dijkstra's algorithms are most efficient for sparse and dense networks, respectively. Pathways are illustrated for two examples: helix unfolding and membrane permeation. Finally, we illustrate that networks based on local kinetic information can lead to incorrect interpretation of molecular mechanisms.

Dataset Information

Application of density estimation algorithms in analyzing co-morbidities of migraine.

Publications

Application of density estimation algorithms in analyzing co-morbidities of migraine.

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