Dataset Information

Thresher: determining the number of clusters while removing outliers.

ABSTRACT: BACKGROUND:Cluster analysis is the most common unsupervised method for finding hidden groups in data. Clustering presents two main challenges: (1) finding the optimal number of clusters, and (2) removing "outliers" among the objects being clustered. Few clustering algorithms currently deal directly with the outlier problem. Furthermore, existing methods for identifying the number of clusters still have some drawbacks. Thus, there is a need for a better algorithm to tackle both challenges. RESULTS:We present a new approach, implemented in an R package called Thresher, to cluster objects in general datasets. Thresher combines ideas from principal component analysis, outlier filtering, and von Mises-Fisher mixture models in order to select the optimal number of clusters. We performed a large Monte Carlo simulation study to compare Thresher with other methods for detecting outliers and determining the number of clusters. We found that Thresher had good sensitivity and specificity for detecting and removing outliers. We also found that Thresher is the best method for estimating the optimal number of clusters when the number of objects being clustered is smaller than the number of variables used for clustering. Finally, we applied Thresher and eleven other methods to 25 sets of breast cancer data downloaded from the Gene Expression Omnibus; only Thresher consistently estimated the number of clusters to lie in the range of 4-7 that is consistent with the literature. CONCLUSIONS:Thresher is effective at automatically detecting and removing outliers. By thus cleaning the data, it produces better estimates of the optimal number of clusters when there are more variables than objects. When we applied Thresher to a variety of breast cancer datasets, it produced estimates that were both self-consistent and consistent with the literature. We expect Thresher to be useful for studying a wide variety of biological datasets.

SUBMITTER: Wang M

PROVIDER: S-EPMC5759208 | biostudies-literature | 2018 Jan

REPOSITORIES: biostudies-literature

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Thresher: determining the number of clusters while removing outliers.

Wang Min M Abrams Zachary B ZB Kornblau Steven M SM Coombes Kevin R KR

BMC bioinformatics 20180108 1

<h4>Background</h4>Cluster analysis is the most common unsupervised method for finding hidden groups in data. Clustering presents two main challenges: (1) finding the optimal number of clusters, and (2) removing "outliers" among the objects being clustered. Few clustering algorithms currently deal directly with the outlier problem. Furthermore, existing methods for identifying the number of clusters still have some drawbacks. Thus, there is a need for a better algorithm to tackle both challenges ...[more]

PMID: 29310570

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Project description:Cognitive diagnosis models (CDMs) allow classifying respondents into a set of discrete attribute profiles. The internal structure of the test is determined in a Q-matrix, whose correct specification is necessary to achieve an accurate attribute profile classification. Several empirical Q-matrix estimation and validation methods have been proposed with the aim of providing well-specified Q-matrices. However, these methods require the number of attributes to be set in advance. No systematic studies about CDMs dimensionality assessment have been conducted, which contrasts with the vast existing literature for the factor analysis framework. To address this gap, the present study evaluates the performance of several dimensionality assessment methods from the factor analysis literature in determining the number of attributes in the context of CDMs. The explored methods were parallel analysis, minimum average partial, very simple structure, DETECT, empirical Kaiser criterion, exploratory graph analysis, and a machine learning factor forest model. Additionally, a model comparison approach was considered, which consists in comparing the model-fit of empirically estimated Q-matrices. The performance of these methods was assessed by means of a comprehensive simulation study that included different generating number of attributes, item qualities, sample sizes, ratios of the number of items to attribute, correlations among the attributes, attributes thresholds, and generating CDM. Results showed that parallel analysis (with Pearson correlations and mean eigenvalue criterion), factor forest model, and model comparison (with AIC) are suitable alternatives to determine the number of attributes in CDM applications, with an overall percentage of correct estimates above 76% of the conditions. The accuracy increased to 97% when these three methods agreed on the number of attributes. In short, the present study supports the use of three methods in assessing the dimensionality of CDMs. This will allow to test the assumption of correct dimensionality present in the Q-matrix estimation and validation methods, as well as to gather evidence of validity to support the use of the scores obtained with these models. The findings of this study are illustrated using real data from an intelligence test to provide guidelines for assessing the dimensionality of CDM data in applied settings.

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Thresher: determining the number of clusters while removing outliers.

Publications

Thresher: determining the number of clusters while removing outliers.

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