Cluster Analyses of a Target Data Set from the IFCS Cluster Benchmark Data Repository: Introduction to the Special Issue

After a brief introduction to benchmarking in data analysis in general and in cluster analysis in particular, we describe the setup of the IFCS Cluster Benchmark Data Repository along with two challenges connected with it. The first of these challenges called for data sets to be contributed to the repository; the second one pertained to cluster analyses of the winning data set of the first challenge. Subsequently, we introduce the winning data set of the first challenge together with relevant meta-data. We conclude with a brief description of the organization of the present special issue, which comprises reports of analyses that have been submitted as contributions to the second challenge

Onset of an outline map to get a hold on the wildwood of clustering methods

The domain of cluster analysis is a meeting point for a very rich multidisciplinary encounter, with cluster-analytic methods being studied and developed in discrete mathematics, numerical analysis, statistics, data analysis and data science, and computer science (including machine learning, data mining, and knowledge discovery), to name but a few. The other side of the coin, however, is that the domain suffers from a major accessibility problem as well as from the fact that it is rife with division across many pretty isolated islands. As a way out, the present paper offers an outline map for the clustering domain as a whole, which takes the form of an overarching conceptual framework and a common language. With this framework we wish to contribute to structuring the domain, to characterizing methods that have often been developed and studied in quite different contexts, to identifying links between them, and to introducing a frame of reference for optimally setting up cluster analyses in data-analytic practice.Comment: 33 pages, 4 figure

Bayesian hierarchical classes analysis

Hierarchical classes models are models for N-way N-mode data that represent the association among the N modes and simultaneously yield, for each mode, a hierarchical classification of its elements. In this paper we present a stochastic extension of the hierarchical classes model for two-way two-mode binary data. In line with the original model, the new probabilistic extension still represents both the association among the two modes and the hierarchical classifications. A fully Bayesian method for fitting the new model is presented and evaluated in a simulation study. Furthermore, we propose tools for model selection and model checking based on Bayes factors and posterior predictive checks. We illustrate the advantages of the new approach with applications in the domain of the psychology of choice and psychiatric diagnosis

Joint mapping of genes and conditions via multidimensional unfolding analysis

<p>Abstract</p> <p>Background</p> <p>Microarray compendia profile the expression of genes in a number of experimental conditions. Such data compendia are useful not only to group genes and conditions based on their similarity in overall expression over profiles but also to gain information on more subtle relations between genes and conditions. Getting a clear visual overview of all these patterns in a single easy-to-grasp representation is a useful preliminary analysis step: We propose to use for this purpose an advanced exploratory method, called multidimensional unfolding.</p> <p>Results</p> <p>We present a novel algorithm for multidimensional unfolding that overcomes both general problems and problems that are specific for the analysis of gene expression data sets. Applying the algorithm to two publicly available microarray compendia illustrates its power as a tool for exploratory data analysis: The unfolding analysis of a first data set resulted in a two-dimensional representation which clearly reveals temporal regulation patterns for the genes and a meaningful structure for the time points, while the analysis of a second data set showed the algorithm's ability to go beyond a mere identification of those genes that discriminate between different patient or tissue types.</p> <p>Conclusion</p> <p>Multidimensional unfolding offers a useful tool for preliminary explorations of microarray data: By relying on an easy-to-grasp low-dimensional geometric framework, relations among genes, among conditions and between genes and conditions are simultaneously represented in an accessible way which may reveal interesting patterns in the data. An additional advantage of the method is that it can be applied to the raw data without necessitating the choice of suitable genewise transformations of the data.</p

Benchmarking in cluster analysis: A white paper

To achieve scientific progress in terms of building a cumulative body of knowledge, careful attention to benchmarking is of the utmost importance. This means that proposals of new methods of data pre-processing, new data-analytic techniques, and new methods of output post-processing, should be extensively and carefully compared with existing alternatives, and that existing methods should be subjected to neutral comparison studies. To date, benchmarking and recommendations for benchmarking have been frequently seen in the context of supervised learning. Unfortunately, there has been a dearth of guidelines for benchmarking in an unsupervised setting, with the area of clustering as an important subdomain. To address this problem, discussion is given to the theoretical conceptual underpinnings of benchmarking in the field of cluster analysis by means of simulated as well as empirical data. Subsequently, the practicalities of how to address benchmarking questions in clustering are dealt with, and foundational recommendations are made