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This article is part of the supplement: Computational Intelligence in Bioinformatics and Biostatistics: new trends from the CIBB conference series

Open Access Research

A methodology to assess the intrinsic discriminative ability of a distance function and its interplay with clustering algorithms for microarray data analysis

Raffaele Giancarlo1, Giosué Lo Bosco1*, Luca Pinello2 and Filippo Utro3

Author affiliations

1 Dipartimento di Matematica ed Informatica, Universitá di Palermo, Via Archirafi 34, 90123 Palermo, Italy

2 Department of Biostatistics at Dana-Farber Cancer Institute and Harvard School of Public Health, 44 Binney Street, Boston, Massachusetts 02115, USA

3 Computational Genomics Group, IBM T.J. Watson Research Center, 1101 Kitchawan Road, Route 134, Yorktown Heights, N.Y. 10598, USA

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Citation and License

BMC Bioinformatics 2013, 14(Suppl 1):S6  doi:10.1186/1471-2105-14-S1-S6

Published: 14 January 2013

Abstract

Background

Clustering is one of the most well known activities in scientific investigation and the object of research in many disciplines, ranging from statistics to computer science. Following Handl et al., it can be summarized as a three step process: (1) choice of a distance function; (2) choice of a clustering algorithm; (3) choice of a validation method. Although such a purist approach to clustering is hardly seen in many areas of science, genomic data require that level of attention, if inferences made from cluster analysis have to be of some relevance to biomedical research.

Results

A procedure is proposed for the assessment of the discriminative ability of a distance function. That is, the evaluation of the ability of a distance function to capture structure in a dataset. It is based on the introduction of a new external validation index, referred to as Balanced Misclassification Index (BMI, for short) and of a nontrivial modification of the well known Receiver Operating Curve (ROC, for short), which we refer to as Corrected ROC (CROC, for short). The main results are: (a) a quantitative and qualitative method to describe the intrinsic separation ability of a distance; (b) a quantitative method to assess the performance of a clustering algorithm in conjunction with the intrinsic separation ability of a distance function. The proposed procedure is more informative than the ones available in the literature due to the adopted tools. Indeed, the first one allows to map distances and clustering solutions as graphical objects on a plane, and gives information about the bias of the clustering algorithm with respect to a distance. The second tool is a new external validity index which shows similar performances with respect to the state of the art, but with more flexibility, allowing for a broader spectrum of applications. In fact, it allows not only to quantify the merit of each clustering solution but also to quantify the agglomerative or divisive errors due to the algorithm.

Conclusions

The new methodology has been used to experimentally study three popular distance functions, namely, Euclidean distance d2, Pearson correlation dr and mutual information dMI. Based on the results of the experiments, we have that the Euclidean and Pearson correlation distances have a good intrinsic discrimination ability. Conversely, the mutual information distance does not seem to offer the same flexibility and versatility as the other two distances. Apparently, that is due to well known problems in its estimation. since it requires that a dataset must have a substantial number of features to be reliable. Nevertheless, taking into account such a fact, together with results presented in Priness et al., one receives an indication that dMI may be superior to the other distances considered in this study only in conjunction with clustering algorithms specifically designed for its use. In addition, it results that K-means, Average Link, and Complete link clustering algorithms are in most cases able to improve the discriminative ability of the distances considered in this study with respect to clustering. The methodology has a range of applicability that goes well beyond microarray data since it is independent of the nature of the input data. The only requirement is that the input data must have the same format of a "feature matrix". In particular it can be used to cluster ChIP-seq data.