COMPACT: A Comparative Package for Clustering Assessment

Roy Varshavsky, Michal Linial, David Horn

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

Abstract

There exist numerous algorithms that cluster data-points from large-scale genomic experiments such as sequencing, gene-expression and proteomics. Such algorithms may employ distinct principles, and lead to different performance and results. The appropriate choice of a clustering method is a significant and often overlooked aspect in extracting information from large-scale datasets. Evidently, such choice may significantly influence the biological interpretation of the data. We present an easy-to-use and intuitive tool that compares some clustering methods within the same framework. The interface is named COMPACT for Comparative-Package-for-Clustering-Assessment. COMPACT first reduces the dataset's dimensionality using the Singular Value Decomposition (SVD) method, and only then employs various clustering techniques. Besides its simplicity, and its ability to perform well on high-dimensional data, it provides visualization tools for evaluating the results. COMPACT was tested on a variety of datasets, from classical benchmarks to large-scale gene-expression experiments. COMPACT is configurable and expendable to newly added algorithms.

Original languageEnglish
Title of host publicationParallel and Distributed Processing and Applications - ISPA 2005 Workshops - ISPA 2005 International Workshops, AEPP, ASTD, BIOS, GCIC, IADS, MASN, SGCA, and WISA, Proceedings
Pages159-167
Number of pages9
DOIs
StatePublished - 2005
EventISPA 2005 International Workshops, AEPP, ASTD, BIOS, GCIC, IADS, MASN, SGCA, and WISA - Nanjing, China
Duration: 2 Nov 20055 Nov 2005

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume3759 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

ConferenceISPA 2005 International Workshops, AEPP, ASTD, BIOS, GCIC, IADS, MASN, SGCA, and WISA
Country/TerritoryChina
CityNanjing
Period2/11/055/11/05

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