title: Combined Mapping of Multiple clUsteriNg ALgorithms (COMMUNAL): A Robust Method for Selection of Cluster Number, K.
abstract: In order to discover new subsets (clusters) of a data set, researchers often use algorithms that perform unsupervised clustering, namely, the algorithmic separation of a dataset into some number of distinct clusters. Deciding whether a particular separation (or number of clusters, K) is correct is a sort of 'dark art', with multiple techniques available for assessing the validity of unsupervised clustering algorithms. Here, we present a new technique for unsupervised clustering that uses multiple clustering algorithms, multiple validity metrics, and progressively bigger subsets of the data to produce an intuitive 3D map of cluster stability that can help determine the optimal number of clusters in a data set, a technique we call COmbined Mapping of Multiple clUsteriNg ALgorithms (COMMUNAL). COMMUNAL locally optimizes algorithms and validity measures for the data being used. We show its application to simulated data with a known K, and then apply this technique to several well-known cancer gene expression datasets, showing that COMMUNAL provides new insights into clustering behavior and stability in all tested cases. COMMUNAL is shown to be a useful tool for determining K in complex biological datasets, and is freely available as a package for R.
authors.affiliation: Institute for Immunity, Transplantation and Infection, Stanford University.|Biomedical Informatics Research, Stanford University, Stanford, CA 94305, United States.
authors.forename: Timothy E
authors.initials: TE
authors.lastname: Sweeney
authors.affiliation: Department of Statistics, Stanford University, Stanford, CA 94305, United States.
authors.forename: Albert C
authors.initials: AC
authors.lastname: Chen
authors.affiliation: Biomedical Informatics Research, Stanford University, Stanford, CA 94305, United States.
authors.forename: Olivier
authors.initials: O
authors.lastname: Gevaert
mesh_terms: D000465:Algorithms; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D030541:Databases, Genetic; D015894:Genome, Human; D006801:Humans; D009369:Neoplasms / Q000235:genetics; D015203:Reproducibility of Results