Progeny Clustering: A Method to Identify Biological Phenotypes

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dc.citation.journalTitleScientific Reports
dc.citation.volumeNumber5
dc.contributor.authorHu, Chenyue W.
dc.contributor.authorKornblau, Steven M.
dc.contributor.authorSlater, John H.
dc.contributor.authorQutub, Amina A.
dc.date.accessioned2015-11-09T18:52:17Z
dc.date.available2015-11-09T18:52:17Z
dc.date.issued2015
dc.description.abstractEstimating the optimal number of clusters is a major challenge in applying cluster analysis to any type of dataset, especially to biomedical datasets, which are high-dimensional and complex. Here, we introduce an improved method, Progeny Clustering, which is stability-based and exceptionally efficient in computing, to find the ideal number of clusters. The algorithm employs a novel Progeny Sampling method to reconstruct cluster identity, a co-occurrence probability matrix to assess the clustering stability, and a set of reference datasets to overcome inherent biases in the algorithm and data space. Our method was shown successful and robust when applied to two synthetic datasets (datasets of two-dimensions and ten-dimensions containing eight dimensions of pure noise), two standard biological datasets (the Iris dataset and Rat CNS dataset) and two biological datasets (a cell phenotype dataset and an acute myeloid leukemia (AML) reverse phase protein array (RPPA) dataset). Progeny Clustering outperformed some popular clustering evaluation methods in the ten-dimensional synthetic dataset as well as in the cell phenotype dataset, and it was the only method that successfully discovered clinically meaningful patient groupings in the AML RPPA dataset.
dc.identifier.citationHu, Chenyue W., Kornblau, Steven M., Slater, John H., et al.. "Progeny Clustering: A Method to Identify Biological Phenotypes." <i>Scientific Reports,</i> 5, (2015) Nature Publishing Group: http://dx.doi.org/10.1038/srep12894.
dc.identifier.doihttp://dx.doi.org/10.1038/srep12894
dc.identifier.urihttps://hdl.handle.net/1911/82035
dc.language.isoeng
dc.publisherNature Publishing Group
dc.rightsThis work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the articleﾒs Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material.
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.titleProgeny Clustering: A Method to Identify Biological Phenotypes
dc.typeJournal article
dc.type.dcmiText
dc.type.publicationpublisher version
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