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Sci Rep. 2015 Aug 12;5:12894. doi: 10.1038/srep12894.

Progeny Clustering: A Method to Identify Biological Phenotypes.

Author information

1
Department of Bioengineering, Rice University.
2
Departments of Leukemia and Stem Cell Transplant, University of Texas MD Anderson Cancer Center.
3
Department of Biomedical Engineering, University of Delaware.

Abstract

Estimating 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.

PMID:
26267476
PMCID:
PMC4533525
DOI:
10.1038/srep12894
[Indexed for MEDLINE]
Free PMC Article

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