Medoid

About: Medoid is a research topic. Over the lifetime, 650 publications have been published within this topic receiving 13839 citations.

Defining clusters from a hierarchical cluster tree

Abstract: Summary: Hierarchical clustering is a widely used method for detecting clusters in genomic data. Clusters are defined by cutting branches off the dendrogram. A common but inflexible method uses a constant height cutoff value; this method exhibits suboptimal performance on complicated dendrograms. We present the Dynamic Tree Cut R package that implements novel dynamic branch cutting methods for detecting clusters in a dendrogram depending on their shape. Compared to the constant height cutoff method, our techniques offer the following advantages: (1) they are capable of identifying nested clusters; (2) they are flexible—cluster shape parameters can be tuned to suit the application at hand; (3) they are suitable for automation; and (4) they can optionally combine the advantages of hierarchical clustering and partitioning around medoids, giving better detection of outliers. We illustrate the use of these methods by applying them to protein–protein interaction network data and to a simulated gene expression data set. Availability: The Dynamic Tree Cut method is implemented in an R package available at http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/BranchCutting Contact: stevitihit@yahoo.com Supplementary information: Supplementary data are available at Bioinformatics online.

A simple and fast algorithm for K-medoids clustering

Abstract: This paper proposes a new algorithm for K-medoids clustering which runs like the K-means algorithm and tests several methods for selecting initial medoids. The proposed algorithm calculates the distance matrix once and uses it for finding new medoids at every iterative step. To evaluate the proposed algorithm, we use some real and artificial data sets and compare with the results of other algorithms in terms of the adjusted Rand index. Experimental results show that the proposed algorithm takes a significantly reduced time in computation with comparable performance against the partitioning around medoids.

Quick Shift and Kernel Methods for Mode Seeking

Abstract: We show that the complexity of the recently introduced medoid-shift algorithm in clustering N points is O(N 2), with a small constant, if the underlying distance is Euclidean. This makes medoid shift considerably faster than mean shift, contrarily to what previously believed. We then exploit kernel methods to extend both mean shift and the improved medoid shift to a large family of distances, with complexity bounded by the effective rank of the resulting kernel matrix, and with explicit regularization constraints. Finally, we show that, under certain conditions, medoid shift fails to cluster data points belonging to the same mode, resulting in over-fragmentation. We propose remedies for this problem, by introducing a novel, simple and extremely efficient clustering algorithm, called quick shift, that explicitly trades off under- and over-fragmentation. Like medoid shift, quick shift operates in non-Euclidean spaces in a straightforward manner. We also show that the accelerated medoid shift can be used to initialize mean shift for increased efficiency. We illustrate our algorithms to clustering data on manifolds, image segmentation, and the automatic discovery of visual categories.