jmlr jmlr2012 jmlr2012-12 jmlr2012-12-reference knowledge-graph by maker-knowledge-mining

12 jmlr-2012-Active Clustering of Biological Sequences


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Author: Konstantin Voevodski, Maria-Florina Balcan, Heiko Röglin, Shang-Hua Teng, Yu Xia

Abstract: Given a point set S and an unknown metric d on S, we study the problem of efficiently partitioning S into k clusters while querying few distances between the points. In our model we assume that we have access to one versus all queries that given a point s ∈ S return the distances between s and all other points. We show that given a natural assumption about the structure of the instance, we can efficiently find an accurate clustering using only O(k) distance queries. Our algorithm uses an active selection strategy to choose a small set of points that we call landmarks, and considers only the distances between landmarks and other points to produce a clustering. We use our procedure to cluster proteins by sequence similarity. This setting nicely fits our model because we can use a fast sequence database search program to query a sequence against an entire data set. We conduct an empirical study that shows that even though we query a small fraction of the distances between the points, we produce clusterings that are close to a desired clustering given by manual classification. Keywords: clustering, active clustering, k-median, approximation algorithms, approximation stability, clustering accuracy, protein sequences ∗. A preliminary version of this article appeared under the title Efficient Clustering with Limited Distance Information in the Proceedings of the Twenty-Sixth Conference on Uncertainty in Artificial Intelligence, AUAI Press, Corvallis, Oregon, 632-641. †. Most of this work was completed at Boston University. c 2012 Konstantin Voevodski, Maria-Florina Balcan, Heiko R¨ glin, Shang-Hua Teng and Yu Xia. o ¨ VOEVODSKI , BALCAN , R OGLIN , T ENG AND X IA


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