Home Page

Papers

Submissions

News

Editorial Board

Special Issues

Open Source Software

Proceedings (PMLR)

Data (DMLR)

Transactions (TMLR)

Search

Statistics

Login

Frequently Asked Questions

Contact Us



RSS Feed

Active Clustering of Biological Sequences

Konstantin Voevodski, Maria-Florina Balcan, Heiko Röglin, Shang-Hua Teng, Yu Xia; 13(7):203−225, 2012.

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.

[abs][pdf][bib]       
© JMLR 2012. (edit, beta)

Mastodon