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Bioinformatics Advance Access originally published online on September 25, 2007
Bioinformatics 2007 23(20):2708-2715; doi:10.1093/bioinformatics/btm414
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Clustering by soft-constraint affinity propagation: applications to gene-expression data

Michele Leone *, Sumedha and Martin Weigt

Institute for Scientific Interchange, Viale Settimio Severo 65, Villa Gualino, I-10133 Torino, Italy

*To whom correspondence should be addressed.


  Abstract

Motivation: Similarity-measure-based clustering is a crucial problem appearing throughout scientific data analysis. Recently, a powerful new algorithm called Affinity Propagation (AP) based on message-passing techniques was proposed by Frey and Dueck (2007a). In AP, each cluster is identified by a common exemplar all other data points of the same cluster refer to, and exemplars have to refer to themselves. Albeit its proved power, AP in its present form suffers from a number of drawbacks. The hard constraint of having exactly one exemplar per cluster restricts AP to classes of regularly shaped clusters, and leads to suboptimal performance, e.g. in analyzing gene expression data.

Results: This limitation can be overcome by relaxing the AP hard constraints. A new parameter controls the importance of the constraints compared to the aim of maximizing the overall similarity, and allows to interpolate between the simple case where each data point selects its closest neighbor as an exemplar and the original AP. The resulting soft-constraint affinity propagation (SCAP) becomes more informative, accurate and leads to more stable clustering. Even though a new a priori free parameter is introduced, the overall dependence of the algorithm on external tuning is reduced, as robustness is increased and an optimal strategy for parameter selection emerges more naturally. SCAP is tested on biological benchmark data, including in particular microarray data related to various cancer types. We show that the algorithm efficiently unveils the hierarchical cluster structure present in the data sets. Further on, it allows to extract sparse gene expression signatures for each cluster.

Contact: leone{at}isi.it, sumedha{at}isi.it and weigt{at}isi.it

Associate Editor: Trey Ideker

Received on May 24, 2007; revised on July 25, 2007; accepted on August 9, 2007

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