APCluster plugin
The APCluster plugin provides a Cytoscape-compliant implementation of
the Affinity Propagation algorithm (Frey and Dueck, Science 2007). The
algorithm identifies meaningful clusters by passing messages which
encode the affinity of one data point to become an examplar for
another data point. The main benefit our implementation is that it
enables the user to run AP on any network straight from the Cytoscape
GUI and immediately visualize the results. APCluster also makes it
easy to control the parameters of the algorithm by keeping track of
parameter settings and results from multiple executions. The
advantages of AP include its speed and ability to cluster a wide range
of networks (both weighted and unweighted, as well as directed and
undirected).
For details on the algorithm, original implementations and references
please visit the official Affinity Propagation website:
http://www.psi.toronto.edu/affinitypropagation/.
This plugin is an open source application (GPL 3 license). The plugin jar file, instructions and sources are available at:
http://bioputer.mimuw.edu.pl/modevo.
Please don't hesitate to contact us with any comments and suggestion or if you are interested in co-developing this
software.
About the authors
This plugin was implemented by Michal Wozniak. Project idea and guidance came from Janusz Dutkowski and Jerzy Tiuryn.
Affiliation: Institute of Informatics, University of Warsaw
E-mail: {m.wozniak,januszd,tiuryn}@mimuw.edu.pl