Package org.nlpub.watset.graph

Class MarkovClusteringBinaryRunner<V,E>

java.lang.Object

org.nlpub.watset.graph.MarkovClusteringBinaryRunner<V,E>

Type Parameters:

V - the type of nodes in the graph

E - the type of edges in the graph

All Implemented Interfaces:

Clustering<V>

public class MarkovClusteringBinaryRunner<V,E>
extends Object
implements Clustering<V>

A wrapper for the official implementation of the Markov Clustering (MCL) algorithm in C.

This is a weird thing. The official implementation of MCL is very fast, but is distributed under GPL. In order to use it we need to run the separate process and speak to it over standard input/output redirection.

See Also:

van Dongen (2000)

Constructor Summary

Constructors

Constructor	Description
MarkovClusteringBinaryRunner(org.jgrapht.Graph<V,E> graph, Path mcl, double r)	Create an instance of the Markov Clustering algorithm wrapper.
MarkovClusteringBinaryRunner(org.jgrapht.Graph<V,E> graph, Path mcl, double r, int threads)	Create an instance of the Markov Clustering algorithm wrapper.

Method Summary

Modifier and Type	Method	Description
void	fit()	Run the algorithm to induce the parameters of the clusters.
Collection<Collection<V>>	getClusters()	Return a collection of clusters, each cluster is a collection of objects.
static <V,E> Function<org.jgrapht.Graph<V,E>,Clustering<V>>	provider(Path mcl, double r)	A factory function that sets up the algorithm for the given graph.
static <V,E> Function<org.jgrapht.Graph<V,E>,Clustering<V>>	provider(Path mcl, double r, int threads)	A factory function that sets up the algorithm for the given graph.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

MarkovClusteringBinaryRunner

public MarkovClusteringBinaryRunner(org.jgrapht.Graph<V,E> graph,
                                    Path mcl,
                                    double r,
                                    int threads)

Create an instance of the Markov Clustering algorithm wrapper.

Parameters:

graph - the graph

mcl - the path to the MCL binary

r - the inflation parameter

threads - the number of threads

MarkovClusteringBinaryRunner

public MarkovClusteringBinaryRunner(org.jgrapht.Graph<V,E> graph,
                                    Path mcl,
                                    double r)

Create an instance of the Markov Clustering algorithm wrapper.

Parameters:

graph - the graph

mcl - the path to the MCL binary

r - the inflation parameter

Method Detail

provider

public static <V,E> Function<org.jgrapht.Graph<V,E>,Clustering<V>> provider(Path mcl,
                                                                                              double r,
                                                                                              int threads)

A factory function that sets up the algorithm for the given graph.

Type Parameters:

V - the type of nodes in the graph

E - the type of edges in the graph

Parameters:

mcl - the path to the MCL binary

r - the inflation parameter

threads - the number of threads

Returns:

a factory function that sets up the algorithm for the given graph

provider

public static <V,E> Function<org.jgrapht.Graph<V,E>,Clustering<V>> provider(Path mcl,
                                                                                              double r)

A factory function that sets up the algorithm for the given graph.

Type Parameters:

V - the type of nodes in the graph

E - the type of edges in the graph

Parameters:

mcl - the path to the MCL binary

r - the inflation parameter

Returns:

a factory function that sets up the algorithm for the given graph

getClusters

public Collection<Collection<V>> getClusters()

Description copied from interface: Clustering

Return a collection of clusters, each cluster is a collection of objects. Usually this method is called after the Clustering.fit() method.

Specified by:

getClusters in interface Clustering<V>

Returns:

clusters

fit

public void fit()

Description copied from interface: Clustering

Run the algorithm to induce the parameters of the clusters.

Specified by:

fit in interface Clustering<V>