Package org.nlpub.watset.graph

Class MarkovClusteringExternal<V,E>

java.lang.Object

org.nlpub.watset.graph.MarkovClusteringExternal<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 MarkovClusteringExternal<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 we need to run the separate process and speak to it over standard input/output redirection.

See Also:

van Dongen (2000), van Dongen (2008), MCL - a cluster algorithm for graphs

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	MarkovClusteringExternal.Builder<V,E>	Builder for MarkovClusteringExternal.

Field Summary

Fields

Modifier and Type	Field	Description
protected org.jgrapht.Graph<V,E>	graph	The graph.
protected Map<V,Integer>	mapping	The mapping of nodes to indices.
protected File	output	The output file.
protected Path	path	The path to the MCL binary.
protected double	r	The inflation parameter.
protected int	threads	The number of threads.

Constructor Summary

Constructors

Constructor	Description
MarkovClusteringExternal(org.jgrapht.Graph<V,E> graph, Path path, double r)	Deprecated. MarkovClusteringExternal(Graph, Path, double, int)
MarkovClusteringExternal(org.jgrapht.Graph<V,E> graph, Path path, 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)	Deprecated. Replaced with provider(Path, double, int)
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

Field Detail

graph

protected final org.jgrapht.Graph<V,E> graph

The graph.

path

protected final Path path

The path to the MCL binary.

r

protected final double r

The inflation parameter.

threads

protected final int threads

The number of threads.

mapping

protected Map<V,Integer> mapping

The mapping of nodes to indices.

output

protected File output

The output file.

Constructor Detail

MarkovClusteringExternal

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

Create an instance of the Markov Clustering algorithm wrapper.

Parameters:

graph - the graph

path - the path to the MCL binary

r - the inflation parameter

threads - the number of threads

MarkovClusteringExternal

@Deprecated
public MarkovClusteringExternal(org.jgrapht.Graph<V,E> graph,
                                Path path,
                                double r)

Deprecated.

MarkovClusteringExternal(Graph, Path, double, int)

Create an instance of the Markov Clustering algorithm wrapper.

Parameters:

graph - the graph

path - 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

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

Deprecated.

Replaced with provider(Path, double, int)

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>