Agglomerative hierarchical clustering

Agglomerative hierarchical clustering analysis and visualization implemented in Java

License	Apache License 2.0
GroupId	com.apporiented
ArtifactId	hierarchical-clustering
Last Version	1.2.0
Release Date	Dec 27, 2018
Type	jar
Description	Agglomerative hierarchical clustering Agglomerative hierarchical clustering analysis and visualization implemented in Java
Project URL	https://github.com/lbehnke/hierarchical-clustering-java
Project Organization	Lars Behnke
Source Code Management	https://github.com/lbehnke/hierarchical-clustering-java

Download hierarchical-clustering

Filename	Size
hierarchical-clustering-1.2.0.pom
hierarchical-clustering-1.2.0.jar	28 KB
hierarchical-clustering-1.2.0-sources.jar	18 KB
hierarchical-clustering-1.2.0-javadoc.jar	119 KB

How to add to project

Apache Maven

<!-- https://jarcasting.com/artifacts/com.apporiented/hierarchical-clustering/ -->
<dependency>
    <groupId>com.apporiented</groupId>
    <artifactId>hierarchical-clustering</artifactId>
    <version>1.2.0</version>
</dependency>

Gradle Groovy

// https://jarcasting.com/artifacts/com.apporiented/hierarchical-clustering/
implementation 'com.apporiented:hierarchical-clustering:1.2.0'

Gradle Kotlin

// https://jarcasting.com/artifacts/com.apporiented/hierarchical-clustering/
implementation ("com.apporiented:hierarchical-clustering:1.2.0")

Apache Buildr

'com.apporiented:hierarchical-clustering:jar:1.2.0'

Apache Ivy

<dependency org="com.apporiented" name="hierarchical-clustering" rev="1.2.0">
  <artifact name="hierarchical-clustering" type="jar" />
</dependency>

Groovy Grape

@Grapes(
@Grab(group='com.apporiented', module='hierarchical-clustering', version='1.2.0')
)

Scala SBT

libraryDependencies += "com.apporiented" % "hierarchical-clustering" % "1.2.0"

Leiningen

[com.apporiented/hierarchical-clustering "1.2.0"]

Dependencies

test (2)

Group / Artifact	Type	Version
junit : junit	jar	4.11
commons-io : commons-io	jar	2.5

Project Modules

There are no modules declared in this project.

hierarchical-clustering-java

Implementation of an agglomerative hierarchical clustering algorithm in Java. Different linkage approaches are supported:

• Single Linkage
• Complete Linkage

What you put in

Pass a distance matrix and a cluster name array along with a linkage strategy to the clustering algorithm:

String[] names = new String[] { "O1", "O2", "O3", "O4", "O5", "O6" };
double[][] distances = new double[][] { 
    { 0, 1, 9, 7, 11, 14 },
    { 1, 0, 4, 3, 8, 10 }, 
    { 9, 4, 0, 9, 2, 8 },
    { 7, 3, 9, 0, 6, 13 }, 
    { 11, 8, 2, 6, 0, 10 },
    { 14, 10, 8, 13, 10, 0 }};

ClusteringAlgorithm alg = new DefaultClusteringAlgorithm();
Cluster cluster = alg.performClustering(distances, names,
    new AverageLinkageStrategy());

Alternatively, you can pass a pdist-like matrix containing one row:

String[] names = new String[] { "O1", "O2", "O3", "O4", "O5", "O6" };
double[][] pdist = new double[][] {
			{1, 9, 7, 11 ,14 ,4 ,3 ,8 ,10 ,9 ,2 ,8 ,6 ,13 ,10}
	};
ClusteringAlgorithm alg = new PDistClusteringAlgorithm();
Cluster cluster = alg.performClustering(pdist, names, new MinimumLinkageStrategy());

What you get out

The algorithm creates a Cluster instance representing an hierachy of cluster nodes based on their distances. You may want to visualize the result using the Swing component DendrogramPanel:

DendrogramPanel dp = new DendrogramPanel();
dp.setModel(cluster);

When embedded into a JFrame the dendrogram panel should display this:

License

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at (http://www.apache.org/licenses/LICENSE-2.0). Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

Versions

Version
1.2.0 Dec 27, 2018
1.1.0 Feb 18, 2015
1.0.3 Oct 15, 2014