de.lmu.ifi.dbs.elki.algorithm.clustering.hierarchical

Class NNChain<O>

java.lang.Object

de.lmu.ifi.dbs.elki.algorithm.AbstractAlgorithm<R>

de.lmu.ifi.dbs.elki.algorithm.AbstractDistanceBasedAlgorithm<O,PointerHierarchyRepresentationResult>

de.lmu.ifi.dbs.elki.algorithm.clustering.hierarchical.AGNES<O>

de.lmu.ifi.dbs.elki.algorithm.clustering.hierarchical.NNChain<O>

Type Parameters:

O - Object type

All Implemented Interfaces:

Algorithm, HierarchicalClusteringAlgorithm, DistanceBasedAlgorithm<O>

@Reference(authors="F. Murtagh",title="A survey of recent advances in hierarchical clustering algorithms",booktitle="The Computer Journal 26(4)",url="https://doi.org/10.1093/comjnl/26.4.354",bibkey="DBLP:journals/cj/Murtagh83") @Reference(authors="D. M\u00fcllner",title="Modern hierarchical, agglomerative clustering algorithms",booktitle="arXiv preprint arXiv:1109.2378",url="https://arxiv.org/abs/1109.2378",bibkey="DBLP:journals/corr/abs-1109-2378")
public class NNChain<O>
extends AGNES<O>

NNchain clustering algorithm.

Reference:

F. Murtagh
A survey of recent advances in hierarchical clustering algorithms
The Computer Journal 26(4)

D. Müllner
Modern hierarchical, agglomerative clustering algorithms
arXiv preprint arXiv:1109.2378

Since:

0.7.5

Author:

Erich Schubert

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	NNChain.Parameterizer<O> Parameterization class.

Field Summary

Fields

Modifier and Type	Field and Description
private static Logging	LOG Class logger.

Fields inherited from class de.lmu.ifi.dbs.elki.algorithm.clustering.hierarchical.AGNES

linkage

Fields inherited from class de.lmu.ifi.dbs.elki.algorithm.AbstractAlgorithm

ALGORITHM_ID

Fields inherited from interface de.lmu.ifi.dbs.elki.algorithm.DistanceBasedAlgorithm

DISTANCE_FUNCTION_ID

Constructor Summary

Constructors

Constructor and Description
NNChain(DistanceFunction<? super O> distanceFunction, Linkage linkage) Constructor.

Method Summary

Modifier and Type	Method and Description
static int	findUnlinked(int pos, int end, DBIDArrayIter ix, PointerHierarchyRepresentationBuilder builder) Find an unlinked object.
protected Logging	getLogger() Get the (STATIC) logger for this class.
private void	nnChainCore(MatrixParadigm mat, PointerHierarchyRepresentationBuilder builder) Uses NNChain as in "Modern hierarchical, agglomerative clustering algorithms" by Daniel Müllner
PointerHierarchyRepresentationResult	run(Database db, Relation<O> relation) Run the algorithm

Methods inherited from class de.lmu.ifi.dbs.elki.algorithm.clustering.hierarchical.AGNES

findMerge, getInputTypeRestriction, initializeDistanceMatrix, merge, shrinkActiveSet, updateMatrix

Methods inherited from class de.lmu.ifi.dbs.elki.algorithm.AbstractDistanceBasedAlgorithm

getDistanceFunction

Methods inherited from class de.lmu.ifi.dbs.elki.algorithm.AbstractAlgorithm

run

Methods inherited from class java.lang.Object

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

Methods inherited from interface de.lmu.ifi.dbs.elki.algorithm.clustering.hierarchical.HierarchicalClusteringAlgorithm

run

Field Detail

LOG

private static final Logging LOG

Class logger.

Constructor Detail

NNChain

public NNChain(DistanceFunction<? super O> distanceFunction,
               Linkage linkage)

Constructor.

Parameters:

distanceFunction - Distance function

Method Detail

run

public PointerHierarchyRepresentationResult run(Database db,
                                                Relation<O> relation)

Run the algorithm

Overrides:

run in class AGNES<O>

Parameters:

db - Database to run on

relation - Data relation

Returns:

Clustering result

nnChainCore

private void nnChainCore(MatrixParadigm mat,
                         PointerHierarchyRepresentationBuilder builder)

Uses NNChain as in "Modern hierarchical, agglomerative clustering algorithms" by Daniel Müllner

Parameters:

mat - Matrix view

builder - Result builder

findUnlinked

public static int findUnlinked(int pos,
                               int end,
                               DBIDArrayIter ix,
                               PointerHierarchyRepresentationBuilder builder)

Find an unlinked object.

Parameters:

pos - Starting position

end - End position

ix - Iterator to translate into DBIDs

builder - Linkage information

Returns:

Position

getLogger

protected Logging getLogger()

Description copied from class: AbstractAlgorithm

Get the (STATIC) logger for this class.

Overrides:

getLogger in class AGNES<O>

Returns:

the static logger