Package elki.clustering.kmedoids

Class FastPAM1<O>

java.lang.Object

elki.clustering.kmedoids.PAM<O>

elki.clustering.kmedoids.FastPAM1<O>

Type Parameters:

O - vector datatype

All Implemented Interfaces:

Algorithm, ClusteringAlgorithm<Clustering<MedoidModel>>, KMedoidsClustering<O>

Direct Known Subclasses:

FastPAM

@Reference(authors="Erich Schubert, Peter J. Rousseeuw",
           title="Faster k-Medoids Clustering: Improving the PAM, CLARA, and CLARANS Algorithms",
           booktitle="Proc. 12th Int. Conf. Similarity Search and Applications (SISAP\'2019)",
           url="https://doi.org/10.1007/978-3-030-32047-8_16",
           bibkey="DBLP:conf/sisap/SchubertR19")
@Priority(-100)
public class FastPAM1<O>
extends PAM<O>

FastPAM1: A version of PAM that is O(k) times faster, i.e., now in O((n-k)²). The change here feels pretty small - we handle all k medoids in parallel using an array. But this means the innermost loop only gets executed in O(1/k) of all iterations, and thus we benefit on average.

This acceleration gives exactly (assuming perfect numerical accuracy) the same results as the original PAM. For further improvements that can affect the result, see also FastPAM, which is recommended for usage in practice.

Reference:

Erich Schubert, Peter J. Rousseeuw
Faster k-Medoids Clustering: Improving the PAM, CLARA, and CLARANS Algorithms
Proc. 12th Int. Conf. Similarity Search and Applications (SISAP'2019)

Since:

0.7.5

Author:

Erich Schubert

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
protected static class	FastPAM1.Instance	Instance for a single dataset.
static class	FastPAM1.Par<V>	Parameterization class.

Nested classes/interfaces inherited from interface elki.Algorithm

Algorithm.Utils

Field Summary

Fields

Modifier and Type	Field	Description
private static java.lang.String	KEY	Key for statistics logging.
private static Logging	LOG	The logger for this class.

Fields inherited from class elki.clustering.kmedoids.PAM

distance, initializer, k, maxiter

Constructor Summary

Constructors

Constructor	Description
FastPAM1(Distance<? super O> distance, int k, int maxiter, KMedoidsInitialization<O> initializer)	Constructor.

Method Summary

Modifier and Type	Method	Description
protected Logging	getLogger()	Get the static class logger.
Clustering<MedoidModel>	run(Relation<O> relation, int k, DistanceQuery<? super O> distQ)	Run k-medoids clustering with a given distance query. Not a very elegant API, but needed for some types of nested k-medoids.

Methods inherited from class elki.clustering.kmedoids.PAM

getInputTypeRestriction, initialMedoids, run, wrapResult

Methods inherited from class java.lang.Object

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

Methods inherited from interface elki.clustering.ClusteringAlgorithm

autorun

Field Detail

LOG

private static final Logging LOG

The logger for this class.

KEY

private static final java.lang.String KEY

Key for statistics logging.

Constructor Detail

FastPAM1

public FastPAM1(Distance<? super O> distance,
                int k,
                int maxiter,
                KMedoidsInitialization<O> initializer)

Constructor.

Parameters:

distance - distance function

k - k parameter

maxiter - Maxiter parameter

initializer - Function to generate the initial means

Method Detail

run

public Clustering<MedoidModel> run(Relation<O> relation,
                                   int k,
                                   DistanceQuery<? super O> distQ)

Description copied from interface: KMedoidsClustering

Run k-medoids clustering with a given distance query.
Not a very elegant API, but needed for some types of nested k-medoids.

Specified by:

run in interface KMedoidsClustering<O>

Overrides:

run in class PAM<O>

Parameters:

relation - relation to use

k - Number of clusters

distQ - Distance query to use

Returns:

result

getLogger

protected Logging getLogger()

Description copied from class: PAM

Get the static class logger.

Overrides:

getLogger in class PAM<O>