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

Class KMedoidsPAM.Instance

java.lang.Object

de.lmu.ifi.dbs.elki.algorithm.clustering.kmeans.KMedoidsPAM.Instance

Direct Known Subclasses:

KMedoidsFastPAM1.Instance, KMedoidsPAMReynolds.Instance

Enclosing class:

KMedoidsPAM<V>

protected static class KMedoidsPAM.Instance
extends java.lang.Object

Instance for a single dataset. Note: we experimented with not caching the distance to nearest and second nearest, but only the assignments. The matrix lookup was more expensive, so this is probably worth the 2*n doubles in storage.

Author:

Erich Schubert

Field Summary

Fields

Modifier and Type	Field and Description
(package private) WritableIntegerDataStore	assignment Cluster mapping.
(package private) DistanceQuery<?>	distQ Distance function to use.
(package private) DBIDs	ids Ids to process.
(package private) WritableDoubleDataStore	nearest Distance to the nearest medoid of each point.
(package private) WritableDoubleDataStore	second Distance to the second nearest medoid.

Constructor Summary

Constructors

Constructor and Description
Instance(DistanceQuery<?> distQ, DBIDs ids, WritableIntegerDataStore assignment) Constructor.

Method Summary

Modifier and Type	Method and Description
protected double	assignToNearestCluster(ArrayDBIDs means) Returns a list of clusters.
protected double	computeReassignmentCost(DBIDRef h, int mnum) Compute the reassignment cost of one swap.
protected double	run(ArrayModifiableDBIDs medoids, int maxiter) Run the PAM optimization phase.

Methods inherited from class java.lang.Object

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

Field Detail

ids

DBIDs ids

Ids to process.

distQ

DistanceQuery<?> distQ

Distance function to use.

nearest

WritableDoubleDataStore nearest

Distance to the nearest medoid of each point.

second

WritableDoubleDataStore second

Distance to the second nearest medoid.

assignment

WritableIntegerDataStore assignment

Cluster mapping.

Constructor Detail

Instance

public Instance(DistanceQuery<?> distQ,
                DBIDs ids,
                WritableIntegerDataStore assignment)

Constructor.

Parameters:

distQ - Distance query

ids - IDs to process

assignment - Cluster assignment

Method Detail

run

protected double run(ArrayModifiableDBIDs medoids,
                     int maxiter)

Run the PAM optimization phase.

Parameters:

medoids - Medoids list

maxiter -

Returns:

final cost

computeReassignmentCost

protected double computeReassignmentCost(DBIDRef h,
                                         int mnum)

Compute the reassignment cost of one swap.

Parameters:

h - Current object to swap with the medoid

mnum - Medoid number to be replaced

Returns:

cost

assignToNearestCluster

protected double assignToNearestCluster(ArrayDBIDs means)

Returns a list of clusters. The k^th cluster contains the ids of those objects, that are nearest to the k^th mean.

Parameters:

means - Object centroids

Returns:

Assignment cost