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

Class SLINK<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.SLINK<O>

Type Parameters:

O - the type of DatabaseObject the algorithm is applied on

All Implemented Interfaces:

Algorithm, HierarchicalClusteringAlgorithm, DistanceBasedAlgorithm<O>

Direct Known Subclasses:

CLINK

@Title(value="SLINK: Single Link Clustering")
 @Description(value="Hierarchical clustering algorithm based on single-link connectivity.")
 @Reference(authors="R. Sibson",
           title="SLINK: An optimally efficient algorithm for the single-link cluster method",
           booktitle="The Computer Journal 16 (1973), No. 1, p. 30-34.",
           url="https://doi.org/10.1093/comjnl/16.1.30",
           bibkey="DBLP:journals/cj/Sibson73")
 @Alias(value={"de.lmu.ifi.dbs.elki.algorithm.clustering.SLINK","clustering.SLINK","single-link","single-linkage"})
 @Priority(value=200)
public class SLINK<O>
extends AbstractDistanceBasedAlgorithm<O,PointerHierarchyRepresentationResult>
implements HierarchicalClusteringAlgorithm

Implementation of the efficient Single-Link Algorithm SLINK of R. Sibson.

This is probably the fastest exact single-link algorithm currently in use.

Reference:

R. Sibson:
SLINK: An optimally efficient algorithm for the single-link cluster method
In: The Computer Journal 16 (1973), No. 1, p. 30-34.

Since:

0.6.0

Author:

Elke Achtert, Erich Schubert

Nested Class Summary

Nested Classes

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

Field Summary

Fields

Modifier and Type	Field and Description
private static Logging	LOG The logger for this class.

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
SLINK(DistanceFunction<? super O> distanceFunction) Constructor.

Method Summary

Modifier and Type	Method and Description
TypeInformation[]	getInputTypeRestriction() Get the input type restriction used for negotiating the data query.
protected Logging	getLogger() Get the (STATIC) logger for this class.
protected void	process(DBIDRef id, ArrayDBIDs ids, DBIDArrayIter it, int n, WritableDBIDDataStore pi, WritableDoubleDataStore lambda, WritableDoubleDataStore m) SLINK main loop.
PointerHierarchyRepresentationResult	run(Database database, Relation<O> relation) Performs the SLINK algorithm on the given database.
private void	slinkstep3(DBIDRef id, DBIDArrayIter it, int n, WritableDBIDDataStore pi, WritableDoubleDataStore lambda, WritableDoubleDataStore m) Third step: Determine the values for P and L
private void	slinkstep4(DBIDRef id, DBIDArrayIter it, int n, WritableDBIDDataStore pi, WritableDoubleDataStore lambda) Fourth step: Actualize the clusters if necessary
private void	step2(DBIDRef id, DBIDArrayIter it, int n, DistanceQuery<? super O> distQuery, WritableDoubleDataStore m) Second step: Determine the pairwise distances from all objects in the pointer representation to the new object with the specified id.
private void	step2primitive(DBIDRef id, DBIDArrayIter it, int n, Relation<? extends O> relation, PrimitiveDistanceFunction<? super O> distFunc, WritableDoubleDataStore m) Second step: Determine the pairwise distances from all objects in the pointer representation to the new object with the specified id.

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

The logger for this class.

Constructor Detail

SLINK

public SLINK(DistanceFunction<? super O> distanceFunction)

Constructor.

Parameters:

distanceFunction - Distance function

Method Detail

run

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

Performs the SLINK algorithm on the given database.

Parameters:

database - Database to process

relation - Data relation to use

step2

private void step2(DBIDRef id,
                   DBIDArrayIter it,
                   int n,
                   DistanceQuery<? super O> distQuery,
                   WritableDoubleDataStore m)

Second step: Determine the pairwise distances from all objects in the pointer representation to the new object with the specified id.

Parameters:

id - the id of the object to be inserted into the pointer representation

it - Array iterator

n - Last object

distQuery - Distance query

m - Data store

step2primitive

private void step2primitive(DBIDRef id,
                            DBIDArrayIter it,
                            int n,
                            Relation<? extends O> relation,
                            PrimitiveDistanceFunction<? super O> distFunc,
                            WritableDoubleDataStore m)

Second step: Determine the pairwise distances from all objects in the pointer representation to the new object with the specified id.

Parameters:

id - the id of the object to be inserted into the pointer representation

it - Array iterator

n - Last object

m - Data store

relation - Data relation

distFunc - Distance function to use

process

protected void process(DBIDRef id,
                       ArrayDBIDs ids,
                       DBIDArrayIter it,
                       int n,
                       WritableDBIDDataStore pi,
                       WritableDoubleDataStore lambda,
                       WritableDoubleDataStore m)

SLINK main loop.

Parameters:

id - Current object

ids - All objects

it - Array iterator

n - Last object to process at this run

pi - Parent

lambda - Height

m - Distance

slinkstep3

private void slinkstep3(DBIDRef id,
                        DBIDArrayIter it,
                        int n,
                        WritableDBIDDataStore pi,
                        WritableDoubleDataStore lambda,
                        WritableDoubleDataStore m)

Third step: Determine the values for P and L

Parameters:

id - the id of the object to be inserted into the pointer representation

it - array iterator

n - Last object to process at this run

pi - Pi data store

lambda - Lambda data store

m - Data store

slinkstep4

private void slinkstep4(DBIDRef id,
                        DBIDArrayIter it,
                        int n,
                        WritableDBIDDataStore pi,
                        WritableDoubleDataStore lambda)

Fourth step: Actualize the clusters if necessary

Parameters:

id - the id of the current object

it - array iterator

n - Last object to process at this run

pi - Pi data store

lambda - Lambda data store

getInputTypeRestriction

public TypeInformation[] getInputTypeRestriction()

Description copied from class: AbstractAlgorithm

Get the input type restriction used for negotiating the data query.

Specified by:

getInputTypeRestriction in interface Algorithm

Specified by:

getInputTypeRestriction in class AbstractAlgorithm<PointerHierarchyRepresentationResult>

Returns:

Type restriction

getLogger

protected Logging getLogger()

Description copied from class: AbstractAlgorithm

Get the (STATIC) logger for this class.

Specified by:

getLogger in class AbstractAlgorithm<PointerHierarchyRepresentationResult>

Returns:

the static logger