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

Class P3C<V extends NumberVector>

java.lang.Object

de.lmu.ifi.dbs.elki.algorithm.AbstractAlgorithm<Clustering<SubspaceModel>>

de.lmu.ifi.dbs.elki.algorithm.clustering.subspace.P3C<V>

Type Parameters:

V - the type of NumberVector handled by this Algorithm.

All Implemented Interfaces:

Algorithm, ClusteringAlgorithm<Clustering<SubspaceModel>>, SubspaceClusteringAlgorithm<SubspaceModel>

@Title(value="P3C: A Robust Projected Clustering Algorithm.")
 @Reference(authors="Gabriela Moise, J\u00f6rg Sander, Martin Ester",
           title="P3C: A Robust Projected Clustering Algorithm",
           booktitle="Proc. Sixth International Conference on Data Mining (ICDM \'06)",
           url="https://doi.org/10.1109/ICDM.2006.123",
           bibkey="DBLP:conf/icdm/MoiseSE06")
 @Priority(value=190)
public class P3C<V extends NumberVector>
extends AbstractAlgorithm<Clustering<SubspaceModel>>
implements SubspaceClusteringAlgorithm<SubspaceModel>

P3C: A Robust Projected Clustering Algorithm.

Reference:
Gabriela Moise, Jörg Sander, Martin Ester
P3C: A Robust Projected Clustering Algorithm
In: Proc. Sixth International Conference on Data Mining (ICDM '06)

This is not a complete implementation of P3C, but good enough for most users. Improvements are welcome. The most obviously missing step is section 3.5 of P3C, where the cluster subspaces are refined.

Since:

0.6.0

Author:

Florian Nuecke, Erich Schubert

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
private static class	P3C.ClusterCandidate This class is used to represent potential clusters.
static class	P3C.Parameterizer<V extends NumberVector> Parameterization class.
private static class	P3C.Signature P3C Cluster signature.

Field Summary

Fields

Modifier and Type	Field and Description
protected double	alpha Alpha threshold for testing.
protected double	emDelta Threshold when to stop EM iterations.
private static Logging	LOG The logger for this class.
protected int	maxEmIterations Maximum number of iterations for the EM step.
protected int	minClusterSize Minimum cluster size for noise flagging.
protected double	poissonThreshold Parameter for the Poisson test threshold.

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

ALGORITHM_ID

Constructor Summary

Constructors

Constructor and Description
P3C(double alpha, double poissonThreshold, int maxEmIterations, double emDelta, int minClusterSize) Constructor.

Method Summary

Modifier and Type	Method and Description
private void	assignUnassigned(Relation<V> relation, WritableDataStore<double[]> probClusterIGivenX, java.util.List<MultivariateGaussianModel> models, ModifiableDBIDs unassigned) Assign unassigned objects to best candidate based on shortest Mahalanobis distance.
private int	chiSquaredUniformTest(SetDBIDs[] parts, long[] marked, int card) Performs a ChiSquared test to determine whether an attribute has a uniform distribution.
private void	computeFuzzyMembership(Relation<V> relation, java.util.ArrayList<P3C.Signature> clusterCores, ModifiableDBIDs unassigned, WritableDataStore<double[]> probClusterIGivenX, java.util.List<MultivariateGaussianModel> models, int dim) Computes a fuzzy membership with the weights based on which cluster cores each data point is part of.
private java.util.ArrayList<P3C.Signature>	constructOneSignatures(SetDBIDs[][] partitions, long[][] markers) Construct the 1-signatures by merging adjacent dense bins.
private void	findOutliers(Relation<V> relation, java.util.List<MultivariateGaussianModel> models, java.util.ArrayList<P3C.ClusterCandidate> clusterCandidates, ModifiableDBIDs noise) Performs outlier detection by testing the Mahalanobis distance of each point in a cluster against the critical value of the ChiSquared distribution with as many degrees of freedom as the cluster has relevant attributes.
TypeInformation[]	getInputTypeRestriction() Get the input type restriction used for negotiating the data query.
protected Logging	getLogger() Get the (STATIC) logger for this class.
private java.util.ArrayList<P3C.ClusterCandidate>	hardClustering(WritableDataStore<double[]> probClusterIGivenX, java.util.List<P3C.Signature> clusterCores, DBIDs dbids) Creates a hard clustering from the specified soft membership matrix.
private java.util.ArrayList<P3C.Signature>	mergeClusterCores(int binCount, java.util.ArrayList<P3C.Signature> signatures) Merge 1-signatures into p-signatures.
protected P3C.Signature	mergeSignatures(P3C.Signature first, P3C.Signature second, int numBins) Generates a merged signature of this and another one, where the other signature must be a 1-signature.
private SetDBIDs[][]	partitionData(Relation<V> relation, int bins) Partition the data set into bins bins in each dimension independently.
private java.util.ArrayList<P3C.Signature>	pruneRedundantClusterCores(java.util.ArrayList<P3C.Signature> clusterCores)
Clustering<SubspaceModel>	run(Database database, Relation<V> relation) Performs the P3C algorithm on the given Database.
protected HashSetModifiableDBIDs	unionDBIDs(DBIDs[] parts, int start, int end) Compute the union of multiple DBID sets.

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.ClusteringAlgorithm

run

Field Detail

LOG

private static final Logging LOG

The logger for this class.

poissonThreshold

protected double poissonThreshold

Parameter for the Poisson test threshold.

maxEmIterations

protected int maxEmIterations

Maximum number of iterations for the EM step.

emDelta

protected double emDelta

Threshold when to stop EM iterations.

minClusterSize

protected int minClusterSize

Minimum cluster size for noise flagging. (Not existing in the original publication).

alpha

protected double alpha

Alpha threshold for testing.

Constructor Detail

P3C

public P3C(double alpha,
           double poissonThreshold,
           int maxEmIterations,
           double emDelta,
           int minClusterSize)

Constructor.

Parameters:

alpha - ChiSquared test threshold

poissonThreshold - Poisson test threshold

maxEmIterations - Maximum number of EM iterations

emDelta - EM stopping threshold

minClusterSize - Minimum cluster size

Method Detail

run

public Clustering<SubspaceModel> run(Database database,
                                     Relation<V> relation)

Performs the P3C algorithm on the given Database.

constructOneSignatures

private java.util.ArrayList<P3C.Signature> constructOneSignatures(SetDBIDs[][] partitions,
                                                                  long[][] markers)

Construct the 1-signatures by merging adjacent dense bins.

Parameters:

partitions - Initial partitions.

markers - Markers for dense partitions.

Returns:

1-signatures

mergeClusterCores

private java.util.ArrayList<P3C.Signature> mergeClusterCores(int binCount,
                                                             java.util.ArrayList<P3C.Signature> signatures)

Merge 1-signatures into p-signatures.

Parameters:

binCount - Number of bins in each dimension.

signatures - 1-signatures

Returns:

p-signatures

pruneRedundantClusterCores

private java.util.ArrayList<P3C.Signature> pruneRedundantClusterCores(java.util.ArrayList<P3C.Signature> clusterCores)

partitionData

private SetDBIDs[][] partitionData(Relation<V> relation,
                                   int bins)

Partition the data set into bins bins in each dimension independently. This can be used to construct a grid approximation of the data using O(d n) memory. When a dimension is found to be constant, it will not be partitioned, but instead the corresponding array will be set to null.

Parameters:

relation - Data relation to partition

bins - Number of bins

Returns:

Partitions of each dimension.

unionDBIDs

protected HashSetModifiableDBIDs unionDBIDs(DBIDs[] parts,
                                            int start,
                                            int end)

Compute the union of multiple DBID sets.

Parameters:

parts - Parts array

start - Array start index

end - Array end index (exclusive)

Returns:

Union

chiSquaredUniformTest

private int chiSquaredUniformTest(SetDBIDs[] parts,
                                  long[] marked,
                                  int card)

Performs a ChiSquared test to determine whether an attribute has a uniform distribution.

Parameters:

parts - Data partitions.

marked - the marked bins that should be ignored.

card - Cardinality

Returns:

Position of maximum, or -1 when uniform.

computeFuzzyMembership

private void computeFuzzyMembership(Relation<V> relation,
                                    java.util.ArrayList<P3C.Signature> clusterCores,
                                    ModifiableDBIDs unassigned,
                                    WritableDataStore<double[]> probClusterIGivenX,
                                    java.util.List<MultivariateGaussianModel> models,
                                    int dim)

Computes a fuzzy membership with the weights based on which cluster cores each data point is part of.

Parameters:

relation - Data relation

clusterCores - the cluster cores.

unassigned - set to which to add unassigned points.

probClusterIGivenX - Membership probabilities.

models - Cluster models.

dim - Dimensionality

assignUnassigned

private void assignUnassigned(Relation<V> relation,
                              WritableDataStore<double[]> probClusterIGivenX,
                              java.util.List<MultivariateGaussianModel> models,
                              ModifiableDBIDs unassigned)

Assign unassigned objects to best candidate based on shortest Mahalanobis distance.

Parameters:

relation - Data relation

probClusterIGivenX - fuzzy membership matrix.

models - Cluster models.

unassigned - the list of points not yet assigned.

hardClustering

private java.util.ArrayList<P3C.ClusterCandidate> hardClustering(WritableDataStore<double[]> probClusterIGivenX,
                                                                 java.util.List<P3C.Signature> clusterCores,
                                                                 DBIDs dbids)

Creates a hard clustering from the specified soft membership matrix.

Parameters:

probClusterIGivenX - the membership matrix.

dbids - mapping matrix row to DBID.

Returns:

a hard clustering based on the matrix.

findOutliers

private void findOutliers(Relation<V> relation,
                          java.util.List<MultivariateGaussianModel> models,
                          java.util.ArrayList<P3C.ClusterCandidate> clusterCandidates,
                          ModifiableDBIDs noise)

Performs outlier detection by testing the Mahalanobis distance of each point in a cluster against the critical value of the ChiSquared distribution with as many degrees of freedom as the cluster has relevant attributes.

Parameters:

relation - Data relation

models - Cluster models

clusterCandidates - the list of clusters to check.

noise - the set to which to add points deemed outliers.

mergeSignatures

protected P3C.Signature mergeSignatures(P3C.Signature first,
                                        P3C.Signature second,
                                        int numBins)

Generates a merged signature of this and another one, where the other signature must be a 1-signature.

Parameters:

first - First signature.

second - Second signature, must be a 1-signature.

numBins - Number of bins per dimension.

Returns:

the merged signature, or null if the merge failed.

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<Clustering<SubspaceModel>>

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<Clustering<SubspaceModel>>

Returns:

the static logger