Package elki.clustering.affinitypropagation

Class AffinityPropagation<O>

  • Type Parameters:
    O - object type
    All Implemented Interfaces:
    elki.Algorithm, ClusteringAlgorithm<Clustering<MedoidModel>>
    @Title("Affinity Propagation: Clustering by Passing Messages Between Data Points")
@Reference(title="Clustering by Passing Messages Between Data Points",
           authors="B. J. Frey, D. Dueck",
           booktitle="Science Vol 315",
           url="https://doi.org/10.1126/science.1136800",
           bibkey="doi:10.1126/science.1136800")
public class AffinityPropagation<O>
extends java.lang.Object
implements ClusteringAlgorithm<Clustering<MedoidModel>>
    Cluster analysis by affinity propagation.

    Reference:

    B. J. Frey, D. Dueck
    Clustering by Passing Messages Between Data Points
    Science Vol 315

    Since:
    0.6.0
    Author:
    Erich Schubert

    • Nested Class Summary

      • Nested classes/interfaces inherited from interface elki.Algorithm

        elki.Algorithm.Utils

    • Field Summary

      Fields 
      Modifier and Type Field Description
      (package private) int convergence
      Terminate after 10 iterations with no changes.
      (package private) AffinityPropagationInitialization<O> initialization
      Similarity initialization
      (package private) double lambda
      Damping factor lambda.
      private static elki.logging.Logging LOG
      Class logger
      (package private) int maxiter
      Maximum number of iterations.

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      private Clustering<MedoidModel> buildResult​(elki.database.ids.ArrayDBIDs ids, int[] assignment)
      Build the clustering result.
      elki.data.type.TypeInformation[] getInputTypeRestriction()  
      private it.unimi.dsi.fastutil.ints.Int2ObjectOpenHashMap<elki.database.ids.ModifiableDBIDs> makeClusterMap​(elki.database.ids.ArrayDBIDs ids, int[] assignment)
      Build an int to DBIDs lookup for the clusters.
      Clustering<MedoidModel> run​(elki.database.relation.Relation<O> relation)
      Perform affinity propagation clustering.
      private int updateAssignment​(double[][] r, double[][] a, int[] assignment)
      Update the cluster assignment.
      private void updateAvailabilities​(double[][] r, double[][] a)
      Update availability matrix
      private void updateResponsibilities​(double[][] s, double[][] a, double[][] r)
      Update the responsibility matrix

      • Methods inherited from class java.lang.Object

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

    • Field Detail

      • LOG

        private static final elki.logging.Logging LOG
        Class logger

      • lambda

        double lambda
        Damping factor lambda.

      • convergence

        int convergence
        Terminate after 10 iterations with no changes.

      • maxiter

        int maxiter
        Maximum number of iterations.

    • Constructor Detail

      • AffinityPropagation

        public AffinityPropagation​(AffinityPropagationInitialization<O> initialization,
                           double lambda,
                           int convergence,
                           int maxiter)
        Constructor.
        Parameters:
        initialization - Similarity initialization
        lambda - Damping factor
        convergence - Termination threshold (Number of stable iterations)
        maxiter - Maximum number of iterations

    • Method Detail

      • getInputTypeRestriction

        public elki.data.type.TypeInformation[] getInputTypeRestriction()
        Specified by:
        getInputTypeRestriction in interface elki.Algorithm

      • run

        public Clustering<MedoidModel> run​(elki.database.relation.Relation<O> relation)
        Perform affinity propagation clustering.
        Parameters:
        relation - Relation
        Returns:
        Clustering result

      • updateResponsibilities

        private void updateResponsibilities​(double[][] s,
                                    double[][] a,
                                    double[][] r)
        Update the responsibility matrix
        Parameters:
        s - Similarities
        a - Availability
        r - Responsibilities

      • updateAvailabilities

        private void updateAvailabilities​(double[][] r,
                                  double[][] a)
        Update availability matrix
        Parameters:
        r - Responsibilities
        a - Availability

      • updateAssignment

        private int updateAssignment​(double[][] r,
                             double[][] a,
                             int[] assignment)
        Update the cluster assignment.
        Parameters:
        r - Responsibilities
        a - Affinities
        assignment - Assignment storage
        Returns:
        Number of changed entries

      • makeClusterMap

        private it.unimi.dsi.fastutil.ints.Int2ObjectOpenHashMap<elki.database.ids.ModifiableDBIDs> makeClusterMap​(elki.database.ids.ArrayDBIDs ids,
                                                                                                           int[] assignment)
        Build an int to DBIDs lookup for the clusters.
        Parameters:
        ids - DBIDs
        assignment - Cluster assignment
        Returns:
        Index

      • buildResult

        private Clustering<MedoidModel> buildResult​(elki.database.ids.ArrayDBIDs ids,
                                            int[] assignment)
        Build the clustering result.
        Parameters:
        ids - DBIDs
        assignment - Assignment index
        Returns:
        Clustering