Class MiniMax<O>

  • Type Parameters:
    O - Object type
    All Implemented Interfaces:
    Algorithm, HierarchicalClusteringAlgorithm
    Direct Known Subclasses:
    MiniMaxAnderberg, MiniMaxNNChain

    @Reference(authors="S. I. Ao, K. Yip, M. Ng, D. Cheung, P.-Y. Fong, I. Melhado, P. C. Sham",title="CLUSTAG: hierarchical clustering and graph methods for selecting tag SNPs",booktitle="Bioinformatics, 21 (8)",url="https://doi.org/10.1093/bioinformatics/bti201",bibkey="DBLP:journals/bioinformatics/AoYNCFMS05") @Reference(authors="J. Bien, R. Tibshirani",title="Hierarchical Clustering with Prototypes via Minimax Linkage",booktitle="Journal of the American Statistical Association 106(495)",url="https://doi.org/10.1198/jasa.2011.tm10183",bibkey="doi:10.1198/jasa.2011.tm10183")
    public class MiniMax<O>
    extends java.lang.Object
    implements HierarchicalClusteringAlgorithm
    Minimax Linkage clustering.

    Reference:

    S. I. Ao, K. Yip, M. Ng, D. Cheung, P.-Y. Fong, I. Melhado, P. C. Sham
    CLUSTAG: hierarchical clustering and graph methods for selecting tag SNPs
    Bioinformatics, 21 (8)

    J. Bien and R. Tibshirani
    Hierarchical Clustering with Prototypes via Minimax Linkage
    Journal of the American Statistical Association 106(495)

    Since:
    0.7.5
    Author:
    Julian Erhard, Erich Schubert
    • Field Detail

      • LOG

        private static final Logging LOG
        Class Logger.
      • distance

        protected Distance<? super O> distance
        Distance function used.
    • Constructor Detail

      • MiniMax

        public MiniMax​(Distance<? super O> distance)
        Constructor.
        Parameters:
        distance - Distance function to use.
    • Method Detail

      • getInputTypeRestriction

        public TypeInformation[] getInputTypeRestriction()
        Description copied from interface: Algorithm
        Get the input type restriction used for negotiating the data query.
        Specified by:
        getInputTypeRestriction in interface Algorithm
        Returns:
        Type restriction
      • initializeMatrices

        protected static <O> ClusterDistanceMatrix initializeMatrices​(ArrayDBIDs ids,
                                                                      ArrayModifiableDBIDs prots,
                                                                      DistanceQuery<O> dq)
        Initializes the inter-cluster distance matrix of possible merges
        Parameters:
        ids - Object ids
        prots - Prototype storage
        dq - The distance query
        Returns:
        mat Cluster distance matrix