readme_cc_current

一种聚类算法,名字是cocluster

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README file for cocluster


USAGE
        cocluster-'uname' [SWITCHES]


DESCRIPTION
        Implements three co-clustering algorithms (in C++):
        information-theoretic co-clustering and two types of
        minimum sum-squared residue co-clustering algorithms


AUTHORS
        Hyuk Cho
        Copyright (c) 2005, 2006
        Hyuk Cho, Yuqiang Guan, and Suvrit Sra
        {hyukcho, yguan, suvrit}@cs.utexas.edu
        Copyright (c) 2003, 2004


REQUIRED SWITCHES
        At least, the following switches are required: -A -C -I -R


DESCRIPTION OF SWITCHES

        -A  algorithmType  (REQUIRED)
            specifies type of coclustering algorithm
              e -- euclidean coclustering algorithm (DEFAULT)
              i -- information theoretic coclustering algorithm
              r -- minimim squared residue coclustering algorithm

        -C  colClusterNum  (REQUIRED)
            specifies number of column clusters (DEFAULT = 1)

        -D  dumpLevel  [dumpAccessMode  dumpFilename]
            specifies level of intermediate information dump
            dumpLevel can be one of
              0 -- minimal information (DEFAULT)
              1 -- objective function value in Batch Update and minimal statistics
              2 -- objective function value in local search and maximal statistics
              3 -- maximal information in a specified file and minimal on stdout
                   dumpAccessMode is required after '-D 3' and one of
                     a -- append mode
                     o -- output mode
                   dumpFilename is required after '-D 3 a/o'

        -E  outputEachClsuter
            specifies detail ouputs in external cluster validattion section
            outputEachCluster can be one of
              0 -- don't output a confusion matrix and each cluster's statistics (DEFAULT)
              1 -- output them in external cluster validation section

        -I  inputMatrixType  inputFormatType  inputFilename  (REQUIRED)
            specifies details of input matrix file
            inputMatrixType can be one of
              d -- dense (i.e., rectangle/square) matrix
                   inputFormatType after '-I d' can be one of
                     s -- dimension and matrix stored separately
                     t -- both dimension and matrix stored together
              s -- sparse matrix in CCS
                   inputFormatType after '-I s' can be one of
                     f -- tfn scaling
                     x -- txx scaling

        -J  oneWay
            specifies to get one-way row/column clustering objective function values
            oneWay can be one of
              0 -- don't compute one-way objective function value(s) (DEFAULT)
              1 -- compute one-way objective function value(s)

        -K  classLabelSelection  classOffsetType  classLabelFilename
            specifies details of class label file
            classLabelSelection can be one of
              b -- both row and column class labels
              c -- column class labels
              r -- row class labels
            classOffsetType can be one of
                     0 -- class label index starts from 0
                     1 -- class label index starts from 1
  
        -M  smoothingType  [rowSmoothingMagnitude  colSmoothingMagnitude]
            specifies details of smoothing techniques
            smoothingType can be one of
              a -- annealing of uniform smoothing (DEFAULT = 1)
              h -- maximum entropy smoothing
              n -- no smoothing (DEFAULT)
              u -- uniform smoothing (DEFAULT = 0)
                   smoothingMagnitude is required for '-M a/h/u'
        -N  runNum
            specifies number of runs to get averaged statistics (DEFAULT = 1)

        -O  outputFileType  [outputLabelType  outputOffsetType]  outputAccessMode  outputFilename
            specifies details of cocluster/objective/statistics file information
            outputFileType can be one of
              c -- output co-clusters
                   outputLabelType is required after '-O c' and can be one of
                     b -- each co-cluster block consisting of three rows like
                            #rows #columns (in 1st row)
                            list of row #s in (1,1)-th co-cluster (in 2nd row)
                            list of column #s in (1,2)-th column co-cluster (in 3rd row)
                            and so on
                     s -- all co-clusters represented in a simple format of two rows like (DEFAULT)
                            list of row cluster labels of all rows (in 1st row)
                            list of column cluster labels of all columns (in 2nd row)
                   outputOffsetType is required after '-O c b' and outputLabelType and can be one of
                            0 -- cluster label index starts from 0
                            1 -- cluster label index starts from 1
              o -- output objective function value(s)
              s -- output satistical information
            outputAccessMode can be one of
                                   a -- append mode, useful with '-N randomRunNum'
                                   o -- output mode

        -R  rowClusterNum  (REQUIRED)
            specifies number of row clusters (DEFAULT = 1)

        -S  seedingType  seedingLabelSelection  [seedingPertValue
                                                 | (seedingOffsetType  numSeedingSet seedingFilename)
                                                 | (numRowPermutation | numColPermutation)]
            specifies details of initial cluster assignment
            seedingType can be one of
              f -- farthest apart assignment
              m -- permute an initial random cluster vector
                   numRowPermutation or/and numColPermutation is/are required after '-S m b/c/r'
                            numRowPermutation  numColPermutation -- after '-S m b'
                            numColPermutation -- after '-S m c'
                            numRowPermutation -- after '-S m r'
              p -- perturbates cluster centroids
                   seedingPertValue is required after '-S p'
              r -- random assignment (DEFAULT)
              s -- read cluster labels from a seeding file
                   seedingOffsetType is required after '-S s b/c/r' and one of
                            0 -- seeding label index starts from 0
                            1 -- seeding label index starts from 1
                   numSeedingSet is required after '-S s b/c/r 0/1'
                                   n -- positive integer (>=1)
                   seedingFilename is required after '-S s b/c/r/ 0/1 n'
            seedingLabelSelection can be one of
                     b -- both row and column cluster labels
                     c -- column cluster labels
                     r -- row cluster labels

        -T  thresholdType  rowThreshold  colThreshold
            specifies details of threshold for either batch update or local search
            thresholdType can be one of
              b -- batch update (default = +0.001)
              l -- local search (default = -1e-06)
            Both rowThreshold and colThreshold are required.

        -U  updateType  [updateSelection  |  (rowLocalSearchLength  colLocalSearchLength)]
            specifies details of cluster-centroid-updating order in batch update or local search
            updateType can be one of
              b -- batch update
                   updateSelection is required after '-U b' and can be one of
                     0 -- single row and single column, respectively (DEFAULT)
                     1 -- single row and single column, in batch mode
                     2 -- single row or single column, flipping a pair coin
                     3 -- multiple run of either row or column, flipping a pair coin
              l -- local search
                   rowLocalSearchLength (DEFAULT = 0) is required after 'l'
                   colLocalSearchLength (DEFAULT = 0) is required after 'l' and rowLocalSearchLength
                   To avoid empty row/column cluster(s), use -1 for row/colLocalSearchLength.

        -X  anticorrelation
            specifies to capture anti-correlated rows (by taking reverse of rows)
            anticorrelation can be one of
              0 -- don't capture anti-correlated rows (DEFAULT)
              1 -- capture anti-correlated rows


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