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

Class ChengAndChurch.BiclusterCandidate

java.lang.Object

de.lmu.ifi.dbs.elki.algorithm.clustering.biclustering.ChengAndChurch.BiclusterCandidate

Enclosing class:

ChengAndChurch<V extends NumberVector>

protected static class ChengAndChurch.BiclusterCandidate
extends Object

Bicluster candidate.

Author:

Erich Schubert

Field Summary

Fields

Modifier and Type	Field and Description
(package private) double	allM Mean of the current bicluster.
(package private) int	colcard Cardinalities.
(package private) double[]	colM Means.
(package private) long[]	cols Row and column bitmasks.
(package private) long[]	irow Row and column bitmasks.
private ChengAndChurch.CellVisitor	MEANVISITOR Visitor for updating the means.
(package private) double	residue The current bicluster score (mean squared residue).
(package private) int	rowcard Cardinalities.
(package private) double[]	rowM Means.
(package private) long[]	rows Row and column bitmasks.

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	ChengAndChurch.BiclusterCandidate(int rows, int cols) Constructor.

Method Summary

Methods

Modifier and Type	Method and Description
protected double	computeColResidue(double[][] mat, int col) Computes the mean column residue of the given col.
protected double	computeMeanSquaredDeviation(double[][] mat) Compute the mean square residue.
protected double	computeRowResidue(double[][] mat, int row, boolean rowinverted) Computes the mean row residue of the given row.
protected void	invertRow(int rnum, boolean b)
protected void	maskMatrix(double[][] mat, Distribution replacement) Updates the mask with replacement values for all data in the given rows and columns.
protected void	reset() Resets the values for the next cluster search.
protected void	selectColumn(int cnum, boolean set) Select or deselect a column.
protected void	selectRow(int rnum, boolean set) Select or deselect a row.
protected double	updateRowAndColumnMeans(double[][] mat, boolean all) Update the row means and column means.
protected void	visitAll(double[][] mat, int mode, ChengAndChurch.CellVisitor visitor) Visit all selected cells in the data matrix.
protected void	visitColumn(double[][] mat, int col, int mode, ChengAndChurch.CellVisitor visitor) Visit a column of the matrix.
protected void	visitRow(double[][] mat, int row, int mode, ChengAndChurch.CellVisitor visitor) Visit a row of the data matrix.

Methods inherited from class java.lang.Object

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

Field Detail

rowcard

int rowcard

Cardinalities.

colcard

int colcard

Cardinalities.

rowM

double[] rowM

Means.

colM

double[] colM

Means.

rows

long[] rows

Row and column bitmasks.

irow

long[] irow

Row and column bitmasks.

cols

long[] cols

Row and column bitmasks.

allM

double allM

Mean of the current bicluster.

residue

double residue

The current bicluster score (mean squared residue).

MEANVISITOR

private final ChengAndChurch.CellVisitor MEANVISITOR

Visitor for updating the means.

Constructor Detail

ChengAndChurch.BiclusterCandidate

protected ChengAndChurch.BiclusterCandidate(int rows,
                                 int cols)

Constructor.

Parameters:

rows - Row dimensionality.

cols - Column dimensionality.

Method Detail

reset

protected void reset()

Resets the values for the next cluster search.

visitAll

protected void visitAll(double[][] mat,
            int mode,
            ChengAndChurch.CellVisitor visitor)

Visit all selected cells in the data matrix.

Parameters:

mat - Data matrix

mode - Operation mode

visitor - Visitor function

visitColumn

protected void visitColumn(double[][] mat,
               int col,
               int mode,
               ChengAndChurch.CellVisitor visitor)

Visit a column of the matrix.

Parameters:

mat - Data matrix

col - Column to visit

mode - Operation mode

visitor - Visitor function

visitRow

protected void visitRow(double[][] mat,
            int row,
            int mode,
            ChengAndChurch.CellVisitor visitor)

Visit a row of the data matrix.

Parameters:

mat - Data matrix

row - Row to visit

visitor - Visitor function

updateRowAndColumnMeans

protected double updateRowAndColumnMeans(double[][] mat,
                             boolean all)

Update the row means and column means.

Parameters:

mat - Data matrix

all - Flag, to update all

Returns:

overall mean

computeMeanSquaredDeviation

protected double computeMeanSquaredDeviation(double[][] mat)

Compute the mean square residue.

Parameters:

mat - Data matrix

Returns:

mean squared residue

computeRowResidue

protected double computeRowResidue(double[][] mat,
                       int row,
                       boolean rowinverted)

Computes the mean row residue of the given row.

Parameters:

mat - Data matrix

row - The row who's residue should be computed.

rowinverted - Indicates if the row should be considered inverted.

Returns:

The row residue of the given row.

computeColResidue

protected double computeColResidue(double[][] mat,
                       int col)

Computes the mean column residue of the given col.

Parameters:

col - The column who's residue should be computed.

Returns:

The row residue of the given colum.

maskMatrix

protected void maskMatrix(double[][] mat,
              Distribution replacement)

Updates the mask with replacement values for all data in the given rows and columns.

Parameters:

mat - Mask to update.

replacement - Distribution to sample replacement values from.

selectColumn

protected void selectColumn(int cnum,
                boolean set)

Select or deselect a column.

Parameters:

cnum - Column to select

set - Value to set

selectRow

protected void selectRow(int rnum,
             boolean set)

Select or deselect a row.

Parameters:

rnum - Row to select

set - Value to set

invertRow

protected void invertRow(int rnum,
             boolean b)