meka.core

Class MatrixUtils

java.lang.Object

meka.core.MatrixUtils

public class MatrixUtils
extends Object

Utility functions relating to matrices.

Version:

$Revision$

Author:

Jesse Read (jesse@tsc.uc3m.es), Joerg Wicker (wicker@uni-mainz.de)

Constructor Summary

Constructors

Constructor and Description
MatrixUtils()

Method Summary

Modifier and Type	Method and Description
static double[][]	abs(double[][] A) absolute value
static double[][]	add(double[][] A, double v)
static double[][]	add(double[][] A, double[][] B)
static double[]	addBias(double[] x)
static double[][]	addBias(double[][] M)
static Jama.Matrix	addBias(Jama.Matrix M)
static double[][]	copy(double[][] P) Copy a 2D array
static int[][]	deep_copy(int[][] M) Deep Copy - Make a deep copy of M[][].
static double	dot(double[] v, double[] u) dot product of two vectors
static double	dsigma(double a) Derivative of the sigmoid function applied to scalar
static double[]	dsigma(double[] v) Derivative of the sigmoid function applied to vector
static double[][]	dsigma(double[][] A) Derivative of the sigmoid function applied to Matrix
static Jama.Matrix	dsigma(Jama.Matrix A) Derivative of the sigmoid function applied to Jama Matrix
static void	fillCol(double[][] M, int k, double val)
static void	fillRow(double[][] M, int k, double val)
static double[]	flatten(double[][] M) Flatten - turn Matrix [0.
static int[]	flatten(int[][] M) Flatten - turn Matrix [0 1; 2 3] into vector [0 1 2 3].
static double[]	getCol(double[][] M, int k) GetCol - return the k-th column of M (as a vector).
static int[]	getCol(int[][] M, int k) GetCol - return the k-th column of M (as a vector).
static String	getDim(double[][] M)
static String	getDim(Jama.Matrix M)
static double[][]	getTranspose(double[][] M)
static weka.core.matrix.Matrix	instancesToMatrix(weka.core.Instances inst) Helper method that transforma an Instances object to a Matrix object.
static weka.core.Instances	matrixToInstances(weka.core.matrix.Matrix mat, weka.core.Instances patternInst) Helper method that transforms a Matrix object to an Instances object.
static int[]	maxIndices(double[][] M) returns argmax_{j,k} M[j][k]
static double	meanSquaredError(double[][] vectorBatch1, double[][] vectorBatch2)
static double[][]	multiply(double[][] A, double K) Multiply - multiply each value in A[][] by constant K.
static double[][]	multiply(double[][] A, double[][] B) Multiply - multiply matrices A and B together.
static double[]	multiply(double[] a, double[] b) Multiply - multiply vectors a and b together.
static double[][]	multiplyTranspose(double[][] A, double[][] B)
static double[]	ones(int L) Ones - return a vector full of 1s.
static void	printDim(double[][] M)
static void	printDim(Jama.Matrix M)
static void	printMatrix(double[][] M_)
static double[][]	randn(int rows, int cols, Random r) A 2D array of Gaussian random numbers
static Jama.Matrix	randomn(int nrows, int ncols, Random r) A matrix of Gaussian random numbers
static double[]	removeBias(double[] x)
static double[][]	removeBias(double[][] M)
static Jama.Matrix	removeBias(Jama.Matrix M)
static double[][]	sample(double[][] M, Random r) Sample - Returns Matrix C where each value C[j][k] is 1 with probability M[j][k] and 0 otherwise.
static double[]	sample(double[] v, Random r) Sample - Returns vector c where each value c[j][k] is 1 with probability v[j][k] and 0 otherwise.
static Jama.Matrix	sample(Jama.Matrix M, Random r) Sample - Returns Matrix C where each value C[j][k] is 1 with probability M[j][k] and 0 otherwise.
static double	sigma(double a) Sigmoid / Logistic function
static double[]	sigma(double[] v) Sigmoid function applied to vector
static double[][]	sigma(double[][] A) Sigmoid function applied to matrix (2D array)
static Jama.Matrix	sigma(Jama.Matrix A) Sigmoid function applied to Matrix
static double	squaredError(double[] vector1, double[] vector2)
static double	SS(double[][] M) squared sum
static double[][]	subtract(double[][] A, double[][] B)
static double[]	sum(double[][] M) Sum - sum this matrix.
static int[]	sum(int[][] M) Sum - sum this matrix.
static double[][]	threshold(double[][] P, double t) Threshold - apply threshold t to matrix P[][].
static double[][]	threshold(double[][] P, Random r) sample from matrix
static double[]	threshold(double[] v, double t) threshold function applied to vector
static Jama.Matrix	threshold(Jama.Matrix M, double t) sigmoid function applied to vector
static String	toString(double[][] M_) ToString - return a String representation.
static String	toString(double[][] M_, int adp) ToString - return a String representation (to adp decimal places).
static String	toString(double[][] M, String name) ToString - return a String representation of 'M', in Matlab format, called 'name'.
static String	toString(int[][] M_) ToString - return a String representation.
static String	toString(Jama.Matrix M)
static double[][]	transposeMultiply(double[][] A, double[][] B)

Methods inherited from class java.lang.Object

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

Constructor Detail

MatrixUtils

public MatrixUtils()

Method Detail

instancesToMatrix

public static weka.core.matrix.Matrix instancesToMatrix(weka.core.Instances inst)

Helper method that transforma an Instances object to a Matrix object.

Parameters:

inst - The Instances to transform.

Returns:

The resulting Matrix object.

matrixToInstances

public static weka.core.Instances matrixToInstances(weka.core.matrix.Matrix mat,
                                                    weka.core.Instances patternInst)

Helper method that transforms a Matrix object to an Instances object.

Parameters:

mat - The Matrix to transform.

patternInst - the Instances template to use

Returns:

The resulting Instances object.

getCol

public static double[] getCol(double[][] M,
                              int k)

GetCol - return the k-th column of M (as a vector).

getCol

public static int[] getCol(int[][] M,
                           int k)

GetCol - return the k-th column of M (as a vector).

addBias

public static double[] addBias(double[] x)

addBias

public static double[][] addBias(double[][] M)

addBias

public static Jama.Matrix addBias(Jama.Matrix M)

removeBias

public static double[] removeBias(double[] x)

removeBias

public static Jama.Matrix removeBias(Jama.Matrix M)

removeBias

public static double[][] removeBias(double[][] M)

multiply

public static double[][] multiply(double[][] A,
                                  double K)

Multiply - multiply each value in A[][] by constant K.

toString

public static String toString(Jama.Matrix M)

toString

public static String toString(double[][] M_,
                              int adp)

ToString - return a String representation (to adp decimal places).

toString

public static String toString(double[][] M_)

ToString - return a String representation.

toString

public static String toString(int[][] M_)

ToString - return a String representation.

toString

public static String toString(double[][] M,
                              String name)

ToString - return a String representation of 'M', in Matlab format, called 'name'.

threshold

public static final double[][] threshold(double[][] P,
                                         double t)

Threshold - apply threshold t to matrix P[][].

flatten

public static int[] flatten(int[][] M)

Flatten - turn Matrix [0 1; 2 3] into vector [0 1 2 3].

flatten

public static double[] flatten(double[][] M)

Flatten - turn Matrix [0. 1.; 2. 3.] into vector [0. 1. 2. 3.].

subtract

public static double[][] subtract(double[][] A,
                                  double[][] B)

abs

public static double[][] abs(double[][] A)

absolute value

SS

public static double SS(double[][] M)

squared sum

sigma

public static final double sigma(double a)

Sigmoid / Logistic function

sigma

public static final double[] sigma(double[] v)

Sigmoid function applied to vector

sigma

public static final double[][] sigma(double[][] A)

Sigmoid function applied to matrix (2D array)

sigma

public static final Jama.Matrix sigma(Jama.Matrix A)

Sigmoid function applied to Matrix

dsigma

public static final double dsigma(double a)

Derivative of the sigmoid function applied to scalar

dsigma

public static final double[] dsigma(double[] v)

Derivative of the sigmoid function applied to vector

dsigma

public static final double[][] dsigma(double[][] A)

Derivative of the sigmoid function applied to Matrix

dsigma

public static final Jama.Matrix dsigma(Jama.Matrix A)

Derivative of the sigmoid function applied to Jama Matrix

deep_copy

public static int[][] deep_copy(int[][] M)

Deep Copy - Make a deep copy of M[][].

ones

public static double[] ones(int L)

Ones - return a vector full of 1s.

sum

public static int[] sum(int[][] M)

Sum - sum this matrix.

sum

public static double[] sum(double[][] M)

Sum - sum this matrix.

fillRow

public static final void fillRow(double[][] M,
                                 int k,
                                 double val)

fillCol

public static final void fillCol(double[][] M,
                                 int k,
                                 double val)

randn

public static double[][] randn(int rows,
                               int cols,
                               Random r)

A 2D array of Gaussian random numbers

randomn

public static Jama.Matrix randomn(int nrows,
                                  int ncols,
                                  Random r)

A matrix of Gaussian random numbers

copy

public static final double[][] copy(double[][] P)

Copy a 2D array

threshold

public static final double[][] threshold(double[][] P,
                                         Random r)

sample from matrix

threshold

public static final double[] threshold(double[] v,
                                       double t)

threshold function applied to vector

threshold

public static final Jama.Matrix threshold(Jama.Matrix M,
                                          double t)

sigmoid function applied to vector

transposeMultiply

public static double[][] transposeMultiply(double[][] A,
                                           double[][] B)

multiplyTranspose

public static double[][] multiplyTranspose(double[][] A,
                                           double[][] B)

multiply

public static double[][] multiply(double[][] A,
                                  double[][] B)

Multiply - multiply matrices A and B together.

multiply

public static double[] multiply(double[] a,
                                double[] b)
                         throws Exception

Multiply - multiply vectors a and b together.

Throws:

Exception

getTranspose

public static double[][] getTranspose(double[][] M)

add

public static double[][] add(double[][] A,
                             double[][] B)

add

public static double[][] add(double[][] A,
                             double v)

squaredError

public static double squaredError(double[] vector1,
                                  double[] vector2)

meanSquaredError

public static double meanSquaredError(double[][] vectorBatch1,
                                      double[][] vectorBatch2)

dot

public static double dot(double[] v,
                         double[] u)

dot product of two vectors

sample

public static double[][] sample(double[][] M,
                                Random r)

Sample - Returns Matrix C where each value C[j][k] is 1 with probability M[j][k] and 0 otherwise. (assume each value is in [0,1])

sample

public static double[] sample(double[] v,
                              Random r)

Sample - Returns vector c where each value c[j][k] is 1 with probability v[j][k] and 0 otherwise. (assume each value is in [0,1])

sample

public static Jama.Matrix sample(Jama.Matrix M,
                                 Random r)

Sample - Returns Matrix C where each value C[j][k] is 1 with probability M[j][k] and 0 otherwise. (assume each value is in [0,1])

printMatrix

public static void printMatrix(double[][] M_)

printDim

public static void printDim(Jama.Matrix M)

printDim

public static void printDim(double[][] M)

getDim

public static String getDim(double[][] M)

getDim

public static String getDim(Jama.Matrix M)

maxIndices

public static int[] maxIndices(double[][] M)

returns argmax_{j,k} M[j][k]