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weka.core.ContingencyTables Maven / Gradle / Ivy
/*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see [email protected] )
* @version $Revision: 10057 $
*/
public class ContingencyTables
implements RevisionHandler {
/** The natural logarithm of 2 */
public static final double log2 = Math.log(2);
/** Cache of integer logs */
private static final double MAX_INT_FOR_CACHE_PLUS_ONE = 10000;
private static final double[] INT_N_LOG_N_CACHE = new double[(int)MAX_INT_FOR_CACHE_PLUS_ONE];
/** Initialize cache */
static {
for (int i = 1; i < MAX_INT_FOR_CACHE_PLUS_ONE; i++) {
double d = (double)i;
INT_N_LOG_N_CACHE[i] = d * Math.log(d);
}
}
/**
* Returns chi-squared probability for a given matrix.
*
* @param matrix the contigency table
* @param yates is Yates' correction to be used?
* @return the chi-squared probability
*/
public static double chiSquared(double [][] matrix, boolean yates) {
int df = (matrix.length - 1) * (matrix[0].length - 1);
return Statistics.chiSquaredProbability(chiVal(matrix, yates), df);
}
/**
* Computes chi-squared statistic for a contingency table.
*
* @param matrix the contigency table
* @param useYates is Yates' correction to be used?
* @return the value of the chi-squared statistic
*/
public static double chiVal(double [][] matrix, boolean useYates) {
int df, nrows, ncols, row, col;
double[] rtotal, ctotal;
double expect = 0, chival = 0, n = 0;
boolean yates = true;
nrows = matrix.length;
ncols = matrix[0].length;
rtotal = new double [nrows];
ctotal = new double [ncols];
for (row = 0; row < nrows; row++) {
for (col = 0; col < ncols; col++) {
rtotal[row] += matrix[row][col];
ctotal[col] += matrix[row][col];
n += matrix[row][col];
}
}
df = (nrows - 1)*(ncols - 1);
if ((df > 1) || (!useYates)) {
yates = false;
} else if (df <= 0) {
return 0;
}
chival = 0.0;
for (row = 0; row < nrows; row++) {
if (Utils.gr(rtotal[row], 0)) {
for (col = 0; col < ncols; col++) {
if (Utils.gr(ctotal[col], 0)) {
expect = (ctotal[col] * rtotal[row]) / n;
chival += chiCell (matrix[row][col], expect, yates);
}
}
}
}
return chival;
}
/**
* Tests if Cochran's criterion is fullfilled for the given
* contingency table. Rows and columns with all zeros are not considered
* relevant.
*
* @param matrix the contigency table to be tested
* @return true if contingency table is ok, false if not
*/
public static boolean cochransCriterion(double[][] matrix) {
double[] rtotal, ctotal;
double n = 0, expect, smallfreq = 5;
int smallcount = 0, nonZeroRows = 0, nonZeroColumns = 0, nrows, ncols,
row, col;
nrows = matrix.length;
ncols = matrix[0].length;
rtotal = new double [nrows];
ctotal = new double [ncols];
for (row = 0; row < nrows; row++) {
for (col = 0; col < ncols; col++) {
rtotal[row] += matrix[row][col];
ctotal[col] += matrix[row][col];
n += matrix[row][col];
}
}
for (row = 0; row < nrows; row++) {
if (Utils.gr(rtotal[row], 0)) {
nonZeroRows++;
}
}
for (col = 0; col < ncols; col++) {
if (Utils.gr(ctotal[col], 0)) {
nonZeroColumns++;
}
}
for (row = 0; row < nrows; row++) {
if (Utils.gr(rtotal[row], 0)) {
for (col = 0; col < ncols; col++) {
if (Utils.gr(ctotal[col], 0)) {
expect = (ctotal[col] * rtotal[row]) / n;
if (Utils.sm(expect, smallfreq)) {
if (Utils.sm(expect, 1)) {
return false;
} else {
smallcount++;
if (smallcount > (nonZeroRows * nonZeroColumns) / smallfreq) {
return false;
}
}
}
}
}
}
}
return true;
}
/**
* Computes Cramer's V for a contingency table.
*
* @param matrix the contingency table
* @return Cramer's V
*/
public static double CramersV(double [][] matrix) {
int row, col, nrows,ncols, min;
double n = 0;
nrows = matrix.length;
ncols = matrix[0].length;
for (row = 0; row < nrows; row++) {
for (col = 0; col < ncols; col++) {
n += matrix[row][col];
}
}
min = nrows < ncols ? nrows-1 : ncols-1;
if ((min == 0) || Utils.eq(n, 0))
return 0;
return Math.sqrt(chiVal(matrix, false) / (n * (double)min));
}
/**
* Computes the entropy of the given array.
*
* @param array the array
* @return the entropy
*/
public static double entropy(double[] array) {
double returnValue = 0, sum = 0;
for (int i = 0; i < array.length; i++) {
returnValue -= lnFunc(array[i]);
sum += array[i];
}
if (Utils.eq(sum, 0)) {
return 0;
} else {
return (returnValue + lnFunc(sum)) / (sum * log2);
}
}
/**
* Computes conditional entropy of the rows given
* the columns.
*
* @param matrix the contingency table
* @return the conditional entropy of the rows given the columns
*/
public static double entropyConditionedOnColumns(double[][] matrix) {
double returnValue = 0, sumForColumn, total = 0;
for (int j = 0; j < matrix[0].length; j++) {
sumForColumn = 0;
for (int i = 0; i < matrix.length; i++) {
returnValue = returnValue + lnFunc(matrix[i][j]);
sumForColumn += matrix[i][j];
}
returnValue = returnValue - lnFunc(sumForColumn);
total += sumForColumn;
}
if (Utils.eq(total, 0)) {
return 0;
}
return -returnValue / (total * log2);
}
/**
* Computes conditional entropy of the columns given
* the rows.
*
* @param matrix the contingency table
* @return the conditional entropy of the columns given the rows
*/
public static double entropyConditionedOnRows(double[][] matrix) {
double returnValue = 0, sumForRow, total = 0;
for (int i = 0; i < matrix.length; i++) {
sumForRow = 0;
for (int j = 0; j < matrix[0].length; j++) {
returnValue = returnValue + lnFunc(matrix[i][j]);
sumForRow += matrix[i][j];
}
returnValue = returnValue - lnFunc(sumForRow);
total += sumForRow;
}
if (Utils.eq(total, 0)) {
return 0;
}
return -returnValue / (total * log2);
}
/**
* Computes conditional entropy of the columns given the rows
* of the test matrix with respect to the train matrix. Uses a
* Laplace prior. Does NOT normalize the entropy.
*
* @param train the train matrix
* @param test the test matrix
* @param numClasses the number of symbols for Laplace
* @return the entropy
*/
public static double entropyConditionedOnRows(double[][] train,
double[][] test,
double numClasses) {
double returnValue = 0, trainSumForRow, testSumForRow, testSum = 0;
for (int i = 0; i < test.length; i++) {
trainSumForRow = 0;
testSumForRow = 0;
for (int j = 0; j < test[0].length; j++) {
returnValue -= test[i][j] * Math.log(train[i][j] + 1);
trainSumForRow += train[i][j];
testSumForRow += test[i][j];
}
testSum = testSumForRow;
returnValue += testSumForRow * Math.log(trainSumForRow +
numClasses);
}
return returnValue / (testSum * log2);
}
/**
* Computes the rows' entropy for the given contingency table.
*
* @param matrix the contingency table
* @return the rows' entropy
*/
public static double entropyOverRows(double[][] matrix) {
double returnValue = 0, sumForRow, total = 0;
for (int i = 0; i < matrix.length; i++) {
sumForRow = 0;
for (int j = 0; j < matrix[0].length; j++) {
sumForRow += matrix[i][j];
}
returnValue = returnValue - lnFunc(sumForRow);
total += sumForRow;
}
if (Utils.eq(total, 0)) {
return 0;
}
return (returnValue + lnFunc(total)) / (total * log2);
}
/**
* Computes the columns' entropy for the given contingency table.
*
* @param matrix the contingency table
* @return the columns' entropy
*/
public static double entropyOverColumns(double[][] matrix){
double returnValue = 0, sumForColumn, total = 0;
for (int j = 0; j < matrix[0].length; j++){
sumForColumn = 0;
for (int i = 0; i < matrix.length; i++) {
sumForColumn += matrix[i][j];
}
returnValue = returnValue - lnFunc(sumForColumn);
total += sumForColumn;
}
if (Utils.eq(total, 0)) {
return 0;
}
return (returnValue + lnFunc(total)) / (total * log2);
}
/**
* Computes gain ratio for contingency table (split on rows).
* Returns Double.MAX_VALUE if the split entropy is 0.
*
* @param matrix the contingency table
* @return the gain ratio
*/
public static double gainRatio(double[][] matrix){
double preSplit = 0, postSplit = 0, splitEnt = 0,
sumForRow, sumForColumn, total = 0, infoGain;
// Compute entropy before split
for (int i = 0; i < matrix[0].length; i++) {
sumForColumn = 0;
for (int j = 0; j < matrix.length; j++)
sumForColumn += matrix[j][i];
preSplit += lnFunc(sumForColumn);
total += sumForColumn;
}
preSplit -= lnFunc(total);
// Compute entropy after split and split entropy
for (int i = 0; i < matrix.length; i++) {
sumForRow = 0;
for (int j = 0; j < matrix[0].length; j++) {
postSplit += lnFunc(matrix[i][j]);
sumForRow += matrix[i][j];
}
splitEnt += lnFunc(sumForRow);
}
postSplit -= splitEnt;
splitEnt -= lnFunc(total);
infoGain = preSplit - postSplit;
if (Utils.eq(splitEnt, 0))
return 0;
return infoGain / splitEnt;
}
/**
* Returns negative base 2 logarithm of multiple hypergeometric
* probability for a contingency table.
*
* @param matrix the contingency table
* @return the log of the hypergeometric probability of the contingency table
*/
public static double log2MultipleHypergeometric(double[][] matrix) {
double sum = 0, sumForRow, sumForColumn, total = 0;
for (int i = 0; i < matrix.length; i++) {
sumForRow = 0;
for (int j = 0; j < matrix[i].length; j++) {
sumForRow += matrix[i][j];
}
sum += SpecialFunctions.lnFactorial(sumForRow);
total += sumForRow;
}
for (int j = 0; j < matrix[0].length; j++) {
sumForColumn = 0;
for (int i = 0; i < matrix.length; i++) {
sumForColumn += matrix [i][j];
}
sum += SpecialFunctions.lnFactorial(sumForColumn);
}
for (int i = 0; i < matrix.length; i++) {
for (int j = 0; j < matrix[i].length; j++) {
sum -= SpecialFunctions.lnFactorial(matrix[i][j]);
}
}
sum -= SpecialFunctions.lnFactorial(total);
return -sum / log2;
}
/**
* Reduces a matrix by deleting all zero rows and columns.
*
* @param matrix the matrix to be reduced
* @return the matrix with all zero rows and columns deleted
*/
public static double[][] reduceMatrix(double[][] matrix) {
int row, col, currCol, currRow, nrows, ncols,
nonZeroRows = 0, nonZeroColumns = 0;
double[] rtotal, ctotal;
double[][] newMatrix;
nrows = matrix.length;
ncols = matrix[0].length;
rtotal = new double [nrows];
ctotal = new double [ncols];
for (row = 0; row < nrows; row++) {
for (col = 0; col < ncols; col++) {
rtotal[row] += matrix[row][col];
ctotal[col] += matrix[row][col];
}
}
for (row = 0; row < nrows; row++) {
if (Utils.gr(rtotal[row],0)) {
nonZeroRows++;
}
}
for (col = 0; col < ncols; col++) {
if (Utils.gr(ctotal[col],0)) {
nonZeroColumns++;
}
}
newMatrix = new double[nonZeroRows][nonZeroColumns];
currRow = 0;
for (row = 0; row < nrows; row++) {
if (Utils.gr(rtotal[row],0)) {
currCol = 0;
for (col = 0; col < ncols; col++) {
if (Utils.gr(ctotal[col],0)) {
newMatrix[currRow][currCol] = matrix[row][col];
currCol++;
}
}
currRow++;
}
}
return newMatrix;
}
/**
* Calculates the symmetrical uncertainty for base 2.
*
* @param matrix the contingency table
* @return the calculated symmetrical uncertainty
*
*/
public static double symmetricalUncertainty(double matrix[][]) {
double sumForColumn, sumForRow, total = 0, columnEntropy = 0,
rowEntropy = 0, entropyConditionedOnRows = 0, infoGain = 0;
// Compute entropy for columns
for (int i = 0; i < matrix[0].length; i++) {
sumForColumn = 0;
for (int j = 0; j < matrix.length; j++) {
sumForColumn += matrix[j][i];
}
columnEntropy += lnFunc(sumForColumn);
total += sumForColumn;
}
columnEntropy -= lnFunc(total);
// Compute entropy for rows and conditional entropy
for (int i = 0; i < matrix.length; i++) {
sumForRow = 0;
for (int j = 0; j < matrix[0].length; j++) {
sumForRow += matrix[i][j];
entropyConditionedOnRows += lnFunc(matrix[i][j]);
}
rowEntropy += lnFunc(sumForRow);
}
entropyConditionedOnRows -= rowEntropy;
rowEntropy -= lnFunc(total);
infoGain = columnEntropy - entropyConditionedOnRows;
if (Utils.eq(columnEntropy, 0) || Utils.eq(rowEntropy, 0))
return 0;
return 2.0 * (infoGain / (columnEntropy + rowEntropy));
}
/**
* Computes Goodman and Kruskal's tau-value for a contingency table.
*
* @param matrix the contingency table
* @return Goodman and Kruskal's tau-value
*/
public static double tauVal(double[][] matrix) {
int nrows, ncols, row, col;
double [] ctotal;
double maxcol = 0, max, maxtotal = 0, n = 0;
nrows = matrix.length;
ncols = matrix[0].length;
ctotal = new double [ncols];
for (row = 0; row < nrows; row++) {
max = 0;
for (col = 0; col < ncols; col++) {
if (Utils.gr(matrix[row][col], max))
max = matrix[row][col];
ctotal[col] += matrix[row][col];
n += matrix[row][col];
}
maxtotal += max;
}
if (Utils.eq(n, 0)) {
return 0;
}
maxcol = ctotal[Utils.maxIndex(ctotal)];
return (maxtotal - maxcol)/(n - maxcol);
}
/**
* Help method for computing entropy.
*/
public static double lnFunc(double num){
if (num <= 0) {
return 0;
} else {
// Use cache if we have a sufficiently small integer
if (num < MAX_INT_FOR_CACHE_PLUS_ONE) {
int n = (int)num;
if ((double)n == num) {
return INT_N_LOG_N_CACHE[n];
}
}
return num * Math.log(num);
}
}
/**
* Computes chi-value for one cell in a contingency table.
*
* @param freq the observed frequency in the cell
* @param expected the expected frequency in the cell
* @return the chi-value for that cell; 0 if the expected value is
* too close to zero
*/
private static double chiCell(double freq, double expected,
boolean yates){
// Cell in empty row and column?
if (Utils.smOrEq(expected, 0)) {
return 0;
}
// Compute difference between observed and expected value
double diff = Math.abs(freq - expected);
if (yates) {
// Apply Yates' correction if wanted
diff -= 0.5;
// The difference should never be negative
if (diff < 0) {
diff = 0;
}
}
// Return chi-value for the cell
return (diff * diff / expected);
}
/**
* Returns the revision string.
*
* @return the revision
*/
public String getRevision() {
return RevisionUtils.extract("$Revision: 10057 $");
}
/**
* Main method for testing this class.
*/
public static void main(String[] ops) {
double[] firstRow = {10, 5, 20};
double[] secondRow = {2, 10, 6};
double[] thirdRow = {5, 10, 10};
double[][] matrix = new double[3][0];
matrix[0] = firstRow; matrix[1] = secondRow; matrix[2] = thirdRow;
for (int i = 0; i < matrix.length; i++) {
for (int j = 0; j < matrix[i].length; j++) {
System.out.print(matrix[i][j] + " ");
}
System.out.println();
}
System.out.println("Chi-squared probability: " +
ContingencyTables.chiSquared(matrix, false));
System.out.println("Chi-squared value: " +
ContingencyTables.chiVal(matrix, false));
System.out.println("Cochran's criterion fullfilled: " +
ContingencyTables.cochransCriterion(matrix));
System.out.println("Cramer's V: " +
ContingencyTables.CramersV(matrix));
System.out.println("Entropy of first row: " +
ContingencyTables.entropy(firstRow));
System.out.println("Entropy conditioned on columns: " +
ContingencyTables.entropyConditionedOnColumns(matrix));
System.out.println("Entropy conditioned on rows: " +
ContingencyTables.entropyConditionedOnRows(matrix));
System.out.println("Entropy conditioned on rows (with Laplace): " +
ContingencyTables.entropyConditionedOnRows(matrix, matrix, 3));
System.out.println("Entropy of rows: " +
ContingencyTables.entropyOverRows(matrix));
System.out.println("Entropy of columns: " +
ContingencyTables.entropyOverColumns(matrix));
System.out.println("Gain ratio: " +
ContingencyTables.gainRatio(matrix));
System.out.println("Negative log2 of multiple hypergeometric probability: " +
ContingencyTables.log2MultipleHypergeometric(matrix));
System.out.println("Symmetrical uncertainty: " +
ContingencyTables.symmetricalUncertainty(matrix));
System.out.println("Tau value: " +
ContingencyTables.tauVal(matrix));
double[][] newMatrix = new double[3][3];
newMatrix[0][0] = 1; newMatrix[0][1] = 0; newMatrix[0][2] = 1;
newMatrix[1][0] = 0; newMatrix[1][1] = 0; newMatrix[1][2] = 0;
newMatrix[2][0] = 1; newMatrix[2][1] = 0; newMatrix[2][2] = 1;
System.out.println("Matrix with empty row and column: ");
for (int i = 0; i < newMatrix.length; i++) {
for (int j = 0; j < newMatrix[i].length; j++) {
System.out.print(newMatrix[i][j] + " ");
}
System.out.println();
}
System.out.println("Reduced matrix: ");
newMatrix = ContingencyTables.reduceMatrix(newMatrix);
for (int i = 0; i < newMatrix.length; i++) {
for (int j = 0; j < newMatrix[i].length; j++) {
System.out.print(newMatrix[i][j] + " ");
}
System.out.println();
}
}
}
