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Open Source Chemistry Library
/*
* Copyright (c) 1997 - 2016
* Actelion Pharmaceuticals Ltd.
* Gewerbestrasse 16
* CH-4123 Allschwil, Switzerland
*
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice, this
* list of conditions and the following disclaimer.
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
* 3. Neither the name of the the copyright holder nor the
* names of its contributors may be used to endorse or promote products
* derived from this software without specific prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
* ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
* DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
* ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
package com.actelion.research.calc.classification;
import com.actelion.research.util.Formatter;
import java.io.Serializable;
import java.util.List;
/**
* PrecisionAndRecall
* @author Modest von Korff
* @version 1.0
* Jun 18, 2015 MvK Start implementation
*/
public class PrecisionAndRecall implements Serializable {
public static final String ATTR_TP = "TP";
public static final String ATTR_TN = "TN";
public static final String ATTR_FP = "FP";
public static final String ATTR_FN = "FN";
public int truePositive=0;
public int trueNegative=0;
public int falsePositive=0;
public int falseNegative=0;
/**
* @param truePositive
* @param trueNegative
* @param falsePositive
* @param falseNegative
*/
public PrecisionAndRecall(int truePositive, int trueNegative,
int falsePositive, int falseNegative) {
super();
this.truePositive = truePositive;
this.trueNegative = trueNegative;
this.falsePositive = falsePositive;
this.falseNegative = falseNegative;
}
/**
*
*/
public PrecisionAndRecall() {
}
public void add(PrecisionAndRecall p){
this.truePositive+=p.truePositive;
this.trueNegative+=p.trueNegative;
this.falsePositive+=p.falsePositive;
this.falseNegative+=p.falseNegative;
}
public void parse2PrecisionAndRecall(String sVal){
if(PrecisionAndRecall.ATTR_TP.equals(sVal)) {
truePositive++;
} else if(PrecisionAndRecall.ATTR_TN.equals(sVal)) {
trueNegative++;
} else if(PrecisionAndRecall.ATTR_FP.equals(sVal)) {
falsePositive++;
} else if(PrecisionAndRecall.ATTR_FN.equals(sVal)) {
falseNegative++;
} else {
throw new RuntimeException("Parsing error for '" + sVal + "'.");
}
}
/**
* @return the truePositive
*/
public int getTruePositive() {
return truePositive;
}
/**
* @param truePositive the truePositive to set
*/
public void setTruePositive(int truePositive) {
this.truePositive = truePositive;
}
/**
* @return the trueNegative
*/
public int getTrueNegative() {
return trueNegative;
}
/**
* @param trueNegative the trueNegative to set
*/
public void setTrueNegative(int trueNegative) {
this.trueNegative = trueNegative;
}
/**
* @return the falsePositive
*/
public int getFalsePositive() {
return falsePositive;
}
/**
* @param falsePositive the falsePositive to set
*/
public void setFalsePositive(int falsePositive) {
this.falsePositive = falsePositive;
}
/**
* @return the falseNegative
*/
public int getFalseNegative() {
return falseNegative;
}
/**
* @param falseNegative the falseNegative to set
*/
public void setFalseNegative(int falseNegative) {
this.falseNegative = falseNegative;
}
public int getSum(){
return trueNegative+truePositive+falsePositive+falseNegative;
}
public double calculatePrecision(){
int tp_fp = truePositive+falsePositive;
if(tp_fp==0){
return 0;
}
return truePositive/(double)(truePositive+falsePositive);
}
public double calculateRecall(){
int tp_fn = truePositive+falseNegative;
if(tp_fn==0){
return 0;
}
return truePositive/(double)(truePositive+falseNegative);
}
public double calculateAccuracy(){
double acc = (truePositive+trueNegative)/(double)getSum();
return acc;
}
/**
* F1 score
* @return
*/
public double calculateHarmonicMean(){
double p = calculatePrecision();
double r = calculateRecall();
if((p+r)==0){
return 0;
}
double f1 = 2.0 * (p*r/(p+r));
return f1;
}
public double calculateCohensKappa(){
double all = getSum();
double pYes = ((truePositive+falseNegative)/all) * ((truePositive+falsePositive)/all);
double pNo = ((falsePositive+trueNegative)/all) * ((falseNegative+trueNegative)/all);
double pe = pYes+pNo;
double po = calculateAccuracy();
double k = (po-pe)/(1.0-pe);
return k;
}
/* (non-Javadoc)
* @see java.lang.Object#toString()
*/
@Override
public String toString() {
StringBuilder sb = new StringBuilder();
sb.append("Accuracy " + Formatter.format3(calculateAccuracy()));
sb.append(", precision " + Formatter.format3(calculatePrecision()));
sb.append(", recall " + Formatter.format3(calculateRecall()));
sb.append(", F1 "+ Formatter.format3(calculateHarmonicMean()));
sb.append(", Cohens' kappa " + Formatter.format3(calculateCohensKappa()));
sb.append("\n");
sb.append("True positive " + truePositive);
sb.append("\n");
sb.append("True negative " + trueNegative);
sb.append("\n");
sb.append("False positive " + falsePositive);
sb.append("\n");
sb.append("False negative " + falseNegative);
return sb.toString();
}
public static double getHarmonicMean(List li){
double sum=0;
for (PrecisionAndRecall precisionAndRecall : li) {
sum += precisionAndRecall.calculateHarmonicMean();
}
return sum / li.size();
}
public static void main(String[] args) {
PrecisionAndRecall pr = new PrecisionAndRecall();
pr.truePositive=20;
pr.trueNegative=15;
pr.falseNegative=5;
pr.falsePositive=10;
System.out.println("Cohen's kappa: " + pr.calculateCohensKappa());
}
}