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[DL-Learner SVN] SF.net SVN: dl-learner:[4267] trunk
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From: <lor...@us...> - 2014-05-09 18:13:07
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Revision: 4267
http://sourceforge.net/p/dl-learner/code/4267
Author: lorenz_b
Date: 2014-05-09 18:13:04 +0000 (Fri, 09 May 2014)
Log Message:
-----------
Modified CV script.
Modified Paths:
--------------
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL2Disjunctive.java
trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QueryTreeHeuristic.java
trunk/components-core/src/main/java/org/dllearner/core/owl/DoubleMinMaxRange.java
trunk/scripts/src/main/java/org/dllearner/scripts/NestedCrossValidation.java
trunk/scripts/src/main/java/org/dllearner/scripts/evaluation/QTLEvaluation.java
trunk/test/qtl/breasttissue/train1.conf
trunk/test/qtl/carcinogenesis/train.conf
trunk/test/qtl/mutagenesis/train1.conf
trunk/test/qtl/parkinsons/train.conf
trunk/test/qtl/suramin/train.conf
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL2Disjunctive.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL2Disjunctive.java 2014-05-08 18:19:32 UTC (rev 4266)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QTL2Disjunctive.java 2014-05-09 18:13:04 UTC (rev 4267)
@@ -102,19 +102,18 @@
@ConfigOption(name = "noisePercentage", defaultValue="0.0", description="the (approximated) percentage of noise within the examples")
private double noisePercentage = 0.0;
@ConfigOption(defaultValue = "10", name = "maxExecutionTimeInSeconds", description = "maximum execution of the algorithm in seconds")
- private int maxExecutionTimeInSeconds = -1;
+ private int maxExecutionTimeInSeconds = 60;
private double coverageWeight = 0.8;
private double specifityWeight = 0.1;
- private double coverageBeta = 0.5;
private double minCoveredPosExamplesFraction = 0.2;
// maximum execution time to compute a part of the solution
private double maxTreeComputationTimeInSeconds = 10;
// how important not to cover negatives
- private double posWeight = 2;
+ private double beta = 1;
// minimum score a query tree must have to be part of the solution
- private double minimumTreeScore = 0.2;
+ private double minimumTreeScore = 0.3;
//If yes, then the algorithm tries to cover all positive examples. Note that while this improves accuracy on the testing set,
//it may lead to overfitting
private boolean tryFullCoverage;
@@ -161,10 +160,10 @@
lggGenerator = new LGGGeneratorImpl<String>();
- if(heuristic == null){
+// if(heuristic == null){
heuristic = new QueryTreeHeuristic();
- heuristic.setPosExamplesWeight(posWeight);
- }
+ heuristic.setPosExamplesWeight(beta);
+// }
logger.info("Initializing...");
treeCache = new QueryTreeCache(model);
@@ -222,7 +221,8 @@
String setup = "Setup:";
setup += "\n#Pos. examples:" + currentPosExamples.size();
setup += "\n#Neg. examples:" + currentNegExamples.size();
- setup += "\nPos. weight(beta):" + posWeight;
+ setup += "Heuristic:" + heuristic.getHeuristicType().name();
+ setup += "\nbeta=" + beta;
logger.info(setup);
logger.info("Running...");
startTime = System.currentTimeMillis();
@@ -236,7 +236,7 @@
logger.info("#Remaining neg. examples:" + currentNegExampleTrees.size());
//compute a (partial) solution
- computeNextPartialSolution();
+ computeBestPartialSolution();
//pick best (partial) solution computed so far
EvaluatedQueryTree<String> bestPartialSolution = currentPartialSolutions.first();
@@ -279,29 +279,31 @@
long endTime = System.currentTimeMillis();
logger.info("Finished in " + (endTime-startTime) + "ms.");
- logger.info("Combined solution:\n" + OWLAPIConverter.getOWLAPIDescription(currentBestSolution.getDescription()));
+ logger.info("Combined solution:" + OWLAPIConverter.getOWLAPIDescription(currentBestSolution.getDescription()).toString().replace("\n", ""));
logger.info(currentBestSolution.getScore());
}
- private void computeNextPartialSolution(){
+ private void computeBestPartialSolution(){
logger.info("Computing best partial solution...");
bestCurrentScore = Double.NEGATIVE_INFINITY;
partialSolutionStartTime = System.currentTimeMillis();
initTodoList(currentPosExampleTrees, currentNegExampleTrees);
EvaluatedQueryTree<String> currentElement;
+ QueryTree<String> currentTree;
while(!partialSolutionTerminationCriteriaSatisfied()){
logger.trace("TODO list size: " + todoList.size());
//pick best element from todo list
currentElement = todoList.poll();
+ currentTree = currentElement.getTree();
//generate the LGG between the chosen tree and each uncovered positive example
- for (QueryTree<String> example : currentElement.getFalseNegatives()) {
- QueryTree<String> tree = currentElement.getTree();
-
+ Iterator<QueryTree<String>> it = currentElement.getFalseNegatives().iterator();
+ while (it.hasNext() && !isPartialSolutionTimeExpired() && !isTimeExpired()) {
+ QueryTree<String> uncoveredTree = it.next();
//compute the LGG
lggMon.start();
- QueryTree<String> lgg = lggGenerator.getLGG(tree, example);
+ QueryTree<String> lgg = lggGenerator.getLGG(currentTree, uncoveredTree);
lggMon.stop();
//evaluate the LGG
@@ -312,8 +314,8 @@
if(score >= bestCurrentScore){
//add to todo list, if not already contained in todo list or solution list
todo(solution);
- if(solution.getScore() > bestCurrentScore){
- logger.info("Got better solution:" + solution.getTreeScore());
+ if(score > bestCurrentScore){
+ logger.info("\tGot better solution:" + solution.getTreeScore());
}
bestCurrentScore = solution.getScore();
} else if(mas < bestCurrentScore){
@@ -330,7 +332,7 @@
logger.info("...finished in " + (endTime-partialSolutionStartTime) + "ms.");
EvaluatedDescription bestPartialSolution = currentPartialSolutions.first().asEvaluatedDescription();
- logger.info("Best partial solution:\n" + OWLAPIConverter.getOWLAPIDescription(bestPartialSolution.getDescription()) + "\n(" + bestPartialSolution.getScore() + ")");
+ logger.info("Best partial solution: " + OWLAPIConverter.getOWLAPIDescription(bestPartialSolution.getDescription()).toString().replace("\n", "") + "\n(" + bestPartialSolution.getScore() + ")");
logger.trace("LGG time: " + lggMon.getTotal() + "ms");
logger.trace("Avg. LGG time: " + lggMon.getAvg() + "ms");
@@ -361,7 +363,7 @@
? 0
: coveredPositiveExamples / (double)(coveredPositiveExamples + coveredNegativeExampleTrees.size());
- double coverageScore = Heuristics.getFScore(recall, precision, coverageBeta);
+ double coverageScore = Heuristics.getFScore(recall, precision, beta);
//2. get a score for the specifity of the query, i.e. how many edges/nodes = precision oriented
int nrOfSpecificNodes = 0;
@@ -400,8 +402,6 @@
private EvaluatedDescription buildCombinedSolution(){
if(partialSolutions.size() == 1){
EvaluatedDescription combinedSolution = partialSolutions.get(0).asEvaluatedDescription();
- double accuracy = lp.getAccuracy(combinedSolution.getDescription());
- System.out.println(accuracy);
return combinedSolution;
}
List<Description> disjuncts = new ArrayList<Description>();
@@ -423,16 +423,13 @@
Set<Individual> posNotCovered = Sets.difference(lp.getPositiveExamples(), posCovered);
Set<Individual> negNotCovered = Sets.difference(lp.getNegativeExamples(), negCovered);
- double accuracy = lp.getAccuracy(unionDescription);
- System.out.println(accuracy);
-
//compute the coverage
double recall = posCovered.size() / (double)lp.getPositiveExamples().size();
double precision = (posCovered.size() + negCovered.size() == 0)
? 0
: posCovered.size() / (double)(posCovered.size() + negCovered.size());
- double coverageScore = Heuristics.getFScore(recall, precision, coverageBeta);
+ double coverageScore = Heuristics.getFScore(recall, precision, beta);
// ScoreTwoValued score = new ScoreTwoValued(posCovered, posNotCovered, negCovered, negNotCovered);
// score.setAccuracy(coverageScore);
@@ -442,6 +439,7 @@
}
private void reset(){
+ currentBestSolution = null;
partialSolutions = new ArrayList<EvaluatedQueryTree<String>>();
stop = false;
@@ -672,17 +670,18 @@
}
/**
- * @param coverageBeta the coverageBeta to set
+ * Default value is 1. Lower values force importance of covering positive examples.
+ * @param beta the beta to set
*/
- public void setCoverageBeta(double coverageBeta) {
- this.coverageBeta = coverageBeta;
+ public void setBeta(double beta) {
+ this.beta = beta;
}
/**
- * @param posWeight the posWeight to set
+ * @param maxTreeComputationTimeInSeconds the maxTreeComputationTimeInSeconds to set
*/
- public void setPosWeight(double posWeight) {
- this.posWeight = posWeight;
+ public void setMaxTreeComputationTimeInSeconds(double maxTreeComputationTimeInSeconds) {
+ this.maxTreeComputationTimeInSeconds = maxTreeComputationTimeInSeconds;
}
/* (non-Javadoc)
Modified: trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QueryTreeHeuristic.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QueryTreeHeuristic.java 2014-05-08 18:19:32 UTC (rev 4266)
+++ trunk/components-core/src/main/java/org/dllearner/algorithms/qtl/QueryTreeHeuristic.java 2014-05-09 18:13:04 UTC (rev 4267)
@@ -26,13 +26,6 @@
private HeuristicType heuristicType = HeuristicType.PRED_ACC;
- // F score beta value
- private double coverageBeta = 1;
-
- private double coverageWeight = 0.8;
-
- private double specifityWeight = 0.1;
-
private double posExamplesWeight = 1;
// syntactic comparison as final comparison criterion
@@ -63,7 +56,7 @@
case FMEASURE :
score = Heuristics.getFScore(tp/(tp+fn), tp/(tp+fp), posExamplesWeight);break;
case PRED_ACC :
- score = (tp + posExamplesWeight * tn) / ((tp + fn) + posExamplesWeight * (tn + fp));break;
+ score = (1/posExamplesWeight * tp + tn) / (1/posExamplesWeight * (tp + fn) + (tn + fp));break;
case ENTROPY :{
double total = tp + fn;
double pp = tp / total;
@@ -154,6 +147,13 @@
}
/**
+ * @return the heuristicType
+ */
+ public HeuristicType getHeuristicType() {
+ return heuristicType;
+ }
+
+ /**
* @param posExamplesWeight the posExamplesWeight to set
*/
public void setPosExamplesWeight(double posExamplesWeight) {
Modified: trunk/components-core/src/main/java/org/dllearner/core/owl/DoubleMinMaxRange.java
===================================================================
--- trunk/components-core/src/main/java/org/dllearner/core/owl/DoubleMinMaxRange.java 2014-05-08 18:19:32 UTC (rev 4266)
+++ trunk/components-core/src/main/java/org/dllearner/core/owl/DoubleMinMaxRange.java 2014-05-09 18:13:04 UTC (rev 4267)
@@ -65,11 +65,11 @@
* @see org.dllearner.core.owl.KBElement#toString(java.lang.String, java.util.Map)
*/
public String toString(String baseURI, Map<String, String> prefixes) {
- return " [>= " + minValue + " <= " + maxValue + "]";
+ return " double[>= " + minValue + " <= " + maxValue + "]";
}
public String toKBSyntaxString(String baseURI, Map<String, String> prefixes) {
- return " [>= " + minValue + " <= " + maxValue + "]";
+ return " double[>= " + minValue + " <= " + maxValue + "]";
}
public void accept(KBElementVisitor visitor) {
@@ -81,7 +81,7 @@
*/
@Override
public String toManchesterSyntaxString(String baseURI, Map<String, String> prefixes) {
- return " [>= " + minValue + " <= " + maxValue + "]";
+ return " double[>= " + minValue + " <= " + maxValue + "]";
}
/* (non-Javadoc)
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/NestedCrossValidation.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/NestedCrossValidation.java 2014-05-08 18:19:32 UTC (rev 4266)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/NestedCrossValidation.java 2014-05-09 18:13:04 UTC (rev 4267)
@@ -22,7 +22,6 @@
import static java.util.Arrays.asList;
import java.io.File;
-import java.io.FileNotFoundException;
import java.io.IOException;
import java.lang.reflect.InvocationTargetException;
import java.text.DecimalFormat;
@@ -43,15 +42,17 @@
import org.apache.commons.beanutils.PropertyUtils;
import org.apache.log4j.ConsoleAppender;
import org.apache.log4j.FileAppender;
+import org.apache.log4j.Layout;
import org.apache.log4j.Level;
import org.apache.log4j.Logger;
+import org.apache.log4j.PatternLayout;
+import org.apache.log4j.Priority;
import org.apache.log4j.SimpleLayout;
import org.dllearner.cli.CLI;
import org.dllearner.core.AbstractCELA;
import org.dllearner.core.AbstractLearningProblem;
import org.dllearner.core.AbstractReasonerComponent;
import org.dllearner.core.ComponentInitException;
-import org.dllearner.core.ComponentManager;
import org.dllearner.core.owl.Description;
import org.dllearner.core.owl.Individual;
import org.dllearner.learningproblems.PosNegLP;
@@ -101,7 +102,10 @@
*/
public class NestedCrossValidation {
- private File outputFile = new File("log/nested-cv.log");
+
+ private static final Logger logger = Logger.getLogger(NestedCrossValidation.class.getName());
+
+ private static File logFile = new File("log/nested-cv.log");
DecimalFormat df = new DecimalFormat();
// overall statistics
@@ -126,7 +130,7 @@
OptionParser parser = new OptionParser();
parser.acceptsAll(asList("h", "?", "help"), "Show help.");
- parser.acceptsAll(asList("c", "conf"), "The comma separated list of conffiles to be used.").withRequiredArg().describedAs("file1, file2, ...");
+ parser.acceptsAll(asList("c", "conf"), "The comma separated list of config files to be used.").withRequiredArg().describedAs("file1, file2, ...");
parser.acceptsAll(asList( "v", "verbose"), "Be more verbose.");
parser.acceptsAll(asList( "o", "outerfolds"), "Number of outer folds.").withRequiredArg().ofType(Integer.class).describedAs("#folds");
parser.acceptsAll(asList( "i", "innerfolds"), "Number of inner folds.").withRequiredArg().ofType(Integer.class).describedAs("#folds");
@@ -167,13 +171,18 @@
// create logger (a simple logger which outputs
// its messages to the console)
- SimpleLayout layout = new SimpleLayout();
+ Layout layout = new PatternLayout("%m%n");
ConsoleAppender consoleAppender = new ConsoleAppender(layout);
Logger logger = Logger.getRootLogger();
logger.removeAllAppenders();
logger.addAppender(consoleAppender);
- logger.setLevel(Level.WARN);
+ logger.setLevel(Level.ERROR);
Logger.getLogger("org.dllearner.algorithms").setLevel(Level.INFO);
+ Logger.getLogger("org.dllearner.scripts").setLevel(Level.INFO);
+
+ FileAppender fileAppender = new FileAppender(layout, logFile.getPath(), false);
+ logger.addAppender(fileAppender);
+ fileAppender.setThreshold(Level.INFO);
// logger.addAppender(new FileAppender(layout, "nested-cv.log", false));
// disable OWL API info output
java.util.logging.Logger.getLogger("").setLevel(java.util.logging.Level.WARNING);
@@ -188,15 +197,6 @@
}
}
-
- private void print(String s){
- try {
- Files.append(s + "\n", outputFile , Charsets.UTF_8);
- } catch (IOException e) {
- e.printStackTrace();
- }
- System.out.println(s);
- }
public NestedCrossValidation(File confFile, int outerFolds, int innerFolds, String parameter, double startValue, double endValue, double stepsize, boolean verbose) throws ComponentInitException, ParseException, org.dllearner.confparser.ParseException, IOException {
this(Lists.newArrayList(confFile), outerFolds, innerFolds, parameter, startValue, endValue, stepsize, verbose);
@@ -205,37 +205,38 @@
public NestedCrossValidation(List<File> confFiles, int outerFolds, int innerFolds, String parameter, double startValue, double endValue, double stepsize, boolean verbose) throws ComponentInitException, ParseException, org.dllearner.confparser.ParseException, IOException {
for (File confFile : confFiles) {
- print(confFile.getPath());
+ logger.info("++++++++++++++++++++++++++++++++++++++++++++++");
+ logger.info(confFile.getPath());
+ logger.info("++++++++++++++++++++++++++++++++++++++++++++++");
validate(confFile, outerFolds, innerFolds, parameter, startValue, endValue, stepsize, verbose);
}
- print("********************************************");
- print("********************************************");
- print("********************************************");
+ logger.info("############################################");
+ logger.info("############################################");
// decide for the best parameter
- print(" Summary over parameter values:");
+ logger.info(" Overall summary over parameter values:");
double bestPara = startValue;
double bestValue = Double.NEGATIVE_INFINITY;
for (Entry<Double, Stat> entry : globalParaStats.entrySet()) {
double para = entry.getKey();
Stat stat = entry.getValue();
- print(" value " + para + ": " + stat.prettyPrint("%"));
+ logger.info(" value " + para + ": " + stat.prettyPrint("%"));
if (stat.getMean() > bestValue) {
bestPara = para;
bestValue = stat.getMean();
}
}
- print(" selected " + bestPara + " as best parameter value (criterion value " + df.format(bestValue) + "%)");
+ logger.info(" selected " + bestPara + " as best parameter value (criterion value " + df.format(bestValue) + "%)");
// overall statistics
- print("*******************");
- print("* Overall Results *");
- print("*******************");
- print("accuracy: " + globalAcc.prettyPrint("%"));
- print("F measure: " + globalF.prettyPrint("%"));
- print("precision: " + globalPrecision.prettyPrint("%"));
- print("recall: " + globalRecall.prettyPrint("%"));
+ logger.info("*******************");
+ logger.info("* Overall Results *");
+ logger.info("*******************");
+ logger.info("accuracy: " + globalAcc.prettyPrint("%"));
+ logger.info("F measure: " + globalF.prettyPrint("%"));
+ logger.info("precision: " + globalPrecision.prettyPrint("%"));
+ logger.info("recall: " + globalRecall.prettyPrint("%"));
}
@@ -255,6 +256,7 @@
Collections.shuffle(negExamples, new Random(2));
AbstractReasonerComponent rc = start.getReasonerComponent();
+ rc.init();
String baseURI = rc.getBaseURI();
List<TrainTestList> posLists = getFolds(posExamples, outerFolds);
@@ -268,7 +270,7 @@
for(int currOuterFold=0; currOuterFold<outerFolds; currOuterFold++) {
- print("Outer fold " + currOuterFold);
+ logger.info("Outer fold " + currOuterFold);
TrainTestList posList = posLists.get(currOuterFold);
TrainTestList negList = negLists.get(currOuterFold);
@@ -277,7 +279,7 @@
for(double currParaValue=startValue; currParaValue<=endValue; currParaValue+=stepsize) {
- print(" Parameter value " + currParaValue + ":");
+ logger.info(" Parameter value " + currParaValue + ":");
// split train folds again (computation of inner folds for each parameter
// value is redundant, but not a big problem)
List<Individual> trainPosList = posList.getTrainList();
@@ -291,7 +293,7 @@
for(int currInnerFold=0; currInnerFold<innerFolds; currInnerFold++) {
- print(" Inner fold " + currInnerFold + ":");
+ logger.info(" Inner fold " + currInnerFold + ":");
// get positive & negative examples for training run
Set<Individual> posEx = new TreeSet<Individual>(innerPosLists.get(currInnerFold).getTrainList());
Set<Individual> negEx = new TreeSet<Individual>(innerNegLists.get(currInnerFold).getTrainList());
@@ -320,13 +322,12 @@
TreeSet<Individual> posTest = new TreeSet<Individual>(innerPosLists.get(currInnerFold).getTestList());
TreeSet<Individual> negTest = new TreeSet<Individual>(innerNegLists.get(currInnerFold).getTestList());
- AbstractReasonerComponent rs = start.getReasonerComponent();
// true positive
- Set<Individual> posCorrect = rs.hasType(concept, posTest);
+ Set<Individual> posCorrect = rc.hasType(concept, posTest);
// false negative
Set<Individual> posError = Helper.difference(posTest, posCorrect);
// false positive
- Set<Individual> negError = rs.hasType(concept, negTest);
+ Set<Individual> negError = rc.hasType(concept, negTest);
// true negative
Set<Individual> negCorrect = Helper.difference(negTest, negError);
@@ -340,19 +341,16 @@
paraCriterionStat.addNumber(accuracy);
- print(" hypothesis: " + concept.toManchesterSyntaxString(baseURI, null));
- print(" accuracy: " + df.format(accuracy) + "%");
- print(" precision: " + df.format(precision) + "%");
- print(" recall: " + df.format(recall) + "%");
- print(" F measure: " + df.format(fmeasure) + "%");
+ logger.info(" hypothesis: " + concept.toManchesterSyntaxString(baseURI, null));
+ logger.info(" accuracy: " + df.format(accuracy) + "%");
+ logger.info(" precision: " + df.format(precision) + "%");
+ logger.info(" recall: " + df.format(recall) + "%");
+ logger.info(" F measure: " + df.format(fmeasure) + "%");
if(verbose) {
- print(" false positives (neg. examples classified as pos.): " + formatIndividualSet(posError, baseURI));
- print(" false negatives (pos. examples classified as neg.): " + formatIndividualSet(negError, baseURI));
+ logger.info(" false positives (neg. examples classified as pos.): " + formatIndividualSet(posError, baseURI));
+ logger.info(" false negatives (pos. examples classified as neg.): " + formatIndividualSet(negError, baseURI));
}
-
- // free memory
- rs.releaseKB();
}
paraStats.put(currParaValue, paraCriterionStat);
@@ -365,20 +363,20 @@
}
// decide for the best parameter
- print(" Summary over parameter values:");
+ logger.info(" Summary over parameter values:");
double bestPara = startValue;
double bestValue = Double.NEGATIVE_INFINITY;
for(Entry<Double,Stat> entry : paraStats.entrySet()) {
double para = entry.getKey();
Stat stat = entry.getValue();
- print(" value " + para + ": " + stat.prettyPrint("%"));
+ logger.info(" value " + para + ": " + stat.prettyPrint("%"));
if(stat.getMean() > bestValue) {
bestPara = para;
bestValue = stat.getMean();
}
}
- print(" selected " + bestPara + " as best parameter value (criterion value " + df.format(bestValue) + "%)");
- print(" Learn on Outer fold:");
+ logger.info(" selected " + bestPara + " as best parameter value (criterion value " + df.format(bestValue) + "%)");
+ logger.info(" Learn on Outer fold:");
// start a learning process with this parameter and evaluate it on the outer fold
start = new CLI(confFile);
@@ -418,15 +416,15 @@
double recall = 100 * (double) posCorrect.size() / (posCorrect.size() + posError.size());
double fmeasure = 2 * (precision * recall) / (precision + recall);
- print(" hypothesis: " + concept.toManchesterSyntaxString(baseURI, null));
- print(" accuracy: " + df.format(accuracy) + "%");
- print(" precision: " + df.format(precision) + "%");
- print(" recall: " + df.format(recall) + "%");
- print(" F measure: " + df.format(fmeasure) + "%");
+ logger.info(" hypothesis: " + concept.toManchesterSyntaxString(baseURI, null));
+ logger.info(" accuracy: " + df.format(accuracy) + "%");
+ logger.info(" precision: " + df.format(precision) + "%");
+ logger.info(" recall: " + df.format(recall) + "%");
+ logger.info(" F measure: " + df.format(fmeasure) + "%");
if(verbose) {
- print(" false positives (neg. examples classified as pos.): " + formatIndividualSet(posError, baseURI));
- print(" false negatives (pos. examples classified as neg.): " + formatIndividualSet(negError, baseURI));
+ logger.info(" false positives (neg. examples classified as pos.): " + formatIndividualSet(posError, baseURI));
+ logger.info(" false negatives (pos. examples classified as neg.): " + formatIndividualSet(negError, baseURI));
}
// update overall statistics
@@ -445,13 +443,13 @@
globalRecall.add(recallOverall);
// overall statistics
- print("*******************");
- print("* Overall Results *");
- print("*******************");
- print("accuracy: " + accOverall.prettyPrint("%"));
- print("F measure: " + fOverall.prettyPrint("%"));
- print("precision: " + precisionOverall.prettyPrint("%"));
- print("recall: " + recallOverall.prettyPrint("%"));
+ logger.info("*******************");
+ logger.info("* Overall Results *");
+ logger.info("*******************");
+ logger.info("accuracy: " + accOverall.prettyPrint("%"));
+ logger.info("F measure: " + fOverall.prettyPrint("%"));
+ logger.info("precision: " + precisionOverall.prettyPrint("%"));
+ logger.info("recall: " + recallOverall.prettyPrint("%"));
}
// convenience methods, which takes a list of examples and divides them in
Modified: trunk/scripts/src/main/java/org/dllearner/scripts/evaluation/QTLEvaluation.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/scripts/evaluation/QTLEvaluation.java 2014-05-08 18:19:32 UTC (rev 4266)
+++ trunk/scripts/src/main/java/org/dllearner/scripts/evaluation/QTLEvaluation.java 2014-05-09 18:13:04 UTC (rev 4267)
@@ -6,43 +6,39 @@
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
+import java.io.IOException;
import java.util.ArrayList;
import java.util.Collections;
import java.util.LinkedList;
import java.util.List;
import java.util.Random;
+import java.util.Set;
import java.util.SortedSet;
import java.util.TreeSet;
-import org.dllearner.algorithms.qtl.QTL2;
import org.dllearner.algorithms.qtl.QTL2Disjunctive;
import org.dllearner.algorithms.qtl.QueryTreeFactory;
import org.dllearner.algorithms.qtl.datastructures.QueryTree;
import org.dllearner.algorithms.qtl.datastructures.impl.QueryTreeImpl;
import org.dllearner.algorithms.qtl.impl.QueryTreeFactoryImpl;
+import org.dllearner.cli.CLI;
import org.dllearner.cli.CrossValidation;
-import org.dllearner.cli.SPARQLCrossValidation;
+import org.dllearner.core.AbstractLearningProblem;
import org.dllearner.core.ComponentInitException;
import org.dllearner.core.LearningProblemUnsupportedException;
import org.dllearner.core.owl.Individual;
-import org.dllearner.kb.LocalModelBasedSparqlEndpointKS;
import org.dllearner.kb.OWLAPIOntology;
import org.dllearner.learningproblems.PosNegLP;
import org.dllearner.learningproblems.PosNegLPStandard;
import org.dllearner.reasoning.FastInstanceChecker;
-import org.dllearner.reasoning.SPARQLReasoner;
+import org.dllearner.scripts.NestedCrossValidation;
import org.semanticweb.owlapi.apibinding.OWLManager;
-import org.semanticweb.owlapi.model.IRI;
-import org.semanticweb.owlapi.model.OWLDataFactory;
import org.semanticweb.owlapi.model.OWLOntology;
-import org.semanticweb.owlapi.model.OWLOntologyChange;
import org.semanticweb.owlapi.model.OWLOntologyCreationException;
import org.semanticweb.owlapi.model.OWLOntologyManager;
-import org.semanticweb.owlapi.reasoner.OWLReasoner;
-import org.semanticweb.owlapi.reasoner.OWLReasonerFactory;
-import com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory;
import com.google.common.collect.Lists;
+import com.google.common.collect.Sets;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
@@ -52,363 +48,20 @@
*/
public class QTLEvaluation {
- int nrOfFolds = 10;
+ int nrOfFolds = 3;
private int nrOfPosExamples = 300;
private int nrOfNegExamples = 300;
- List<String> posExamples = Lists.newArrayList(
- "http://dl-learner.org/carcinogenesis#d1",
- "http://dl-learner.org/carcinogenesis#d10",
- "http://dl-learner.org/carcinogenesis#d101",
- "http://dl-learner.org/carcinogenesis#d102",
- "http://dl-learner.org/carcinogenesis#d103",
- "http://dl-learner.org/carcinogenesis#d106",
- "http://dl-learner.org/carcinogenesis#d107",
- "http://dl-learner.org/carcinogenesis#d108",
- "http://dl-learner.org/carcinogenesis#d11",
- "http://dl-learner.org/carcinogenesis#d12",
- "http://dl-learner.org/carcinogenesis#d13",
- "http://dl-learner.org/carcinogenesis#d134",
- "http://dl-learner.org/carcinogenesis#d135",
- "http://dl-learner.org/carcinogenesis#d136",
- "http://dl-learner.org/carcinogenesis#d138",
- "http://dl-learner.org/carcinogenesis#d140",
- "http://dl-learner.org/carcinogenesis#d141",
- "http://dl-learner.org/carcinogenesis#d144",
- "http://dl-learner.org/carcinogenesis#d145",
- "http://dl-learner.org/carcinogenesis#d146",
- "http://dl-learner.org/carcinogenesis#d147",
- "http://dl-learner.org/carcinogenesis#d15",
- "http://dl-learner.org/carcinogenesis#d17",
- "http://dl-learner.org/carcinogenesis#d19",
- "http://dl-learner.org/carcinogenesis#d192",
- "http://dl-learner.org/carcinogenesis#d193",
- "http://dl-learner.org/carcinogenesis#d195",
- "http://dl-learner.org/carcinogenesis#d196",
- "http://dl-learner.org/carcinogenesis#d197",
- "http://dl-learner.org/carcinogenesis#d198",
- "http://dl-learner.org/carcinogenesis#d199",
- "http://dl-learner.org/carcinogenesis#d2",
- "http://dl-learner.org/carcinogenesis#d20",
- "http://dl-learner.org/carcinogenesis#d200",
- "http://dl-learner.org/carcinogenesis#d201",
- "http://dl-learner.org/carcinogenesis#d202",
- "http://dl-learner.org/carcinogenesis#d203",
- "http://dl-learner.org/carcinogenesis#d204",
- "http://dl-learner.org/carcinogenesis#d205",
- "http://dl-learner.org/carcinogenesis#d21",
- "http://dl-learner.org/carcinogenesis#d22",
- "http://dl-learner.org/carcinogenesis#d226",
- "http://dl-learner.org/carcinogenesis#d227",
- "http://dl-learner.org/carcinogenesis#d228",
- "http://dl-learner.org/carcinogenesis#d229",
- "http://dl-learner.org/carcinogenesis#d231",
- "http://dl-learner.org/carcinogenesis#d232",
- "http://dl-learner.org/carcinogenesis#d234",
- "http://dl-learner.org/carcinogenesis#d236",
- "http://dl-learner.org/carcinogenesis#d239",
- "http://dl-learner.org/carcinogenesis#d23_2",
- "http://dl-learner.org/carcinogenesis#d242",
- "http://dl-learner.org/carcinogenesis#d245",
- "http://dl-learner.org/carcinogenesis#d247",
- "http://dl-learner.org/carcinogenesis#d249",
- "http://dl-learner.org/carcinogenesis#d25",
- "http://dl-learner.org/carcinogenesis#d252",
- "http://dl-learner.org/carcinogenesis#d253",
- "http://dl-learner.org/carcinogenesis#d254",
- "http://dl-learner.org/carcinogenesis#d255",
- "http://dl-learner.org/carcinogenesis#d26",
- "http://dl-learner.org/carcinogenesis#d272",
- "http://dl-learner.org/carcinogenesis#d275",
- "http://dl-learner.org/carcinogenesis#d277",
- "http://dl-learner.org/carcinogenesis#d279",
- "http://dl-learner.org/carcinogenesis#d28",
- "http://dl-learner.org/carcinogenesis#d281",
- "http://dl-learner.org/carcinogenesis#d283",
- "http://dl-learner.org/carcinogenesis#d284",
- "http://dl-learner.org/carcinogenesis#d288",
- "http://dl-learner.org/carcinogenesis#d29",
- "http://dl-learner.org/carcinogenesis#d290",
- "http://dl-learner.org/carcinogenesis#d291",
- "http://dl-learner.org/carcinogenesis#d292",
- "http://dl-learner.org/carcinogenesis#d30",
- "http://dl-learner.org/carcinogenesis#d31",
- "http://dl-learner.org/carcinogenesis#d32",
- "http://dl-learner.org/carcinogenesis#d33",
- "http://dl-learner.org/carcinogenesis#d34",
- "http://dl-learner.org/carcinogenesis#d35",
- "http://dl-learner.org/carcinogenesis#d36",
- "http://dl-learner.org/carcinogenesis#d37",
- "http://dl-learner.org/carcinogenesis#d38",
- "http://dl-learner.org/carcinogenesis#d42",
- "http://dl-learner.org/carcinogenesis#d43",
- "http://dl-learner.org/carcinogenesis#d44",
- "http://dl-learner.org/carcinogenesis#d45",
- "http://dl-learner.org/carcinogenesis#d46",
- "http://dl-learner.org/carcinogenesis#d47",
- "http://dl-learner.org/carcinogenesis#d48",
- "http://dl-learner.org/carcinogenesis#d49",
- "http://dl-learner.org/carcinogenesis#d5",
- "http://dl-learner.org/carcinogenesis#d51",
- "http://dl-learner.org/carcinogenesis#d52",
- "http://dl-learner.org/carcinogenesis#d53",
- "http://dl-learner.org/carcinogenesis#d55",
- "http://dl-learner.org/carcinogenesis#d58",
- "http://dl-learner.org/carcinogenesis#d6",
- "http://dl-learner.org/carcinogenesis#d7",
- "http://dl-learner.org/carcinogenesis#d84",
- "http://dl-learner.org/carcinogenesis#d85_2",
- "http://dl-learner.org/carcinogenesis#d86",
- "http://dl-learner.org/carcinogenesis#d87",
- "http://dl-learner.org/carcinogenesis#d88",
- "http://dl-learner.org/carcinogenesis#d89",
- "http://dl-learner.org/carcinogenesis#d9",
- "http://dl-learner.org/carcinogenesis#d91",
- "http://dl-learner.org/carcinogenesis#d92",
- "http://dl-learner.org/carcinogenesis#d93",
- "http://dl-learner.org/carcinogenesis#d95",
- "http://dl-learner.org/carcinogenesis#d96",
- "http://dl-learner.org/carcinogenesis#d98",
- "http://dl-learner.org/carcinogenesis#d99",
- "http://dl-learner.org/carcinogenesis#d100",
- "http://dl-learner.org/carcinogenesis#d104",
- "http://dl-learner.org/carcinogenesis#d105",
- "http://dl-learner.org/carcinogenesis#d109",
- "http://dl-learner.org/carcinogenesis#d137",
- "http://dl-learner.org/carcinogenesis#d139",
- "http://dl-learner.org/carcinogenesis#d14",
- "http://dl-learner.org/carcinogenesis#d142",
- "http://dl-learner.org/carcinogenesis#d143",
- "http://dl-learner.org/carcinogenesis#d148",
- "http://dl-learner.org/carcinogenesis#d16",
- "http://dl-learner.org/carcinogenesis#d18",
- "http://dl-learner.org/carcinogenesis#d191",
- "http://dl-learner.org/carcinogenesis#d206",
- "http://dl-learner.org/carcinogenesis#d230",
- "http://dl-learner.org/carcinogenesis#d233",
- "http://dl-learner.org/carcinogenesis#d235",
- "http://dl-learner.org/carcinogenesis#d237",
- "http://dl-learner.org/carcinogenesis#d238",
- "http://dl-learner.org/carcinogenesis#d23_1",
- "http://dl-learner.org/carcinogenesis#d24",
- "http://dl-learner.org/carcinogenesis#d240",
- "http://dl-learner.org/carcinogenesis#d241",
- "http://dl-learner.org/carcinogenesis#d243",
- "http://dl-learner.org/carcinogenesis#d244",
- "http://dl-learner.org/carcinogenesis#d246",
- "http://dl-learner.org/carcinogenesis#d248",
- "http://dl-learner.org/carcinogenesis#d250",
- "http://dl-learner.org/carcinogenesis#d251",
- "http://dl-learner.org/carcinogenesis#d27",
- "http://dl-learner.org/carcinogenesis#d273",
- "http://dl-learner.org/carcinogenesis#d274",
- "http://dl-learner.org/carcinogenesis#d278",
- "http://dl-learner.org/carcinogenesis#d286",
- "http://dl-learner.org/carcinogenesis#d289",
- "http://dl-learner.org/carcinogenesis#d3",
- "http://dl-learner.org/carcinogenesis#d39",
- "http://dl-learner.org/carcinogenesis#d4",
- "http://dl-learner.org/carcinogenesis#d40",
- "http://dl-learner.org/carcinogenesis#d41",
- "http://dl-learner.org/carcinogenesis#d50",
- "http://dl-learner.org/carcinogenesis#d54",
- "http://dl-learner.org/carcinogenesis#d56",
- "http://dl-learner.org/carcinogenesis#d57",
- "http://dl-learner.org/carcinogenesis#d8",
- "http://dl-learner.org/carcinogenesis#d85_1",
- "http://dl-learner.org/carcinogenesis#d90",
- "http://dl-learner.org/carcinogenesis#d94",
- "http://dl-learner.org/carcinogenesis#d97",
- "http://dl-learner.org/carcinogenesis#d296",
- "http://dl-learner.org/carcinogenesis#d305",
- "http://dl-learner.org/carcinogenesis#d306",
- "http://dl-learner.org/carcinogenesis#d307",
- "http://dl-learner.org/carcinogenesis#d308",
- "http://dl-learner.org/carcinogenesis#d311",
- "http://dl-learner.org/carcinogenesis#d314",
- "http://dl-learner.org/carcinogenesis#d315",
- "http://dl-learner.org/carcinogenesis#d316",
- "http://dl-learner.org/carcinogenesis#d320",
- "http://dl-learner.org/carcinogenesis#d322",
- "http://dl-learner.org/carcinogenesis#d323",
- "http://dl-learner.org/carcinogenesis#d325",
- "http://dl-learner.org/carcinogenesis#d329",
- "http://dl-learner.org/carcinogenesis#d330",
- "http://dl-learner.org/carcinogenesis#d331",
- "http://dl-learner.org/carcinogenesis#d332",
- "http://dl-learner.org/carcinogenesis#d333",
- "http://dl-learner.org/carcinogenesis#d336",
- "http://dl-learner.org/carcinogenesis#d337"
- );
+ CLI cli = new CLI(new File("../test/qtl/carcinogenesis/train.conf"));
- List<String> negExamples = Lists.newArrayList(
- "http://dl-learner.org/carcinogenesis#d110",
- "http://dl-learner.org/carcinogenesis#d111",
- "http://dl-learner.org/carcinogenesis#d114",
- "http://dl-learner.org/carcinogenesis#d116",
- "http://dl-learner.org/carcinogenesis#d117",
- "http://dl-learner.org/carcinogenesis#d119",
- "http://dl-learner.org/carcinogenesis#d121",
- "http://dl-learner.org/carcinogenesis#d123",
- "http://dl-learner.org/carcinogenesis#d124",
- "http://dl-learner.org/carcinogenesis#d125",
- "http://dl-learner.org/carcinogenesis#d127",
- "http://dl-learner.org/carcinogenesis#d128",
- "http://dl-learner.org/carcinogenesis#d130",
- "http://dl-learner.org/carcinogenesis#d133",
- "http://dl-learner.org/carcinogenesis#d150",
- "http://dl-learner.org/carcinogenesis#d151",
- "http://dl-learner.org/carcinogenesis#d154",
- "http://dl-learner.org/carcinogenesis#d155",
- "http://dl-learner.org/carcinogenesis#d156",
- "http://dl-learner.org/carcinogenesis#d159",
- "http://dl-learner.org/carcinogenesis#d160",
- "http://dl-learner.org/carcinogenesis#d161",
- "http://dl-learner.org/carcinogenesis#d162",
- "http://dl-learner.org/carcinogenesis#d163",
- "http://dl-learner.org/carcinogenesis#d164",
- "http://dl-learner.org/carcinogenesis#d165",
- "http://dl-learner.org/carcinogenesis#d166",
- "http://dl-learner.org/carcinogenesis#d169",
- "http://dl-learner.org/carcinogenesis#d170",
- "http://dl-learner.org/carcinogenesis#d171",
- "http://dl-learner.org/carcinogenesis#d172",
- "http://dl-learner.org/carcinogenesis#d173",
- "http://dl-learner.org/carcinogenesis#d174",
- "http://dl-learner.org/carcinogenesis#d178",
- "http://dl-learner.org/carcinogenesis#d179",
- "http://dl-learner.org/carcinogenesis#d180",
- "http://dl-learner.org/carcinogenesis#d181",
- "http://dl-learner.org/carcinogenesis#d183",
- "http://dl-learner.org/carcinogenesis#d184",
- "http://dl-learner.org/carcinogenesis#d185",
- "http://dl-learner.org/carcinogenesis#d186",
- "http://dl-learner.org/carcinogenesis#d188",
- "http://dl-learner.org/carcinogenesis#d190",
- "http://dl-learner.org/carcinogenesis#d194",
- "http://dl-learner.org/carcinogenesis#d207",
- "http://dl-learner.org/carcinogenesis#d208_1",
- "http://dl-learner.org/carcinogenesis#d209",
- "http://dl-learner.org/carcinogenesis#d210",
- "http://dl-learner.org/carcinogenesis#d211",
- "http://dl-learner.org/carcinogenesis#d212",
- "http://dl-learner.org/carcinogenesis#d213",
- "http://dl-learner.org/carcinogenesis#d214",
- "http://dl-learner.org/carcinogenesis#d215",
- "http://dl-learner.org/carcinogenesis#d217",
- "http://dl-learner.org/carcinogenesis#d218",
- "http://dl-learner.org/carcinogenesis#d219",
- "http://dl-learner.org/carcinogenesis#d220",
- "http://dl-learner.org/carcinogenesis#d224",
- "http://dl-learner.org/carcinogenesis#d256",
- "http://dl-learner.org/carcinogenesis#d257",
- "http://dl-learner.org/carcinogenesis#d258",
- "http://dl-learner.org/carcinogenesis#d261",
- "http://dl-learner.org/carcinogenesis#d262",
- "http://dl-learner.org/carcinogenesis#d263",
- "http://dl-learner.org/carcinogenesis#d264",
- "http://dl-learner.org/carcinogenesis#d265",
- "http://dl-learner.org/carcinogenesis#d266",
- "http://dl-learner.org/carcinogenesis#d267",
- "http://dl-learner.org/carcinogenesis#d269",
- "http://dl-learner.org/carcinogenesis#d271",
- "http://dl-learner.org/carcinogenesis#d276",
- "http://dl-learner.org/carcinogenesis#d280",
- "http://dl-learner.org/carcinogenesis#d285",
- "http://dl-learner.org/carcinogenesis#d287",
- "http://dl-learner.org/carcinogenesis#d293",
- "http://dl-learner.org/carcinogenesis#d294",
- "http://dl-learner.org/carcinogenesis#d59",
- "http://dl-learner.org/carcinogenesis#d60",
- "http://dl-learner.org/carcinogenesis#d61",
- "http://dl-learner.org/carcinogenesis#d63",
- "http://dl-learner.org/carcinogenesis#d64",
- "http://dl-learner.org/carcinogenesis#d65",
- "http://dl-learner.org/carcinogenesis#d69",
- "http://dl-learner.org/carcinogenesis#d70",
- "http://dl-learner.org/carcinogenesis#d71",
- "http://dl-learner.org/carcinogenesis#d72",
- "http://dl-learner.org/carcinogenesis#d73",
- "http://dl-learner.org/carcinogenesis#d74",
- "http://dl-learner.org/carcinogenesis#d75",
- "http://dl-learner.org/carcinogenesis#d76",
- "http://dl-learner.org/carcinogenesis#d77",
- "http://dl-learner.org/carcinogenesis#d78",
- "http://dl-learner.org/carcinogenesis#d79",
- "http://dl-learner.org/carcinogenesis#d80",
- "http://dl-learner.org/carcinogenesis#d81",
- "http://dl-learner.org/carcinogenesis#d82",
- "http://dl-learner.org/carcinogenesis#d112",
- "http://dl-learner.org/carcinogenesis#d113",
- "http://dl-learner.org/carcinogenesis#d115",
- "http://dl-learner.org/carcinogenesis#d118",
- "http://dl-learner.org/carcinogenesis#d120",
- "http://dl-learner.org/carcinogenesis#d122",
- "http://dl-learner.org/carcinogenesis#d126",
- "http://dl-learner.org/carcinogenesis#d129",
- "http://dl-learner.org/carcinogenesis#d131",
- "http://dl-learner.org/carcinogenesis#d132",
- "http://dl-learner.org/carcinogenesis#d149",
- "http://dl-learner.org/carcinogenesis#d152",
- "http://dl-learner.org/carcinogenesis#d153",
- "http://dl-learner.org/carcinogenesis#d157",
- "http://dl-learner.org/carcinogenesis#d158",
- "http://dl-learner.org/carcinogenesis#d167",
- "http://dl-learner.org/carcinogenesis#d168",
- "http://dl-learner.org/carcinogenesis#d175",
- "http://dl-learner.org/carcinogenesis#d176",
- "http://dl-learner.org/carcinogenesis#d177",
- "http://dl-learner.org/carcinogenesis#d182",
- "http://dl-learner.org/carcinogenesis#d187",
- "http://dl-learner.org/carcinogenesis#d189",
- "http://dl-learner.org/carcinogenesis#d208_2",
- "http://dl-learner.org/carcinogenesis#d216",
- "http://dl-learner.org/carcinogenesis#d221",
- "http://dl-learner.org/carcinogenesis#d222",
- "http://dl-learner.org/carcinogenesis#d223",
- "http://dl-learner.org/carcinogenesis#d225",
- "http://dl-learner.org/carcinogenesis#d259",
- "http://dl-learner.org/carcinogenesis#d260",
- "http://dl-learner.org/carcinogenesis#d268",
- "http://dl-learner.org/carcinogenesis#d270",
- "http://dl-learner.org/carcinogenesis#d282",
- "http://dl-learner.org/carcinogenesis#d295",
- "http://dl-learner.org/carcinogenesis#d62",
- "http://dl-learner.org/carcinogenesis#d66",
- "http://dl-learner.org/carcinogenesis#d67",
- "http://dl-learner.org/carcinogenesis#d68",
- "http://dl-learner.org/carcinogenesis#d83",
- "http://dl-learner.org/carcinogenesis#d297",
- "http://dl-learner.org/carcinogenesis#d298",
- "http://dl-learner.org/carcinogenesis#d299",
- "http://dl-learner.org/carcinogenesis#d300",
- "http://dl-learner.org/carcinogenesis#d302",
- "http://dl-learner.org/carcinogenesis#d303",
- "http://dl-learner.org/carcinogenesis#d304",
- "http://dl-learner.org/carcinogenesis#d309",
- "http://dl-learner.org/carcinogenesis#d312",
- "http://dl-learner.org/carcinogenesis#d313",
- "http://dl-learner.org/carcinogenesis#d317",
- "http://dl-learner.org/carcinogenesis#d318",
- "http://dl-learner.org/carcinogenesis#d319",
- "http://dl-learner.org/carcinogenesis#d324",
- "http://dl-learner.org/carcinogenesis#d326",
- "http://dl-learner.org/carcinogenesis#d327",
- "http://dl-learner.org/carcinogenesis#d328",
- "http://dl-learner.org/carcinogenesis#d334",
- "http://dl-learner.org/carcinogenesis#d335"
- );
-
private Model model;
private OWLOntology ontology;
private QueryTreeFactory<String> queryTreeFactory;
- private List<QueryTree<String>> posExampleTrees;
- private List<QueryTree<String>> negExampleTrees;
private PosNegLP lp;
- public QTLEvaluation() throws ComponentInitException {
+ public QTLEvaluation() throws ComponentInitException, IOException {
queryTreeFactory = new QueryTreeFactoryImpl();
queryTreeFactory.setMaxDepth(3);
@@ -434,59 +87,29 @@
}
}
- private void loadExamples() throws ComponentInitException{
+ private void loadExamples() throws ComponentInitException, IOException{
- Collections.shuffle(posExamples, new Random(1));
- Collections.shuffle(negExamples, new Random(2));
+ cli.init();
+ lp = (PosNegLP) cli.getLearningProblem();
+
+ // get examples and shuffle them
+ List<Individual> posExamples = new LinkedList<Individual>(((PosNegLP)lp).getPositiveExamples());
+ Collections.shuffle(posExamples, new Random(1));
+ List<Individual> negExamples = new LinkedList<Individual>(((PosNegLP)lp).getNegativeExamples());
+ Collections.shuffle(negExamples, new Random(2));
posExamples = posExamples.subList(0, Math.min(posExamples.size(), nrOfPosExamples));
negExamples = negExamples.subList(0, Math.min(negExamples.size(), nrOfNegExamples));
-// posExamples.clear();
-// String string = "http://dl-learner.org/carcinogenesis#d101, http://dl-learner.org/carcinogenesis#d103, http://dl-learner.org/carcinogenesis#d107, http://dl-learner.org/carcinogenesis#d108, http://dl-learner.org/carcinogenesis#d135, http://dl-learner.org/carcinogenesis#d139, http://dl-learner.org/carcinogenesis#d14, http://dl-learner.org/carcinogenesis#d141, http://dl-learner.org/carcinogenesis#d143, http://dl-learner.org/carcinogenesis#d147, http://dl-learner.org/carcinogenesis#d17, http://dl-learner.org/carcinogenesis#d19, http://dl-learner.org/carcinogenesis#d193, http://dl-learner.org/carcinogenesis#d198, http://dl-learner.org/carcinogenesis#d228, http://dl-learner.org/carcinogenesis#d236, http://dl-learner.org/carcinogenesis#d242, http://dl-learner.org/carcinogenesis#d244, http://dl-learner.org/carcinogenesis#d273, http://dl-learner.org/carcinogenesis#d275, http://dl-learner.org/carcinogenesis#d28, http://dl-learner.org/carcinogenesis#d283, http://dl-learner.org/carcinogenesis#d286, http://dl-learner.org/carcinogenesis#d291, http://dl-learner.org/carcinogenesis#d292, http://dl-learner.org/carcinogenesis#d307, http://dl-learner.org/carcinogenesis#d31, http://dl-learner.org/carcinogenesis#d325, http://dl-learner.org/carcinogenesis#d33, http://dl-learner.org/carcinogenesis#d333, http://dl-learner.org/carcinogenesis#d34, http://dl-learner.org/carcinogenesis#d36, http://dl-learner.org/carcinogenesis#d38, http://dl-learner.org/carcinogenesis#d4, http://dl-learner.org/carcinogenesis#d40, http://dl-learner.org/carcinogenesis#d44, http://dl-learner.org/carcinogenesis#d51, http://dl-learner.org/carcinogenesis#d85_2, http://dl-learner.org/carcinogenesis#d98, http://dl-learner.org/carcinogenesis#d99";
-// String[] split = string.split(",");
-// for (String s : split) {
-// posExamples.add(s.trim());
-// }
-// negExamples.clear();
-// string = "http://dl-learner.org/carcinogenesis#d112, http://dl-learner.org/carcinogenesis#d116, http://dl-learner.org/carcinogenesis#d117, http://dl-learner.org/carcinogenesis#d119, http://dl-learner.org/carcinogenesis#d157, http://dl-learner.org/carcinogenesis#d160, http://dl-learner.org/carcinogenesis#d161, http://dl-learner.org/carcinogenesis#d162, http://dl-learner.org/carcinogenesis#d163, http://dl-learner.org/carcinogenesis#d167, http://dl-learner.org/carcinogenesis#d169, http://dl-learner.org/carcinogenesis#d175, http://dl-learner.org/carcinogenesis#d177, http://dl-learner.org/carcinogenesis#d184, http://dl-learner.org/carcinogenesis#d194, http://dl-learner.org/carcinogenesis#d208_2, http://dl-learner.org/carcinogenesis#d209, http://dl-learner.org/carcinogenesis#d217, http://dl-learner.org/carcinogenesis#d256, http://dl-learner.org/carcinogenesis#d257, http://dl-learner.org/carcinogenesis#d260, http://dl-learner.org/carcinogenesis#d271, http://dl-learner.org/carcinogenesis#d276, http://dl-learner.org/carcinogenesis#d282, http://dl-learner.org/carcinogenesis#d287, http://dl-learner.org/carcinogenesis#d294, http://dl-learner.org/carcinogenesis#d298, http://dl-learner.org/carcinogenesis#d300, http://dl-learner.org/carcinogenesis#d309, http://dl-learner.org/carcinogenesis#d319, http://dl-learner.org/carcinogenesis#d326, http://dl-learner.org/carcinogenesis#d328, http://dl-learner.org/carcinogenesis#d334, http://dl-learner.org/carcinogenesis#d60, http://dl-learner.org/carcinogenesis#d61, http://dl-learner.org/carcinogenesis#d66, http://dl-learner.org/carcinogenesis#d75, http://dl-learner.org/carcinogenesis#d79, http://dl-learner.org/carcinogenesis#d80, http://dl-learner.org/carcinogenesis#d83";
-// split = string.split(",");
-// for (String s : split) {
-// negExamples.add(s.trim());
-// }
+ Set<Individual> posSet = new TreeSet<Individual>(
+ NestedCrossValidation.getFolds(NestedCrossValidation.getFolds(posExamples, 3).get(0).getTrainList(), 3).get(0).getTrainList());
+ Set<Individual> negSet = new TreeSet<Individual>(
+ NestedCrossValidation.getFolds(NestedCrossValidation.getFolds(negExamples, 3).get(0).getTrainList(), 3).get(0).getTrainList());
- posExampleTrees = new ArrayList<QueryTree<String>>();
- for (String ex : posExamples) {
- QueryTreeImpl<String> tree = queryTreeFactory.getQueryTree(ex, model);
- posExampleTrees.add(tree);
- }
- negExampleTrees = new ArrayList<QueryTree<String>>();
- for (String ex : negExamples) {
- QueryTreeImpl<String> tree = queryTreeFactory.getQueryTree(ex, model);
- negExampleTrees.add(tree);
- }
- int cnt = 1;
- for(QueryTree<String> tree : posExampleTrees){
-// System.out.println("TREE " + cnt);
-// tree.dump();
-//
-// System.out.println("-----------------------------");
- cnt++;
-// System.out.println(((QueryTreeImpl<String>)tree).toQuery());
- }
-
- SortedSet<Individual> pos = new TreeSet<Individual>();
- for (String ex : posExamples) {
- pos.add(new Individual(ex));
- }
- SortedSet<Individual> neg = new TreeSet<Individual>();
- for (String ex : negExamples) {
- neg.add(new Individual(ex));
- }
- lp = new PosNegLPStandard();
- lp.setPositiveExamples(pos);
- lp.setNegativeExamples(neg);
+ this.lp = new PosNegLPStandard();
+ this.lp.setPositiveExamples(posSet);
+ this.lp.setNegativeExamples(negSet);
}
public void run(boolean multiThreaded) throws ComponentInitException, LearningProblemUnsupportedException{
@@ -496,13 +119,14 @@
lp.setReasoner(reasoner);
lp.init();
QTL2Disjunctive la = new QTL2Disjunctive(lp, reasoner);
-// la.init();
-// la.start();
+ la.setBeta(0.5);
+ la.init();
+ la.start();
CrossValidation.outputFile = new File("log/qtl-cv.log");
CrossValidation.writeToFile = true;
CrossValidation.multiThreaded = multiThreaded;
- CrossValidation cv = new CrossValidation(la, lp, reasoner, nrOfFolds, false);
+// CrossValidation cv = new CrossValidation(la, lp, reasoner, nrOfFolds, false);
long endTime = System.currentTimeMillis();
System.err.println((endTime - startTime) + "ms");
}
Modified: trunk/test/qtl/breasttissue/train1.conf
===================================================================
--- trunk/test/qtl/breasttissue/train1.conf 2014-05-08 18:19:32 UTC (rev 4266)
+++ trunk/test/qtl/breasttissue/train1.conf 2014-05-09 18:13:04 UTC (rev 4267)
@@ -8,6 +8,8 @@
// QTL configuration
alg.type = "qtl2dis"
+alg.maxExecutionTimeInSeconds = 60
+alg.maxTreeComputationTimeInSeconds = 10
// learning problem
lp.type = "posNegStandard"
Modified: trunk/test/qtl/carcinogenesis/train.conf
===================================================================
--- trunk/test/qtl/carcinogenesis/train.conf 2014-05-08 18:19:32 UTC (rev 4266)
+++ trunk/test/qtl/carcinogenesis/train.conf 2014-05-09 18:13:04 UTC (rev 4267)
@@ -8,6 +8,11 @@
reasoner.type = "fast instance checker"
reasoner.sources = { ks }
+// QTL configuration
+alg.type = "qtl2dis"
+alg.maxExecutionTimeInSeconds = 60
+alg.maxTreeComputationTimeInSeconds = 10
+
// learning problem
lp.type = "posNegStandard"
lp.positiveExamples = {
@@ -352,5 +357,3 @@
"kb:d335"
}
-// QTL configuration
-alg.type = "qtl2dis"
Modified: trunk/test/qtl/mutagenesis/train1.conf
===================================================================
--- trunk/test/qtl/mutagenesis/train1.conf 2014-05-08 18:19:32 UTC (rev 4266)
+++ trunk/test/qtl/mutagenesis/train1.conf 2014-05-09 18:13:04 UTC (rev 4267)
@@ -11,6 +11,8 @@
// QTL configuration
alg.type = "qtl2dis"
+alg.maxExecutionTimeInSeconds = 60
+alg.maxTreeComputationTimeInSeconds = 10
// learning problem
lp.type = "posNegStandard"
Modified: trunk/test/qtl/parkinsons/train.conf
===================================================================
--- trunk/test/qtl/parkinsons/train.conf 2014-05-08 18:19:32 UTC (rev 4266)
+++ trunk/test/qtl/parkinsons/train.conf 2014-05-09 18:13:04 UTC (rev 4267)
@@ -7,6 +7,8 @@
// QTL configuration
alg.type = "qtl2dis"
+alg.maxExecutionTimeInSeconds = 60
+alg.maxTreeComputationTimeInSeconds = 10
// learning problem
lp.type = "posNegStandard"
Modified: trunk/test/qtl/suramin/train.conf
===================================================================
--- trunk/test/qtl/suramin/train.conf 2014-05-08 18:19:32 UTC (rev 4266)
+++ trunk/test/qtl/suramin/train.conf 2014-05-09 18:13:04 UTC (rev 4267)
@@ -30,4 +30,6 @@
}
// QTL configuration
-alg.type = "qtl2dis"
\ No newline at end of file
+alg.type = "qtl2dis"
+alg.maxExecutionTimeInSeconds = 60
+alg.maxTreeComputationTimeInSeconds = 10
\ No newline at end of file
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