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[DL-Learner SVN] SF.net SVN: dl-learner:[2042] trunk/src/dl-learner/org/dllearner
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From: <ku...@us...> - 2010-02-16 01:08:48
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Revision: 2042
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=2042&view=rev
Author: kurzum
Date: 2010-02-16 00:17:05 +0000 (Tue, 16 Feb 2010)
Log Message:
-----------
almost finished DescriptionSubsumptionTree,
still a NullPointer somewhere...
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/scripts/tiger/TestIterativeLearning.java
trunk/src/dl-learner/org/dllearner/utilities/experiments/ExperimentCollector.java
trunk/src/dl-learner/org/dllearner/utilities/experiments/ExperimentConfig.java
trunk/src/dl-learner/org/dllearner/utilities/experiments/IteratedConfig.java
trunk/src/dl-learner/org/dllearner/utilities/experiments/Table.java
trunk/src/dl-learner/org/dllearner/utilities/experiments/TableRowColumn.java
Added Paths:
-----------
trunk/src/dl-learner/org/dllearner/utilities/datastructures/DescriptionSubsumptionTree.java
Modified: trunk/src/dl-learner/org/dllearner/scripts/tiger/TestIterativeLearning.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/tiger/TestIterativeLearning.java 2010-02-15 18:40:49 UTC (rev 2041)
+++ trunk/src/dl-learner/org/dllearner/scripts/tiger/TestIterativeLearning.java 2010-02-16 00:17:05 UTC (rev 2042)
@@ -47,8 +47,8 @@
import org.dllearner.utilities.experiments.ExperimentCollector;
import org.dllearner.utilities.experiments.IteratedConfig;
import org.dllearner.utilities.experiments.Jamon;
+import org.dllearner.utilities.experiments.Table;
-import com.jamonapi.MonKey;
import com.jamonapi.MonKeyImp;
import com.jamonapi.Monitor;
@@ -114,7 +114,7 @@
}
folds = 2;
- iterations = 1;
+ iterations = 2;
long n = System.currentTimeMillis();
passiveNoZU();
// passiveWithZu();
@@ -144,25 +144,27 @@
// ExMakerCrossFolds.printFolds(folds);
List<IteratedConfig> configs = getConfigs();
for (IteratedConfig experimentConfig : configs) {
- logger.warn("next: passiveNoZU."+experimentConfig.label);
+ experimentConfig.init(mks);
+ logger.warn("next: passiveNoZU."+experimentConfig.experimentName);
int i = 1;
for (Examples examples : folds) {
-
- for(MonKeyImp m : mks){
- experimentConfig.init(m);
- }
-
logger.warn("beginning fold: "+(i++));
conductExperiment( examples, experimentConfig);
+
}
+ Table t = new Table();
+ t.addTableRowColumn(experimentConfig.getTableRows());
+ t.sortByLabel();
+ JamonMonitorLogger.writeHTMLReport("/tmp/tiger.html");
+ System.out.println(t.getGnuPlotAsColumn());
if (true) {
System.exit(0);
}
- eColl_passiveNoZU.addExperimentConfig(experimentConfig);
+// eColl_passiveNoZU.addExperimentConfig(experimentConfig);
logger.info(experimentConfig);
- eColl_passiveNoZU.write(iterations);
+// eColl_passiveNoZU.write(iterations);
}
@@ -192,7 +194,7 @@
List<IteratedConfig> configs = getConfigs();
for (IteratedConfig experimentConfig : configs) {
- logger.warn("next: passiveWithZu."+experimentConfig.label);
+ logger.warn("next: passiveWithZu."+experimentConfig.experimentName);
int i=1;
for (Examples examples : runs) {
logger.warn("beginning run: "+(i++));
@@ -259,6 +261,17 @@
for(int i = 0 ; config.stopCondition(i, precision, recall, fmeasure, lastConcept) ;i++ ) {
Monitor iterationTime = JamonMonitorLogger.getTimeMonitor(TestIterativeLearning.class, "iterationTime").start();
Monitor literationTime = config.start(logIterationTime, i);
+// try {
+// Thread.sleep(2000);
+// } catch (InterruptedException e) {
+// // TODO Auto-generated catch block
+// e.printStackTrace();
+// }
+// literationTime.stop();
+// System.out.println(literationTime);
+// if (true) {
+// System.exit(0);
+// }
/*LEARNING*/
Monitor lLearningTime = config.start(logLearningTime, i);
Added: trunk/src/dl-learner/org/dllearner/utilities/datastructures/DescriptionSubsumptionTree.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/datastructures/DescriptionSubsumptionTree.java (rev 0)
+++ trunk/src/dl-learner/org/dllearner/utilities/datastructures/DescriptionSubsumptionTree.java 2010-02-16 00:17:05 UTC (rev 2042)
@@ -0,0 +1,127 @@
+package org.dllearner.utilities.datastructures;
+
+import java.util.Collection;
+import java.util.SortedSet;
+import java.util.TreeSet;
+
+import org.dllearner.core.EvaluatedDescription;
+import org.dllearner.core.ReasonerComponent;
+import org.dllearner.core.owl.Description;
+import org.dllearner.learningproblems.EvaluatedDescriptionPosNeg;
+
+public class DescriptionSubsumptionTree {
+ public class Node {
+ public Node parent;
+ public double accuracy;
+
+ //by length?
+ public SortedSet<EvaluatedDescription> equivalents = new TreeSet<EvaluatedDescription>();
+
+ //by accuracy
+ public SortedSet<Node> subClasses = new TreeSet<Node>();
+
+ public Node(EvaluatedDescription ed){
+ if(ed!=null) {equivalents.add(ed);};
+ accuracy = ed.getAccuracy();
+ }
+
+ //happens only if n is sure to be a subclass
+ public void insert(Node n){
+ if(subClasses.isEmpty()){
+ subClasses.add(n);
+ }else{
+ SortedSet<Node> toBeRemoved = new TreeSet<Node>();
+ for (Node sub : subClasses) {
+ if(rc.isSuperClassOf(getDesc(), sub.getDesc())){
+ //subClass of subclass
+ sub.insert(n);
+ n.parent = sub;
+ }else if(rc.isEquivalentClass(getDesc(), sub.getDesc())){
+ //EquivalentClass of subclass
+ sub.equivalents.add(n.getEvalDesc());
+ }else{
+ //superclass of subclass
+ n.parent = this;
+ n.subClasses.add(sub);
+ toBeRemoved.add(sub);
+ }
+ }
+ //needs to be done outside, concurrent exception
+ for (Node node : toBeRemoved) {
+ subClasses.remove(node);
+ }
+ }
+ }
+
+
+ public boolean isRoot(){
+ return (parent == null);
+ }
+
+ public EvaluatedDescription getEvalDesc(){
+ return equivalents.first();
+ }
+ public Description getDesc(){
+ return equivalents.first().getDescription();
+ }
+ @Override
+ public String toString(){
+ return getEvalDesc().toString();
+ }
+
+ public String _toString(String tab){
+ String ret = (isRoot())?"Thing\n":"";
+
+ if(subClasses.isEmpty()){
+ ret+= this+"\n";
+ }
+ tab+=" ";
+ for (Node sub : subClasses) {
+ ret += sub.toString()+"\n";
+ }
+ return ret;
+ }
+
+
+ }
+ private Node root;
+
+ private final ReasonerComponent rc;
+
+ public DescriptionSubsumptionTree(ReasonerComponent rc){
+ this.rc = rc;
+ this.root = new Node(null);
+ this.root.parent = null;
+ }
+
+ public static void main(String[] args) {
+
+ }
+
+ public void insert(Collection<EvaluatedDescription> evaluatedDescriptions){
+ for (EvaluatedDescription evaluatedDescription : evaluatedDescriptions) {
+ System.out.println("Adding: "+evaluatedDescription.toString());
+ Node n = new Node(evaluatedDescription);
+ this.root.insert(n);
+ }
+ }
+ public void insertEdPosNeg(Collection<EvaluatedDescriptionPosNeg> evaluatedDescriptions, int limit){
+ int i=0;
+ for (EvaluatedDescription evaluatedDescription : evaluatedDescriptions) {
+
+ System.out.println("Adding: "+evaluatedDescription.toString());
+ Node n = new Node(evaluatedDescription);
+ this.root.insert(n);
+ if(i>limit){break;}
+ i++;
+ }
+ }
+
+ @Override
+ public String toString(){
+ return root._toString("");
+ }
+
+
+
+}
Modified: trunk/src/dl-learner/org/dllearner/utilities/experiments/ExperimentCollector.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/experiments/ExperimentCollector.java 2010-02-15 18:40:49 UTC (rev 2041)
+++ trunk/src/dl-learner/org/dllearner/utilities/experiments/ExperimentCollector.java 2010-02-16 00:17:05 UTC (rev 2042)
@@ -20,6 +20,8 @@
public static DecimalFormat dfhuman = new DecimalFormat("##.##%");
public static DecimalFormat dfRuntime = new DecimalFormat("####.");
List<IteratedConfig> experimentConfigs = new ArrayList<IteratedConfig>();
+
+
public ExperimentCollector(String filePrefix) {
details = dir + filePrefix + "_" + "details";
@@ -42,7 +44,7 @@
String headerGNU = "\t";
String headerLatex = "\t&\t";
for (IteratedConfig ec : experimentConfigs) {
- headerGNU += ec.label + "\t";
+ headerGNU += ec.experimentName + "\t";
Files.appendFile(new File(details), ec.toString());
}
for (int i = 0; i < iterations; i++) {
@@ -67,7 +69,7 @@
}
for (IteratedConfig ec : experimentConfigs) {
- String label = ec.label ;
+ String label = ec.experimentName ;
String learningTimeLatex = label+" learn"+ "\t&\t";
String totalTimeLatex = label+" total"+ "\t&\t";
String fmeasureLatex = label+ "\t&\t";
@@ -83,7 +85,7 @@
}
for (IteratedConfig ec : experimentConfigs) {
- String label = ec.label;
+ String label = ec.experimentName;
String learningTimeHuman = label+" learn" + "\t&\t";
String totalTimeHuman = label+" total" + "\t&\t";
String fmeasureHuman = label + "\t&\t";
Modified: trunk/src/dl-learner/org/dllearner/utilities/experiments/ExperimentConfig.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/experiments/ExperimentConfig.java 2010-02-15 18:40:49 UTC (rev 2041)
+++ trunk/src/dl-learner/org/dllearner/utilities/experiments/ExperimentConfig.java 2010-02-16 00:17:05 UTC (rev 2042)
@@ -15,8 +15,8 @@
public class ExperimentConfig {
private static final Logger logger = Logger.getLogger(ExperimentConfig.class);
- public final String label;
- public final int iterations;
+ public final String experimentName;
+ public final int sizeOfResultVector;
protected List<MonitorComposite> mcs = new ArrayList<MonitorComposite>();
protected Map<String,MonitorComposite> mcsMap = new HashMap<String, MonitorComposite>();
@@ -25,47 +25,89 @@
public ExperimentConfig(String label){
this(label,1);
}
- public ExperimentConfig(String label, int iterations){
- this.label = label;
- this.iterations = iterations;
+ public ExperimentConfig(String experimentName, int sizeOfResultVector){
+ this.experimentName = experimentName;
+ this.sizeOfResultVector = sizeOfResultVector;
}
@Override
public String toString(){
- return this.label+" with "+iterations+" iterations";
+ return this.experimentName+" with "+sizeOfResultVector+" iterations";
}
public List<TableRowColumn> getTableRows(){
List<TableRowColumn> l = new ArrayList<TableRowColumn>();
+ if(sizeOfResultVector == 1) {
+ Monitor[] monitors = new Monitor[mcs.size()];
+// TableRowColumn trc =
+ for (int i = 0; i < monitors.length; i++) {
+ monitors[i] = mcs.get(i).getMonitors()[0];
+ }
+ l.add(new TableRowColumn(monitors, experimentName, ""));
+
+ }else{
+ for(MonitorComposite mc :mcs){
+ l.add(new TableRowColumn(mc.getMonitors(), experimentName, getRev(mc)));
+ }
+ }
+
return l;
}
- public void init(MonKeyImp monkey){
- Monitor[] marr = new Monitor[iterations];
- for (int i = 0; i < iterations; i++) {
- marr[i] = MonitorFactory.getMonitor(mon(monkey, i));
+ private MonitorComposite get(MonKeyImp m){
+ return mcsMap.get(mon(m).getLabel());
+ }
+ private String getRev(MonitorComposite mc){
+ return mcsMapRev.get(mc);
+ }
+
+ private void put(MonKeyImp m ,MonitorComposite mc ){
+ mcsMap.put(mon(m).getLabel(), mc);
+ }
+ private void putRev(MonitorComposite mc , MonKeyImp m ){
+ mcsMapRev.put( mc, m.getLabel());
+ }
+
+ public void init(List<MonKeyImp> monkeys){
+ for (MonKeyImp monKeyImp : monkeys) {
+ init(monKeyImp);
}
+// JamonMonitorLogger.writeHTMLReport("/tmp/tiger.html");
+ }
+
+ public void init(MonKeyImp oldMonkey){
+ Monitor[] marr = new Monitor[sizeOfResultVector];
+ for (int i = 0; i < sizeOfResultVector; i++) {
+ MonKeyImp newMonKey = mon(oldMonkey, i);
+ if(newMonKey.getUnits().equals(Jamon.MS)){
+ marr[i] = MonitorFactory.getTimeMonitor(newMonKey);
+ }else{
+ marr[i] = MonitorFactory.getMonitor(newMonKey);
+ }
+ }
MonitorComposite m = new MonitorComposite(marr);
mcs.add(m);
- mcsMap.put( monkey.getLabel(),m);
- mcsMapRev.put(m, monkey.getLabel());
+ put( oldMonkey,m);
+ putRev(m, oldMonkey);
+
}
protected MonKeyImp mon(MonKeyImp monkey){
- return (monkey.getLabel().startsWith(label))?monkey:new MonKeyImp(label+monkey.getLabel(), monkey.getUnits());
+ MonKeyImp m = (monkey.getLabel().startsWith(experimentName))?monkey:new MonKeyImp(experimentName+"_"+monkey.getLabel(), monkey.getUnits());
+ return m;
}
- protected MonKeyImp mon(MonKeyImp monkey, int index){
+ protected MonKeyImp mon(MonKeyImp oldMonkey, int index){
//narrensicher
- MonKeyImp l = mon(monkey);
- return (iterations==1)?monkey:new MonKeyImp(l.getLabel()+"_"+index, l.getUnits()) ;
+ MonKeyImp newMonkey = mon(oldMonkey);
+ return new MonKeyImp(newMonkey.getLabel()+"_"+index, newMonkey.getUnits()) ;
}
public void add(MonKeyImp monkey, int index, double value){
try{
- mcsMap.get(monkey.getLabel()).getMonitors()[index].add(value);
+ get(monkey).getMonitors()[index].add(value);
}catch (Exception e) {
e.printStackTrace();
logger.error("index too big, max = "+index);
@@ -73,7 +115,7 @@
}
public Monitor start(MonKeyImp monkey, int index){
- return mcsMap.get(monkey.getLabel()).getMonitors()[index].start();
+ return get(monkey).getMonitors()[index].start();
}
// public static boolean higher(Monitor[] a, double current){
Modified: trunk/src/dl-learner/org/dllearner/utilities/experiments/IteratedConfig.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/experiments/IteratedConfig.java 2010-02-15 18:40:49 UTC (rev 2041)
+++ trunk/src/dl-learner/org/dllearner/utilities/experiments/IteratedConfig.java 2010-02-16 00:17:05 UTC (rev 2042)
@@ -43,7 +43,7 @@
// if(higher(iterationRecall, recall)){highestRecall=concept;}
// if(higher(iterationFmeasure, fmeasure)){highestFMeasure=concept;}
- boolean condIter = (iteration<this.iterations);
+ boolean condIter = (iteration<this.sizeOfResultVector);
boolean condPrec = fmeasure <=1.0d;
if(!condIter){
logger.info("iterations reached, stopping");
Modified: trunk/src/dl-learner/org/dllearner/utilities/experiments/Table.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/experiments/Table.java 2010-02-15 18:40:49 UTC (rev 2041)
+++ trunk/src/dl-learner/org/dllearner/utilities/experiments/Table.java 2010-02-16 00:17:05 UTC (rev 2042)
@@ -3,6 +3,8 @@
import java.util.ArrayList;
import java.util.List;
import java.util.Random;
+import java.util.SortedSet;
+import java.util.TreeSet;
import org.apache.log4j.Logger;
import org.dllearner.utilities.JamonMonitorLogger;
@@ -19,6 +21,11 @@
LATEX, GNUPLOT
};
+
+// private Map<String, TableRowColumn> m = new HashMap<String, TableRowColumn>();
+ private SortedSet<String> experimentNames = new TreeSet<String>();
+ private SortedSet<String> labels = new TreeSet<String>();
+
private List<TableRowColumn> tableRowColumns = new ArrayList<TableRowColumn>();
private int length;
@@ -43,8 +50,8 @@
}
// System.out.println("avg: " + m[a].getAvg());
}
- TableRowColumn trc = new TableRowColumn(m, "entry_" + i);
- trc.deleteAll();
+ TableRowColumn trc = new TableRowColumn(m, "Test","entry_" + i);
+// trc.deleteAll();
trc.useStdDev=false;
t.addTableRowColumn(trc);
}
@@ -58,11 +65,19 @@
JamonMonitorLogger.writeHTMLReport("log/tiger.html");
}
+ public void addTableRowColumn(List<TableRowColumn> trcs) {
+ for (TableRowColumn tableRowColumn : trcs) {
+ labels.add(tableRowColumn.getLabel());
+ experimentNames.add(tableRowColumn.getExperimentName());
+ addTableRowColumn(tableRowColumn);
+ }
+ }
+
public void addTableRowColumn(TableRowColumn trc) {
try{
trc.toLatexRow();
}catch (NullPointerException e) {
- logger.error("TableRowColumn was not initialized, ignoring it, label: "+trc.label);
+ logger.error("TableRowColumn was not initialized, ignoring it: "+trc);
e.printStackTrace();
}
@@ -73,7 +88,7 @@
if (trc.size() != length) {
logger.error("Added TableRowColumn does not match previous set length (" + length + ") but has size "
- + trc.size() + "), \nignoring it, label: "+trc.label+", value: " + trc.toLatexRow());
+ + trc.size() + "), \nignoring it: "+trc);
}
@@ -116,13 +131,13 @@
boolean first = (i==1);
switch (f) {
case LATEX:
- rows[0] += (first?trc.label+TableRowColumn.latexSep:"");
+ rows[0] += (first?trc.getHeader()+TableRowColumn.latexSep:"");
rows[i] += (firstColumn&&addNumbersInFront?i+TableRowColumn.latexSep:"");
rows[i] += trc.getLatexEntry(i-1)
+ ((last) ? TableRowColumn.latexSep : TableRowColumn.latexSep);
break;
case GNUPLOT:
- rows[0] += (first?"#"+trc.label+"\t":"");
+ rows[0] += (first?"#"+trc.getHeader()+"\t":"");
rows[i] += (firstColumn&&addNumbersInFront?i+"\t":"");
rows[i] += trc.getGnuPlotEntry(i-1) + ((last) ?"" : "\t");
break;
@@ -152,5 +167,45 @@
}
return (replaceCommaByPoints)?ret.replace(",","."):ret;
}
+
+ public void sortByExperimentName(){
+ _sortByLabel();
+ _sortByExperimentName();
+
+ }
+ public void sortByLabel(){
+ _sortByExperimentName();
+ _sortByLabel();
+ }
+
+ private void _sortByLabel(){
+ List<String> l = new ArrayList<String>(labels);
+ List<TableRowColumn> newTrc = new ArrayList<TableRowColumn>();
+
+ for (String s : l) {
+ for (TableRowColumn trc : tableRowColumns) {
+ if(trc.getLabel().equals(s)){
+ newTrc.add(trc);
+ }
+ }
+ }
+ tableRowColumns = newTrc;
+ }
+ private void _sortByExperimentName(){
+ List<String> l = new ArrayList<String>(experimentNames);
+ List<TableRowColumn> newTrc = new ArrayList<TableRowColumn>();
+
+ for (String s : l) {
+ for (TableRowColumn trc : tableRowColumns) {
+ if(trc.getExperimentName().equals(s)){
+ newTrc.add(trc);
+ }
+ }
+ }
+ tableRowColumns = newTrc;
+ }
+
+
+
}
Modified: trunk/src/dl-learner/org/dllearner/utilities/experiments/TableRowColumn.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/utilities/experiments/TableRowColumn.java 2010-02-15 18:40:49 UTC (rev 2041)
+++ trunk/src/dl-learner/org/dllearner/utilities/experiments/TableRowColumn.java 2010-02-16 00:17:05 UTC (rev 2042)
@@ -5,7 +5,6 @@
import org.dllearner.utilities.JamonMonitorLogger;
import com.jamonapi.Monitor;
-import com.jamonapi.MonitorFactory;
public class TableRowColumn {
@@ -16,12 +15,13 @@
public static String latexSep = "\t&\t";
public static String latexEnd = "\\\\";
- String label = "";
+ private final String label ;
+ private final String experimentName;
Monitor[] monitors;
boolean useStdDev = false;
- DecimalFormat dfGnuPlotDefault = new DecimalFormat("#######.######");
+ DecimalFormat dfGnuPlotDefault = new DecimalFormat("######0.00####");
// DecimalFormat dfStdDevLatex = new DecimalFormat("##.##%");
DecimalFormat dfLatexDefault = new DecimalFormat("####.####");
@@ -30,9 +30,10 @@
// public TableRowColumn(Monitor[] monitors){
// this.monitors = monitors;
// }
- public TableRowColumn(Monitor[] monitors, String label) {
+ public TableRowColumn(Monitor[] monitors, String experimentName, String label) {
this.monitors = monitors;
this.label = label;
+ this.experimentName = experimentName;
}
@@ -44,10 +45,19 @@
public void deleteAll(){
for (int i = 0; i < monitors.length; i++) {
- MonitorFactory.remove(monitors[i].getMonKey());
+// MonitorFactory.remove(monitors[i].getMonKey());
}
}
+ @Override
+ public String toString(){
+ return experimentName+" "+label+" "+toGnuPlotRow();
+ }
+
+ public String getHeader(){
+ return experimentName+" "+label;
+ }
+
public int size() {
return monitors.length;
}
@@ -59,13 +69,17 @@
public String getLabel() {
return label;
}
+
+ public String getExperimentName() {
+ return experimentName;
+ }
public String toGnuPlotRow() {
return toRow(Formats.GNUPLOT);
}
private String toRow(Formats f) {
- String ret = label;
+ String ret = experimentName+ " "+ label;
for (int i = 0; i < monitors.length; i++) {
boolean last = (i + 1 == monitors.length);
switch (f) {
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