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[DL-Learner SVN] SF.net SVN: dl-learner:[1583] trunk/src/dl-learner/org/dllearner
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From: <jen...@us...> - 2009-01-26 13:15:30
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Revision: 1583
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=1583&view=rev
Author: jenslehmann
Date: 2009-01-26 11:55:26 +0000 (Mon, 26 Jan 2009)
Log Message:
-----------
benchmarks with monitoring mostly deactivated
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/algorithms/el/ELDescriptionNode.java
trunk/src/dl-learner/org/dllearner/algorithms/el/ELDescriptionTree.java
trunk/src/dl-learner/org/dllearner/refinementoperators/ELDown2.java
trunk/src/dl-learner/org/dllearner/scripts/evaluation/ELOperatorBenchmark.java
trunk/src/dl-learner/org/dllearner/test/junit/ELDownTests.java
trunk/src/dl-learner/org/dllearner/test/junit/TestOntologies.java
Modified: trunk/src/dl-learner/org/dllearner/algorithms/el/ELDescriptionNode.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/el/ELDescriptionNode.java 2009-01-25 19:16:38 UTC (rev 1582)
+++ trunk/src/dl-learner/org/dllearner/algorithms/el/ELDescriptionNode.java 2009-01-26 11:55:26 UTC (rev 1583)
@@ -137,7 +137,7 @@
tree.addNodeToLevel(this, level);
// simulation update
- Monitor mon = MonitorFactory.start("simulation update");
+// Monitor mon = MonitorFactory.start("simulation update");
// the nodes, which need to be updated
Set<ELDescriptionNode> update = new HashSet<ELDescriptionNode>();
@@ -188,7 +188,7 @@
// apply updates recursively top-down
tree.updateSimulation(update);
- mon.stop();
+// mon.stop();
// add all classes in label
for(NamedClass nc : label) {
@@ -350,7 +350,7 @@
// simulation update when extending or refining label
// (same in both cases)
private void labelSimulationUpdate() {
- Monitor mon = MonitorFactory.start("simulation update");
+// Monitor mon = MonitorFactory.start("simulation update");
// compute the nodes, which need to be updated
Set<ELDescriptionNode> update = new HashSet<ELDescriptionNode>();
@@ -411,13 +411,13 @@
// apply updates recursively top-down
tree.updateSimulation(update);
- mon.stop();
+// mon.stop();
}
public void refineEdge(int edgeNumber, ObjectProperty op) {
edges.get(edgeNumber).setLabel(op);
- Monitor mon = MonitorFactory.start("simulation update");
+// Monitor mon = MonitorFactory.start("simulation update");
// compute the nodes, which need to be updated
Set<ELDescriptionNode> update = new HashSet<ELDescriptionNode>();
update.add(this);
@@ -451,7 +451,7 @@
// apply updates recursively top-down
tree.updateSimulation(update);
- mon.stop();
+// mon.stop();
}
/**
Modified: trunk/src/dl-learner/org/dllearner/algorithms/el/ELDescriptionTree.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/el/ELDescriptionTree.java 2009-01-25 19:16:38 UTC (rev 1582)
+++ trunk/src/dl-learner/org/dllearner/algorithms/el/ELDescriptionTree.java 2009-01-26 11:55:26 UTC (rev 1583)
@@ -42,9 +42,6 @@
import org.dllearner.core.owl.Thing;
import org.dllearner.core.owl.UnsupportedLanguageException;
-import com.jamonapi.Monitor;
-import com.jamonapi.MonitorFactory;
-
/**
* Represents an EL description tree. Unlike {@link ELDescriptionNode}, this is
* a tree-wide structure, i.e. it does not implement the tree structure itself,
@@ -467,7 +464,7 @@
@Override
@SuppressWarnings("unchecked")
public ELDescriptionTree clone() {
- Monitor mon = MonitorFactory.start("tree clone");
+// Monitor mon = MonitorFactory.start("tree clone");
// clone "global" tree
ELDescriptionTree treeClone = new ELDescriptionTree(rs);
@@ -553,7 +550,7 @@
treeClone.levelNodeMapping.put(i, newNodes);
}
- mon.stop();
+// mon.stop();
return treeClone;
}
Modified: trunk/src/dl-learner/org/dllearner/refinementoperators/ELDown2.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/refinementoperators/ELDown2.java 2009-01-25 19:16:38 UTC (rev 1582)
+++ trunk/src/dl-learner/org/dllearner/refinementoperators/ELDown2.java 2009-01-26 11:55:26 UTC (rev 1583)
@@ -51,8 +51,8 @@
import org.dllearner.core.owl.Thing;
import org.dllearner.utilities.Helper;
-import com.jamonapi.Monitor;
-import com.jamonapi.MonitorFactory;
+//import com.jamonapi.Monitor;
+//import com.jamonapi.MonitorFactory;
/**
* EL downward refinement operator constructed by Jens Lehmann
@@ -168,7 +168,7 @@
// operation 1: label extension
private List<ELDescriptionTree> extendLabel(ELDescriptionTree tree, ELDescriptionNode v, int[] position) {
- Monitor mon = MonitorFactory.start("extend label");
+// Monitor mon = MonitorFactory.start("extend label");
List<ELDescriptionTree> refinements = new LinkedList<ELDescriptionTree>();
// the index is the range of role in the edge pointing to the parent of this node
@@ -193,13 +193,13 @@
}
}
- mon.stop();
+// mon.stop();
return refinements;
}
// operation 2: label refinement
private List<ELDescriptionTree> refineLabel(ELDescriptionTree tree, ELDescriptionNode v, int[] position) {
- Monitor mon = MonitorFactory.start("refine label");
+// Monitor mon = MonitorFactory.start("refine label");
List<ELDescriptionTree> refinements = new LinkedList<ELDescriptionTree>();
// loop through all classes in label
@@ -220,13 +220,13 @@
}
}
}
- mon.stop();
+// mon.stop();
return refinements;
}
// operation 3: refine edge
private List<ELDescriptionTree> refineEdge(ELDescriptionTree tree, ELDescriptionNode v, int[] position) {
- Monitor mon = MonitorFactory.start("refine edge");
+// Monitor mon = MonitorFactory.start("refine edge");
List<ELDescriptionTree> refinements = new LinkedList<ELDescriptionTree>();
for(int edgeNumber = 0; edgeNumber < v.getEdges().size(); edgeNumber++) {
@@ -251,13 +251,13 @@
}
}
}
- mon.stop();
+// mon.stop();
return refinements;
}
// operation 4: attach tree
private Collection<ELDescriptionTree> attachSubtree(ELDescriptionTree tree, ELDescriptionNode v, int[] position) {
- Monitor mon = MonitorFactory.start("attach tree");
+// Monitor mon = MonitorFactory.start("attach tree");
List<ELDescriptionTree> refinements = new LinkedList<ELDescriptionTree>();
// compute the set of most general roles such that the domain of each role is not disjoint
@@ -311,7 +311,7 @@
// we check equivalence by a minimality test (TODO: can we still do this?)
boolean minimal = mergedTree.isMinimal();
- MonitorFactory.add("as.minimal", "boolean", minimal ? 1 : 0);
+// MonitorFactory.add("as.minimal", "boolean", minimal ? 1 : 0);
if(minimal) {
logger.trace("Merged tree is minimal, i.e. not equivalent.");
// it is not equivalent, i.e. we found a refinement
@@ -321,7 +321,7 @@
// perform complex check in merged tree
boolean check = asCheck(wClone);
logger.trace("Result of complex check: " + check);
- MonitorFactory.add("as.check", "boolean", check ? 1 : 0);
+// MonitorFactory.add("as.check", "boolean", check ? 1 : 0);
if(check) {
// refine property
@@ -331,9 +331,9 @@
// refine tree using recursive operator call
logger.trace("Recursive Call");
// do not monitor recursive calls (counts time twice or more)
- mon.stop();
+// mon.stop();
List<ELDescriptionTree> recRefs = refine(tp);
- mon.start();
+// mon.start();
logger.trace("Recursive Call Done");
for(ELDescriptionTree tpp : recRefs) {
m.add(new ELDescriptionEdge(r, tpp.getRootNode()));
@@ -344,13 +344,13 @@
logger.trace("M: " + m);
}
}
- mon.stop();
+// mon.stop();
return refinements;
}
// new version of as
private Collection<ELDescriptionTree> attachSubtree2(ELDescriptionTree tree, ELDescriptionNode v, int[] position) {
- Monitor mon = MonitorFactory.start("attach tree");
+// Monitor mon = MonitorFactory.start("attach tree");
Set<ELDescriptionTree> refinements = new TreeSet<ELDescriptionTree>(treeComp);
// create and initialise M
@@ -401,13 +401,13 @@
ELDescriptionNode w = tpp.getNode(wPosition);
boolean minimal = tpp.isMinimal();
- MonitorFactory.add("as.minimal", "boolean", minimal ? 1 : 0);
+// MonitorFactory.add("as.minimal", "boolean", minimal ? 1 : 0);
if(minimal) {
refinements.add(tpp);
// logger.trace("tree is minimal; added to T");
} else {
boolean check = asCheck(w);
- MonitorFactory.add("as.check", "boolean", check ? 1 : 0);
+// MonitorFactory.add("as.check", "boolean", check ? 1 : 0);
// logger.trace("tree is not minimal; result of complex check: " + check);
if(check) {
@@ -429,11 +429,11 @@
if(rppSet.size() != 0) {
// recursive call
- mon.stop();
+// mon.stop();
// logger.trace("recursive call start");
List<ELDescriptionTree> recRefs = refine(tp);
// logger.trace("recursive call end");
- mon.start();
+// mon.start();
for(ELDescriptionTree tStar : recRefs) {
m.add(new TreeAndRoleSet(tStar, rppSet));
@@ -443,14 +443,14 @@
}
- mon.stop();
+// mon.stop();
return refinements;
}
// create a new tree which is obtained by attaching the new tree at the given node in the tree via role r
private ELDescriptionTree mergeTrees(ELDescriptionTree tree, ELDescriptionNode node, int[] position, ObjectProperty r, ELDescriptionTree newTree) {
- Monitor mon = MonitorFactory.start("as.merge trees");
+// Monitor mon = MonitorFactory.start("as.merge trees");
// System.out.println("merge start");
// System.out.println(tree);
// System.out.println(newTree);
@@ -497,13 +497,13 @@
// mon2.stop();
- mon.stop();
+// mon.stop();
return mergedTree;
}
// TODO: variables have been renamed in article
public boolean asCheck(ELDescriptionNode v) {
- Monitor mon = MonitorFactory.start("as.complex check");
+// Monitor mon = MonitorFactory.start("as.complex check");
// System.out.println("asCheck: " + v.getTree().toSimulationString());
// find all edges up to the root node
@@ -541,7 +541,7 @@
}
}
- mon.stop();
+// mon.stop();
return true;
}
Modified: trunk/src/dl-learner/org/dllearner/scripts/evaluation/ELOperatorBenchmark.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/evaluation/ELOperatorBenchmark.java 2009-01-25 19:16:38 UTC (rev 1582)
+++ trunk/src/dl-learner/org/dllearner/scripts/evaluation/ELOperatorBenchmark.java 2009-01-26 11:55:26 UTC (rev 1583)
@@ -86,43 +86,45 @@
"cton",
// is ok at length 8
"earthrealm2",
- // cannot even be read "fma_owl_dl_component_1.4.0",
- // ontology file seems broken "iso_19115",
- // ontology file seems broken "nci",
// is ok at length 8
"process",
- // takes too long to read in "pto",
// is ok at length 8
"tambis",
// ontology file seems broken "thesaurus",
// is ok at length 8
- "transportation"
+ "transportation",
+ // takes too long to read in
+ "pto",
+ // ontology file seems broken "iso_19115",
+ // ontology file seems broken "nci",
+ // cannot even be read
+ "fma_owl_dl_component_1.4.0"
};
for(String ont : onts) {
String file = base + ont + ".owl";
rand = new Random(1);
- testOntology(statDir, file, 100, 8);
+ testOntology(statDir, file, 100, 7);
}
// artificial ontology tests //
-
+ /*
// number of concepts and roles
int[] conceptCounts = new int[] { 5, 10, 50, 100 }; //, 500, 1000 };
int[] roleCounts = new int[] { 5, 10, 50, 100, 500, 1000};
- base = "/home/jl/downloads/uni-leipzig/OTAGen-v1/generated/generated_";
+ String base = "/home/jl/downloads/uni-leipzig/OTAGen-v1/generated/generated_";
// loop through all artificial ontologies
for(int conceptCount : conceptCounts) {
for(int roleCount : roleCounts) {
String file = base + "c" + conceptCount + "_r" + roleCount + ".owl";
rand = new Random(1);
- testOntology(statDir, file, 100, 9);
+ testOntology(statDir, file, 100, 7);
}
}
System.exit(0);
-
+ */
/*
// number of applications of operator
@@ -190,6 +192,7 @@
File statFile = new File(statDir + statFileName);
String statString = "";
+ int refinementMaxSizeOverall = 0;
MonitorFactory.reset();
for(int loop = 0; loop < nrOfChains; loop++) {
@@ -216,18 +219,32 @@
int sizeSum = 0;
for(ELDescriptionTree tree : refinements) {
// System.out.println(" " + tree.toDescriptionString());
- sizeSum += tree.getSize();
+ int size = tree.getSize();
+ sizeSum += size;
+ refinementMaxSizeOverall = Math.max(size, refinementMaxSizeOverall);
}
MonitorFactory.add("refinement size", "count", sizeSum/(double)refinements.size());
MonitorFactory.add("refinement size increase", "count", (sizeSum-refinements.size()*currTree.getSize())/(double)refinements.size());
System.out.println(" [has " + refinements.size() + " refinements]");
- // pick a refinement randomly (which is kind of slow for a set, but
- // this does not matter here)
+
+ // pick a refinement randomly - this has the disadvantage that we have huge
+ // variations over different runs
int index = rand.nextInt(refinements.size());
-// currTree = new ArrayList<ELDescriptionTree>(refinements).get(index);
currTree = refinements.get(index);
+
+ // we pick a/the median of the refinements as next refinement
+// ELDescriptionTreeComparator treeComp = new ELDescriptionTreeComparator();
+// TreeSet<ELDescriptionTree> refinementsSet = new TreeSet<ELDescriptionTree>(treeComp);
+// refinementsSet.addAll(refinements);
+// List<ELDescriptionTree> refinementList = new LinkedList<ELDescriptionTree>(refinements);
+ // sort by size (first criterion of comparator)
+// Collections.sort(refinementList, treeComp);
+// currTree = refinementList.get((int)(refinementList.size()*0.5));
+// System.out.println(rand.nextGaussian());
+// currTree = refinementList.get((int)(refinementList.size()*rand.nextGaussian()));
+
MonitorFactory.add("picked refinement size", "count", currTree.getSize());
}
System.out.println("operator time: " + runtime.prettyPrint("ms"));
@@ -246,23 +263,26 @@
statString += getMonitorDataCount(MonitorFactory.getMonitor("refinement count", "count"));
statString += getMonitorDataCount(MonitorFactory.getMonitor("refinement size", "count"));
+ statString += "refinement max size overall: " + refinementMaxSizeOverall + "\n";
statString += getMonitorDataCount(MonitorFactory.getMonitor("picked refinement size", "count"));
statString += getMonitorDataCount(MonitorFactory.getMonitor("refinement size increase", "count"));
statString += "\n";
- statString += getMonitorData(MonitorFactory.getMonitor("extend label", "ms."));
- statString += getMonitorData(MonitorFactory.getMonitor("refine label", "ms."));
- statString += getMonitorData(MonitorFactory.getMonitor("refine edge", "ms."));
- statString += getMonitorData(MonitorFactory.getMonitor("attach tree", "ms."));
- statString += getMonitorData(MonitorFactory.getMonitor("as.merge trees", "ms."));
- statString += getMonitorData(MonitorFactory.getMonitor("as.complex check", "ms."));
+// statString += getMonitorData(MonitorFactory.getMonitor("extend label", "ms."));
+// statString += getMonitorData(MonitorFactory.getMonitor("refine label", "ms."));
+// statString += getMonitorData(MonitorFactory.getMonitor("refine edge", "ms."));
+// statString += getMonitorData(MonitorFactory.getMonitor("attach tree", "ms."));
+// statString += getMonitorData(MonitorFactory.getMonitor("as.merge trees", "ms."));
+// statString += getMonitorData(MonitorFactory.getMonitor("as.complex check", "ms."));
// statString += getMonitorData(MonitorFactory.getMonitor("as.tmp", "ms."));
// statString += getMonitorData(MonitorFactory.getMonitor("el.tmp", "ms."));
- statString += getMonitorDataBoolean(MonitorFactory.getMonitor("as.minimal", "boolean"));
- statString += getMonitorDataBoolean(MonitorFactory.getMonitor("as.check", "boolean"));
- statString += getMonitorData(MonitorFactory.getMonitor("tree clone", "ms."));
- statString += getMonitorData(MonitorFactory.getMonitor("simulation update", "ms."));
+// statString += getMonitorDataBoolean(MonitorFactory.getMonitor("as.minimal", "boolean"));
+// statString += getMonitorDataBoolean(MonitorFactory.getMonitor("as.check", "boolean"));
+// statString += getMonitorData(MonitorFactory.getMonitor("tree clone", "ms."));
+// statString += getMonitorData(MonitorFactory.getMonitor("simulation update", "ms."));
statString += getMonitorData(MonitorFactory.getMonitor("disjointness reasoning", "ms."));
+ double reasoningPercentage = 100 * MonitorFactory.getMonitor("disjointness reasoning", "ms.").getTotal()/MonitorFactory.getMonitor("operator application time", "ms.").getTotal();
+ statString += "disjointness reasoning percentage: " + df.format(reasoningPercentage) + "%\n";
Files.createFile(statFile, statString);
@@ -278,6 +298,7 @@
return mon.getLabel() + ": av " + df.format(mon.getAvg()) + " (stddev " + df.format(mon.getStdDev()) + ", min " + df.format(mon.getMin()) + ", max " + df.format(mon.getMax()) + ", " + df.format(mon.getTotal()) + " total, " + (int)mon.getHits() + " hits)\n";
}
+ @SuppressWarnings("unused")
private static String getMonitorDataBoolean(Monitor mon) {
return mon.getLabel() + ": " + df.format(mon.getAvg()*100) + "%\n";
}
Modified: trunk/src/dl-learner/org/dllearner/test/junit/ELDownTests.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/test/junit/ELDownTests.java 2009-01-25 19:16:38 UTC (rev 1582)
+++ trunk/src/dl-learner/org/dllearner/test/junit/ELDownTests.java 2009-01-26 11:55:26 UTC (rev 1583)
@@ -66,6 +66,7 @@
*/
public class ELDownTests {
+ @SuppressWarnings("unused")
private static Logger logger = Logger.getLogger(ELDownTests.class);
/**
Modified: trunk/src/dl-learner/org/dllearner/test/junit/TestOntologies.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/test/junit/TestOntologies.java 2009-01-25 19:16:38 UTC (rev 1582)
+++ trunk/src/dl-learner/org/dllearner/test/junit/TestOntologies.java 2009-01-26 11:55:26 UTC (rev 1583)
@@ -36,7 +36,7 @@
*/
public final class TestOntologies {
- public enum TestOntology { EMPTY, SIMPLE, SIMPLE_NO_DR, SIMPLE_NO_DISJOINT, SIMPLE2, SIMPLE3, R1SUBR2, DATA1, FIVE_ROLES };
+ public enum TestOntology { EMPTY, SIMPLE, SIMPLE_NO_DR, SIMPLE_NO_DISJOINT, SIMPLE_NO_DR_DISJOINT, SIMPLE2, SIMPLE3, R1SUBR2, DATA1, FIVE_ROLES };
public static ReasonerComponent getTestOntology(TestOntology ont) {
String kbString = "";
@@ -70,6 +70,12 @@
kbString += "bird SUB animal.\n";
kbString += "cat SUB animal.\n";
kbString += "human SUB TOP.\n";
+ } else if(ont.equals(TestOntology.SIMPLE_NO_DR_DISJOINT)) {
+ kbString += "Subrole(hasChild, has).\n";
+ kbString += "Subrole(hasPet, has).\n";
+ kbString += "bird SUB animal.\n";
+ kbString += "cat SUB animal.\n";
+ kbString += "human SUB TOP.\n";
} else if(ont.equals(TestOntology.SIMPLE2)) {
kbString += "Subrole(r2,r3).\n";
kbString += "a1 SUB TOP.\n";
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