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[DL-Learner SVN] SF.net SVN: dl-learner:[1520] trunk
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From: <jen...@us...> - 2008-11-21 12:07:02
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Revision: 1520
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=1520&view=rev
Author: jenslehmann
Date: 2008-11-21 12:06:58 +0000 (Fri, 21 Nov 2008)
Log Message:
-----------
continued work on EL simulations
Modified Paths:
--------------
trunk/examples/carcinogenesis/train.conf
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/reasoning/OWLAPIReasoner.java
trunk/src/dl-learner/org/dllearner/test/junit/SimulationTests.java
trunk/src/dl-learner/org/dllearner/test/junit/TestOntologies.java
Modified: trunk/examples/carcinogenesis/train.conf
===================================================================
--- trunk/examples/carcinogenesis/train.conf 2008-11-18 18:05:10 UTC (rev 1519)
+++ trunk/examples/carcinogenesis/train.conf 2008-11-21 12:06:58 UTC (rev 1520)
@@ -10,7 +10,7 @@
refexamples.writeSearchTree = false;
refexamples.searchTreeFile = "log/carcinogenesis/searchTree.log";
-// store some default settings to make the experiment reproducable in the future
+// store some settings to make the experiment reproducable in the future
refexamples.negativeWeight = 0.8;
refexamples.startNodeBonus = 1.0;
refexamples.forceRefinementLengthIncrease = false;
Modified: trunk/src/dl-learner/org/dllearner/algorithms/el/ELDescriptionNode.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/el/ELDescriptionNode.java 2008-11-18 18:05:10 UTC (rev 1519)
+++ trunk/src/dl-learner/org/dllearner/algorithms/el/ELDescriptionNode.java 2008-11-21 12:06:58 UTC (rev 1520)
@@ -58,7 +58,7 @@
// the reference tree for storing values, must not be null
protected ELDescriptionTree tree;
- protected TreeSet<NamedClass> label;
+ protected TreeSet<NamedClass> label = new TreeSet<NamedClass>();
protected List<ELDescriptionEdge> edges = new LinkedList<ELDescriptionEdge>();
@@ -111,7 +111,9 @@
}
public ELDescriptionNode(ELDescriptionNode parentNode, ObjectProperty parentProperty, TreeSet<NamedClass> label) {
- this.label = label;
+// this.label = label;
+ // we first need to add the edge and update the simulation and then add
+ // all classes iteratively to the label (each time updating the simulation again)
this.edges = new LinkedList<ELDescriptionEdge>();
parent = parentNode;
// the reference tree is the same as for the parent tree
@@ -122,36 +124,63 @@
ELDescriptionEdge edge = new ELDescriptionEdge(parentProperty, this);
parent.edges.add(edge);
// we need to update the set of nodes on a particular level
- tree.addNodeToLevel(this, level);
+ tree.addNodeToLevel(this, level);
// simulation update
// the nodes, which need to be updated
- Set<ELDescriptionNode> update = new TreeSet<ELDescriptionNode>();
+ Set<ELDescriptionNode> update = new HashSet<ELDescriptionNode>();
// loop over all nodes on the same level, which are not in the in set
Set<ELDescriptionNode> nodes = tree.getNodesOnLevel(level);
for(ELDescriptionNode w : nodes) {
- if(w.label.size() == 0) {
+ // to save space, we do not add reflexive relations
+ if(w != this) {
+ // (w,v') is automatically added
+ tree.extendSimulation(w, this);
- }
-
- if(inSC1.contains(w) && tree.checkSC2(this, w)) {
- tree.extendSimulation(this, w);
+ // check conditions for (v',w)
+ boolean sc1 = false, sc2 = false;
+
+ if(w.label.size() == 0) {
+ tree.extendSimulationSC1(this, w);
+ sc1 = true;
+ }
+
+ if(w.edges.size() == 0) {
+ tree.extendSimulationSC2(this, w);
+ sc2 = true;
+ }
+
+ if(sc1 && sc2) {
+ tree.extendSimulationSC12(this, w);
+ }
+
update.add(w.parent);
}
}
+ update.add(this.parent);
+// if(inSC1.contains(w) && tree.checkSC2(this, w)) {
+// tree.extendSimulation(this, w);
+// update.add(w.parent);
+// }
+
// loop over all nodes in out set
- for(ELDescriptionNode w : out) {
- if(!tree.checkSC1(this, w)) {
- tree.shrinkSimulation(this, w);
- update.add(w.parent);
- }
- }
+// for(ELDescriptionNode w : out) {
+// if(!tree.checkSC1(this, w)) {
+// tree.shrinkSimulation(this, w);
+// update.add(w.parent);
+// }
+// }
// apply updates recursively top-down
tree.updateSimulation(update);
+ // add all classes in label
+ for(NamedClass nc : label) {
+ extendLabel(nc);
+ }
+
}
/**
@@ -304,21 +333,25 @@
Set<ELDescriptionNode> update = new TreeSet<ELDescriptionNode>();
// loop over all nodes on the same level, which are not in the in set
- Set<ELDescriptionNode> nodes = tree.getNodesOnLevel(level);
- Set<ELDescriptionNode> tmp = Helper.difference(nodes, in);
+ Set<ELDescriptionNode> tmp = new HashSet<ELDescriptionNode>(tree.getNodesOnLevel(level));
+ tmp.removeAll(in);
for(ELDescriptionNode w : tmp) {
- // we only need to recompute SC2
- if(inSC1.contains(w) && tree.checkSC2(this, w)) {
- tree.extendSimulation(this, w);
- update.add(w.parent);
+ if(w != this) {
+ // we only need to recompute SC2
+ if(inSC1.contains(w) && tree.checkSC2(this, w)) {
+ tree.extendSimulation(this, w);
+ update.add(w.parent);
+ }
}
}
// loop over all nodes in out set
for(ELDescriptionNode w : out) {
- if(!tree.checkSC1(this, w)) {
- tree.shrinkSimulation(this, w);
- update.add(w.parent);
+ if(w != this) {
+ if(!tree.checkSC1(w, this)) {
+ tree.shrinkSimulation(w, this);
+ update.add(w.parent);
+ }
}
}
@@ -330,24 +363,28 @@
edges.get(edgeNumber).setLabel(op);
// compute the nodes, which need to be updated
- Set<ELDescriptionNode> update = new TreeSet<ELDescriptionNode>();
+ Set<ELDescriptionNode> update = new HashSet<ELDescriptionNode>();
// loop over all nodes on the same level, which are not in the in set
- Set<ELDescriptionNode> nodes = tree.getNodesOnLevel(level);
- Set<ELDescriptionNode> tmp = Helper.difference(nodes, in);
+ Set<ELDescriptionNode> tmp = new HashSet<ELDescriptionNode>(tree.getNodesOnLevel(level));
+ tmp.removeAll(in);
for(ELDescriptionNode w : tmp) {
- // we only need to recompute SC1
- if(inSC2.contains(w) && tree.checkSC1(this, w)) {
- tree.extendSimulation(this, w);
- update.add(w.parent);
+ if(w != this) {
+ // we only need to recompute SC1
+ if(inSC2.contains(w) && tree.checkSC1(this, w)) {
+ tree.extendSimulation(this, w);
+ update.add(w.parent);
+ }
}
}
// loop over all nodes in out set
for(ELDescriptionNode w : out) {
- if(!tree.checkSC2(this, w)) {
- tree.shrinkSimulation(this, w);
- update.add(w.parent);
+ if(w != this) {
+ if(!tree.checkSC2(this, w)) {
+ tree.shrinkSimulation(this, w);
+ update.add(w.parent);
+ }
}
}
@@ -422,6 +459,32 @@
return str;
}
+ private String toDescriptionString(Set<ELDescriptionNode> nodes) {
+ String str = "";
+ // comma separated list of descriptions
+ for(ELDescriptionNode node : nodes) {
+ str += node.toDescriptionString() + ",";
+ }
+ // remove last comma
+ if(str.length() > 0) {
+ str = str.substring(0, str.length()-1);
+ }
+ return str;
+ }
+
+ public String toSimulationString() {
+ String str = "";
+ str += "in: " + toDescriptionString(in) + "\n";
+ str += "inSC1: " + toDescriptionString(inSC1) + "\n";
+ str += "inSC2: " + toDescriptionString(inSC2) + "\n";
+ str += "out: " + toDescriptionString(out) + "\n";
+ str += "outSC1: " + toDescriptionString(outSC1) + "\n";
+ str += "outSC2: " + toDescriptionString(outSC2) + "\n";
+ return str;
+ }
+
+
+
public ELDescriptionNode getParent() {
return parent;
}
Modified: trunk/src/dl-learner/org/dllearner/algorithms/el/ELDescriptionTree.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/el/ELDescriptionTree.java 2008-11-18 18:05:10 UTC (rev 1519)
+++ trunk/src/dl-learner/org/dllearner/algorithms/el/ELDescriptionTree.java 2008-11-21 12:06:58 UTC (rev 1520)
@@ -234,17 +234,20 @@
// same level are tested before any node of a lower level is tested)
ELDescriptionNode v = list.pollFirst();
// loop through all nodes on same level
- for(ELDescriptionNode w : levelNodeMapping.get(v.getLevel())) {
- if(!v.out.contains(w) && v.outSC1.contains(w) && checkSC2(v,w)) {
- extendSimulation(v,w);
- list.add(v.getParent());
- list.add(w.getParent());
+ Set<ELDescriptionNode> sameLevel = levelNodeMapping.get(v.getLevel());
+ for(ELDescriptionNode w : sameLevel) {
+ if(v != w) {
+ if(!v.out.contains(w) && v.outSC1.contains(w) && checkSC2(v,w)) {
+ extendSimulation(v,w);
+ list.add(v.getParent());
+ list.add(w.getParent());
+ }
+ if(!w.out.contains(v) && w.outSC1.contains(v) && checkSC2(w,v)) {
+ extendSimulation(w,v);
+ list.add(v.getParent());
+ list.add(w.getParent());
+ }
}
- if(!w.out.contains(v) && w.outSC1.contains(v) && checkSC2(w,v)) {
- extendSimulation(w,v);
- list.add(v.getParent());
- list.add(w.getParent());
- }
}
}
}
@@ -327,6 +330,21 @@
node2.inSC2.add(node1);
}
+ public void extendSimulationSC1(ELDescriptionNode node1, ELDescriptionNode node2) {
+ node1.outSC1.add(node2);
+ node2.inSC1.add(node1);
+ }
+
+ public void extendSimulationSC2(ELDescriptionNode node1, ELDescriptionNode node2) {
+ node1.outSC2.add(node2);
+ node2.inSC2.add(node1);
+ }
+
+ public void extendSimulationSC12(ELDescriptionNode node1, ELDescriptionNode node2) {
+ node1.out.add(node2);
+ node2.in.add(node1);
+ }
+
// removes (node1,node2) from simulation, takes care of all helper sets
public void shrinkSimulation(ELDescriptionNode node1, ELDescriptionNode node2) {
node1.out.remove(node2);
@@ -337,6 +355,21 @@
node2.inSC2.remove(node1);
}
+ public void shrinkSimulationSC1(ELDescriptionNode node1, ELDescriptionNode node2) {
+ node1.outSC1.remove(node2);
+ node2.inSC1.remove(node1);
+ }
+
+ public void shrinkSimulationSC2(ELDescriptionNode node1, ELDescriptionNode node2) {
+ node1.outSC2.remove(node2);
+ node2.inSC2.remove(node1);
+ }
+
+ public void shrinkSimulationSC12(ELDescriptionNode node1, ELDescriptionNode node2) {
+ node1.out.remove(node2);
+ node2.in.remove(node1);
+ }
+
@Override
@SuppressWarnings("unchecked")
public ELDescriptionTree clone() {
Modified: trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java 2008-11-18 18:05:10 UTC (rev 1519)
+++ trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java 2008-11-21 12:06:58 UTC (rev 1520)
@@ -49,7 +49,6 @@
import org.dllearner.core.owl.Constant;
import org.dllearner.core.owl.Datatype;
import org.dllearner.core.owl.DatatypeProperty;
-import org.dllearner.core.owl.DatatypePropertyHierarchy;
import org.dllearner.core.owl.Description;
import org.dllearner.core.owl.Entity;
import org.dllearner.core.owl.Individual;
@@ -126,7 +125,7 @@
private RoleComparator roleComparator = new RoleComparator();
// private ClassHierarchy subsumptionHierarchy;
// private ObjectPropertyHierarchy roleHierarchy;
- private DatatypePropertyHierarchy datatypePropertyHierarchy;
+// private DatatypePropertyHierarchy datatypePropertyHierarchy;
// private Set<Description> allowedConceptsInSubsumptionHierarchy;
// primitives
Modified: trunk/src/dl-learner/org/dllearner/test/junit/SimulationTests.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/test/junit/SimulationTests.java 2008-11-18 18:05:10 UTC (rev 1519)
+++ trunk/src/dl-learner/org/dllearner/test/junit/SimulationTests.java 2008-11-21 12:06:58 UTC (rev 1520)
@@ -71,12 +71,14 @@
// perform test with empty background knowledge and A1 AND EXISTS r1.TOP AND EXISTS r2.TOP
ReasonerComponent rs = TestOntologies.getTestOntology(TestOntology.EMPTY);
ELDescriptionTree tree = new ELDescriptionTree(rs);
+ NamedClass a1 = new NamedClass("a1");
ELDescriptionNode v1 = new ELDescriptionNode(tree);
+ v1.extendLabel(a1);
ObjectProperty r1 = new ObjectProperty("r1");
ELDescriptionNode v2 = new ELDescriptionNode(v1, r1, new TreeSet<NamedClass>());
ObjectProperty r2 = new ObjectProperty("r2");
ELDescriptionNode v3 = new ELDescriptionNode(v1, r2, new TreeSet<NamedClass>());
-
+
assertEmpty(v1);
assertAll(v2, v3);
assertAll(v3, v2);
@@ -109,6 +111,11 @@
ObjectProperty r2 = new ObjectProperty("r2");
ELDescriptionNode v4 = new ELDescriptionNode(v1, r2, a1);
+ System.out.println("v1:\n" + v1.toSimulationString());
+ System.out.println("v2:\n" + v2.toSimulationString());
+ System.out.println("v3:\n" + v3.toSimulationString());
+ System.out.println("v4:\n" + v4.toSimulationString());
+
assertEmpty(v1);
assertAllIn(v2, v3, v4);
@@ -160,7 +167,8 @@
ELDescriptionNode v2 = new ELDescriptionNode(v1, r1, a2, a3);
ELDescriptionNode v3 = new ELDescriptionNode(v1, r1);
ELDescriptionNode v4 = new ELDescriptionNode(v2, r1, a1);
- ELDescriptionNode v5 = new ELDescriptionNode(v2, r2, a1, a2);
+ ELDescriptionNode v5 = new ELDescriptionNode(v2, r3, a1, a2);
+ v2.refineEdge(1, r2);
ELDescriptionNode v6 = new ELDescriptionNode(v3, r3, a3);
assertEmpty(v1);
Modified: trunk/src/dl-learner/org/dllearner/test/junit/TestOntologies.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/test/junit/TestOntologies.java 2008-11-18 18:05:10 UTC (rev 1519)
+++ trunk/src/dl-learner/org/dllearner/test/junit/TestOntologies.java 2008-11-21 12:06:58 UTC (rev 1520)
@@ -56,7 +56,7 @@
kbString += "(human AND animal) = BOTTOM.\n";
} else if(ont.equals(TestOntology.SIMPLE2)) {
kbString += "Subrole(r2,r3).";
- kbString += "a2 SUB a4";
+ kbString += "a2 SUB a4.";
} else if(ont.equals(TestOntology.R1SUBR2)) {
kbString += "Subrole(r1,r2).\n";
} else if(ont.equals(TestOntology.DATA1)) {
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