dl-learner-svn Mailing List for DL-Learner (Page 109)

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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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