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[DL-Learner SVN] SF.net SVN: dl-learner:[1927] trunk
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From: <jen...@us...> - 2009-12-01 17:59:18
|
Revision: 1927
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=1927&view=rev
Author: jenslehmann
Date: 2009-12-01 17:59:11 +0000 (Tue, 01 Dec 2009)
Log Message:
-----------
- max execution time for EL base algorithm implemented
- cross benchmark extended
- several small changes
Modified Paths:
--------------
trunk/src/dl-learner/org/dllearner/algorithms/celoe/CELOE.java
trunk/src/dl-learner/org/dllearner/algorithms/celoe/OEHeuristicRuntime.java
trunk/src/dl-learner/org/dllearner/algorithms/el/ELLearningAlgorithm.java
trunk/src/dl-learner/org/dllearner/algorithms/el/ELLearningAlgorithmDisjunctive.java
trunk/src/dl-learner/org/dllearner/core/configurators/ELLearningAlgorithmConfigurator.java
trunk/src/dl-learner/org/dllearner/core/configurators/ELLearningAlgorithmDisjunctiveConfigurator.java
trunk/src/dl-learner/org/dllearner/core/configurators/PosNegLPStandardConfigurator.java
trunk/src/dl-learner/org/dllearner/core/options/CommonConfigOptions.java
trunk/src/dl-learner/org/dllearner/examples/MonogenicDiseases.java
trunk/src/dl-learner/org/dllearner/learningproblems/ClassLearningProblem.java
trunk/src/dl-learner/org/dllearner/learningproblems/PosNegLPStandard.java
trunk/src/dl-learner/org/dllearner/refinementoperators/ELDown2.java
trunk/src/dl-learner/org/dllearner/refinementoperators/Utility.java
trunk/src/dl-learner/org/dllearner/scripts/PaperStatistics.java
trunk/src/dl-learner/org/dllearner/test/junit/ELDownTests.java
trunk/src/dl-learner/org/dllearner/test/junit/TestOntologies.java
Added Paths:
-----------
trunk/examples/cross-benchmark/arch/arch_el.conf
trunk/examples/cross-benchmark/arch/arch_el_disjunctive.conf
trunk/examples/cross-benchmark/forte/uncle_el.conf
trunk/examples/cross-benchmark/forte/uncle_el_disjunctive.conf
trunk/examples/cross-benchmark/moral_reasoner/moral_43examples_complex_el.conf
trunk/examples/cross-benchmark/moral_reasoner/moral_43examples_complex_el_disjunctive.conf
trunk/examples/cross-benchmark/moral_reasoner/moral_43examples_simple_el.conf
trunk/examples/cross-benchmark/moral_reasoner/moral_43examples_simple_el_disjunctive.conf
trunk/examples/cross-benchmark/poker/pair_el.conf
trunk/examples/cross-benchmark/poker/pair_el_disjunctive.conf
trunk/examples/cross-benchmark/poker/straight_el.conf
trunk/examples/cross-benchmark/poker/straight_el_disjunctive.conf
trunk/examples/cross-benchmark/trains/trains_el.conf
trunk/examples/cross-benchmark/trains/trains_el_disjunctive.conf
Added: trunk/examples/cross-benchmark/arch/arch_el.conf
===================================================================
--- trunk/examples/cross-benchmark/arch/arch_el.conf (rev 0)
+++ trunk/examples/cross-benchmark/arch/arch_el.conf 2009-12-01 17:59:11 UTC (rev 1927)
@@ -0,0 +1,10 @@
+algorithm = el;
+el.instanceBasedDisjoints = false;
+reasoner = owlAPIReasoner;
+import("arch.owl");
+
++c1
++c4
+-c2
+-c3
+-c5
Added: trunk/examples/cross-benchmark/arch/arch_el_disjunctive.conf
===================================================================
--- trunk/examples/cross-benchmark/arch/arch_el_disjunctive.conf (rev 0)
+++ trunk/examples/cross-benchmark/arch/arch_el_disjunctive.conf 2009-12-01 17:59:11 UTC (rev 1927)
@@ -0,0 +1,10 @@
+algorithm = disjunctiveEL;
+disjunctiveEL.instanceBasedDisjoints = false;
+reasoner = owlAPIReasoner;
+import("arch.owl");
+
++c1
++c4
+-c2
+-c3
+-c5
Added: trunk/examples/cross-benchmark/forte/uncle_el.conf
===================================================================
--- trunk/examples/cross-benchmark/forte/uncle_el.conf (rev 0)
+++ trunk/examples/cross-benchmark/forte/uncle_el.conf 2009-12-01 17:59:11 UTC (rev 1927)
@@ -0,0 +1,116 @@
+/**
+ * Extracted from the FORTE (First Order Revision of Theories from Examples)
+ * data set:
+ *
+ * http://www.cs.utexas.edu/users/ml/forte.html
+ *
+ * The goal of this learning problem is to learn the concept of an uncle.
+ *
+ * In the file forte_family.kb, you can find a graphical representation of the
+ * family tree corresponding to the facts in this file.
+ *
+ * possible solution: (male AND (EXISTS hasSibling.EXISTS hasChild.TOP
+ * OR EXISTS married.EXISTS hasSibling.EXISTS hasChild.TOP))
+ *
+ * Copyright (C) 2007, Jens Lehmann
+ */
+
+
+algorithm = el;
+el.instanceBasedDisjoints = false;
+refexamples.useCardinalityRestrictions = false;
+reasoner = owlAPIReasoner;
+import("forte_family.owl");
+
+/** examples **/
+
+
+// complete example set
++art
++calvin
++carlos
++david
++eric
++fred
++frederick
++george
++harry
++jack
++james
++jonas
++karl
++leon
++mark
++melvin
++neil
++nero
++owen
++paul
++peter
++umo
++walt
+
+-alfred
+-alice
+-angela
+-ann
+-beatrice
+-bob
+-callie
+-carl
+-christy
+-cornelia
+-deanna
+-elisa
+-f12
+-f14
+-f19
+-f2
+-f20
+-f21
+-f22
+-f23
+-f25
+-f26
+-f28
+-f8
+-fannie
+-gail
+-helen
+-jane
+-janet
+-kari
+-lorrie
+-m1
+-m10
+-m11
+-m13
+-m15
+-m16
+-m17
+-m18
+-m24
+-m27
+-m29
+-m3
+-m4
+-m5
+-m6
+-m7
+-m9
+-maria
+-martha
+-nancy
+-nonnie
+-oma
+-paula
+-prissie
+-rachel
+-ray
+-regina
+-steve
+-susan
+-terri
+-terry
+-wendy
+
Added: trunk/examples/cross-benchmark/forte/uncle_el_disjunctive.conf
===================================================================
--- trunk/examples/cross-benchmark/forte/uncle_el_disjunctive.conf (rev 0)
+++ trunk/examples/cross-benchmark/forte/uncle_el_disjunctive.conf 2009-12-01 17:59:11 UTC (rev 1927)
@@ -0,0 +1,116 @@
+/**
+ * Extracted from the FORTE (First Order Revision of Theories from Examples)
+ * data set:
+ *
+ * http://www.cs.utexas.edu/users/ml/forte.html
+ *
+ * The goal of this learning problem is to learn the concept of an uncle.
+ *
+ * In the file forte_family.kb, you can find a graphical representation of the
+ * family tree corresponding to the facts in this file.
+ *
+ * possible solution: (male AND (EXISTS hasSibling.EXISTS hasChild.TOP
+ * OR EXISTS married.EXISTS hasSibling.EXISTS hasChild.TOP))
+ *
+ * Copyright (C) 2007, Jens Lehmann
+ */
+
+
+algorithm = disjunctiveEL;
+disjunctiveEL.instanceBasedDisjoints = false;
+refexamples.useCardinalityRestrictions = false;
+reasoner = owlAPIReasoner;
+import("forte_family.owl");
+
+/** examples **/
+
+
+// complete example set
++art
++calvin
++carlos
++david
++eric
++fred
++frederick
++george
++harry
++jack
++james
++jonas
++karl
++leon
++mark
++melvin
++neil
++nero
++owen
++paul
++peter
++umo
++walt
+
+-alfred
+-alice
+-angela
+-ann
+-beatrice
+-bob
+-callie
+-carl
+-christy
+-cornelia
+-deanna
+-elisa
+-f12
+-f14
+-f19
+-f2
+-f20
+-f21
+-f22
+-f23
+-f25
+-f26
+-f28
+-f8
+-fannie
+-gail
+-helen
+-jane
+-janet
+-kari
+-lorrie
+-m1
+-m10
+-m11
+-m13
+-m15
+-m16
+-m17
+-m18
+-m24
+-m27
+-m29
+-m3
+-m4
+-m5
+-m6
+-m7
+-m9
+-maria
+-martha
+-nancy
+-nonnie
+-oma
+-paula
+-prissie
+-rachel
+-ray
+-regina
+-steve
+-susan
+-terri
+-terry
+-wendy
+
Added: trunk/examples/cross-benchmark/moral_reasoner/moral_43examples_complex_el.conf
===================================================================
--- trunk/examples/cross-benchmark/moral_reasoner/moral_43examples_complex_el.conf (rev 0)
+++ trunk/examples/cross-benchmark/moral_reasoner/moral_43examples_complex_el.conf 2009-12-01 17:59:11 UTC (rev 1927)
@@ -0,0 +1,63 @@
+ /***********************
+ solution is:
+(severity_harm AND (NOT benefit_victim) AND (vicarious OR voluntary))
+
+
+ Examples:
+ 23 positive
+ 20 negative
+
+ ***********************/
+ algorithm = el;
+el.instanceBasedDisjoints = false;
+refexamples.useCardinalityRestrictions = false;
+reasoner = owlAPIReasoner;
+/** background knowledge **/
+import("moral_43instances_complex.owl");
+
+
+/** Examples **/
++p0
++p1
++p2
++p3
++p4
++p5
++p6
++p7
++p8
++p9
++p10
++p90
++p91
++p92
++p93
++p94
++p95
++p96
++p97
++p98
++p99
++p100
++p101
+-n0
+-n1
+-n2
+-n3
+//-n4
+-n5
+-n6
+-n7
+-n8
+-n9
+-n10
+-n90
+-n91
+-n92
+-n93
+-n94
+-n95
+-n96
+-n97
+-n98
+-n99
Added: trunk/examples/cross-benchmark/moral_reasoner/moral_43examples_complex_el_disjunctive.conf
===================================================================
--- trunk/examples/cross-benchmark/moral_reasoner/moral_43examples_complex_el_disjunctive.conf (rev 0)
+++ trunk/examples/cross-benchmark/moral_reasoner/moral_43examples_complex_el_disjunctive.conf 2009-12-01 17:59:11 UTC (rev 1927)
@@ -0,0 +1,63 @@
+ /***********************
+ solution is:
+(severity_harm AND (NOT benefit_victim) AND (vicarious OR voluntary))
+
+
+ Examples:
+ 23 positive
+ 20 negative
+
+ ***********************/
+ algorithm = disjunctiveEL;
+disjunctiveEL.instanceBasedDisjoints = false;
+refexamples.useCardinalityRestrictions = false;
+reasoner = owlAPIReasoner;
+/** background knowledge **/
+import("moral_43instances_complex.owl");
+
+
+/** Examples **/
++p0
++p1
++p2
++p3
++p4
++p5
++p6
++p7
++p8
++p9
++p10
++p90
++p91
++p92
++p93
++p94
++p95
++p96
++p97
++p98
++p99
++p100
++p101
+-n0
+-n1
+-n2
+-n3
+//-n4
+-n5
+-n6
+-n7
+-n8
+-n9
+-n10
+-n90
+-n91
+-n92
+-n93
+-n94
+-n95
+-n96
+-n97
+-n98
+-n99
Added: trunk/examples/cross-benchmark/moral_reasoner/moral_43examples_simple_el.conf
===================================================================
--- trunk/examples/cross-benchmark/moral_reasoner/moral_43examples_simple_el.conf (rev 0)
+++ trunk/examples/cross-benchmark/moral_reasoner/moral_43examples_simple_el.conf 2009-12-01 17:59:11 UTC (rev 1927)
@@ -0,0 +1,63 @@
+ /***********************
+ solution should be:
+ guilty = (blameworthy OR vicarious_blame ).
+
+
+ Examples:
+ 23 positive
+ 20 negative
+
+ ***********************/
+algorithm = el;
+el.instanceBasedDisjoints = false;
+refexamples.useCardinalityRestrictions = false;
+reasoner = owlAPIReasoner;
+ /** background knowledge **/
+ import("moral_43instances.owl");
+
+
+ /** Examples **/
+ +p0
+ +p1
+ +p2
+ +p3
+ +p4
+ +p5
+ +p6
+ +p7
+ +p8
+ +p9
+ +p10
+ +p90
+ +p91
+ +p92
+ +p93
+ +p94
+ +p95
+ +p96
+ +p97
+ +p98
+ +p99
+ +p100
+ +p101
+ -n0
+ -n1
+ -n2
+ -n3
+ //-n4
+ -n5
+ -n6
+ -n7
+ -n8
+ -n9
+ -n10
+ -n90
+ -n91
+ -n92
+ -n93
+ -n94
+ -n95
+ -n96
+ -n97
+ -n98
+ -n99
Added: trunk/examples/cross-benchmark/moral_reasoner/moral_43examples_simple_el_disjunctive.conf
===================================================================
--- trunk/examples/cross-benchmark/moral_reasoner/moral_43examples_simple_el_disjunctive.conf (rev 0)
+++ trunk/examples/cross-benchmark/moral_reasoner/moral_43examples_simple_el_disjunctive.conf 2009-12-01 17:59:11 UTC (rev 1927)
@@ -0,0 +1,63 @@
+ /***********************
+ solution should be:
+ guilty = (blameworthy OR vicarious_blame ).
+
+
+ Examples:
+ 23 positive
+ 20 negative
+
+ ***********************/
+algorithm = disjunctiveEL;
+disjunctiveEL.instanceBasedDisjoints = false;
+refexamples.useCardinalityRestrictions = false;
+reasoner = owlAPIReasoner;
+ /** background knowledge **/
+ import("moral_43instances.owl");
+
+
+ /** Examples **/
+ +p0
+ +p1
+ +p2
+ +p3
+ +p4
+ +p5
+ +p6
+ +p7
+ +p8
+ +p9
+ +p10
+ +p90
+ +p91
+ +p92
+ +p93
+ +p94
+ +p95
+ +p96
+ +p97
+ +p98
+ +p99
+ +p100
+ +p101
+ -n0
+ -n1
+ -n2
+ -n3
+ //-n4
+ -n5
+ -n6
+ -n7
+ -n8
+ -n9
+ -n10
+ -n90
+ -n91
+ -n92
+ -n93
+ -n94
+ -n95
+ -n96
+ -n97
+ -n98
+ -n99
Added: trunk/examples/cross-benchmark/poker/pair_el.conf
===================================================================
--- trunk/examples/cross-benchmark/poker/pair_el.conf (rev 0)
+++ trunk/examples/cross-benchmark/poker/pair_el.conf 2009-12-01 17:59:11 UTC (rev 1927)
@@ -0,0 +1,64 @@
+/**
+ * See pair.conf. This is the same learning problem, but loading
+ * background knowledge from an OWL file instead.
+ *
+ * Copyright (C) 2007, Jens Lehmann
+ */
+algorithm = el;
+el.instanceBasedDisjoints = false;
+refexamples.useCardinalityRestrictions = false;
+reasoner = owlAPIReasoner;
+
+/*Background knowledge*/
+import("pair50.owl");
+
+/*Examples*/
+-"http://localhost/foo#hand0"
+-"http://localhost/foo#hand1"
+-"http://localhost/foo#hand2"
+-"http://localhost/foo#hand3"
+-"http://localhost/foo#hand4"
+-"http://localhost/foo#hand5"
+-"http://localhost/foo#hand6"
+-"http://localhost/foo#hand7"
+-"http://localhost/foo#hand8"
++"http://localhost/foo#hand9"
+-"http://localhost/foo#hand10"
+-"http://localhost/foo#hand11"
+-"http://localhost/foo#hand12"
++"http://localhost/foo#hand13"
+-"http://localhost/foo#hand14"
+-"http://localhost/foo#hand15"
+-"http://localhost/foo#hand16"
+-"http://localhost/foo#hand17"
++"http://localhost/foo#hand18"
++"http://localhost/foo#hand19"
+-"http://localhost/foo#hand20"
++"http://localhost/foo#hand21"
++"http://localhost/foo#hand22"
++"http://localhost/foo#hand23"
++"http://localhost/foo#hand24"
++"http://localhost/foo#hand25"
++"http://localhost/foo#hand26"
+-"http://localhost/foo#hand27"
+-"http://localhost/foo#hand28"
++"http://localhost/foo#hand29"
+-"http://localhost/foo#hand30"
+-"http://localhost/foo#hand31"
+-"http://localhost/foo#hand32"
+-"http://localhost/foo#hand33"
+-"http://localhost/foo#hand34"
++"http://localhost/foo#hand35"
++"http://localhost/foo#hand36"
+-"http://localhost/foo#hand37"
++"http://localhost/foo#hand38"
++"http://localhost/foo#hand39"
++"http://localhost/foo#hand40"
++"http://localhost/foo#hand41"
+-"http://localhost/foo#hand42"
++"http://localhost/foo#hand43"
+-"http://localhost/foo#hand44"
+-"http://localhost/foo#hand45"
+-"http://localhost/foo#hand46"
++"http://localhost/foo#hand47"
++"http://localhost/foo#hand48"
Added: trunk/examples/cross-benchmark/poker/pair_el_disjunctive.conf
===================================================================
--- trunk/examples/cross-benchmark/poker/pair_el_disjunctive.conf (rev 0)
+++ trunk/examples/cross-benchmark/poker/pair_el_disjunctive.conf 2009-12-01 17:59:11 UTC (rev 1927)
@@ -0,0 +1,64 @@
+/**
+ * See pair.conf. This is the same learning problem, but loading
+ * background knowledge from an OWL file instead.
+ *
+ * Copyright (C) 2007, Jens Lehmann
+ */
+algorithm = disjunctiveEL;
+disjunctiveEL.instanceBasedDisjoints = false;
+refexamples.useCardinalityRestrictions = false;
+reasoner = owlAPIReasoner;
+
+/*Background knowledge*/
+import("pair50.owl");
+
+/*Examples*/
+-"http://localhost/foo#hand0"
+-"http://localhost/foo#hand1"
+-"http://localhost/foo#hand2"
+-"http://localhost/foo#hand3"
+-"http://localhost/foo#hand4"
+-"http://localhost/foo#hand5"
+-"http://localhost/foo#hand6"
+-"http://localhost/foo#hand7"
+-"http://localhost/foo#hand8"
++"http://localhost/foo#hand9"
+-"http://localhost/foo#hand10"
+-"http://localhost/foo#hand11"
+-"http://localhost/foo#hand12"
++"http://localhost/foo#hand13"
+-"http://localhost/foo#hand14"
+-"http://localhost/foo#hand15"
+-"http://localhost/foo#hand16"
+-"http://localhost/foo#hand17"
++"http://localhost/foo#hand18"
++"http://localhost/foo#hand19"
+-"http://localhost/foo#hand20"
++"http://localhost/foo#hand21"
++"http://localhost/foo#hand22"
++"http://localhost/foo#hand23"
++"http://localhost/foo#hand24"
++"http://localhost/foo#hand25"
++"http://localhost/foo#hand26"
+-"http://localhost/foo#hand27"
+-"http://localhost/foo#hand28"
++"http://localhost/foo#hand29"
+-"http://localhost/foo#hand30"
+-"http://localhost/foo#hand31"
+-"http://localhost/foo#hand32"
+-"http://localhost/foo#hand33"
+-"http://localhost/foo#hand34"
++"http://localhost/foo#hand35"
++"http://localhost/foo#hand36"
+-"http://localhost/foo#hand37"
++"http://localhost/foo#hand38"
++"http://localhost/foo#hand39"
++"http://localhost/foo#hand40"
++"http://localhost/foo#hand41"
+-"http://localhost/foo#hand42"
++"http://localhost/foo#hand43"
+-"http://localhost/foo#hand44"
+-"http://localhost/foo#hand45"
+-"http://localhost/foo#hand46"
++"http://localhost/foo#hand47"
++"http://localhost/foo#hand48"
Added: trunk/examples/cross-benchmark/poker/straight_el.conf
===================================================================
--- trunk/examples/cross-benchmark/poker/straight_el.conf (rev 0)
+++ trunk/examples/cross-benchmark/poker/straight_el.conf 2009-12-01 17:59:11 UTC (rev 1927)
@@ -0,0 +1,71 @@
+/**
+ * See straight.conf. This is the same learning problem, but loading
+ * background knowledge from an OWL file instead.
+ *
+ * Copyright (C) 2007, Jens Lehmann
+ */
+
+/*Background knowledge*/
+algorithm = el;
+el.instanceBasedDisjoints = false;
+refexamples.useCardinalityRestrictions = false;
+reasoner = owlAPIReasoner;
+import("straight.owl");
+
+/*Examples*/
++"http://localhost/foo#hand1"
++"http://localhost/foo#hand22"
++"http://localhost/foo#hand40"
++"http://localhost/foo#hand44"
+
+-"http://localhost/foo#hand0"
+-"http://localhost/foo#hand2"
+-"http://localhost/foo#hand3"
+-"http://localhost/foo#hand4"
+-"http://localhost/foo#hand5"
+-"http://localhost/foo#hand6"
+-"http://localhost/foo#hand7"
+-"http://localhost/foo#hand8"
+-"http://localhost/foo#hand9"
+-"http://localhost/foo#hand10"
+-"http://localhost/foo#hand11"
+-"http://localhost/foo#hand12"
+-"http://localhost/foo#hand13"
+-"http://localhost/foo#hand14"
+-"http://localhost/foo#hand15"
+-"http://localhost/foo#hand16"
+-"http://localhost/foo#hand17"
+-"http://localhost/foo#hand18"
+-"http://localhost/foo#hand19"
+-"http://localhost/foo#hand20"
+-"http://localhost/foo#hand21"
+-"http://localhost/foo#hand23"
+-"http://localhost/foo#hand24"
+-"http://localhost/foo#hand25"
+-"http://localhost/foo#hand26"
+-"http://localhost/foo#hand27"
+-"http://localhost/foo#hand28"
+-"http://localhost/foo#hand29"
+-"http://localhost/foo#hand30"
+-"http://localhost/foo#hand31"
+-"http://localhost/foo#hand32"
+-"http://localhost/foo#hand33"
+-"http://localhost/foo#hand34"
+-"http://localhost/foo#hand35"
+-"http://localhost/foo#hand36"
+-"http://localhost/foo#hand37"
+-"http://localhost/foo#hand38"
+-"http://localhost/foo#hand39"
+-"http://localhost/foo#hand41"
+-"http://localhost/foo#hand42"
+-"http://localhost/foo#hand43"
+-"http://localhost/foo#hand45"
+-"http://localhost/foo#hand46"
+-"http://localhost/foo#hand47"
+-"http://localhost/foo#hand48"
+-"http://localhost/foo#hand49"
+-"http://localhost/foo#hand50"
+-"http://localhost/foo#hand51"
+-"http://localhost/foo#hand52"
+-"http://localhost/foo#hand53"
+-"http://localhost/foo#hand54"
Added: trunk/examples/cross-benchmark/poker/straight_el_disjunctive.conf
===================================================================
--- trunk/examples/cross-benchmark/poker/straight_el_disjunctive.conf (rev 0)
+++ trunk/examples/cross-benchmark/poker/straight_el_disjunctive.conf 2009-12-01 17:59:11 UTC (rev 1927)
@@ -0,0 +1,71 @@
+/**
+ * See straight.conf. This is the same learning problem, but loading
+ * background knowledge from an OWL file instead.
+ *
+ * Copyright (C) 2007, Jens Lehmann
+ */
+
+/*Background knowledge*/
+algorithm = disjunctiveEL;
+disjunctiveEL.instanceBasedDisjoints = false;
+refexamples.useCardinalityRestrictions = false;
+reasoner = owlAPIReasoner;
+import("straight.owl");
+
+/*Examples*/
++"http://localhost/foo#hand1"
++"http://localhost/foo#hand22"
++"http://localhost/foo#hand40"
++"http://localhost/foo#hand44"
+
+-"http://localhost/foo#hand0"
+-"http://localhost/foo#hand2"
+-"http://localhost/foo#hand3"
+-"http://localhost/foo#hand4"
+-"http://localhost/foo#hand5"
+-"http://localhost/foo#hand6"
+-"http://localhost/foo#hand7"
+-"http://localhost/foo#hand8"
+-"http://localhost/foo#hand9"
+-"http://localhost/foo#hand10"
+-"http://localhost/foo#hand11"
+-"http://localhost/foo#hand12"
+-"http://localhost/foo#hand13"
+-"http://localhost/foo#hand14"
+-"http://localhost/foo#hand15"
+-"http://localhost/foo#hand16"
+-"http://localhost/foo#hand17"
+-"http://localhost/foo#hand18"
+-"http://localhost/foo#hand19"
+-"http://localhost/foo#hand20"
+-"http://localhost/foo#hand21"
+-"http://localhost/foo#hand23"
+-"http://localhost/foo#hand24"
+-"http://localhost/foo#hand25"
+-"http://localhost/foo#hand26"
+-"http://localhost/foo#hand27"
+-"http://localhost/foo#hand28"
+-"http://localhost/foo#hand29"
+-"http://localhost/foo#hand30"
+-"http://localhost/foo#hand31"
+-"http://localhost/foo#hand32"
+-"http://localhost/foo#hand33"
+-"http://localhost/foo#hand34"
+-"http://localhost/foo#hand35"
+-"http://localhost/foo#hand36"
+-"http://localhost/foo#hand37"
+-"http://localhost/foo#hand38"
+-"http://localhost/foo#hand39"
+-"http://localhost/foo#hand41"
+-"http://localhost/foo#hand42"
+-"http://localhost/foo#hand43"
+-"http://localhost/foo#hand45"
+-"http://localhost/foo#hand46"
+-"http://localhost/foo#hand47"
+-"http://localhost/foo#hand48"
+-"http://localhost/foo#hand49"
+-"http://localhost/foo#hand50"
+-"http://localhost/foo#hand51"
+-"http://localhost/foo#hand52"
+-"http://localhost/foo#hand53"
+-"http://localhost/foo#hand54"
Added: trunk/examples/cross-benchmark/trains/trains_el.conf
===================================================================
--- trunk/examples/cross-benchmark/trains/trains_el.conf (rev 0)
+++ trunk/examples/cross-benchmark/trains/trains_el.conf 2009-12-01 17:59:11 UTC (rev 1927)
@@ -0,0 +1,28 @@
+/**
+ * See arch.conf. This is the same learning problem, but loading background
+ * knowledge from an OWL file instead.
+ *
+ * Copyright (C) 2007, Jens Lehmann
+ */
+
+algorithm = el;
+el.instanceBasedDisjoints = false;
+refexamples.useCardinalityRestrictions = false;
+reasoner = owlAPIReasoner;
+hidePrefix = "http://example.com/foo#";
+
+/*Background knowledge*/
+
+import("trains.owl");
+
+/*Examples*/
++"http://example.com/foo#east1"
++"http://example.com/foo#east2"
++"http://example.com/foo#east3"
++"http://example.com/foo#east4"
++"http://example.com/foo#east5"
+-"http://example.com/foo#west6"
+-"http://example.com/foo#west7"
+-"http://example.com/foo#west8"
+-"http://example.com/foo#west9"
+-"http://example.com/foo#west10"
Added: trunk/examples/cross-benchmark/trains/trains_el_disjunctive.conf
===================================================================
--- trunk/examples/cross-benchmark/trains/trains_el_disjunctive.conf (rev 0)
+++ trunk/examples/cross-benchmark/trains/trains_el_disjunctive.conf 2009-12-01 17:59:11 UTC (rev 1927)
@@ -0,0 +1,28 @@
+/**
+ * See arch.conf. This is the same learning problem, but loading background
+ * knowledge from an OWL file instead.
+ *
+ * Copyright (C) 2007, Jens Lehmann
+ */
+
+algorithm = disjunctiveEL;
+disjunctiveEL.instanceBasedDisjoints = false;
+refexamples.useCardinalityRestrictions = false;
+reasoner = owlAPIReasoner;
+hidePrefix = "http://example.com/foo#";
+
+/*Background knowledge*/
+
+import("trains.owl");
+
+/*Examples*/
++"http://example.com/foo#east1"
++"http://example.com/foo#east2"
++"http://example.com/foo#east3"
++"http://example.com/foo#east4"
++"http://example.com/foo#east5"
+-"http://example.com/foo#west6"
+-"http://example.com/foo#west7"
+-"http://example.com/foo#west8"
+-"http://example.com/foo#west9"
+-"http://example.com/foo#west10"
Modified: trunk/src/dl-learner/org/dllearner/algorithms/celoe/CELOE.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/celoe/CELOE.java 2009-11-30 15:49:23 UTC (rev 1926)
+++ trunk/src/dl-learner/org/dllearner/algorithms/celoe/CELOE.java 2009-12-01 17:59:11 UTC (rev 1927)
@@ -49,6 +49,7 @@
import org.dllearner.core.owl.Thing;
import org.dllearner.learningproblems.ClassLearningProblem;
import org.dllearner.learningproblems.PosNegLP;
+import org.dllearner.learningproblems.PosNegLPStandard;
import org.dllearner.learningproblems.PosOnlyLP;
import org.dllearner.refinementoperators.RefinementOperator;
import org.dllearner.refinementoperators.RhoDRDown;
@@ -393,7 +394,7 @@
if(accuracy > bestAccuracy) {
bestAccuracy = accuracy;
bestDescription = description;
- logger.info("more accurate (" + dfPercent.format(bestAccuracy) + ") class expression found: " + descriptionToString(bestDescription));
+ logger.info("more accurate (" + dfPercent.format(bestAccuracy) + ") class expression found: " + descriptionToString(bestDescription)); // + getTemporaryString(bestDescription));
}
return true;
}
@@ -574,12 +575,21 @@
int current = 1;
String str = "";
for(EvaluatedDescription ed : bestEvaluatedDescriptions.getSet().descendingSet()) {
- str += current + ": " + descriptionToString(ed.getDescription()) + " " + dfPercent.format(ed.getAccuracy()) + "\n";
+ // temporary code
+ if(learningProblem instanceof PosNegLPStandard) {
+ str += current + ": " + descriptionToString(ed.getDescription()) + " (pred. acc.: " + dfPercent.format(((PosNegLPStandard)learningProblem).getPredAccuracyOrTooWeakExact(ed.getDescription(),1)) + ", F-measure: "+ dfPercent.format(((PosNegLPStandard)learningProblem).getFMeasureOrTooWeakExact(ed.getDescription(),1)) + ")\n";
+ } else {
+ str += current + ": " + descriptionToString(ed.getDescription()) + " " + dfPercent.format(ed.getAccuracy()) + "\n";
+ }
current++;
}
return str;
}
+// private String getTemporaryString(Description description) {
+// return descriptionToString(description) + " (pred. acc.: " + dfPercent.format(((PosNegLPStandard)learningProblem).getPredAccuracyOrTooWeakExact(description,1)) + ", F-measure: "+ dfPercent.format(((PosNegLPStandard)learningProblem).getFMeasureOrTooWeakExact(description,1)) + ")";
+// }
+
private void updateMinMaxHorizExp(OENode node) {
int newHorizExp = node.getHorizontalExpansion();
Modified: trunk/src/dl-learner/org/dllearner/algorithms/celoe/OEHeuristicRuntime.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/celoe/OEHeuristicRuntime.java 2009-11-30 15:49:23 UTC (rev 1926)
+++ trunk/src/dl-learner/org/dllearner/algorithms/celoe/OEHeuristicRuntime.java 2009-12-01 17:59:11 UTC (rev 1927)
@@ -34,7 +34,7 @@
public class OEHeuristicRuntime implements Comparator<OENode>{
// strong penalty for long descriptions
- private double expansionPenaltyFactor = 0.1;
+ private double expansionPenaltyFactor = 0.01; // 0.1;
// bonus for being better than parent node
private double gainBonusFactor = 0.3;
// penalty if a node description has very many refinements since exploring
Modified: trunk/src/dl-learner/org/dllearner/algorithms/el/ELLearningAlgorithm.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/el/ELLearningAlgorithm.java 2009-11-30 15:49:23 UTC (rev 1926)
+++ trunk/src/dl-learner/org/dllearner/algorithms/el/ELLearningAlgorithm.java 2009-12-01 17:59:11 UTC (rev 1927)
@@ -32,6 +32,9 @@
import org.dllearner.core.ReasonerComponent;
import org.dllearner.core.configurators.Configurator;
import org.dllearner.core.configurators.ELLearningAlgorithmConfigurator;
+import org.dllearner.core.options.CommonConfigOptions;
+import org.dllearner.core.options.ConfigOption;
+import org.dllearner.core.options.StringConfigOption;
import org.dllearner.core.owl.Description;
import org.dllearner.core.owl.Thing;
import org.dllearner.learningproblems.EvaluatedDescriptionPosNeg;
@@ -59,6 +62,9 @@
private boolean isRunning = false;
private boolean stop = false;
+ private double treeSearchTimeSeconds = 1.0;
+ private long treeStartTime;
+
// a set with limited size (currently the ordering is defined in the class itself)
private EvaluatedDescriptionSet bestEvaluatedDescriptions = new EvaluatedDescriptionSet(LearningAlgorithm.MAX_NR_OF_RESULTS);
@@ -68,6 +74,7 @@
public ELLearningAlgorithm(PosNegLP problem, ReasonerComponent reasoner) {
super(problem, reasoner);
+ configurator = new ELLearningAlgorithmConfigurator(this);
}
public static String getName() {
@@ -90,13 +97,21 @@
return configurator;
}
+ public static Collection<ConfigOption<?>> createConfigOptions() {
+ Collection<ConfigOption<?>> options = new LinkedList<ConfigOption<?>>();
+// options.add(CommonConfigOptions.getNoisePercentage());
+// options.add(new StringConfigOption("startClass", "the named class which should be used to start the algorithm (GUI: needs a widget for selecting a class)"));
+ options.add(CommonConfigOptions.getInstanceBasedDisjoints());
+ return options;
+ }
+
@Override
public void init() throws ComponentInitException {
// currently we use the stable heuristic
heuristic = new StableHeuristic();
candidates = new TreeSet<SearchTreeNode>(heuristic);
- operator = new ELDown2(reasoner);
+ operator = new ELDown2(reasoner, configurator.getInstanceBasedDisjoints());
}
@Override
@@ -104,6 +119,7 @@
stop = false;
isRunning = true;
reset();
+ treeStartTime = System.nanoTime();
// create start node
ELDescriptionTree top = new ELDescriptionTree(reasoner, Thing.instance);
@@ -157,9 +173,13 @@
parentNode.addChild(node);
}
+// System.out.println("TEST");
+
if(!node.isTooWeak()) {
// add as candidate
candidates.add(node);
+
+// System.out.println("TEST2");
// check whether we want to add it to the best evaluated descriptions;
// to do this we pick the worst considered evaluated description
@@ -178,6 +198,19 @@
}
private boolean stoppingCriteriaSatisfied() {
+ // in some cases, there could be no candidate left ...
+ if(candidates.isEmpty()) {
+ return true;
+ }
+
+ // stop when max time is reached
+ long runTime = System.nanoTime() - treeStartTime;
+ double runTimeSeconds = runTime / (double) 1000000000;
+
+ if(runTimeSeconds >= treeSearchTimeSeconds) {
+ return true;
+ }
+
// stop if we have a node covering all positives and none of the negatives
SearchTreeNode bestNode = candidates.last();
return (bestNode.getCoveredNegatives() == 0);
Modified: trunk/src/dl-learner/org/dllearner/algorithms/el/ELLearningAlgorithmDisjunctive.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/algorithms/el/ELLearningAlgorithmDisjunctive.java 2009-11-30 15:49:23 UTC (rev 1926)
+++ trunk/src/dl-learner/org/dllearner/algorithms/el/ELLearningAlgorithmDisjunctive.java 2009-12-01 17:59:11 UTC (rev 1927)
@@ -141,6 +141,7 @@
Collection<ConfigOption<?>> options = new LinkedList<ConfigOption<?>>();
options.add(CommonConfigOptions.getNoisePercentage());
options.add(new StringConfigOption("startClass", "the named class which should be used to start the algorithm (GUI: needs a widget for selecting a class)"));
+ options.add(CommonConfigOptions.getInstanceBasedDisjoints());
return options;
}
@@ -165,7 +166,7 @@
} else {
startClass = Thing.instance;
}
- operator = new ELDown2(reasoner);
+ operator = new ELDown2(reasoner, configurator.getInstanceBasedDisjoints());
// noise = configurator.getNoisePercentage()/(double)100;
@@ -365,6 +366,11 @@
}
private boolean treeCriteriaSatisfied() {
+ // stop if there are no more candidates (unlikely, but can happen)
+ if(candidates.isEmpty()) {
+ return true;
+ }
+
long runTime = System.nanoTime() - treeStartTime;
double runTimeSeconds = runTime / (double) 1000000000;
@@ -376,6 +382,7 @@
}
private boolean stoppingCriteriaSatisfied() {
+
// stop if we have a node covering all positives and none of the negatives
// SearchTreeNode bestNode = candidates.last();
// return (bestNode.getCoveredNegatives() == 0);
Modified: trunk/src/dl-learner/org/dllearner/core/configurators/ELLearningAlgorithmConfigurator.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/configurators/ELLearningAlgorithmConfigurator.java 2009-11-30 15:49:23 UTC (rev 1926)
+++ trunk/src/dl-learner/org/dllearner/core/configurators/ELLearningAlgorithmConfigurator.java 2009-12-01 17:59:11 UTC (rev 1927)
@@ -55,7 +55,25 @@
return component;
}
+/**
+* instanceBasedDisjoints Specifies whether to use real disjointness checks or instance based ones (no common instances) in the refinement operator..
+* mandatory: false| reinit necessary: true
+* default value: true
+* @return boolean
+**/
+public boolean getInstanceBasedDisjoints() {
+return (Boolean) ComponentManager.getInstance().getConfigOptionValue(eLLearningAlgorithm, "instanceBasedDisjoints") ;
+}
+/**
+* @param instanceBasedDisjoints Specifies whether to use real disjointness checks or instance based ones (no common instances) in the refinement operator..
+* mandatory: false| reinit necessary: true
+* default value: true
+**/
+public void setInstanceBasedDisjoints(boolean instanceBasedDisjoints) {
+ComponentManager.getInstance().applyConfigEntry(eLLearningAlgorithm, "instanceBasedDisjoints", instanceBasedDisjoints);
+reinitNecessary = true;
+}
/**
* true, if this component needs reinitializsation.
Modified: trunk/src/dl-learner/org/dllearner/core/configurators/ELLearningAlgorithmDisjunctiveConfigurator.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/configurators/ELLearningAlgorithmDisjunctiveConfigurator.java 2009-11-30 15:49:23 UTC (rev 1926)
+++ trunk/src/dl-learner/org/dllearner/core/configurators/ELLearningAlgorithmDisjunctiveConfigurator.java 2009-12-01 17:59:11 UTC (rev 1927)
@@ -73,6 +73,15 @@
public String getStartClass() {
return (String) ComponentManager.getInstance().getConfigOptionValue(eLLearningAlgorithmDisjunctive, "startClass") ;
}
+/**
+* instanceBasedDisjoints Specifies whether to use real disjointness checks or instance based ones (no common instances) in the refinement operator..
+* mandatory: false| reinit necessary: true
+* default value: true
+* @return boolean
+**/
+public boolean getInstanceBasedDisjoints() {
+return (Boolean) ComponentManager.getInstance().getConfigOptionValue(eLLearningAlgorithmDisjunctive, "instanceBasedDisjoints") ;
+}
/**
* @param noisePercentage the (approximated) percentage of noise within the examples.
@@ -92,6 +101,15 @@
ComponentManager.getInstance().applyConfigEntry(eLLearningAlgorithmDisjunctive, "startClass", startClass);
reinitNecessary = true;
}
+/**
+* @param instanceBasedDisjoints Specifies whether to use real disjointness checks or instance based ones (no common instances) in the refinement operator..
+* mandatory: false| reinit necessary: true
+* default value: true
+**/
+public void setInstanceBasedDisjoints(boolean instanceBasedDisjoints) {
+ComponentManager.getInstance().applyConfigEntry(eLLearningAlgorithmDisjunctive, "instanceBasedDisjoints", instanceBasedDisjoints);
+reinitNecessary = true;
+}
/**
* true, if this component needs reinitializsation.
Modified: trunk/src/dl-learner/org/dllearner/core/configurators/PosNegLPStandardConfigurator.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/configurators/PosNegLPStandardConfigurator.java 2009-11-30 15:49:23 UTC (rev 1926)
+++ trunk/src/dl-learner/org/dllearner/core/configurators/PosNegLPStandardConfigurator.java 2009-12-01 17:59:11 UTC (rev 1927)
@@ -106,7 +106,7 @@
/**
* useApproximations whether to use stochastic approximations for computing accuracy.
* mandatory: false| reinit necessary: true
-* default value: true
+* default value: false
* @return boolean
**/
public boolean getUseApproximations() {
@@ -124,7 +124,7 @@
/**
* accuracyMethod Specifies, which method/function to use for computing accuracy..
* mandatory: false| reinit necessary: true
-* default value: standard
+* default value: predacc
* @return String
**/
public String getAccuracyMethod() {
@@ -177,7 +177,7 @@
/**
* @param useApproximations whether to use stochastic approximations for computing accuracy.
* mandatory: false| reinit necessary: true
-* default value: true
+* default value: false
**/
public void setUseApproximations(boolean useApproximations) {
ComponentManager.getInstance().applyConfigEntry(posNegLPStandard, "useApproximations", useApproximations);
@@ -195,7 +195,7 @@
/**
* @param accuracyMethod Specifies, which method/function to use for computing accuracy..
* mandatory: false| reinit necessary: true
-* default value: standard
+* default value: predacc
**/
public void setAccuracyMethod(String accuracyMethod) {
ComponentManager.getInstance().applyConfigEntry(posNegLPStandard, "accuracyMethod", accuracyMethod);
Modified: trunk/src/dl-learner/org/dllearner/core/options/CommonConfigOptions.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/core/options/CommonConfigOptions.java 2009-11-30 15:49:23 UTC (rev 1926)
+++ trunk/src/dl-learner/org/dllearner/core/options/CommonConfigOptions.java 2009-12-01 17:59:11 UTC (rev 1927)
@@ -57,6 +57,7 @@
public static String logLevelDefault = "DEBUG";
public static double noisePercentageDefault = 0.0;
public static boolean terminateOnNoiseReachedDefault = true;
+ public static boolean instanceBasedDisjointsDefault = true;
public static StringConfigOption getVerbosityOption() {
StringConfigOption verbosityOption = new StringConfigOption("verbosity", "control verbosity of output for this component", "warning");
@@ -195,4 +196,8 @@
public static StringConfigOption getLogLevel() {
return new StringConfigOption("logLevel", "determines the logLevel for this component, can be {TRACE, DEBUG, INFO}",logLevelDefault);
}
+
+ public static BooleanConfigOption getInstanceBasedDisjoints() {
+ return new BooleanConfigOption("instanceBasedDisjoints", "Specifies whether to use real disjointness checks or instance based ones (no common instances) in the refinement operator.", instanceBasedDisjointsDefault);
+ }
}
Modified: trunk/src/dl-learner/org/dllearner/examples/MonogenicDiseases.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/examples/MonogenicDiseases.java 2009-11-30 15:49:23 UTC (rev 1926)
+++ trunk/src/dl-learner/org/dllearner/examples/MonogenicDiseases.java 2009-12-01 17:59:11 UTC (rev 1927)
@@ -371,7 +371,7 @@
// generate a class with all positive examples (optional)
if(generatePosExampleClass) {
String phenotype = rs.getString("phenotype");
- if(phenotype.toLowerCase().contains("polymorphism")) {
+ if(!phenotype.toLowerCase().contains("polymorphism")) {
kb.addAxiom(new ClassAssertionAxiom(deleteriousMutationClass, mutationInd));
}
}
@@ -385,13 +385,13 @@
long startWriteTime = System.nanoTime();
OWLAPIReasoner.exportKBToOWL(owlFile, kb, ontologyURI);
long writeDuration = System.nanoTime() - startWriteTime;
- System.out.println("OK (time: " + Helper.prettyPrintNanoSeconds(writeDuration) + "; file size: " + owlFile.length()/1024 + " KB).");
+ System.out.println("OK (entities: " + count + "; time: " + Helper.prettyPrintNanoSeconds(writeDuration) + "; file size: " + owlFile.length()/1024 + " KB).");
// selecting examples
// -> only a fraction of examples are selected as positive/negative
if(pgSQL) {
rs = stmt.executeQuery("SELECT * FROM fiche_mutant, mutants WHERE fiche_mutant.id=mutants.id AND " //lower(phenotype) not like 'polymorphism' AND "
- + " (gain_contact is not null) AND (gain_contact != 0)");
+ + " (gain_contact is not null)"); // AND (gain_contact != 0)");
} else {
rs = stmt.executeQuery("SELECT * FROM " + table + " WHERE " //lower(phenotype) not like 'polymorphism' AND "
+ " (gain_contact is not null) AND (gain_contact != 0)");
@@ -407,33 +407,28 @@
posExamples.add(new Individual(getURI("mutation" + mutationID)));
}
}
-
- // conf example:
-
-// import("mutation.owl");
-//
-// reasoner = fastInstanceChecker;
-//
-// problem = classLearning;
-// classLearning.classToDescribe = "http://dl-learner.org/mutation#DeletoriousMutation";
-// classLearning.accuracyMethod = "fmeasure";
-// classLearning.approxAccuracy = 0.03;
-//
-// algorithm = celoe;
-// celoe.maxExecutionTimeInSeconds = 10;
-// celoe.noisePercentage = 10;
-// celoe.maxNrOfResults = 1;
-// celoe.singleSuggestionMode = true;
-
+
// writing conf file
Files.clearFile(confFile);
String confHeader = "import(\"" + owlFile.getName() + "\");\n\n";
confHeader += "reasoner = fastInstanceChecker;\n";
+
confHeader += "problem = classLearning;\n";
- confHeader += "classLearning.classToDescribe = \"" + deleteriousMutationClass + "\";\n";
+ confHeader += "classLearning.classToDescribe = \"" + deleteriousMutationClass + "\";\n";
+ confHeader += "classLearning.accuracyMethod = \"fmeasure\";\n";
+ confHeader += "classLearning.approxAccuracy = 0.03;\n";
+
+// confHeader += "problem = posNegLPStandard;\n";
+// confHeader += "posNegLPStandard.useApproximations = true;\n";
+// confHeader += "posNegLPStandard.accuracyMethod = \"fmeasure\";\n";
+// confHeader += "posNegLPStandard.approxAccuracy = 0.03;\n";
+
confHeader += "algorithm = celoe;\n";
- confHeader += "celoe.maxExecutionTimeInSeconds = 100;\n";
- confHeader += "celoe.noisePercentage = 25;\n";
+ confHeader += "celoe.maxExecutionTimeInSeconds = 10;\n";
+ confHeader += "celoe.noisePercentage = 10;\n";
+ confHeader += "celoe.singleSuggestionMode = true;\n";
+ confHeader += "celoe.useNegation = true;\n";
+
// confHeader += "refexamples.noisePercentage = 15;\n";
// confHeader += "refexamples.startClass = \"" + getURI("Mutation") + "\";\n";
// confHeader += "refexamples.writeSearchTree = false;\n";
@@ -446,6 +441,7 @@
}
long runTime = System.nanoTime() - startTime;
+ System.out.println("Conf file written with " + posExamples.size() + " positive and " + negExamples.size() + " negative examples.");
System.out.println("Database successfully converted in " + Helper.prettyPrintNanoSeconds(runTime) + ".");
}
Modified: trunk/src/dl-learner/org/dllearner/learningproblems/ClassLearningProblem.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/learningproblems/ClassLearningProblem.java 2009-11-30 15:49:23 UTC (rev 1926)
+++ trunk/src/dl-learner/org/dllearner/learningproblems/ClassLearningProblem.java 2009-12-01 17:59:11 UTC (rev 1927)
@@ -138,6 +138,8 @@
Random rand = new Random(1);
Collections.shuffle(classInstances, rand);
Collections.shuffle(superClassInstances, rand);
+
+ System.out.println(classInstances.size() + " " + superClassInstances.size());
}
/**
Modified: trunk/src/dl-learner/org/dllearner/learningproblems/PosNegLPStandard.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/learningproblems/PosNegLPStandard.java 2009-11-30 15:49:23 UTC (rev 1926)
+++ trunk/src/dl-learner/org/dllearner/learningproblems/PosNegLPStandard.java 2009-12-01 17:59:11 UTC (rev 1927)
@@ -293,14 +293,14 @@
throw new Error("approximating pred. acc not implemented");
}
} else {
- return getAccuracyOrTooWeakExact(description, noise);
+ return getPredAccuracyOrTooWeakExact(description, noise);
}
}
/* (non-Javadoc)
* @see org.dllearner.core.LearningProblem#getAccuracyOrTooWeak(org.dllearner.core.owl.Description, double)
*/
- public double getAccuracyOrTooWeakExact(Description description, double noise) {
+ public double getPredAccuracyOrTooWeakExact(Description description, double noise) {
int maxNotCovered = (int) Math.ceil(noise*positiveExamples.size());
@@ -321,9 +321,41 @@
}
}
- return positiveExamples.size() - notCoveredPos + notCoveredNeg / (double) allExamples.size();
+// if(useFMeasure) {
+// double recall = (positiveExamples.size() - notCoveredPos) / (double) positiveExamples.size();
+// double precision = (positiveExamples.size() - notCoveredPos) / (double) (allExamples.size() - notCoveredPos - notCoveredNeg);
+// return getFMeasure(recall, precision);
+// } else {
+ return (positiveExamples.size() - notCoveredPos + notCoveredNeg) / (double) allExamples.size();
+// }
}
+ public double getFMeasureOrTooWeakExact(Description description, double noise) {
+ int additionalInstances = 0;
+ for(Individual ind : negativeExamples) {
+ if(reasoner.hasType(description, ind)) {
+ additionalInstances++;
+ }
+ }
+
+ int coveredInstances = 0;
+ for(Individual ind : positiveExamples) {
+ if(reasoner.hasType(description, ind)) {
+ coveredInstances++;
+ }
+ }
+
+ double recall = coveredInstances/(double)positiveExamples.size();
+
+ if(recall < 1 - noise) {
+ return -1;
+ }
+
+ double precision = (additionalInstances + coveredInstances == 0) ? 0 : coveredInstances / (double) (coveredInstances + additionalInstances);
+
+ return getFMeasure(recall, precision);
+ }
+
// instead of using the standard operation, we use optimisation
// and approximation here
public double getFMeasureOrTooWeakApprox(Description description, double noise) {
@@ -438,6 +470,12 @@
precision = 0;
}
+// System.out.println("description: " + description);
+// System.out.println("recall: " + recall);
+// System.out.println("precision: " + precision);
+// System.out.println("F-measure: " + getFMeasure(recall, precision));
+// System.out.println("exact: " + getAccuracyOrTooWeakExact(description, noise));
+
return getFMeasure(recall, precision);
}
Modified: trunk/src/dl-learner/org/dllearner/refinementoperators/ELDown2.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/refinementoperators/ELDown2.java 2009-11-30 15:49:23 UTC (rev 1926)
+++ trunk/src/dl-learner/org/dllearner/refinementoperators/ELDown2.java 2009-12-01 17:59:11 UTC (rev 1927)
@@ -103,6 +103,10 @@
private TreeAndRoleSetComparator mComp = new TreeAndRoleSetComparator();
public ELDown2(ReasonerComponent rs) {
+ this(rs, true);
+ }
+
+ public ELDown2(ReasonerComponent rs, boolean instanceBasedDisjoints) {
this.rs = rs;
subsumptionHierarchy = rs.getClassHierarchy();
opHierarchy = rs.getObjectPropertyHierarchy();
@@ -114,7 +118,7 @@
opRanges.put(op, rs.getRange(op));
}
- utility = new Utility(rs, opDomains);
+ utility = new Utility(rs, opDomains, instanceBasedDisjoints);
}
/* (non-Javadoc)
@@ -182,6 +186,9 @@
// call ncc (see paper)
Set<NamedClass> candidates = utility.getClassCandidates(index, v.getLabel());
+// System.out.println("index: " + index + " label: " + v.getLabel());
+// System.out.println("candidates: " + candidates);
+
for(NamedClass nc : candidates) {
// clone operation
ELDescriptionTree clonedTree = tree.clone();
Modified: trunk/src/dl-learner/org/dllearner/refinementoperators/Utility.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/refinementoperators/Utility.java 2009-11-30 15:49:23 UTC (rev 1926)
+++ trunk/src/dl-learner/org/dllearner/refinementoperators/Utility.java 2009-12-01 17:59:11 UTC (rev 1927)
@@ -58,7 +58,6 @@
// specifies whether to do real disjoint tests or check that
// two named classes do not have common instances
- // TODO: turn this into a parameter
private boolean instanceBasedDisjoints = true;
// cache for reasoner queries
@@ -71,11 +70,12 @@
throw new Error("not implemented yet");
}
- public Utility(ReasonerComponent rs, Map<ObjectProperty,Description> opDomains) {
+ public Utility(ReasonerComponent rs, Map<ObjectProperty,Description> opDomains, boolean instanceBasedDisjoints) {
this.reasoner = rs;
sh = rs.getClassHierarchy();
// we cache object property domains
this.opDomains = opDomains;
+ this.instanceBasedDisjoints = instanceBasedDisjoints;
}
/**
@@ -134,6 +134,7 @@
// for 2 of them we can stop further traversal in the subsumption
// hierarchy
for(Description d : sh.getSubClasses(upperClass)) {
+// System.out.println("d: " + d);
// owl:Nothing is never a candidate (not in EL)
if(!(d instanceof Nothing)) {
NamedClass candidate = (NamedClass) d;
@@ -151,6 +152,7 @@
// candidate went successfully through all checks
candidates.add(candidate);
} else {
+// System.out.println("k32: " + candidate + " index " + index + " cond1 " + isDisjoint(new Negation(candidate),index) + " cond2 " + checkSuperClasses(existingClasses,candidate));
// descend subsumption hierarchy to find candidates
candidates.addAll(getClassCandidatesRecursive(index, existingClasses, candidate));
}
Modified: trunk/src/dl-learner/org/dllearner/scripts/PaperStatistics.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/scripts/PaperStatistics.java 2009-11-30 15:49:23 UTC (rev 1926)
+++ trunk/src/dl-learner/org/dllearner/scripts/PaperStatistics.java 2009-12-01 17:59:11 UTC (rev 1927)
@@ -119,8 +119,10 @@
String[] algorithmPostfix = new String[4];
algorithmPostfix[0] = "_refexamples";
algorithmPostfix[1] = "_refexamples_fast";
- algorithmPostfix[2] = "_gp";
- algorithmPostfix[3] = "_hybrid";
+ algorithmPostfix[2] = "_el";
+ algorithmPostfix[3] = "_el_disjunctive";
+// algorithmPostfix[4] = "_gp";
+// algorithmPostfix[5] = "_hybrid";
int startAlgorithmNr = 0;
// only max. 4 folds for straight problem
Modified: trunk/src/dl-learner/org/dllearner/test/junit/ELDownTests.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/test/junit/ELDownTests.java 2009-11-30 15:49:23 UTC (rev 1926)
+++ trunk/src/dl-learner/org/dllearner/test/junit/ELDownTests.java 2009-12-01 17:59:11 UTC (rev 1927)
@@ -41,6 +41,7 @@
import org.dllearner.core.owl.Description;
import org.dllearner.core.owl.NamedClass;
import org.dllearner.core.owl.ObjectProperty;
+import org.dllearner.core.owl.Thing;
import org.dllearner.kb.OWLFile;
import org.dllearner.parser.KBParser;
import org.dllearner.parser.ParseException;
@@ -313,6 +314,21 @@
}
+ @Test
+ public void test5() {
+ ReasonerComponent rs = TestOntologies.getTestOntology(TestOntology.TRAINS_OWL);
+ RefinementOperator operator = new ELDown2(rs);
+ Set<Description> refinements = operator.refine(Thing.instance);
+ for(Description refinement : refinements) {
+ System.out.println(refinement);
+ }
+
+// Set<Description> subClasses = rs.getSubClasses(Thing.instance);
+// for(Description cl : subClasses) {
+// System.out.println(cl);
+// }
+ }
+
// not part of the regular test suite, since Galen 2 is required
// @Test
public void asTest() throws ComponentInitException, MalformedURLException {
Modified: trunk/src/dl-learner/org/dllearner/test/junit/TestOntologies.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/test/junit/TestOntologies.java 2009-11-30 15:49:23 UTC (rev 1926)
+++ trunk/src/dl-learner/org/dllearner/test/junit/TestOntologies.java 2009-12-01 17:59:11 UTC (rev 1927)
@@ -32,6 +32,7 @@
import org.dllearner.parser.KBParser;
import org.dllearner.parser.ParseException;
import org.dllearner.reasoning.FastInstanceChecker;
+import org.dllearner.reasoning.OWLAPIReasoner;
/**
* Some ontologies to simplify unit tests.
@@ -41,7 +42,7 @@
*/
public final class TestOntologies {
- public enum TestOntology { EMPTY, SIMPLE, SIMPLE_NO_DR, SIMPLE_NO_DISJOINT, SIMPLE_NO_DR_DISJOINT, SIMPLE2, SIMPLE3, R1SUBR2, DATA1, FIVE_ROLES, FATHER_OE, CARCINOGENESIS, EPC_OE, KRK_ZERO_ONE, DBPEDIA_OWL };
+ public enum TestOntology { EMPTY, SIMPLE, SIMPLE_NO_DR, SIMPLE_NO_DISJOINT, SIMPLE_NO_DR_DISJOINT, SIMPLE2, SIMPLE3, R1SUBR2, DATA1, FIVE_ROLES, FATHER_OE, CARCINOGENESIS, EPC_OE, KRK_ZERO_ONE, DBPEDIA_OWL, TRAINS_OWL };
public static ReasonerComponent getTestOntology(TestOntology ont) {
String kbString = "";
@@ -119,7 +120,9 @@
owlFile = "examples/krk/KRK_ZERO_ONE.owl";
} else if(ont.equals(TestOntology.DBPEDIA_OWL)) {
owlFile = "/home/jl/promotion/ontologien/dbpedia.owl";
- }
+ } else if(ont.equals(TestOntology.TRAINS_OWL)) {
+ owlFile = "examples/cross-benchmark/trains/trains.owl";
+ }
try {
ComponentManager cm = ComponentManager.getInstance();
@@ -139,7 +142,8 @@
}
}
- ReasonerComponent rc = cm.reasoner(FastInstanceChecker.class, source);
+ ReasonerComponent rc = cm.reasoner(OWLAPIReasoner.class, source);
+// ReasonerComponent rc = cm.reasoner(FastInstanceChecker.class, source);
source.init();
rc.init();
return rc;
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