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Posted to commits@ctakes.apache.org by ja...@apache.org on 2013/08/02 18:48:16 UTC
svn commit: r1509770 [3/4] - in /ctakes/branches/ctakes-3.1.0: ./
ctakes-assertion-res/ ctakes-assertion-zoner-res/ ctakes-assertion-zoner/
ctakes-assertion/
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/attributes/features/selection/
ctak...
Modified: ctakes/branches/ctakes-3.1.0/ctakes-preprocessor/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-preprocessor/pom.xml?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-preprocessor/pom.xml (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-preprocessor/pom.xml Fri Aug 2 16:48:14 2013
@@ -1,53 +1,53 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!--
-
- Licensed to the Apache Software Foundation (ASF) under one
- or more contributor license agreements. See the NOTICE file
- distributed with this work for additional information
- regarding copyright ownership. The ASF licenses this file
- to you under the Apache License, Version 2.0 (the
- "License"); you may not use this file except in compliance
- with the License. You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
- Unless required by applicable law or agreed to in writing,
- software distributed under the License is distributed on an
- "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- KIND, either express or implied. See the License for the
- specific language governing permissions and limitations
- under the License.
-
--->
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
- <modelVersion>4.0.0</modelVersion>
- <artifactId>ctakes-preprocessor</artifactId>
- <name>Apache cTAKES document preprocessor</name>
- <parent>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes</artifactId>
- <version>3.1.0-SNAPSHOT</version>
- </parent>
- <dependencies>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-type-system</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-core</artifactId>
- </dependency>
- <dependency>
- <groupId>xerces</groupId>
- <artifactId>xercesImpl</artifactId>
- </dependency>
- <dependency>
- <groupId>log4j</groupId>
- <artifactId>log4j</artifactId>
- </dependency>
- <dependency>
- <groupId>junit</groupId>
- <artifactId>junit</artifactId>
- </dependency>
- </dependencies>
-</project>
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+ Licensed to the Apache Software Foundation (ASF) under one
+ or more contributor license agreements. See the NOTICE file
+ distributed with this work for additional information
+ regarding copyright ownership. The ASF licenses this file
+ to you under the Apache License, Version 2.0 (the
+ "License"); you may not use this file except in compliance
+ with the License. You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing,
+ software distributed under the License is distributed on an
+ "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ KIND, either express or implied. See the License for the
+ specific language governing permissions and limitations
+ under the License.
+
+-->
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <artifactId>ctakes-preprocessor</artifactId>
+ <name>Apache cTAKES document preprocessor</name>
+ <parent>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes</artifactId>
+ <version>3.1.0</version>
+ </parent>
+ <dependencies>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-type-system</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-core</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>xerces</groupId>
+ <artifactId>xercesImpl</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>log4j</groupId>
+ <artifactId>log4j</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>junit</groupId>
+ <artifactId>junit</artifactId>
+ </dependency>
+ </dependencies>
+</project>
Modified: ctakes/branches/ctakes-3.1.0/ctakes-regression-test/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-regression-test/pom.xml?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-regression-test/pom.xml (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-regression-test/pom.xml Fri Aug 2 16:48:14 2013
@@ -3,7 +3,7 @@
<parent>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes</artifactId>
- <version>3.1.0-SNAPSHOT</version>
+ <version>3.1.0</version>
</parent>
<artifactId>ctakes-regression-test</artifactId>
<name>Apache cTAKES Regression-test</name>
Modified: ctakes/branches/ctakes-3.1.0/ctakes-regression-test/src/test/java/org/apache/ctakes/regression/test/RegressionPipelineTest.java
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-regression-test/src/test/java/org/apache/ctakes/regression/test/RegressionPipelineTest.java?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-regression-test/src/test/java/org/apache/ctakes/regression/test/RegressionPipelineTest.java (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-regression-test/src/test/java/org/apache/ctakes/regression/test/RegressionPipelineTest.java Fri Aug 2 16:48:14 2013
@@ -88,7 +88,7 @@ public class RegressionPipelineTest exte
+ file.getName().substring(0,
file.getName().indexOf(".")));
- logger.info("Creating Dir" + generated);
+ logger.info("Creating directory: " + generated);
Assert.assertTrue(
"Unable to create " + generated.getAbsolutePath(),
Modified: ctakes/branches/ctakes-3.1.0/ctakes-relation-extractor-res/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-relation-extractor-res/pom.xml?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-relation-extractor-res/pom.xml (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-relation-extractor-res/pom.xml Fri Aug 2 16:48:14 2013
@@ -24,7 +24,7 @@
<parent>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes</artifactId>
- <version>3.1.0-SNAPSHOT</version>
+ <version>3.1.0</version>
</parent>
<artifactId>ctakes-relation-extractor-res</artifactId>
<name>Apache cTAKES Resources relation-extractor</name>
Modified: ctakes/branches/ctakes-3.1.0/ctakes-relation-extractor/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-relation-extractor/pom.xml?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-relation-extractor/pom.xml (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-relation-extractor/pom.xml Fri Aug 2 16:48:14 2013
@@ -1,168 +1,168 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!--
-
- Licensed to the Apache Software Foundation (ASF) under one
- or more contributor license agreements. See the NOTICE file
- distributed with this work for additional information
- regarding copyright ownership. The ASF licenses this file
- to you under the Apache License, Version 2.0 (the
- "License"); you may not use this file except in compliance
- with the License. You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
- Unless required by applicable law or agreed to in writing,
- software distributed under the License is distributed on an
- "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- KIND, either express or implied. See the License for the
- specific language governing permissions and limitations
- under the License.
-
--->
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
- <modelVersion>4.0.0</modelVersion>
- <artifactId>ctakes-relation-extractor</artifactId>
- <name>Apache cTAKES Relation Extractor</name>
- <parent>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes</artifactId>
- <version>3.1.0-SNAPSHOT</version>
- </parent>
- <dependencies>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-relation-extractor-res</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-type-system</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-core</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-utils</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-pos-tagger</artifactId>
- </dependency>
- <dependency>
- <groupId>org.cleartk</groupId>
- <artifactId>cleartk-eval</artifactId>
- </dependency>
- <dependency>
- <groupId>org.cleartk</groupId>
- <artifactId>cleartk-ml</artifactId>
- </dependency>
- <dependency>
- <groupId>org.cleartk</groupId>
- <artifactId>cleartk-ml-libsvm</artifactId>
- </dependency>
- <dependency>
- <groupId>org.cleartk</groupId>
- <artifactId>cleartk-ml-opennlp-maxent</artifactId>
- </dependency>
- <dependency>
- <groupId>org.cleartk</groupId>
- <artifactId>cleartk-util</artifactId>
- </dependency>
- <dependency>
- <groupId>com.lexicalscope.jewelcli</groupId>
- <artifactId>jewelcli</artifactId>
- </dependency>
- <dependency>
- <groupId>commons-io</groupId>
- <artifactId>commons-io</artifactId>
- </dependency>
- <dependency>
- <groupId>commons-lang</groupId>
- <artifactId>commons-lang</artifactId>
- </dependency>
- <dependency>
- <groupId>commons-logging</groupId>
- <artifactId>commons-logging</artifactId>
- </dependency>
- <dependency>
- <groupId>com.google.guava</groupId>
- <artifactId>guava</artifactId>
- </dependency>
-
- <dependency>
- <groupId>com.carrotsearch</groupId>
- <artifactId>hppc</artifactId>
- </dependency>
-
-
- <dependency>
- <groupId>jdom</groupId>
- <artifactId>jdom</artifactId>
- </dependency>
-
- <dependency>
- <groupId>log4j</groupId>
- <artifactId>log4j</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.opennlp</groupId>
- <artifactId>opennlp-maxent</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.opennlp</groupId>
- <artifactId>opennlp-tools</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.lucene</groupId>
- <artifactId>lucene-core</artifactId>
- </dependency>
- <dependency>
- <groupId>tw.edu.ntu.csie</groupId>
- <artifactId>libsvm</artifactId>
- </dependency>
-
- <dependency>
- <groupId>org.springframework</groupId>
- <artifactId>spring-core</artifactId>
- </dependency>
-
- <dependency>
- <groupId>junit</groupId>
- <artifactId>junit</artifactId>
- </dependency>
- <dependency>
- <groupId>org.uimafit</groupId>
- <artifactId>uimafit</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-context-tokenizer</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-constituency-parser</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-ne-contexts</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-chunker</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-dependency-parser</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-dictionary-lookup</artifactId>
- </dependency>
- <dependency>
- <groupId>edu.mit</groupId>
- <artifactId>jwi</artifactId>
- <version>2.2.3</version>
- </dependency>
- </dependencies>
-</project>
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+ Licensed to the Apache Software Foundation (ASF) under one
+ or more contributor license agreements. See the NOTICE file
+ distributed with this work for additional information
+ regarding copyright ownership. The ASF licenses this file
+ to you under the Apache License, Version 2.0 (the
+ "License"); you may not use this file except in compliance
+ with the License. You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing,
+ software distributed under the License is distributed on an
+ "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ KIND, either express or implied. See the License for the
+ specific language governing permissions and limitations
+ under the License.
+
+-->
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <artifactId>ctakes-relation-extractor</artifactId>
+ <name>Apache cTAKES Relation Extractor</name>
+ <parent>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes</artifactId>
+ <version>3.1.0</version>
+ </parent>
+ <dependencies>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-relation-extractor-res</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-type-system</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-core</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-utils</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-pos-tagger</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.cleartk</groupId>
+ <artifactId>cleartk-eval</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.cleartk</groupId>
+ <artifactId>cleartk-ml</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.cleartk</groupId>
+ <artifactId>cleartk-ml-libsvm</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.cleartk</groupId>
+ <artifactId>cleartk-ml-opennlp-maxent</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.cleartk</groupId>
+ <artifactId>cleartk-util</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>com.lexicalscope.jewelcli</groupId>
+ <artifactId>jewelcli</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>commons-io</groupId>
+ <artifactId>commons-io</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>commons-lang</groupId>
+ <artifactId>commons-lang</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>commons-logging</groupId>
+ <artifactId>commons-logging</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>com.google.guava</groupId>
+ <artifactId>guava</artifactId>
+ </dependency>
+
+ <dependency>
+ <groupId>com.carrotsearch</groupId>
+ <artifactId>hppc</artifactId>
+ </dependency>
+
+
+ <dependency>
+ <groupId>jdom</groupId>
+ <artifactId>jdom</artifactId>
+ </dependency>
+
+ <dependency>
+ <groupId>log4j</groupId>
+ <artifactId>log4j</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.opennlp</groupId>
+ <artifactId>opennlp-maxent</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.opennlp</groupId>
+ <artifactId>opennlp-tools</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.lucene</groupId>
+ <artifactId>lucene-core</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>tw.edu.ntu.csie</groupId>
+ <artifactId>libsvm</artifactId>
+ </dependency>
+
+ <dependency>
+ <groupId>org.springframework</groupId>
+ <artifactId>spring-core</artifactId>
+ </dependency>
+
+ <dependency>
+ <groupId>junit</groupId>
+ <artifactId>junit</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.uimafit</groupId>
+ <artifactId>uimafit</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-context-tokenizer</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-constituency-parser</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-ne-contexts</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-chunker</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-dependency-parser</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-dictionary-lookup</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>edu.mit</groupId>
+ <artifactId>jwi</artifactId>
+ <version>2.2.3</version>
+ </dependency>
+ </dependencies>
+</project>
Modified: ctakes/branches/ctakes-3.1.0/ctakes-side-effect-res/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-side-effect-res/pom.xml?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-side-effect-res/pom.xml (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-side-effect-res/pom.xml Fri Aug 2 16:48:14 2013
@@ -24,7 +24,7 @@
<parent>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes</artifactId>
- <version>3.1.0-SNAPSHOT</version>
+ <version>3.1.0</version>
</parent>
<artifactId>ctakes-side-effect-res</artifactId>
<name>Apache cTAKES Resources side-effect</name>
Modified: ctakes/branches/ctakes-3.1.0/ctakes-side-effect/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-side-effect/pom.xml?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-side-effect/pom.xml (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-side-effect/pom.xml Fri Aug 2 16:48:14 2013
@@ -1,89 +1,89 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!--
-
- Licensed to the Apache Software Foundation (ASF) under one
- or more contributor license agreements. See the NOTICE file
- distributed with this work for additional information
- regarding copyright ownership. The ASF licenses this file
- to you under the Apache License, Version 2.0 (the
- "License"); you may not use this file except in compliance
- with the License. You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
- Unless required by applicable law or agreed to in writing,
- software distributed under the License is distributed on an
- "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- KIND, either express or implied. See the License for the
- specific language governing permissions and limitations
- under the License.
-
--->
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
- <modelVersion>4.0.0</modelVersion>
- <artifactId>ctakes-side-effect</artifactId>
- <name>Apache cTAKES Side Effects</name>
- <parent>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes</artifactId>
- <version>3.1.0-SNAPSHOT</version>
- </parent>
-
- <dependencies>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-side-effect-res</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-type-system</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-core</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-dictionary-lookup</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-drug-ner</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-utils</artifactId>
- </dependency>
- <dependency>
- <groupId>log4j</groupId>
- <artifactId>log4j</artifactId>
- </dependency>
- <dependency>
- <groupId>jdom</groupId>
- <artifactId>jdom</artifactId>
- </dependency>
- <dependency>
- <groupId>junit</groupId>
- <artifactId>junit</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.lucene</groupId>
- <artifactId>lucene-core</artifactId>
- </dependency>
- <dependency>
- <groupId>tw.edu.ntu.csie</groupId>
- <artifactId>libsvm</artifactId>
- </dependency>
- </dependencies>
- <build>
- <plugins>
- <plugin>
- <groupId>org.cleartk</groupId>
- <artifactId>jcasgen-maven-plugin</artifactId>
- <configuration>
- <typeSystem>src/main/resources/org/apache/ctakes/sideeffect/types/TypeSystem.xml</typeSystem>
- </configuration>
- </plugin>
- </plugins>
- </build>
-</project>
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+ Licensed to the Apache Software Foundation (ASF) under one
+ or more contributor license agreements. See the NOTICE file
+ distributed with this work for additional information
+ regarding copyright ownership. The ASF licenses this file
+ to you under the Apache License, Version 2.0 (the
+ "License"); you may not use this file except in compliance
+ with the License. You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing,
+ software distributed under the License is distributed on an
+ "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ KIND, either express or implied. See the License for the
+ specific language governing permissions and limitations
+ under the License.
+
+-->
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <artifactId>ctakes-side-effect</artifactId>
+ <name>Apache cTAKES Side Effects</name>
+ <parent>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes</artifactId>
+ <version>3.1.0</version>
+ </parent>
+
+ <dependencies>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-side-effect-res</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-type-system</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-core</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-dictionary-lookup</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-drug-ner</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-utils</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>log4j</groupId>
+ <artifactId>log4j</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>jdom</groupId>
+ <artifactId>jdom</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>junit</groupId>
+ <artifactId>junit</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.lucene</groupId>
+ <artifactId>lucene-core</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>tw.edu.ntu.csie</groupId>
+ <artifactId>libsvm</artifactId>
+ </dependency>
+ </dependencies>
+ <build>
+ <plugins>
+ <plugin>
+ <groupId>org.cleartk</groupId>
+ <artifactId>jcasgen-maven-plugin</artifactId>
+ <configuration>
+ <typeSystem>src/main/resources/org/apache/ctakes/sideeffect/types/TypeSystem.xml</typeSystem>
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
+</project>
Modified: ctakes/branches/ctakes-3.1.0/ctakes-smoking-status-res/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-smoking-status-res/pom.xml?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-smoking-status-res/pom.xml (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-smoking-status-res/pom.xml Fri Aug 2 16:48:14 2013
@@ -24,7 +24,7 @@
<parent>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes</artifactId>
- <version>3.1.0-SNAPSHOT</version>
+ <version>3.1.0</version>
</parent>
<artifactId>ctakes-smoking-status-res</artifactId>
<name>Apache cTAKES Resources smoking-status</name>
Modified: ctakes/branches/ctakes-3.1.0/ctakes-smoking-status/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-smoking-status/pom.xml?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-smoking-status/pom.xml (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-smoking-status/pom.xml Fri Aug 2 16:48:14 2013
@@ -1,89 +1,89 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!--
-
- Licensed to the Apache Software Foundation (ASF) under one
- or more contributor license agreements. See the NOTICE file
- distributed with this work for additional information
- regarding copyright ownership. The ASF licenses this file
- to you under the Apache License, Version 2.0 (the
- "License"); you may not use this file except in compliance
- with the License. You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
- Unless required by applicable law or agreed to in writing,
- software distributed under the License is distributed on an
- "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- KIND, either express or implied. See the License for the
- specific language governing permissions and limitations
- under the License.
-
--->
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
- <modelVersion>4.0.0</modelVersion>
- <artifactId>ctakes-smoking-status</artifactId>
- <name>Apache cTAKES Smoking Status</name>
- <parent>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes</artifactId>
- <version>3.1.0-SNAPSHOT</version>
- </parent>
-
- <dependencies>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-smoking-status-res</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-type-system</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-core</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-dictionary-lookup</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-drug-ner</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-utils</artifactId>
- </dependency>
- <dependency>
- <groupId>log4j</groupId>
- <artifactId>log4j</artifactId>
- </dependency>
- <dependency>
- <groupId>jdom</groupId>
- <artifactId>jdom</artifactId>
- </dependency>
- <dependency>
- <groupId>junit</groupId>
- <artifactId>junit</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.lucene</groupId>
- <artifactId>lucene-core</artifactId>
- </dependency>
- <dependency>
- <groupId>tw.edu.ntu.csie</groupId>
- <artifactId>libsvm</artifactId>
- </dependency>
- </dependencies>
- <build>
- <plugins>
- <plugin>
- <groupId>org.cleartk</groupId>
- <artifactId>jcasgen-maven-plugin</artifactId>
- <configuration>
- <typeSystem>src/main/resources/org/apache/ctakes/smokingstatus/types/TypeSystem.xml</typeSystem>
- </configuration>
- </plugin>
- </plugins>
- </build>
-</project>
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+ Licensed to the Apache Software Foundation (ASF) under one
+ or more contributor license agreements. See the NOTICE file
+ distributed with this work for additional information
+ regarding copyright ownership. The ASF licenses this file
+ to you under the Apache License, Version 2.0 (the
+ "License"); you may not use this file except in compliance
+ with the License. You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing,
+ software distributed under the License is distributed on an
+ "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ KIND, either express or implied. See the License for the
+ specific language governing permissions and limitations
+ under the License.
+
+-->
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <artifactId>ctakes-smoking-status</artifactId>
+ <name>Apache cTAKES Smoking Status</name>
+ <parent>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes</artifactId>
+ <version>3.1.0</version>
+ </parent>
+
+ <dependencies>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-smoking-status-res</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-type-system</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-core</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-dictionary-lookup</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-drug-ner</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-utils</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>log4j</groupId>
+ <artifactId>log4j</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>jdom</groupId>
+ <artifactId>jdom</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>junit</groupId>
+ <artifactId>junit</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.lucene</groupId>
+ <artifactId>lucene-core</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>tw.edu.ntu.csie</groupId>
+ <artifactId>libsvm</artifactId>
+ </dependency>
+ </dependencies>
+ <build>
+ <plugins>
+ <plugin>
+ <groupId>org.cleartk</groupId>
+ <artifactId>jcasgen-maven-plugin</artifactId>
+ <configuration>
+ <typeSystem>src/main/resources/org/apache/ctakes/smokingstatus/types/TypeSystem.xml</typeSystem>
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
+</project>
Modified: ctakes/branches/ctakes-3.1.0/ctakes-template-filler/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-template-filler/pom.xml?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-template-filler/pom.xml (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-template-filler/pom.xml Fri Aug 2 16:48:14 2013
@@ -27,7 +27,7 @@
<parent>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes</artifactId>
- <version>3.1.0-SNAPSHOT</version>
+ <version>3.1.0</version>
</parent>
<dependencies>
<dependency>
Modified: ctakes/branches/ctakes-3.1.0/ctakes-temporal-res/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-temporal-res/pom.xml?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-temporal-res/pom.xml (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-temporal-res/pom.xml Fri Aug 2 16:48:14 2013
@@ -24,7 +24,7 @@
<parent>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes</artifactId>
- <version>3.1.0-SNAPSHOT</version>
+ <version>3.1.0</version>
</parent>
<artifactId>ctakes-temporal-res</artifactId>
<name>Apache cTAKES Resources temporal</name>
Modified: ctakes/branches/ctakes-3.1.0/ctakes-temporal/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-temporal/pom.xml?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-temporal/pom.xml (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-temporal/pom.xml Fri Aug 2 16:48:14 2013
@@ -19,8 +19,7 @@
under the License.
-->
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<artifactId>ctakes-temporal</artifactId>
<packaging>jar</packaging>
@@ -28,7 +27,7 @@
<parent>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes</artifactId>
- <version>3.1.0-SNAPSHOT</version>
+ <version>3.1.0</version>
</parent>
<dependencies>
<dependency>
Modified: ctakes/branches/ctakes-3.1.0/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventAnnotator.java?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventAnnotator.java (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventAnnotator.java Fri Aug 2 16:48:14 2013
@@ -88,12 +88,12 @@ public class EventAnnotator extends Temp
protected Float featureSelectionThreshold = 1f; //default is not using feature selection, i.e. select 100% of all features.
public static final String PARAM_SMOTE_NUM_NEIGHBORS = "NumOfNeighborForSMOTE";
-
+
@ConfigurationParameter(
- name = PARAM_SMOTE_NUM_NEIGHBORS,
- mandatory = false,
- description = "the number of neighbors used for minority instances for SMOTE algorithm")
- protected Float smoteNumOfNeighbors = 0f;
+ name = PARAM_SMOTE_NUM_NEIGHBORS,
+ mandatory = false,
+ description = "the number of neighbors used for minority instances for SMOTE algorithm")
+ protected Float smoteNumOfNeighbors = 0f;
public static final String PARAM_FEATURE_SELECTION_URI = "FeatureSelectionURI";
Modified: ctakes/branches/ctakes-3.1.0/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimeAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimeAnnotator.java?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimeAnnotator.java (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimeAnnotator.java Fri Aug 2 16:48:14 2013
@@ -28,6 +28,7 @@ import org.apache.ctakes.temporal.ae.fea
import org.apache.ctakes.temporal.ae.feature.TimeWordTypeExtractor;
import org.apache.ctakes.temporal.ae.feature.selection.Chi2FeatureSelection;
import org.apache.ctakes.temporal.ae.feature.selection.FeatureSelection;
+import org.apache.ctakes.temporal.utils.SMOTEplus;
import org.apache.ctakes.typesystem.type.syntax.BaseToken;
import org.apache.ctakes.typesystem.type.textsem.TimeMention;
import org.apache.ctakes.typesystem.type.textspan.Segment;
@@ -67,7 +68,7 @@ public class TimeAnnotator extends Tempo
name = PARAM_FEATURE_SELECTION_THRESHOLD,
mandatory = false,
description = "the Chi-squared threshold at which features should be removed")
- protected Float featureSelectionThreshold = 0f;
+ protected Float featureSelectionThreshold = 1f;
public static final String PARAM_FEATURE_SELECTION_URI = "FeatureSelectionURI";
@@ -76,13 +77,22 @@ public class TimeAnnotator extends Tempo
name = PARAM_FEATURE_SELECTION_URI,
description = "provides a URI where the feature selection data will be written")
protected URI featureSelectionURI;
+
+ public static final String PARAM_SMOTE_NUM_NEIGHBORS = "NumOfNeighborForSMOTE";
+
+ @ConfigurationParameter(
+ name = PARAM_SMOTE_NUM_NEIGHBORS,
+ mandatory = false,
+ description = "the number of neighbors used for minority instances for SMOTE algorithm")
+ protected Float smoteNumOfNeighbors = 0f;
public static final String TIMEX_VIEW = "TimexView";
public static AnalysisEngineDescription createDataWriterDescription(
Class<?> dataWriterClass,
File outputDirectory,
- float featureSelect) throws ResourceInitializationException {
+ float featureSelect,
+ float smoteNeighborNumber) throws ResourceInitializationException {
return AnalysisEngineFactory.createPrimitiveDescription(
TimeAnnotator.class,
CleartkAnnotator.PARAM_IS_TRAINING,
@@ -92,7 +102,9 @@ public class TimeAnnotator extends Tempo
DirectoryDataWriterFactory.PARAM_OUTPUT_DIRECTORY,
outputDirectory,
TimeAnnotator.PARAM_FEATURE_SELECTION_THRESHOLD,
- featureSelect);
+ featureSelect,
+ EventAnnotator.PARAM_SMOTE_NUM_NEIGHBORS,
+ smoteNeighborNumber);
}
public static AnalysisEngineDescription createAnnotatorDescription(File modelDirectory)
@@ -121,7 +133,7 @@ public class TimeAnnotator extends Tempo
private static final String FEATURE_SELECTION_NAME = "SelectNeighborFeatures";
public static FeatureSelection<String> createFeatureSelection(double threshold) {
- return new Chi2FeatureSelection<String>(TimeAnnotator.FEATURE_SELECTION_NAME, threshold);
+ return new Chi2FeatureSelection<String>(TimeAnnotator.FEATURE_SELECTION_NAME, threshold, true);
}
public static URI createFeatureSelectionURI(File outputDirectoryName) {
@@ -159,7 +171,7 @@ public class TimeAnnotator extends Tempo
parseExtractor = new ParseSpanFeatureExtractor();
//initialize feature selection
- if (featureSelectionThreshold == 0) {
+ if (featureSelectionThreshold == 1) {
this.featureSelection = null;
} else {
this.featureSelection = TimeAnnotator.createFeatureSelection(this.featureSelectionThreshold);
@@ -176,10 +188,13 @@ public class TimeAnnotator extends Tempo
@Override
public void process(JCas jCas, Segment segment) throws AnalysisEngineProcessException {
+ //TRY SMOTE algorithm here to generate more minority class samples
+ SMOTEplus smote = new SMOTEplus((int)Math.ceil(this.smoteNumOfNeighbors));
+
// classify tokens within each sentence
for (Sentence sentence : JCasUtil.selectCovered(jCas, Sentence.class, segment)) {
List<BaseToken> tokens = JCasUtil.selectCovered(jCas, BaseToken.class, sentence);
-
+
// during training, the list of all outcomes for the tokens
List<String> outcomes;
if (this.isTraining()) {
@@ -234,12 +249,20 @@ public class TimeAnnotator extends Tempo
}
// if training, write to data file
- if (this.isTraining()) {
- String outcome = outcomes.get(tokenIndex);
- this.dataWriter.write(new Instance<String>(outcome, features));
- }else {// if predicting, add prediction to outcomes
- outcomes.add(this.classifier.classify(features));
- }
+ if (this.isTraining()) {
+ String outcome = outcomes.get(tokenIndex);
+ // if it is an "O" down-sample it
+ if (outcome.equals("O")) {
+ this.dataWriter.write(new Instance<String>(outcome, features));
+
+ }else{//for minority instances:
+ Instance<String> minorityInst = new Instance<String>(outcome, features);
+ this.dataWriter.write(minorityInst);
+ smote.addInstance(minorityInst);//add minority instances to SMOTE algorithm
+ }
+ }else {// if predicting, add prediction to outcomes
+ outcomes.add(this.classifier.classify(features));
+ }
}
// during prediction, convert chunk labels to times and add them to the CAS
@@ -253,5 +276,11 @@ public class TimeAnnotator extends Tempo
this.timeChunking.createChunks(timexCas, tokens, outcomes);
}
}
+ if(this.isTraining() && this.smoteNumOfNeighbors >= 1){ //add synthetic instances to datawriter, if smote is selected
+ Iterable<Instance<String>> syntheticInsts = smote.populateMinorityClass();
+ for( Instance<String> sytheticInst: syntheticInsts){
+ this.dataWriter.write(sytheticInst);
+ }
+ }
}
}
Modified: ctakes/branches/ctakes-3.1.0/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/selection/Chi2FeatureSelection.java
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/selection/Chi2FeatureSelection.java?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/selection/Chi2FeatureSelection.java (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/selection/Chi2FeatureSelection.java Fri Aug 2 16:48:14 2013
@@ -7,6 +7,7 @@ import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
import java.net.URI;
+import java.util.LinkedHashSet;
import java.util.Set;
import org.cleartk.classifier.Feature;
@@ -133,6 +134,8 @@ public class Chi2FeatureSelection<OUTCOM
private boolean yates = false;
+ private LinkedHashSet<String> discardedFeatureNames;
+
public Chi2FeatureSelection(String name) {
this(name, 0.0);
}
@@ -199,6 +202,7 @@ public class Chi2FeatureSelection<OUTCOM
this.selectedFeatureNames = Sets.newLinkedHashSet(ordering.immutableSortedCopy(featureNames).subList(
0,
this.numFeatures));
+ this.discardedFeatureNames = Sets.newLinkedHashSet(ordering.immutableSortedCopy(featureNames).subList(this.numFeatures, totalFeatures));
this.isTrained = true;
}
@@ -209,13 +213,24 @@ public class Chi2FeatureSelection<OUTCOM
throw new IllegalStateException("Cannot save before training");
}
File out = new File(uri);
+ final String uriPath = uri.getPath();
+ final int lastIndex = uriPath.lastIndexOf('.');
+ final String discardPath = (lastIndex >= 0 ? uriPath.substring(0, lastIndex) : uriPath ) + "_discarded.dat";
+ final File discardOut = new File( discardPath );
+// File discardOut = new File(uri.getPath().substring(0,uri.getPath().lastIndexOf(".")) + "_discarded.dat");
BufferedWriter writer = new BufferedWriter(new FileWriter(out));
+ BufferedWriter diswriter = new BufferedWriter(new FileWriter(discardOut));
for (String feature : this.selectedFeatureNames) {
writer.append(String.format("%s\t%f\n", feature, this.chi2Function.score(feature)));
}
+
+ for (String feature : this.discardedFeatureNames ){
+ diswriter.append(String.format("%s\t%f\n", feature, this.chi2Function.score(feature)));
+ }
writer.close();
+ diswriter.close();
}
@Override
Modified: ctakes/branches/ctakes-3.1.0/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTimeSpans.java
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTimeSpans.java?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTimeSpans.java (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfTimeSpans.java Fri Aug 2 16:48:14 2013
@@ -64,8 +64,11 @@ public class EvaluationOfTimeSpans exten
static interface Options extends Evaluation_ImplBase.Options {
- @Option(longName = "featureSelectionThreshold", defaultValue = "0")
+ @Option(longName = "featureSelectionThreshold", defaultValue = "1")
public float getFeatureSelectionThreshold();
+
+ @Option(longName = "SMOTENeighborNumber", defaultValue = "0")
+ public float getSMOTENeighborNumber();
}
public static void main(String[] args) throws Exception {
@@ -99,6 +102,7 @@ public class EvaluationOfTimeSpans exten
options.getXMIDirectory(),
options.getTreebankDirectory(),
options.getFeatureSelectionThreshold(),
+ options.getSMOTENeighborNumber(),
annotatorClass,
options.getPrintOverlappingSpans(),
annotatorTrainingArguments.get(annotatorClass));
@@ -131,6 +135,8 @@ public class EvaluationOfTimeSpans exten
private String[] trainingArguments;
private float featureSelectionThreshold;
+
+ private float smoteNeighborNumber;
public EvaluationOfTimeSpans(
File baseDirectory,
@@ -140,6 +146,7 @@ public class EvaluationOfTimeSpans exten
File xmiDirectory,
File treebankDirectory,
float featureSelectionThreshold,
+ float numOfSmoteNeighbors,
Class<? extends JCasAnnotator_ImplBase> annotatorClass,
boolean printOverlapping,
String[] trainingArguments) {
@@ -148,6 +155,7 @@ public class EvaluationOfTimeSpans exten
this.featureSelectionThreshold = featureSelectionThreshold;
this.trainingArguments = trainingArguments;
this.printOverlapping = printOverlapping;
+ this.smoteNeighborNumber = numOfSmoteNeighbors;
}
@Override
@@ -164,7 +172,8 @@ public class EvaluationOfTimeSpans exten
return TimeAnnotator.createDataWriterDescription(
dataWriterClass,
this.getModelDirectory(directory),
- this.featureSelectionThreshold);
+ this.featureSelectionThreshold,
+ this.smoteNeighborNumber);
}
return AnalysisEngineFactory.createPrimitiveDescription(
this.annotatorClass,
Modified: ctakes/branches/ctakes-3.1.0/ctakes-type-system/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-type-system/pom.xml?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-type-system/pom.xml (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-type-system/pom.xml Fri Aug 2 16:48:14 2013
@@ -1,63 +1,63 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!--
-
- Licensed to the Apache Software Foundation (ASF) under one
- or more contributor license agreements. See the NOTICE file
- distributed with this work for additional information
- regarding copyright ownership. The ASF licenses this file
- to you under the Apache License, Version 2.0 (the
- "License"); you may not use this file except in compliance
- with the License. You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
- Unless required by applicable law or agreed to in writing,
- software distributed under the License is distributed on an
- "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- KIND, either express or implied. See the License for the
- specific language governing permissions and limitations
- under the License.
-
--->
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
- <modelVersion>4.0.0</modelVersion>
- <artifactId>ctakes-type-system</artifactId>
- <name>Apache cTAKES common type system</name>
- <description>Defines the cTAKES type system UIMA annotation classes.</description>
- <parent>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes</artifactId>
- <version>3.1.0-SNAPSHOT</version>
- </parent>
- <dependencies>
- <dependency>
- <groupId>org.apache.uima</groupId>
- <artifactId>uimaj-core</artifactId>
- </dependency>
- <dependency>
- <groupId>org.uimafit</groupId>
- <artifactId>uimafit</artifactId>
- </dependency>
- <dependency>
- <groupId>tw.edu.ntu.csie</groupId>
- <artifactId>libsvm</artifactId>
- </dependency>
- <dependency>
- <groupId>junit</groupId>
- <artifactId>junit</artifactId>
- <scope>test</scope>
- </dependency>
- </dependencies>
-
- <build>
- <plugins>
- <plugin>
- <groupId>org.cleartk</groupId>
- <artifactId>jcasgen-maven-plugin</artifactId>
- <configuration>
- <typeSystem>src/main/resources/org/apache/ctakes/typesystem/types/TypeSystem.xml</typeSystem>
- </configuration>
- </plugin>
- </plugins>
- </build>
-</project>
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+ Licensed to the Apache Software Foundation (ASF) under one
+ or more contributor license agreements. See the NOTICE file
+ distributed with this work for additional information
+ regarding copyright ownership. The ASF licenses this file
+ to you under the Apache License, Version 2.0 (the
+ "License"); you may not use this file except in compliance
+ with the License. You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing,
+ software distributed under the License is distributed on an
+ "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ KIND, either express or implied. See the License for the
+ specific language governing permissions and limitations
+ under the License.
+
+-->
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <artifactId>ctakes-type-system</artifactId>
+ <name>Apache cTAKES common type system</name>
+ <description>Defines the cTAKES type system UIMA annotation classes.</description>
+ <parent>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes</artifactId>
+ <version>3.1.0</version>
+ </parent>
+ <dependencies>
+ <dependency>
+ <groupId>org.apache.uima</groupId>
+ <artifactId>uimaj-core</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.uimafit</groupId>
+ <artifactId>uimafit</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>tw.edu.ntu.csie</groupId>
+ <artifactId>libsvm</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>junit</groupId>
+ <artifactId>junit</artifactId>
+ <scope>test</scope>
+ </dependency>
+ </dependencies>
+
+ <build>
+ <plugins>
+ <plugin>
+ <groupId>org.cleartk</groupId>
+ <artifactId>jcasgen-maven-plugin</artifactId>
+ <configuration>
+ <typeSystem>src/main/resources/org/apache/ctakes/typesystem/types/TypeSystem.xml</typeSystem>
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
+</project>
Modified: ctakes/branches/ctakes-3.1.0/ctakes-utils/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.1.0/ctakes-utils/pom.xml?rev=1509770&r1=1509769&r2=1509770&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.1.0/ctakes-utils/pom.xml (original)
+++ ctakes/branches/ctakes-3.1.0/ctakes-utils/pom.xml Fri Aug 2 16:48:14 2013
@@ -1,62 +1,62 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!--
-
- Licensed to the Apache Software Foundation (ASF) under one
- or more contributor license agreements. See the NOTICE file
- distributed with this work for additional information
- regarding copyright ownership. The ASF licenses this file
- to you under the Apache License, Version 2.0 (the
- "License"); you may not use this file except in compliance
- with the License. You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
- Unless required by applicable law or agreed to in writing,
- software distributed under the License is distributed on an
- "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- KIND, either express or implied. See the License for the
- specific language governing permissions and limitations
- under the License.
-
--->
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
- <modelVersion>4.0.0</modelVersion>
- <artifactId>ctakes-utils</artifactId>
- <name>Apache cTAKES utils</name>
- <parent>
- <artifactId>ctakes</artifactId>
- <groupId>org.apache.ctakes</groupId>
- <version>3.1.0-SNAPSHOT</version>
- </parent>
- <dependencies>
- <dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-type-system</artifactId>
- </dependency>
- <dependency>
- <groupId>log4j</groupId>
- <artifactId>log4j</artifactId>
- </dependency>
- <dependency>
- <groupId>junit</groupId>
- <artifactId>junit</artifactId>
- <scope>compile</scope>
- </dependency>
- <dependency>
- <groupId>org.apache.lucene</groupId>
- <artifactId>lucene-core</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.lucene</groupId>
- <artifactId>lucene-queries</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.lucene</groupId>
- <artifactId>lucene-queryparser</artifactId>
- </dependency>
- <dependency>
- <groupId>org.apache.lucene</groupId>
- <artifactId>lucene-analyzers-common</artifactId>
- </dependency>
- </dependencies>
-</project>
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+ Licensed to the Apache Software Foundation (ASF) under one
+ or more contributor license agreements. See the NOTICE file
+ distributed with this work for additional information
+ regarding copyright ownership. The ASF licenses this file
+ to you under the Apache License, Version 2.0 (the
+ "License"); you may not use this file except in compliance
+ with the License. You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing,
+ software distributed under the License is distributed on an
+ "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ KIND, either express or implied. See the License for the
+ specific language governing permissions and limitations
+ under the License.
+
+-->
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <artifactId>ctakes-utils</artifactId>
+ <name>Apache cTAKES utils</name>
+ <parent>
+ <artifactId>ctakes</artifactId>
+ <groupId>org.apache.ctakes</groupId>
+ <version>3.1.0</version>
+ </parent>
+ <dependencies>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-type-system</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>log4j</groupId>
+ <artifactId>log4j</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>junit</groupId>
+ <artifactId>junit</artifactId>
+ <scope>compile</scope>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.lucene</groupId>
+ <artifactId>lucene-core</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.lucene</groupId>
+ <artifactId>lucene-queries</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.lucene</groupId>
+ <artifactId>lucene-queryparser</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.lucene</groupId>
+ <artifactId>lucene-analyzers-common</artifactId>
+ </dependency>
+ </dependencies>
+</project>