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Posted to commits@ctakes.apache.org by sw...@apache.org on 2013/08/16 20:42:20 UTC
svn commit: r1514842 - in /ctakes/trunk/ctakes-assertion: build.xml
src/main/java/org/apache/ctakes/assertion/train/PolarityCotrainingTests.java
src/main/java/org/apache/ctakes/assertion/train/PolarityCotrainingTrain.java
Author: swu
Date: Fri Aug 16 18:42:20 2013
New Revision: 1514842
URL: http://svn.apache.org/r1514842
Log:
polarity paper #1 test scripts
Added:
ctakes/trunk/ctakes-assertion/build.xml (with props)
ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/PolarityCotrainingTests.java (with props)
ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/PolarityCotrainingTrain.java (with props)
Added: ctakes/trunk/ctakes-assertion/build.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/build.xml?rev=1514842&view=auto
==============================================================================
--- ctakes/trunk/ctakes-assertion/build.xml (added)
+++ ctakes/trunk/ctakes-assertion/build.xml Fri Aug 16 18:42:20 2013
@@ -0,0 +1,377 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<!-- WARNING: Eclipse auto-generated file.
+ Any modifications will be overwritten.
+ To include a user specific buildfile here, simply create one in the same
+ directory with the processing instruction <?eclipse.ant.import?>
+ as the first entry and export the buildfile again. --><project basedir="." default="build" name="ctakes-assertion">
+ <property environment="env"/>
+ <property name="ECLIPSE_HOME" value="../../../tools/eclipse"/>
+ <property name="debuglevel" value="source,lines,vars"/>
+ <property name="target" value="1.6"/>
+ <property name="source" value="1.6"/>
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+ <path id="Maven Dependencies.libraryclasspath">
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+ <target name="init">
+ <mkdir dir="target/classes"/>
+ <mkdir dir="target/test-classes"/>
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+ <fileset dir="src/main/java">
+ <exclude name="**/*.java"/>
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+ <fileset dir="target/generated-sources/jcasgen">
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+ <target name="clean">
+ <delete dir="target/classes"/>
+ <delete dir="target/test-classes"/>
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+ <target depends="clean" name="cleanall"/>
+ <target depends="build-subprojects,build-project" name="build"/>
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+ <src path="src/test/java"/>
+ <classpath refid="ctakes-assertion.classpath"/>
+ </javac>
+ </target>
+ <target description="Build all projects which reference this project. Useful to propagate changes." name="build-refprojects"/>
+ <target description="copy Eclipse compiler jars to ant lib directory" name="init-eclipse-compiler">
+ <copy todir="${ant.library.dir}">
+ <fileset dir="${ECLIPSE_HOME}/plugins" includes="org.eclipse.jdt.core_*.jar"/>
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+ <unzip dest="${ant.library.dir}">
+ <patternset includes="jdtCompilerAdapter.jar"/>
+ <fileset dir="${ECLIPSE_HOME}/plugins" includes="org.eclipse.jdt.core_*.jar"/>
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+ </target>
+ <target description="compile project with Eclipse compiler" name="build-eclipse-compiler">
+ <property name="build.compiler" value="org.eclipse.jdt.core.JDTCompilerAdapter"/>
+ <antcall target="build"/>
+ </target>
+ <target name="CrossValidateAttributeModels">
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+ <jvmarg line="-Xmx1600M"/>
+ <classpath refid="run.CrossValidateAttributeModels.classpath"/>
+ </java>
+ </target>
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+ <java classname="org.apache.ctakes.assertion.train.CrossValidateChi2GridSearch" failonerror="true" fork="yes">
+ <jvmarg line="-Xmx2g"/>
+ <classpath refid="run.CrossValidateChi2GridSearch.classpath"/>
+ </java>
+ </target>
+ <target name="NegExCorpusReader">
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+ <arg line="/Users/m081914/work/data/negextestset/rsAnnotations-1-120-random.txt"/>
+ <classpath refid="run.NegExCorpusReader.classpath"/>
+ </java>
+ </target>
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+ <jvmarg line="-Xmx2g"/>
+ <classpath refid="run.ReadAndPreprocessForAttributeModels.classpath"/>
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+ <classpath refid="run.TestAttributeModels.classpath"/>
+ </java>
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+ <classpath refid="run.TestFeatureSelection.classpath"/>
+ </java>
+ </target>
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+ <jvmarg line="-Xmx1600M"/>
+ <classpath refid="run.TrainAttributeModels.classpath"/>
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+ </target>
+ <target name="ctakes_assertion_read_gold_and_preprocess">
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+ <classpath refid="run.ctakes_assertion_read_gold_and_preprocess.classpath"/>
+ </java>
+ </target>
+ <target name="ctakes_assertion_evaluation_on_test">
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+ <jvmarg line="-Xmx1600M"/>
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+ <classpath refid="run.ctakes_assertion_evaluation_on_test.classpath"/>
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+ <classpath refid="run.ctakes_assertion_evaluation_on_output.classpath"/>
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+ <classpath refid="run.ctakes_assertion_crossvalidation.classpath"/>
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+ <classpath refid="run.ctakes__assertion_eval_preprocess.classpath"/>
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+ <classpath refid="run.ctakes__assertion_eval.classpath"/>
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+ <classpath refid="run.ctakes_assertion_evaluation_on_test.classpath"/>
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+ <classpath refid="run.ctakes_assertion_evaluation_on_output.classpath"/>
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+ <java classname="org.apache.ctakes.assertion.eval.AssertionEvaluation" failonerror="true" fork="yes">
+ <jvmarg line="-Xmx1600M"/>
+ <arg line="--train-dir /Users/m081914/work/data/assertion/fromtim_sharp_data/train --models-dir ../ctakes-assertion-res/resources/model/sharptrain-xval --cross-validation 5"/>
+ <classpath refid="run.ctakes_assertion_crossvalidation.classpath"/>
+ </java>
+ </target>
+ <target name="ctakes__assertion_eval_preprocess">
+ <java classname="org.apache.ctakes.assertion.eval.AssertionEvaluation" failonerror="true" fork="yes">
+ <arg line="--train-dir data/train --test-dir data/test --models-dir data/model/eval.model --dev-dir data/dev --preprocess-only "H:\SHARP\Corpora\\Mayo\UMLS_CEM""/>
+ <classpath refid="run.ctakes__assertion_eval_preprocess.classpath"/>
+ </java>
+ </target>
+ <target name="ctakes__assertion_eval">
+ <java classname="org.apache.ctakes.assertion.eval.AssertionEvaluation" failonerror="true" fork="yes">
+ <arg line="--train-dir data/train --test-dir data/test --models-dir data/model/eval.model --dev-dir data/dev"/>
+ <classpath refid="run.ctakes__assertion_eval.classpath"/>
+ </java>
+ </target>
+ <target name="PolarityCotrainingTrain">
+ <java classname="org.apache.ctakes.assertion.train.PolarityCotrainingTrain" failonerror="true" fork="yes">
+ <classpath refid="run.PolarityCotrainingTrain.classpath"/>
+ </java>
+ </target>
+ <target name="PolarityCotrainingTests">
+ <java classname="org.apache.ctakes.assertion.train.PolarityCotrainingTests" failonerror="true" fork="yes">
+ <classpath refid="run.PolarityCotrainingTests.classpath"/>
+ </java>
+ </target>
+</project>
Propchange: ctakes/trunk/ctakes-assertion/build.xml
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Added: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/PolarityCotrainingTests.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/PolarityCotrainingTests.java?rev=1514842&view=auto
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/PolarityCotrainingTests.java (added)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/PolarityCotrainingTests.java Fri Aug 16 18:42:20 2013
@@ -0,0 +1,99 @@
+package org.apache.ctakes.assertion.train;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Map.Entry;
+
+import org.apache.ctakes.assertion.eval.AssertionEvaluation;
+import org.apache.ctakes.assertion.util.AssertionConst;
+import org.apache.ctakes.assertion.train.PolarityCotrainingTrain.*;
+
+import scala.actors.threadpool.Arrays;
+
+
+/**
+ * For each assertion attribute (polarity, conditional, etc), run against the test directories
+ * for that attribute, using models that are under the models-dir.
+ * Note that this uses constants within {@link AssertionConst} for the directory names.
+ */
+public class PolarityCotrainingTests {
+
+ protected final static String SHARP_TEST = AssertionConst.DATA_DIR + "preprocessed_data/sharp/test";
+ protected final static String I2B2_TEST = AssertionConst.DATA_DIR + "preprocessed_data/i2b2/test";
+ protected final static String MIPACQ_TEST = AssertionConst.DATA_DIR + "preprocessed_data/mipacq/cTAKES-xmi";
+ protected final static String NEGEX_TEST = AssertionConst.DATA_DIR + "preprocessed_data/negex";
+
+ public static void main(String[] args) throws Exception {
+
+ AssertionEvaluation.useEvaluationLogFile = true;
+
+ HashMap<String,String> testGrid = new HashMap<String,String>();
+ testGrid.put(PolarityCotrainingTrain.SHARP_MODEL, SHARP_TEST);
+ testGrid.put(PolarityCotrainingTrain.SHARP_MODEL, I2B2_TEST);
+ testGrid.put(PolarityCotrainingTrain.SHARP_MODEL, MIPACQ_TEST);
+ testGrid.put(PolarityCotrainingTrain.SHARP_MODEL, NEGEX_TEST);
+ testGrid.put(PolarityCotrainingTrain.I2B2_MODEL, SHARP_TEST);
+ testGrid.put(PolarityCotrainingTrain.I2B2_MODEL, I2B2_TEST);
+ testGrid.put(PolarityCotrainingTrain.I2B2_MODEL, MIPACQ_TEST);
+ testGrid.put(PolarityCotrainingTrain.I2B2_MODEL, NEGEX_TEST);
+ testGrid.put(PolarityCotrainingTrain.MIPACQ_MODEL, SHARP_TEST);
+ testGrid.put(PolarityCotrainingTrain.MIPACQ_MODEL, I2B2_TEST);
+ testGrid.put(PolarityCotrainingTrain.MIPACQ_MODEL, MIPACQ_TEST); // not valid
+ testGrid.put(PolarityCotrainingTrain.MIPACQ_MODEL, NEGEX_TEST);
+ testGrid.put(PolarityCotrainingTrain.NEGEX_MODEL, SHARP_TEST);
+ testGrid.put(PolarityCotrainingTrain.NEGEX_MODEL, I2B2_TEST);
+ testGrid.put(PolarityCotrainingTrain.NEGEX_MODEL, MIPACQ_TEST);
+ testGrid.put(PolarityCotrainingTrain.NEGEX_MODEL, NEGEX_TEST); // not valid
+ testGrid.put(PolarityCotrainingTrain.SHARP_I2B2_MODEL, SHARP_TEST);
+ testGrid.put(PolarityCotrainingTrain.SHARP_I2B2_MODEL, I2B2_TEST);
+ testGrid.put(PolarityCotrainingTrain.SHARP_I2B2_MODEL, MIPACQ_TEST);
+ testGrid.put(PolarityCotrainingTrain.SHARP_I2B2_MODEL, NEGEX_TEST);
+ testGrid.put(PolarityCotrainingTrain.SHARP_MIPACQ_MODEL, SHARP_TEST);
+ testGrid.put(PolarityCotrainingTrain.SHARP_MIPACQ_MODEL, I2B2_TEST);
+ testGrid.put(PolarityCotrainingTrain.SHARP_MIPACQ_MODEL, MIPACQ_TEST); // not valid
+ testGrid.put(PolarityCotrainingTrain.SHARP_MIPACQ_MODEL, NEGEX_TEST);
+ testGrid.put(PolarityCotrainingTrain.SHARP_NEGEX_MODEL, SHARP_TEST);
+ testGrid.put(PolarityCotrainingTrain.SHARP_NEGEX_MODEL, I2B2_TEST);
+ testGrid.put(PolarityCotrainingTrain.SHARP_NEGEX_MODEL, MIPACQ_TEST);
+ testGrid.put(PolarityCotrainingTrain.SHARP_NEGEX_MODEL, NEGEX_TEST); // not valid
+ testGrid.put(PolarityCotrainingTrain.SHARP_I2B2_MIPACQ_NEGEX_MODEL, SHARP_TEST);
+ testGrid.put(PolarityCotrainingTrain.SHARP_I2B2_MIPACQ_NEGEX_MODEL, I2B2_TEST);
+ testGrid.put(PolarityCotrainingTrain.SHARP_I2B2_MIPACQ_NEGEX_MODEL, MIPACQ_TEST);
+ testGrid.put(PolarityCotrainingTrain.SHARP_I2B2_MIPACQ_NEGEX_MODEL, NEGEX_TEST);
+
+
+ String attribute = "polarity";
+
+ for (Entry<String, String> oneTest : testGrid.entrySet()) {
+ ArrayList<String> params = new ArrayList<String>();
+
+ params.add("--test-dir"); params.add(oneTest.getValue());
+ params.add("--models-dir"); params.add(oneTest.getKey());
+ // params.add("--ytex-negation");
+ // params.add("--evaluation-output-dir"); params.add(AssertionConst.evalOutputDir);
+ params.add("--test-only");
+ params.add("--print-errors");
+
+ // Build up an "ignore" string
+ for (String ignoreAttribute : AssertionConst.allAnnotationTypes) {
+ if (!ignoreAttribute.equals(attribute)) {
+
+ if (ignoreAttribute.equals("historyOf")) {
+ ignoreAttribute = ignoreAttribute.substring(0, ignoreAttribute.length()-2);
+ }
+
+ params.add("--ignore-" + ignoreAttribute);
+ }
+ }
+ String[] paramList = params.toArray(new String[]{});
+
+ System.out.println(Arrays.asList(paramList).toString());
+
+ // Run the actual assertion test on just one attribute
+ AssertionEvaluation.main( paramList );
+ }
+ }
+
+
+
+}
Propchange: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/PolarityCotrainingTests.java
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Added: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/PolarityCotrainingTrain.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/PolarityCotrainingTrain.java?rev=1514842&view=auto
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/PolarityCotrainingTrain.java (added)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/PolarityCotrainingTrain.java Fri Aug 16 18:42:20 2013
@@ -0,0 +1,79 @@
+package org.apache.ctakes.assertion.train;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Map.Entry;
+
+import org.apache.ctakes.assertion.eval.AssertionEvaluation;
+import org.apache.ctakes.assertion.util.AssertionConst;
+
+import scala.actors.threadpool.Arrays;
+/**
+ * For each assertion attribute (polarity, conditional, etc), train a model using the data
+ * in the training directories for that attribute, and store the model under the models-dir
+ * Note that this uses constants within {@link AssertionConst} for the directory names.
+ */
+public class PolarityCotrainingTrain {
+ protected final static String SHARP_TRAIN = AssertionConst.DATA_DIR + "preprocessed_data/sharp/train";
+ protected final static String I2B2_TRAIN = AssertionConst.DATA_DIR + "preprocessed_data/i2b2/train";
+ protected final static String MIPACQ_TRAIN = AssertionConst.DATA_DIR + "preprocessed_data/mipacq/cTAKES-xmi"; // actually test
+ protected final static String NEGEX_TRAIN = AssertionConst.DATA_DIR + "preprocessed_data/negex"; // actually test
+
+ protected final static String SHARP_MODEL = "../ctakes-assertion-res/resources/model/sharptrain";
+ protected final static String I2B2_MODEL = "../ctakes-assertion-res/resources/model/i2b2train";
+ protected final static String MIPACQ_MODEL = "../ctakes-assertion-res/resources/model/mipacqtest";
+ protected final static String NEGEX_MODEL = "../ctakes-assertion-res/resources/model/negextest";
+ protected final static String SHARP_I2B2_MODEL = "../ctakes-assertion-res/resources/model/sharptrain+i2b2train";
+ protected final static String SHARP_MIPACQ_MODEL = "../ctakes-assertion-res/resources/model/sharptrain+mipacqtest";
+ protected final static String SHARP_NEGEX_MODEL = "../ctakes-assertion-res/resources/model/sharptrain+negextest";
+ protected final static String SHARP_I2B2_MIPACQ_NEGEX_MODEL = "../ctakes-assertion-res/resources/model/sharpi2b2mipacqnegex";
+
+ public static void main(String[] args) throws Exception {
+
+ String attribute = "polarity";
+
+ HashMap<String,String> trainGrid = new HashMap<String,String>();
+ trainGrid.put(SHARP_TRAIN, SHARP_MODEL);
+ trainGrid.put(I2B2_TRAIN, I2B2_MODEL);
+ trainGrid.put(MIPACQ_TRAIN, MIPACQ_MODEL);
+ trainGrid.put(NEGEX_TRAIN, NEGEX_MODEL);
+ trainGrid.put(SHARP_TRAIN+":"+I2B2_TRAIN, SHARP_I2B2_MODEL);
+ trainGrid.put(SHARP_TRAIN+":"+MIPACQ_TRAIN, SHARP_MIPACQ_MODEL);
+ trainGrid.put(SHARP_TRAIN+":"+NEGEX_TRAIN, SHARP_NEGEX_MODEL);
+ trainGrid.put(SHARP_TRAIN+":"+I2B2_TRAIN+":"+MIPACQ_TRAIN+":"+NEGEX_TRAIN,
+ SHARP_I2B2_MIPACQ_NEGEX_MODEL);
+
+ for (Entry<String, String> oneTrain : trainGrid.entrySet()) {
+
+ ArrayList<String> params = new ArrayList<String>();
+
+ params.add("--train-dir"); params.add(oneTrain.getKey());
+// params.add("--test-dir"); params.add("sharp_data/dev");
+ params.add("--models-dir"); params.add(oneTrain.getValue());
+// params.add("--evaluation-output-dir"); params.add(AssertionConst.evalOutputDir);
+ params.add("--train-only");
+// params.add("--feature-selection"); params.add("1.0");
+
+ // Build up an "ignore" string
+ for (String ignoreAttribute : AssertionConst.allAnnotationTypes) {
+ if (!ignoreAttribute.equals(attribute)) {
+
+ if (ignoreAttribute.equals("historyOf")) {
+ ignoreAttribute = ignoreAttribute.substring(0, ignoreAttribute.length()-2);
+ }
+
+ params.add("--ignore-" + ignoreAttribute);
+ }
+ }
+ String[] paramList = params.toArray(new String[]{});
+
+// System.out.println(Arrays.asList(paramList).toString());
+
+ // Run the actual assertion training on just one attribute
+ AssertionEvaluation.main( paramList );
+ }
+
+
+
+ }
+}
Propchange: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/train/PolarityCotrainingTrain.java
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