New algorithms and functionalities

News algorithms Improvements in configuration files Documentation and API update
kdis-lab · Apr 4, 2024 · f0e7525 · f0e7525
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diff --git a/documentation/apidoc/.DS_Store → .DS_Store b/documentation/apidoc/.DS_Store → .DS_Store
diff --git a/dist/configurations/MIMLClassifier/DMIMLkNN.config b/dist/configurations/MIMLClassifier/DMIMLkNN.config
diff --git a/dist/configurations/MIMLClassifier/EnMIMLNNMetric.config b/dist/configurations/MIMLClassifier/EnMIMLNNMetric.config
diff --git a/dist/configurations/MIMLClassifier/KiSar.config b/dist/configurations/MIMLClassifier/KiSar.config
diff --git a/dist/configurations/MIMLClassifier/MIMLBRkNN.config b/dist/configurations/MIMLClassifier/MIMLBRkNN.config
diff --git a/dist/configurations/MIMLClassifier/MIMLBagging.config b/dist/configurations/MIMLClassifier/MIMLBagging.config
diff --git a/dist/configurations/MIMLClassifier/MIMLDGC.config b/dist/configurations/MIMLClassifier/MIMLDGC.config
diff --git a/dist/configurations/MIMLClassifier/MIMLFast.config b/dist/configurations/MIMLClassifier/MIMLFast.config
diff --git a/dist/configurations/MIMLClassifier/MIMLIBLR.config b/dist/configurations/MIMLClassifier/MIMLIBLR.config
diff --git a/dist/configurations/MIMLClassifier/MIMLMAPkNN.config b/dist/configurations/MIMLClassifier/MIMLMAPkNN.config
diff --git a/dist/configurations/MIMLClassifier/MIMLNN.config b/dist/configurations/MIMLClassifier/MIMLNN.config
diff --git a/dist/configurations/MIMLClassifier/MIMLRBF.config b/dist/configurations/MIMLClassifier/MIMLRBF.config
diff --git a/dist/configurations/MIMLClassifier/MIMLSVM.config b/dist/configurations/MIMLClassifier/MIMLSVM.config
diff --git a/dist/configurations/MIMLClassifier/MIMLWel.config b/dist/configurations/MIMLClassifier/MIMLWel.config
diff --git a/dist/configurations/MIMLClassifier/MIMLkNN.config b/dist/configurations/MIMLClassifier/MIMLkNN.config
diff --git a/dist/configurations/toMI/MIMLtoMI_BR_CitationKNN.config b/dist/configurations/toMI/MIMLtoMI_BR_CitationKNN.config
diff --git a/dist/configurations/toMI/MIMLtoMI_BR_MDD.config b/dist/configurations/toMI/MIMLtoMI_BR_MDD.config
diff --git a/dist/configurations/toMI/MIMLtoMI_BR_MIBoost.config b/dist/configurations/toMI/MIMLtoMI_BR_MIBoost.config
diff --git a/dist/configurations/toMI/MIMLtoMI_BR_MIDD.config b/dist/configurations/toMI/MIMLtoMI_BR_MIDD.config
diff --git a/dist/configurations/toMI/MIMLtoMI_BR_MILR.config b/dist/configurations/toMI/MIMLtoMI_BR_MILR.config
diff --git a/dist/configurations/toMI/MIMLtoMI_BR_MINND.config b/dist/configurations/toMI/MIMLtoMI_BR_MINND.config
@@ -0,0 +1,35 @@
+<configuration>
+
+	<classifier name="miml.classifiers.miml.mimlTOmi.MIMLClassifierToMI">
+
+		<transformationMethod name="miml.classifiers.miml.mimlTOmi.MIMLBinaryRelevance"/>
+
+		<multiInstanceClassifier name="weka.classifiers.mi.MINND">
+			<listOptions>
+				-K 10 -S 1 -E 1
+			</listOptions>
+        </multiInstanceClassifier>
+
+	</classifier>
+
+	<evaluator name="miml.evaluation.EvaluatorHoldout">
+		<data>
+			<trainFile>data/miml_birds_random_80train.arff</trainFile>
+			<testFile>data/miml_birds_random_20test.arff</testFile>
+			<xmlFile>data/miml_birds.xml</xmlFile>
+		</data>
+	</evaluator>
+
+	<report name="miml.report.BaseMIMLReport">
+		<fileName>results/toMI/BR_MINND.csv</fileName>
+		<standardDeviation>false</standardDeviation>
+		<header>true</header>
+		<measures perLabel="false">
+			<measure>Hamming Loss</measure>
+			<measure>Subset Accuracy</measure>
+			<measure>Macro-averaged Precision</measure>
+			<measure>Macro-averaged F-Measure</measure>
+		</measures>
+	</report>
+
+</configuration>
diff --git a/dist/configurations/toMI/MIMLtoMI_BR_MIOptimalBall.config b/dist/configurations/toMI/MIMLtoMI_BR_MIOptimalBall.config
diff --git a/dist/configurations/toMI/MIMLtoMI_BR_MIRI.config b/dist/configurations/toMI/MIMLtoMI_BR_MIRI.config
diff --git a/dist/configurations/toMI/MIMLtoMI_BR_MISMO.config b/dist/configurations/toMI/MIMLtoMI_BR_MISMO.config
diff --git a/dist/configurations/toMI/MIMLtoMI_BR_MISVM.config b/dist/configurations/toMI/MIMLtoMI_BR_MISVM.config
diff --git a/dist/configurations/toMI/MIMLtoMI_BR_MITI.config b/dist/configurations/toMI/MIMLtoMI_BR_MITI.config
diff --git a/dist/configurations/toMI/MIMLtoMI_BR_MIWrapper.config b/dist/configurations/toMI/MIMLtoMI_BR_MIWrapper.config
diff --git a/dist/configurations/toMI/MIMLtoMI_BR_SimpleMI.config b/dist/configurations/toMI/MIMLtoMI_BR_SimpleMI.config
diff --git a/dist/configurations/toMI/MIMLtoMI_BR_TLC.config b/dist/configurations/toMI/MIMLtoMI_BR_TLC.config
@@ -0,0 +1,35 @@
+<configuration>
+
+	<classifier name="miml.classifiers.miml.mimlTOmi.MIMLClassifierToMI">
+
+		<transformationMethod name="miml.classifiers.miml.mimlTOmi.MIMLBinaryRelevance"/>
+
+        <multiInstanceClassifier name="weka.classifiers.mi.TLC">
+			<listOptions>
+				-P weka.classifiers.trees.J48 -W weka.classifiers.meta.LogitBoost -- -S 1 -I 10 -W weka.classifiers.trees.DecisionStump
+			</listOptions>
+        </multiInstanceClassifier>
+
+	</classifier>
+
+	<evaluator name="miml.evaluation.EvaluatorHoldout">
+		<data>
+			<trainFile>data/miml_birds_random_80train.arff</trainFile>
+			<testFile>data/miml_birds_random_20test.arff</testFile>
+			<xmlFile>data/miml_birds.xml</xmlFile>
+		</data>
+	</evaluator>
+
+	<report name="miml.report.BaseMIMLReport">
+		<fileName>results/toMI/BR_TLC.csv</fileName>
+		<standardDeviation>false</standardDeviation>
+		<header>true</header>
+		<measures perLabel="false">
+			<measure>Hamming Loss</measure>
+			<measure>Subset Accuracy</measure>
+			<measure>Macro-averaged Precision</measure>
+			<measure>Macro-averaged F-Measure</measure>
+		</measures>
+	</report>
+
+</configuration>
diff --git a/dist/configurations/toMI/MIMLtoMI_LP_CitationKNN.config b/dist/configurations/toMI/MIMLtoMI_LP_CitationKNN.config
diff --git a/dist/configurations/toMI/MIMLtoMI_LP_MINND.config b/dist/configurations/toMI/MIMLtoMI_LP_MINND.config
@@ -0,0 +1,35 @@
+<configuration>
+
+	<classifier name="miml.classifiers.miml.mimlTOmi.MIMLClassifierToMI">
+
+		<transformationMethod name="miml.classifiers.miml.mimlTOmi.MIMLLabelPowerset"/>
+
+		<multiInstanceClassifier name="weka.classifiers.mi.MINND">
+			<listOptions>
+				-K 10 -S 1 -E 1
+			</listOptions>
+        </multiInstanceClassifier>
+
+	</classifier>
+
+	<evaluator name="miml.evaluation.EvaluatorHoldout">
+		<data>
+			<trainFile>data/miml_birds_random_80train.arff</trainFile>
+			<testFile>data/miml_birds_random_20test.arff</testFile>
+			<xmlFile>data/miml_birds.xml</xmlFile>
+		</data>
+	</evaluator>
+
+	<report name="miml.report.BaseMIMLReport">
+		<fileName>results/toMI/LP_MINND.csv</fileName>
+		<standardDeviation>false</standardDeviation>
+		<header>true</header>
+		<measures perLabel="false">
+			<measure>Hamming Loss</measure>
+			<measure>Subset Accuracy</measure>
+			<measure>Macro-averaged Precision</measure>
+			<measure>Macro-averaged F-Measure</measure>
+		</measures>
+	</report>
+
+</configuration>
diff --git a/dist/configurations/toMI/MIMLtoMI_LP_MISMO.config b/dist/configurations/toMI/MIMLtoMI_LP_MISMO.config
@@ -0,0 +1,35 @@
+<configuration>
+
+	<classifier name="miml.classifiers.miml.mimlTOmi.MIMLClassifierToMI">
+
+		<transformationMethod name="miml.classifiers.miml.mimlTOmi.MIMLLabelPowerset"/>
+
+		<multiInstanceClassifier name="miml.classifiers.mi.MISMOWrapper">
+			<listOptions>
+				-L 1.0e-3 -P 1.0e-12 -N 0 -V 5
+			</listOptions>
+        </multiInstanceClassifier>
+
+	</classifier>
+
+	<evaluator name="miml.evaluation.EvaluatorHoldout">
+		<data>
+			<trainFile>data/miml_birds_random_80train.arff</trainFile>
+			<testFile>data/miml_birds_random_20test.arff</testFile>
+			<xmlFile>data/miml_birds.xml</xmlFile>
+		</data>
+	</evaluator>
+
+	<report name="miml.report.BaseMIMLReport">
+		<fileName>results/toMI/LP_MISMO.csv</fileName>
+		<standardDeviation>false</standardDeviation>
+		<header>true</header>
+		<measures perLabel="false">
+			<measure>Hamming Loss</measure>
+			<measure>Subset Accuracy</measure>
+			<measure>Macro-averaged Precision</measure>
+			<measure>Macro-averaged F-Measure</measure>
+		</measures>
+	</report>
+
+</configuration>
diff --git a/dist/configurations/toMI/MIMLtoMI_LP_MIWrapper.config b/dist/configurations/toMI/MIMLtoMI_LP_MIWrapper.config
diff --git a/dist/configurations/toMI/MIMLtoMI_LP_SimpleMI.config b/dist/configurations/toMI/MIMLtoMI_LP_SimpleMI.config
diff --git a/dist/configurations/toMI/MIMLtoMI_LP_TLC.config b/dist/configurations/toMI/MIMLtoMI_LP_TLC.config
@@ -0,0 +1,35 @@
+<configuration>
+
+	<classifier name="miml.classifiers.miml.mimlTOmi.MIMLClassifierToMI">
+
+		<transformationMethod name="miml.classifiers.miml.mimlTOmi.MIMLLabelPowerset"/>
+
+		<multiInstanceClassifier name="weka.classifiers.mi.TLC">
+			<listOptions>
+				-P weka.classifiers.trees.J48 -W weka.classifiers.meta.LogitBoost -- -S 1 -I 10 -W weka.classifiers.trees.DecisionStump
+			</listOptions>
+        </multiInstanceClassifier>
+
+	</classifier>
+
+	<evaluator name="miml.evaluation.EvaluatorHoldout">
+		<data>
+			<trainFile>data/miml_birds_random_80train.arff</trainFile>
+			<testFile>data/miml_birds_random_20test.arff</testFile>
+			<xmlFile>data/miml_birds.xml</xmlFile>
+		</data>
+	</evaluator>
+
+	<report name="miml.report.BaseMIMLReport">
+		<fileName>results/toMI/LP_TLC.csv</fileName>
+		<standardDeviation>false</standardDeviation>
+		<header>true</header>
+		<measures perLabel="false">
+			<measure>Hamming Loss</measure>
+			<measure>Subset Accuracy</measure>
+			<measure>Macro-averaged Precision</measure>
+			<measure>Macro-averaged F-Measure</measure>
+		</measures>
+	</report>
+
+</configuration>
diff --git a/dist/configurations/toML/MIMLtoML_AT_BR.config b/dist/configurations/toML/MIMLtoML_AT_BR.config
diff --git a/dist/configurations/toML/MIMLtoML_AT_BRkNN.config b/dist/configurations/toML/MIMLtoML_AT_BRkNN.config
diff --git a/dist/configurations/toML/MIMLtoML_AT_CC.config b/dist/configurations/toML/MIMLtoML_AT_CC.config
diff --git a/dist/configurations/toML/MIMLtoML_AT_CLR.config b/dist/configurations/toML/MIMLtoML_AT_CLR.config
diff --git a/dist/configurations/toML/MIMLtoML_AT_DMLkNN.config b/dist/configurations/toML/MIMLtoML_AT_DMLkNN.config
diff --git a/dist/configurations/toML/MIMLtoML_AT_ECC.config b/dist/configurations/toML/MIMLtoML_AT_ECC.config
diff --git a/dist/configurations/toML/MIMLtoML_AT_EPS.config b/dist/configurations/toML/MIMLtoML_AT_EPS.config
diff --git a/dist/configurations/toML/MIMLtoML_AT_HOMER.config b/dist/configurations/toML/MIMLtoML_AT_HOMER.config
diff --git a/dist/configurations/toML/MIMLtoML_AT_IBLR_ML.config b/dist/configurations/toML/MIMLtoML_AT_IBLR_ML.config
diff --git a/dist/configurations/toML/MIMLtoML_AT_LP.config b/dist/configurations/toML/MIMLtoML_AT_LP.config
diff --git a/dist/configurations/toML/MIMLtoML_AT_MLDGC.config b/dist/configurations/toML/MIMLtoML_AT_MLDGC.config
@@ -0,0 +1,33 @@
+<configuration>
+
+	<classifier name="miml.classifiers.miml.mimlTOml.MIMLClassifierToML">
+
+		<multiLabelClassifier name="miml.classifiers.ml.MLDGC">
+			<parameters>
+				<parameter class="int.class" value="10"/>
+			</parameters>
+		</multiLabelClassifier>
+		<transformationMethod name="miml.transformation.mimlTOml.ArithmeticTransformation"/>
+	</classifier>
+
+	<evaluator name="miml.evaluation.EvaluatorCV">
+		<numFolds>5</numFolds>
+		<data>
+			<file>data/miml_birds.arff</file>
+			<xmlFile>data/miml_birds.xml</xmlFile>
+		</data>
+	</evaluator>	
+
+	<report name="miml.report.BaseMIMLReport">
+		<fileName>results/toML/AT_MLDGC.csv</fileName>
+		<standardDeviation>false</standardDeviation>
+		<header>true</header>
+		<measures perLabel="false">
+			<measure>Hamming Loss</measure>
+			<measure>Subset Accuracy</measure>
+			<measure>Macro-averaged Precision</measure>
+			<measure>Macro-averaged F-Measure</measure>
+		</measures>
+	</report>
+
+</configuration>
diff --git a/dist/configurations/toML/MIMLtoML_AT_MLStacking.config b/dist/configurations/toML/MIMLtoML_AT_MLStacking.config
diff --git a/dist/configurations/toML/MIMLtoML_AT_MLkNN.config b/dist/configurations/toML/MIMLtoML_AT_MLkNN.config
diff --git a/dist/configurations/toML/MIMLtoML_AT_PS.config b/dist/configurations/toML/MIMLtoML_AT_PS.config
diff --git a/dist/configurations/toML/MIMLtoML_AT_RAkEL.config b/dist/configurations/toML/MIMLtoML_AT_RAkEL.config
diff --git a/dist/configurations/toML/MIMLtoML_AT_RFPCT.config b/dist/configurations/toML/MIMLtoML_AT_RFPCT.config
@@ -0,0 +1,39 @@
+<configuration>
+
+	<classifier name="miml.classifiers.miml.mimlTOml.MIMLClassifierToML">
+
+		<multiLabelClassifier name="miml.classifiers.ml.RFPCT">
+			<parameters>
+				<parameter class="String.class" value="clusFolder"/>
+				<parameter class="String.class" value="clusBirds"/>
+				<parameter class="int.class" value="10"/>
+				<parameter class="long.class" value="1"/>
+			</parameters>
+		</multiLabelClassifier>
+		<transformationMethod name="miml.transformation.mimlTOml.ArithmeticTransformation"/>
+	</classifier>
+
+	<evaluator name="miml.evaluation.EvaluatorHoldoutClus">
+		<data>
+			<trainFile>data/miml_birds_random_80train.arff</trainFile>
+			<testFile>data/miml_birds_random_20test.arff</testFile>
+			<xmlFile>data/miml_birds.xml</xmlFile>
+		</data>
+		<clusWorkingDir>clusFolder</clusWorkingDir>
+		<clusDataset>clusBirds</clusDataset>
+	</evaluator>
+
+
+	<report name="miml.report.BaseMIMLReport">
+		<fileName>results/toML/AT_RFPCT.csv</fileName>
+		<standardDeviation>false</standardDeviation>
+		<header>true</header>
+		<measures perLabel="false">
+			<measure>Hamming Loss</measure>
+			<measure>Subset Accuracy</measure>
+			<measure>Macro-averaged Precision</measure>
+			<measure>Macro-averaged F-Measure</measure>
+		</measures>
+	</report>
+
+</configuration>
diff --git a/dist/configurations/toML/MIMLtoML_AT_RPC.config b/dist/configurations/toML/MIMLtoML_AT_RPC.config
diff --git a/dist/configurations/toML/MIMLtoML_GT_BR.config b/dist/configurations/toML/MIMLtoML_GT_BR.config
diff --git a/dist/configurations/toML/MIMLtoML_GT_BRkNN.config b/dist/configurations/toML/MIMLtoML_GT_BRkNN.config
diff --git a/dist/configurations/toML/MIMLtoML_GT_CC.config b/dist/configurations/toML/MIMLtoML_GT_CC.config
diff --git a/dist/configurations/toML/MIMLtoML_GT_CLR.config b/dist/configurations/toML/MIMLtoML_GT_CLR.config
diff --git a/dist/configurations/toML/MIMLtoML_GT_DMLkNN.config b/dist/configurations/toML/MIMLtoML_GT_DMLkNN.config
diff --git a/dist/configurations/toML/MIMLtoML_GT_ECC.config b/dist/configurations/toML/MIMLtoML_GT_ECC.config
diff --git a/dist/configurations/toML/MIMLtoML_GT_EPS.config b/dist/configurations/toML/MIMLtoML_GT_EPS.config
diff --git a/dist/configurations/toML/MIMLtoML_GT_HOMER.config b/dist/configurations/toML/MIMLtoML_GT_HOMER.config
diff --git a/dist/configurations/toML/MIMLtoML_GT_IBLR_ML.config b/dist/configurations/toML/MIMLtoML_GT_IBLR_ML.config
diff --git a/dist/configurations/toML/MIMLtoML_GT_LP.config b/dist/configurations/toML/MIMLtoML_GT_LP.config
diff --git a/dist/configurations/toML/MIMLtoML_GT_MLDGC.config b/dist/configurations/toML/MIMLtoML_GT_MLDGC.config
@@ -0,0 +1,29 @@
+<configuration>
+
+	<classifier name="miml.classifiers.miml.mimlTOml.MIMLClassifierToML">
+
+		<multiLabelClassifier name="miml.classifiers.ml.MLDGC"/>		
+		<transformationMethod name="miml.transformation.mimlTOml.GeometricTransformation"/>
+	</classifier>
+
+	<evaluator name="miml.evaluation.EvaluatorCV">
+		<numFolds>5</numFolds>
+		<data>
+			<file>data/miml_birds.arff</file>
+			<xmlFile>data/miml_birds.xml</xmlFile>
+		</data>
+	</evaluator>	
+
+	<report name="miml.report.BaseMIMLReport">
+		<fileName>results/toML/GT_MLDGC.csv</fileName>
+		<standardDeviation>false</standardDeviation>
+		<header>true</header>
+		<measures perLabel="false">
+			<measure>Hamming Loss</measure>
+			<measure>Subset Accuracy</measure>
+			<measure>Macro-averaged Precision</measure>
+			<measure>Macro-averaged F-Measure</measure>
+		</measures>
+	</report>
+
+</configuration>
diff --git a/dist/configurations/toML/MIMLtoML_GT_MLStacking.config b/dist/configurations/toML/MIMLtoML_GT_MLStacking.config
diff --git a/dist/configurations/toML/MIMLtoML_GT_MLkNN.config b/dist/configurations/toML/MIMLtoML_GT_MLkNN.config
diff --git a/dist/configurations/toML/MIMLtoML_GT_PS.config b/dist/configurations/toML/MIMLtoML_GT_PS.config
diff --git a/dist/configurations/toML/MIMLtoML_GT_RAkEL.config b/dist/configurations/toML/MIMLtoML_GT_RAkEL.config
diff --git a/dist/configurations/toML/MIMLtoML_GT_RFPCT.config b/dist/configurations/toML/MIMLtoML_GT_RFPCT.config
@@ -0,0 +1,39 @@
+<configuration>
+
+	<classifier name="miml.classifiers.miml.mimlTOml.MIMLClassifierToML">
+
+		<multiLabelClassifier name="miml.classifiers.ml.RFPCT">
+			<parameters>
+				<parameter class="String.class" value="clusFolder"/>
+				<parameter class="String.class" value="clusBirds"/>
+				<parameter class="int.class" value="10"/>
+				<parameter class="long.class" value="1"/>
+			</parameters>
+		</multiLabelClassifier>
+		<transformationMethod name="miml.transformation.mimlTOml.GeometricTransformation"/>
+	</classifier>
+
+	<evaluator name="miml.evaluation.EvaluatorHoldoutClus">
+		<data>
+			<trainFile>data/miml_birds_random_80train.arff</trainFile>
+			<testFile>data/miml_birds_random_20test.arff</testFile>
+			<xmlFile>data/miml_birds.xml</xmlFile>
+		</data>
+		<clusWorkingDir>clusFolder</clusWorkingDir>
+		<clusDataset>clusBirds</clusDataset>
+	</evaluator>
+
+
+	<report name="miml.report.BaseMIMLReport">
+		<fileName>results/toML/GT_RFPCT.csv</fileName>
+		<standardDeviation>false</standardDeviation>
+		<header>true</header>
+		<measures perLabel="false">
+			<measure>Hamming Loss</measure>
+			<measure>Subset Accuracy</measure>
+			<measure>Macro-averaged Precision</measure>
+			<measure>Macro-averaged F-Measure</measure>
+		</measures>
+	</report>
+
+</configuration>
diff --git a/dist/configurations/toML/MIMLtoML_GT_RPC.config b/dist/configurations/toML/MIMLtoML_GT_RPC.config
diff --git a/dist/configurations/toML/MIMLtoML_KMT_BR.config b/dist/configurations/toML/MIMLtoML_KMT_BR.config
@@ -0,0 +1,34 @@
+<configuration>
+
+	<classifier name="miml.classifiers.miml.mimlTOml.MIMLClassifierToML">
+
+		<multiLabelClassifier name="mulan.classifier.transformation.BinaryRelevance">
+			<parameters>
+				<parameter class="weka.classifiers.Classifier" value="weka.classifiers.lazy.IBk" listOptions="-K 3 -I"/>
+			</parameters>
+		</multiLabelClassifier>
+		<transformationMethod name="miml.transformation.mimlTOml.KMeansTransformation"/>
+	</classifier>
+
+	<evaluator name="miml.evaluation.EvaluatorHoldout">
+		<data>
+			<trainFile>data/miml_birds_random_80train.arff</trainFile>
+			<testFile>data/miml_birds_random_20test.arff</testFile>
+			<xmlFile>data/miml_birds.xml</xmlFile>
+		</data>
+	</evaluator>
+
+
+	<report name="miml.report.BaseMIMLReport">
+		<fileName>results/toML/KMT_BR.csv</fileName>
+		<standardDeviation>false</standardDeviation>
+		<header>true</header>
+		<measures perLabel="false">
+			<measure>Hamming Loss</measure>
+			<measure>Subset Accuracy</measure>
+			<measure>Macro-averaged Precision</measure>
+			<measure>Macro-averaged F-Measure</measure>
+		</measures>
+	</report>
+
+</configuration>