dimont_motif_discovery: test-data/predictor

annotate test-data/predictor_test.xml @ 2:31963c6688ef draft default tip

Deleted selected files

author	grau
date	Wed, 20 Nov 2013 04:33:37 -0500
parents	b7d6db3ba6bc
children

rev	line source
0 b7d6db3ba6bc Uploaded grau parents: diff changeset	1 <gendismix-classifier>
b7d6db3ba6bc Uploaded grau parents: diff changeset	2 <alphabetcontainer><className>de.jstacs.data.alphabets.DNAAlphabetContainer</className></alphabetcontainer><length><className>java.lang.Integer</className>0</length><classWeights><className>[D</className><length>2</length><pos val="0">-2.034267647272289</pos><pos val="1">-0.2525781403291907</pos></classWeights><params><className>de.jstacs.classifiers.differentiableSequenceScoreBased.gendismix.GenDisMixClassifierParameterSet</className><sequenceScoringParameterSet>
b7d6db3ba6bc Uploaded grau parents: diff changeset	3 <superParameters>
b7d6db3ba6bc Uploaded grau parents: diff changeset	4 <instanceParameterSet>
b7d6db3ba6bc Uploaded grau parents: diff changeset	5 <superParameterSet>
b7d6db3ba6bc Uploaded grau parents: diff changeset	6 <parameterSet>
b7d6db3ba6bc Uploaded grau parents: diff changeset	7 <set>
b7d6db3ba6bc Uploaded grau parents: diff changeset	8 <numberOfParameters><className>java.lang.Integer</className>8</numberOfParameters><parameter><className>de.jstacs.parameters.SelectionParameter</className><collectionParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	9 <name><className>java.lang.String</className>algorithm</name><comment><className>java.lang.String</className>the algorithm that should be used for numerical optimization</comment><datatype><className>de.jstacs.DataType</className><name>BYTE</name></datatype><required><className>java.lang.Boolean</className>true</required><userSelected><className>java.lang.Boolean</className>true</userSelected><errorMessage>null</errorMessage><rangeable><className>java.lang.Boolean</className>true</rangeable><collection><className>de.jstacs.parameters.SimpleParameterSet</className><parameterSet>
b7d6db3ba6bc Uploaded grau parents: diff changeset	10 <set>
b7d6db3ba6bc Uploaded grau parents: diff changeset	11 <numberOfParameters><className>java.lang.Integer</className>13</numberOfParameters><parameter><className>de.jstacs.parameters.SimpleParameter</className><simpleParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	12 <name><className>java.lang.String</className>steepest descent</name><comment>null</comment><datatype><className>de.jstacs.DataType</className><name>BYTE</name></datatype><required><className>java.lang.Boolean</className>false</required><isSet><className>java.lang.Boolean</className>true</isSet><errorMessage><className>java.lang.String</className></errorMessage><isRangeable><className>java.lang.Boolean</className>true</isRangeable><validator>null</validator><defaultValue>null</defaultValue><value><className>java.lang.Byte</className>16</value></simpleParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	13 </parameter><parameter><className>de.jstacs.parameters.SimpleParameter</className><simpleParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	14 <name><className>java.lang.String</className>conjugate gradients (F., R.)</name><comment>null</comment><datatype><className>de.jstacs.DataType</className><name>BYTE</name></datatype><required><className>java.lang.Boolean</className>false</required><isSet><className>java.lang.Boolean</className>true</isSet><errorMessage><className>java.lang.String</className></errorMessage><isRangeable><className>java.lang.Boolean</className>true</isRangeable><validator>null</validator><defaultValue>null</defaultValue><value><className>java.lang.Byte</className>17</value></simpleParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	15 </parameter><parameter><className>de.jstacs.parameters.SimpleParameter</className><simpleParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	16 <name><className>java.lang.String</className>conjugate gradients (P., R. positive)</name><comment>null</comment><datatype><className>de.jstacs.DataType</className><name>BYTE</name></datatype><required><className>java.lang.Boolean</className>false</required><isSet><className>java.lang.Boolean</className>true</isSet><errorMessage><className>java.lang.String</className></errorMessage><isRangeable><className>java.lang.Boolean</className>true</isRangeable><validator>null</validator><defaultValue>null</defaultValue><value><className>java.lang.Byte</className>18</value></simpleParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	17 </parameter><parameter><className>de.jstacs.parameters.SimpleParameter</className><simpleParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	18 <name><className>java.lang.String</className>quasi newton (D., F., P.)</name><comment>null</comment><datatype><className>de.jstacs.DataType</className><name>BYTE</name></datatype><required><className>java.lang.Boolean</className>false</required><isSet><className>java.lang.Boolean</className>true</isSet><errorMessage><className>java.lang.String</className></errorMessage><isRangeable><className>java.lang.Boolean</className>true</isRangeable><validator>null</validator><defaultValue>null</defaultValue><value><className>java.lang.Byte</className>19</value></simpleParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	19 </parameter><parameter><className>de.jstacs.parameters.SimpleParameter</className><simpleParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	20 <name><className>java.lang.String</className>quasi newton (B., F., G., S.)</name><comment>null</comment><datatype><className>de.jstacs.DataType</className><name>BYTE</name></datatype><required><className>java.lang.Boolean</className>false</required><isSet><className>java.lang.Boolean</className>true</isSet><errorMessage><className>java.lang.String</className></errorMessage><isRangeable><className>java.lang.Boolean</className>true</isRangeable><validator>null</validator><defaultValue>null</defaultValue><value><className>java.lang.Byte</className>20</value></simpleParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	21 </parameter><parameter><className>de.jstacs.parameters.SimpleParameter</className><simpleParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	22 <name><className>java.lang.String</className>limited memory quasi newton (B., F., G., S.; n=3)</name><comment>null</comment><datatype><className>de.jstacs.DataType</className><name>BYTE</name></datatype><required><className>java.lang.Boolean</className>false</required><isSet><className>java.lang.Boolean</className>true</isSet><errorMessage><className>java.lang.String</className></errorMessage><isRangeable><className>java.lang.Boolean</className>true</isRangeable><validator>null</validator><defaultValue>null</defaultValue><value><className>java.lang.Byte</className>3</value></simpleParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	23 </parameter><parameter><className>de.jstacs.parameters.SimpleParameter</className><simpleParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	24 <name><className>java.lang.String</className>limited memory quasi newton (B., F., G., S.; n=4)</name><comment>null</comment><datatype><className>de.jstacs.DataType</className><name>BYTE</name></datatype><required><className>java.lang.Boolean</className>false</required><isSet><className>java.lang.Boolean</className>true</isSet><errorMessage><className>java.lang.String</className></errorMessage><isRangeable><className>java.lang.Boolean</className>true</isRangeable><validator>null</validator><defaultValue>null</defaultValue><value><className>java.lang.Byte</className>4</value></simpleParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	25 </parameter><parameter><className>de.jstacs.parameters.SimpleParameter</className><simpleParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	26 <name><className>java.lang.String</className>limited memory quasi newton (B., F., G., S.; n=5)</name><comment>null</comment><datatype><className>de.jstacs.DataType</className><name>BYTE</name></datatype><required><className>java.lang.Boolean</className>false</required><isSet><className>java.lang.Boolean</className>true</isSet><errorMessage><className>java.lang.String</className></errorMessage><isRangeable><className>java.lang.Boolean</className>true</isRangeable><validator>null</validator><defaultValue>null</defaultValue><value><className>java.lang.Byte</className>5</value></simpleParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	27 </parameter><parameter><className>de.jstacs.parameters.SimpleParameter</className><simpleParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	28 <name><className>java.lang.String</className>limited memory quasi newton (B., F., G., S.; n=6)</name><comment>null</comment><datatype><className>de.jstacs.DataType</className><name>BYTE</name></datatype><required><className>java.lang.Boolean</className>false</required><isSet><className>java.lang.Boolean</className>true</isSet><errorMessage><className>java.lang.String</className></errorMessage><isRangeable><className>java.lang.Boolean</className>true</isRangeable><validator>null</validator><defaultValue>null</defaultValue><value><className>java.lang.Byte</className>6</value></simpleParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	29 </parameter><parameter><className>de.jstacs.parameters.SimpleParameter</className><simpleParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	30 <name><className>java.lang.String</className>limited memory quasi newton (B., F., G., S.; n=7)</name><comment>null</comment><datatype><className>de.jstacs.DataType</className><name>BYTE</name></datatype><required><className>java.lang.Boolean</className>false</required><isSet><className>java.lang.Boolean</className>true</isSet><errorMessage><className>java.lang.String</className></errorMessage><isRangeable><className>java.lang.Boolean</className>true</isRangeable><validator>null</validator><defaultValue>null</defaultValue><value><className>java.lang.Byte</className>7</value></simpleParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	31 </parameter><parameter><className>de.jstacs.parameters.SimpleParameter</className><simpleParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	32 <name><className>java.lang.String</className>limited memory quasi newton (B., F., G., S.; n=8)</name><comment>null</comment><datatype><className>de.jstacs.DataType</className><name>BYTE</name></datatype><required><className>java.lang.Boolean</className>false</required><isSet><className>java.lang.Boolean</className>true</isSet><errorMessage><className>java.lang.String</className></errorMessage><isRangeable><className>java.lang.Boolean</className>true</isRangeable><validator>null</validator><defaultValue>null</defaultValue><value><className>java.lang.Byte</className>8</value></simpleParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	33 </parameter><parameter><className>de.jstacs.parameters.SimpleParameter</className><simpleParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	34 <name><className>java.lang.String</className>limited memory quasi newton (B., F., G., S.; n=9)</name><comment>null</comment><datatype><className>de.jstacs.DataType</className><name>BYTE</name></datatype><required><className>java.lang.Boolean</className>false</required><isSet><className>java.lang.Boolean</className>true</isSet><errorMessage><className>java.lang.String</className></errorMessage><isRangeable><className>java.lang.Boolean</className>true</isRangeable><validator>null</validator><defaultValue>null</defaultValue><value><className>java.lang.Byte</className>9</value></simpleParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	35 </parameter><parameter><className>de.jstacs.parameters.SimpleParameter</className><simpleParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	36 <name><className>java.lang.String</className>limited memory quasi newton (B., F., G., S.; n=10)</name><comment>null</comment><datatype><className>de.jstacs.DataType</className><name>BYTE</name></datatype><required><className>java.lang.Boolean</className>false</required><isSet><className>java.lang.Boolean</className>true</isSet><errorMessage><className>java.lang.String</className></errorMessage><isRangeable><className>java.lang.Boolean</className>true</isRangeable><validator>null</validator><defaultValue>null</defaultValue><value><className>java.lang.Byte</className>10</value></simpleParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	37 </parameter></set>
b7d6db3ba6bc Uploaded grau parents: diff changeset	38 </parameterSet>
b7d6db3ba6bc Uploaded grau parents: diff changeset	39 </collection><selected><className>java.lang.Integer</className>2</selected><defaultSelected><className>java.lang.Integer</className>4</defaultSelected></collectionParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	40 </parameter><parameter><className>de.jstacs.parameters.SelectionParameter</className><collectionParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	41 <name><className>java.lang.String</className>termination condition</name><comment><className>java.lang.String</className>the terminantion condition for stopping the training algorithm</comment><datatype><className>de.jstacs.DataType</className><name>PARAMETERSET</name></datatype><required><className>java.lang.Boolean</className>true</required><userSelected><className>java.lang.Boolean</className>true</userSelected><errorMessage>null</errorMessage><rangeable><className>java.lang.Boolean</className>true</rangeable><collection><className>de.jstacs.parameters.SimpleParameterSet</className><parameterSet>
b7d6db3ba6bc Uploaded grau parents: diff changeset	42 <set>
b7d6db3ba6bc Uploaded grau parents: diff changeset	43 <numberOfParameters><className>java.lang.Integer</className>8</numberOfParameters><parameter><className>de.jstacs.parameters.ParameterSetContainer</className><parameterSetContainer>
b7d6db3ba6bc Uploaded grau parents: diff changeset	44 <name><className>java.lang.String</className>AbsoluteValueConditionParameterSet</name><comment><className>java.lang.String</className></comment><datatype><className>de.jstacs.DataType</className><name>PARAMETERSET</name></datatype><errorMessage>null</errorMessage><parameterClass><className>java.lang.Class</className><name>de.jstacs.algorithms.optimization.termination.AbsoluteValueCondition$AbsoluteValueConditionParameterSet</name></parameterClass></parameterSetContainer>
b7d6db3ba6bc Uploaded grau parents: diff changeset	45 </parameter><parameter><className>de.jstacs.parameters.ParameterSetContainer</className><parameterSetContainer>
b7d6db3ba6bc Uploaded grau parents: diff changeset	46 <name><className>java.lang.String</className>CombinedConditionParameterSet</name><comment><className>java.lang.String</className></comment><datatype><className>de.jstacs.DataType</className><name>PARAMETERSET</name></datatype><errorMessage>null</errorMessage><parameterClass><className>java.lang.Class</className><name>de.jstacs.algorithms.optimization.termination.CombinedCondition$CombinedConditionParameterSet</name></parameterClass></parameterSetContainer>
b7d6db3ba6bc Uploaded grau parents: diff changeset	47 </parameter><parameter><className>de.jstacs.parameters.ParameterSetContainer</className><parameterSetContainer>
b7d6db3ba6bc Uploaded grau parents: diff changeset	48 <name><className>java.lang.String</className>IterationConditionParameterSet</name><comment><className>java.lang.String</className></comment><datatype><className>de.jstacs.DataType</className><name>PARAMETERSET</name></datatype><errorMessage>null</errorMessage><parameterClass><className>java.lang.Class</className><name>de.jstacs.algorithms.optimization.termination.IterationCondition$IterationConditionParameterSet</name></parameterClass></parameterSetContainer>
b7d6db3ba6bc Uploaded grau parents: diff changeset	49 </parameter><parameter><className>de.jstacs.parameters.ParameterSetContainer</className><parameterSetContainer>
b7d6db3ba6bc Uploaded grau parents: diff changeset	50 <name><className>java.lang.String</className>MultipleIterationsConditionParameterSet</name><comment><className>java.lang.String</className></comment><datatype><className>de.jstacs.DataType</className><name>PARAMETERSET</name></datatype><errorMessage>null</errorMessage><parameterClass><className>java.lang.Class</className><name>de.jstacs.algorithms.optimization.termination.MultipleIterationsCondition$MultipleIterationsConditionParameterSet</name></parameterClass></parameterSetContainer>
b7d6db3ba6bc Uploaded grau parents: diff changeset	51 </parameter><parameter><className>de.jstacs.parameters.ParameterSetContainer</className><parameterSetContainer>
b7d6db3ba6bc Uploaded grau parents: diff changeset	52 <name><className>java.lang.String</className>SmallDifferenceOfFunctionEvaluationsConditionParameterSet</name><comment><className>java.lang.String</className></comment><datatype><className>de.jstacs.DataType</className><name>PARAMETERSET</name></datatype><errorMessage>null</errorMessage><parameters><className>de.jstacs.algorithms.optimization.termination.SmallDifferenceOfFunctionEvaluationsCondition$SmallDifferenceOfFunctionEvaluationsConditionParameterSet</className><instanceParameterSet>
b7d6db3ba6bc Uploaded grau parents: diff changeset	53 <superParameterSet>
b7d6db3ba6bc Uploaded grau parents: diff changeset	54 <parameterSet>
b7d6db3ba6bc Uploaded grau parents: diff changeset	55 <set>
b7d6db3ba6bc Uploaded grau parents: diff changeset	56 <numberOfParameters><className>java.lang.Integer</className>1</numberOfParameters><parameter><className>de.jstacs.parameters.SimpleParameter</className><simpleParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	57 <name><className>java.lang.String</className>epsilon</name><comment><className>java.lang.String</className>the epsilon for the difference of function evaluations used for deciding whether to stop the algorithm or not</comment><datatype><className>de.jstacs.DataType</className><name>DOUBLE</name></datatype><required><className>java.lang.Boolean</className>true</required><isSet><className>java.lang.Boolean</className>true</isSet><errorMessage>null</errorMessage><isRangeable><className>java.lang.Boolean</className>true</isRangeable><validator><className>de.jstacs.parameters.validation.NumberValidator</className><NumberValidator>
b7d6db3ba6bc Uploaded grau parents: diff changeset	58 <className><className>java.lang.String</className>java.lang.Double</className><lowerBound><className>java.lang.String</className>0.0</lowerBound><upperBound><className>java.lang.String</className>1.7976931348623157E308</upperBound></NumberValidator>
b7d6db3ba6bc Uploaded grau parents: diff changeset	59 </validator><defaultValue><className>java.lang.Double</className>1.0E-6</defaultValue><value><className>java.lang.Double</className>1.0E-4</value></simpleParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	60 </parameter></set>
b7d6db3ba6bc Uploaded grau parents: diff changeset	61 </parameterSet>
b7d6db3ba6bc Uploaded grau parents: diff changeset	62 </superParameterSet>
b7d6db3ba6bc Uploaded grau parents: diff changeset	63 <instanceClass><className>java.lang.Class</className><name>de.jstacs.algorithms.optimization.termination.SmallDifferenceOfFunctionEvaluationsCondition</name></instanceClass></instanceParameterSet>
b7d6db3ba6bc Uploaded grau parents: diff changeset	64 </parameters></parameterSetContainer>
b7d6db3ba6bc Uploaded grau parents: diff changeset	65 </parameter><parameter><className>de.jstacs.parameters.ParameterSetContainer</className><parameterSetContainer>
b7d6db3ba6bc Uploaded grau parents: diff changeset	66 <name><className>java.lang.String</className>SmallGradientConditonParameterSet</name><comment><className>java.lang.String</className></comment><datatype><className>de.jstacs.DataType</className><name>PARAMETERSET</name></datatype><errorMessage>null</errorMessage><parameterClass><className>java.lang.Class</className><name>de.jstacs.algorithms.optimization.termination.SmallGradientConditon$SmallGradientConditonParameterSet</name></parameterClass></parameterSetContainer>
b7d6db3ba6bc Uploaded grau parents: diff changeset	67 </parameter><parameter><className>de.jstacs.parameters.ParameterSetContainer</className><parameterSetContainer>
b7d6db3ba6bc Uploaded grau parents: diff changeset	68 <name><className>java.lang.String</className>SmallStepConditionParameterSet</name><comment><className>java.lang.String</className></comment><datatype><className>de.jstacs.DataType</className><name>PARAMETERSET</name></datatype><errorMessage>null</errorMessage><parameterClass><className>java.lang.Class</className><name>de.jstacs.algorithms.optimization.termination.SmallStepCondition$SmallStepConditionParameterSet</name></parameterClass></parameterSetContainer>
b7d6db3ba6bc Uploaded grau parents: diff changeset	69 </parameter><parameter><className>de.jstacs.parameters.ParameterSetContainer</className><parameterSetContainer>
b7d6db3ba6bc Uploaded grau parents: diff changeset	70 <name><className>java.lang.String</className>TimeConditionParameterSet</name><comment><className>java.lang.String</className></comment><datatype><className>de.jstacs.DataType</className><name>PARAMETERSET</name></datatype><errorMessage>null</errorMessage><parameterClass><className>java.lang.Class</className><name>de.jstacs.algorithms.optimization.termination.TimeCondition$TimeConditionParameterSet</name></parameterClass></parameterSetContainer>
b7d6db3ba6bc Uploaded grau parents: diff changeset	71 </parameter></set>
b7d6db3ba6bc Uploaded grau parents: diff changeset	72 </parameterSet>
b7d6db3ba6bc Uploaded grau parents: diff changeset	73 </collection><selected><className>java.lang.Integer</className>4</selected><defaultSelected><className>java.lang.Integer</className>4</defaultSelected></collectionParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	74 </parameter><parameter><className>de.jstacs.parameters.SimpleParameter</className><simpleParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	75 <name><className>java.lang.String</className>line epsilon</name><comment><className>java.lang.String</className>the threshold for stopping the line search in the numerical training</comment><datatype><className>de.jstacs.DataType</className><name>DOUBLE</name></datatype><required><className>java.lang.Boolean</className>true</required><isSet><className>java.lang.Boolean</className>true</isSet><errorMessage>null</errorMessage><isRangeable><className>java.lang.Boolean</className>true</isRangeable><validator><className>de.jstacs.parameters.validation.NumberValidator</className><NumberValidator>
b7d6db3ba6bc Uploaded grau parents: diff changeset	76 <className><className>java.lang.String</className>java.lang.Double</className><lowerBound><className>java.lang.String</className>0.0</lowerBound><upperBound><className>java.lang.String</className>1.7976931348623157E308</upperBound></NumberValidator>
b7d6db3ba6bc Uploaded grau parents: diff changeset	77 </validator><defaultValue><className>java.lang.Double</className>1.0E-9</defaultValue><value><className>java.lang.Double</className>1.0E-5</value></simpleParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	78 </parameter><parameter><className>de.jstacs.parameters.SimpleParameter</className><simpleParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	79 <name><className>java.lang.String</className>start distance</name><comment><className>java.lang.String</className>the start distance for the line search in the numerical training</comment><datatype><className>de.jstacs.DataType</className><name>DOUBLE</name></datatype><required><className>java.lang.Boolean</className>true</required><isSet><className>java.lang.Boolean</className>true</isSet><errorMessage>null</errorMessage><isRangeable><className>java.lang.Boolean</className>true</isRangeable><validator><className>de.jstacs.parameters.validation.NumberValidator</className><NumberValidator>
b7d6db3ba6bc Uploaded grau parents: diff changeset	80 <className><className>java.lang.String</className>java.lang.Double</className><lowerBound><className>java.lang.String</className>0.0</lowerBound><upperBound><className>java.lang.String</className>1.7976931348623157E308</upperBound></NumberValidator>
b7d6db3ba6bc Uploaded grau parents: diff changeset	81 </validator><defaultValue><className>java.lang.Double</className>1.0</defaultValue><value><className>java.lang.Double</className>1.0</value></simpleParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	82 </parameter><parameter><className>de.jstacs.parameters.SimpleParameter</className><simpleParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	83 <name><className>java.lang.String</className>free parameters</name><comment><className>java.lang.String</className>Indicates whether only the free parameters or all parameters should be used.</comment><datatype><className>de.jstacs.DataType</className><name>BOOLEAN</name></datatype><required><className>java.lang.Boolean</className>true</required><isSet><className>java.lang.Boolean</className>true</isSet><errorMessage><className>java.lang.String</className></errorMessage><isRangeable><className>java.lang.Boolean</className>true</isRangeable><validator>null</validator><defaultValue><className>java.lang.Boolean</className>false</defaultValue><value><className>java.lang.Boolean</className>false</value></simpleParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	84 </parameter><parameter><className>de.jstacs.parameters.EnumParameter</className><collectionParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	85 <name><className>java.lang.String</className>KindOfParameter</name><comment><className>java.lang.String</className>Indicates whether special plugIn parameters or the zero vector should be used as start parameters. For non-concave problems it is highly recommended to use plugIn parameters.</comment><datatype><className>de.jstacs.DataType</className><name>STRING</name></datatype><required><className>java.lang.Boolean</className>true</required><userSelected><className>java.lang.Boolean</className>true</userSelected><errorMessage>null</errorMessage><rangeable><className>java.lang.Boolean</className>true</rangeable><collection><className>de.jstacs.parameters.SimpleParameterSet</className><parameterSet>
b7d6db3ba6bc Uploaded grau parents: diff changeset	86 <set>
b7d6db3ba6bc Uploaded grau parents: diff changeset	87 <numberOfParameters><className>java.lang.Integer</className>3</numberOfParameters><parameter><className>de.jstacs.parameters.SimpleParameter</className><simpleParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	88 <name><className>java.lang.String</className>ZEROS</name><comment>null</comment><datatype><className>de.jstacs.DataType</className><name>STRING</name></datatype><required><className>java.lang.Boolean</className>false</required><isSet><className>java.lang.Boolean</className>true</isSet><errorMessage><className>java.lang.String</className></errorMessage><isRangeable><className>java.lang.Boolean</className>false</isRangeable><validator>null</validator><defaultValue>null</defaultValue><value><className>java.lang.String</className>ZEROS</value></simpleParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	89 </parameter><parameter><className>de.jstacs.parameters.SimpleParameter</className><simpleParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	90 <name><className>java.lang.String</className>LAST</name><comment>null</comment><datatype><className>de.jstacs.DataType</className><name>STRING</name></datatype><required><className>java.lang.Boolean</className>false</required><isSet><className>java.lang.Boolean</className>true</isSet><errorMessage><className>java.lang.String</className></errorMessage><isRangeable><className>java.lang.Boolean</className>false</isRangeable><validator>null</validator><defaultValue>null</defaultValue><value><className>java.lang.String</className>LAST</value></simpleParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	91 </parameter><parameter><className>de.jstacs.parameters.SimpleParameter</className><simpleParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	92 <name><className>java.lang.String</className>PLUGIN</name><comment>null</comment><datatype><className>de.jstacs.DataType</className><name>STRING</name></datatype><required><className>java.lang.Boolean</className>false</required><isSet><className>java.lang.Boolean</className>true</isSet><errorMessage><className>java.lang.String</className></errorMessage><isRangeable><className>java.lang.Boolean</className>false</isRangeable><validator>null</validator><defaultValue>null</defaultValue><value><className>java.lang.String</className>PLUGIN</value></simpleParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	93 </parameter></set>
b7d6db3ba6bc Uploaded grau parents: diff changeset	94 </parameterSet>
b7d6db3ba6bc Uploaded grau parents: diff changeset	95 </collection><selected><className>java.lang.Integer</className>2</selected><defaultSelected><className>java.lang.Integer</className>2</defaultSelected><selectedEnum><className>java.lang.String</className>PLUGIN</selectedEnum><defaultSelectedEnum><className>java.lang.String</className>PLUGIN</defaultSelectedEnum><enumName><className>java.lang.Class</className><name>de.jstacs.classifiers.differentiableSequenceScoreBased.OptimizableFunction$KindOfParameter</name></enumName></collectionParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	96 </parameter><parameter><className>de.jstacs.parameters.SimpleParameter</className><simpleParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	97 <name><className>java.lang.String</className>Normalize</name><comment><className>java.lang.String</className>If true the conditional likelihood will be normalized to the number of data sets.</comment><datatype><className>de.jstacs.DataType</className><name>BOOLEAN</name></datatype><required><className>java.lang.Boolean</className>true</required><isSet><className>java.lang.Boolean</className>true</isSet><errorMessage><className>java.lang.String</className></errorMessage><isRangeable><className>java.lang.Boolean</className>true</isRangeable><validator>null</validator><defaultValue><className>java.lang.Boolean</className>true</defaultValue><value><className>java.lang.Boolean</className>true</value></simpleParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	98 </parameter><parameter><className>de.jstacs.parameters.SimpleParameter</className><simpleParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	99 <name><className>java.lang.String</className>Threads</name><comment><className>java.lang.String</className>The number of threads that is used during an optimization.</comment><datatype><className>de.jstacs.DataType</className><name>INT</name></datatype><required><className>java.lang.Boolean</className>true</required><isSet><className>java.lang.Boolean</className>true</isSet><errorMessage>null</errorMessage><isRangeable><className>java.lang.Boolean</className>true</isRangeable><validator><className>de.jstacs.parameters.validation.NumberValidator</className><NumberValidator>
b7d6db3ba6bc Uploaded grau parents: diff changeset	100 <className><className>java.lang.String</className>java.lang.Integer</className><lowerBound><className>java.lang.String</className>1</lowerBound><upperBound><className>java.lang.String</className>128</upperBound></NumberValidator>
b7d6db3ba6bc Uploaded grau parents: diff changeset	101 </validator><defaultValue><className>java.lang.Integer</className>1</defaultValue><value><className>java.lang.Integer</className>1</value></simpleParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	102 </parameter></set>
b7d6db3ba6bc Uploaded grau parents: diff changeset	103 </parameterSet>
b7d6db3ba6bc Uploaded grau parents: diff changeset	104 </superParameterSet>
b7d6db3ba6bc Uploaded grau parents: diff changeset	105 <instanceClass><className>java.lang.Class</className><name>de.jstacs.classifiers.differentiableSequenceScoreBased.gendismix.GenDisMixClassifier</name></instanceClass></instanceParameterSet>
b7d6db3ba6bc Uploaded grau parents: diff changeset	106 </superParameters>
b7d6db3ba6bc Uploaded grau parents: diff changeset	107 <variableLength><className>java.lang.Boolean</className>true</variableLength><alphabet><className>de.jstacs.parameters.SelectionParameter</className><collectionParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	108 <name><className>java.lang.String</className>Alphabet</name><comment><className>java.lang.String</className>The alphabet the model works on</comment><datatype><className>de.jstacs.DataType</className><name>PARAMETERSET</name></datatype><required><className>java.lang.Boolean</className>true</required><userSelected><className>java.lang.Boolean</className>true</userSelected><errorMessage>null</errorMessage><rangeable><className>java.lang.Boolean</className>true</rangeable><collection><className>de.jstacs.parameters.SimpleParameterSet</className><parameterSet>
b7d6db3ba6bc Uploaded grau parents: diff changeset	109 <set>
b7d6db3ba6bc Uploaded grau parents: diff changeset	110 <numberOfParameters><className>java.lang.Integer</className>2</numberOfParameters><parameter><className>de.jstacs.parameters.ParameterSetContainer</className><parameterSetContainer>
b7d6db3ba6bc Uploaded grau parents: diff changeset	111 <name><className>java.lang.String</className>AlphabetContainerParameterSet</name><comment><className>java.lang.String</className></comment><datatype><className>de.jstacs.DataType</className><name>PARAMETERSET</name></datatype><errorMessage>null</errorMessage><parameters><className>de.jstacs.data.AlphabetContainerParameterSet</className><alphabetContainerParameterSet>
b7d6db3ba6bc Uploaded grau parents: diff changeset	112 <superParameters>
b7d6db3ba6bc Uploaded grau parents: diff changeset	113 <instanceParameterSet>
b7d6db3ba6bc Uploaded grau parents: diff changeset	114 <superParameterSet>
b7d6db3ba6bc Uploaded grau parents: diff changeset	115 <parameterSet>
b7d6db3ba6bc Uploaded grau parents: diff changeset	116 <set>
b7d6db3ba6bc Uploaded grau parents: diff changeset	117 <numberOfParameters><className>java.lang.Integer</className>1</numberOfParameters><parameter><className>de.jstacs.parameters.SelectionParameter</className><collectionParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	118 <name><className>java.lang.String</className>Alphabet</name><comment><className>java.lang.String</className>Select a discrete alphabet</comment><datatype><className>de.jstacs.DataType</className><name>PARAMETERSET</name></datatype><required><className>java.lang.Boolean</className>true</required><userSelected><className>java.lang.Boolean</className>false</userSelected><errorMessage>null</errorMessage><rangeable><className>java.lang.Boolean</className>true</rangeable><collection><className>de.jstacs.parameters.SimpleParameterSet</className><parameterSet>
b7d6db3ba6bc Uploaded grau parents: diff changeset	119 <set>
b7d6db3ba6bc Uploaded grau parents: diff changeset	120 <numberOfParameters><className>java.lang.Integer</className>4</numberOfParameters><parameter><className>de.jstacs.parameters.ParameterSetContainer</className><parameterSetContainer>
b7d6db3ba6bc Uploaded grau parents: diff changeset	121 <name><className>java.lang.String</className>DNAAlphabetParameterSet</name><comment><className>java.lang.String</className></comment><datatype><className>de.jstacs.DataType</className><name>PARAMETERSET</name></datatype><errorMessage>null</errorMessage><parameters><className>de.jstacs.data.alphabets.DNAAlphabet$DNAAlphabetParameterSet</className></parameters></parameterSetContainer>
b7d6db3ba6bc Uploaded grau parents: diff changeset	122 </parameter><parameter><className>de.jstacs.parameters.ParameterSetContainer</className><parameterSetContainer>
b7d6db3ba6bc Uploaded grau parents: diff changeset	123 <name><className>java.lang.String</className>ProteinAlphabetParameterSet</name><comment><className>java.lang.String</className></comment><datatype><className>de.jstacs.DataType</className><name>PARAMETERSET</name></datatype><errorMessage>null</errorMessage><parameters><className>de.jstacs.data.alphabets.ProteinAlphabet$ProteinAlphabetParameterSet</className></parameters></parameterSetContainer>
b7d6db3ba6bc Uploaded grau parents: diff changeset	124 </parameter><parameter><className>de.jstacs.parameters.ParameterSetContainer</className><parameterSetContainer>
b7d6db3ba6bc Uploaded grau parents: diff changeset	125 <name><className>java.lang.String</className>GenericComplementableDiscreteAlphabetParameterSet</name><comment><className>java.lang.String</className></comment><datatype><className>de.jstacs.DataType</className><name>PARAMETERSET</name></datatype><errorMessage>null</errorMessage><parameters><className>de.jstacs.data.alphabets.GenericComplementableDiscreteAlphabet$GenericComplementableDiscreteAlphabetParameterSet</className><instanceParameterSet>
b7d6db3ba6bc Uploaded grau parents: diff changeset	126 <superParameterSet>
b7d6db3ba6bc Uploaded grau parents: diff changeset	127 <parameterSet>
b7d6db3ba6bc Uploaded grau parents: diff changeset	128 <set>
b7d6db3ba6bc Uploaded grau parents: diff changeset	129 <numberOfParameters><className>java.lang.Integer</className>1</numberOfParameters><parameter><className>de.jstacs.parameters.SimpleParameter</className><simpleParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	130 <name><className>java.lang.String</className>Values of the index for computings the reverse complement</name><comment><className>java.lang.String</className></comment><datatype><className>de.jstacs.DataType</className><name>STRING</name></datatype><required><className>java.lang.Boolean</className>true</required><isSet><className>java.lang.Boolean</className>false</isSet><errorMessage>null</errorMessage><isRangeable><className>java.lang.Boolean</className>false</isRangeable><validator>null</validator><defaultValue>null</defaultValue><value>null</value></simpleParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	131 </parameter></set>
b7d6db3ba6bc Uploaded grau parents: diff changeset	132 </parameterSet>
b7d6db3ba6bc Uploaded grau parents: diff changeset	133 </superParameterSet>
b7d6db3ba6bc Uploaded grau parents: diff changeset	134 <instanceClass><className>java.lang.Class</className><name>de.jstacs.data.alphabets.GenericComplementableDiscreteAlphabet</name></instanceClass></instanceParameterSet>
b7d6db3ba6bc Uploaded grau parents: diff changeset	135 </parameters></parameterSetContainer>
b7d6db3ba6bc Uploaded grau parents: diff changeset	136 </parameter><parameter><className>de.jstacs.parameters.ParameterSetContainer</className><parameterSetContainer>
b7d6db3ba6bc Uploaded grau parents: diff changeset	137 <name><className>java.lang.String</className>DiscreteAlphabetParameterSet</name><comment><className>java.lang.String</className></comment><datatype><className>de.jstacs.DataType</className><name>PARAMETERSET</name></datatype><errorMessage>null</errorMessage><parameters><className>de.jstacs.data.alphabets.DiscreteAlphabet$DiscreteAlphabetParameterSet</className><instanceParameterSet>
b7d6db3ba6bc Uploaded grau parents: diff changeset	138 <superParameterSet>
b7d6db3ba6bc Uploaded grau parents: diff changeset	139 <parameterSet>
b7d6db3ba6bc Uploaded grau parents: diff changeset	140 <set>
b7d6db3ba6bc Uploaded grau parents: diff changeset	141 <numberOfParameters><className>java.lang.Integer</className>2</numberOfParameters><parameter><className>de.jstacs.parameters.SimpleParameter</className><simpleParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	142 <name><className>java.lang.String</className>Values of the alphabet</name><comment><className>java.lang.String</className>The possible values of the discrete alphabet.If the alphabet consists of single characters, e.g. A, C, G, and T, the values may be set as a single string, e.g. &quot;ACGT&quot;.If the alphabet consists of multi-character symbols, e.g. Gly, Asp, Ser,the symbols must be separated by spaces.</comment><datatype><className>de.jstacs.DataType</className><name>STRING</name></datatype><required><className>java.lang.Boolean</className>true</required><isSet><className>java.lang.Boolean</className>false</isSet><errorMessage>null</errorMessage><isRangeable><className>java.lang.Boolean</className>false</isRangeable><validator>null</validator><defaultValue>null</defaultValue><value>null</value></simpleParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	143 </parameter><parameter><className>de.jstacs.parameters.SelectionParameter</className><collectionParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	144 <name><className>java.lang.String</className>Case insensitive</name><comment><className>java.lang.String</className>Use the alphabet case insensitive</comment><datatype><className>de.jstacs.DataType</className><name>BOOLEAN</name></datatype><required><className>java.lang.Boolean</className>true</required><userSelected><className>java.lang.Boolean</className>false</userSelected><errorMessage>null</errorMessage><rangeable><className>java.lang.Boolean</className>true</rangeable><collection><className>de.jstacs.parameters.SimpleParameterSet</className><parameterSet>
b7d6db3ba6bc Uploaded grau parents: diff changeset	145 <set>
b7d6db3ba6bc Uploaded grau parents: diff changeset	146 <numberOfParameters><className>java.lang.Integer</className>2</numberOfParameters><parameter><className>de.jstacs.parameters.SimpleParameter</className><simpleParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	147 <name><className>java.lang.String</className>Case insensitive</name><comment>null</comment><datatype><className>de.jstacs.DataType</className><name>BOOLEAN</name></datatype><required><className>java.lang.Boolean</className>false</required><isSet><className>java.lang.Boolean</className>true</isSet><errorMessage><className>java.lang.String</className></errorMessage><isRangeable><className>java.lang.Boolean</className>true</isRangeable><validator>null</validator><defaultValue>null</defaultValue><value><className>java.lang.Boolean</className>true</value></simpleParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	148 </parameter><parameter><className>de.jstacs.parameters.SimpleParameter</className><simpleParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	149 <name><className>java.lang.String</className>Case sensitive</name><comment>null</comment><datatype><className>de.jstacs.DataType</className><name>BOOLEAN</name></datatype><required><className>java.lang.Boolean</className>false</required><isSet><className>java.lang.Boolean</className>true</isSet><errorMessage><className>java.lang.String</className></errorMessage><isRangeable><className>java.lang.Boolean</className>true</isRangeable><validator>null</validator><defaultValue>null</defaultValue><value><className>java.lang.Boolean</className>false</value></simpleParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	150 </parameter></set>
b7d6db3ba6bc Uploaded grau parents: diff changeset	151 </parameterSet>
b7d6db3ba6bc Uploaded grau parents: diff changeset	152 </collection><selected><className>java.lang.Integer</className>0</selected><defaultSelected><className>java.lang.Integer</className>0</defaultSelected></collectionParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	153 </parameter></set>
b7d6db3ba6bc Uploaded grau parents: diff changeset	154 </parameterSet>
b7d6db3ba6bc Uploaded grau parents: diff changeset	155 </superParameterSet>
b7d6db3ba6bc Uploaded grau parents: diff changeset	156 <instanceClass><className>java.lang.Class</className><name>de.jstacs.data.alphabets.DiscreteAlphabet</name></instanceClass></instanceParameterSet>
b7d6db3ba6bc Uploaded grau parents: diff changeset	157 </parameters></parameterSetContainer>
b7d6db3ba6bc Uploaded grau parents: diff changeset	158 </parameter></set>
b7d6db3ba6bc Uploaded grau parents: diff changeset	159 </parameterSet>
b7d6db3ba6bc Uploaded grau parents: diff changeset	160 </collection><selected><className>java.lang.Integer</className>0</selected><defaultSelected><className>java.lang.Integer</className>0</defaultSelected></collectionParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	161 </parameter></set>
b7d6db3ba6bc Uploaded grau parents: diff changeset	162 </parameterSet>
b7d6db3ba6bc Uploaded grau parents: diff changeset	163 </superParameterSet>
b7d6db3ba6bc Uploaded grau parents: diff changeset	164 <instanceClass><className>java.lang.Class</className><name>de.jstacs.data.AlphabetContainer</name></instanceClass></instanceParameterSet>
b7d6db3ba6bc Uploaded grau parents: diff changeset	165 </superParameters>
b7d6db3ba6bc Uploaded grau parents: diff changeset	166 <type><className>de.jstacs.data.AlphabetContainer$AlphabetContainerType</className><name>DISCRETE</name></type><simple><className>java.lang.Boolean</className>true</simple></alphabetContainerParameterSet>
b7d6db3ba6bc Uploaded grau parents: diff changeset	167 </parameters></parameterSetContainer>
b7d6db3ba6bc Uploaded grau parents: diff changeset	168 </parameter><parameter><className>de.jstacs.parameters.ParameterSetContainer</className><parameterSetContainer>
b7d6db3ba6bc Uploaded grau parents: diff changeset	169 <name><className>java.lang.String</className>DNAAlphabetContainerParameterSet</name><comment><className>java.lang.String</className></comment><datatype><className>de.jstacs.DataType</className><name>PARAMETERSET</name></datatype><errorMessage>null</errorMessage><parameters><className>de.jstacs.data.alphabets.DNAAlphabetContainer$DNAAlphabetContainerParameterSet</className></parameters></parameterSetContainer>
b7d6db3ba6bc Uploaded grau parents: diff changeset	170 </parameter></set>
b7d6db3ba6bc Uploaded grau parents: diff changeset	171 </parameterSet>
b7d6db3ba6bc Uploaded grau parents: diff changeset	172 </collection><selected><className>java.lang.Integer</className>1</selected><defaultSelected><className>java.lang.Integer</className>0</defaultSelected></collectionParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	173 </alphabet><length><className>de.jstacs.parameters.SimpleParameter</className><simpleParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	174 <name><className>java.lang.String</className>Length</name><comment><className>java.lang.String</className>The length of sequences the model can work on</comment><datatype><className>de.jstacs.DataType</className><name>INT</name></datatype><required><className>java.lang.Boolean</className>true</required><isSet><className>java.lang.Boolean</className>true</isSet><errorMessage>null</errorMessage><isRangeable><className>java.lang.Boolean</className>true</isRangeable><validator><className>de.jstacs.parameters.validation.NumberValidator</className><NumberValidator>
b7d6db3ba6bc Uploaded grau parents: diff changeset	175 <className><className>java.lang.String</className>java.lang.Integer</className><lowerBound><className>java.lang.String</className>0</lowerBound><upperBound><className>java.lang.String</className>0</upperBound></NumberValidator>
b7d6db3ba6bc Uploaded grau parents: diff changeset	176 </validator><defaultValue><className>java.lang.Integer</className>0</defaultValue><value><className>java.lang.Integer</className>0</value></simpleParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	177 </length></sequenceScoringParameterSet>
b7d6db3ba6bc Uploaded grau parents: diff changeset	178 </params><hasBeenOptimized><className>java.lang.Boolean</className>false</hasBeenOptimized><lastScore><className>java.lang.Double</className>-0.29019836129972626</lastScore><score><className>[Lde.jstacs.sequenceScores.statisticalModels.differentiable.DifferentiableStatisticalModel;</className><length>2</length><pos val="0"><className>projects.dimont.ThresholdedStrandChIPper</className><ThresholdedStrandChIPper>
b7d6db3ba6bc Uploaded grau parents: diff changeset	179 <length><className>java.lang.Integer</className>0</length><starts><className>java.lang.Integer</className>1</starts><freeParams><className>java.lang.Boolean</className>false</freeParams><function><className>[Lde.jstacs.sequenceScores.statisticalModels.differentiable.DifferentiableStatisticalModel;</className><length>1</length><pos val="0"><className>de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.MarkovModelDiffSM</className><MarkovModelDiffSM>
b7d6db3ba6bc Uploaded grau parents: diff changeset	180 <bayesianNetworkSF>
b7d6db3ba6bc Uploaded grau parents: diff changeset	181 <alphabets><className>de.jstacs.data.alphabets.DNAAlphabetContainer</className></alphabets><length><className>java.lang.Integer</className>7</length><trees><className>[Lde.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameterTree;</className><length>7</length><pos val="0"><className>de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameterTree</className><parameterTree>
b7d6db3ba6bc Uploaded grau parents: diff changeset	182 <pos><className>java.lang.Integer</className>0</pos><contextPoss><className>[I</className><length>0</length></contextPoss><root><className>de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameterTree$TreeElement</className><treeElement>
b7d6db3ba6bc Uploaded grau parents: diff changeset	183 <contNum><className>java.lang.Integer</className>0</contNum><contextPos><className>java.lang.Integer</className>-1</contextPos><children>null</children><pars><className>[Lde.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameter;</className><length>4</length><pos val="0"><className>de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameter</className><parameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	184 <value><className>java.lang.Double</className>-1.8882500938776798</value><symbol><className>java.lang.Byte</className>0</symbol><index><className>java.lang.Integer</className>0</index><pseudoCount><className>java.lang.Double</className>1.0</pseudoCount><position><className>java.lang.Integer</className>0</position><context><className>[[I</className><length>0</length></context><count><className>java.lang.Double</className>1.0</count><free><className>java.lang.Boolean</className>true</free><z><className>java.lang.Double</className>0.0</z><t><className>java.lang.Double</className>0.0</t></parameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	185 </pos><pos val="1"><className>de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameter</className><parameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	186 <value><className>java.lang.Double</className>-2.3929793553147585</value><symbol><className>java.lang.Byte</className>1</symbol><index><className>java.lang.Integer</className>1</index><pseudoCount><className>java.lang.Double</className>1.0</pseudoCount><position><className>java.lang.Integer</className>0</position><context><className>[[I</className><length>0</length></context><count><className>java.lang.Double</className>1.0</count><free><className>java.lang.Boolean</className>true</free><z><className>java.lang.Double</className>0.0</z><t><className>java.lang.Double</className>0.0</t></parameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	187 </pos><pos val="2"><className>de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameter</className><parameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	188 <value><className>java.lang.Double</className>-0.27411896862354784</value><symbol><className>java.lang.Byte</className>2</symbol><index><className>java.lang.Integer</className>2</index><pseudoCount><className>java.lang.Double</className>1.0</pseudoCount><position><className>java.lang.Integer</className>0</position><context><className>[[I</className><length>0</length></context><count><className>java.lang.Double</className>1.0</count><free><className>java.lang.Boolean</className>true</free><z><className>java.lang.Double</className>0.0</z><t><className>java.lang.Double</className>0.0</t></parameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	189 </pos><pos val="3"><className>de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameter</className><parameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	190 <value><className>java.lang.Double</className>-3.074727770552047</value><symbol><className>java.lang.Byte</className>3</symbol><index><className>java.lang.Integer</className>3</index><pseudoCount><className>java.lang.Double</className>1.0</pseudoCount><position><className>java.lang.Integer</className>0</position><context><className>[[I</className><length>0</length></context><count><className>java.lang.Double</className>1.0</count><free><className>java.lang.Boolean</className>true</free><z><className>java.lang.Double</className>0.0</z><t><className>java.lang.Double</className>0.0</t></parameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	191 </pos></pars></treeElement>
b7d6db3ba6bc Uploaded grau parents: diff changeset	192 </root><firstParent><className>java.lang.Integer</className>-1</firstParent><firstChildren><className>[I</className><length>0</length></firstChildren></parameterTree>
b7d6db3ba6bc Uploaded grau parents: diff changeset	193 </pos><pos val="1"><className>de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameterTree</className><parameterTree>
b7d6db3ba6bc Uploaded grau parents: diff changeset	194 <pos><className>java.lang.Integer</className>1</pos><contextPoss><className>[I</className><length>0</length></contextPoss><root><className>de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameterTree$TreeElement</className><treeElement>
b7d6db3ba6bc Uploaded grau parents: diff changeset	195 <contNum><className>java.lang.Integer</className>0</contNum><contextPos><className>java.lang.Integer</className>-1</contextPos><children>null</children><pars><className>[Lde.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameter;</className><length>4</length><pos val="0"><className>de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameter</className><parameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	196 <value><className>java.lang.Double</className>-3.143173615307912</value><symbol><className>java.lang.Byte</className>0</symbol><index><className>java.lang.Integer</className>4</index><pseudoCount><className>java.lang.Double</className>1.0</pseudoCount><position><className>java.lang.Integer</className>1</position><context><className>[[I</className><length>0</length></context><count><className>java.lang.Double</className>1.0</count><free><className>java.lang.Boolean</className>true</free><z><className>java.lang.Double</className>0.0</z><t><className>java.lang.Double</className>0.0</t></parameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	197 </pos><pos val="1"><className>de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameter</className><parameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	198 <value><className>java.lang.Double</className>-3.0349593264798793</value><symbol><className>java.lang.Byte</className>1</symbol><index><className>java.lang.Integer</className>5</index><pseudoCount><className>java.lang.Double</className>1.0</pseudoCount><position><className>java.lang.Integer</className>1</position><context><className>[[I</className><length>0</length></context><count><className>java.lang.Double</className>1.0</count><free><className>java.lang.Boolean</className>true</free><z><className>java.lang.Double</className>0.0</z><t><className>java.lang.Double</className>0.0</t></parameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	199 </pos><pos val="2"><className>de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameter</className><parameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	200 <value><className>java.lang.Double</className>-0.07796546434673289</value><symbol><className>java.lang.Byte</className>2</symbol><index><className>java.lang.Integer</className>6</index><pseudoCount><className>java.lang.Double</className>1.0</pseudoCount><position><className>java.lang.Integer</className>1</position><context><className>[[I</className><length>0</length></context><count><className>java.lang.Double</className>1.0</count><free><className>java.lang.Boolean</className>true</free><z><className>java.lang.Double</className>0.0</z><t><className>java.lang.Double</className>0.0</t></parameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	201 </pos><pos val="3"><className>de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameter</className><parameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	202 <value><className>java.lang.Double</className>-3.0037566140099474</value><symbol><className>java.lang.Byte</className>3</symbol><index><className>java.lang.Integer</className>7</index><pseudoCount><className>java.lang.Double</className>1.0</pseudoCount><position><className>java.lang.Integer</className>1</position><context><className>[[I</className><length>0</length></context><count><className>java.lang.Double</className>1.0</count><free><className>java.lang.Boolean</className>true</free><z><className>java.lang.Double</className>0.0</z><t><className>java.lang.Double</className>0.0</t></parameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	203 </pos></pars></treeElement>
b7d6db3ba6bc Uploaded grau parents: diff changeset	204 </root><firstParent><className>java.lang.Integer</className>-1</firstParent><firstChildren><className>[I</className><length>0</length></firstChildren></parameterTree>
b7d6db3ba6bc Uploaded grau parents: diff changeset	205 </pos><pos val="2"><className>de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameterTree</className><parameterTree>
b7d6db3ba6bc Uploaded grau parents: diff changeset	206 <pos><className>java.lang.Integer</className>2</pos><contextPoss><className>[I</className><length>0</length></contextPoss><root><className>de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameterTree$TreeElement</className><treeElement>
b7d6db3ba6bc Uploaded grau parents: diff changeset	207 <contNum><className>java.lang.Integer</className>0</contNum><contextPos><className>java.lang.Integer</className>-1</contextPos><children>null</children><pars><className>[Lde.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameter;</className><length>4</length><pos val="0"><className>de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameter</className><parameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	208 <value><className>java.lang.Double</className>-0.31188945615131514</value><symbol><className>java.lang.Byte</className>0</symbol><index><className>java.lang.Integer</className>8</index><pseudoCount><className>java.lang.Double</className>1.0</pseudoCount><position><className>java.lang.Integer</className>2</position><context><className>[[I</className><length>0</length></context><count><className>java.lang.Double</className>1.0</count><free><className>java.lang.Boolean</className>true</free><z><className>java.lang.Double</className>0.0</z><t><className>java.lang.Double</className>0.0</t></parameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	209 </pos><pos val="1"><className>de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameter</className><parameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	210 <value><className>java.lang.Double</className>-1.6066576296875537</value><symbol><className>java.lang.Byte</className>1</symbol><index><className>java.lang.Integer</className>9</index><pseudoCount><className>java.lang.Double</className>1.0</pseudoCount><position><className>java.lang.Integer</className>2</position><context><className>[[I</className><length>0</length></context><count><className>java.lang.Double</className>1.0</count><free><className>java.lang.Boolean</className>true</free><z><className>java.lang.Double</className>0.0</z><t><className>java.lang.Double</className>0.0</t></parameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	211 </pos><pos val="2"><className>de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameter</className><parameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	212 <value><className>java.lang.Double</className>-2.730887292275338</value><symbol><className>java.lang.Byte</className>2</symbol><index><className>java.lang.Integer</className>10</index><pseudoCount><className>java.lang.Double</className>1.0</pseudoCount><position><className>java.lang.Integer</className>2</position><context><className>[[I</className><length>0</length></context><count><className>java.lang.Double</className>1.0</count><free><className>java.lang.Boolean</className>true</free><z><className>java.lang.Double</className>0.0</z><t><className>java.lang.Double</className>0.0</t></parameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	213 </pos><pos val="3"><className>de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameter</className><parameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	214 <value><className>java.lang.Double</className>-2.6732170295356927</value><symbol><className>java.lang.Byte</className>3</symbol><index><className>java.lang.Integer</className>11</index><pseudoCount><className>java.lang.Double</className>1.0</pseudoCount><position><className>java.lang.Integer</className>2</position><context><className>[[I</className><length>0</length></context><count><className>java.lang.Double</className>1.0</count><free><className>java.lang.Boolean</className>true</free><z><className>java.lang.Double</className>0.0</z><t><className>java.lang.Double</className>0.0</t></parameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	215 </pos></pars></treeElement>
b7d6db3ba6bc Uploaded grau parents: diff changeset	216 </root><firstParent><className>java.lang.Integer</className>-1</firstParent><firstChildren><className>[I</className><length>0</length></firstChildren></parameterTree>
b7d6db3ba6bc Uploaded grau parents: diff changeset	217 </pos><pos val="3"><className>de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameterTree</className><parameterTree>
b7d6db3ba6bc Uploaded grau parents: diff changeset	218 <pos><className>java.lang.Integer</className>3</pos><contextPoss><className>[I</className><length>0</length></contextPoss><root><className>de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameterTree$TreeElement</className><treeElement>
b7d6db3ba6bc Uploaded grau parents: diff changeset	219 <contNum><className>java.lang.Integer</className>0</contNum><contextPos><className>java.lang.Integer</className>-1</contextPos><children>null</children><pars><className>[Lde.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameter;</className><length>4</length><pos val="0"><className>de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameter</className><parameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	220 <value><className>java.lang.Double</className>-3.001513214238137</value><symbol><className>java.lang.Byte</className>0</symbol><index><className>java.lang.Integer</className>12</index><pseudoCount><className>java.lang.Double</className>1.0</pseudoCount><position><className>java.lang.Integer</className>3</position><context><className>[[I</className><length>0</length></context><count><className>java.lang.Double</className>1.0</count><free><className>java.lang.Boolean</className>true</free><z><className>java.lang.Double</className>0.0</z><t><className>java.lang.Double</className>0.0</t></parameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	221 </pos><pos val="1"><className>de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameter</className><parameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	222 <value><className>java.lang.Double</className>-2.085566919294928</value><symbol><className>java.lang.Byte</className>1</symbol><index><className>java.lang.Integer</className>13</index><pseudoCount><className>java.lang.Double</className>1.0</pseudoCount><position><className>java.lang.Integer</className>3</position><context><className>[[I</className><length>0</length></context><count><className>java.lang.Double</className>1.0</count><free><className>java.lang.Boolean</className>true</free><z><className>java.lang.Double</className>0.0</z><t><className>java.lang.Double</className>0.0</t></parameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	223 </pos><pos val="2"><className>de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameter</className><parameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	224 <value><className>java.lang.Double</className>-2.9231013926680576</value><symbol><className>java.lang.Byte</className>2</symbol><index><className>java.lang.Integer</className>14</index><pseudoCount><className>java.lang.Double</className>1.0</pseudoCount><position><className>java.lang.Integer</className>3</position><context><className>[[I</className><length>0</length></context><count><className>java.lang.Double</className>1.0</count><free><className>java.lang.Boolean</className>true</free><z><className>java.lang.Double</className>0.0</z><t><className>java.lang.Double</className>0.0</t></parameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	225 </pos><pos val="3"><className>de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameter</className><parameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	226 <value><className>java.lang.Double</className>-0.21048803951371753</value><symbol><className>java.lang.Byte</className>3</symbol><index><className>java.lang.Integer</className>15</index><pseudoCount><className>java.lang.Double</className>1.0</pseudoCount><position><className>java.lang.Integer</className>3</position><context><className>[[I</className><length>0</length></context><count><className>java.lang.Double</className>1.0</count><free><className>java.lang.Boolean</className>true</free><z><className>java.lang.Double</className>0.0</z><t><className>java.lang.Double</className>0.0</t></parameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	227 </pos></pars></treeElement>
b7d6db3ba6bc Uploaded grau parents: diff changeset	228 </root><firstParent><className>java.lang.Integer</className>-1</firstParent><firstChildren><className>[I</className><length>0</length></firstChildren></parameterTree>
b7d6db3ba6bc Uploaded grau parents: diff changeset	229 </pos><pos val="4"><className>de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameterTree</className><parameterTree>
b7d6db3ba6bc Uploaded grau parents: diff changeset	230 <pos><className>java.lang.Integer</className>4</pos><contextPoss><className>[I</className><length>0</length></contextPoss><root><className>de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameterTree$TreeElement</className><treeElement>
b7d6db3ba6bc Uploaded grau parents: diff changeset	231 <contNum><className>java.lang.Integer</className>0</contNum><contextPos><className>java.lang.Integer</className>-1</contextPos><children>null</children><pars><className>[Lde.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameter;</className><length>4</length><pos val="0"><className>de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameter</className><parameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	232 <value><className>java.lang.Double</className>-2.8821327963137757</value><symbol><className>java.lang.Byte</className>0</symbol><index><className>java.lang.Integer</className>16</index><pseudoCount><className>java.lang.Double</className>1.0</pseudoCount><position><className>java.lang.Integer</className>4</position><context><className>[[I</className><length>0</length></context><count><className>java.lang.Double</className>1.0</count><free><className>java.lang.Boolean</className>true</free><z><className>java.lang.Double</className>0.0</z><t><className>java.lang.Double</className>0.0</t></parameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	233 </pos><pos val="1"><className>de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameter</className><parameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	234 <value><className>java.lang.Double</className>-2.0159864932010403</value><symbol><className>java.lang.Byte</className>1</symbol><index><className>java.lang.Integer</className>17</index><pseudoCount><className>java.lang.Double</className>1.0</pseudoCount><position><className>java.lang.Integer</className>4</position><context><className>[[I</className><length>0</length></context><count><className>java.lang.Double</className>1.0</count><free><className>java.lang.Boolean</className>true</free><z><className>java.lang.Double</className>0.0</z><t><className>java.lang.Double</className>0.0</t></parameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	235 </pos><pos val="2"><className>de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameter</className><parameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	236 <value><className>java.lang.Double</className>-3.198141984146207</value><symbol><className>java.lang.Byte</className>2</symbol><index><className>java.lang.Integer</className>18</index><pseudoCount><className>java.lang.Double</className>1.0</pseudoCount><position><className>java.lang.Integer</className>4</position><context><className>[[I</className><length>0</length></context><count><className>java.lang.Double</className>1.0</count><free><className>java.lang.Boolean</className>true</free><z><className>java.lang.Double</className>0.0</z><t><className>java.lang.Double</className>0.0</t></parameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	237 </pos><pos val="3"><className>de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameter</className><parameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	238 <value><className>java.lang.Double</className>-0.22982042448197193</value><symbol><className>java.lang.Byte</className>3</symbol><index><className>java.lang.Integer</className>19</index><pseudoCount><className>java.lang.Double</className>1.0</pseudoCount><position><className>java.lang.Integer</className>4</position><context><className>[[I</className><length>0</length></context><count><className>java.lang.Double</className>1.0</count><free><className>java.lang.Boolean</className>true</free><z><className>java.lang.Double</className>0.0</z><t><className>java.lang.Double</className>0.0</t></parameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	239 </pos></pars></treeElement>
b7d6db3ba6bc Uploaded grau parents: diff changeset	240 </root><firstParent><className>java.lang.Integer</className>-1</firstParent><firstChildren><className>[I</className><length>0</length></firstChildren></parameterTree>
b7d6db3ba6bc Uploaded grau parents: diff changeset	241 </pos><pos val="5"><className>de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameterTree</className><parameterTree>
b7d6db3ba6bc Uploaded grau parents: diff changeset	242 <pos><className>java.lang.Integer</className>5</pos><contextPoss><className>[I</className><length>0</length></contextPoss><root><className>de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameterTree$TreeElement</className><treeElement>
b7d6db3ba6bc Uploaded grau parents: diff changeset	243 <contNum><className>java.lang.Integer</className>0</contNum><contextPos><className>java.lang.Integer</className>-1</contextPos><children>null</children><pars><className>[Lde.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameter;</className><length>4</length><pos val="0"><className>de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameter</className><parameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	244 <value><className>java.lang.Double</className>-0.34246698237242884</value><symbol><className>java.lang.Byte</className>0</symbol><index><className>java.lang.Integer</className>20</index><pseudoCount><className>java.lang.Double</className>1.0</pseudoCount><position><className>java.lang.Integer</className>5</position><context><className>[[I</className><length>0</length></context><count><className>java.lang.Double</className>1.0</count><free><className>java.lang.Boolean</className>true</free><z><className>java.lang.Double</className>0.0</z><t><className>java.lang.Double</className>0.0</t></parameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	245 </pos><pos val="1"><className>de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameter</className><parameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	246 <value><className>java.lang.Double</className>-2.7005991646867735</value><symbol><className>java.lang.Byte</className>1</symbol><index><className>java.lang.Integer</className>21</index><pseudoCount><className>java.lang.Double</className>1.0</pseudoCount><position><className>java.lang.Integer</className>5</position><context><className>[[I</className><length>0</length></context><count><className>java.lang.Double</className>1.0</count><free><className>java.lang.Boolean</className>true</free><z><className>java.lang.Double</className>0.0</z><t><className>java.lang.Double</className>0.0</t></parameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	247 </pos><pos val="2"><className>de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameter</className><parameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	248 <value><className>java.lang.Double</className>-2.8704352256363097</value><symbol><className>java.lang.Byte</className>2</symbol><index><className>java.lang.Integer</className>22</index><pseudoCount><className>java.lang.Double</className>1.0</pseudoCount><position><className>java.lang.Integer</className>5</position><context><className>[[I</className><length>0</length></context><count><className>java.lang.Double</className>1.0</count><free><className>java.lang.Boolean</className>true</free><z><className>java.lang.Double</className>0.0</z><t><className>java.lang.Double</className>0.0</t></parameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	249 </pos><pos val="3"><className>de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameter</className><parameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	250 <value><className>java.lang.Double</className>-1.8031374642502886</value><symbol><className>java.lang.Byte</className>3</symbol><index><className>java.lang.Integer</className>23</index><pseudoCount><className>java.lang.Double</className>1.0</pseudoCount><position><className>java.lang.Integer</className>5</position><context><className>[[I</className><length>0</length></context><count><className>java.lang.Double</className>1.0</count><free><className>java.lang.Boolean</className>true</free><z><className>java.lang.Double</className>0.0</z><t><className>java.lang.Double</className>0.0</t></parameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	251 </pos></pars></treeElement>
b7d6db3ba6bc Uploaded grau parents: diff changeset	252 </root><firstParent><className>java.lang.Integer</className>-1</firstParent><firstChildren><className>[I</className><length>0</length></firstChildren></parameterTree>
b7d6db3ba6bc Uploaded grau parents: diff changeset	253 </pos><pos val="6"><className>de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameterTree</className><parameterTree>
b7d6db3ba6bc Uploaded grau parents: diff changeset	254 <pos><className>java.lang.Integer</className>6</pos><contextPoss><className>[I</className><length>0</length></contextPoss><root><className>de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameterTree$TreeElement</className><treeElement>
b7d6db3ba6bc Uploaded grau parents: diff changeset	255 <contNum><className>java.lang.Integer</className>0</contNum><contextPos><className>java.lang.Integer</className>-1</contextPos><children>null</children><pars><className>[Lde.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameter;</className><length>4</length><pos val="0"><className>de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameter</className><parameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	256 <value><className>java.lang.Double</className>-1.1813946371662982</value><symbol><className>java.lang.Byte</className>0</symbol><index><className>java.lang.Integer</className>24</index><pseudoCount><className>java.lang.Double</className>1.0</pseudoCount><position><className>java.lang.Integer</className>6</position><context><className>[[I</className><length>0</length></context><count><className>java.lang.Double</className>1.0</count><free><className>java.lang.Boolean</className>true</free><z><className>java.lang.Double</className>0.0</z><t><className>java.lang.Double</className>0.0</t></parameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	257 </pos><pos val="1"><className>de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameter</className><parameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	258 <value><className>java.lang.Double</className>-2.5623116795403806</value><symbol><className>java.lang.Byte</className>1</symbol><index><className>java.lang.Integer</className>25</index><pseudoCount><className>java.lang.Double</className>1.0</pseudoCount><position><className>java.lang.Integer</className>6</position><context><className>[[I</className><length>0</length></context><count><className>java.lang.Double</className>1.0</count><free><className>java.lang.Boolean</className>true</free><z><className>java.lang.Double</className>0.0</z><t><className>java.lang.Double</className>0.0</t></parameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	259 </pos><pos val="2"><className>de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameter</className><parameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	260 <value><className>java.lang.Double</className>-0.8967765906261282</value><symbol><className>java.lang.Byte</className>2</symbol><index><className>java.lang.Integer</className>26</index><pseudoCount><className>java.lang.Double</className>1.0</pseudoCount><position><className>java.lang.Integer</className>6</position><context><className>[[I</className><length>0</length></context><count><className>java.lang.Double</className>1.0</count><free><className>java.lang.Boolean</className>true</free><z><className>java.lang.Double</className>0.0</z><t><className>java.lang.Double</className>0.0</t></parameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	261 </pos><pos val="3"><className>de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameter</className><parameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	262 <value><className>java.lang.Double</className>-1.7730354775995691</value><symbol><className>java.lang.Byte</className>3</symbol><index><className>java.lang.Integer</className>27</index><pseudoCount><className>java.lang.Double</className>1.0</pseudoCount><position><className>java.lang.Integer</className>6</position><context><className>[[I</className><length>0</length></context><count><className>java.lang.Double</className>1.0</count><free><className>java.lang.Boolean</className>true</free><z><className>java.lang.Double</className>0.0</z><t><className>java.lang.Double</className>0.0</t></parameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	263 </pos></pars></treeElement>
b7d6db3ba6bc Uploaded grau parents: diff changeset	264 </root><firstParent><className>java.lang.Integer</className>-1</firstParent><firstChildren><className>[I</className><length>0</length></firstChildren></parameterTree>
b7d6db3ba6bc Uploaded grau parents: diff changeset	265 </pos></trees><isTrained><className>java.lang.Boolean</className>true</isTrained><ess><className>java.lang.Double</className>4.0</ess><numFreePars><className>java.lang.Integer</className>28</numFreePars><nums><className>[I</className><length>28</length><pos val="0">0</pos><pos val="1">1</pos><pos val="2">2</pos><pos val="3">3</pos><pos val="4">4</pos><pos val="5">5</pos><pos val="6">6</pos><pos val="7">7</pos><pos val="8">8</pos><pos val="9">9</pos><pos val="10">10</pos><pos val="11">11</pos><pos val="12">12</pos><pos val="13">13</pos><pos val="14">14</pos><pos val="15">15</pos><pos val="16">16</pos><pos val="17">17</pos><pos val="18">18</pos><pos val="19">19</pos><pos val="20">20</pos><pos val="21">21</pos><pos val="22">22</pos><pos val="23">23</pos><pos val="24">24</pos><pos val="25">25</pos><pos val="26">26</pos><pos val="27">27</pos></nums><structureMeasure><className>de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.InhomogeneousMarkov</className><inhomogeneousMarkov>
b7d6db3ba6bc Uploaded grau parents: diff changeset	266 <parameters><className>de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.InhomogeneousMarkov$InhomogeneousMarkovParameterSet</className><instanceParameterSet>
b7d6db3ba6bc Uploaded grau parents: diff changeset	267 <superParameterSet>
b7d6db3ba6bc Uploaded grau parents: diff changeset	268 <parameterSet>
b7d6db3ba6bc Uploaded grau parents: diff changeset	269 <set>
b7d6db3ba6bc Uploaded grau parents: diff changeset	270 <numberOfParameters><className>java.lang.Integer</className>1</numberOfParameters><parameter><className>de.jstacs.parameters.SimpleParameter</className><simpleParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	271 <name><className>java.lang.String</className>Order</name><comment><className>java.lang.String</className>The order of the Markov model.</comment><datatype><className>de.jstacs.DataType</className><name>INT</name></datatype><required><className>java.lang.Boolean</className>true</required><isSet><className>java.lang.Boolean</className>true</isSet><errorMessage><className>java.lang.String</className></errorMessage><isRangeable><className>java.lang.Boolean</className>true</isRangeable><validator>null</validator><defaultValue>null</defaultValue><value><className>java.lang.Integer</className>0</value></simpleParameter>
b7d6db3ba6bc Uploaded grau parents: diff changeset	272 </parameter></set>
b7d6db3ba6bc Uploaded grau parents: diff changeset	273 </parameterSet>
b7d6db3ba6bc Uploaded grau parents: diff changeset	274 </superParameterSet>
b7d6db3ba6bc Uploaded grau parents: diff changeset	275 <instanceClass><className>java.lang.Class</className><name>de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.InhomogeneousMarkov</name></instanceClass></instanceParameterSet>
b7d6db3ba6bc Uploaded grau parents: diff changeset	276 </parameters></inhomogeneousMarkov>
b7d6db3ba6bc Uploaded grau parents: diff changeset	277 </structureMeasure><plugInParameters><className>java.lang.Boolean</className>true</plugInParameters><order><className>[[I</className><length>7</length><pos val="0"><className>[I</className><length>2</length><pos val="0">0</pos><pos val="1">0</pos></pos><pos val="1"><className>[I</className><length>2</length><pos val="0">1</pos><pos val="1">1</pos></pos><pos val="2"><className>[I</className><length>2</length><pos val="0">2</pos><pos val="1">2</pos></pos><pos val="3"><className>[I</className><length>2</length><pos val="0">3</pos><pos val="1">3</pos></pos><pos val="4"><className>[I</className><length>2</length><pos val="0">4</pos><pos val="1">4</pos></pos><pos val="5"><className>[I</className><length>2</length><pos val="0">5</pos><pos val="1">5</pos></pos><pos val="6"><className>[I</className><length>2</length><pos val="0">6</pos><pos val="1">6</pos></pos></order><roots><className>[I</className><length>7</length><pos val="0">0</pos><pos val="1">1</pos><pos val="2">2</pos><pos val="3">3</pos><pos val="4">4</pos><pos val="5">5</pos><pos val="6">6</pos></roots><freeParams><className>java.lang.Boolean</className>false</freeParams></bayesianNetworkSF>
b7d6db3ba6bc Uploaded grau parents: diff changeset	278 <lengthPenalty>null</lengthPenalty></MarkovModelDiffSM>
b7d6db3ba6bc Uploaded grau parents: diff changeset	279 </pos></function><optimizeHidden><className>java.lang.Boolean</className>true</optimizeHidden><plugIn><className>java.lang.Boolean</className>true</plugIn><hiddenParameter><className>[D</className><length>2</length><pos val="0">0.9933095080065826</pos><pos val="1">-1.0769418964449786</pos></hiddenParameter><threshold><className>java.lang.Double</className>0.5</threshold></ThresholdedStrandChIPper>
b7d6db3ba6bc Uploaded grau parents: diff changeset	280 </pos><pos val="1"><className>de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous.UniformHomogeneousDiffSM</className><UniformHomogeneousDiffSM>
b7d6db3ba6bc Uploaded grau parents: diff changeset	281 <length><className>java.lang.Integer</className>0</length><alphabets><className>de.jstacs.data.alphabets.DNAAlphabetContainer</className></alphabets><ess><className>java.lang.Double</className>16.0</ess></UniformHomogeneousDiffSM>
b7d6db3ba6bc Uploaded grau parents: diff changeset	282 </pos></score><beta><className>[D</className><length>3</length><pos val="0">0.5</pos><pos val="1">0.0</pos><pos val="2">0.5</pos></beta><prior>
b7d6db3ba6bc Uploaded grau parents: diff changeset	283 <class><className>java.lang.Class</className><name>de.jstacs.classifiers.differentiableSequenceScoreBased.logPrior.CompositeLogPrior</name></class> </prior>
b7d6db3ba6bc Uploaded grau parents: diff changeset	284 </gendismix-classifier>
b7d6db3ba6bc Uploaded grau parents: diff changeset	285

Mercurial > repos > grau > dimont_motif_discovery

annotate test-data/predictor_test.xml @ 2:31963c6688ef draft default tip