Package adams.flow.transformer

Class WekaBootstrapping

  • All Implemented Interfaces:
    adams.core.AdditionalInformationHandler, adams.core.CleanUpHandler, adams.core.Destroyable, adams.core.GlobalInfoSupporter, adams.core.logging.LoggingLevelHandler, adams.core.logging.LoggingSupporter, adams.core.option.OptionHandler, adams.core.QuickInfoSupporter, adams.core.Randomizable, adams.core.ShallowCopySupporter<adams.flow.core.Actor>, adams.core.SizeOfHandler, adams.core.Stoppable, adams.core.StoppableWithFeedback, adams.core.VariablesInspectionHandler, adams.event.VariableChangeListener, adams.flow.core.Actor, adams.flow.core.ErrorHandler, adams.flow.core.InputConsumer, adams.flow.core.OutputProducer, Serializable, Comparable
    public class WekaBootstrapping
extends adams.flow.transformer.AbstractTransformer
implements adams.core.Randomizable
    Performs bootstrapping on the incoming evaluation and outputs a spreadsheet where each row represents the results from bootstrapping sub-sample.

    Input/output:
    - accepts:
       weka.classifiers.Evaluation
       adams.flow.container.WekaEvaluationContainer
    - generates:
       adams.data.spreadsheet.SpreadSheet


    Container information:
    - adams.flow.container.WekaEvaluationContainer: Evaluation, Model, Prediction output, Original indices 

    -logging-level <OFF|SEVERE|WARNING|INFO|CONFIG|FINE|FINER|FINEST> (property: loggingLevel)
    The logging level for outputting errors and debugging output.
    default: WARNING
 
    -name <java.lang.String> (property: name)
    The name of the actor.
    default: WekaBootstrapping
 
    -annotation <adams.core.base.BaseAnnotation> (property: annotations)
    The annotations to attach to this actor.
    default: 
 
    -skip <boolean> (property: skip)
    If set to true, transformation is skipped and the input token is just forwarded 
    as it is.
    default: false
 
    -stop-flow-on-error <boolean> (property: stopFlowOnError)
    If set to true, the flow execution at this level gets stopped in case this 
    actor encounters an error; the error gets propagated; useful for critical 
    actors.
    default: false
 
    -silent <boolean> (property: silent)
    If enabled, then no errors are output in the console; Note: the enclosing 
    actor handler must have this enabled as well.
    default: false
 
    -seed <long> (property: seed)
    The seed for generating the random sub-samples.
    default: 1
 
    -num-subsamples <int> (property: numSubSamples)
    The number of random sub-samples to generate.
    default: 10
    minimum: 1
 
    -percentage <double> (property: percentage)
    The percentage of the sub-sample size (between 0 and 1).
    default: 0.66
    minimum: 1.0E-4
    maximum: 1.0
 
    -statistic <Number correct|Number incorrect|Number unclassified|Percent correct|Percent incorrect|Percent unclassified|Kappa statistic|Mean absolute error|Root mean squared error|Relative absolute error|Root relative squared error|Correlation coefficient|SF prior entropy|SF scheme entropy|SF entropy gain|SF mean prior entropy|SF mean scheme entropy|SF mean entropy gain|KB information|KB mean information|KB relative information|True positive rate|Num true positives|False positive rate|Num false positives|True negative rate|Num true negatives|False negative rate|Num false negatives|IR precision|IR recall|F measure|Matthews correlation coefficient|Area under ROC|Area under PRC|Weighted true positive rate|Weighted false positive rate|Weighted true negative rate|Weighted false negative rate|Weighted IR precision|Weighted IR recall|Weighted F measure|Weighted Matthews correlation coefficient|Weighted area under ROC|Weighted area under PRC|Unweighted Macro F measure|Unweighted Micro F measure|Bias|R^2> [-statistic ...] (property: statisticValues)
    The evaluation values to extract and turn into a spreadsheet.
    default: 
 
    -class-index <adams.data.weka.WekaLabelIndex> (property: classIndex)
    The index of class label (eg used for AUC).
    default: first
    example: An index is a number starting with 1; apart from label names (case-sensitive), the following placeholders can be used as well: first, second, third, last_2, last_1, last; numeric indices can be enforced by preceding them with '#' (eg '#12'); label names can be surrounded by double quotes.
 
    -percentile <adams.core.base.BaseDouble> [-percentile ...] (property: percentiles)
    The percentiles to calculate for the errors (0-1; 0.95 is 95th percentile
    ).
    default: 
 
    -error-calculation <ACTUAL_MINUS_PREDICTED|PREDICTED_MINUS_ACTUAL|BOTH|ABSOLUTE> (property: errorCalculation)
    Determines how to calculate the error.
    default: ACTUAL_MINUS_PREDICTED
 
    -with-replacement <boolean> (property: withReplacement)
    If enabled, predictions are drawn using with replacement (i.e., duplicates 
    are possible).
    default: true
    Version:
    $Revision$
    Author:
    FracPete (fracpete at waikato dot ac dot nz)
    See Also:
    Serialized Form

    • Field Summary

      Fields 
      Modifier and Type Field Description
      protected WekaLabelIndex m_ClassIndex
      the index of the class label.
      protected WekaBootstrapping.ErrorCalculation m_ErrorCalculation
      the error calculation.
      protected int m_NumSubSamples
      the number of random sub-samples to generate.
      protected double m_Percentage
      the size for the sub-samples (0-1).
      protected adams.core.base.BaseDouble[] m_Percentiles
      the percentiles to output (0-1).
      protected long m_Seed
      the random number seed.
      protected EvaluationStatistic[] m_StatisticValues
      the comparison fields.
      protected boolean m_WithReplacement
      whether to use with replacement or not.

      • Fields inherited from class adams.flow.transformer.AbstractTransformer

        BACKUP_INPUT, BACKUP_OUTPUT, m_InputToken, m_OutputToken

      • Fields inherited from class adams.flow.core.AbstractActor

        m_Annotations, m_BackupState, m_DetectedObjectVariables, m_DetectedVariables, m_ErrorHandler, m_Executed, m_Executing, m_ExecutionListeningSupporter, m_FullName, m_LoggingPrefix, m_Name, m_Parent, m_ScopeHandler, m_Self, m_Silent, m_Skip, m_StopFlowOnError, m_StopMessage, m_Stopped, m_StorageHandler, m_VariablesUpdated

      • Fields inherited from class adams.core.option.AbstractOptionHandler

        m_OptionManager

      • Fields inherited from class adams.core.logging.LoggingObject

        m_Logger, m_LoggingIsEnabled, m_LoggingLevel

      • Fields inherited from interface adams.flow.core.Actor

        FILE_EXTENSION, FILE_EXTENSION_GZ

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      Class[] accepts()
      Returns the class that the consumer accepts.
      String classIndexTipText()
      Returns the tip text for this property.
      void defineOptions()
      Adds options to the internal list of options.
      protected String doExecute()
      Executes the flow item.
      String errorCalculationTipText()
      Returns the tip text for this property.
      Class[] generates()
      Returns the class of objects that it generates.
      WekaLabelIndex getClassIndex()
      Returns the current index of class label (1-based).
      WekaBootstrapping.ErrorCalculation getErrorCalculation()
      Returns how to calculate the errors for the percentiles.
      int getNumSubSamples()
      Returns the number of sub-samples to generate.
      double getPercentage()
      Returns the percentage (0-1).
      adams.core.base.BaseDouble[] getPercentiles()
      Returns the percentiles to calculate for the errors.
      String getQuickInfo()
      Returns a quick info about the actor, which will be displayed in the GUI.
      long getSeed()
      Returns the seed value.
      EvaluationStatistic[] getStatisticValues()
      Returns the values to extract.
      boolean getWithReplacement()
      Returns whether to draw predictions using replacement.
      String globalInfo()
      Returns a string describing the object.
      String numSubSamplesTipText()
      Returns the tip text for this property.
      String percentageTipText()
      Returns the tip text for this property.
      String percentilesTipText()
      Returns the tip text for this property.
      String seedTipText()
      Returns the tip text for this property.
      void setClassIndex​(WekaLabelIndex value)
      Sets the index of class label index (1-based).
      void setErrorCalculation​(WekaBootstrapping.ErrorCalculation value)
      Sets how to calculate the errors for the percentiles.
      void setNumSubSamples​(int value)
      Sets the number sub-samples to generate.
      void setPercentage​(double value)
      Sets the percentage (0-1).
      void setPercentiles​(adams.core.base.BaseDouble[] value)
      Sets the percentiles to calculate for the errors.
      void setSeed​(long value)
      Sets the seed value.
      void setStatisticValues​(EvaluationStatistic[] value)
      Sets the values to extract.
      void setWithReplacement​(boolean value)
      Sets whether to draw predictions using replacement.
      String statisticValuesTipText()
      Returns the tip text for this property.
      String withReplacementTipText()
      Returns the tip text for this property.

      • Methods inherited from class adams.flow.transformer.AbstractTransformer

        backupState, currentInput, execute, hasInput, hasPendingOutput, input, output, postExecute, restoreState, wrapUp

      • Methods inherited from class adams.flow.core.AbstractActor

        annotationsTipText, canInspectOptions, canPerformSetUpCheck, cleanUp, compareTo, configureLogger, destroy, equals, finalUpdateVariables, findVariables, findVariables, forceVariables, forCommandLine, forName, forName, getAdditionalInformation, getAnnotations, getDefaultName, getDetectedVariables, getErrorHandler, getFlowActors, getFlowExecutionListeningSupporter, getFullName, getName, getNextSibling, getParent, getParentComponent, getPreviousSibling, getRoot, getScopeHandler, getSilent, getSkip, getStopFlowOnError, getStopMessage, getStorageHandler, getVariables, handleError, handleException, hasErrorHandler, hasStopMessage, index, initialize, isBackedUp, isExecuted, isExecuting, isFinished, isHeadless, isStopped, nameTipText, performSetUpChecks, performVariableChecks, preExecute, pruneBackup, pruneBackup, reset, setAnnotations, setErrorHandler, setName, setParent, setSilent, setSkip, setStopFlowOnError, setUp, setVariables, shallowCopy, shallowCopy, silentTipText, sizeOf, skipTipText, stopExecution, stopExecution, stopFlowOnErrorTipText, updateDetectedVariables, updatePrefix, updateVariables, variableChanged

      • Methods inherited from class adams.core.option.AbstractOptionHandler

        cleanUpOptions, finishInit, getDefaultLoggingLevel, getOptionManager, loggingLevelTipText, newOptionManager, setLoggingLevel, toCommandLine, toString

      • Methods inherited from class adams.core.logging.LoggingObject

        getLogger, getLoggingLevel, initializeLogging, isLoggingEnabled

      • Methods inherited from interface adams.flow.core.Actor

        cleanUp, compareTo, destroy, equals, findVariables, getAnnotations, getDefaultName, getDetectedVariables, getErrorHandler, getFlowExecutionListeningSupporter, getFullName, getName, getNextSibling, getParent, getParentComponent, getPreviousSibling, getRoot, getScopeHandler, getSilent, getSkip, getStopFlowOnError, getStopMessage, getStorageHandler, getVariables, handleError, hasErrorHandler, hasStopMessage, index, isExecuted, isFinished, isHeadless, isStopped, setAnnotations, setErrorHandler, setName, setParent, setSilent, setSkip, setStopFlowOnError, setUp, setVariables, shallowCopy, shallowCopy, sizeOf, stopExecution, stopExecution, toCommandLine, variableChanged

      • Methods inherited from interface adams.core.AdditionalInformationHandler

        getAdditionalInformation

      • Methods inherited from interface adams.core.logging.LoggingLevelHandler

        getLoggingLevel, setLoggingLevel

      • Methods inherited from interface adams.core.logging.LoggingSupporter

        getLogger, isLoggingEnabled

      • Methods inherited from interface adams.core.option.OptionHandler

        cleanUpOptions, getOptionManager

      • Methods inherited from interface adams.core.VariablesInspectionHandler

        canInspectOptions

    • Field Detail

      • m_Seed

        protected long m_Seed
        the random number seed.

      • m_NumSubSamples

        protected int m_NumSubSamples
        the number of random sub-samples to generate.

      • m_Percentage

        protected double m_Percentage
        the size for the sub-samples (0-1).

      • m_ClassIndex

        protected WekaLabelIndex m_ClassIndex
        the index of the class label.

      • m_Percentiles

        protected adams.core.base.BaseDouble[] m_Percentiles
        the percentiles to output (0-1).

      • m_WithReplacement

        protected boolean m_WithReplacement
        whether to use with replacement or not.

    • Constructor Detail

      • WekaBootstrapping

        public WekaBootstrapping()

    • Method Detail

      • globalInfo

        public String globalInfo()
        Returns a string describing the object.
        Specified by:
        globalInfo in interface adams.core.GlobalInfoSupporter
        Specified by:
        globalInfo in class adams.core.option.AbstractOptionHandler
        Returns:
        a description suitable for displaying in the gui

      • defineOptions

        public void defineOptions()
        Adds options to the internal list of options.
        Specified by:
        defineOptions in interface adams.core.option.OptionHandler
        Overrides:
        defineOptions in class adams.flow.core.AbstractActor

      • setSeed

        public void setSeed​(long value)
        Sets the seed value.
        Specified by:
        setSeed in interface adams.core.Randomizable
        Parameters:
        value - the seed

      • getSeed

        public long getSeed()
        Returns the seed value.
        Specified by:
        getSeed in interface adams.core.Randomizable
        Returns:
        the seed

      • seedTipText

        public String seedTipText()
        Returns the tip text for this property.
        Specified by:
        seedTipText in interface adams.core.Randomizable
        Returns:
        tip text for this property suitable for displaying in the GUI or for listing the options.

      • setNumSubSamples

        public void setNumSubSamples​(int value)
        Sets the number sub-samples to generate.
        Parameters:
        value - the number of sub-samples

      • getNumSubSamples

        public int getNumSubSamples()
        Returns the number of sub-samples to generate.
        Returns:
        the number of sub-samples

      • numSubSamplesTipText

        public String numSubSamplesTipText()
        Returns the tip text for this property.
        Returns:
        tip text for this property suitable for displaying in the GUI or for listing the options.

      • setPercentage

        public void setPercentage​(double value)
        Sets the percentage (0-1).
        Parameters:
        value - the percentage

      • getPercentage

        public double getPercentage()
        Returns the percentage (0-1).
        Returns:
        the percentage

      • percentageTipText

        public String percentageTipText()
        Returns the tip text for this property.
        Returns:
        tip text for this property suitable for displaying in the GUI or for listing the options.

      • setStatisticValues

        public void setStatisticValues​(EvaluationStatistic[] value)
        Sets the values to extract.
        Parameters:
        value - the value

      • getStatisticValues

        public EvaluationStatistic[] getStatisticValues()
        Returns the values to extract.
        Returns:
        the value

      • statisticValuesTipText

        public String statisticValuesTipText()
        Returns the tip text for this property.
        Returns:
        tip text for this property suitable for displaying in the GUI or for listing the options.

      • setClassIndex

        public void setClassIndex​(WekaLabelIndex value)
        Sets the index of class label index (1-based).
        Parameters:
        value - the label index

      • getClassIndex

        public WekaLabelIndex getClassIndex()
        Returns the current index of class label (1-based).
        Returns:
        the label index

      • classIndexTipText

        public String classIndexTipText()
        Returns the tip text for this property.
        Returns:
        tip text for this property suitable for displaying in the GUI or for listing the options.

      • setPercentiles

        public void setPercentiles​(adams.core.base.BaseDouble[] value)
        Sets the percentiles to calculate for the errors.
        Parameters:
        value - the percentiles (0-1; 0.95 is 95th percentile)

      • getPercentiles

        public adams.core.base.BaseDouble[] getPercentiles()
        Returns the percentiles to calculate for the errors.
        Returns:
        the percentiles (0-1; 0.95 is 95th percentile)

      • percentilesTipText

        public String percentilesTipText()
        Returns the tip text for this property.
        Returns:
        tip text for this property suitable for displaying in the GUI or for listing the options.

      • setErrorCalculation

        public void setErrorCalculation​(WekaBootstrapping.ErrorCalculation value)
        Sets how to calculate the errors for the percentiles.
        Parameters:
        value - the type

      • errorCalculationTipText

        public String errorCalculationTipText()
        Returns the tip text for this property.
        Returns:
        tip text for this property suitable for displaying in the GUI or for listing the options.

      • setWithReplacement

        public void setWithReplacement​(boolean value)
        Sets whether to draw predictions using replacement.
        Parameters:
        value - true if with replacement

      • getWithReplacement

        public boolean getWithReplacement()
        Returns whether to draw predictions using replacement.
        Returns:
        true if with replacement

      • withReplacementTipText

        public String withReplacementTipText()
        Returns the tip text for this property.
        Returns:
        tip text for this property suitable for displaying in the GUI or for listing the options.

      • getQuickInfo

        public String getQuickInfo()
        Returns a quick info about the actor, which will be displayed in the GUI.
        Specified by:
        getQuickInfo in interface adams.flow.core.Actor
        Specified by:
        getQuickInfo in interface adams.core.QuickInfoSupporter
        Overrides:
        getQuickInfo in class adams.flow.core.AbstractActor
        Returns:
        null if no info available, otherwise short string

      • accepts

        public Class[] accepts()
        Returns the class that the consumer accepts.
        Specified by:
        accepts in interface adams.flow.core.InputConsumer
        Returns:
        the Class of objects that can be processed

      • generates

        public Class[] generates()
        Returns the class of objects that it generates.
        Specified by:
        generates in interface adams.flow.core.OutputProducer
        Returns:
        the Class of the generated tokens

      • doExecute

        protected String doExecute()
        Executes the flow item.
        Specified by:
        doExecute in class adams.flow.core.AbstractActor
        Returns:
        null if everything is fine, otherwise error message