Package weka.filters.supervised.attribute

Class SIMPLSMatrixFilterFromGeneticString

  • All Implemented Interfaces:
    Serializable, weka.core.CapabilitiesHandler, weka.core.CapabilitiesIgnorer, weka.core.CommandlineRunnable, weka.core.OptionHandler, weka.core.RevisionHandler, weka.core.TechnicalInformationHandler, weka.filters.SupervisedFilter
    public class SIMPLSMatrixFilterFromGeneticString
extends weka.filters.supervised.attribute.PLSFilter
    Runs Partial Least Square Regression over the given instances and computes the resulting beta matrix for prediction.
    By default it replaces missing values and centers the data.

    Allows access to the internal matrices.

    For more information see:

    Tormod Naes, Tomas Isaksson, Tom Fearn, Tony Davies (2002). A User Friendly Guide to Multivariate Calibration and Classification. NIR Publications.

    StatSoft, Inc.. Partial Least Squares (PLS).

    Bent Jorgensen, Yuri Goegebeur. Module 7: Partial least squares regression I.

    S. de Jong (1993). SIMPLS: an alternative approach to partial least squares regression. Chemometrics and Intelligent Laboratory Systems. 18:251-263.

    BibTeX: 
     @book{Naes2002,
    author = {Tormod Naes and Tomas Isaksson and Tom Fearn and Tony Davies},
    publisher = {NIR Publications},
    title = {A User Friendly Guide to Multivariate Calibration and Classification},
    year = {2002},
    ISBN = {0-9528666-2-5}
 }
 
 @misc{missing_id,
    author = {StatSoft, Inc.},
    booktitle = {Electronic Textbook StatSoft},
    title = {Partial Least Squares (PLS)},
    HTTP = {http://www.statsoft.com/textbook/stpls.html}
 }
 
 @misc{missing_id,
    author = {Bent Jorgensen and Yuri Goegebeur},
    booktitle = {ST02: Multivariate Data Analysis and Chemometrics},
    title = {Module 7: Partial least squares regression I},
    HTTP = {http://statmaster.sdu.dk/courses/ST02/module07/}
 }
 
 @article{Jong1993,
    author = {S. de Jong},
    journal = {Chemometrics and Intelligent Laboratory Systems},
    pages = {251-263},
    title = {SIMPLS: an alternative approach to partial least squares regression},
    volume = {18},
    year = {1993}
 }


    Valid options are: 

     -D
  Turns on output of debugging information.
     -C <num>
  The number of components to compute.
  (default: 20)
     -U
  Updates the class attribute as well.
  (default: off)
     -M
  Turns replacing of missing values on.
  (default: off)
     -A <SIMPLS|PLS1>
  The algorithm to use.
  (default: PLS1)
     -P <none|center|standardize>
  The type of preprocessing that is applied to the data.
  (default: center)
    Version:
    $Revision: 10824 $
    Author:
    FracPete (fracpete at waikato dot ac dot nz)
    See Also:
    Serialized Form

    • Field Summary

      Fields 
      Modifier and Type Field Description
      static String BITSTRING  
      static String COLUMNS  
      protected String m_BitString  
      protected int m_Columns  
      protected double m_Max  
      protected double m_Min  
      protected int m_Rows  
      protected weka.core.matrix.Matrix m_SIMPLS_MATRIX_LOCAL  
      protected int m_Splits  
      static String MAX  
      static String MIN  
      static String ROWS  
      static String SPLITS  

      • Fields inherited from class weka.filters.supervised.attribute.PLSFilter

        ALGORITHM_PLS1, ALGORITHM_SIMPLS, m_Algorithm, m_ClassMean, m_ClassStdDev, m_Filter, m_Missing, m_NumComponents, m_PerformPrediction, m_PLS1_b_hat, m_PLS1_P, m_PLS1_RegVector, m_PLS1_W, m_Preprocessing, m_ReplaceMissing, m_SIMPLS_B, m_SIMPLS_W, PREPROCESSING_CENTER, PREPROCESSING_NONE, PREPROCESSING_STANDARDIZE, TAGS_ALGORITHM, TAGS_PREPROCESSING

      • Fields inherited from class weka.filters.Filter

        m_Debug, m_DoNotCheckCapabilities, m_FirstBatchDone, m_InputRelAtts, m_InputStringAtts, m_NewBatch, m_OutputRelAtts, m_OutputStringAtts

    • Method Summary

      All Methods Static Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      String bitstringTipText()  
      protected int calcNumBits()
      Calculates the number of bits to use.
      String columnsTipText()  
      String getBitstring()  
      int getColumns()  
      weka.core.matrix.Matrix getMatrix()  
      double getMax()  
      double getMin()  
      String[] getOptions()
      Gets the current option settings for the OptionHandler.
      int getRows()  
      int getSplits()  
      String globalInfo()
      Returns a string describing this classifier.
      void initialiseW​(weka.core.Instances ins)  
      void initialiseWeights()  
      Enumeration listOptions()
      Returns an enumeration describing the available options.
      static void main​(String[] args)
      runs the filter with the given arguments.
      String maxTipText()  
      String minTipText()  
      protected weka.core.Instances processSIMPLS​(weka.core.Instances instances)  
      protected void reset()
      Resets the cleaner.
      String rowsTipText()  
      void setBitstring​(String bits)  
      void setColumns​(int columns)  
      void setMatrix​(weka.core.matrix.Matrix m)  
      void setMax​(double max)  
      void setMin​(double min)  
      void setOptions​(String[] options)
      Sets the OptionHandler's options using the given list.
      void setRows​(int rows)  
      void setSplits​(int splits)  
      String splitsTipText()  

      • Methods inherited from class weka.filters.supervised.attribute.PLSFilter

        algorithmTipText, columnAsVector, determineOutputFormat, getAlgorithm, getCapabilities, getDominantEigenVector, getNumComponents, getPerformPrediction, getPreprocessing, getReplaceMissing, getRevision, getTechnicalInformation, getVector, getX, getX, getY, getY, normalizeVector, numComponentsTipText, performPredictionTipText, preprocessingTipText, process, processPLS1, replaceMissingTipText, setAlgorithm, setNumComponents, setPerformPrediction, setPreprocessing, setReplaceMissing, setVector, toInstances

      • Methods inherited from class weka.filters.SimpleBatchFilter

        allowAccessToFullInputFormat, batchFinished, hasImmediateOutputFormat, input, input

      • Methods inherited from class weka.filters.SimpleFilter

        setInputFormat

      • Methods inherited from class weka.filters.Filter

        batchFilterFile, bufferInput, copyValues, copyValues, debugTipText, doNotCheckCapabilitiesTipText, filterFile, flushInput, getCapabilities, getCopyOfInputFormat, getDebug, getDoNotCheckCapabilities, getInputFormat, getOutputFormat, initInputLocators, initOutputLocators, inputFormatPeek, isFirstBatchDone, isNewBatch, isOutputFormatDefined, makeCopies, makeCopy, mayRemoveInstanceAfterFirstBatchDone, numPendingOutput, output, outputFormatPeek, outputPeek, postExecution, preExecution, push, push, resetQueue, run, runFilter, setDebug, setDoNotCheckCapabilities, setOutputFormat, testInputFormat, toString, useFilter, wekaStaticWrapper

    • Constructor Detail

      • SIMPLSMatrixFilterFromGeneticString

        public SIMPLSMatrixFilterFromGeneticString()

    • Method Detail

      • setBitstring

        public void setBitstring​(String bits)

      • getBitstring

        public String getBitstring()

      • bitstringTipText

        public String bitstringTipText()

      • setMin

        public void setMin​(double min)

      • getMin

        public double getMin()

      • minTipText

        public String minTipText()

      • setMax

        public void setMax​(double max)

      • getMax

        public double getMax()

      • maxTipText

        public String maxTipText()

      • setSplits

        public void setSplits​(int splits)

      • getSplits

        public int getSplits()

      • splitsTipText

        public String splitsTipText()

      • setRows

        public void setRows​(int rows)

      • getRows

        public int getRows()

      • rowsTipText

        public String rowsTipText()

      • setColumns

        public void setColumns​(int columns)

      • getColumns

        public int getColumns()

      • columnsTipText

        public String columnsTipText()

      • initialiseWeights

        public void initialiseWeights()

      • initialiseW

        public void initialiseW​(weka.core.Instances ins)
                 throws Exception
        Throws:
        Exception

      • calcNumBits

        protected int calcNumBits()
        Calculates the number of bits to use.
        Returns:
        the number of bits

      • setMatrix

        public void setMatrix​(weka.core.matrix.Matrix m)

      • getMatrix

        public weka.core.matrix.Matrix getMatrix()

      • processSIMPLS

        protected weka.core.Instances processSIMPLS​(weka.core.Instances instances)
                                     throws Exception
        Overrides:
        processSIMPLS in class weka.filters.supervised.attribute.PLSFilter
        Throws:
        Exception

      • listOptions

        public Enumeration listOptions()
        Returns an enumeration describing the available options.
        Specified by:
        listOptions in interface weka.core.OptionHandler
        Overrides:
        listOptions in class weka.filters.supervised.attribute.PLSFilter
        Returns:
        an enumeration of all the available options.

      • setOptions

        public void setOptions​(String[] options)
                throws Exception
        Sets the OptionHandler's options using the given list. All options will be set (or reset) during this call (i.e. incremental setting of options is not possible).
        Specified by:
        setOptions in interface weka.core.OptionHandler
        Overrides:
        setOptions in class weka.filters.supervised.attribute.PLSFilter
        Parameters:
        options - the list of options as an array of strings
        Throws:
        Exception - if an option is not supported

      • getOptions

        public String[] getOptions()
        Gets the current option settings for the OptionHandler.
        Specified by:
        getOptions in interface weka.core.OptionHandler
        Overrides:
        getOptions in class weka.filters.supervised.attribute.PLSFilter
        Returns:
        the list of current option settings as an array of strings

      • globalInfo

        public String globalInfo()
        Returns a string describing this classifier.
        Overrides:
        globalInfo in class weka.filters.supervised.attribute.PLSFilter
        Returns:
        a description of the classifier suitable for displaying in the explorer/experimenter gui

      • reset

        protected void reset()
        Resets the cleaner.
        Overrides:
        reset in class weka.filters.SimpleFilter

      • main

        public static void main​(String[] args)
        runs the filter with the given arguments.
        Parameters:
        args - the commandline arguments