Package weka.filters.unsupervised.attribute

Class KernelFilter

java.lang.Object
weka.filters.Filter
weka.filters.SimpleFilter
weka.filters.SimpleBatchFilter
weka.filters.unsupervised.attribute.KernelFilter
All Implemented Interfaces:
Serializable, CapabilitiesHandler, CapabilitiesIgnorer, CommandlineRunnable, OptionHandler, RevisionHandler, TechnicalInformationHandler, UnsupervisedFilter
public class KernelFilter extends SimpleBatchFilter implements UnsupervisedFilter, TechnicalInformationHandler
Converts the given set of data into a kernel matrix. The class value remains unchanged as long as the chosen preprocessing filter does not change it.
By default, the data is preprocessed with the Center filter, but the user can choose any filter. (NB: one must be careful that the filter does not alter the class attribute unintentionally.) With weka.filters.AllFilter the preprocessing gets disabled.

For more information regarding preprocessing the data, see:

K.P. Bennett, M.J. Embrechts: An Optimization Perspective on Kernel Partial Least Squares Regression. In: Advances in Learning Theory: Methods, Models and Applications, 227-249, 2003.

BibTeX: 

 @inproceedings{Bennett2003,
    author = {K.P. Bennett and M.J. Embrechts},
    booktitle = {Advances in Learning Theory: Methods, Models and Applications},
    editor = {J. Suykens et al.},
    pages = {227-249},
    publisher = {IOS Press, Amsterdam, The Netherlands},
    series = {NATO Science Series, Series III: Computer and System Sciences},
    title = {An Optimization Perspective on Kernel Partial Least Squares Regression},
    volume = {190},
    year = {2003}
 }

Valid options are: 

 -output-debug-info
  Turns on output of debugging information.
 
 -no-checks
  Turns off all checks - use with caution!
  Turning them off assumes that data is purely numeric, doesn't
  contain any missing values, and has a nominal class. Turning them
  off also means that no header information will be stored if the
  machine is linear. Finally, it also assumes that no instance has
  a weight equal to 0.
  (default: checks on)
 
 -F <filename>
  The file to initialize the filter with (optional).
 
 -C <num>
  The class index for the file to initialize with,
  First and last are valid (optional, default: last).
 
 -K <classname and parameters>
  The Kernel to use.
  (default: weka.classifiers.functions.supportVector.PolyKernel)
 
 -kernel-factor
  Defines a factor for the kernel.
   - RBFKernel: a factor for gamma
    Standardize: 1/(2*N)
    Normalize..: 6/N
  Available parameters are:
   N for # of instances, A for # of attributes
  (default: 1)
 
 -P <classname and parameters>
  The Filter used for preprocessing (use weka.filters.AllFilter
  to disable preprocessing).
  (default: weka.filters.unsupervised.attribute.Center)
 
 Options specific to kernel weka.classifiers.functions.supportVector.PolyKernel:
 
 -D
  Enables debugging output (if available) to be printed.
  (default: off)
 
 -no-checks
  Turns off all checks - use with caution!
  (default: checks on)
 
 -C <num>
  The size of the cache (a prime number), 0 for full cache and 
  -1 to turn it off.
  (default: 250007)
 
 -E <num>
  The Exponent to use.
  (default: 1.0)
 
 -L
  Use lower-order terms.
  (default: no)
 
 Options specific to preprocessing filter weka.filters.unsupervised.attribute.Center:
 
 -unset-class-temporarily
  Unsets the class index temporarily before the filter is
  applied to the data.
  (default: no)
Version:
$Revision: 14266 $
Author:
Jonathan Miles (jdm18@cs.waikato.ac.nz), FracPete (fracpete at waikato dot ac dot nz)
See Also:

  • Constructor Details

    • KernelFilter

      public KernelFilter()

  • Method Details

    • globalInfo

      public String globalInfo()
      Returns a string describing this filter.
      Specified by:
      globalInfo in class SimpleFilter
      Returns:
      a description of the filter suitable for displaying in the explorer/experimenter gui

    • getTechnicalInformation

      public TechnicalInformation getTechnicalInformation()
      Returns an instance of a TechnicalInformation object, containing detailed information about the technical background of this class, e.g., paper reference or book this class is based on.
      Specified by:
      getTechnicalInformation in interface TechnicalInformationHandler
      Returns:
      the technical information about this class

    • listOptions

      public Enumeration<Option> listOptions()
      Returns an enumeration describing the available options.
      Specified by:
      listOptions in interface OptionHandler
      Overrides:
      listOptions in class Filter
      Returns:
      an enumeration of all the available options.

    • getOptions

      public String[] getOptions()
      Gets the current settings of the filter.
      Specified by:
      getOptions in interface OptionHandler
      Overrides:
      getOptions in class Filter
      Returns:
      an array of strings suitable for passing to setOptions

    • setOptions

      public void setOptions(String[] options) throws Exception
      Parses a given list of options.

      Valid options are: 

       -D
  Turns on output of debugging information.
 
       -no-checks
  Turns off all checks - use with caution!
  Turning them off assumes that data is purely numeric, doesn't
  contain any missing values, and has a nominal class. Turning them
  off also means that no header information will be stored if the
  machine is linear. Finally, it also assumes that no instance has
  a weight equal to 0.
  (default: checks on)
 
       -F <filename>
  The file to initialize the filter with (optional).
 
       -C <num>
  The class index for the file to initialize with,
  First and last are valid (optional, default: last).
 
       -K <classname and parameters>
  The Kernel to use.
  (default: weka.classifiers.functions.supportVector.PolyKernel)
 
       -kernel-factor
  Defines a factor for the kernel.
   - RBFKernel: a factor for gamma
    Standardize: 1/(2*N)
    Normalize..: 6/N
  Available parameters are:
   N for # of instances, A for # of attributes
  (default: 1)
 
       -P <classname and parameters>
  The Filter used for preprocessing (use weka.filters.AllFilter
  to disable preprocessing).
  (default: weka.filters.unsupervised.attribute.Center)
 
       Options specific to kernel weka.classifiers.functions.supportVector.PolyKernel:
 
       -D
  Enables debugging output (if available) to be printed.
  (default: off)
 
       -no-checks
  Turns off all checks - use with caution!
  (default: checks on)
 
       -C <num>
  The size of the cache (a prime number), 0 for full cache and 
  -1 to turn it off.
  (default: 250007)
 
       -E <num>
  The Exponent to use.
  (default: 1.0)
 
       -L
  Use lower-order terms.
  (default: no)
 
       Options specific to preprocessing filter weka.filters.unsupervised.attribute.Center:
 
       -unset-class-temporarily
  Unsets the class index temporarily before the filter is
  applied to the data.
  (default: no)
      Specified by:
      setOptions in interface OptionHandler
      Overrides:
      setOptions in class Filter
      Parameters:
      options - the list of options as an array of strings
      Throws:
      Exception - if an option is not supported

    • initFileTipText

      public String initFileTipText()
      Returns the tip text for this property
      Returns:
      tip text for this property suitable for displaying in the explorer/experimenter gui

    • getInitFile

      public File getInitFile()
      Gets the file to initialize the filter with, can be null.
      Returns:
      the file

    • setInitFile

      public void setInitFile(File value)
      Sets the file to initialize the filter with, can be null.
      Parameters:
      value - the file

    • initFileClassIndexTipText

      public String initFileClassIndexTipText()
      Returns the tip text for this property
      Returns:
      tip text for this property suitable for displaying in the explorer/experimenter gui

    • getInitFileClassIndex

      public String getInitFileClassIndex()
      Gets the class index of the file to initialize the filter with.
      Returns:
      the class index

    • setInitFileClassIndex

      public void setInitFileClassIndex(String value)
      Sets class index of the file to initialize the filter with.
      Parameters:
      value - the class index

    • kernelTipText

      public String kernelTipText()
      Returns the tip text for this property
      Returns:
      tip text for this property suitable for displaying in the explorer/experimenter gui

    • getKernel

      public Kernel getKernel()
      Gets the kernel to use.
      Returns:
      the kernel

    • setKernel

      public void setKernel(Kernel value)
      Sets the kernel to use.
      Parameters:
      value - the kernel

    • setChecksTurnedOff

      public void setChecksTurnedOff(boolean value)
      Disables or enables the checks (which could be time-consuming). Use with caution!
      Parameters:
      value - if true turns off all checks

    • getChecksTurnedOff

      public boolean getChecksTurnedOff()
      Returns whether the checks are turned off or not.
      Returns:
      true if the checks are turned off

    • checksTurnedOffTipText

      public String checksTurnedOffTipText()
      Returns the tip text for this property
      Returns:
      tip text for this property suitable for displaying in the explorer/experimenter gui

    • kernelFactorExpressionTipText

      public String kernelFactorExpressionTipText()
      Returns the tip text for this property
      Returns:
      tip text for this property suitable for displaying in the explorer/experimenter gui

    • getKernelFactorExpression

      public String getKernelFactorExpression()
      Gets the expression for the kernel.
      Returns:
      the expression

    • setKernelFactorExpression

      public void setKernelFactorExpression(String value)
      Sets the expression for the kernel.
      Parameters:
      value - the file

    • preprocessingTipText

      public String preprocessingTipText()
      Returns the tip text for this property
      Returns:
      tip text for this property suitable for displaying in the explorer/experimenter gui

    • setPreprocessing

      public void setPreprocessing(Filter value)
      Sets the filter to use for preprocessing (use the AllFilter for no preprocessing)
      Parameters:
      value - the preprocessing filter

    • getPreprocessing

      public Filter getPreprocessing()
      Gets the filter used for preprocessing
      Returns:
      the current preprocessing filter.

    • initFilter

      public void initFilter(Instances instances) throws Exception
      initializes the filter with the given dataset, i.e., the kernel gets built. Needs to be called before the first call of Filter.useFilter or batchFinished(), if not the -F option (or setInitFile(File) is used).
      Parameters:
      instances - the data to initialize with
      Throws:
      Exception - if building of kernel fails

    • getCapabilities

      public Capabilities getCapabilities()
      Returns the Capabilities of this filter.
      Specified by:
      getCapabilities in interface CapabilitiesHandler
      Overrides:
      getCapabilities in class Filter
      Returns:
      the capabilities of this object
      See Also:

    • getRevision

      public String getRevision()
      Returns the revision string.
      Specified by:
      getRevision in interface RevisionHandler
      Overrides:
      getRevision in class Filter
      Returns:
      the revision

    • main

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