KernelFilter

java.lang.Object
- weka.filters.Filter
- - weka.filters.SimpleFilter
  - - weka.filters.SimpleBatchFilter
    - - weka.filters.unsupervised.attribute.KernelFilter

All Implemented Interfaces:: java.io.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: 14271 $
Author:: Jonathan Miles (jdm18@cs.waikato.ac.nz), FracPete (fracpete at waikato dot ac dot nz)
See Also:: Serialized Form

Constructor Summary

Constructors
Constructor and Description

KernelFilter()

Constructors
Constructor and Description
`KernelFilter()`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`java.lang.String`	`checksTurnedOffTipText()` Returns the tip text for this property
`Capabilities`	`getCapabilities()` Returns the Capabilities of this filter.
`boolean`	`getChecksTurnedOff()` Returns whether the checks are turned off or not.
`java.io.File`	`getInitFile()` Gets the file to initialize the filter with, can be null.
`java.lang.String`	`getInitFileClassIndex()` Gets the class index of the file to initialize the filter with.
`Kernel`	`getKernel()` Gets the kernel to use.
`java.lang.String`	`getKernelFactorExpression()` Gets the expression for the kernel.
`java.lang.String[]`	`getOptions()` Gets the current settings of the filter.
`Filter`	`getPreprocessing()` Gets the filter used for preprocessing
`java.lang.String`	`getRevision()` Returns the revision string.
`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.
`java.lang.String`	`globalInfo()` Returns a string describing this filter.
`java.lang.String`	`initFileClassIndexTipText()` Returns the tip text for this property
`java.lang.String`	`initFileTipText()` Returns the tip text for this property
`void`	`initFilter(Instances instances)` initializes the filter with the given dataset, i.e., the kernel gets built.
`java.lang.String`	`kernelFactorExpressionTipText()` Returns the tip text for this property
`java.lang.String`	`kernelTipText()` Returns the tip text for this property
`java.util.Enumeration<Option>`	`listOptions()` Returns an enumeration describing the available options.
`static void`	`main(java.lang.String[] args)` runs the filter with the given arguments
`java.lang.String`	`preprocessingTipText()` Returns the tip text for this property
`void`	`setChecksTurnedOff(boolean value)` Disables or enables the checks (which could be time-consuming).
`void`	`setInitFile(java.io.File value)` Sets the file to initialize the filter with, can be null.
`void`	`setInitFileClassIndex(java.lang.String value)` Sets class index of the file to initialize the filter with.
`void`	`setKernel(Kernel value)` Sets the kernel to use.
`void`	`setKernelFactorExpression(java.lang.String value)` Sets the expression for the kernel.
`void`	`setOptions(java.lang.String[] options)` Parses a given list of options.
`void`	`setPreprocessing(Filter value)` Sets the filter to use for preprocessing (use the AllFilter for no preprocessing)

Methods inherited from class weka.filters.SimpleBatchFilter
allowAccessToFullInputFormat, batchFinished, input, input

Methods inherited from class weka.filters.SimpleFilter
setInputFormat

Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface weka.core.OptionHandler
makeCopy

- Constructor Detail
  - KernelFilter
```
public KernelFilter()
```
- Method Detail
  - globalInfo
```
public java.lang.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 java.util.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 java.lang.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(java.lang.String[] options)
                throws java.lang.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:
    
    java.lang.Exception - if an option is not supported
  - initFileTipText
```
public java.lang.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 java.io.File getInitFile()
```
    Gets the file to initialize the filter with, can be null.
    
    Returns:
    
    the file
  - setInitFile
```
public void setInitFile(java.io.File value)
```
    Sets the file to initialize the filter with, can be null.
    
    Parameters:
    
    value - the file
  - initFileClassIndexTipText
```
public java.lang.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 java.lang.String getInitFileClassIndex()
```
    Gets the class index of the file to initialize the filter with.
    
    Returns:
    
    the class index
  - setInitFileClassIndex
```
public void setInitFileClassIndex(java.lang.String value)
```
    Sets class index of the file to initialize the filter with.
    
    Parameters:
    
    value - the class index
  - kernelTipText
```
public java.lang.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 java.lang.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 java.lang.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 java.lang.String getKernelFactorExpression()
```
    Gets the expression for the kernel.
    
    Returns:
    
    the expression
  - setKernelFactorExpression
```
public void setKernelFactorExpression(java.lang.String value)
```
    Sets the expression for the kernel.
    
    Parameters:
    
    value - the file
  - preprocessingTipText
```
public java.lang.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 java.lang.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:
    
    java.lang.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:
    
    Capabilities
  - getRevision
```
public java.lang.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(java.lang.String[] args)
```
    runs the filter with the given arguments
    
    Parameters:
    
    args - the commandline arguments

Class KernelFilter

Constructor Summary

Method Summary

Methods inherited from class weka.filters.SimpleBatchFilter

Methods inherited from class weka.filters.SimpleFilter

Methods inherited from class weka.filters.Filter

Methods inherited from class java.lang.Object

Methods inherited from interface weka.core.OptionHandler

Constructor Detail

KernelFilter

Method Detail

globalInfo

getTechnicalInformation

listOptions

getOptions

setOptions

initFileTipText

getInitFile

setInitFile

initFileClassIndexTipText

getInitFileClassIndex

setInitFileClassIndex

kernelTipText

getKernel

setKernel

setChecksTurnedOff

getChecksTurnedOff

checksTurnedOffTipText

kernelFactorExpressionTipText

getKernelFactorExpression

setKernelFactorExpression

preprocessingTipText

setPreprocessing

getPreprocessing

initFilter

getCapabilities

getRevision

main