Cobweb (interruptible-weka 0.1.2 API)

java.lang.Object
- weka.clusterers.AbstractClusterer
- - weka.clusterers.RandomizableClusterer
  - - weka.clusterers.Cobweb

All Implemented Interfaces:: java.io.Serializable, java.lang.Cloneable, Clusterer, UpdateableClusterer, CapabilitiesHandler, CapabilitiesIgnorer, CommandlineRunnable, Drawable, OptionHandler, Randomizable, RevisionHandler, TechnicalInformationHandler

public class Cobweb
extends RandomizableClusterer
implements Drawable, TechnicalInformationHandler, UpdateableClusterer

Class implementing the Cobweb and Classit clustering algorithms.

Note: the application of node operators (merging, splitting etc.) in terms of ordering and priority differs (and is somewhat ambiguous) between the original Cobweb and Classit papers. This algorithm always compares the best host, adding a new leaf, merging the two best hosts, and splitting the best host when considering where to place a new instance.

For more information see:

D. Fisher (1987). Knowledge acquisition via incremental conceptual clustering. Machine Learning. 2(2):139-172.

J. H. Gennari, P. Langley, D. Fisher (1990). Models of incremental concept formation. Artificial Intelligence. 40:11-61.

BibTeX:

 @article{Fisher1987,
    author = {D. Fisher},
    journal = {Machine Learning},
    number = {2},
    pages = {139-172},
    title = {Knowledge acquisition via incremental conceptual clustering},
    volume = {2},
    year = {1987}
 }
 
 @article{Gennari1990,
    author = {J. H. Gennari and P. Langley and D. Fisher},
    journal = {Artificial Intelligence},
    pages = {11-61},
    title = {Models of incremental concept formation},
    volume = {40},
    year = {1990}
 }

Valid options are:

 -A <acuity>
  Acuity.
  (default=1.0)

 -C <cutoff>
  Cutoff.
  (default=0.002)

 -save-data
  Save instance data.

 -S <num>
  Random number seed.
  (default 42)

 -output-debug-info
  If set, clusterer is run in debug mode and
  may output additional info to the console

 -do-not-check-capabilities
  If set, clusterer capabilities are not checked before clusterer is built
  (use with caution).

See Also:: RandomizableClusterer, Drawable, Serialized Form

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

class Cobweb.CNode
Inner class handling node operations for Cobweb.

Nested Classes
Modifier and Type	Class and Description
`class`	`Cobweb.CNode` Inner class handling node operations for Cobweb.

Field Summary

Fields
Modifier and Type	Field and Description
`protected double`	`m_acuity` Acuity (minimum standard deviation).
`protected Cobweb.CNode`	`m_cobwebTree` Holds the root of the Cobweb tree.
`protected double`	`m_cutoff` Cutoff (minimum category utility).
`protected static double`	`m_normal` Normal constant.
`protected int`	`m_numberMerges` the number of merges that happened
`protected int`	`m_numberOfClusters` Number of clusters (nodes in the tree).
`protected boolean`	`m_numberOfClustersDetermined` whether the number of clusters was already determined
`protected int`	`m_numberSplits` the number of splits that happened
`protected boolean`	`m_saveInstances` Output instances in graph representation of Cobweb tree (Allows instances at nodes in the tree to be visualized in the Explorer).

Fields inherited from class weka.clusterers.RandomizableClusterer
m_Seed, m_SeedDefault

Fields inherited from class weka.clusterers.AbstractClusterer
m_Debug, m_DoNotCheckCapabilities

Fields inherited from interface weka.core.Drawable
BayesNet, Newick, NOT_DRAWABLE, TREE

Constructor Summary

Constructors
Constructor and Description

Cobweb()
default constructor

Constructors
Constructor and Description
`Cobweb()` default constructor

Method Summary

All Methods Static Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method and Description
`java.lang.String`	`acuityTipText()` Returns the tip text for this property
`void`	`addInstance(Instance newInstance)` Deprecated. updateClusterer(Instance) should be used instead
`void`	`buildClusterer(Instances data)` Builds the clusterer.
`int`	`clusterInstance(Instance instance)` Classifies a given instance.
`java.lang.String`	`cutoffTipText()` Returns the tip text for this property
`protected void`	`determineNumberOfClusters()` determines the number of clusters if necessary
`double`	`getAcuity()` get the acuity value
`Capabilities`	`getCapabilities()` Returns default capabilities of the clusterer.
`double`	`getCutoff()` get the cutoff
`java.lang.String[]`	`getOptions()` Gets the current settings of Cobweb.
`java.lang.String`	`getRevision()` Returns the revision string.
`boolean`	`getSaveInstanceData()` Get the value of saveInstances.
`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.
`Cobweb.CNode`	`getTreeRoot()` Get the root of the tree.
`java.lang.String`	`globalInfo()` Returns a string describing this clusterer
`java.lang.String`	`graph()` Generates the graph string of the Cobweb tree
`int`	`graphType()` Returns the type of graphs this class represents
`java.util.Enumeration<Option>`	`listOptions()` Returns an enumeration describing the available options.
`static void`	`main(java.lang.String[] argv)` Main method.
`int`	`numberOfClusters()` Returns the number of clusters.
`java.lang.String`	`saveInstanceDataTipText()` Returns the tip text for this property
`java.lang.String`	`seedTipText()` Returns the tip text for this property
`void`	`setAcuity(double a)` set the acuity.
`void`	`setCutoff(double c)` set the cutoff
`void`	`setOptions(java.lang.String[] options)` Parses a given list of options.
`void`	`setSaveInstanceData(boolean newsaveInstances)` Set the value of saveInstances.
`java.lang.String`	`toString()` Returns a description of the clusterer as a string.
`void`	`updateClusterer(Instance newInstance)` Adds an instance to the clusterer.
`void`	`updateFinished()` Singals the end of the updating.

Methods inherited from class weka.clusterers.RandomizableClusterer
getSeed, setSeed

Methods inherited from class weka.clusterers.AbstractClusterer
debugTipText, distributionForInstance, doNotCheckCapabilitiesTipText, forName, getDebug, getDoNotCheckCapabilities, makeCopies, makeCopy, postExecution, preExecution, run, runClusterer, setDebug, setDoNotCheckCapabilities

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

- Field Detail
  - m_normal
```
protected static final double m_normal
```
    Normal constant.
  - m_acuity
```
protected double m_acuity
```
    Acuity (minimum standard deviation).
  - m_cutoff
```
protected double m_cutoff
```
    Cutoff (minimum category utility).
  - m_cobwebTree
```
protected Cobweb.CNode m_cobwebTree
```
    Holds the root of the Cobweb tree.
  - m_numberOfClusters
```
protected int m_numberOfClusters
```
    Number of clusters (nodes in the tree). Must never be queried directly, only via the method numberOfClusters(). Otherwise it's not guaranteed that it contains the correct value.
    
    See Also:
    
    numberOfClusters(), m_numberOfClustersDetermined
  - m_numberOfClustersDetermined
```
protected boolean m_numberOfClustersDetermined
```
    whether the number of clusters was already determined
  - m_numberSplits
```
protected int m_numberSplits
```
    the number of splits that happened
  - m_numberMerges
```
protected int m_numberMerges
```
    the number of merges that happened
  - m_saveInstances
```
protected boolean m_saveInstances
```
    Output instances in graph representation of Cobweb tree (Allows instances at nodes in the tree to be visualized in the Explorer).
- Constructor Detail
  - Cobweb
```
public Cobweb()
```
    default constructor
- Method Detail
  - globalInfo
```
public java.lang.String globalInfo()
```
    Returns a string describing this clusterer
    
    Returns:
    
    a description of the evaluator 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
  - getCapabilities
```
public Capabilities getCapabilities()
```
    Returns default capabilities of the clusterer.
    
    Specified by:
    
    getCapabilities in interface Clusterer
    
    Specified by:
    
    getCapabilities in interface CapabilitiesHandler
    
    Overrides:
    
    getCapabilities in class AbstractClusterer
    
    Returns:
    
    the capabilities of this clusterer
    
    See Also:
    
    Capabilities
  - buildClusterer
```
public void buildClusterer(Instances data)
                    throws java.lang.Exception
```
    Builds the clusterer.
    
    Specified by:
    
    buildClusterer in interface Clusterer
    
    Specified by:
    
    buildClusterer in class AbstractClusterer
    
    Parameters:
    
    data - the training instances.
    
    Throws:
    
    java.lang.Exception - if something goes wrong.
  - updateFinished
```
public void updateFinished()
```
    Singals the end of the updating.
    
    Specified by:
    
    updateFinished in interface UpdateableClusterer
  - clusterInstance
```
public int clusterInstance(Instance instance)
                    throws java.lang.Exception
```
    Classifies a given instance.
    
    Specified by:
    
    clusterInstance in interface Clusterer
    
    Overrides:
    
    clusterInstance in class AbstractClusterer
    
    Parameters:
    
    instance - the instance to be assigned to a cluster
    
    Returns:
    
    the number of the assigned cluster as an interger if the class is enumerated, otherwise the predicted value
    
    Throws:
    
    java.lang.Exception - if instance could not be classified successfully
  - determineNumberOfClusters
```
protected void determineNumberOfClusters()
```
    determines the number of clusters if necessary
    
    See Also:
    
    m_numberOfClusters, m_numberOfClustersDetermined
  - numberOfClusters
```
public int numberOfClusters()
```
    Returns the number of clusters.
    
    Specified by:
    
    numberOfClusters in interface Clusterer
    
    Specified by:
    
    numberOfClusters in class AbstractClusterer
    
    Returns:
    
    the number of clusters
  - getTreeRoot
```
public Cobweb.CNode getTreeRoot()
```
    Get the root of the tree.
    
    Returns:
    
    the root of the tree.
  - updateClusterer
```
public void updateClusterer(Instance newInstance)
                     throws java.lang.Exception
```
    Adds an instance to the clusterer.
    
    Specified by:
    
    updateClusterer in interface UpdateableClusterer
    
    Parameters:
    
    newInstance - the instance to be added
    
    Throws:
    
    java.lang.Exception - if something goes wrong
  - addInstance
```
@Deprecated
public void addInstance(Instance newInstance)
                              throws java.lang.Exception
```
    Deprecated. updateClusterer(Instance) should be used instead
    
    Adds an instance to the Cobweb tree.
    
    Parameters:
    
    newInstance - the instance to be added
    
    Throws:
    
    java.lang.Exception - if something goes wrong
    
    See Also:
    
    updateClusterer(Instance)
  - listOptions
```
public java.util.Enumeration<Option> listOptions()
```
    Returns an enumeration describing the available options.
    
    Specified by:
    
    listOptions in interface OptionHandler
    
    Overrides:
    
    listOptions in class RandomizableClusterer
    
    Returns:
    
    an enumeration of all the available options.
  - setOptions
```
public void setOptions(java.lang.String[] options)
                throws java.lang.Exception
```
    Parses a given list of options.
    Valid options are:
```
 -A <acuity>
  Acuity.
  (default=1.0)
```
```
 -C <cutoff>
  Cutoff.
  (default=0.002)
```
```
 -save-data
  Save instance data.
```
```
 -S <num>
  Random number seed.
  (default 42)
```
```
 -output-debug-info
  If set, clusterer is run in debug mode and
  may output additional info to the console
```
```
 -do-not-check-capabilities
  If set, clusterer capabilities are not checked before clusterer is built
  (use with caution).
```
    Specified by:
    
    setOptions in interface OptionHandler
    
    Overrides:
    
    setOptions in class RandomizableClusterer
    
    Parameters:
    
    options - the list of options as an array of strings
    
    Throws:
    
    java.lang.Exception - if an option is not supported
  - acuityTipText
```
public java.lang.String acuityTipText()
```
    Returns the tip text for this property
    
    Returns:
    
    tip text for this property suitable for displaying in the explorer/experimenter gui
  - setAcuity
```
public void setAcuity(double a)
```
    set the acuity.
    
    Parameters:
    
    a - the acuity value
  - getAcuity
```
public double getAcuity()
```
    get the acuity value
    
    Returns:
    
    the acuity
  - cutoffTipText
```
public java.lang.String cutoffTipText()
```
    Returns the tip text for this property
    
    Returns:
    
    tip text for this property suitable for displaying in the explorer/experimenter gui
  - setCutoff
```
public void setCutoff(double c)
```
    set the cutoff
    
    Parameters:
    
    c - the cutof
  - getCutoff
```
public double getCutoff()
```
    get the cutoff
    
    Returns:
    
    the cutoff
  - saveInstanceDataTipText
```
public java.lang.String saveInstanceDataTipText()
```
    Returns the tip text for this property
    
    Returns:
    
    tip text for this property suitable for displaying in the explorer/experimenter gui
  - getSaveInstanceData
```
public boolean getSaveInstanceData()
```
    Get the value of saveInstances.
    
    Returns:
    
    Value of saveInstances.
  - setSaveInstanceData
```
public void setSaveInstanceData(boolean newsaveInstances)
```
    Set the value of saveInstances.
    
    Parameters:
    
    newsaveInstances - Value to assign to saveInstances.
  - getOptions
```
public java.lang.String[] getOptions()
```
    Gets the current settings of Cobweb.
    
    Specified by:
    
    getOptions in interface OptionHandler
    
    Overrides:
    
    getOptions in class RandomizableClusterer
    
    Returns:
    
    an array of strings suitable for passing to setOptions()
  - toString
```
public java.lang.String toString()
```
    Returns a description of the clusterer as a string.
    
    Overrides:
    
    toString in class java.lang.Object
    
    Returns:
    
    a string describing the clusterer.
  - graphType
```
public int graphType()
```
    Returns the type of graphs this class represents
    
    Specified by:
    
    graphType in interface Drawable
    
    Returns:
    
    Drawable.TREE
  - graph
```
public java.lang.String graph()
                       throws java.lang.Exception
```
    Generates the graph string of the Cobweb tree
    
    Specified by:
    
    graph in interface Drawable
    
    Returns:
    
    a String value
    
    Throws:
    
    java.lang.Exception - if an error occurs
  - getRevision
```
public java.lang.String getRevision()
```
    Returns the revision string.
    
    Specified by:
    
    getRevision in interface RevisionHandler
    
    Overrides:
    
    getRevision in class AbstractClusterer
    
    Returns:
    
    the revision
  - seedTipText
```
public java.lang.String seedTipText()
```
    Returns the tip text for this property
    
    Overrides:
    
    seedTipText in class RandomizableClusterer
    
    Returns:
    
    tip text for this property suitable for displaying in the explorer/experimenter gui
  - main
```
public static void main(java.lang.String[] argv)
```
    Main method.
    
    Parameters:
    
    argv - the commandline options

Class Cobweb

Nested Class Summary

Field Summary

Fields inherited from class weka.clusterers.RandomizableClusterer

Fields inherited from class weka.clusterers.AbstractClusterer

Fields inherited from interface weka.core.Drawable

Constructor Summary

Method Summary

Methods inherited from class weka.clusterers.RandomizableClusterer

Methods inherited from class weka.clusterers.AbstractClusterer

Methods inherited from class java.lang.Object

Field Detail

m_normal

m_acuity

m_cutoff

m_cobwebTree

m_numberOfClusters

m_numberOfClustersDetermined

m_numberSplits

m_numberMerges

m_saveInstances

Constructor Detail

Cobweb

Method Detail

globalInfo

getTechnicalInformation

getCapabilities

buildClusterer

updateFinished

clusterInstance

determineNumberOfClusters

numberOfClusters

getTreeRoot

updateClusterer

addInstance

listOptions

setOptions

acuityTipText

setAcuity

getAcuity

cutoffTipText

setCutoff

getCutoff

saveInstanceDataTipText

getSaveInstanceData

setSaveInstanceData

getOptions

toString

graphType

graph

getRevision

seedTipText

main