org.biojava.stats.svm

Class NormalizingKernel

java.lang.Object

org.biojava.stats.svm.NestedKernel

org.biojava.stats.svm.NormalizingKernel

All Implemented Interfaces:

Serializable, SVMKernel

public class NormalizingKernel
extends NestedKernel

Performs a normalization on the results of a nested kernel.

This is equivalent to making the locations in feature space of the nested kernel unit vectors lying on a unit sphere. The dot product in feature space then becomes just cos theta rather than ||a|| * ||b|| * cos theta as both lengths are 1. The length of a in the feature space of kernel k is sqrt( k(a, a) ), so that the normalizing kernel ends up calculating k(a, b) / sqrt( k(a, a) * k(b, b) ).

As the values of k(x, x) are required repeatedly, it may be worth making the nested kernel a DiagonalCachingKernel.

Author:

Thomas Down, Matthew Pocock

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
NormalizingKernel()
NormalizingKernel(SVMKernel k)

Method Summary

Methods

Modifier and Type	Method and Description
double	evaluate(Object a, Object b) Return the dot product of two vectors in an arbitrary feature space.
String	toString()

Methods inherited from class org.biojava.stats.svm.NestedKernel

getNestedKernel, setNestedKernel

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

NormalizingKernel

public NormalizingKernel()

NormalizingKernel

public NormalizingKernel(SVMKernel k)

Method Detail

evaluate

public double evaluate(Object a,
              Object b)

Description copied from interface: SVMKernel

Return the dot product of two vectors in an arbitrary feature space. In this implementation, the `vectors' can actually be arbitrary objects.

toString

public String toString()

Overrides:

toString in class Object