org.biojava.stats.svm

Class DiagonalCachingKernel

java.lang.Object

org.biojava.stats.svm.NestedKernel

org.biojava.stats.svm.DiagonalCachingKernel

All Implemented Interfaces:

Serializable, SVMKernel

public class DiagonalCachingKernel
extends NestedKernel

Caches the leading diagonal of a kernel matrix.

Several kernels need to repeatedly access k(x,x) to do things like normalization, or to calculate distances. This kernel wraps k so that these leading diagonal elements do not need to be calculated each time.

This kernel is thread-safe. However, care must be taken when setting the nested kernel that no other thread is retrieving values at the same time. This would cause a race condition in which the newly flushed cache may contain a value from the previous kernel.

Author:

Matthew Pocock, Thomas Down

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
DiagonalCachingKernel() Create a new CachingKernel.
DiagonalCachingKernel(SVMKernel k) Creates a new DiagonalCachingKernel that nests k.

Method Summary

Methods

Modifier and Type	Method and Description
double	evaluate(Object x, Object y) Returns the kernel product of two Objects.
void	setNestedKernel(SVMKernel k) Set the kernel to nest.
String	toString()

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

getNestedKernel

Methods inherited from class java.lang.Object

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

Constructor Detail

DiagonalCachingKernel

public DiagonalCachingKernel()

Create a new CachingKernel.

DiagonalCachingKernel

public DiagonalCachingKernel(SVMKernel k)

Creates a new DiagonalCachingKernel that nests k.

Method Detail

setNestedKernel

public void setNestedKernel(SVMKernel k)

Set the kernel to nest.

This will flush the cache.

Overrides:

setNestedKernel in class NestedKernel

Parameters:

k - the kernel to nest.

evaluate

public double evaluate(Object x,
              Object y)

Returns the kernel product of two Objects.

This returns getNestedKernel.evaluate(x, y). If x.equals(y) then it will cache the result first time, and do a hash table look up to retrieve the value in subsequent calls.

toString

public String toString()

Overrides:

toString in class Object