Uses of Interface
org.biojava.stats.svm.SVMKernel

Packages that use SVMKernel

Package	Description
org.biojava.stats.svm	Support Vector Machine classification and regression.
org.biojava.stats.svm.tools	Tools for use of the SVM package.

Uses of SVMKernel in org.biojava.stats.svm

Classes in org.biojava.stats.svm that implement SVMKernel

Modifier and Type	Class and Description
class	CachingKernel Caches the results of a nested kernel so that k(a, b) need only be calculated once.
class	DiagonalAddKernel Adds a class specific constant to k(x, x).
class	DiagonalCachingKernel Caches the leading diagonal of a kernel matrix.
class	LinearKernel Deprecated. Just use SparseVector.kernel instead...
class	ListSumKernel This kernel computes the sum of the dot products between items of two lists at corresponding indexes.
class	NestedKernel Encapsulates a kernel that wraps another kernel up.
class	NormalizingKernel Performs a normalization on the results of a nested kernel.
class	PolynomialKernel This kernel computes all possible products of order features in feature space.
class	RadialBaseKernel This kernel computes the radial base kernel that corresponds to a gausian distribution.
class	SigmoidKernel This kernel implements a three layer neural net.
static class	SparseVector.NormalizingKernel A version of the standard dot-product kernel that scales each column independently.

Fields in org.biojava.stats.svm declared as SVMKernel

Modifier and Type	Field and Description
static SVMKernel	SparseVector.kernel

Methods in org.biojava.stats.svm that return SVMKernel

Modifier and Type	Method and Description
SVMKernel	SVMRegressionModel.getKernel()
SVMKernel	SVMClassifierModel.getKernel()
SVMKernel	SimpleSVMClassifierModel.getKernel()
SVMKernel	NestedKernel.getNestedKernel() Retrieve the currently nested SVMKernel.
SVMKernel	SigmoidKernel.getWrappedKernel()

Methods in org.biojava.stats.svm with parameters of type SVMKernel

Modifier and Type	Method and Description
void	SVMRegressionModel.setKernel(SVMKernel k)
void	NestedKernel.setNestedKernel(SVMKernel k) Set the SVMKernel to nest to k.
void	DiagonalCachingKernel.setNestedKernel(SVMKernel k) Set the kernel to nest.
void	CachingKernel.setNestedKernel(SVMKernel k)
void	SigmoidKernel.setWrappedKernel(SVMKernel kernel)
SVMClassifierModel	SMOTrainer.trainModel(SVMTarget target, SVMKernel kernel, TrainingListener l)

Constructors in org.biojava.stats.svm with parameters of type SVMKernel

Constructor and Description
CachingKernel(SVMKernel k)
DiagonalCachingKernel(SVMKernel k) Creates a new DiagonalCachingKernel that nests k.
NestedKernel(SVMKernel k) Create a new NestedKernel that wraps k.
NormalizingKernel(SVMKernel k)
PolynomialKernel(SVMKernel nested, double order, double a, double c)
RadialBaseKernel(SVMKernel nested, double width)
SimpleSVMClassifierModel(SVMKernel kernel)
SimpleSVMClassifierModel(SVMKernel kernel, Collection items)
SimpleSVMClassifierModel(SVMKernel kernel, SVMTarget target)

Uses of SVMKernel in org.biojava.stats.svm.tools

Classes in org.biojava.stats.svm.tools that implement SVMKernel

Modifier and Type	Class and Description
class	SuffixTreeKernel Computes the dot-product of two suffix-trees as the sum of the products of the counts of all nodes they have in common.

Fields in org.biojava.stats.svm.tools declared as SVMKernel

Modifier and Type	Field and Description
static SVMKernel	ClassifierExample.PointClassifier.polyKernel
static SVMKernel	ClassifierExample.PointClassifier.rbfKernel

Methods in org.biojava.stats.svm.tools that return SVMKernel

Modifier and Type	Method and Description
SVMKernel	ClassifierExample.PointClassifier.getKernel() Retrieve the currently used kernel

Methods in org.biojava.stats.svm.tools with parameters of type SVMKernel

Modifier and Type	Method and Description
void	ClassifierExample.PointClassifier.setKernel(SVMKernel kernel) Set the kernel used for classification.