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

Packages that use SVMKernel
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
 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
static SVMKernel SparseVector.kernel
           
 

Methods in org.biojava.stats.svm that return SVMKernel
 SVMKernel SimpleSVMClassifierModel.getKernel()
           
 SVMKernel SVMClassifierModel.getKernel()
           
 SVMKernel SVMRegressionModel.getKernel()
           
 SVMKernel NestedKernel.getNestedKernel()
          Retrieve the currently nested SVMKernel.
 SVMKernel SigmoidKernel.getWrappedKernel()
           
 

Methods in org.biojava.stats.svm with parameters of type SVMKernel
 void SVMRegressionModel.setKernel(SVMKernel k)
           
 void CachingKernel.setNestedKernel(SVMKernel k)
           
 void DiagonalCachingKernel.setNestedKernel(SVMKernel k)
           Set the kernel to nest.
 void NestedKernel.setNestedKernel(SVMKernel k)
          Set the SVMKernel to nest to 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
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
 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
static SVMKernel ClassifierExample.PointClassifier.polyKernel
           
static SVMKernel ClassifierExample.PointClassifier.rbfKernel
           
 

Methods in org.biojava.stats.svm.tools that return SVMKernel
 SVMKernel ClassifierExample.PointClassifier.getKernel()
          Retrieve the currently used kernel
 

Methods in org.biojava.stats.svm.tools with parameters of type SVMKernel
 void ClassifierExample.PointClassifier.setKernel(SVMKernel kernel)
          Set the kernel used for classification.