Package org.biojava.stats.svm.tools
Class SuffixTreeKernel
java.lang.Object
org.biojava.stats.svm.tools.SuffixTreeKernel
- All Implemented Interfaces:
Serializable
,SVMKernel
Computes the dot-product of two suffix-trees as the sum of the products
of the counts of all nodes they have in common.
This implementation allows you to scale the sub-space for each word length independently.
- Author:
- Matthew Pocock
- See Also:
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Nested Class Summary
Nested ClassesModifier and TypeClassDescriptionstatic interface
Encapsulates the scale factor to apply at a given depth.static class
Scale using a multiple of two DepthScalers.static class
Scales by 4^depth - equivalent to dividing by a probablistic flatt prior null modelstatic class
Scale using a BitSet to allow/disallow depths.static class
Scale all depths by 1.0 -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptiondouble
Calculate the dot product between the SuffixTrees a and b.Retrieve the current DepthScaler.void
setDepthScaler
(SuffixTreeKernel.DepthScaler depthScaler) Change the current DepthScaler to depthScaler.toString()
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Constructor Details
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SuffixTreeKernel
public SuffixTreeKernel()
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Method Details
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getDepthScaler
Retrieve the current DepthScaler.- Returns:
- the current DepthScaler
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setDepthScaler
Change the current DepthScaler to depthScaler.- Parameters:
depthScaler
- the new DepthScaler to use
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evaluate
Calculate the dot product between the SuffixTrees a and b.This is the sum of the dot products of each subspace for a given word length. Each subspace is scaled using the DepthScaler returned by getDepthScaler.
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toString
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