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java.lang.Objectde.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.Measure
de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.InhomogeneousMarkov
public class InhomogeneousMarkov
Class for a network structure of a BayesianNetworkScoringFunction
that is an inhomogeneous Markov model. The order of the Markov model can be defined by the user. A Markov model
of order 0
is also know as position weight matrix (PWM), a Markov model of order 1
is also known as weight array matrix (WAM) model.
Constructor Summary | |
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InhomogeneousMarkov(int order)
Creates the structure of an inhomogeneous Markov model of order order . |
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InhomogeneousMarkov(StringBuffer buf)
Re-creates an InhomogeneousMarkov structure from its XML-representation as returned by toXML() . |
Method Summary | |
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InhomogeneousMarkov |
clone()
|
String |
getInstanceName()
Returns the name of the Measure and possibly some additional information about the current instance. |
int |
getOrder()
Returns the order of the Markov model as defined in the constructor |
int[][] |
getParents(Sample fg,
Sample bg,
double[] weightsFg,
double[] weightsBg,
int length)
Returns the optimal parents for the given data and weights. |
boolean |
isShiftable()
Indicates if Measure supports shifts. |
StringBuffer |
toXML()
This method returns an XML-representation of an instance of the implementing class. |
Methods inherited from class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.Measure |
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fillTensor, fillTensor, getCMI, getCMI, getEAR, getEAR, getMI, getMI, getStatistics, getStatisticsOrderTwo, sum, toParents, union |
Methods inherited from class java.lang.Object |
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equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public InhomogeneousMarkov(int order)
order
.
order
- the orderpublic InhomogeneousMarkov(StringBuffer buf) throws NonParsableException
InhomogeneousMarkov
structure from its XML-representation as returned by toXML()
.
buf
- the XML-representation
NonParsableException
- is thrown if the XML-code could not be parsedMethod Detail |
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public int getOrder()
public InhomogeneousMarkov clone() throws CloneNotSupportedException
clone
in class Measure
CloneNotSupportedException
public String getInstanceName()
Measure
Measure
and possibly some additional information about the current instance.
getInstanceName
in class Measure
public int[][] getParents(Sample fg, Sample bg, double[] weightsFg, double[] weightsBg, int length) throws Exception
Measure
p
at each position i
is build as follows:
p[i][p.length - 1]
contains the index i
itselfp[i][p.length - 2]
contains the "most important" parentp[i][0]
contains the "least important parent
getParents
in class Measure
fg
- the data of the current (foreground) classbg
- the data of the negative (background) classweightsFg
- the weights for the sequences of fg
weightsBg
- the weights for the sequences of bg
length
- the length of the model, must be equal to the length of the sequences
Exception
- thrown if the lengths do not match or other problems concerning the data occurpublic boolean isShiftable()
Measure
Measure
supports shifts.
isShiftable
in class Measure
Measure
supports shiftspublic StringBuffer toXML()
Storable
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