ambit2.similarity.knn

Class NearestNeighborsSimilarity<ID,Features>

java.lang.Object

ambit2.model.AbstractModel<ID,Features,ResultType>

ambit2.similarity.AbstractSimilarityModel<ID,Features,Double>

ambit2.similarity.knn.NearestNeighborsSimilarity<ID,Features>

All Implemented Interfaces:

IModelDefinition<ID,Features,Double>

Direct Known Subclasses:

NNAtomEnvironmentSimilarity, NNFingerprintSimilarity

public abstract class NearestNeighborsSimilarity<ID,Features>
extends AbstractSimilarityModel<ID,Features,Double>

Calculates average distance to kNN nearest neighbors, as defined by IDistanceFunction.

Author:

Nina Jeliazkova nina@acad.bg Modified Feb 4, 2007

Field Summary

Fields

Modifier and Type	Field and Description
protected IAttributeSelection<Features>	attributeSelection
protected int	kNN
protected NearestNeighborsSearch<Features>	nearestNeighborsSearch

Fields inherited from class ambit2.similarity.AbstractSimilarityModel

result

Fields inherited from class ambit2.model.AbstractModel

built, logger, p_model, p_stats, parameters, ps, stats

Constructor Summary

Constructors

Constructor and Description
NearestNeighborsSimilarity(IDistanceFunction<Features> distanceFunction, int knn)

Method Summary

Modifier and Type	Method and Description
void	buildInitialize()
protected double	calculateAverageDistance(Features query, List<DistanceComparable<Features>> neighbors) Weighted average Sum((1/distance)*property).
protected Object	classifyQuery(Features query, List<DistanceComparable<Features>> neighbors)
void	close()
int	getKNN()
NearestNeighborsSearch<Features>	getNearestNeighborsSearch()
double	getPairwise(Features features1, Features features2)
Object	getParameter(Object parameter)
protected abstract Features	getSelectedAttributes(Features attributes)
Double	learn(ID id, Features features, Double observed, Double predicted)
Double	predict(ID id, Features features, Double observed, Double predicted, IModelStatistics<Double> stats)
void	setKNN(int knn)
void	setNearestNeighborsSearch(NearestNeighborsSearch<Features> nnSearch)
void	setParameter(Object parameter, Object value)
String	toString()
protected Features	transformAttributes(Features attributes)

Methods inherited from class ambit2.similarity.AbstractSimilarityModel

getPairwise, getResult, learn, setResult

Methods inherited from class ambit2.model.AbstractModel

getAttributeSelection, getStats, isBuilt, predict, setAttributeSelection, setStats

Methods inherited from class java.lang.Object

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

Field Detail

nearestNeighborsSearch

protected NearestNeighborsSearch<Features> nearestNeighborsSearch

attributeSelection

protected IAttributeSelection<Features> attributeSelection

kNN

protected int kNN

Constructor Detail

NearestNeighborsSimilarity

public NearestNeighborsSimilarity(IDistanceFunction<Features> distanceFunction,
                                  int knn)

Method Detail

buildInitialize

public void buildInitialize()
                     throws net.idea.modbcum.i.exceptions.AmbitException

Overrides:

buildInitialize in class AbstractSimilarityModel<ID,Features,Double>

Throws:

net.idea.modbcum.i.exceptions.AmbitException

learn

public Double learn(ID id,
                    Features features,
                    Double observed,
                    Double predicted)
             throws net.idea.modbcum.i.exceptions.AmbitException,
                    UnsupportedOperationException

Throws:

net.idea.modbcum.i.exceptions.AmbitException

UnsupportedOperationException

getSelectedAttributes

protected abstract Features getSelectedAttributes(Features attributes)

transformAttributes

protected Features transformAttributes(Features attributes)

classifyQuery

protected Object classifyQuery(Features query,
                               List<DistanceComparable<Features>> neighbors)
                        throws Exception

Throws:

Exception

calculateAverageDistance

protected double calculateAverageDistance(Features query,
                                          List<DistanceComparable<Features>> neighbors)
                                   throws Exception

Weighted average Sum((1/distance)*property).

Parameters:

query -

neighbors -

Returns:

the property

Throws:

Exception

predict

public Double predict(ID id,
                      Features features,
                      Double observed,
                      Double predicted,
                      IModelStatistics<Double> stats)
               throws net.idea.modbcum.i.exceptions.AmbitException

Throws:

net.idea.modbcum.i.exceptions.AmbitException

getPairwise

public double getPairwise(Features features1,
                          Features features2)
                   throws net.idea.modbcum.i.exceptions.AmbitException

Specified by:

getPairwise in class AbstractSimilarityModel<ID,Features,Double>

Throws:

net.idea.modbcum.i.exceptions.AmbitException

close

public void close()

toString

public String toString()

Overrides:

toString in class Object

setParameter

public void setParameter(Object parameter,
                         Object value)

Specified by:

setParameter in interface IModelDefinition<ID,Features,Double>

Overrides:

setParameter in class AbstractModel<ID,Features,Double>

getParameter

public Object getParameter(Object parameter)

Specified by:

getParameter in interface IModelDefinition<ID,Features,Double>

Overrides:

getParameter in class AbstractModel<ID,Features,Double>

getNearestNeighborsSearch

public NearestNeighborsSearch<Features> getNearestNeighborsSearch()

setNearestNeighborsSearch

public void setNearestNeighborsSearch(NearestNeighborsSearch<Features> nnSearch)

getKNN

public int getKNN()

setKNN

public void setKNN(int knn)