edu.ucla.sspace.matrix

Class NearestNeighborAffinityMatrixCreator

java.lang.Object

edu.ucla.sspace.matrix.NearestNeighborAffinityMatrixCreator

All Implemented Interfaces:

AffinityMatrixCreator

public class NearestNeighborAffinityMatrixCreator
extends Object
implements AffinityMatrixCreator

This AffinityMatrixCreator adds an edge added between two data points, i and j, if j is in the k nearest neighbors of i. This relationship is not symmetric.

Author:

David Jurgens, Keith Stevens

Constructor Summary

Constructors

Constructor and Description
NearestNeighborAffinityMatrixCreator()

Method Summary

Methods

Modifier and Type	Method and Description
MatrixFile	calculate(Matrix input) Computes the affinity matrix for the input matrix according to the specified similarity metrics, returning the result as a file on disk.
MatrixFile	calculate(MatrixFile input) Computes the affinity matrix for the input matrix according to the specified similarity metrics, returning the result as a file on disk.
MatrixFile	calculate(MatrixFile input, boolean useColumns) Computes the affinity matrix for the input matrix according to the specified similarity metrics, optionally treating the columns as data points, and returning the result as a file on disk.
void	setFunctions(SimilarityFunction edgeSim, SimilarityFunction kernelSim) Sets the SimilarityFunctions to be used for selecting edges and then weighting edges.
void	setParams(double... params) Sets any numeric parameters, such as thresholds, for this AffinityMatrixCreator.

Methods inherited from class java.lang.Object

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

Constructor Detail

NearestNeighborAffinityMatrixCreator

public NearestNeighborAffinityMatrixCreator()

Method Detail

setParams

public void setParams(double... params)

Description copied from interface: AffinityMatrixCreator

Sets any numeric parameters, such as thresholds, for this AffinityMatrixCreator. Each AffinityMatrixCreator should specify how many parameters it expects and in what order.

Specified by:

setParams in interface AffinityMatrixCreator

setFunctions

public void setFunctions(SimilarityFunction edgeSim,
                SimilarityFunction kernelSim)

Sets the SimilarityFunctions to be used for selecting edges and then weighting edges. edgeSim will be computed over every possible edge. The returned scores will be used to filter out valid edges in the graph. kernelSim will be used to compute the final edge weight between two valid edges in the graph, this is also called a kernel function.

Specified by:

setFunctions in interface AffinityMatrixCreator

Parameters:

edgeSim - The SimilarityFunction used to filter edges. This metric is assumed to be symmetric.

kernelSim - The SimilarityFunction used to weight valid edges. This metric may or may not be symmetric.

calculate

public MatrixFile calculate(Matrix input)

Computes the affinity matrix for the input matrix according to the specified similarity metrics, returning the result as a file on disk. Because the input matrix is provided already in memory, all similarity comparisons are performed in memory, which offers a significant speed-up compared to the off-core overloads of this method that operate on a MatrixFile as input.

Specified by:

calculate in interface AffinityMatrixCreator

Parameters:

input - The Matrix that contains data points that are to be formed into an affinity matrix.

Returns:

the affinity matrix as a file on disk. The result may be read back into memory with MatrixFile.read().

calculate

public MatrixFile calculate(MatrixFile input)

Computes the affinity matrix for the input matrix according to the specified similarity metrics, returning the result as a file on disk. The similarity comparisons are all performed off-core, which ensures that the input matrix does not need to be loaded in memory in its entirety in order to compute the affinity matrix.

Specified by:

calculate in interface AffinityMatrixCreator

Parameters:

input - The MatrixFile that contains data points that are to be formed into an affinity matrix.

Returns:

the affinity matrix as a file on disk. The result may be read back into memory with MatrixFile.read().

calculate

public MatrixFile calculate(MatrixFile input,
                   boolean useColumns)

Computes the affinity matrix for the input matrix according to the specified similarity metrics, optionally treating the columns as data points, and returning the result as a file on disk. The similarity comparisons are all performed off-core, which ensures that the input matrix does not need to be loaded in memory in its entirety in order to compute the affinity matrix.

This method is primiarily intended to support computing the affinity matrix for the SVDLIBC_SPARSE_BINARY format which is stored in column-major order.

Specified by:

calculate in interface AffinityMatrixCreator

Parameters:

input - The MatrixFile that contains data points that are to be formed into an affinity matrix.

useColumns - true if the affinity matrix should be calculated for the columns of the input matrix, not the rows.

Returns:

the affinity matrix as a file on disk. The result may be read back into memory with MatrixFile.read().