Package elki.projection
Class GaussianAffinityMatrixBuilder<O>
- java.lang.Object
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- elki.projection.GaussianAffinityMatrixBuilder<O>
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- Type Parameters:
O
- Vector type
- All Implemented Interfaces:
AffinityMatrixBuilder<O>
- Direct Known Subclasses:
PerplexityAffinityMatrixBuilder
@Reference(authors="G. Hinton, S. Roweis", title="Stochastic Neighbor Embedding", booktitle="Advances in Neural Information Processing Systems 15", url="http://papers.nips.cc/paper/2276-stochastic-neighbor-embedding", bibkey="DBLP:conf/nips/HintonR02") public class GaussianAffinityMatrixBuilder<O> extends java.lang.Object implements AffinityMatrixBuilder<O>
Compute the affinity matrix for SNE and tSNE using a Gaussian distribution with a constant sigma.Reference:
G. Hinton, S. Roweis
Stochastic Neighbor Embedding
Advances in Neural Information Processing Systems 15- Since:
- 0.7.5
- Author:
- Erich Schubert
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
GaussianAffinityMatrixBuilder.Par<O>
Parameterization class.
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Constructor Summary
Constructors Constructor Description GaussianAffinityMatrixBuilder(Distance<? super O> distance, double sigma)
Constructor.
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description protected double[][]
buildDistanceMatrix(ArrayDBIDs ids, DistanceQuery<?> dq)
Build a distance matrix of squared distances.<T extends O>
AffinityMatrixcomputeAffinityMatrix(Relation<T> relation, double initialScale)
Compute the affinity matrix.protected static double
computeH(int i, double[] dist_i, double[] pij_i, double mbeta)
Compute H (observed perplexity) for row i, and the row pij_i.protected static double[][]
computePij(double[][] dist, double sigma, double initialScale)
Compute the pij from the distance matrix.TypeInformation
getInputTypeRestriction()
Supported input data.
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Field Detail
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LOG
private static final Logging LOG
Class logger.
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MIN_PIJ
protected static final double MIN_PIJ
Minimum value for pij entries (even when duplicate)- See Also:
- Constant Field Values
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sigma
protected double sigma
Kernel bandwidth sigma.
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Method Detail
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computeAffinityMatrix
public <T extends O> AffinityMatrix computeAffinityMatrix(Relation<T> relation, double initialScale)
Description copied from interface:AffinityMatrixBuilder
Compute the affinity matrix.- Specified by:
computeAffinityMatrix
in interfaceAffinityMatrixBuilder<O>
- Type Parameters:
T
- Relation type- Parameters:
relation
- Data relationinitialScale
- initial scale- Returns:
- Affinity matrix
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buildDistanceMatrix
protected double[][] buildDistanceMatrix(ArrayDBIDs ids, DistanceQuery<?> dq)
Build a distance matrix of squared distances.- Parameters:
ids
- DBIDsdq
- Distance query- Returns:
- Distance matrix
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computePij
protected static double[][] computePij(double[][] dist, double sigma, double initialScale)
Compute the pij from the distance matrix.- Parameters:
dist
- Distance matrix.sigma
- Kernel bandwidth sigmainitialScale
- Initial scale- Returns:
- Affinity matrix pij
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computeH
protected static double computeH(int i, double[] dist_i, double[] pij_i, double mbeta)
Compute H (observed perplexity) for row i, and the row pij_i.- Parameters:
i
- Current point i (entry i will be ignored)dist_i
- Distance matrix row (input)pij_i
- Row pij[i] (output)mbeta
--1. / (2 * sigma * sigma)
- Returns:
- Observed perplexity
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getInputTypeRestriction
public TypeInformation getInputTypeRestriction()
Supported input data.- Specified by:
getInputTypeRestriction
in interfaceAffinityMatrixBuilder<O>
- Returns:
- Input data type information.
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