NeighbourhoodCA Class Reference

#include <nca.h>

Inheritance diagram for NeighbourhoodCA:

Collaboration diagram for NeighbourhoodCA:

Public Member Functions
void	setLabels (const Matrix1D< unsigned char > &labels)
	Set labels. More...
void	setSpecificParameters (double lambda=0., int K=12)
	Set specific parameters. More...
double	objectiveFunction ()
void	reduceDimensionality ()
	Reduce dimensionality. More...
Public Member Functions inherited from DimRedAlgorithm
	DimRedAlgorithm ()
	Empty constructor. More...
void	setInputData (Matrix2D< double > &X)
	Set input data. More...
void	setOutputDimensionality (size_t outputDim)
	Set output dimensionality. More...
const Matrix2D< double > &	getReducedData ()
	Get reduced data. More...

Public Attributes
double	lambda
	Weight factor for regularization. More...
Matrix1D< unsigned char >	labels
	Labels. More...
int	K
	Number of neighbours. More...
Matrix2D< double >	D2Y
Matrix2D< double >	A
Matrix1D< double >	D2YRowSum
Matrix2D< int >	idx
Public Attributes inherited from DimRedAlgorithm
Matrix2D< double > *	X
	Pointer to input data. More...
size_t	outputDim
	Output dim. More...
Matrix2D< double >	Y
	Output data. More...
DimRedDistance2	distance
	Distance function. More...
FileName	fnMapping
	Save mapping. More...

Detailed Description

Class for making a NCA dimensionality reduction

Definition at line 20 of file nca.h.

Member Function Documentation

objectiveFunction()

double NeighbourhoodCA::objectiveFunction

(

)

Definition at line 40 of file nca.cpp.

{
    // Project X onto the subspace given by A, Y=X*A
    matrixOperation_AB(*X,A,Y);

    // Compute the distance between the nearest neighbours of each observation
    // in this new subspace
    D2Y.resizeNoCopy(MAT_YSIZE(Y),K);
    FOR_ALL_ELEMENTS_IN_MATRIX2D(D2Y)
    {
        double aux=0.;
        int actualj=MAT_ELEM(idx,i,j);
        for (int l=0; l<MAT_XSIZE(Y); ++l)
        {
            double diff=MAT_ELEM(Y,i,l)-MAT_ELEM(Y,actualj,l);
            aux+=diff*diff;
        }
        MAT_ELEM(D2Y,i,j)=exp(-aux);
    }
    D2Y.rowSum(D2YRowSum);

    // Compute F
    double F=0.;
    for (int i=0; i<MAT_YSIZE(Y); ++i)
    {
        double sumClassi=0.;
        int labeli=VEC_ELEM(labels,i);
        for (int j=0; j<K; ++j)
        {
            int actualj=MAT_ELEM(idx,i,j);
            if (VEC_ELEM(labels,actualj)==labeli)
                sumClassi+=MAT_ELEM(D2Y,i,j);
        }
        if (fabs(VEC_ELEM(D2YRowSum,i))>1e-16)
            F+=sumClassi/VEC_ELEM(D2YRowSum,i);
    }

    // Compute regularization
    double sumA2=0.0;
    FOR_ALL_ELEMENTS_IN_MATRIX2D(A)
        sumA2+=MAT_ELEM(A,i,j)*MAT_ELEM(A,i,j);
    sumA2/=MAT_XSIZE(A)*MAT_YSIZE(A);

    return -(F-lambda*sumA2);
}

reduceDimensionality()

void NeighbourhoodCA::reduceDimensionality ( )

virtual

Reduce dimensionality.

Implements DimRedAlgorithm.

Definition at line 95 of file nca.cpp.

{
    Matrix2D<double> D2;
    subtractColumnMeans(*X);
    kNearestNeighbours(*X, K, idx, D2, distance, false);

    size_t d=MAT_XSIZE(*X);
    A.initGaussian(d,outputDim,0,0.01);

    // Optimize A
    Matrix1D<double> pA(MAT_XSIZE(A)*MAT_YSIZE(A)), steps(MAT_XSIZE(A)*MAT_YSIZE(A));
    steps.initConstant(1);
    memcpy(&VEC_ELEM(pA,0),&MAT_ELEM(A,0,0),VEC_XSIZE(pA)*sizeof(double));
    double goal;
    int iter;
    powellOptimizer(pA,1,VEC_XSIZE(pA),&ncaObjectiveFuntion,this,0.001,goal,iter,steps,false);
    memcpy(&MAT_ELEM(A,0,0),&VEC_ELEM(pA,0),VEC_XSIZE(pA)*sizeof(double));

    // Reduction
    matrixOperation_AB(*X,A,Y);
}

setLabels()

void NeighbourhoodCA::setLabels

(

const Matrix1D< unsigned char > &

labels

)

Set labels.

Definition at line 29 of file nca.cpp.

{
    this->labels=labels;
}

setSpecificParameters()

void NeighbourhoodCA::setSpecificParameters	(	double	lambda = 0.,
		int	K = 12
	)

Set specific parameters.

Definition at line 34 of file nca.cpp.

{
    this->lambda=lambda;
    this->K=K;
}

Member Data Documentation

A

Matrix2D<double> NeighbourhoodCA::A

Definition at line 33 of file nca.h.

D2Y

Matrix2D<double> NeighbourhoodCA::D2Y

Definition at line 33 of file nca.h.

D2YRowSum

Matrix1D<double> NeighbourhoodCA::D2YRowSum

Definition at line 34 of file nca.h.

idx

Matrix2D<int> NeighbourhoodCA::idx

Definition at line 37 of file nca.h.

K

int NeighbourhoodCA::K

Number of neighbours.

Definition at line 30 of file nca.h.

labels

Matrix1D<unsigned char> NeighbourhoodCA::labels

Labels.

Definition at line 27 of file nca.h.

lambda

double NeighbourhoodCA::lambda

Weight factor for regularization.

Definition at line 24 of file nca.h.

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The documentation for this class was generated from the following files:

• xmipp/libraries/dimred/nca.h
• xmipp/libraries/dimred/nca.cpp