Detailed Description

Manifold Sculpting. A non-linear dimensionality reduction algorithm. (See Gashler, Michael S. and Ventura, Dan and Martinez, Tony. Iterative non-linear dimensionality reduction with manifold sculpting. In Advances in Neural Information Processing Systems 20, pages 513–520, MIT Press, Cambridge, MA, 2008.)

#include <GManifold.h>

Inheritance diagram for GClasses::GManifoldSculpting:

Public Member Functions
	GManifoldSculpting (size_t nNeighbors, size_t targetDims, GRand *pRand)

virtual	~GManifoldSculpting ()

double	aveNeighborDist ()
	Returns the average distance between neighbors. More...

void	beginTransform (const GMatrix *pRealSpaceData)
	Call this before calling SquishPass. pRealSpaceData should be a dataset of all real values. More...

void	clampPoint (size_t n)
	Partially supervise the specified point. More...

size_t	countShortcuts (size_t nThreshold)
	Counts the number of times that a point has a neighbor with an index that is >= nThreshold away from this points index. (If the manifold is sampled in order such that points are expected to find neighbors with indexes close to their own, this can serve to identify when parts of the manifold are too close to other parts for so many neighbors to be used.) More...

GMatrix &	data ()

double	learningRate ()
	Returns the current learning rate. More...

virtual GMatrix *	reduce (const GMatrix &in)
	Perform NLDR. More...

const GRelation &	relationAfter ()

void	setMinAndMaxNeighborDist (double min, double max)
	Neighbors that are closer than min or farther than max will be ignored. The default is [0, 1e20]. It is common to make nNeighbors big and max small so that the hyper-sphere will define the neighborhood. More...

void	setNeighborFinder (GNeighborFinderGeneralizing *pNF)
	Specifies to use the neighborhoods determined by the specified neighbor-finder instead of the nearest Euclidean-distance neighbors. If this method is called, pNF should have the same number of neighbors and the same dataset as is passed into this class. More...

void	setPreprocessedData (GMatrix *pData)
	This will takes ownership of pData. (It will modify pData too.) Specifies reduced dimensionality data created by another algorithm, which should be refined using Manifold Sculpting. More...

void	setSquishingRate (double d)
	Set the rate of squishing. (.99 is a good value) More...

double	squishPass (size_t nSeedDataPoint)
	Perform one iteration of squishing. Returns a heuristical error value. More...

Public Member Functions inherited from GClasses::GTransform
	GTransform ()

	GTransform (const GDomNode *pNode)

virtual	~GTransform ()

Protected Member Functions
size_t	adjustDataPoint (size_t nPoint, double *pError)

double	averageNeighborDistance (size_t nDims)

void	calculateMetadata (const GMatrix *pData)

double	computeError (size_t nPoint)

void	moveMeanToOrigin ()

struct GManifoldSculptingNeighbor *	record (size_t n)

struct GManifoldSculptingStuff *	stuff (size_t n)

virtual double	supervisedError (size_t nPoint)
	You can overload this to add some intelligent supervision to the heuristic. More...

double	vectorCorrelation (const double pdA, const double pdV, const double *pdB)

double	vectorCorrelation2 (double squaredScale, size_t a, size_t vertex, struct GManifoldSculptingNeighbor *pNeighborRec)

Protected Member Functions inherited from GClasses::GTransform
virtual GDomNode *	baseDomNode (GDom pDoc, const char szClassName) const
	Child classes should use this in their implementation of serialize. More...

Protected Attributes
double	m_dAveNeighborDist

double	m_dLearningRate

double	m_dSquishingRate

double	m_maxNeighborDist

double	m_minNeighborDist

size_t	m_nCurrentDimension

size_t	m_nDimensions

size_t	m_nNeighbors

size_t	m_nPass

size_t	m_nRecordSize

size_t	m_nStuffIndex

size_t	m_nTargetDims

GMatrix *	m_pData

unsigned char *	m_pMetaData

GNeighborFinderGeneralizing *	m_pNF

GRand *	m_pRand

GRelation *	m_pRelationAfter

std::deque< size_t >	m_q

double	m_scale

Constructor & Destructor Documentation

GClasses::GManifoldSculpting::GManifoldSculpting	(	size_t	nNeighbors,
		size_t	targetDims,
		GRand *	pRand
	)

virtual GClasses::GManifoldSculpting::~GManifoldSculpting ( )

virtual

Member Function Documentation

size_t GClasses::GManifoldSculpting::adjustDataPoint	(	size_t	nPoint,
		double *	pError
	)

protected

double GClasses::GManifoldSculpting::aveNeighborDist ( )

inline

Returns the average distance between neighbors.

double GClasses::GManifoldSculpting::averageNeighborDistance ( size_t nDims )

protected

void GClasses::GManifoldSculpting::beginTransform ( const GMatrix * pRealSpaceData )

Call this before calling SquishPass. pRealSpaceData should be a dataset of all real values.

void GClasses::GManifoldSculpting::calculateMetadata ( const GMatrix * pData )

protected

void GClasses::GManifoldSculpting::clampPoint ( size_t n )

Partially supervise the specified point.

double GClasses::GManifoldSculpting::computeError ( size_t nPoint )

protected

size_t GClasses::GManifoldSculpting::countShortcuts ( size_t nThreshold )

Counts the number of times that a point has a neighbor with an index that is >= nThreshold away from this points index. (If the manifold is sampled in order such that points are expected to find neighbors with indexes close to their own, this can serve to identify when parts of the manifold are too close to other parts for so many neighbors to be used.)

GMatrix& GClasses::GManifoldSculpting::data ( )

inline

double GClasses::GManifoldSculpting::learningRate ( )

inline

Returns the current learning rate.

void GClasses::GManifoldSculpting::moveMeanToOrigin ( )

protected

struct GManifoldSculptingNeighbor* GClasses::GManifoldSculpting::record ( size_t n )

inlineprotected

virtual GMatrix* GClasses::GManifoldSculpting::reduce ( const GMatrix & in )

virtual

Perform NLDR.

Implements GClasses::GTransform.

const GRelation& GClasses::GManifoldSculpting::relationAfter ( )

inline

void GClasses::GManifoldSculpting::setMinAndMaxNeighborDist	(	double	min,
		double	max
	)

inline

Neighbors that are closer than min or farther than max will be ignored. The default is [0, 1e20]. It is common to make nNeighbors big and max small so that the hyper-sphere will define the neighborhood.

void GClasses::GManifoldSculpting::setNeighborFinder ( GNeighborFinderGeneralizing * pNF )

inline

Specifies to use the neighborhoods determined by the specified neighbor-finder instead of the nearest Euclidean-distance neighbors. If this method is called, pNF should have the same number of neighbors and the same dataset as is passed into this class.

void GClasses::GManifoldSculpting::setPreprocessedData ( GMatrix * pData )

This will takes ownership of pData. (It will modify pData too.) Specifies reduced dimensionality data created by another algorithm, which should be refined using Manifold Sculpting.

void GClasses::GManifoldSculpting::setSquishingRate ( double d )

inline

Set the rate of squishing. (.99 is a good value)

double GClasses::GManifoldSculpting::squishPass ( size_t nSeedDataPoint )

Perform one iteration of squishing. Returns a heuristical error value.

struct GManifoldSculptingStuff* GClasses::GManifoldSculpting::stuff ( size_t n )

inlineprotected

virtual double GClasses::GManifoldSculpting::supervisedError ( size_t nPoint )

inlineprotectedvirtual

You can overload this to add some intelligent supervision to the heuristic.

double GClasses::GManifoldSculpting::vectorCorrelation	(	const double *	pdA,
		const double *	pdV,
		const double *	pdB
	)

protected

double GClasses::GManifoldSculpting::vectorCorrelation2	(	double	squaredScale,
		size_t	a,
		size_t	vertex,
		struct GManifoldSculptingNeighbor *	pNeighborRec
	)

protected

Member Data Documentation

double GClasses::GManifoldSculpting::m_dAveNeighborDist

protected

double GClasses::GManifoldSculpting::m_dLearningRate

protected

double GClasses::GManifoldSculpting::m_dSquishingRate

protected

double GClasses::GManifoldSculpting::m_maxNeighborDist

protected

double GClasses::GManifoldSculpting::m_minNeighborDist

protected

size_t GClasses::GManifoldSculpting::m_nCurrentDimension

protected

size_t GClasses::GManifoldSculpting::m_nDimensions

protected

size_t GClasses::GManifoldSculpting::m_nNeighbors

protected

size_t GClasses::GManifoldSculpting::m_nPass

protected

size_t GClasses::GManifoldSculpting::m_nRecordSize

protected

size_t GClasses::GManifoldSculpting::m_nStuffIndex

protected

size_t GClasses::GManifoldSculpting::m_nTargetDims

protected

GMatrix* GClasses::GManifoldSculpting::m_pData

protected

unsigned char* GClasses::GManifoldSculpting::m_pMetaData

protected

GNeighborFinderGeneralizing* GClasses::GManifoldSculpting::m_pNF

protected

GRand* GClasses::GManifoldSculpting::m_pRand

protected

GRelation* GClasses::GManifoldSculpting::m_pRelationAfter

protected

std::deque<size_t> GClasses::GManifoldSculpting::m_q

protected

double GClasses::GManifoldSculpting::m_scale

protected

Detailed Description

Public Member Functions

Protected Member Functions

Protected Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation