CIsomap Class Reference

Detailed Description

the class Isomap used to preprocess data using K-Isomap algorithm as described in

Silva, V. D., & Tenenbaum, J. B. (2003). Global versus local methods in nonlinear dimensionality reduction. Advances in Neural Information Processing Systems 15, 15(Figure 2), 721-728. MIT Press. Retrieved from http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.9.3407&rep=rep1&type=pdf

Shortest paths are being computed with Dijkstra's algorithm with heap in parallel. Due to sparsity of the kNN graph Fibonacci Heap with amortized O(1) Extract-Min operation time complexity is used.

It is possible to apply preprocessor to specified distance using apply_to_distance.

Definition at line 45 of file Isomap.h.

Inheritance diagram for CIsomap:

Public Member Functions
	CIsomap ()
virtual	~CIsomap ()
const char *	get_name () const
void	set_k (int32_t k)
int32_t	get_k () const
Public Member Functions inherited from CMultidimensionalScaling
	CMultidimensionalScaling ()
virtual	~CMultidimensionalScaling ()
virtual CSimpleFeatures < float64_t > *	embed_distance (CDistance *distance)
virtual CFeatures *	apply (CFeatures *features)
SGVector< float64_t >	get_eigenvalues () const
void	set_landmark_number (int32_t num)
int32_t	get_landmark_number () const
void	set_landmark (bool landmark)
bool	get_landmark () const
Public Member Functions inherited from CEmbeddingConverter
	CEmbeddingConverter ()
virtual	~CEmbeddingConverter ()
virtual CSimpleFeatures < float64_t > *	embed (CFeatures *features)
void	set_target_dim (int32_t dim)
int32_t	get_target_dim () const
void	set_distance (CDistance *distance)
CDistance *	get_distance () const
void	set_kernel (CKernel *kernel)
CKernel *	get_kernel () const
Public Member Functions inherited from CConverter
	CConverter ()
virtual	~CConverter ()
Public Member Functions inherited from CSGObject
	CSGObject ()
	CSGObject (const CSGObject &orig)
virtual	~CSGObject ()
virtual bool	is_generic (EPrimitiveType *generic) const
template<class T >
void	set_generic ()
void	unset_generic ()
virtual void	print_serializable (const char *prefix="")
virtual bool	save_serializable (CSerializableFile *file, const char *prefix="")
virtual bool	load_serializable (CSerializableFile *file, const char *prefix="")
void	set_global_io (SGIO *io)
SGIO *	get_global_io ()
void	set_global_parallel (Parallel *parallel)
Parallel *	get_global_parallel ()
void	set_global_version (Version *version)
Version *	get_global_version ()
SGVector< char * >	get_modelsel_names ()
char *	get_modsel_param_descr (const char *param_name)
index_t	get_modsel_param_index (const char *param_name)

Protected Member Functions
virtual void	init ()
	HELPERS.
virtual SGMatrix< float64_t >	process_distance_matrix (SGMatrix< float64_t > distance_matrix)
SGMatrix< float64_t >	isomap_distance (SGMatrix< float64_t > D_matrix)
Protected Member Functions inherited from CMultidimensionalScaling
SGMatrix< float64_t >	classic_embedding (SGMatrix< float64_t > distance_matrix)
SGMatrix< float64_t >	landmark_embedding (SGMatrix< float64_t > distance_matrix)

Static Protected Member Functions
static void *	run_dijkstra_thread (void *p)
	THREADS.
Static Protected Member Functions inherited from CMultidimensionalScaling
static void *	run_triangulation_thread (void *p)
	STATIC.
static SGVector< int32_t >	shuffle (int32_t count, int32_t total_count)

Protected Attributes
int32_t	m_k
	FIELDS.
Protected Attributes inherited from CMultidimensionalScaling
SGVector< float64_t >	m_eigenvalues
	FIELDS.
bool	m_landmark
int32_t	m_landmark_number
Protected Attributes inherited from CEmbeddingConverter
int32_t	m_target_dim
CDistance *	m_distance
CKernel *	m_kernel

Additional Inherited Members
Public Attributes inherited from CSGObject
SGIO *	io
Parallel *	parallel
Version *	version
Parameter *	m_parameters
Parameter *	m_model_selection_parameters

Constructor & Destructor Documentation

CIsomap

(

)

Definition at line 56 of file Isomap.cpp.

~CIsomap ( )

virtual

Definition at line 68 of file Isomap.cpp.

Member Function Documentation

int32_t get_k

(

)

const

getter for k parameter

Returns

k value

Definition at line 78 of file Isomap.cpp.

const char * get_name ( ) const

virtual

get name

Reimplemented from CMultidimensionalScaling.

Definition at line 83 of file Isomap.cpp.

void init ( )

protectedvirtual

HELPERS.

default init

Reimplemented from CMultidimensionalScaling.

Definition at line 63 of file Isomap.cpp.

SGMatrix< float64_t > isomap_distance ( SGMatrix< float64_t >  D_matrix )

protected

approximate geodesic distance with shortest path in kNN graph

Parameters

D_matrix

distance matrix (deleted on exit)

Returns

approximate geodesic distance matrix

Definition at line 93 of file Isomap.cpp.

SGMatrix< float64_t > process_distance_matrix ( SGMatrix< float64_t >  distance_matrix )

protectedvirtual

process distance matrix (redefined in isomap, for mds does nothing)

Parameters

distance_matrix

distance matrix

Returns

processed distance matrix

Reimplemented from CMultidimensionalScaling.

Definition at line 88 of file Isomap.cpp.

void * run_dijkstra_thread ( void *  p )

staticprotected

THREADS.

run dijkstra thread

Parameters

p	thread params

Definition at line 211 of file Isomap.cpp.

void set_k

(

int32_t

k

)

setter for k parameter

Parameters

k

value

Definition at line 72 of file Isomap.cpp.

Member Data Documentation

int32_t m_k

protected

FIELDS.

k, number of neighbors for K-Isomap

Definition at line 85 of file Isomap.h.

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

• Isomap.h
• Isomap.cpp