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:

[legend]

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)

const char *	get_name () const

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)

template<>
void	set_generic ()

template<>
void	set_generic ()

template<>
void	set_generic ()

template<>
void	set_generic ()

template<>
void	set_generic ()

template<>
void	set_generic ()

template<>
void	set_generic ()

template<>
void	set_generic ()

template<>
void	set_generic ()

template<>
void	set_generic ()

template<>
void	set_generic ()

template<>
void	set_generic ()

template<>
void	set_generic ()

Protected Member Functions
virtual void	init ()
	HELPERS. More...

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)

Protected Member Functions inherited from CEmbeddingConverter
void	init ()

Protected Member Functions inherited from CSGObject
virtual void	load_serializable_pre () throw (ShogunException)

virtual void	load_serializable_post () throw (ShogunException)

virtual void	save_serializable_pre () throw (ShogunException)

virtual void	save_serializable_post () throw (ShogunException)

Static Protected Member Functions
static void *	run_dijkstra_thread (void *p)
	THREADS. More...

Static Protected Member Functions inherited from CMultidimensionalScaling
static void *	run_triangulation_thread (void *p)
	STATIC. More...

static SGVector< int32_t >	shuffle (int32_t count, int32_t total_count)

Protected Attributes
int32_t	m_k
	FIELDS. More...

Protected Attributes inherited from CMultidimensionalScaling
SGVector< float64_t >	m_eigenvalues
	FIELDS. More...

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 CEmbeddingConverter.

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.

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

Detailed Description

Public Member Functions

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation