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CStochasticProximityEmbedding Class Reference

Detailed Description

class StochasticProximityEmbedding used to construct embeddings of data using the Stochastic Proximity algorithm.

Agrafiotis, D. K. (2002) Stochastic Proximity Embedding Retrieved from: http://www.dimitris-agrafiotis.com/Papers/jcc20078.pdf

This class provides two different strategies for the computation of the embedding. In each iteration, both strategies choose two sets of feature vectors whose representation in the embedded space is updated. The first set is randomly chosen in both strategies. However, the second set is obtained differently depending on the strategy used. In the SPE_GLOBAL strategy, the second set is still chosen at random. On the other hand, if SPE_LOCAL is used, first of all, the K-Nearest Neighbors of each of the feature vectors in the first set is obtained and secondly, a number of feature vectors among these K-Nearest Neighbors is chosen to form the second set.

The parameter K for K-Nearest Neighbors in SPE_LOCAL corresponds to the class member "m_k". Each of the two sets used on every iteration is formed by "m_nupdates" feature vectors. Therefore, the number of feature vectors given must be always at least two times the value of "m_nupdates".

In order to avoid problems with memory in case a large number of features vectors is to be embedded, the distance matrix is never computed explicitily. This has the drawback that it is likely that the same distances are computed several times during the process.

Uses implementation from the Tapkee library.

Only CEuclideanDistance distance is supported for the moment.

Definition at line 63 of file StochasticProximityEmbedding.h.

Inheritance diagram for CStochasticProximityEmbedding:
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Public Member Functions

 CStochasticProximityEmbedding ()
 
virtual ~CStochasticProximityEmbedding ()
 
virtual CFeatures * apply (CFeatures *features)
 
void set_k (int32_t k)
 
int32_t get_k () const
 
void set_strategy (ESPEStrategy strategy)
 
ESPEStrategy get_strategy () const
 
void set_tolerance (float32_t tolerance)
 
int32_t get_tolerance () const
 
void set_nupdates (int32_t nupdates)
 
int32_t get_nupdates () const
 
void set_max_iteration (const int32_t max_iteration)
 
int32_t get_max_iteration () const
 
virtual const char * get_name () const
 
virtual CDenseFeatures
< 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
 
virtual CSGObject * shallow_copy () const
 
virtual CSGObject * deep_copy () const
 
virtual bool is_generic (EPrimitiveType *generic) const
 
template<class T >
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 ()
 
template<>
void set_generic ()
 
template<>
void set_generic ()
 
template<>
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 ()
 
SGStringList< char > get_modelsel_names ()
 
void print_modsel_params ()
 
char * get_modsel_param_descr (const char *param_name)
 
index_t get_modsel_param_index (const char *param_name)
 
void build_gradient_parameter_dictionary (CMap< TParameter *, CSGObject * > *dict)
 
virtual void update_parameter_hash ()
 
virtual bool parameter_hash_changed ()
 
virtual bool equals (CSGObject *other, float64_t accuracy=0.0, bool tolerant=false)
 
virtual CSGObject * clone ()
 

Public Attributes

SGIO * io
 
Parallel * parallel
 
Version * version
 
Parameter * m_parameters
 
Parameter * m_model_selection_parameters
 
Parameter * m_gradient_parameters
 
uint32_t m_hash
 

Protected Member Functions

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)
 

Protected Attributes

int32_t m_target_dim
 
CDistance * m_distance
 
CKernel * m_kernel
 

Constructor & Destructor Documentation

CStochasticProximityEmbedding ( )

constructor

Definition at line 19 of file StochasticProximityEmbedding.cpp.

~CStochasticProximityEmbedding ( )
virtual

destructor

Definition at line 43 of file StochasticProximityEmbedding.cpp.

Member Function Documentation

CFeatures * apply ( CFeatures *  features)
virtual

apply to features

Parameters
featuresfeatures to embed
Returns
embedding features

Implements CEmbeddingConverter.

Definition at line 112 of file StochasticProximityEmbedding.cpp.

void build_gradient_parameter_dictionary ( CMap< TParameter *, CSGObject * > *  dict)
inherited

Builds a dictionary of all parameters in SGObject as well of those of SGObjects that are parameters of this object. Dictionary maps parameters to the objects that own them.

Parameters
dictdictionary of parameters to be built.

Definition at line 597 of file SGObject.cpp.

CSGObject * clone ( )
virtualinherited

Creates a clone of the current object. This is done via recursively traversing all parameters, which corresponds to a deep copy. Calling equals on the cloned object always returns true although none of the memory of both objects overlaps.

Returns
an identical copy of the given object, which is disjoint in memory. NULL if the clone fails. Note that the returned object is SG_REF'ed

Definition at line 714 of file SGObject.cpp.

CSGObject * deep_copy ( ) const
virtualinherited

A deep copy. All the instance variables will also be copied.

Definition at line 198 of file SGObject.cpp.

CDenseFeatures< float64_t > * embed ( CFeatures *  features)
virtualinherited

embed given features, acts the same as apply, but returns DenseFeatures

Parameters
featuresfeatures to embed
Returns
embedding simple features

Definition at line 35 of file EmbeddingConverter.cpp.

bool equals ( CSGObject *  other,
float64_t  accuracy = 0.0,
bool  tolerant = false 
)
virtualinherited

Recursively compares the current SGObject to another one. Compares all registered numerical parameters, recursion upon complex (SGObject) parameters. Does not compare pointers!

May be overwritten but please do with care! Should not be necessary in most cases.

Parameters
otherobject to compare with
accuracyaccuracy to use for comparison (optional)
tolerantallows linient check on float equality (within accuracy)
Returns
true if all parameters were equal, false if not

Definition at line 618 of file SGObject.cpp.

CDistance * get_distance ( ) const
inherited

getter for distance

Returns
distance

Definition at line 58 of file EmbeddingConverter.cpp.

SGIO * get_global_io ( )
inherited

get the io object

Returns
io object

Definition at line 235 of file SGObject.cpp.

Parallel * get_global_parallel ( )
inherited

get the parallel object

Returns
parallel object

Definition at line 277 of file SGObject.cpp.

Version * get_global_version ( )
inherited

get the version object

Returns
version object

Definition at line 290 of file SGObject.cpp.

int32_t get_k ( ) const

getter for number of neighbors k in local strategy

Returns
k value

Definition at line 55 of file StochasticProximityEmbedding.cpp.

CKernel * get_kernel ( ) const
inherited

getter for kernel

Returns
kernel

Definition at line 71 of file EmbeddingConverter.cpp.

int32_t get_max_iteration ( ) const

getter for the maximum number of iterations

Returns
the maximum number of iterations

Definition at line 102 of file StochasticProximityEmbedding.cpp.

SGStringList< char > get_modelsel_names ( )
inherited
Returns
vector of names of all parameters which are registered for model selection

Definition at line 498 of file SGObject.cpp.

char * get_modsel_param_descr ( const char *  param_name)
inherited

Returns description of a given parameter string, if it exists. SG_ERROR otherwise

Parameters
param_namename of the parameter
Returns
description of the parameter

Definition at line 522 of file SGObject.cpp.

index_t get_modsel_param_index ( const char *  param_name)
inherited

Returns index of model selection parameter with provided index

Parameters
param_namename of model selection parameter
Returns
index of model selection parameter with provided name, -1 if there is no such

Definition at line 535 of file SGObject.cpp.

const char * get_name ( ) const
virtual

get name

Reimplemented from CEmbeddingConverter.

Definition at line 107 of file StochasticProximityEmbedding.cpp.

int32_t get_nupdates ( ) const

getter for number of updates per iteration

Returns
nupdates value

Definition at line 92 of file StochasticProximityEmbedding.cpp.

ESPEStrategy get_strategy ( ) const

getter for type of SPE strategy

Returns
strategy value

Definition at line 65 of file StochasticProximityEmbedding.cpp.

int32_t get_target_dim ( ) const
inherited

getter for target dimension

Returns
target dimension

Definition at line 46 of file EmbeddingConverter.cpp.

int32_t get_tolerance ( ) const

getter for regularization parameter

Returns
regularization value

Definition at line 79 of file StochasticProximityEmbedding.cpp.

bool is_generic ( EPrimitiveType *  generic) const
virtualinherited

If the SGSerializable is a class template then TRUE will be returned and GENERIC is set to the type of the generic.

Parameters
genericset to the type of the generic if returning TRUE
Returns
TRUE if a class template.

Definition at line 296 of file SGObject.cpp.

bool load_serializable ( CSerializableFile *  file,
const char *  prefix = "" 
)
virtualinherited

Load this object from file. If it will fail (returning FALSE) then this object will contain inconsistent data and should not be used!

Parameters
filewhere to load from
prefixprefix for members
Returns
TRUE if done, otherwise FALSE

Definition at line 369 of file SGObject.cpp.

void load_serializable_post ( )
throw (ShogunException
)
protectedvirtualinherited

Can (optionally) be overridden to post-initialize some member variables which are not PARAMETER::ADD'ed. Make sure that at first the overridden method BASE_CLASS::LOAD_SERIALIZABLE_POST is called.

Exceptions
ShogunExceptionwill be thrown if an error occurs.

Reimplemented in CKernel, CWeightedDegreePositionStringKernel, CList, CAlphabet, CLinearHMM, CGaussianKernel, CInverseMultiQuadricKernel, CCircularKernel, and CExponentialKernel.

Definition at line 426 of file SGObject.cpp.

void load_serializable_pre ( )
throw (ShogunException
)
protectedvirtualinherited

Can (optionally) be overridden to pre-initialize some member variables which are not PARAMETER::ADD'ed. Make sure that at first the overridden method BASE_CLASS::LOAD_SERIALIZABLE_PRE is called.

Exceptions
ShogunExceptionwill be thrown if an error occurs.

Reimplemented in CDynamicArray< T >, CDynamicArray< float64_t >, CDynamicArray< float32_t >, CDynamicArray< int32_t >, CDynamicArray< char >, CDynamicArray< bool >, and CDynamicObjectArray.

Definition at line 421 of file SGObject.cpp.

bool parameter_hash_changed ( )
virtualinherited
Returns
whether parameter combination has changed since last update

Definition at line 262 of file SGObject.cpp.

void print_modsel_params ( )
inherited

prints all parameter registered for model selection and their type

Definition at line 474 of file SGObject.cpp.

void print_serializable ( const char *  prefix = "")
virtualinherited

prints registered parameters out

Parameters
prefixprefix for members

Definition at line 308 of file SGObject.cpp.

bool save_serializable ( CSerializableFile *  file,
const char *  prefix = "" 
)
virtualinherited

Save this object to file.

Parameters
filewhere to save the object; will be closed during returning if PREFIX is an empty string.
prefixprefix for members
Returns
TRUE if done, otherwise FALSE

Definition at line 314 of file SGObject.cpp.

void save_serializable_post ( )
throw (ShogunException
)
protectedvirtualinherited

Can (optionally) be overridden to post-initialize some member variables which are not PARAMETER::ADD'ed. Make sure that at first the overridden method BASE_CLASS::SAVE_SERIALIZABLE_POST is called.

Exceptions
ShogunExceptionwill be thrown if an error occurs.

Reimplemented in CKernel.

Definition at line 436 of file SGObject.cpp.

void save_serializable_pre ( )
throw (ShogunException
)
protectedvirtualinherited

Can (optionally) be overridden to pre-initialize some member variables which are not PARAMETER::ADD'ed. Make sure that at first the overridden method BASE_CLASS::SAVE_SERIALIZABLE_PRE is called.

Exceptions
ShogunExceptionwill be thrown if an error occurs.

Reimplemented in CKernel, CDynamicArray< T >, CDynamicArray< float64_t >, CDynamicArray< float32_t >, CDynamicArray< int32_t >, CDynamicArray< char >, CDynamicArray< bool >, and CDynamicObjectArray.

Definition at line 431 of file SGObject.cpp.

void set_distance ( CDistance *  distance)
inherited

setter for distance

Parameters
distancedistance to set

Definition at line 51 of file EmbeddingConverter.cpp.

void set_generic ( )
inherited

Definition at line 41 of file SGObject.cpp.

void set_generic ( )
inherited

Definition at line 46 of file SGObject.cpp.

void set_generic ( )
inherited

Definition at line 51 of file SGObject.cpp.

void set_generic ( )
inherited

Definition at line 56 of file SGObject.cpp.

void set_generic ( )
inherited

Definition at line 61 of file SGObject.cpp.

void set_generic ( )
inherited

Definition at line 66 of file SGObject.cpp.

void set_generic ( )
inherited

Definition at line 71 of file SGObject.cpp.

void set_generic ( )
inherited

Definition at line 76 of file SGObject.cpp.

void set_generic ( )
inherited

Definition at line 81 of file SGObject.cpp.

void set_generic ( )
inherited

Definition at line 86 of file SGObject.cpp.

void set_generic ( )
inherited

Definition at line 91 of file SGObject.cpp.

void set_generic ( )
inherited

Definition at line 96 of file SGObject.cpp.

void set_generic ( )
inherited

Definition at line 101 of file SGObject.cpp.

void set_generic ( )
inherited

Definition at line 106 of file SGObject.cpp.

void set_generic ( )
inherited

Definition at line 111 of file SGObject.cpp.

void set_generic ( )
inherited

set generic type to T

void set_global_io ( SGIO *  io)
inherited

set the io object

Parameters
ioio object to use

Definition at line 228 of file SGObject.cpp.

void set_global_parallel ( Parallel *  parallel)
inherited

set the parallel object

Parameters
parallelparallel object to use

Definition at line 241 of file SGObject.cpp.

void set_global_version ( Version *  version)
inherited

set the version object

Parameters
versionversion object to use

Definition at line 283 of file SGObject.cpp.

void set_k ( int32_t  k)

setter for number of neighbors k in local strategy

Parameters
kk value

Definition at line 47 of file StochasticProximityEmbedding.cpp.

void set_kernel ( CKernel *  kernel)
inherited

setter for kernel

Parameters
kernelkernel to set

Definition at line 64 of file EmbeddingConverter.cpp.

void set_max_iteration ( const int32_t  max_iteration)

setter for the maximum number of iterations

Parameters
max_iterationthe maximum number of iterations

Definition at line 97 of file StochasticProximityEmbedding.cpp.

void set_nupdates ( int32_t  nupdates)

setter for number of updates per iteration

Parameters
nupdatesnumber of updates per SPE iteration

Definition at line 84 of file StochasticProximityEmbedding.cpp.

void set_strategy ( ESPEStrategy  strategy)

setter for strategy parameter

Parameters
strategytype of SPE strategy

Definition at line 60 of file StochasticProximityEmbedding.cpp.

void set_target_dim ( int32_t  dim)
inherited

setter for target dimension

Parameters
dimtarget dimension

Definition at line 40 of file EmbeddingConverter.cpp.

void set_tolerance ( float32_t  tolerance)

setter for regularization parameter

Parameters
toleranceregularization value

Definition at line 70 of file StochasticProximityEmbedding.cpp.

CSGObject * shallow_copy ( ) const
virtualinherited

A shallow copy. All the SGObject instance variables will be simply assigned and SG_REF-ed.

Reimplemented in CGaussianKernel.

Definition at line 192 of file SGObject.cpp.

void unset_generic ( )
inherited

unset generic type

this has to be called in classes specializing a template class

Definition at line 303 of file SGObject.cpp.

void update_parameter_hash ( )
virtualinherited

Updates the hash of current parameter combination

Definition at line 248 of file SGObject.cpp.

Member Data Documentation

SGIO* io
inherited

io

Definition at line 369 of file SGObject.h.

CDistance* m_distance
protectedinherited

distance to be used

Definition at line 99 of file EmbeddingConverter.h.

Parameter* m_gradient_parameters
inherited

parameters wrt which we can compute gradients

Definition at line 384 of file SGObject.h.

uint32_t m_hash
inherited

Hash of parameter values

Definition at line 387 of file SGObject.h.

CKernel* m_kernel
protectedinherited

kernel to be used

Definition at line 102 of file EmbeddingConverter.h.

Parameter* m_model_selection_parameters
inherited

model selection parameters

Definition at line 381 of file SGObject.h.

Parameter* m_parameters
inherited

parameters

Definition at line 378 of file SGObject.h.

int32_t m_target_dim
protectedinherited

target dim of dimensionality reduction preprocessor

Definition at line 96 of file EmbeddingConverter.h.

Parallel* parallel
inherited

parallel

Definition at line 372 of file SGObject.h.

Version* version
inherited

version

Definition at line 375 of file SGObject.h.

The documentation for this class was generated from the following files:
SHOGUN Machine Learning Toolbox - Documentation