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CKernelPCA Class Reference

Detailed Description

Preprocessor KernelPCA performs kernel principal component analysis.

Schoelkopf, B., Smola, A. J., & Mueller, K. R. (1999). Kernel Principal Component Analysis. Advances in kernel methods support vector learning, 1327(3), 327-352. MIT Press. Retrieved from http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.32.8744

Definition at line 35 of file KernelPCA.h.

Inheritance diagram for CKernelPCA:
Inheritance graph
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Public Member Functions

 CKernelPCA ()
 CKernelPCA (CKernel *k)
virtual ~CKernelPCA ()
virtual bool init (CFeatures *features)
 initialize preprocessor from features
virtual void cleanup ()
 cleanup
virtual SGMatrix< float64_tapply_to_feature_matrix (CFeatures *features)
virtual SGVector< float64_tapply_to_feature_vector (SGVector< float64_t > vector)
virtual CDenseFeatures
< float64_t > * 
apply_to_string_features (CFeatures *features)
SGMatrix< float64_tget_transformation_matrix () const
SGVector< float64_tget_bias_vector () const
virtual const char * get_name () const
virtual EPreprocessorType get_type () const
void set_target_dim (int32_t dim)
int32_t get_target_dim () const
void set_distance (CDistance *distance)
CDistanceget_distance () const
void set_kernel (CKernel *kernel)
CKernelget_kernel () const
virtual EFeatureClass get_feature_class ()
 return that we are dense features (just fixed size matrices)
virtual EFeatureType get_feature_type ()
 return feature type
virtual CSGObjectshallow_copy () const
virtual CSGObjectdeep_copy () const
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="", int32_t param_version=VERSION_PARAMETER)
virtual bool load_serializable (CSerializableFile *file, const char *prefix="", int32_t param_version=VERSION_PARAMETER)
DynArray< TParameter * > * load_file_parameters (const SGParamInfo *param_info, int32_t file_version, CSerializableFile *file, const char *prefix="")
DynArray< TParameter * > * load_all_file_parameters (int32_t file_version, int32_t current_version, CSerializableFile *file, const char *prefix="")
void map_parameters (DynArray< TParameter * > *param_base, int32_t &base_version, DynArray< const SGParamInfo * > *target_param_infos)
void set_global_io (SGIO *io)
SGIOget_global_io ()
void set_global_parallel (Parallel *parallel)
Parallelget_global_parallel ()
void set_global_version (Version *version)
Versionget_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_parameter_dictionary (CMap< TParameter *, CSGObject * > &dict)

Public Attributes

SGIOio
Parallelparallel
Versionversion
Parameterm_parameters
Parameterm_model_selection_parameters
ParameterMapm_parameter_map
uint32_t m_hash

Protected Member Functions

void init ()
virtual TParametermigrate (DynArray< TParameter * > *param_base, const SGParamInfo *target)
virtual void one_to_one_migration_prepare (DynArray< TParameter * > *param_base, const SGParamInfo *target, TParameter *&replacement, TParameter *&to_migrate, char *old_name=NULL)
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)
virtual bool update_parameter_hash ()

Protected Attributes

CFeaturesm_init_features
SGMatrix< float64_tm_transformation_matrix
SGVector< float64_tm_bias_vector
bool m_initialized
int32_t m_target_dim
CDistancem_distance
CKernelm_kernel
CEmbeddingConverterm_converter

Constructor & Destructor Documentation

default constructor

Definition at line 28 of file KernelPCA.cpp.

CKernelPCA ( CKernel k)

constructor

Parameters
kkernel to be used

Definition at line 33 of file KernelPCA.cpp.

~CKernelPCA ( )
virtual

Definition at line 62 of file KernelPCA.cpp.

Member Function Documentation

SGMatrix< float64_t > apply_to_feature_matrix ( CFeatures features)
virtual

apply preproc on feature matrix result in feature matrix return pointer to feature_matrix, i.e. f->get_feature_matrix();

Reimplemented from CDimensionReductionPreprocessor.

Definition at line 128 of file KernelPCA.cpp.

SGVector< float64_t > apply_to_feature_vector ( SGVector< float64_t vector)
virtual

apply preproc on single feature vector result in feature matrix

Reimplemented from CDimensionReductionPreprocessor.

Definition at line 160 of file KernelPCA.cpp.

CDenseFeatures< float64_t > * apply_to_string_features ( CFeatures features)
virtual

apply to string features

Parameters
features

Definition at line 185 of file KernelPCA.cpp.

void build_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 1204 of file SGObject.cpp.

void cleanup ( )
virtual

cleanup

Reimplemented from CDimensionReductionPreprocessor.

Definition at line 52 of file KernelPCA.cpp.

virtual CSGObject* deep_copy ( ) const
virtualinherited

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

Definition at line 131 of file SGObject.h.

SGVector<float64_t> get_bias_vector ( ) const

get bias of KPCA

Definition at line 79 of file KernelPCA.h.

CDistance * get_distance ( ) const
inherited

getter for distance

Returns
distance

Definition at line 88 of file DimensionReductionPreprocessor.cpp.

virtual EFeatureClass get_feature_class ( )
virtualinherited

return that we are dense features (just fixed size matrices)

Implements CPreprocessor.

Reimplemented in CRandomFourierGaussPreproc.

virtual EFeatureType get_feature_type ( )
virtualinherited

return feature type

Implements CPreprocessor.

Reimplemented in CRandomFourierGaussPreproc.

SGIO * get_global_io ( )
inherited

get the io object

Returns
io object

Definition at line 224 of file SGObject.cpp.

Parallel * get_global_parallel ( )
inherited

get the parallel object

Returns
parallel object

Definition at line 259 of file SGObject.cpp.

Version * get_global_version ( )
inherited

get the version object

Returns
version object

Definition at line 272 of file SGObject.cpp.

CKernel * get_kernel ( ) const
inherited

getter for kernel

Returns
kernel

Definition at line 101 of file DimensionReductionPreprocessor.cpp.

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

Definition at line 1108 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 1132 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 1145 of file SGObject.cpp.

virtual const char* get_name ( ) const
virtual
Returns
object name

Reimplemented from CDimensionReductionPreprocessor.

Definition at line 85 of file KernelPCA.h.

int32_t get_target_dim ( ) const
inherited

getter for target dimension

Returns
target dimension

Definition at line 76 of file DimensionReductionPreprocessor.cpp.

SGMatrix<float64_t> get_transformation_matrix ( ) const

get transformation matrix, i.e. eigenvectors

Definition at line 71 of file KernelPCA.h.

virtual EPreprocessorType get_type ( ) const
virtual
Returns
the type of preprocessor

Reimplemented from CDimensionReductionPreprocessor.

Definition at line 88 of file KernelPCA.h.

bool init ( CFeatures features)
virtual

initialize preprocessor from features

Reimplemented from CDimensionReductionPreprocessor.

Definition at line 68 of file KernelPCA.cpp.

void init ( )
protected

default init

Reimplemented from CDimensionReductionPreprocessor.

Definition at line 39 of file KernelPCA.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 278 of file SGObject.cpp.

DynArray< TParameter * > * load_all_file_parameters ( int32_t  file_version,
int32_t  current_version,
CSerializableFile file,
const char *  prefix = "" 
)
inherited

maps all parameters of this instance to the provided file version and loads all parameter data from the file into an array, which is sorted (basically calls load_file_parameter(...) for all parameters and puts all results into a sorted array)

Parameters
file_versionparameter version of the file
current_versionversion from which mapping begins (you want to use VERSION_PARAMETER for this in most cases)
filefile to load from
prefixprefix for members
Returns
(sorted) array of created TParameter instances with file data

Definition at line 679 of file SGObject.cpp.

DynArray< TParameter * > * load_file_parameters ( const SGParamInfo param_info,
int32_t  file_version,
CSerializableFile file,
const char *  prefix = "" 
)
inherited

loads some specified parameters from a file with a specified version The provided parameter info has a version which is recursively mapped until the file parameter version is reached. Note that there may be possibly multiple parameters in the mapping, therefore, a set of TParameter instances is returned

Parameters
param_infoinformation of parameter
file_versionparameter version of the file, must be <= provided parameter version
filefile to load from
prefixprefix for members
Returns
new array with TParameter instances with the attached data

Definition at line 523 of file SGObject.cpp.

bool load_serializable ( CSerializableFile file,
const char *  prefix = "",
int32_t  param_version = VERSION_PARAMETER 
)
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
param_version(optional) a parameter version different to (this is mainly for testing, better do not use)
Returns
TRUE if done, otherwise FALSE

Reimplemented in CModelSelectionParameters.

Definition at line 354 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 occurres.

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

Definition at line 1033 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 occurres.

Definition at line 1028 of file SGObject.cpp.

void map_parameters ( DynArray< TParameter * > *  param_base,
int32_t &  base_version,
DynArray< const SGParamInfo * > *  target_param_infos 
)
inherited

Takes a set of TParameter instances (base) with a certain version and a set of target parameter infos and recursively maps the base level wise to the current version using CSGObject::migrate(...). The base is replaced. After this call, the base version containing parameters should be of same version/type as the initial target parameter infos. Note for this to work, the migrate methods and all the internal parameter mappings have to match

Parameters
param_baseset of TParameter instances that are mapped to the provided target parameter infos
base_versionversion of the parameter base
target_param_infosset of SGParamInfo instances that specify the target parameter base

Definition at line 717 of file SGObject.cpp.

TParameter * migrate ( DynArray< TParameter * > *  param_base,
const SGParamInfo target 
)
protectedvirtualinherited

creates a new TParameter instance, which contains migrated data from the version that is provided. The provided parameter data base is used for migration, this base is a collection of all parameter data of the previous version. Migration is done FROM the data in param_base TO the provided param info Migration is always one version step. Method has to be implemented in subclasses, if no match is found, base method has to be called.

If there is an element in the param_base which equals the target, a copy of the element is returned. This represents the case when nothing has changed and therefore, the migrate method is not overloaded in a subclass

Parameters
param_baseset of TParameter instances to use for migration
targetparameter info for the resulting TParameter
Returns
a new TParameter instance with migrated data from the base of the type which is specified by the target parameter

Definition at line 923 of file SGObject.cpp.

void one_to_one_migration_prepare ( DynArray< TParameter * > *  param_base,
const SGParamInfo target,
TParameter *&  replacement,
TParameter *&  to_migrate,
char *  old_name = NULL 
)
protectedvirtualinherited

This method prepares everything for a one-to-one parameter migration. One to one here means that only ONE element of the parameter base is needed for the migration (the one with the same name as the target). Data is allocated for the target (in the type as provided in the target SGParamInfo), and a corresponding new TParameter instance is written to replacement. The to_migrate pointer points to the single needed TParameter instance needed for migration. If a name change happened, the old name may be specified by old_name. In addition, the m_delete_data flag of to_migrate is set to true. So if you want to migrate data, the only thing to do after this call is converting the data in the m_parameter fields. If unsure how to use - have a look into an example for this. (base_migration_type_conversion.cpp for example)

Parameters
param_baseset of TParameter instances to use for migration
targetparameter info for the resulting TParameter
replacement(used as output) here the TParameter instance which is returned by migration is created into
to_migratethe only source that is used for migration
old_namewith this parameter, a name change may be specified

Definition at line 864 of file SGObject.cpp.

void print_modsel_params ( )
inherited

prints all parameter registered for model selection and their type

Definition at line 1084 of file SGObject.cpp.

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

prints registered parameters out

Parameters
prefixprefix for members

Definition at line 290 of file SGObject.cpp.

bool save_serializable ( CSerializableFile file,
const char *  prefix = "",
int32_t  param_version = VERSION_PARAMETER 
)
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
param_version(optional) a parameter version different to (this is mainly for testing, better do not use)
Returns
TRUE if done, otherwise FALSE

Reimplemented in CModelSelectionParameters.

Definition at line 296 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 occurres.

Reimplemented in CKernel.

Definition at line 1043 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 occurres.

Reimplemented in CKernel.

Definition at line 1038 of file SGObject.cpp.

void set_distance ( CDistance distance)
inherited

setter for distance

Parameters
distancedistance to set

Definition at line 81 of file DimensionReductionPreprocessor.cpp.

void set_generic< floatmax_t > ( )
inherited

set generic type to T

Definition at line 41 of file SGObject.cpp.

void set_global_io ( SGIO io)
inherited

set the io object

Parameters
ioio object to use

Definition at line 217 of file SGObject.cpp.

void set_global_parallel ( Parallel parallel)
inherited

set the parallel object

Parameters
parallelparallel object to use

Definition at line 230 of file SGObject.cpp.

void set_global_version ( Version version)
inherited

set the version object

Parameters
versionversion object to use

Definition at line 265 of file SGObject.cpp.

void set_kernel ( CKernel kernel)
inherited

setter for kernel

Parameters
kernelkernel to set

Definition at line 94 of file DimensionReductionPreprocessor.cpp.

void set_target_dim ( int32_t  dim)
inherited

setter for target dimension

Parameters
dimtarget dimension

Definition at line 70 of file DimensionReductionPreprocessor.cpp.

virtual 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 122 of file SGObject.h.

void unset_generic ( )
inherited

unset generic type

this has to be called in classes specializing a template class

Definition at line 285 of file SGObject.cpp.

bool update_parameter_hash ( )
protectedvirtualinherited

Updates the hash of current parameter combination.

Returns
bool if parameter combination has changed since last update.

Definition at line 237 of file SGObject.cpp.

Member Data Documentation

SGIO* io
inherited

io

Definition at line 462 of file SGObject.h.

SGVector<float64_t> m_bias_vector
protected

bias vector

Definition at line 104 of file KernelPCA.h.

CEmbeddingConverter* m_converter
protectedinherited

embedding converter to be used

Definition at line 125 of file DimensionReductionPreprocessor.h.

CDistance* m_distance
protectedinherited

distance to be used

Definition at line 119 of file DimensionReductionPreprocessor.h.

uint32_t m_hash
inherited

Hash of parameter values

Definition at line 480 of file SGObject.h.

CFeatures* m_init_features
protected

features used by init. needed for apply

Definition at line 98 of file KernelPCA.h.

bool m_initialized
protected

true when already initialized

Definition at line 107 of file KernelPCA.h.

CKernel* m_kernel
protectedinherited

kernel to be used

Definition at line 122 of file DimensionReductionPreprocessor.h.

Parameter* m_model_selection_parameters
inherited

model selection parameters

Definition at line 474 of file SGObject.h.

ParameterMap* m_parameter_map
inherited

map for different parameter versions

Definition at line 477 of file SGObject.h.

Parameter* m_parameters
inherited

parameters

Definition at line 471 of file SGObject.h.

int32_t m_target_dim
protectedinherited

target dim of dimensionality reduction preprocessor

Definition at line 116 of file DimensionReductionPreprocessor.h.

SGMatrix<float64_t> m_transformation_matrix
protected

transformation matrix

Definition at line 101 of file KernelPCA.h.

Parallel* parallel
inherited

parallel

Definition at line 465 of file SGObject.h.

Version* version
inherited

version

Definition at line 468 of file SGObject.h.


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

SHOGUN Machine Learning Toolbox - Documentation