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CExplicitSpecFeatures Class Reference

Detailed Description

Features that compute the Spectrum Kernel feature space explicitly.

See Also
CCommWordStringKernel

Definition at line 26 of file ExplicitSpecFeatures.h.

Inheritance diagram for CExplicitSpecFeatures:
Inheritance graph
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Public Member Functions

 CExplicitSpecFeatures ()
 CExplicitSpecFeatures (CStringFeatures< uint16_t > *str, bool normalize=true)
 CExplicitSpecFeatures (const CExplicitSpecFeatures &orig)
virtual ~CExplicitSpecFeatures ()
virtual CFeaturesduplicate () const
virtual int32_t get_dim_feature_space () const
virtual float64_t dot (int32_t vec_idx1, CDotFeatures *df, int32_t vec_idx2)
virtual float64_t dense_dot (int32_t vec_idx1, const float64_t *vec2, int32_t vec2_len)
virtual void add_to_dense_vec (float64_t alpha, int32_t vec_idx1, float64_t *vec2, int32_t vec2_len, bool abs_val=false)
virtual void * get_feature_iterator (int32_t vector_index)
virtual bool get_next_feature (int32_t &index, float64_t &value, void *iterator)
virtual void free_feature_iterator (void *iterator)
virtual int32_t get_nnz_features_for_vector (int32_t num)
virtual EFeatureType get_feature_type ()
virtual EFeatureClass get_feature_class ()
virtual int32_t get_num_vectors () const
virtual int32_t get_size ()
virtual const char * get_name () const
- Public Member Functions inherited from CDotFeatures
 CDotFeatures (int32_t size=0)
 CDotFeatures (const CDotFeatures &orig)
 CDotFeatures (CFile *loader)
virtual ~CDotFeatures ()
virtual void dense_dot_range (float64_t *output, int32_t start, int32_t stop, float64_t *alphas, float64_t *vec, int32_t dim, float64_t b)
virtual void dense_dot_range_subset (int32_t *sub_index, int32_t num, float64_t *output, float64_t *alphas, float64_t *vec, int32_t dim, float64_t b)
float64_t get_combined_feature_weight ()
void set_combined_feature_weight (float64_t nw)
SGMatrix< float64_tget_computed_dot_feature_matrix ()
SGVector< float64_tget_computed_dot_feature_vector (int32_t num)
void benchmark_add_to_dense_vector (int32_t repeats=5)
void benchmark_dense_dot_range (int32_t repeats=5)
virtual SGVector< float64_tget_mean ()
virtual SGMatrix< float64_tget_cov ()
- Public Member Functions inherited from CFeatures
 CFeatures (int32_t size=0)
 CFeatures (const CFeatures &orig)
 CFeatures (CFile *loader)
virtual ~CFeatures ()
virtual int32_t add_preprocessor (CPreprocessor *p)
 set preprocessor
virtual CPreprocessordel_preprocessor (int32_t num)
 del current preprocessor
CPreprocessorget_preprocessor (int32_t num)
 get current preprocessor
void set_preprocessed (int32_t num)
bool is_preprocessed (int32_t num)
int32_t get_num_preprocessed ()
 get whether specified preprocessor (or all if num=1) was/were already applied
int32_t get_num_preprocessors () const
void clean_preprocessors ()
int32_t get_cache_size ()
virtual bool reshape (int32_t num_features, int32_t num_vectors)
void list_feature_obj ()
virtual void load (CFile *loader)
virtual void save (CFile *writer)
bool check_feature_compatibility (CFeatures *f)
bool has_property (EFeatureProperty p)
void set_property (EFeatureProperty p)
void unset_property (EFeatureProperty p)
virtual void set_subset (CSubset *subset)
virtual void remove_subset ()
virtual void subset_changed_post ()
index_t subset_idx_conversion (index_t idx) const
bool has_subset () const
virtual CFeaturescopy_subset (SGVector< index_t > indices)
- 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)
SGIOget_global_io ()
void set_global_parallel (Parallel *parallel)
Parallelget_global_parallel ()
void set_global_version (Version *version)
Versionget_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

void obtain_kmer_spectrum (CStringFeatures< uint16_t > *str)
void delete_kmer_spectrum ()
- Protected Member Functions inherited from CDotFeatures
void display_progress (int32_t start, int32_t stop, int32_t v)

Protected Attributes

bool use_normalization
int32_t num_strings
int32_t alphabet_size
int32_t spec_size
float64_t ** k_spectrum
- Protected Attributes inherited from CDotFeatures
float64_t combined_weight
 feature weighting in combined dot features
- Protected Attributes inherited from CFeatures
CSubsetm_subset

Additional Inherited Members

- Static Public Member Functions inherited from CDotFeatures
static void * dense_dot_range_helper (void *p)
- Public Attributes inherited from CSGObject
SGIOio
Parallelparallel
Versionversion
Parameterm_parameters
Parameterm_model_selection_parameters

Constructor & Destructor Documentation

default constructor

Definition at line 16 of file ExplicitSpecFeatures.cpp.

CExplicitSpecFeatures ( CStringFeatures< uint16_t > *  str,
bool  normalize = true 
)

constructor

Parameters
strstringfeatures (of words)
normalizewhether to use sqrtdiag normalization

Definition at line 30 of file ExplicitSpecFeatures.cpp.

copy constructor

Definition at line 43 of file ExplicitSpecFeatures.cpp.

~CExplicitSpecFeatures ( )
virtual

destructor

Definition at line 51 of file ExplicitSpecFeatures.cpp.

Member Function Documentation

void add_to_dense_vec ( float64_t  alpha,
int32_t  vec_idx1,
float64_t vec2,
int32_t  vec2_len,
bool  abs_val = false 
)
virtual

add vector 1 multiplied with alpha to dense vector2

Parameters
alphascalar alpha
vec_idx1index of first vector
vec2pointer to real valued vector
vec2_lenlength of real valued vector
abs_valif true add the absolute value

Implements CDotFeatures.

Definition at line 89 of file ExplicitSpecFeatures.cpp.

void delete_kmer_spectrum ( )
protected

free kmer spectrum

Definition at line 139 of file ExplicitSpecFeatures.cpp.

float64_t dense_dot ( int32_t  vec_idx1,
const float64_t vec2,
int32_t  vec2_len 
)
virtual

compute dot product between vector1 and a dense vector

Parameters
vec_idx1index of first vector
vec2pointer to real valued vector
vec2_lenlength of real valued vector

Implements CDotFeatures.

Definition at line 76 of file ExplicitSpecFeatures.cpp.

float64_t dot ( int32_t  vec_idx1,
CDotFeatures df,
int32_t  vec_idx2 
)
virtual

compute dot product between vector1 and vector2, appointed by their indices

Parameters
vec_idx1index of first vector
dfDotFeatures (of same kind) to compute dot product with
vec_idx2index of second vector

Implements CDotFeatures.

Definition at line 61 of file ExplicitSpecFeatures.cpp.

CFeatures * duplicate ( ) const
virtual

duplicate feature object

Returns
feature object

Implements CFeatures.

Definition at line 148 of file ExplicitSpecFeatures.cpp.

void free_feature_iterator ( void *  iterator)
virtual

clean up iterator call this function with the iterator returned by get_first_feature

Parameters
iteratoras returned by get_first_feature

Implements CDotFeatures.

Definition at line 167 of file ExplicitSpecFeatures.cpp.

int32_t get_dim_feature_space ( ) const
virtual

obtain the dimensionality of the feature space

(not mix this up with the dimensionality of the input space, usually obtained via get_num_features())

Returns
dimensionality

Implements CDotFeatures.

Definition at line 56 of file ExplicitSpecFeatures.cpp.

EFeatureClass get_feature_class ( )
virtual

get feature class

Returns
feature class

Implements CFeatures.

Definition at line 183 of file ExplicitSpecFeatures.cpp.

void * get_feature_iterator ( int32_t  vector_index)
virtual

iterate over the non-zero features

call get_feature_iterator first, followed by get_next_feature and free_feature_iterator to cleanup

Parameters
vector_indexthe index of the vector over whose components to iterate over
Returns
feature iterator (to be passed to get_next_feature)

Implements CDotFeatures.

Definition at line 155 of file ExplicitSpecFeatures.cpp.

EFeatureType get_feature_type ( )
virtual

get feature type

Returns
templated feature type

Implements CFeatures.

Definition at line 178 of file ExplicitSpecFeatures.cpp.

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

Implements CSGObject.

Definition at line 169 of file ExplicitSpecFeatures.h.

bool get_next_feature ( int32_t &  index,
float64_t value,
void *  iterator 
)
virtual

iterate over the non-zero features

call this function with the iterator returned by get_first_feature and call free_feature_iterator to cleanup

Parameters
indexis returned by reference (-1 when not available)
valueis returned by reference
iteratoras returned by get_first_feature
Returns
true if a new non-zero feature got returned

Implements CDotFeatures.

Definition at line 161 of file ExplicitSpecFeatures.cpp.

int32_t get_nnz_features_for_vector ( int32_t  num)
virtual

get number of non-zero features in vector

Parameters
numwhich vector
Returns
number of non-zero features in vector

Implements CDotFeatures.

Definition at line 172 of file ExplicitSpecFeatures.cpp.

int32_t get_num_vectors ( ) const
virtual

get number of strings

Returns
number of strings

Implements CFeatures.

Definition at line 188 of file ExplicitSpecFeatures.cpp.

int32_t get_size ( )
virtual

get size of one element

Returns
size of one element

Implements CFeatures.

Definition at line 193 of file ExplicitSpecFeatures.cpp.

void obtain_kmer_spectrum ( CStringFeatures< uint16_t > *  str)
protected

obtain the k-spectrum from a list of strings

Parameters
strthe string feature object already in k-mer format

Definition at line 107 of file ExplicitSpecFeatures.cpp.

Member Data Documentation

int32_t alphabet_size
protected

size of alphabet

Definition at line 187 of file ExplicitSpecFeatures.h.

float64_t** k_spectrum
protected

k-mer counts for all strings

Definition at line 192 of file ExplicitSpecFeatures.h.

int32_t num_strings
protected

number of strings

Definition at line 185 of file ExplicitSpecFeatures.h.

int32_t spec_size
protected

size of k-mer spectrum

Definition at line 190 of file ExplicitSpecFeatures.h.

bool use_normalization
protected

use sqrtdiag normalization

Definition at line 183 of file ExplicitSpecFeatures.h.


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

SHOGUN Machine Learning Toolbox - Documentation