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CImplicitWeightedSpecFeatures Class Reference

Detailed Description

Features that compute the Weighted Spectrum Kernel feature space explicitly.

See Also
CWeightedCommWordStringKernel

Definition at line 30 of file ImplicitWeightedSpecFeatures.h.

Inheritance diagram for CImplicitWeightedSpecFeatures:
Inheritance graph
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Public Member Functions

 CImplicitWeightedSpecFeatures ()
 CImplicitWeightedSpecFeatures (CStringFeatures< uint16_t > *str, bool normalize=true)
 CImplicitWeightedSpecFeatures (const CImplicitWeightedSpecFeatures &orig)
virtual ~CImplicitWeightedSpecFeatures ()
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 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 ()
bool set_wd_weights ()
bool set_weights (float64_t *w, int32_t d)
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 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 compute_normalization_const ()
- Protected Member Functions inherited from CDotFeatures
void display_progress (int32_t start, int32_t stop, int32_t v)

Protected Attributes

CStringFeatures< uint16_t > * strings
float64_tnormalization_factors
int32_t num_strings
int32_t alphabet_size
int32_t degree
int32_t spec_size
float64_tspec_weights
- 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 ImplicitWeightedSpecFeatures.cpp.

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

constructor

Parameters
strstringfeatures (of words)
normalizewhether to use sqrtdiag normalization

Definition at line 32 of file ImplicitWeightedSpecFeatures.cpp.

copy constructor

Definition at line 94 of file ImplicitWeightedSpecFeatures.cpp.

Definition at line 102 of file ImplicitWeightedSpecFeatures.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 211 of file ImplicitWeightedSpecFeatures.cpp.

void compute_normalization_const ( )
protected

compute the sqrt diag normalization constant per string

See Also
CSqrtDiagKernelNormalization

Definition at line 51 of file ImplicitWeightedSpecFeatures.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 172 of file ImplicitWeightedSpecFeatures.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 109 of file ImplicitWeightedSpecFeatures.cpp.

CFeatures * duplicate ( ) const
virtual

duplicate feature object

Returns
feature object

Implements CFeatures.

Definition at line 243 of file ImplicitWeightedSpecFeatures.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 304 of file ImplicitWeightedSpecFeatures.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 248 of file ImplicitWeightedSpecFeatures.cpp.

EFeatureClass get_feature_class ( )
virtual

get feature class

Returns
feature class

Implements CFeatures.

Definition at line 330 of file ImplicitWeightedSpecFeatures.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 253 of file ImplicitWeightedSpecFeatures.cpp.

EFeatureType get_feature_type ( )
virtual

get feature type

Returns
templated feature type

Implements CFeatures.

Definition at line 325 of file ImplicitWeightedSpecFeatures.cpp.

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

Implements CSGObject.

Definition at line 193 of file ImplicitWeightedSpecFeatures.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 274 of file ImplicitWeightedSpecFeatures.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 313 of file ImplicitWeightedSpecFeatures.cpp.

int32_t get_num_vectors ( ) const
virtual

get number of strings

Returns
number of strings

Implements CFeatures.

Definition at line 335 of file ImplicitWeightedSpecFeatures.cpp.

int32_t get_size ( )
virtual

get size of one element

Returns
size of one element

Implements CFeatures.

Definition at line 340 of file ImplicitWeightedSpecFeatures.cpp.

bool set_wd_weights ( )

set weighted degree weights

Returns
if setting was successful

Definition at line 62 of file ImplicitWeightedSpecFeatures.cpp.

bool set_weights ( float64_t w,
int32_t  d 
)

set custom weights (swig compatible)

Parameters
wweights
ddegree (must match number of weights)
Returns
if setting was successful

Definition at line 83 of file ImplicitWeightedSpecFeatures.cpp.

Member Data Documentation

int32_t alphabet_size
protected

size of alphabet

Definition at line 211 of file ImplicitWeightedSpecFeatures.h.

int32_t degree
protected

degree

Definition at line 214 of file ImplicitWeightedSpecFeatures.h.

float64_t* normalization_factors
protected

use sqrtdiag normalization

Definition at line 207 of file ImplicitWeightedSpecFeatures.h.

int32_t num_strings
protected

number of strings

Definition at line 209 of file ImplicitWeightedSpecFeatures.h.

int32_t spec_size
protected

size of k-mer spectrum

Definition at line 216 of file ImplicitWeightedSpecFeatures.h.

float64_t* spec_weights
protected

weights for each of the subkernels of degree 1...d

Definition at line 219 of file ImplicitWeightedSpecFeatures.h.

CStringFeatures<uint16_t>* strings
protected

reference to strings

Definition at line 204 of file ImplicitWeightedSpecFeatures.h.


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

SHOGUN Machine Learning Toolbox - Documentation