Public Member Functions | Protected Member Functions | Protected Attributes

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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List of all members.

Public Member Functions

 CImplicitWeightedSpecFeatures ()
 CImplicitWeightedSpecFeatures (CStringFeatures< uint16_t > *str, bool normalize=true)
 CImplicitWeightedSpecFeatures (const CImplicitWeightedSpecFeatures &orig)
virtual ~CImplicitWeightedSpecFeatures ()
virtual CFeatures * duplicate () 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

Protected Member Functions

void compute_normalization_const ()

Protected Attributes

CStringFeatures< uint16_t > * strings
float64_t * normalization_factors
int32_t num_strings
int32_t alphabet_size
int32_t degree
int32_t spec_size
float64_t * spec_weights

Constructor & Destructor Documentation

CImplicitWeightedSpecFeatures (  ) 

default constructor

Definition at line 16 of file ImplicitWeightedSpecFeatures.cpp.

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

constructor

Parameters:
str stringfeatures (of words)
normalize whether to use sqrtdiag normalization

Definition at line 32 of file ImplicitWeightedSpecFeatures.cpp.

CImplicitWeightedSpecFeatures ( const CImplicitWeightedSpecFeatures &  orig  ) 

copy constructor

Definition at line 94 of file ImplicitWeightedSpecFeatures.cpp.

~CImplicitWeightedSpecFeatures (  )  [virtual]

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:
alpha scalar alpha
vec_idx1 index of first vector
vec2 pointer to real valued vector
vec2_len length of real valued vector
abs_val if 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_idx1 index of first vector
vec2 pointer to real valued vector
vec2_len length 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_idx1 index of first vector
df DotFeatures (of same kind) to compute dot product with
vec_idx2 index 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:
iterator as 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_index the 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:
index is returned by reference (-1 when not available)
value is returned by reference
iterator as 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:
num which 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:
w weights
d degree (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.

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