Features that compute the Weighted Spectrum Kernel feature space explicitly.
Definition at line 30 of file ImplicitWeightedSpecFeatures.h.
Public Member Functions | |
CImplicitWeightedSpecFeatures (void) | |
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 |
CImplicitWeightedSpecFeatures | ( | void | ) |
default constructor
Definition at line 16 of file ImplicitWeightedSpecFeatures.cpp.
CImplicitWeightedSpecFeatures | ( | CStringFeatures< uint16_t > * | str, | |
bool | normalize = true | |||
) |
constructor
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.
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
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
Definition at line 51 of file ImplicitWeightedSpecFeatures.cpp.
compute dot product between vector1 and a dense vector
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
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
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
iterator | as returned by get_first_feature |
Implements CDotFeatures.
Definition at line 299 of file ImplicitWeightedSpecFeatures.cpp.
virtual 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())
Implements CDotFeatures.
Definition at line 61 of file ImplicitWeightedSpecFeatures.h.
virtual EFeatureClass get_feature_class | ( | ) | [virtual] |
get feature class
Implements CFeatures.
Definition at line 123 of file ImplicitWeightedSpecFeatures.h.
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
vector_index | the index of the vector over whose components to iterate over |
Implements CDotFeatures.
Definition at line 248 of file ImplicitWeightedSpecFeatures.cpp.
virtual EFeatureType get_feature_type | ( | ) | [virtual] |
get feature type
Implements CFeatures.
Definition at line 114 of file ImplicitWeightedSpecFeatures.h.
virtual const char* get_name | ( | void | ) | const [virtual] |
Implements CSGObject.
Definition at line 217 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
index | is returned by reference (-1 when not available) | |
value | is returned by reference | |
iterator | as returned by get_first_feature |
Implements CDotFeatures.
Definition at line 269 of file ImplicitWeightedSpecFeatures.cpp.
virtual int32_t get_nnz_features_for_vector | ( | int32_t | num | ) | [virtual] |
get number of non-zero features in vector
num | which vector |
Implements CDotFeatures.
Definition at line 98 of file ImplicitWeightedSpecFeatures.h.
virtual int32_t get_num_vectors | ( | ) | const [virtual] |
get number of strings
Implements CFeatures.
Definition at line 132 of file ImplicitWeightedSpecFeatures.h.
virtual int32_t get_size | ( | ) | [virtual] |
get size of one element
Implements CFeatures.
Definition at line 141 of file ImplicitWeightedSpecFeatures.h.
bool set_wd_weights | ( | ) |
set weighted degree weights
Definition at line 62 of file ImplicitWeightedSpecFeatures.cpp.
bool set_weights | ( | float64_t * | w, | |
int32_t | d | |||
) |
set custom weights (swig compatible)
w | weights | |
d | degree (must match number of weights) |
Definition at line 83 of file ImplicitWeightedSpecFeatures.cpp.
int32_t alphabet_size [protected] |
size of alphabet
Definition at line 235 of file ImplicitWeightedSpecFeatures.h.
int32_t degree [protected] |
degree
Definition at line 238 of file ImplicitWeightedSpecFeatures.h.
float64_t* normalization_factors [protected] |
use sqrtdiag normalization
Definition at line 231 of file ImplicitWeightedSpecFeatures.h.
int32_t num_strings [protected] |
number of strings
Definition at line 233 of file ImplicitWeightedSpecFeatures.h.
int32_t spec_size [protected] |
size of k-mer spectrum
Definition at line 240 of file ImplicitWeightedSpecFeatures.h.
float64_t* spec_weights [protected] |
weights for each of the subkernels of degree 1...d
Definition at line 243 of file ImplicitWeightedSpecFeatures.h.
CStringFeatures<uint16_t>* strings [protected] |
reference to strings
Definition at line 228 of file ImplicitWeightedSpecFeatures.h.