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CFKFeatures Class Reference

Detailed Description

The class FKFeatures implements Fischer kernel features obtained from two Hidden Markov models.

It was used in

K. Tsuda, M. Kawanabe, G. Raetsch, S. Sonnenburg, and K.R. Mueller. A new discriminative kernel from probabilistic models. Neural Computation, 14:2397-2414, 2002.

which also has the details.

Note that FK-features are computed on the fly, so to be effective feature caching should be enabled.

It inherits its functionality from CDenseFeatures, which should be consulted for further reference.

Definition at line 43 of file FKFeatures.h.

Inheritance diagram for CFKFeatures:
[legend]

Public Member Functions

 CFKFeatures ()
 
 CFKFeatures (int32_t size, CHMM *p, CHMM *n)
 
 CFKFeatures (const CFKFeatures &orig)
 
virtual ~CFKFeatures ()
 
void set_models (CHMM *p, CHMM *n)
 
void set_a (float64_t a)
 
float64_t get_a ()
 
virtual float64_tset_feature_matrix ()
 
float64_t set_opt_a (float64_t a=-1)
 
float64_t get_weight_a ()
 
virtual const char * get_name () const
 
virtual CFeaturesduplicate () const
 
void free_feature_matrix ()
 
void free_features ()
 
float64_tget_feature_vector (int32_t num, int32_t &len, bool &dofree)
 
SGVector< float64_tget_feature_vector (int32_t num)
 
void set_feature_vector (SGVector< float64_t > vector, int32_t num)
 
void free_feature_vector (float64_t *feat_vec, int32_t num, bool dofree)
 
void free_feature_vector (SGVector< float64_t > vec, int32_t num)
 
void vector_subset (int32_t *idx, int32_t idx_len)
 
void feature_subset (int32_t *idx, int32_t idx_len)
 
SGMatrix< float64_tget_feature_matrix ()
 
float64_tget_feature_matrix (int32_t &num_feat, int32_t &num_vec)
 
SGMatrix< float64_tsteal_feature_matrix ()
 
void set_feature_matrix (SGMatrix< float64_t > matrix)
 
CDenseFeatures< float64_t > * get_transposed ()
 
float64_tget_transposed (int32_t &num_feat, int32_t &num_vec)
 
virtual void copy_feature_matrix (SGMatrix< float64_t > src)
 
void obtain_from_dot (CDotFeatures *df)
 
virtual bool apply_preprocessor (bool force_preprocessing=false)
 
virtual int32_t get_num_vectors () const
 
int32_t get_num_features () const
 
void set_num_features (int32_t num)
 
void set_num_vectors (int32_t num)
 
void initialize_cache ()
 
virtual EFeatureClass get_feature_class () const
 
virtual EFeatureType get_feature_type () const
 
virtual bool reshape (int32_t p_num_features, int32_t p_num_vectors)
 
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 void load (CFile *loader)
 
virtual void save (CFile *saver)
 
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 CFeaturescopy_subset (SGVector< index_t > indices)
 
virtual CFeaturescopy_dimension_subset (SGVector< index_t > dims)
 
virtual bool is_equal (CDenseFeatures *rhs)
 
CFeaturescreate_merged_copy (CList *other)
 
CFeaturescreate_merged_copy (CFeatures *other)
 
virtual CFeaturesshallow_subset_copy ()
 
virtual float64_t dense_dot_sgvec (int32_t vec_idx1, const SGVector< float64_t > vec2)
 
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 ()
 
virtual void add_preprocessor (CPreprocessor *p)
 
virtual void del_preprocessor (int32_t num)
 
CPreprocessorget_preprocessor (int32_t num) const
 
void set_preprocessed (int32_t num)
 
bool is_preprocessed (int32_t num) const
 
int32_t get_num_preprocessed () const
 
int32_t get_num_preprocessors () const
 
void clean_preprocessors ()
 
void list_preprocessors ()
 
int32_t get_cache_size () const
 
void list_feature_obj () const
 
bool check_feature_compatibility (CFeatures *f) const
 
bool has_property (EFeatureProperty p) const
 
void set_property (EFeatureProperty p)
 
void unset_property (EFeatureProperty p)
 
virtual void add_subset (SGVector< index_t > subset)
 
virtual void add_subset_in_place (SGVector< index_t > subset)
 
virtual void remove_subset ()
 
virtual void remove_all_subsets ()
 
virtual CSubsetStackget_subset_stack ()
 
virtual void subset_changed_post ()
 
virtual bool support_compatible_class () const
 
virtual bool get_feature_class_compatibility (EFeatureClass rhs) const
 
virtual CSGObjectshallow_copy () const
 
virtual CSGObjectdeep_copy () const
 
virtual bool is_generic (EPrimitiveType *generic) const
 
template<class T >
void set_generic ()
 
template<>
void set_generic ()
 
template<>
void set_generic ()
 
template<>
void set_generic ()
 
template<>
void set_generic ()
 
template<>
void set_generic ()
 
template<>
void set_generic ()
 
template<>
void set_generic ()
 
template<>
void set_generic ()
 
template<>
void set_generic ()
 
template<>
void set_generic ()
 
template<>
void set_generic ()
 
template<>
void set_generic ()
 
template<>
void set_generic ()
 
template<>
void set_generic ()
 
template<>
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 ()
 
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_gradient_parameter_dictionary (CMap< TParameter *, CSGObject * > *dict)
 
bool has (const std::string &name) const
 
template<typename T >
bool has (const Tag< T > &tag) const
 
template<typename T , typename U = void>
bool has (const std::string &name) const
 
template<typename T >
void set (const Tag< T > &_tag, const T &value)
 
template<typename T , typename U = void>
void set (const std::string &name, const T &value)
 
template<typename T >
get (const Tag< T > &_tag) const
 
template<typename T , typename U = void>
get (const std::string &name) const
 
virtual void update_parameter_hash ()
 
virtual bool parameter_hash_changed ()
 
virtual bool equals (CSGObject *other, float64_t accuracy=0.0, bool tolerant=false)
 
virtual CSGObjectclone ()
 

Static Public Member Functions

static CDenseFeaturesobtain_from_generic (CFeatures *const base_features)
 
static void * dense_dot_range_helper (void *p)
 
static SGVector< float64_tget_mean (CDotFeatures *lhs, CDotFeatures *rhs)
 
static SGMatrix< float64_tcompute_cov (CDotFeatures *lhs, CDotFeatures *rhs)
 

Public Attributes

SGIOio
 
Parallelparallel
 
Versionversion
 
Parameterm_parameters
 
Parameterm_model_selection_parameters
 
Parameterm_gradient_parameters
 
uint32_t m_hash
 

Protected Member Functions

virtual float64_tcompute_feature_vector (int32_t num, int32_t &len, float64_t *target=NULL)
 
void compute_feature_vector (float64_t *addr, int32_t num, int32_t &len)
 
float64_t deriv_a (float64_t a, int32_t dimension=-1)
 
void display_progress (int32_t start, int32_t stop, int32_t v)
 
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)
 
template<typename T >
void register_param (Tag< T > &_tag, const T &value)
 
template<typename T >
void register_param (const std::string &name, const T &value)
 

Protected Attributes

CHMMpos
 
CHMMneg
 
float64_tpos_prob
 
float64_tneg_prob
 
float64_t weight_a
 
int32_t num_vectors
 number of vectors in cache More...
 
int32_t num_features
 number of features in cache More...
 
SGMatrix< float64_tfeature_matrix
 
CCache< float64_t > * feature_cache
 
float64_t combined_weight
 feature weighting in combined dot features More...
 
CSubsetStackm_subset_stack
 

Constructor & Destructor Documentation

default constructor

Definition at line 19 of file FKFeatures.cpp.

CFKFeatures ( int32_t  size,
CHMM p,
CHMM n 
)

constructor

Parameters
sizecache size
ppositive HMM
nnegative HMM

Definition at line 24 of file FKFeatures.cpp.

CFKFeatures ( const CFKFeatures orig)

copy constructor

Definition at line 32 of file FKFeatures.cpp.

~CFKFeatures ( )
virtual

Definition at line 37 of file FKFeatures.cpp.

Member Function Documentation

void add_preprocessor ( CPreprocessor p)
virtualinherited

add preprocessor

Parameters
ppreprocessor to set

Definition at line 85 of file Features.cpp.

void add_subset ( SGVector< index_t subset)
virtualinherited

Adds a subset of indices on top of the current subsets (possibly subset of subset). Every call causes a new active index vector to be stored. Added subsets can be removed one-by-one. If this is not needed, add_subset_in_place() should be used (does not store intermediate index vectors)

Calls subset_changed_post() afterwards

Parameters
subsetsubset of indices to add

Reimplemented in CCombinedFeatures.

Definition at line 310 of file Features.cpp.

void add_subset_in_place ( SGVector< index_t subset)
virtualinherited

Sets/changes latest added subset. This allows to add multiple subsets with in-place memory requirements. They cannot be removed one-by-one afterwards, only the latest active can. If this is needed, use add_subset(). If no subset is active, this just adds.

Calls subset_changed_post() afterwards

Parameters
subsetsubset of indices to replace the latest one with.

Definition at line 316 of file Features.cpp.

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

add vector 1 multiplied with alpha to dense vector2

possible with subset

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.

virtual bool apply_preprocessor ( bool  force_preprocessing = false)
virtualinherited

apply preprocessor

applies preprocessors to ALL features (subset removed before and restored afterwards)

not possible with subset

Parameters
force_preprocessingif preprocssing shall be forced
Returns
if applying was successful
void benchmark_add_to_dense_vector ( int32_t  repeats = 5)
inherited

run benchmark for add_to_dense_vec

Definition at line 318 of file DotFeatures.cpp.

void benchmark_dense_dot_range ( int32_t  repeats = 5)
inherited

run benchmark for dense_dot_range

Definition at line 341 of file DotFeatures.cpp.

void build_gradient_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 630 of file SGObject.cpp.

bool check_feature_compatibility ( CFeatures f) const
inherited

check feature compatibility

Parameters
ffeatures to check for compatibility
Returns
if features are compatible

Definition at line 283 of file Features.cpp.

void clean_preprocessors ( )
inherited

clears all preprocs

Definition at line 116 of file Features.cpp.

CSGObject * clone ( )
virtualinherited

Creates a clone of the current object. This is done via recursively traversing all parameters, which corresponds to a deep copy. Calling equals on the cloned object always returns true although none of the memory of both objects overlaps.

Returns
an identical copy of the given object, which is disjoint in memory. NULL if the clone fails. Note that the returned object is SG_REF'ed

Definition at line 747 of file SGObject.cpp.

SGMatrix< float64_t > compute_cov ( CDotFeatures lhs,
CDotFeatures rhs 
)
staticinherited

compute the covariance of two CDotFeatures together

Returns
covariance

Definition at line 469 of file DotFeatures.cpp.

float64_t * compute_feature_vector ( int32_t  num,
int32_t &  len,
float64_t target = NULL 
)
protectedvirtual

compute feature vector

Parameters
numnum
lenlen
target
Returns
something floaty

Reimplemented from CDenseFeatures< float64_t >.

Definition at line 148 of file FKFeatures.cpp.

void compute_feature_vector ( float64_t addr,
int32_t  num,
int32_t &  len 
)
protected

computes the feature vector to the address addr

Parameters
addraddress
numnum
lenlen

Definition at line 168 of file FKFeatures.cpp.

virtual CFeatures* copy_dimension_subset ( SGVector< index_t dims)
virtualinherited

Creates a new CFeatures instance containing only the dimensions of the feature vector which are specified by the provided indices.

This method is needed for feature selection tasks

possible with subset

Parameters
dimsindices of feature dimensions to copy
Returns
new CFeatures instance with copies of specified features

Reimplemented from CFeatures.

virtual void copy_feature_matrix ( SGMatrix< float64_t src)
virtualinherited

copy feature matrix store copy of feature_matrix, where num_features is the column offset, and columns are linear in memory see below for definition of feature_matrix

not possible with subset

Parameters
srcfeature matrix to copy
virtual CFeatures* copy_subset ( SGVector< index_t indices)
virtualinherited

Creates a new CFeatures instance containing copies of the elements which are specified by the provided indices.

possible with subset

Parameters
indicesindices of feature elements to copy
Returns
new CFeatures instance with copies of feature data

Reimplemented from CFeatures.

CFeatures* create_merged_copy ( CList other)
virtualinherited

Takes a list of feature instances and returns a new instance which is a concatenation of a copy if this instace's data and the given instancess data. Note that the feature types have to be equal.

Parameters
otherfeature object to append
Returns
new feature object which contains copy of data of this instance and of given one

Reimplemented from CFeatures.

CFeatures* create_merged_copy ( CFeatures other)
virtualinherited

Convenience method for method with same name and list as parameter.

Parameters
otherfeature object to append
Returns
new feature object which contains copy of data of this instance and of given one

Reimplemented from CFeatures.

CSGObject * deep_copy ( ) const
virtualinherited

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

Definition at line 231 of file SGObject.cpp.

void del_preprocessor ( int32_t  num)
virtualinherited

delete preprocessor from list

Parameters
numindex of preprocessor in list

Definition at line 122 of file Features.cpp.

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

compute dot product between vector1 and a dense vector

possible with subset

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

Implements CDotFeatures.

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 
)
virtualinherited

Compute the dot product for a range of vectors. This function makes use of dense_dot alphas[i] * sparse[i]^T * w + b

Parameters
outputresult for the given vector range
startstart vector range from this idx
stopstop vector range at this idx
alphasscalars to multiply with, may be NULL
vecdense vector to compute dot product with
dimlength of the dense vector
bbias

note that the result will be written to output[0...(stop-start-1)]

Reimplemented in CCombinedDotFeatures, and CHashedWDFeaturesTransposed.

Definition at line 67 of file DotFeatures.cpp.

void * dense_dot_range_helper ( void *  p)
staticinherited

Compute the dot product for a range of vectors. This function is called by the threads created in dense_dot_range

Definition at line 231 of file DotFeatures.cpp.

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 
)
virtualinherited

Compute the dot product for a subset of vectors. This function makes use of dense_dot alphas[i] * sparse[i]^T * w + b

Parameters
sub_indexindex for which to compute outputs
numlength of index
outputresult for the given vector range
alphasscalars to multiply with, may be NULL
vecdense vector to compute dot product with
dimlength of the dense vector
bbias

Reimplemented in CCombinedDotFeatures, and CHashedWDFeaturesTransposed.

Definition at line 153 of file DotFeatures.cpp.

float64_t dense_dot_sgvec ( int32_t  vec_idx1,
const SGVector< float64_t vec2 
)
virtualinherited

compute dot product between vector1 and a dense vector

Parameters
vec_idx1index of first vector
vec2dense vector

Reimplemented in CHashedDocDotFeatures.

Definition at line 62 of file DotFeatures.cpp.

float64_t deriv_a ( float64_t  a,
int32_t  dimension = -1 
)
protected

deriv a

Parameters
aa
dimensiondimension

Definition at line 43 of file FKFeatures.cpp.

void display_progress ( int32_t  start,
int32_t  stop,
int32_t  v 
)
protectedinherited

display progress output

Parameters
startminimum value
stopmaximum value
vcurrent value

Definition at line 528 of file DotFeatures.cpp.

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

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

possible with subset

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

Implements CDotFeatures.

virtual CFeatures* duplicate ( ) const
virtualinherited

duplicate feature object

Returns
feature object

Implements CFeatures.

bool equals ( CSGObject other,
float64_t  accuracy = 0.0,
bool  tolerant = false 
)
virtualinherited

Recursively compares the current SGObject to another one. Compares all registered numerical parameters, recursion upon complex (SGObject) parameters. Does not compare pointers!

May be overwritten but please do with care! Should not be necessary in most cases.

Parameters
otherobject to compare with
accuracyaccuracy to use for comparison (optional)
tolerantallows linient check on float equality (within accuracy)
Returns
true if all parameters were equal, false if not

Definition at line 651 of file SGObject.cpp.

void feature_subset ( int32_t *  idx,
int32_t  idx_len 
)
inherited

Extracts the features mentioned in idx and replaces them in feature matrix in place.

It does not resize the allocated memory block.

Not possible with subset.

Parameters
idxindex with features that shall remain in the feature matrix
idx_lenlength of the index

Note: assumes idx is sorted

virtual void free_feature_iterator ( void *  iterator)
virtualinherited

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

Parameters
iteratoras returned by get_first_feature

Implements CDotFeatures.

void free_feature_matrix ( )
inherited

free feature matrix

Any subset is removed

void free_feature_vector ( float64_t feat_vec,
int32_t  num,
bool  dofree 
)
inherited

free feature vector

possible with subset

Parameters
feat_vecfeature vector to free
numindex in feature cache
dofreeif vector should be really deleted
void free_feature_vector ( SGVector< float64_t vec,
int32_t  num 
)
inherited

free feature vector

possible with subset

Parameters
vecfeature vector to free
numindex in feature cache
void free_features ( )
inherited

free feature matrix and cache

Any subset is removed

T get ( const Tag< T > &  _tag) const
inherited

Getter for a class parameter, identified by a Tag. Throws an exception if the class does not have such a parameter.

Parameters
_tagname and type information of parameter
Returns
value of the parameter identified by the input tag

Definition at line 367 of file SGObject.h.

T get ( const std::string &  name) const
inherited

Getter for a class parameter, identified by a name. Throws an exception if the class does not have such a parameter.

Parameters
namename of the parameter
Returns
value of the parameter corresponding to the input name and type

Definition at line 388 of file SGObject.h.

float64_t get_a ( )

get weight a

Returns
weight a

Definition at line 82 of file FKFeatures.h.

int32_t get_cache_size ( ) const
inherited

get cache size

Returns
cache size

Definition at line 160 of file Features.cpp.

float64_t get_combined_feature_weight ( )
inherited

get combined feature weight

Returns
combined feature weight

Definition at line 154 of file DotFeatures.h.

SGMatrix< float64_t > get_computed_dot_feature_matrix ( )
inherited

compute the feature matrix in feature space

Returns
computed feature matrix

Definition at line 284 of file DotFeatures.cpp.

SGVector< float64_t > get_computed_dot_feature_vector ( int32_t  num)
inherited

compute the feature vector in feature space

Returns
computed feature vector

Definition at line 305 of file DotFeatures.cpp.

SGMatrix< float64_t > get_cov ( )
virtualinherited

get covariance

Returns
covariance

Definition at line 427 of file DotFeatures.cpp.

virtual int32_t get_dim_feature_space ( ) const
virtualinherited

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.

virtual EFeatureClass get_feature_class ( ) const
virtualinherited

get feature class

Returns
feature class DENSE

Implements CFeatures.

bool get_feature_class_compatibility ( EFeatureClass  rhs) const
virtualinherited

Given a class in right hand side, does this class support compatible computation?

for example, is this->dot(rhs_prt) valid, where rhs_prt is the class in right hand side

Parameters
rhsthe class in right hand side
Returns
whether this class supports compatible computation

Reimplemented in CDenseSubSamplesFeatures< ST >.

Definition at line 355 of file Features.cpp.

virtual void* get_feature_iterator ( int32_t  vector_index)
virtualinherited

iterate over the non-zero features

call get_feature_iterator first, followed by get_next_feature and free_feature_iterator to cleanup

possible with subset

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.

SGMatrix<float64_t > get_feature_matrix ( )
inherited

Getter the feature matrix

in-place without subset a copy with subset

Returns
matrix feature matrix
float64_t * get_feature_matrix ( int32_t &  num_feat,
int32_t &  num_vec 
)
inherited

get the pointer to the feature matrix num_feat,num_vectors are returned by reference

subset is ignored

Parameters
num_featnumber of features in matrix
num_vecnumber of vectors in matrix
Returns
feature matrix
virtual EFeatureType get_feature_type ( ) const
virtualinherited

get feature type

Returns
templated feature type

Implements CFeatures.

float64_t * get_feature_vector ( int32_t  num,
int32_t &  len,
bool &  dofree 
)
inherited

get feature vector for sample num from the matrix as it is if matrix is initialized, else return preprocessed compute_feature_vector (not implemented)

Parameters
numindex of feature vector
lenlength is returned by reference
dofreewhether returned vector must be freed by caller via free_feature_vector
Returns
feature vector
SGVector<float64_t > get_feature_vector ( int32_t  num)
inherited

get feature vector num

possible with subset

Parameters
numindex of vector
Returns
feature vector
SGIO * get_global_io ( )
inherited

get the io object

Returns
io object

Definition at line 268 of file SGObject.cpp.

Parallel * get_global_parallel ( )
inherited

get the parallel object

Returns
parallel object

Definition at line 310 of file SGObject.cpp.

Version * get_global_version ( )
inherited

get the version object

Returns
version object

Definition at line 323 of file SGObject.cpp.

SGVector< float64_t > get_mean ( )
virtualinherited

get mean

Returns
mean returned

Definition at line 384 of file DotFeatures.cpp.

SGVector< float64_t > get_mean ( CDotFeatures lhs,
CDotFeatures rhs 
)
staticinherited

get mean of two CDotFeature objects

Returns
mean returned

Definition at line 402 of file DotFeatures.cpp.

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

Definition at line 531 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 555 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 568 of file SGObject.cpp.

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

Reimplemented from CDenseFeatures< float64_t >.

Definition at line 107 of file FKFeatures.h.

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

iterate over the non-zero features

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

possible with subset

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.

virtual int32_t get_nnz_features_for_vector ( int32_t  num)
virtualinherited

get number of non-zero features in vector

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

Implements CDotFeatures.

int32_t get_num_features ( ) const
inherited

get number of features (of possible subset)

Returns
number of features
int32_t get_num_preprocessed ( ) const
inherited

get the number of applied preprocs

Returns
number of applied preprocessors

Definition at line 103 of file Features.cpp.

int32_t get_num_preprocessors ( ) const
inherited

get number of preprocessors

Returns
number of preprocessors

Definition at line 155 of file Features.cpp.

virtual int32_t get_num_vectors ( ) const
virtualinherited

get number of feature vectors

Returns
number of feature vectors

Implements CFeatures.

CPreprocessor * get_preprocessor ( int32_t  num) const
inherited

get specified preprocessor

Parameters
numindex of preprocessor in list

Definition at line 93 of file Features.cpp.

CSubsetStack * get_subset_stack ( )
virtualinherited

returns subset stack

Returns
subset stack

Definition at line 334 of file Features.cpp.

CDenseFeatures<float64_t >* get_transposed ( )
inherited

get a transposed copy of the features

possible with subset

Returns
transposed copy
float64_t * get_transposed ( int32_t &  num_feat,
int32_t &  num_vec 
)
inherited

compute and return the transpose of the feature matrix which will be prepocessed. num_feat, num_vectors are returned by reference caller has to clean up

possible with subset

Parameters
num_featnumber of features in matrix
num_vecnumber of vectors in matrix
Returns
transposed sparse feature matrix
float64_t get_weight_a ( )

get weight_a

Returns
weight_a

Definition at line 104 of file FKFeatures.h.

bool has ( const std::string &  name) const
inherited

Checks if object has a class parameter identified by a name.

Parameters
namename of the parameter
Returns
true if the parameter exists with the input name

Definition at line 289 of file SGObject.h.

bool has ( const Tag< T > &  tag) const
inherited

Checks if object has a class parameter identified by a Tag.

Parameters
tagtag of the parameter containing name and type information
Returns
true if the parameter exists with the input tag

Definition at line 301 of file SGObject.h.

bool has ( const std::string &  name) const
inherited

Checks if a type exists for a class parameter identified by a name.

Parameters
namename of the parameter
Returns
true if the parameter exists with the input name and type

Definition at line 312 of file SGObject.h.

bool has_property ( EFeatureProperty  p) const
inherited

check if features have given property

Parameters
pfeature property
Returns
if features have given property

Definition at line 295 of file Features.cpp.

void initialize_cache ( )
inherited

Initialize cache

not possible with subset

virtual bool is_equal ( CDenseFeatures< float64_t > *  rhs)
virtualinherited

checks if the contents of this CDenseFeatures object are the same to the contents of rhs

Parameters
rhsother CDenseFeatures object to compare to this one
Returns
whether they represent the same information
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 329 of file SGObject.cpp.

bool is_preprocessed ( int32_t  num) const
inherited

get whether specified preprocessor was already applied

Parameters
numindex of preprocessor in list

Definition at line 149 of file Features.cpp.

void list_feature_obj ( ) const
inherited

list feature object

Definition at line 171 of file Features.cpp.

void list_preprocessors ( )
inherited

print preprocessors

Definition at line 131 of file Features.cpp.

virtual void load ( CFile loader)
virtualinherited

load features from file

Parameters
loaderFile object via which to load data

Reimplemented from CFeatures.

bool load_serializable ( CSerializableFile file,
const char *  prefix = "" 
)
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
Returns
TRUE if done, otherwise FALSE

Definition at line 402 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 occurs.

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

Definition at line 459 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 occurs.

Reimplemented in CDynamicArray< T >, CDynamicArray< float64_t >, CDynamicArray< float32_t >, CDynamicArray< int32_t >, CDynamicArray< char >, CDynamicArray< bool >, and CDynamicObjectArray.

Definition at line 454 of file SGObject.cpp.

void obtain_from_dot ( CDotFeatures df)
inherited

obtain dense features from other dotfeatures

removes any subset before

Parameters
dfdotfeatures to obtain features from
static CDenseFeatures* obtain_from_generic ( CFeatures *const  base_features)
staticinherited

helper method used to specialize a base class instance

bool parameter_hash_changed ( )
virtualinherited
Returns
whether parameter combination has changed since last update

Definition at line 295 of file SGObject.cpp.

void print_modsel_params ( )
inherited

prints all parameter registered for model selection and their type

Definition at line 507 of file SGObject.cpp.

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

prints registered parameters out

Parameters
prefixprefix for members

Definition at line 341 of file SGObject.cpp.

void register_param ( Tag< T > &  _tag,
const T &  value 
)
protectedinherited

Registers a class parameter which is identified by a tag. This enables the parameter to be modified by set() and retrieved by get(). Parameters can be registered in the constructor of the class.

Parameters
_tagname and type information of parameter
valuevalue of the parameter

Definition at line 439 of file SGObject.h.

void register_param ( const std::string &  name,
const T &  value 
)
protectedinherited

Registers a class parameter which is identified by a name. This enables the parameter to be modified by set() and retrieved by get(). Parameters can be registered in the constructor of the class.

Parameters
namename of the parameter
valuevalue of the parameter along with type information

Definition at line 452 of file SGObject.h.

void remove_all_subsets ( )
virtualinherited

removes all subsets Calls subset_changed_post() afterwards

Reimplemented in CCombinedFeatures.

Definition at line 328 of file Features.cpp.

void remove_subset ( )
virtualinherited

removes that last added subset from subset stack, if existing Calls subset_changed_post() afterwards

Reimplemented in CCombinedFeatures.

Definition at line 322 of file Features.cpp.

virtual bool reshape ( int32_t  p_num_features,
int32_t  p_num_vectors 
)
virtualinherited

reshape

not possible with subset

Parameters
p_num_featuresnew number of features
p_num_vectorsnew number of vectors
Returns
if reshaping was successful

Reimplemented from CFeatures.

virtual void save ( CFile saver)
virtualinherited

save features to file

Parameters
saverFile object via which to save data

Reimplemented from CFeatures.

bool save_serializable ( CSerializableFile file,
const char *  prefix = "" 
)
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
Returns
TRUE if done, otherwise FALSE

Definition at line 347 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 occurs.

Reimplemented in CKernel.

Definition at line 469 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 occurs.

Reimplemented in CKernel, CDynamicArray< T >, CDynamicArray< float64_t >, CDynamicArray< float32_t >, CDynamicArray< int32_t >, CDynamicArray< char >, CDynamicArray< bool >, and CDynamicObjectArray.

Definition at line 464 of file SGObject.cpp.

void set ( const Tag< T > &  _tag,
const T &  value 
)
inherited

Setter for a class parameter, identified by a Tag. Throws an exception if the class does not have such a parameter.

Parameters
_tagname and type information of parameter
valuevalue of the parameter

Definition at line 328 of file SGObject.h.

void set ( const std::string &  name,
const T &  value 
)
inherited

Setter for a class parameter, identified by a name. Throws an exception if the class does not have such a parameter.

Parameters
namename of the parameter
valuevalue of the parameter along with type information

Definition at line 354 of file SGObject.h.

void set_a ( float64_t  a)

set weight a

Parameters
aweight a

Definition at line 73 of file FKFeatures.h.

void set_combined_feature_weight ( float64_t  nw)
inherited

set combined kernel weight

Parameters
nwnew combined feature weight

Definition at line 160 of file DotFeatures.h.

float64_t * set_feature_matrix ( )
virtual

set feature matrix

Returns
something floaty

Definition at line 214 of file FKFeatures.cpp.

void set_feature_matrix ( SGMatrix< float64_t matrix)
inherited

Setter for feature matrix

any subset is removed

num_cols is number of feature vectors num_rows is number of dims of vectors see below for definition of feature_matrix

Parameters
matrixfeature matrix to set
void set_feature_vector ( SGVector< float64_t vector,
int32_t  num 
)
inherited

set feature vector num

possible with subset

Parameters
vectorvector
numindex if vector to set
void set_generic ( )
inherited

Definition at line 74 of file SGObject.cpp.

void set_generic ( )
inherited

Definition at line 79 of file SGObject.cpp.

void set_generic ( )
inherited

Definition at line 84 of file SGObject.cpp.

void set_generic ( )
inherited

Definition at line 89 of file SGObject.cpp.

void set_generic ( )
inherited

Definition at line 94 of file SGObject.cpp.

void set_generic ( )
inherited

Definition at line 99 of file SGObject.cpp.

void set_generic ( )
inherited

Definition at line 104 of file SGObject.cpp.

void set_generic ( )
inherited

Definition at line 109 of file SGObject.cpp.

void set_generic ( )
inherited

Definition at line 114 of file SGObject.cpp.

void set_generic ( )
inherited

Definition at line 119 of file SGObject.cpp.

void set_generic ( )
inherited

Definition at line 124 of file SGObject.cpp.

void set_generic ( )
inherited

Definition at line 129 of file SGObject.cpp.

void set_generic ( )
inherited

Definition at line 134 of file SGObject.cpp.

void set_generic ( )
inherited

Definition at line 139 of file SGObject.cpp.

void set_generic ( )
inherited

Definition at line 144 of file SGObject.cpp.

void set_generic ( )
inherited

set generic type to T

void set_global_io ( SGIO io)
inherited

set the io object

Parameters
ioio object to use

Definition at line 261 of file SGObject.cpp.

void set_global_parallel ( Parallel parallel)
inherited

set the parallel object

Parameters
parallelparallel object to use

Definition at line 274 of file SGObject.cpp.

void set_global_version ( Version version)
inherited

set the version object

Parameters
versionversion object to use

Definition at line 316 of file SGObject.cpp.

void set_models ( CHMM p,
CHMM n 
)

set HMMs

Parameters
ppositive HMM
nnegative HMM

Definition at line 128 of file FKFeatures.cpp.

void set_num_features ( int32_t  num)
inherited

set number of features

Parameters
numnumber to set
void set_num_vectors ( int32_t  num)
inherited

set number of vectors

not possible with subset

Parameters
numnumber to set
float64_t set_opt_a ( float64_t  a = -1)

set opt a

Parameters
aa
Returns
something floaty

Definition at line 91 of file FKFeatures.cpp.

void set_preprocessed ( int32_t  num)
inherited

set applied flag for preprocessor

Parameters
numindex of preprocessor in list

Definition at line 143 of file Features.cpp.

void set_property ( EFeatureProperty  p)
inherited

set property

Parameters
pkernel property to set

Definition at line 300 of file Features.cpp.

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 225 of file SGObject.cpp.

virtual CFeatures* shallow_subset_copy ( )
virtualinherited

Reimplemented from CFeatures.

SGMatrix<float64_t > steal_feature_matrix ( )
inherited

steals feature matrix, i.e. returns matrix and forget about it subset is ignored

Returns
matrix feature matrix
virtual void subset_changed_post ( )
virtualinherited

method may be overwritten to update things that depend on subset

Reimplemented in CStringFeatures< ST >, CStringFeatures< T >, CStringFeatures< uint8_t >, CStringFeatures< char >, and CStringFeatures< uint16_t >.

Definition at line 293 of file Features.h.

virtual bool support_compatible_class ( ) const
virtualinherited

does this class support compatible computation bewteen difference classes? for example, this->dot(rhs_prt), can rhs_prt be an instance of a difference class?

Returns
whether this class supports compatible computation

Reimplemented in CDenseSubSamplesFeatures< ST >.

Definition at line 323 of file Features.h.

void unset_generic ( )
inherited

unset generic type

this has to be called in classes specializing a template class

Definition at line 336 of file SGObject.cpp.

void unset_property ( EFeatureProperty  p)
inherited

unset property

Parameters
pkernel property to unset

Definition at line 305 of file Features.cpp.

void update_parameter_hash ( )
virtualinherited

Updates the hash of current parameter combination

Definition at line 281 of file SGObject.cpp.

void vector_subset ( int32_t *  idx,
int32_t  idx_len 
)
inherited

Extracts the feature vectors mentioned in idx and replaces them in feature matrix in place.

It does not resize the allocated memory block.

not possible with subset

Parameters
idxindex with examples that shall remain in the feature matrix
idx_lenlength of the index

Note: assumes idx is sorted

Member Data Documentation

float64_t combined_weight
protectedinherited

feature weighting in combined dot features

Definition at line 249 of file DotFeatures.h.

CCache<float64_t >* feature_cache
protectedinherited

feature cache

Definition at line 557 of file DenseFeatures.h.

SGMatrix<float64_t > feature_matrix
protectedinherited

Feature matrix and its associated number of vectors and features. Note that num_vectors / num_features above match matrix sizes if feature_matrix.matrix != NULL

Definition at line 554 of file DenseFeatures.h.

SGIO* io
inherited

io

Definition at line 537 of file SGObject.h.

Parameter* m_gradient_parameters
inherited

parameters wrt which we can compute gradients

Definition at line 552 of file SGObject.h.

uint32_t m_hash
inherited

Hash of parameter values

Definition at line 555 of file SGObject.h.

Parameter* m_model_selection_parameters
inherited

model selection parameters

Definition at line 549 of file SGObject.h.

Parameter* m_parameters
inherited

parameters

Definition at line 546 of file SGObject.h.

CSubsetStack* m_subset_stack
protectedinherited

subset used for index transformations

Definition at line 361 of file Features.h.

CHMM* neg
protected

negative HMM

Definition at line 142 of file FKFeatures.h.

float64_t* neg_prob
protected

negative prob

Definition at line 146 of file FKFeatures.h.

int32_t num_features
protectedinherited

number of features in cache

Definition at line 548 of file DenseFeatures.h.

int32_t num_vectors
protectedinherited

number of vectors in cache

Definition at line 545 of file DenseFeatures.h.

Parallel* parallel
inherited

parallel

Definition at line 540 of file SGObject.h.

CHMM* pos
protected

positive HMM

Definition at line 140 of file FKFeatures.h.

float64_t* pos_prob
protected

positive prob

Definition at line 144 of file FKFeatures.h.

Version* version
inherited

version

Definition at line 543 of file SGObject.h.

float64_t weight_a
protected

weight a

Definition at line 148 of file FKFeatures.h.


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

SHOGUN Machine Learning Toolbox - Documentation