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CSpectrumRBFKernel Class Reference

Detailed Description

spectrum rbf kernel

Definition at line 31 of file SpectrumRBFKernel.h.

Inheritance diagram for CSpectrumRBFKernel:
Inheritance graph
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Public Member Functions

 CSpectrumRBFKernel ()
 
 CSpectrumRBFKernel (int32_t size, float64_t *AA_matrix, int32_t degree, float64_t width)
 
 CSpectrumRBFKernel (CStringFeatures< char > *l, CStringFeatures< char > *r, int32_t size, float64_t *AA_matrix, int32_t degree, float64_t width)
 
virtual ~CSpectrumRBFKernel ()
 
virtual bool init (CFeatures *l, CFeatures *r)
 
virtual void cleanup ()
 
int32_t get_degree () const
 
virtual EKernelType get_kernel_type ()
 
virtual const char * get_name () const
 
bool set_degree (int32_t deg)
 
int32_t get_degree ()
 
bool set_AA_matrix (float64_t *AA_matrix_)
 
- Public Member Functions inherited from CStringKernel< char >
 CStringKernel (int32_t cachesize=0)
 
 CStringKernel (CFeatures *l, CFeatures *r)
 
virtual EFeatureClass get_feature_class ()
 
virtual EFeatureType get_feature_type ()
 
- Public Member Functions inherited from CKernel
 CKernel ()
 
 CKernel (int32_t size)
 
 CKernel (CFeatures *l, CFeatures *r, int32_t size)
 
virtual ~CKernel ()
 
float64_t kernel (int32_t idx_a, int32_t idx_b)
 
SGMatrix< float64_t > get_kernel_matrix ()
 
virtual SGVector< float64_t > get_kernel_col (int32_t j)
 
virtual SGVector< float64_t > get_kernel_row (int32_t i)
 
template<class T >
SGMatrix< T > get_kernel_matrix ()
 
virtual bool set_normalizer (CKernelNormalizer *normalizer)
 
virtual CKernelNormalizer * get_normalizer ()
 
virtual bool init_normalizer ()
 
void load (CFile *loader)
 
void save (CFile *writer)
 
CFeatures * get_lhs ()
 
CFeatures * get_rhs ()
 
virtual int32_t get_num_vec_lhs ()
 
virtual int32_t get_num_vec_rhs ()
 
virtual bool has_features ()
 
bool get_lhs_equals_rhs ()
 
virtual void remove_lhs_and_rhs ()
 
virtual void remove_rhs ()
 takes all necessary steps if the rhs is removed from kernel More...
 
void set_cache_size (int32_t size)
 
int32_t get_cache_size ()
 
void list_kernel ()
 
bool has_property (EKernelProperty p)
 
virtual void clear_normal ()
 
virtual void add_to_normal (int32_t vector_idx, float64_t weight)
 
EOptimizationType get_optimization_type ()
 
virtual void set_optimization_type (EOptimizationType t)
 
bool get_is_initialized ()
 
virtual bool init_optimization (int32_t count, int32_t *IDX, float64_t *weights)
 
virtual bool delete_optimization ()
 
bool init_optimization_svm (CSVM *svm)
 
virtual float64_t compute_optimized (int32_t vector_idx)
 
virtual void compute_batch (int32_t num_vec, int32_t *vec_idx, float64_t *target, int32_t num_suppvec, int32_t *IDX, float64_t *alphas, float64_t factor=1.0)
 
float64_t get_combined_kernel_weight ()
 
void set_combined_kernel_weight (float64_t nw)
 
virtual int32_t get_num_subkernels ()
 
virtual void compute_by_subkernel (int32_t vector_idx, float64_t *subkernel_contrib)
 
virtual const float64_t * get_subkernel_weights (int32_t &num_weights)
 
virtual void set_subkernel_weights (SGVector< float64_t > weights)
 
- 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)
 
SGIO * get_global_io ()
 
void set_global_parallel (Parallel *parallel)
 
Parallel * get_global_parallel ()
 
void set_global_version (Version *version)
 
Version * get_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)
 
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 ()
 

Protected Member Functions

float64_t AA_helper (const char *path, const int degree, const char *joint_seq, unsigned int index)
 
void read_profiles_and_sequences ()
 
float64_t compute (int32_t idx_a, int32_t idx_b)
 
virtual void remove_lhs ()
 
virtual void register_param ()
 
void register_alphabet ()
 
- Protected Member Functions inherited from CKernel
void set_property (EKernelProperty p)
 
void unset_property (EKernelProperty p)
 
void set_is_initialized (bool p_init)
 
int32_t compute_row_start (int64_t offs, int32_t n, bool symmetric)
 
virtual void load_serializable_post () throw (ShogunException)
 
virtual void save_serializable_pre () throw (ShogunException)
 
virtual void save_serializable_post () throw (ShogunException)
 
virtual void register_params ()
 
- Protected Member Functions inherited from CSGObject
virtual void load_serializable_pre () throw (ShogunException)
 

Protected Attributes

CAlphabet * alphabet
 
int32_t degree
 
int32_t max_mismatch
 
float64_t * AA_matrix
 
int32_t AA_matrix_length
 
float64_t width
 
std::vector< std::vector
< float64_t > > 		profiles
 
std::vector< std::string > sequence_labels
 
SGString< char > * sequences
 
CStringFeatures< char > * string_features
 
int32_t nof_sequences
 
int32_t max_sequence_length
 
bool initialized
 
CArray2< float64_t > kernel_matrix
 
int32_t target_letter_0
 
- Protected Attributes inherited from CKernel
int32_t cache_size
 cache_size in MB More...
 
KERNELCACHE_ELEM * kernel_matrix
 
CFeatures * lhs
 feature vectors to occur on left hand side More...
 
CFeatures * rhs
 feature vectors to occur on right hand side More...
 
bool lhs_equals_rhs
 lhs More...
 
int32_t num_lhs
 number of feature vectors on left hand side More...
 
int32_t num_rhs
 number of feature vectors on right hand side More...
 
float64_t combined_kernel_weight
 
bool optimization_initialized
 
EOptimizationType opt_type
 
uint64_t properties
 
CKernelNormalizer * normalizer
 

Additional Inherited Members

- Public Attributes inherited from CSGObject
SGIO * io
 
Parallel * parallel
 
Version * version
 
Parameter * m_parameters
 
Parameter * m_model_selection_parameters
 
- Static Protected Member Functions inherited from CKernel
template<class T >
static void * get_kernel_matrix_helper (void *p)
 

Constructor & Destructor Documentation

CSpectrumRBFKernel ( )

default constructor

Definition at line 39 of file SpectrumRBFKernel.cpp.

CSpectrumRBFKernel ( int32_t  size,
float64_t *  AA_matrix,
int32_t  degree,
float64_t  width 
)

constructor

Parameters
size
AA_matrix
degree
width

Definition at line 46 of file SpectrumRBFKernel.cpp.

CSpectrumRBFKernel ( CStringFeatures< char > *  l,
CStringFeatures< char > *  r,
int32_t  size,
float64_t *  AA_matrix,
int32_t  degree,
float64_t  width 
)

constructor

Parameters
lfeatures of left-hand side
rfeatures of right-hand side
size
AA_matrix
degree
width

Definition at line 71 of file SpectrumRBFKernel.cpp.

~CSpectrumRBFKernel ( )
virtual

destructor

Definition at line 84 of file SpectrumRBFKernel.cpp.

Member Function Documentation

float64_t AA_helper ( const char *  path,
const int  degree,
const char *  joint_seq,
unsigned int  index 
)
protected

AA helper

Parameters
path
degree
joint_seq
index

Definition at line 336 of file SpectrumRBFKernel.cpp.

void cleanup ( )
virtual

clean up kernel

Reimplemented from CKernel.

Definition at line 320 of file SpectrumRBFKernel.cpp.

float64_t compute ( int32_t  idx_a,
int32_t  idx_b 
)
protectedvirtual

compute kernel function for features a and b idx_{a,b} denote the index of the feature vectors in the corresponding feature object

Parameters
idx_aindex a
idx_bindex b
Returns
computed kernel function at indices a,b

Implements CKernel.

Definition at line 358 of file SpectrumRBFKernel.cpp.

int32_t get_degree ( ) const

get degree

Returns
degree of the kernel

Definition at line 75 of file SpectrumRBFKernel.h.

int32_t get_degree ( )

get degree

Returns
degree

Definition at line 103 of file SpectrumRBFKernel.h.

virtual EKernelType get_kernel_type ( )
virtual

return what type of kernel we are

Returns
kernel type

Implements CStringKernel< char >.

Definition at line 84 of file SpectrumRBFKernel.h.

virtual const char* get_name ( ) const
virtual

return the kernel's name

Returns
name

Reimplemented from CStringKernel< char >.

Definition at line 90 of file SpectrumRBFKernel.h.

bool init ( CFeatures *  l,
CFeatures *  r 
)
virtual

initialize kernel

Parameters
lfeatures of left-hand side
rfeatures of right-hand side
Returns
if initializing was successful

Reimplemented from CStringKernel< char >.

Definition at line 285 of file SpectrumRBFKernel.cpp.

void read_profiles_and_sequences ( )
protected

read profiles and sequences

Definition at line 97 of file SpectrumRBFKernel.cpp.

void register_alphabet ( )
protected

register the alphabet

Definition at line 406 of file SpectrumRBFKernel.cpp.

void register_param ( )
protectedvirtual

register the parameters

Definition at line 395 of file SpectrumRBFKernel.cpp.

void remove_lhs ( )
protectedvirtual

remove lhs from kernel

Reimplemented from CKernel.

Definition at line 91 of file SpectrumRBFKernel.cpp.

bool set_AA_matrix ( float64_t *  AA_matrix_)

set AA matrix

Parameters
AA_matrix_

Definition at line 381 of file SpectrumRBFKernel.cpp.

bool set_degree ( int32_t  deg)

set degree

Parameters
degnew degree
Returns
if setting was successful

Definition at line 97 of file SpectrumRBFKernel.h.

Member Data Documentation

float64_t* AA_matrix
protected

128x128 scalar product matrix

Definition at line 149 of file SpectrumRBFKernel.h.

int32_t AA_matrix_length
protected

length of the AA_matrix – for registration

Definition at line 151 of file SpectrumRBFKernel.h.

CAlphabet* alphabet
protected

alphabet of features

Definition at line 143 of file SpectrumRBFKernel.h.

int32_t degree
protected

degree

Definition at line 145 of file SpectrumRBFKernel.h.

bool initialized
protected

if kernel is initialized

Definition at line 172 of file SpectrumRBFKernel.h.

CArray2<float64_t> kernel_matrix
protected

kernel matrix

Definition at line 174 of file SpectrumRBFKernel.h.

int32_t max_mismatch
protected

maximum mismatch

Definition at line 147 of file SpectrumRBFKernel.h.

int32_t max_sequence_length
protected

max sequence length

Definition at line 169 of file SpectrumRBFKernel.h.

int32_t nof_sequences
protected

nof sequences

Definition at line 167 of file SpectrumRBFKernel.h.

std::vector< std::vector<float64_t> > profiles
protected

profiles

Definition at line 159 of file SpectrumRBFKernel.h.

std::vector<std::string> sequence_labels
protected

sequence labels

Definition at line 161 of file SpectrumRBFKernel.h.

SGString<char>* sequences
protected

sequences

Definition at line 163 of file SpectrumRBFKernel.h.

CStringFeatures<char>* string_features
protected

string features

Definition at line 165 of file SpectrumRBFKernel.h.

int32_t target_letter_0
protected

target letter 0

Definition at line 176 of file SpectrumRBFKernel.h.

float64_t width
protected

width of Gaussian

Definition at line 153 of file SpectrumRBFKernel.h.

The documentation for this class was generated from the following files:
SHOGUN Machine Learning Toolbox - Documentation