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CSpectrumMismatchRBFKernel Class Reference

Detailed Description

spectrum mismatch rbf kernel

Definition at line 42 of file SpectrumMismatchRBFKernel.h.

Inheritance diagram for CSpectrumMismatchRBFKernel:
Inheritance graph
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Public Member Functions

 CSpectrumMismatchRBFKernel ()
 CSpectrumMismatchRBFKernel (int32_t size, float64_t *AA_matrix_, int32_t nr_, int32_t nc_, int32_t degree, int32_t max_mismatch, float64_t width)
 CSpectrumMismatchRBFKernel (CStringFeatures< char > *l, CStringFeatures< char > *r, int32_t size, float64_t *AA_matrix_, int32_t nr_, int32_t nc_, int32_t degree, int32_t max_mismatch, float64_t width)
virtual ~CSpectrumMismatchRBFKernel ()
virtual bool init (CFeatures *l, CFeatures *r)
virtual void cleanup ()
virtual EKernelType get_kernel_type ()
virtual const char * get_name () const
bool set_max_mismatch (int32_t max)
int32_t get_max_mismatch () const
bool set_degree (int32_t deg)
int32_t get_degree () const
bool set_AA_matrix (float64_t *AA_matrix_=NULL, int32_t nr=128, int32_t nc=128)
- 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_tget_kernel_matrix ()
virtual SGVector< float64_tget_kernel_col (int32_t j)
virtual SGVector< float64_tget_kernel_row (int32_t i)
template<class T >
SGMatrix< T > get_kernel_matrix ()
virtual bool set_normalizer (CKernelNormalizer *normalizer)
virtual CKernelNormalizerget_normalizer ()
virtual bool init_normalizer ()
void load (CFile *loader)
void save (CFile *writer)
CFeaturesget_lhs ()
CFeaturesget_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
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_tget_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)
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

float64_t AA_helper (std::string &path, const char *joint_seq, unsigned int index)
float64_t compute_helper (const char *joint_seq, std::vector< unsigned int > joint_index, std::vector< unsigned int > joint_mismatch, std::string path, unsigned int d, const int &alen)
void compute_helper_all (const char *joint_seq, std::vector< struct joint_list_struct > &joint_list, std::string path, unsigned int d)
void compute_all ()
float64_t compute (int32_t idx_a, int32_t idx_b)
virtual void remove_lhs ()
virtual void register_params ()
void register_alphabet ()

Protected Attributes

CAlphabetalphabet
int32_t degree
int32_t max_mismatch
float64_tAA_matrix
int32_t AA_matrix_length
float64_t width
bool initialized
CArray2< float64_tkernel_matrix
int32_t kernel_matrix_length
int32_t target_letter_0

Additional Inherited Members

- Public Attributes inherited from CSGObject
SGIOio
Parallelparallel
Versionversion
Parameterm_parameters
Parameterm_model_selection_parameters
- Static Protected Member Functions inherited from CKernel
template<class T >
static void * get_kernel_matrix_helper (void *p)

Constructor & Destructor Documentation

default constructor

Definition at line 36 of file SpectrumMismatchRBFKernel.cpp.

CSpectrumMismatchRBFKernel ( int32_t  size,
float64_t AA_matrix_,
int32_t  nr_,
int32_t  nc_,
int32_t  degree,
int32_t  max_mismatch,
float64_t  width 
)

constructor

Parameters
size
AA_matrix_
nr_
nc_
degree
max_mismatch
width

Definition at line 43 of file SpectrumMismatchRBFKernel.cpp.

CSpectrumMismatchRBFKernel ( CStringFeatures< char > *  l,
CStringFeatures< char > *  r,
int32_t  size,
float64_t AA_matrix_,
int32_t  nr_,
int32_t  nc_,
int32_t  degree,
int32_t  max_mismatch,
float64_t  width 
)

constructor

Parameters
lfeatures of left-hand side
rfeatures of right-hand side
size
AA_matrix_
nr_
nc_
degree
max_mismatch
width

Definition at line 58 of file SpectrumMismatchRBFKernel.cpp.

destructor

Definition at line 70 of file SpectrumMismatchRBFKernel.cpp.

Member Function Documentation

float64_t AA_helper ( std::string &  path,
const char *  joint_seq,
unsigned int  index 
)
protected

AA helper

Parameters
path
joint_seq
index
Returns
AA helper

Definition at line 120 of file SpectrumMismatchRBFKernel.cpp.

void cleanup ( )
virtual

clean up kernel

Reimplemented from CKernel.

Definition at line 111 of file SpectrumMismatchRBFKernel.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 360 of file SpectrumMismatchRBFKernel.cpp.

void compute_all ( )
protected

computer all

Definition at line 324 of file SpectrumMismatchRBFKernel.cpp.

float64_t compute_helper ( const char *  joint_seq,
std::vector< unsigned int >  joint_index,
std::vector< unsigned int >  joint_mismatch,
std::string  path,
unsigned int  d,
const int &  alen 
)
protected

compute helper

Parameters
joint_seq
joint_index
joint_mismatch
path
d
alen
Returns
helper
void compute_helper_all ( const char *  joint_seq,
std::vector< struct joint_list_struct > &  joint_list,
std::string  path,
unsigned int  d 
)
protected

compute helper all

Parameters
joint_seq
joint_list
path
d
Returns
helper

Definition at line 227 of file SpectrumMismatchRBFKernel.cpp.

int32_t get_degree ( ) const

get degree

Returns
degree

Definition at line 127 of file SpectrumMismatchRBFKernel.h.

virtual EKernelType get_kernel_type ( )
virtual

return what type of kernel we are

Returns
kernel type

Implements CStringKernel< char >.

Definition at line 95 of file SpectrumMismatchRBFKernel.h.

int32_t get_max_mismatch ( ) const

get maximum mismatch

Returns
maximum mismatch

Definition at line 114 of file SpectrumMismatchRBFKernel.h.

virtual const char* get_name ( ) const
virtual

return the kernel's name

Returns
name

Reimplemented from CStringKernel< char >.

Definition at line 101 of file SpectrumMismatchRBFKernel.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 83 of file SpectrumMismatchRBFKernel.cpp.

void register_alphabet ( )
protected

register the alphabet

Definition at line 452 of file SpectrumMismatchRBFKernel.cpp.

void register_params ( )
protectedvirtual

register the parameters

Reimplemented from CKernel.

Definition at line 441 of file SpectrumMismatchRBFKernel.cpp.

void remove_lhs ( )
protectedvirtual

remove lhs from kernel

Reimplemented from CKernel.

Definition at line 77 of file SpectrumMismatchRBFKernel.cpp.

bool set_AA_matrix ( float64_t AA_matrix_ = NULL,
int32_t  nr = 128,
int32_t  nc = 128 
)

set AA matrix

Parameters
AA_matrix_
nr
nc
Returns
true if set

Definition at line 414 of file SpectrumMismatchRBFKernel.cpp.

bool set_degree ( int32_t  deg)

set degree

Parameters
degnew degree
Returns
if setting was successful

Definition at line 121 of file SpectrumMismatchRBFKernel.h.

bool set_max_mismatch ( int32_t  max)

set maximum mismatch

Parameters
maxnew maximum mismatch
Returns
if setting was successful

Definition at line 431 of file SpectrumMismatchRBFKernel.cpp.

Member Data Documentation

float64_t* AA_matrix
protected

128x128 scalar product matrix

Definition at line 203 of file SpectrumMismatchRBFKernel.h.

int32_t AA_matrix_length
protected

length of the AA_matrix – for registration

Definition at line 205 of file SpectrumMismatchRBFKernel.h.

CAlphabet* alphabet
protected

alphabet of features

Definition at line 197 of file SpectrumMismatchRBFKernel.h.

int32_t degree
protected

degree

Definition at line 199 of file SpectrumMismatchRBFKernel.h.

bool initialized
protected

if kernel is initialized

Definition at line 210 of file SpectrumMismatchRBFKernel.h.

CArray2<float64_t> kernel_matrix
protected

kernel matrix

Definition at line 213 of file SpectrumMismatchRBFKernel.h.

int32_t kernel_matrix_length
protected

kernel matrix length

Definition at line 215 of file SpectrumMismatchRBFKernel.h.

int32_t max_mismatch
protected

maximum mismatch

Definition at line 201 of file SpectrumMismatchRBFKernel.h.

int32_t target_letter_0
protected

target letter 0

Definition at line 217 of file SpectrumMismatchRBFKernel.h.

float64_t width
protected

width of Gaussian

Definition at line 207 of file SpectrumMismatchRBFKernel.h.


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

SHOGUN Machine Learning Toolbox - Documentation