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CSalzbergWordStringKernel Class Reference

Detailed Description

The SalzbergWordString kernel implements the Salzberg kernel.

It is described in

Engineering Support Vector Machine Kernels That Recognize Translation Initiation Sites A. Zien, G.Raetsch, S. Mika, B. Schoelkopf, T. Lengauer, K.-R. Mueller

Definition at line 29 of file SalzbergWordStringKernel.h.

Inheritance diagram for CSalzbergWordStringKernel:
Inheritance graph
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Public Member Functions

 CSalzbergWordStringKernel ()
 CSalzbergWordStringKernel (int32_t size, CPluginEstimate *pie, CLabels *labels=NULL)
 CSalzbergWordStringKernel (CStringFeatures< uint16_t > *l, CStringFeatures< uint16_t > *r, CPluginEstimate *pie, CLabels *labels=NULL)
virtual ~CSalzbergWordStringKernel ()
void set_prior_probs (float64_t pos_prior_, float64_t neg_prior_)
void set_prior_probs_from_labels (CLabels *labels)
virtual bool init (CFeatures *l, CFeatures *r)
virtual void cleanup ()
virtual EKernelType get_kernel_type ()
virtual const char * get_name () const
- Public Member Functions inherited from CStringKernel< uint16_t >
 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_lhs ()
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 compute (int32_t idx_a, int32_t idx_b)
int32_t compute_index (int32_t position, uint16_t symbol)

Protected Attributes

CPluginEstimateestimate
float64_tmean
float64_tvariance
float64_tsqrtdiag_lhs
float64_tsqrtdiag_rhs
float64_tld_mean_lhs
float64_tld_mean_rhs
int32_t num_params
int32_t num_symbols
float64_t sum_m2_s2
float64_t pos_prior
float64_t neg_prior
bool initialized

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 21 of file SalzbergWordStringKernel.cpp.

CSalzbergWordStringKernel ( int32_t  size,
CPluginEstimate pie,
CLabels labels = NULL 
)

constructor

Parameters
sizecache size
piethe plugin estimate
labelsoptional labels to set prior from

Definition at line 27 of file SalzbergWordStringKernel.cpp.

CSalzbergWordStringKernel ( CStringFeatures< uint16_t > *  l,
CStringFeatures< uint16_t > *  r,
CPluginEstimate pie,
CLabels labels = NULL 
)

constructor

Parameters
lfeatures of left-hand side
rfeatures of right-hand side
piethe plugin estimate
labelsoptional labels to set prior from

Definition at line 37 of file SalzbergWordStringKernel.cpp.

Definition at line 51 of file SalzbergWordStringKernel.cpp.

Member Function Documentation

void cleanup ( )
virtual

clean up kernel

Reimplemented from CKernel.

Definition at line 292 of file SalzbergWordStringKernel.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 317 of file SalzbergWordStringKernel.cpp.

int32_t compute_index ( int32_t  position,
uint16_t  symbol 
)
protected

compute index of given symbol at given position

Parameters
positionposition
symbolsymbol
Returns
index

Definition at line 116 of file SalzbergWordStringKernel.h.

virtual EKernelType get_kernel_type ( )
virtual

return what type of kernel we are

Returns
kernel type SALZBERG

Implements CStringKernel< uint16_t >.

Definition at line 90 of file SalzbergWordStringKernel.h.

virtual const char* get_name ( ) const
virtual

return the kernel's name

Returns
name Salzberg

Reimplemented from CStringKernel< uint16_t >.

Definition at line 96 of file SalzbergWordStringKernel.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< uint16_t >.

Definition at line 56 of file SalzbergWordStringKernel.cpp.

void set_prior_probs ( float64_t  pos_prior_,
float64_t  neg_prior_ 
)

set prior probs

Parameters
pos_prior_positive prior
neg_prior_negative prior

Definition at line 61 of file SalzbergWordStringKernel.h.

void set_prior_probs_from_labels ( CLabels labels)

set prior probs from labels

Parameters
labelslabels to set prior probabilites from

Definition at line 352 of file SalzbergWordStringKernel.cpp.

Member Data Documentation

CPluginEstimate* estimate
protected

the plugin estimate

Definition at line 125 of file SalzbergWordStringKernel.h.

bool initialized
protected

if kernel is initialized

Definition at line 153 of file SalzbergWordStringKernel.h.

float64_t* ld_mean_lhs
protected

ld mean left-hand side

Definition at line 138 of file SalzbergWordStringKernel.h.

float64_t* ld_mean_rhs
protected

ld mean right-hand side

Definition at line 140 of file SalzbergWordStringKernel.h.

float64_t* mean
protected

mean

Definition at line 128 of file SalzbergWordStringKernel.h.

float64_t neg_prior
protected

negative prior

Definition at line 151 of file SalzbergWordStringKernel.h.

int32_t num_params
protected

number of params

Definition at line 143 of file SalzbergWordStringKernel.h.

int32_t num_symbols
protected

number of symbols

Definition at line 145 of file SalzbergWordStringKernel.h.

float64_t pos_prior
protected

positive prior

Definition at line 149 of file SalzbergWordStringKernel.h.

float64_t* sqrtdiag_lhs
protected

sqrt diagonal of left-hand side

Definition at line 133 of file SalzbergWordStringKernel.h.

float64_t* sqrtdiag_rhs
protected

sqrt diagonal of right-hand side

Definition at line 135 of file SalzbergWordStringKernel.h.

float64_t sum_m2_s2
protected

sum m2 s2

Definition at line 147 of file SalzbergWordStringKernel.h.

float64_t* variance
protected

variance

Definition at line 130 of file SalzbergWordStringKernel.h.


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

SHOGUN Machine Learning Toolbox - Documentation