CSalzbergWordStringKernel Class Reference

Inheritance diagram for CSalzbergWordStringKernel:

Inheritance graph
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List of all members.

Public Member Functions

 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 ()
bool load_init (FILE *src)
bool save_init (FILE *dest)
virtual EKernelType get_kernel_type ()
virtual const char * get_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

CPluginEstimate * estimate
float64_t * mean
float64_t * variance
float64_t * sqrtdiag_lhs
float64_t * sqrtdiag_rhs
float64_t * ld_mean_lhs
float64_t * ld_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

Detailed Description

The SalzbergWordString kernel implements the Salzberg kernel as 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 25 of file SalzbergWordStringKernel.h.

Constructor & Destructor Documentation

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

constructor

Parameters:
size cache size
pie the plugin estimate
labels optional labels to set prior from

Definition at line 19 of file SalzbergWordStringKernel.cpp.

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

constructor

Parameters:
l features of left-hand side
r features of right-hand side
pie the plugin estimate
labels optional labels to set prior from

Definition at line 30 of file SalzbergWordStringKernel.cpp.

CSalzbergWordStringKernel::~CSalzbergWordStringKernel (  )  [virtual]

Definition at line 45 of file SalzbergWordStringKernel.cpp.

Member Function Documentation

void CSalzbergWordStringKernel::cleanup (  )  [virtual]

clean up kernel

Reimplemented from CKernel.

Definition at line 275 of file SalzbergWordStringKernel.cpp.

float64_t CSalzbergWordStringKernel::compute ( int32_t  idx_a,
int32_t  idx_b 
) [protected, virtual]

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_a index a
idx_b index b
Returns:
computed kernel function at indices a,b

Implements CKernel.

Definition at line 312 of file SalzbergWordStringKernel.cpp.

int32_t CSalzbergWordStringKernel::compute_index ( int32_t  position,
uint16_t  symbol 
) [protected]

compute index of given symbol at given position

Parameters:
position position
symbol symbol
Returns:
index

Definition at line 123 of file SalzbergWordStringKernel.h.

virtual EKernelType CSalzbergWordStringKernel::get_kernel_type (  )  [virtual]

return what type of kernel we are

Returns:
kernel type SALZBERG

Implements CKernel.

Definition at line 97 of file SalzbergWordStringKernel.h.

virtual const char* CSalzbergWordStringKernel::get_name (  )  [virtual]

return the kernel's name

Returns:
name Salzberg

Implements CKernel.

Definition at line 103 of file SalzbergWordStringKernel.h.

bool CSalzbergWordStringKernel::init ( CFeatures *  l,
CFeatures *  r 
) [virtual]

initialize kernel

Parameters:
l features of left-hand side
r features of right-hand side
Returns:
if initializing was successful

Reimplemented from CStringKernel< uint16_t >.

Definition at line 50 of file SalzbergWordStringKernel.cpp.

bool CSalzbergWordStringKernel::load_init ( FILE *  src  )  [virtual]

load kernel init_data

Parameters:
src file to load from
Returns:
if loading was successful

Implements CKernel.

Definition at line 300 of file SalzbergWordStringKernel.cpp.

bool CSalzbergWordStringKernel::save_init ( FILE *  dest  )  [virtual]

save kernel init_data

Parameters:
dest file to save to
Returns:
if saving was successful

Implements CKernel.

Definition at line 305 of file SalzbergWordStringKernel.cpp.

void CSalzbergWordStringKernel::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 54 of file SalzbergWordStringKernel.h.

void CSalzbergWordStringKernel::set_prior_probs_from_labels ( CLabels *  labels  ) 

set prior probs from labels

Parameters:
labels labels to set prior probabilites from

Definition at line 344 of file SalzbergWordStringKernel.cpp.

Member Data Documentation

CPluginEstimate* CSalzbergWordStringKernel::estimate [protected]

the plugin estimate

Definition at line 130 of file SalzbergWordStringKernel.h.

bool CSalzbergWordStringKernel::initialized [protected]

if kernel is initialized

Definition at line 158 of file SalzbergWordStringKernel.h.

float64_t* CSalzbergWordStringKernel::ld_mean_lhs [protected]

ld mean left-hand side

Definition at line 143 of file SalzbergWordStringKernel.h.

float64_t* CSalzbergWordStringKernel::ld_mean_rhs [protected]

ld mean right-hand side

Definition at line 145 of file SalzbergWordStringKernel.h.

float64_t* CSalzbergWordStringKernel::mean [protected]

mean

Definition at line 133 of file SalzbergWordStringKernel.h.

float64_t CSalzbergWordStringKernel::neg_prior [protected]

negative prior

Definition at line 156 of file SalzbergWordStringKernel.h.

int32_t CSalzbergWordStringKernel::num_params [protected]

number of params

Definition at line 148 of file SalzbergWordStringKernel.h.

int32_t CSalzbergWordStringKernel::num_symbols [protected]

number of symbols

Definition at line 150 of file SalzbergWordStringKernel.h.

float64_t CSalzbergWordStringKernel::pos_prior [protected]

positive prior

Definition at line 154 of file SalzbergWordStringKernel.h.

float64_t* CSalzbergWordStringKernel::sqrtdiag_lhs [protected]

sqrt diagonal of left-hand side

Definition at line 138 of file SalzbergWordStringKernel.h.

float64_t* CSalzbergWordStringKernel::sqrtdiag_rhs [protected]

sqrt diagonal of right-hand side

Definition at line 140 of file SalzbergWordStringKernel.h.

float64_t CSalzbergWordStringKernel::sum_m2_s2 [protected]

sum m2 s2

Definition at line 152 of file SalzbergWordStringKernel.h.

float64_t* CSalzbergWordStringKernel::variance [protected]

variance

Definition at line 135 of file SalzbergWordStringKernel.h.

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