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.
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 () |
virtual EKernelType | get_kernel_type () |
virtual const char * | get_name () const |
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 |
CSalzbergWordStringKernel | ( | int32_t | size, | |
CPluginEstimate * | pie, | |||
CLabels * | labels = NULL | |||
) |
constructor
size | cache size | |
pie | the plugin estimate | |
labels | optional labels to set prior from |
Definition at line 21 of file SalzbergWordStringKernel.cpp.
CSalzbergWordStringKernel | ( | CStringFeatures< uint16_t > * | l, | |
CStringFeatures< uint16_t > * | r, | |||
CPluginEstimate * | pie, | |||
CLabels * | labels = NULL | |||
) |
constructor
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 32 of file SalzbergWordStringKernel.cpp.
~CSalzbergWordStringKernel | ( | ) | [virtual] |
Definition at line 47 of file SalzbergWordStringKernel.cpp.
void cleanup | ( | ) | [virtual] |
clean up kernel
Reimplemented from CKernel.
Definition at line 288 of file SalzbergWordStringKernel.cpp.
float64_t 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
idx_a | index a | |
idx_b | index b |
Implements CKernel.
Definition at line 313 of file SalzbergWordStringKernel.cpp.
int32_t compute_index | ( | int32_t | position, | |
uint16_t | symbol | |||
) | [protected] |
compute index of given symbol at given position
position | position | |
symbol | symbol |
Definition at line 113 of file SalzbergWordStringKernel.h.
virtual EKernelType get_kernel_type | ( | ) | [virtual] |
return what type of kernel we are
Implements CKernel.
Definition at line 87 of file SalzbergWordStringKernel.h.
virtual const char* get_name | ( | ) | const [virtual] |
return the kernel's name
Implements CSGObject.
Definition at line 93 of file SalzbergWordStringKernel.h.
initialize kernel
l | features of left-hand side | |
r | features of right-hand side |
Reimplemented from CStringKernel< uint16_t >.
Definition at line 52 of file SalzbergWordStringKernel.cpp.
set prior probs
pos_prior_ | positive prior | |
neg_prior_ | negative prior |
Definition at line 58 of file SalzbergWordStringKernel.h.
void set_prior_probs_from_labels | ( | CLabels * | labels | ) |
set prior probs from labels
labels | labels to set prior probabilites from |
Definition at line 348 of file SalzbergWordStringKernel.cpp.
CPluginEstimate* estimate [protected] |
the plugin estimate
Definition at line 120 of file SalzbergWordStringKernel.h.
bool initialized [protected] |
if kernel is initialized
Definition at line 148 of file SalzbergWordStringKernel.h.
float64_t* ld_mean_lhs [protected] |
ld mean left-hand side
Definition at line 133 of file SalzbergWordStringKernel.h.
float64_t* ld_mean_rhs [protected] |
ld mean right-hand side
Definition at line 135 of file SalzbergWordStringKernel.h.
mean
Definition at line 123 of file SalzbergWordStringKernel.h.
negative prior
Definition at line 146 of file SalzbergWordStringKernel.h.
int32_t num_params [protected] |
number of params
Definition at line 138 of file SalzbergWordStringKernel.h.
int32_t num_symbols [protected] |
number of symbols
Definition at line 140 of file SalzbergWordStringKernel.h.
positive prior
Definition at line 144 of file SalzbergWordStringKernel.h.
float64_t* sqrtdiag_lhs [protected] |
sqrt diagonal of left-hand side
Definition at line 128 of file SalzbergWordStringKernel.h.
float64_t* sqrtdiag_rhs [protected] |
sqrt diagonal of right-hand side
Definition at line 130 of file SalzbergWordStringKernel.h.
sum m2 s2
Definition at line 142 of file SalzbergWordStringKernel.h.
variance
Definition at line 125 of file SalzbergWordStringKernel.h.