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 27 of file SalzbergWordStringKernel.h.
CSalzbergWordStringKernel::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 19 of file SalzbergWordStringKernel.cpp.
CSalzbergWordStringKernel::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 30 of file SalzbergWordStringKernel.cpp.
CSalzbergWordStringKernel::~CSalzbergWordStringKernel | ( | ) | [virtual] |
Definition at line 45 of file SalzbergWordStringKernel.cpp.
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
idx_a | index a | |
idx_b | index 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
position | position | |
symbol | symbol |
Definition at line 125 of file SalzbergWordStringKernel.h.
virtual EKernelType CSalzbergWordStringKernel::get_kernel_type | ( | ) | [virtual] |
return what type of kernel we are
Implements CKernel.
Definition at line 99 of file SalzbergWordStringKernel.h.
virtual const char* CSalzbergWordStringKernel::get_name | ( | ) | const [virtual] |
return the kernel's name
Implements CSGObject.
Definition at line 105 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 50 of file SalzbergWordStringKernel.cpp.
bool CSalzbergWordStringKernel::load_init | ( | FILE * | src | ) | [virtual] |
load kernel init_data
src | file to load from |
Implements CKernel.
Definition at line 300 of file SalzbergWordStringKernel.cpp.
bool CSalzbergWordStringKernel::save_init | ( | FILE * | dest | ) | [virtual] |
save kernel init_data
dest | file to save to |
Implements CKernel.
Definition at line 305 of file SalzbergWordStringKernel.cpp.
set prior probs
pos_prior_ | positive prior | |
neg_prior_ | negative prior |
Definition at line 56 of file SalzbergWordStringKernel.h.
void CSalzbergWordStringKernel::set_prior_probs_from_labels | ( | CLabels * | labels | ) |
set prior probs from labels
labels | labels to set prior probabilites from |
Definition at line 344 of file SalzbergWordStringKernel.cpp.
CPluginEstimate* CSalzbergWordStringKernel::estimate [protected] |
the plugin estimate
Definition at line 132 of file SalzbergWordStringKernel.h.
bool CSalzbergWordStringKernel::initialized [protected] |
if kernel is initialized
Definition at line 160 of file SalzbergWordStringKernel.h.
float64_t* CSalzbergWordStringKernel::ld_mean_lhs [protected] |
ld mean left-hand side
Definition at line 145 of file SalzbergWordStringKernel.h.
float64_t* CSalzbergWordStringKernel::ld_mean_rhs [protected] |
ld mean right-hand side
Definition at line 147 of file SalzbergWordStringKernel.h.
float64_t* CSalzbergWordStringKernel::mean [protected] |
mean
Definition at line 135 of file SalzbergWordStringKernel.h.
float64_t CSalzbergWordStringKernel::neg_prior [protected] |
negative prior
Definition at line 158 of file SalzbergWordStringKernel.h.
int32_t CSalzbergWordStringKernel::num_params [protected] |
number of params
Definition at line 150 of file SalzbergWordStringKernel.h.
int32_t CSalzbergWordStringKernel::num_symbols [protected] |
number of symbols
Definition at line 152 of file SalzbergWordStringKernel.h.
float64_t CSalzbergWordStringKernel::pos_prior [protected] |
positive prior
Definition at line 156 of file SalzbergWordStringKernel.h.
float64_t* CSalzbergWordStringKernel::sqrtdiag_lhs [protected] |
sqrt diagonal of left-hand side
Definition at line 140 of file SalzbergWordStringKernel.h.
float64_t* CSalzbergWordStringKernel::sqrtdiag_rhs [protected] |
sqrt diagonal of right-hand side
Definition at line 142 of file SalzbergWordStringKernel.h.
float64_t CSalzbergWordStringKernel::sum_m2_s2 [protected] |
sum m2 s2
Definition at line 154 of file SalzbergWordStringKernel.h.
float64_t* CSalzbergWordStringKernel::variance [protected] |
variance
Definition at line 137 of file SalzbergWordStringKernel.h.