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.
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 123 of file SalzbergWordStringKernel.h.
virtual EKernelType CSalzbergWordStringKernel::get_kernel_type | ( | ) | [virtual] |
return what type of kernel we are
Implements CKernel.
Definition at line 97 of file SalzbergWordStringKernel.h.
virtual const char* CSalzbergWordStringKernel::get_name | ( | ) | [virtual] |
return the kernel's name
Implements CKernel.
Definition at line 103 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 54 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 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.