spectrum mismatch rbf kernel
Definition at line 42 of file SpectrumMismatchRBFKernel.h.
Public Member Functions | |
CSpectrumMismatchRBFKernel (void) | |
CSpectrumMismatchRBFKernel (int32_t size, float64_t *AA_matrix_, int32_t nr_, int32_t nc_, int32_t degree, int32_t max_mismatch, float64_t width) | |
CSpectrumMismatchRBFKernel (CStringFeatures< char > *l, CStringFeatures< char > *r, int32_t size, float64_t *AA_matrix_, int32_t nr_, int32_t nc_, int32_t degree, int32_t max_mismatch, float64_t width) | |
virtual | ~CSpectrumMismatchRBFKernel () |
virtual bool | init (CFeatures *l, CFeatures *r) |
virtual void | cleanup () |
virtual EKernelType | get_kernel_type () |
virtual const char * | get_name () const |
bool | set_max_mismatch (int32_t max) |
int32_t | get_max_mismatch () const |
bool | set_degree (int32_t deg) |
int32_t | get_degree () const |
bool | set_AA_matrix (float64_t *AA_matrix_=NULL, int32_t nr=128, int32_t nc=128) |
Protected Member Functions | |
float64_t | AA_helper (std::string &path, const char *joint_seq, unsigned int index) |
float64_t | compute_helper (const char *joint_seq, std::vector< unsigned int > joint_index, std::vector< unsigned int > joint_mismatch, std::string path, unsigned int d, const int &alen) |
void | compute_helper_all (const char *joint_seq, std::vector< struct joint_list_struct > &joint_list, std::string path, unsigned int d) |
void | compute_all () |
float64_t | compute (int32_t idx_a, int32_t idx_b) |
virtual void | remove_lhs () |
virtual void | register_params () |
void | register_alphabet () |
Protected Attributes | |
CAlphabet * | alphabet |
int32_t | degree |
int32_t | max_mismatch |
float64_t * | AA_matrix |
int32_t | AA_matrix_length |
float64_t | width |
bool | initialized |
CArray2< float64_t > | kernel_matrix |
int32_t | kernel_matrix_length |
int32_t | target_letter_0 |
CSpectrumMismatchRBFKernel | ( | void | ) |
default constructor
Definition at line 36 of file SpectrumMismatchRBFKernel.cpp.
CSpectrumMismatchRBFKernel | ( | int32_t | size, | |
float64_t * | AA_matrix_, | |||
int32_t | nr_, | |||
int32_t | nc_, | |||
int32_t | degree, | |||
int32_t | max_mismatch, | |||
float64_t | width | |||
) |
constructor
size | ||
AA_matrix_ | ||
nr_ | ||
nc_ | ||
degree | ||
max_mismatch | ||
width |
Definition at line 43 of file SpectrumMismatchRBFKernel.cpp.
CSpectrumMismatchRBFKernel | ( | CStringFeatures< char > * | l, | |
CStringFeatures< char > * | r, | |||
int32_t | size, | |||
float64_t * | AA_matrix_, | |||
int32_t | nr_, | |||
int32_t | nc_, | |||
int32_t | degree, | |||
int32_t | max_mismatch, | |||
float64_t | width | |||
) |
constructor
l | features of left-hand side | |
r | features of right-hand side | |
size | ||
AA_matrix_ | ||
nr_ | ||
nc_ | ||
degree | ||
max_mismatch | ||
width |
Definition at line 58 of file SpectrumMismatchRBFKernel.cpp.
~CSpectrumMismatchRBFKernel | ( | ) | [virtual] |
destructor
Definition at line 70 of file SpectrumMismatchRBFKernel.cpp.
float64_t AA_helper | ( | std::string & | path, | |
const char * | joint_seq, | |||
unsigned int | index | |||
) | [protected] |
AA helper
path | ||
joint_seq | ||
index |
Definition at line 120 of file SpectrumMismatchRBFKernel.cpp.
void cleanup | ( | ) | [virtual] |
clean up kernel
Reimplemented from CKernel.
Definition at line 111 of file SpectrumMismatchRBFKernel.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 360 of file SpectrumMismatchRBFKernel.cpp.
void compute_all | ( | ) | [protected] |
computer all
Definition at line 324 of file SpectrumMismatchRBFKernel.cpp.
float64_t compute_helper | ( | const char * | joint_seq, | |
std::vector< unsigned int > | joint_index, | |||
std::vector< unsigned int > | joint_mismatch, | |||
std::string | path, | |||
unsigned int | d, | |||
const int & | alen | |||
) | [protected] |
compute helper
joint_seq | ||
joint_index | ||
joint_mismatch | ||
path | ||
d | ||
alen |
void compute_helper_all | ( | const char * | joint_seq, | |
std::vector< struct joint_list_struct > & | joint_list, | |||
std::string | path, | |||
unsigned int | d | |||
) | [protected] |
compute helper all
joint_seq | ||
joint_list | ||
path | ||
d |
Definition at line 227 of file SpectrumMismatchRBFKernel.cpp.
int32_t get_degree | ( | ) | const |
virtual EKernelType get_kernel_type | ( | ) | [virtual] |
return what type of kernel we are
Implements CStringKernel< char >.
Definition at line 95 of file SpectrumMismatchRBFKernel.h.
int32_t get_max_mismatch | ( | ) | const |
get maximum mismatch
Definition at line 114 of file SpectrumMismatchRBFKernel.h.
virtual const char* get_name | ( | void | ) | const [virtual] |
return the kernel's name
Reimplemented from CStringKernel< char >.
Definition at line 101 of file SpectrumMismatchRBFKernel.h.
initialize kernel
l | features of left-hand side | |
r | features of right-hand side |
Reimplemented from CStringKernel< char >.
Definition at line 83 of file SpectrumMismatchRBFKernel.cpp.
void register_alphabet | ( | ) | [protected] |
register the alphabet
Definition at line 452 of file SpectrumMismatchRBFKernel.cpp.
void register_params | ( | ) | [protected, virtual] |
register the parameters
Reimplemented from CKernel.
Definition at line 441 of file SpectrumMismatchRBFKernel.cpp.
void remove_lhs | ( | ) | [protected, virtual] |
remove lhs from kernel
Reimplemented from CKernel.
Definition at line 77 of file SpectrumMismatchRBFKernel.cpp.
bool set_AA_matrix | ( | float64_t * | AA_matrix_ = NULL , |
|
int32_t | nr = 128 , |
|||
int32_t | nc = 128 | |||
) |
set AA matrix
AA_matrix_ | ||
nr | ||
nc |
Definition at line 414 of file SpectrumMismatchRBFKernel.cpp.
bool set_degree | ( | int32_t | deg | ) |
set degree
deg | new degree |
Definition at line 121 of file SpectrumMismatchRBFKernel.h.
bool set_max_mismatch | ( | int32_t | max | ) |
set maximum mismatch
max | new maximum mismatch |
Definition at line 431 of file SpectrumMismatchRBFKernel.cpp.
128x128 scalar product matrix
Definition at line 203 of file SpectrumMismatchRBFKernel.h.
int32_t AA_matrix_length [protected] |
length of the AA_matrix -- for registration
Definition at line 205 of file SpectrumMismatchRBFKernel.h.
alphabet of features
Definition at line 197 of file SpectrumMismatchRBFKernel.h.
int32_t degree [protected] |
degree
Definition at line 199 of file SpectrumMismatchRBFKernel.h.
bool initialized [protected] |
if kernel is initialized
Definition at line 210 of file SpectrumMismatchRBFKernel.h.
CArray2<float64_t> kernel_matrix [protected] |
kernel matrix
Reimplemented from CKernel.
Definition at line 213 of file SpectrumMismatchRBFKernel.h.
int32_t kernel_matrix_length [protected] |
kernel matrix length
Definition at line 215 of file SpectrumMismatchRBFKernel.h.
int32_t max_mismatch [protected] |
maximum mismatch
Definition at line 201 of file SpectrumMismatchRBFKernel.h.
int32_t target_letter_0 [protected] |
target letter 0
Definition at line 217 of file SpectrumMismatchRBFKernel.h.
width of Gaussian
Definition at line 207 of file SpectrumMismatchRBFKernel.h.