spectrum rbf kernel
Definition at line 31 of file SpectrumRBFKernel.h.
Public Member Functions | |
CSpectrumRBFKernel (void) | |
CSpectrumRBFKernel (int32_t size, float64_t *AA_matrix, int32_t degree, float64_t width) | |
CSpectrumRBFKernel (CStringFeatures< char > *l, CStringFeatures< char > *r, int32_t size, float64_t *AA_matrix, int32_t degree, float64_t width) | |
virtual | ~CSpectrumRBFKernel () |
virtual bool | init (CFeatures *l, CFeatures *r) |
virtual void | cleanup () |
int32_t | get_degree () const |
virtual EKernelType | get_kernel_type () |
virtual const char * | get_name () const |
bool | set_degree (int32_t deg) |
int32_t | get_degree () |
bool | set_AA_matrix (float64_t *AA_matrix_) |
Protected Member Functions | |
float64_t | AA_helper (const char *path, const int degree, const char *joint_seq, unsigned int index) |
void | read_profiles_and_sequences () |
float64_t | compute (int32_t idx_a, int32_t idx_b) |
virtual void | remove_lhs () |
virtual void | register_param () |
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 |
std::vector< std::vector < float64_t > > | profiles |
std::vector< std::string > | sequence_labels |
SGString< char > * | sequences |
CStringFeatures< char > * | string_features |
int32_t | nof_sequences |
int32_t | max_sequence_length |
bool | initialized |
CArray2< float64_t > | kernel_matrix |
int32_t | target_letter_0 |
CSpectrumRBFKernel | ( | void | ) |
default constructor
Definition at line 39 of file SpectrumRBFKernel.cpp.
CSpectrumRBFKernel | ( | int32_t | size, | |
float64_t * | AA_matrix, | |||
int32_t | degree, | |||
float64_t | width | |||
) |
constructor
size | ||
AA_matrix | ||
degree | ||
width |
Definition at line 46 of file SpectrumRBFKernel.cpp.
CSpectrumRBFKernel | ( | CStringFeatures< char > * | l, | |
CStringFeatures< char > * | r, | |||
int32_t | size, | |||
float64_t * | AA_matrix, | |||
int32_t | degree, | |||
float64_t | width | |||
) |
constructor
l | features of left-hand side | |
r | features of right-hand side | |
size | ||
AA_matrix | ||
degree | ||
width |
Definition at line 71 of file SpectrumRBFKernel.cpp.
~CSpectrumRBFKernel | ( | ) | [virtual] |
destructor
Definition at line 84 of file SpectrumRBFKernel.cpp.
float64_t AA_helper | ( | const char * | path, | |
const int | degree, | |||
const char * | joint_seq, | |||
unsigned int | index | |||
) | [protected] |
AA helper
path | ||
degree | ||
joint_seq | ||
index |
Definition at line 336 of file SpectrumRBFKernel.cpp.
void cleanup | ( | ) | [virtual] |
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 358 of file SpectrumRBFKernel.cpp.
int32_t get_degree | ( | ) | const |
int32_t get_degree | ( | ) |
virtual EKernelType get_kernel_type | ( | ) | [virtual] |
return what type of kernel we are
Implements CStringKernel< char >.
Definition at line 84 of file SpectrumRBFKernel.h.
virtual const char* get_name | ( | void | ) | const [virtual] |
return the kernel's name
Reimplemented from CStringKernel< char >.
Definition at line 90 of file SpectrumRBFKernel.h.
initialize kernel
l | features of left-hand side | |
r | features of right-hand side |
Reimplemented from CStringKernel< char >.
Definition at line 285 of file SpectrumRBFKernel.cpp.
void read_profiles_and_sequences | ( | ) | [protected] |
read profiles and sequences
Definition at line 97 of file SpectrumRBFKernel.cpp.
void register_alphabet | ( | ) | [protected] |
register the alphabet
Definition at line 406 of file SpectrumRBFKernel.cpp.
void register_param | ( | ) | [protected, virtual] |
register the parameters
Definition at line 395 of file SpectrumRBFKernel.cpp.
void remove_lhs | ( | ) | [protected, virtual] |
remove lhs from kernel
Reimplemented from CKernel.
Definition at line 91 of file SpectrumRBFKernel.cpp.
bool set_AA_matrix | ( | float64_t * | AA_matrix_ | ) |
bool set_degree | ( | int32_t | deg | ) |
set degree
deg | new degree |
Definition at line 97 of file SpectrumRBFKernel.h.
128x128 scalar product matrix
Definition at line 149 of file SpectrumRBFKernel.h.
int32_t AA_matrix_length [protected] |
length of the AA_matrix -- for registration
Definition at line 151 of file SpectrumRBFKernel.h.
alphabet of features
Definition at line 143 of file SpectrumRBFKernel.h.
int32_t degree [protected] |
degree
Definition at line 145 of file SpectrumRBFKernel.h.
bool initialized [protected] |
if kernel is initialized
Definition at line 172 of file SpectrumRBFKernel.h.
CArray2<float64_t> kernel_matrix [protected] |
int32_t max_mismatch [protected] |
maximum mismatch
Definition at line 147 of file SpectrumRBFKernel.h.
int32_t max_sequence_length [protected] |
max sequence length
Definition at line 169 of file SpectrumRBFKernel.h.
int32_t nof_sequences [protected] |
nof sequences
Definition at line 167 of file SpectrumRBFKernel.h.
profiles
Definition at line 159 of file SpectrumRBFKernel.h.
std::vector<std::string> sequence_labels [protected] |
sequence labels
Definition at line 161 of file SpectrumRBFKernel.h.
sequences
Definition at line 163 of file SpectrumRBFKernel.h.
CStringFeatures<char>* string_features [protected] |
string features
Definition at line 165 of file SpectrumRBFKernel.h.
int32_t target_letter_0 [protected] |
target letter 0
Definition at line 176 of file SpectrumRBFKernel.h.
width of Gaussian
Definition at line 153 of file SpectrumRBFKernel.h.