spectrum rbf kernel
Definition at line 31 of file SpectrumRBFKernel.h.
Public Member Functions | |
| CSpectrumRBFKernel () | |
| 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 |
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 | ( | ) | 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.
