SHOGUN
v1.1.0
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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_) |
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CStringKernel (int32_t cachesize=0) | |
CStringKernel (CFeatures *l, CFeatures *r) | |
virtual EFeatureClass | get_feature_class () |
virtual EFeatureType | get_feature_type () |
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CKernel () | |
CKernel (int32_t size) | |
CKernel (CFeatures *l, CFeatures *r, int32_t size) | |
virtual | ~CKernel () |
float64_t | kernel (int32_t idx_a, int32_t idx_b) |
SGMatrix< float64_t > | get_kernel_matrix () |
virtual SGVector< float64_t > | get_kernel_col (int32_t j) |
virtual SGVector< float64_t > | get_kernel_row (int32_t i) |
template<class T > | |
SGMatrix< T > | get_kernel_matrix () |
virtual bool | set_normalizer (CKernelNormalizer *normalizer) |
virtual CKernelNormalizer * | get_normalizer () |
virtual bool | init_normalizer () |
void | load (CFile *loader) |
void | save (CFile *writer) |
CFeatures * | get_lhs () |
CFeatures * | get_rhs () |
virtual int32_t | get_num_vec_lhs () |
virtual int32_t | get_num_vec_rhs () |
virtual bool | has_features () |
bool | get_lhs_equals_rhs () |
virtual void | remove_lhs_and_rhs () |
virtual void | remove_rhs () |
takes all necessary steps if the rhs is removed from kernel | |
void | set_cache_size (int32_t size) |
int32_t | get_cache_size () |
void | list_kernel () |
bool | has_property (EKernelProperty p) |
virtual void | clear_normal () |
virtual void | add_to_normal (int32_t vector_idx, float64_t weight) |
EOptimizationType | get_optimization_type () |
virtual void | set_optimization_type (EOptimizationType t) |
bool | get_is_initialized () |
virtual bool | init_optimization (int32_t count, int32_t *IDX, float64_t *weights) |
virtual bool | delete_optimization () |
bool | init_optimization_svm (CSVM *svm) |
virtual float64_t | compute_optimized (int32_t vector_idx) |
virtual void | compute_batch (int32_t num_vec, int32_t *vec_idx, float64_t *target, int32_t num_suppvec, int32_t *IDX, float64_t *alphas, float64_t factor=1.0) |
float64_t | get_combined_kernel_weight () |
void | set_combined_kernel_weight (float64_t nw) |
virtual int32_t | get_num_subkernels () |
virtual void | compute_by_subkernel (int32_t vector_idx, float64_t *subkernel_contrib) |
virtual const float64_t * | get_subkernel_weights (int32_t &num_weights) |
virtual void | set_subkernel_weights (SGVector< float64_t > weights) |
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CSGObject () | |
CSGObject (const CSGObject &orig) | |
virtual | ~CSGObject () |
virtual bool | is_generic (EPrimitiveType *generic) const |
template<class T > | |
void | set_generic () |
void | unset_generic () |
virtual void | print_serializable (const char *prefix="") |
virtual bool | save_serializable (CSerializableFile *file, const char *prefix="") |
virtual bool | load_serializable (CSerializableFile *file, const char *prefix="") |
void | set_global_io (SGIO *io) |
SGIO * | get_global_io () |
void | set_global_parallel (Parallel *parallel) |
Parallel * | get_global_parallel () |
void | set_global_version (Version *version) |
Version * | get_global_version () |
SGVector< char * > | get_modelsel_names () |
char * | get_modsel_param_descr (const char *param_name) |
index_t | get_modsel_param_index (const char *param_name) |
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 |
Additional Inherited Members | |
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SGIO * | io |
Parallel * | parallel |
Version * | version |
Parameter * | m_parameters |
Parameter * | m_model_selection_parameters |
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template<class T > | |
static void * | get_kernel_matrix_helper (void *p) |
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.
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destructor
Definition at line 84 of file SpectrumRBFKernel.cpp.
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AA helper
path | |
degree | |
joint_seq | |
index |
Definition at line 336 of file SpectrumRBFKernel.cpp.
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virtual |
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protectedvirtual |
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 | ( | ) |
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return what type of kernel we are
Implements CStringKernel< char >.
Definition at line 84 of file SpectrumRBFKernel.h.
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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.
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read profiles and sequences
Definition at line 97 of file SpectrumRBFKernel.cpp.
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register the alphabet
Definition at line 406 of file SpectrumRBFKernel.cpp.
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register the parameters
Definition at line 395 of file SpectrumRBFKernel.cpp.
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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.
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128x128 scalar product matrix
Definition at line 149 of file SpectrumRBFKernel.h.
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length of the AA_matrix – for registration
Definition at line 151 of file SpectrumRBFKernel.h.
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alphabet of features
Definition at line 143 of file SpectrumRBFKernel.h.
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degree
Definition at line 145 of file SpectrumRBFKernel.h.
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if kernel is initialized
Definition at line 172 of file SpectrumRBFKernel.h.
kernel matrix
Definition at line 174 of file SpectrumRBFKernel.h.
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maximum mismatch
Definition at line 147 of file SpectrumRBFKernel.h.
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max sequence length
Definition at line 169 of file SpectrumRBFKernel.h.
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nof sequences
Definition at line 167 of file SpectrumRBFKernel.h.
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profiles
Definition at line 159 of file SpectrumRBFKernel.h.
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sequence labels
Definition at line 161 of file SpectrumRBFKernel.h.
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sequences
Definition at line 163 of file SpectrumRBFKernel.h.
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string features
Definition at line 165 of file SpectrumRBFKernel.h.
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target letter 0
Definition at line 176 of file SpectrumRBFKernel.h.
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width of Gaussian
Definition at line 153 of file SpectrumRBFKernel.h.