SHOGUN
v1.1.0
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The SalzbergWordString kernel implements the Salzberg kernel.
It is described in
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 29 of file SalzbergWordStringKernel.h.
Public Member Functions | |
CSalzbergWordStringKernel () | |
CSalzbergWordStringKernel (int32_t size, CPluginEstimate *pie, CLabels *labels=NULL) | |
CSalzbergWordStringKernel (CStringFeatures< uint16_t > *l, CStringFeatures< uint16_t > *r, CPluginEstimate *pie, CLabels *labels=NULL) | |
virtual | ~CSalzbergWordStringKernel () |
void | set_prior_probs (float64_t pos_prior_, float64_t neg_prior_) |
void | set_prior_probs_from_labels (CLabels *labels) |
virtual bool | init (CFeatures *l, CFeatures *r) |
virtual void | cleanup () |
virtual EKernelType | get_kernel_type () |
virtual const char * | get_name () const |
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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_lhs () |
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 | compute (int32_t idx_a, int32_t idx_b) |
int32_t | compute_index (int32_t position, uint16_t symbol) |
Protected Attributes | |
CPluginEstimate * | estimate |
float64_t * | mean |
float64_t * | variance |
float64_t * | sqrtdiag_lhs |
float64_t * | sqrtdiag_rhs |
float64_t * | ld_mean_lhs |
float64_t * | ld_mean_rhs |
int32_t | num_params |
int32_t | num_symbols |
float64_t | sum_m2_s2 |
float64_t | pos_prior |
float64_t | neg_prior |
bool | initialized |
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 21 of file SalzbergWordStringKernel.cpp.
CSalzbergWordStringKernel | ( | int32_t | size, |
CPluginEstimate * | pie, | ||
CLabels * | labels = NULL |
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constructor
size | cache size |
pie | the plugin estimate |
labels | optional labels to set prior from |
Definition at line 27 of file SalzbergWordStringKernel.cpp.
CSalzbergWordStringKernel | ( | CStringFeatures< uint16_t > * | l, |
CStringFeatures< uint16_t > * | r, | ||
CPluginEstimate * | pie, | ||
CLabels * | labels = NULL |
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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 37 of file SalzbergWordStringKernel.cpp.
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virtual |
Definition at line 51 of file SalzbergWordStringKernel.cpp.
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clean up kernel
Reimplemented from CKernel.
Definition at line 292 of file SalzbergWordStringKernel.cpp.
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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 317 of file SalzbergWordStringKernel.cpp.
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compute index of given symbol at given position
position | position |
symbol | symbol |
Definition at line 116 of file SalzbergWordStringKernel.h.
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return what type of kernel we are
Implements CStringKernel< uint16_t >.
Definition at line 90 of file SalzbergWordStringKernel.h.
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return the kernel's name
Reimplemented from CStringKernel< uint16_t >.
Definition at line 96 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 56 of file SalzbergWordStringKernel.cpp.
set prior probs
pos_prior_ | positive prior |
neg_prior_ | negative prior |
Definition at line 61 of file SalzbergWordStringKernel.h.
void set_prior_probs_from_labels | ( | CLabels * | labels | ) |
set prior probs from labels
labels | labels to set prior probabilites from |
Definition at line 352 of file SalzbergWordStringKernel.cpp.
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the plugin estimate
Definition at line 125 of file SalzbergWordStringKernel.h.
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if kernel is initialized
Definition at line 153 of file SalzbergWordStringKernel.h.
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ld mean left-hand side
Definition at line 138 of file SalzbergWordStringKernel.h.
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ld mean right-hand side
Definition at line 140 of file SalzbergWordStringKernel.h.
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mean
Definition at line 128 of file SalzbergWordStringKernel.h.
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negative prior
Definition at line 151 of file SalzbergWordStringKernel.h.
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number of params
Definition at line 143 of file SalzbergWordStringKernel.h.
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number of symbols
Definition at line 145 of file SalzbergWordStringKernel.h.
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positive prior
Definition at line 149 of file SalzbergWordStringKernel.h.
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sqrt diagonal of left-hand side
Definition at line 133 of file SalzbergWordStringKernel.h.
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sqrt diagonal of right-hand side
Definition at line 135 of file SalzbergWordStringKernel.h.
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sum m2 s2
Definition at line 147 of file SalzbergWordStringKernel.h.
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variance
Definition at line 130 of file SalzbergWordStringKernel.h.