SHOGUN
v1.1.0
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The Regulaty Modules kernel, based on the WD kernel, as published in Schultheiss et al., Bioinformatics (2009) on regulatory sequences.
Definition at line 25 of file RegulatoryModulesStringKernel.h.
Public Member Functions | |
CRegulatoryModulesStringKernel () | |
CRegulatoryModulesStringKernel (int32_t size, float64_t width, int32_t degree, int32_t shift, int32_t window) | |
CRegulatoryModulesStringKernel (CStringFeatures< char > *lstr, CStringFeatures< char > *rstr, CSimpleFeatures< uint16_t > *lpos, CSimpleFeatures< uint16_t > *rpos, float64_t width, int32_t degree, int32_t shift, int32_t window, int32_t size=10) | |
virtual | ~CRegulatoryModulesStringKernel () |
virtual bool | init (CFeatures *l, CFeatures *r) |
virtual EKernelType | get_kernel_type () |
virtual const char * | get_name () const |
void | set_motif_positions (CSimpleFeatures< uint16_t > *positions_lhs, CSimpleFeatures< uint16_t > *positions_rhs) |
virtual void | register_params () |
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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 () |
virtual void | cleanup () |
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 | |
virtual float64_t | compute (int32_t idx_a, int32_t idx_b) |
float64_t | compute_wds (char *avec, char *bvec, int32_t len) |
void | set_wd_weights () |
Protected Attributes | |
float64_t | width |
int32_t | degree |
int32_t | shift |
int32_t | window |
CSimpleFeatures< uint16_t > * | motif_positions_lhs |
CSimpleFeatures< uint16_t > * | motif_positions_rhs |
int32_t | alen |
int32_t | blen |
float64_t * | position_weights |
float64_t * | weights |
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 19 of file RegulatoryModulesStringKernel.cpp.
CRegulatoryModulesStringKernel | ( | int32_t | size, |
float64_t | width, | ||
int32_t | degree, | ||
int32_t | shift, | ||
int32_t | window | ||
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constructor
size | cache size |
width | width of gaussian kernel |
degree | degree of wds kernel |
shift | shift of wds kernel |
window | size of window around motifs to compute wds kernels on |
Definition at line 27 of file RegulatoryModulesStringKernel.cpp.
CRegulatoryModulesStringKernel | ( | CStringFeatures< char > * | lstr, |
CStringFeatures< char > * | rstr, | ||
CSimpleFeatures< uint16_t > * | lpos, | ||
CSimpleFeatures< uint16_t > * | rpos, | ||
float64_t | width, | ||
int32_t | degree, | ||
int32_t | shift, | ||
int32_t | window, | ||
int32_t | size = 10 |
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) |
constructor
lstr | string features of left-hand side |
rstr | string features of right-hand side |
lpos | motif positions on lhs |
rpos | motif positions on rhs |
width | width of gaussian kernel |
degree | degree of wds kernel |
shift | shift of wds kernel |
window | size of window around motifs to compute wds kernels on |
size | cache size |
Definition at line 35 of file RegulatoryModulesStringKernel.cpp.
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default destructor
Definition at line 46 of file RegulatoryModulesStringKernel.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 85 of file RegulatoryModulesStringKernel.cpp.
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compute WDS kernel for features a and b
avec | vector a |
bvec | vector b |
len | length of string |
Definition at line 133 of file RegulatoryModulesStringKernel.cpp.
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return what type of kernel we are
Implements CStringKernel< char >.
Definition at line 72 of file RegulatoryModulesStringKernel.h.
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return the kernel's name
Reimplemented from CStringKernel< char >.
Definition at line 78 of file RegulatoryModulesStringKernel.h.
initialize kernel
l | features of left-hand side |
r | features of right-hand side |
Reimplemented from CStringKernel< char >.
Definition at line 52 of file RegulatoryModulesStringKernel.cpp.
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Separate the function of parameter registration This can be the first stage of a general framework for cross-validation or other parameter-based operations
Reimplemented from CKernel.
Definition at line 217 of file RegulatoryModulesStringKernel.cpp.
void set_motif_positions | ( | CSimpleFeatures< uint16_t > * | positions_lhs, |
CSimpleFeatures< uint16_t > * | positions_rhs | ||
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set motif positions
positions_lhs | motif positions on lhs |
positions_rhs | motif positions on rhs |
Definition at line 69 of file RegulatoryModulesStringKernel.cpp.
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set standard weighted degree kernel weighting
Definition at line 198 of file RegulatoryModulesStringKernel.cpp.
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the length of matrix of motif positions – for serialization purposes
Definition at line 134 of file RegulatoryModulesStringKernel.h.
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the length of matrix of motif positions – for serialization purposes
Definition at line 136 of file RegulatoryModulesStringKernel.h.
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degree of Weighted Degree kernel part
Definition at line 120 of file RegulatoryModulesStringKernel.h.
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Matrix of motif positions from sequences left-hand side
Definition at line 128 of file RegulatoryModulesStringKernel.h.
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Matrix of motif positions from sequences right-hand side
Definition at line 131 of file RegulatoryModulesStringKernel.h.
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scaling weights in window
Definition at line 139 of file RegulatoryModulesStringKernel.h.
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shift of Weighted Degree with Shifts kernel part
Definition at line 122 of file RegulatoryModulesStringKernel.h.
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weights of WD kernel
Definition at line 142 of file RegulatoryModulesStringKernel.h.
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width of Gaussian kernel part
Definition at line 117 of file RegulatoryModulesStringKernel.h.
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size of window around motifs
Definition at line 125 of file RegulatoryModulesStringKernel.h.