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CRegulatoryModulesStringKernel Class Reference

Detailed Description

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.

Inheritance diagram for CRegulatoryModulesStringKernel:
Inheritance graph
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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 ()
- Public Member Functions inherited from CStringKernel< char >
 CStringKernel (int32_t cachesize=0)
 CStringKernel (CFeatures *l, CFeatures *r)
virtual EFeatureClass get_feature_class ()
virtual EFeatureType get_feature_type ()
- Public Member Functions inherited from CKernel
 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_tget_kernel_matrix ()
virtual SGVector< float64_tget_kernel_col (int32_t j)
virtual SGVector< float64_tget_kernel_row (int32_t i)
template<class T >
SGMatrix< T > get_kernel_matrix ()
virtual bool set_normalizer (CKernelNormalizer *normalizer)
virtual CKernelNormalizerget_normalizer ()
virtual bool init_normalizer ()
virtual void cleanup ()
void load (CFile *loader)
void save (CFile *writer)
CFeaturesget_lhs ()
CFeaturesget_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_tget_subkernel_weights (int32_t &num_weights)
virtual void set_subkernel_weights (SGVector< float64_t > weights)
- Public Member Functions inherited from CSGObject
 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)
SGIOget_global_io ()
void set_global_parallel (Parallel *parallel)
Parallelget_global_parallel ()
void set_global_version (Version *version)
Versionget_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_tposition_weights
float64_tweights

Additional Inherited Members

- Public Attributes inherited from CSGObject
SGIOio
Parallelparallel
Versionversion
Parameterm_parameters
Parameterm_model_selection_parameters
- Static Protected Member Functions inherited from CKernel
template<class T >
static void * get_kernel_matrix_helper (void *p)

Constructor & Destructor Documentation

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 
)

constructor

Parameters
sizecache size
widthwidth of gaussian kernel
degreedegree of wds kernel
shiftshift of wds kernel
windowsize 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 
)

constructor

Parameters
lstrstring features of left-hand side
rstrstring features of right-hand side
lposmotif positions on lhs
rposmotif positions on rhs
widthwidth of gaussian kernel
degreedegree of wds kernel
shiftshift of wds kernel
windowsize of window around motifs to compute wds kernels on
sizecache size

Definition at line 35 of file RegulatoryModulesStringKernel.cpp.

default destructor

Definition at line 46 of file RegulatoryModulesStringKernel.cpp.

Member Function Documentation

float64_t compute ( int32_t  idx_a,
int32_t  idx_b 
)
protectedvirtual

compute kernel function for features a and b idx_{a,b} denote the index of the feature vectors in the corresponding feature object

Parameters
idx_aindex a
idx_bindex b
Returns
computed kernel function at indices a,b

Implements CKernel.

Definition at line 85 of file RegulatoryModulesStringKernel.cpp.

float64_t compute_wds ( char *  avec,
char *  bvec,
int32_t  len 
)
protected

compute WDS kernel for features a and b

Parameters
avecvector a
bvecvector b
lenlength of string
Returns
computed kernel function

Definition at line 133 of file RegulatoryModulesStringKernel.cpp.

virtual EKernelType get_kernel_type ( )
virtual

return what type of kernel we are

Returns
kernel type

Implements CStringKernel< char >.

Definition at line 72 of file RegulatoryModulesStringKernel.h.

virtual const char* get_name ( ) const
virtual

return the kernel's name

Returns
name Regulatory Modules

Reimplemented from CStringKernel< char >.

Definition at line 78 of file RegulatoryModulesStringKernel.h.

bool init ( CFeatures l,
CFeatures r 
)
virtual

initialize kernel

Parameters
lfeatures of left-hand side
rfeatures of right-hand side
Returns
if initializing was successful

Reimplemented from CStringKernel< char >.

Definition at line 52 of file RegulatoryModulesStringKernel.cpp.

void register_params ( )
virtual

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 
)

set motif positions

Parameters
positions_lhsmotif positions on lhs
positions_rhsmotif positions on rhs

Definition at line 69 of file RegulatoryModulesStringKernel.cpp.

void set_wd_weights ( )
protected

set standard weighted degree kernel weighting

Definition at line 198 of file RegulatoryModulesStringKernel.cpp.

Member Data Documentation

int32_t alen
protected

the length of matrix of motif positions – for serialization purposes

Definition at line 134 of file RegulatoryModulesStringKernel.h.

int32_t blen
protected

the length of matrix of motif positions – for serialization purposes

Definition at line 136 of file RegulatoryModulesStringKernel.h.

int32_t degree
protected

degree of Weighted Degree kernel part

Definition at line 120 of file RegulatoryModulesStringKernel.h.

CSimpleFeatures<uint16_t>* motif_positions_lhs
protected

Matrix of motif positions from sequences left-hand side

Definition at line 128 of file RegulatoryModulesStringKernel.h.

CSimpleFeatures<uint16_t>* motif_positions_rhs
protected

Matrix of motif positions from sequences right-hand side

Definition at line 131 of file RegulatoryModulesStringKernel.h.

float64_t* position_weights
protected

scaling weights in window

Definition at line 139 of file RegulatoryModulesStringKernel.h.

int32_t shift
protected

shift of Weighted Degree with Shifts kernel part

Definition at line 122 of file RegulatoryModulesStringKernel.h.

float64_t* weights
protected

weights of WD kernel

Definition at line 142 of file RegulatoryModulesStringKernel.h.

float64_t width
protected

width of Gaussian kernel part

Definition at line 117 of file RegulatoryModulesStringKernel.h.

int32_t window
protected

size of window around motifs

Definition at line 125 of file RegulatoryModulesStringKernel.h.


The documentation for this class was generated from the following files:

SHOGUN Machine Learning Toolbox - Documentation