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CWeightedDegreePositionStringKernel Class Reference

Detailed Description

The Weighted Degree Position String kernel (Weighted Degree kernel with shifts).

The WD-shift kernel of order d compares two sequences \({\bf x}\) and \({\bf x'}\) of length L by summing all contributions of k-mer matches of lengths \(k\in\{1,\dots,d\}\), weighted by coefficients \(\beta_k\) allowing for a positional tolerance of up to shift s.

It is formally defined as

\begin{eqnarray*} &&\!\!\!\!\!\!\!k({\bf x}_i,{\bf x}_j)=\sum_{k=1}^d\beta_k\sum_{l=1}^{\!\!\!\!L-k+1\!\!\!\!}\gamma_l\sum_{\begin{array}{c}s=0\\ \!\!\!\!s+l\leq L\!\!\!\!\end{array}}^{S(l)} \delta_s\;\mu_{k,l,s,{{\bf x}_i},{{\bf x}_j}},\\ &&\!\!\!\!\!\!\!\!\!\! {\footnotesize \mu_{k,l,s,{{\bf x}_i},{{\bf x}_j}}\!\!\! =\!\! I({\bf u}_{k,l+s}({\bf x}_i)\! =\!{\bf u}_{k,l}({\bf x}_j))\! +\!I({\bf u}_{k,l}({\bf x}_i)\! =\!{\bf u}_{k,l+s}({\bf x}_j))},\nonumber \end{eqnarray*}

where \(\beta_j\) are the weighting coefficients of the j-mers, \(\gamma_l\) is a weighting over the position in the sequence, \(\delta_s=1/(2(s+1))\) is the weight assigned to shifts (in either direction) of extent s, and S(l) determines the shift range at position l.

Definition at line 48 of file WeightedDegreePositionStringKernel.h.

Inheritance diagram for CWeightedDegreePositionStringKernel:
Inheritance graph
[legend]

List of all members.

Public Member Functions

 CWeightedDegreePositionStringKernel ()
 CWeightedDegreePositionStringKernel (int32_t size, int32_t degree, int32_t max_mismatch=0, int32_t mkl_stepsize=1)
 CWeightedDegreePositionStringKernel (int32_t size, SGVector< float64_t > weights, int32_t degree, int32_t max_mismatch, SGVector< int32_t > shifts, int32_t mkl_stepsize=1)
 CWeightedDegreePositionStringKernel (CStringFeatures< char > *l, CStringFeatures< char > *r, int32_t degree)
virtual ~CWeightedDegreePositionStringKernel ()
virtual bool init (CFeatures *l, CFeatures *r)
virtual void cleanup ()
virtual EKernelType get_kernel_type ()
virtual const char * get_name () const
virtual bool init_optimization (int32_t p_count, int32_t *IDX, float64_t *alphas)
virtual bool init_optimization (int32_t count, int32_t *IDX, float64_t *alphas, int32_t tree_num, int32_t upto_tree=-1)
virtual bool delete_optimization ()
virtual float64_t compute_optimized (int32_t 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)
virtual void clear_normal ()
virtual void add_to_normal (int32_t idx, float64_t weight)
virtual int32_t get_num_subkernels ()
void compute_by_subkernel (int32_t idx, float64_t *subkernel_contrib)
const float64_tget_subkernel_weights (int32_t &num_weights)
virtual void set_subkernel_weights (SGVector< float64_t > w)
float64_tcompute_abs_weights (int32_t &len)
bool is_tree_initialized ()
int32_t get_max_mismatch ()
int32_t get_degree ()
float64_tget_degree_weights (int32_t &d, int32_t &len)
float64_tget_weights (int32_t &num_weights)
float64_tget_position_weights (int32_t &len)
void set_shifts (SGVector< int32_t > shifts)
bool set_weights (SGMatrix< float64_t > new_weights)
virtual bool set_wd_weights ()
virtual void set_position_weights (SGVector< float64_t > pws)
bool set_position_weights_lhs (float64_t *pws, int32_t len, int32_t num)
bool set_position_weights_rhs (float64_t *pws, int32_t len, int32_t num)
bool init_block_weights ()
bool init_block_weights_from_wd ()
bool init_block_weights_from_wd_external ()
bool init_block_weights_const ()
bool init_block_weights_linear ()
bool init_block_weights_sqpoly ()
bool init_block_weights_cubicpoly ()
bool init_block_weights_exp ()
bool init_block_weights_log ()
bool delete_position_weights ()
bool delete_position_weights_lhs ()
bool delete_position_weights_rhs ()
virtual float64_t compute_by_tree (int32_t idx)
virtual void compute_by_tree (int32_t idx, float64_t *LevelContrib)
float64_tcompute_scoring (int32_t max_degree, int32_t &num_feat, int32_t &num_sym, float64_t *target, int32_t num_suppvec, int32_t *IDX, float64_t *weights)
char * compute_consensus (int32_t &num_feat, int32_t num_suppvec, int32_t *IDX, float64_t *alphas)
float64_textract_w (int32_t max_degree, int32_t &num_feat, int32_t &num_sym, float64_t *w_result, int32_t num_suppvec, int32_t *IDX, float64_t *alphas)
float64_tcompute_POIM (int32_t max_degree, int32_t &num_feat, int32_t &num_sym, float64_t *poim_result, int32_t num_suppvec, int32_t *IDX, float64_t *alphas, float64_t *distrib)
void prepare_POIM2 (SGMatrix< float64_t > distrib)
void compute_POIM2 (int32_t max_degree, CSVM *svm)
SGVector< float64_tget_POIM2 ()
void cleanup_POIM2 ()
 cleanup POIM2
virtual EFeatureClass get_feature_class ()
virtual EFeatureType get_feature_type ()
float64_t kernel (int32_t idx_a, int32_t idx_b)
SGMatrix< float64_tget_kernel_matrix ()
template<class T >
SGMatrix< T > get_kernel_matrix ()
SGVector< float64_tget_kernel_diagonal (SGVector< float64_t > preallocated=SGVector< float64_t >())
virtual SGVector< float64_tget_kernel_col (int32_t j)
virtual SGVector< float64_tget_kernel_row (int32_t i)
void get_kernel_row (int32_t docnum, int32_t *active2dnum, float64_t *buffer, bool full_line=false)
virtual bool set_normalizer (CKernelNormalizer *normalizer)
virtual CKernelNormalizerget_normalizer ()
virtual bool init_normalizer ()
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_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 cache_reset ()
int32_t get_max_elems_cache ()
int32_t get_activenum_cache ()
void cache_kernel_row (int32_t x)
void cache_multiple_kernel_rows (int32_t *key, int32_t varnum)
void kernel_cache_reset_lru ()
void kernel_cache_shrink (int32_t totdoc, int32_t num_shrink, int32_t *after)
void resize_kernel_cache (KERNELCACHE_IDX size, bool regression_hack=false)
void set_time (int32_t t)
int32_t kernel_cache_touch (int32_t cacheidx)
int32_t kernel_cache_check (int32_t cacheidx)
int32_t kernel_cache_space_available ()
void kernel_cache_init (int32_t size, bool regression_hack=false)
void kernel_cache_cleanup ()
void list_kernel ()
bool has_property (EKernelProperty p)
EOptimizationType get_optimization_type ()
virtual void set_optimization_type (EOptimizationType t)
bool get_is_initialized ()
bool init_optimization_svm (CSVM *svm)
float64_t get_combined_kernel_weight ()
void set_combined_kernel_weight (float64_t nw)
virtual SGVector< float64_tget_subkernel_weights ()
virtual SGMatrix< float64_tget_parameter_gradient (const TParameter *param, index_t index=-1)
virtual CSGObjectshallow_copy () const
virtual CSGObjectdeep_copy () const
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="", int32_t param_version=Version::get_version_parameter())
virtual bool load_serializable (CSerializableFile *file, const char *prefix="", int32_t param_version=Version::get_version_parameter())
DynArray< TParameter * > * load_file_parameters (const SGParamInfo *param_info, int32_t file_version, CSerializableFile *file, const char *prefix="")
DynArray< TParameter * > * load_all_file_parameters (int32_t file_version, int32_t current_version, CSerializableFile *file, const char *prefix="")
void map_parameters (DynArray< TParameter * > *param_base, int32_t &base_version, DynArray< const SGParamInfo * > *target_param_infos)
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 ()
SGStringList< char > get_modelsel_names ()
void print_modsel_params ()
char * get_modsel_param_descr (const char *param_name)
index_t get_modsel_param_index (const char *param_name)
void build_gradient_parameter_dictionary (CMap< TParameter *, CSGObject * > *dict)
virtual bool update_parameter_hash ()
virtual bool equals (CSGObject *other, float64_t accuracy=0.0)
virtual CSGObjectclone ()

Static Public Member Functions

static void * compute_batch_helper (void *p)
static CKernelobtain_from_generic (CSGObject *kernel)

Public Attributes

SGIOio
Parallelparallel
Versionversion
Parameterm_parameters
Parameterm_model_selection_parameters
Parameterm_gradient_parameters
ParameterMapm_parameter_map
uint32_t m_hash

Protected Member Functions

void create_empty_tries ()
virtual void add_example_to_tree (int32_t idx, float64_t weight)
void add_example_to_single_tree (int32_t idx, float64_t weight, int32_t tree_num)
virtual float64_t compute (int32_t idx_a, int32_t idx_b)
float64_t compute_with_mismatch (char *avec, int32_t alen, char *bvec, int32_t blen)
float64_t compute_without_mismatch (char *avec, int32_t alen, char *bvec, int32_t blen)
float64_t compute_without_mismatch_matrix (char *avec, int32_t alen, char *bvec, int32_t blen)
float64_t compute_without_mismatch_position_weights (char *avec, float64_t *posweights_lhs, int32_t alen, char *bvec, float64_t *posweights_rhs, int32_t blen)
virtual void remove_lhs ()
virtual void load_serializable_post () throw (ShogunException)
void set_property (EKernelProperty p)
void unset_property (EKernelProperty p)
void set_is_initialized (bool p_init)
int32_t compute_row_start (int64_t offs, int32_t n, bool symmetric)
virtual void save_serializable_pre () throw (ShogunException)
virtual void save_serializable_post () throw (ShogunException)
virtual void register_params ()
virtual TParametermigrate (DynArray< TParameter * > *param_base, const SGParamInfo *target)
virtual void one_to_one_migration_prepare (DynArray< TParameter * > *param_base, const SGParamInfo *target, TParameter *&replacement, TParameter *&to_migrate, char *old_name=NULL)
virtual void load_serializable_pre () throw (ShogunException)

Static Protected Member Functions

template<class T >
static void * get_kernel_matrix_helper (void *p)

Protected Attributes

float64_tweights
int32_t weights_degree
int32_t weights_length
float64_tposition_weights
int32_t position_weights_len
float64_tposition_weights_lhs
int32_t position_weights_lhs_len
float64_tposition_weights_rhs
int32_t position_weights_rhs_len
bool * position_mask
float64_tweights_buffer
int32_t mkl_stepsize
int32_t degree
int32_t length
int32_t max_mismatch
int32_t seq_length
int32_t * shift
int32_t shift_len
int32_t max_shift
bool block_computation
float64_tblock_weights
EWDKernType type
int32_t which_degree
CTrie< DNATrie > tries
CTrie< POIMTrie > poim_tries
bool tree_initialized
bool use_poim_tries
float64_tm_poim_distrib
float64_tm_poim
int32_t m_poim_num_sym
int32_t m_poim_num_feat
int32_t m_poim_result_len
CAlphabetalphabet
int32_t cache_size
 cache_size in MB
KERNEL_CACHE kernel_cache
 kernel cache
KERNELCACHE_ELEMkernel_matrix
CFeatureslhs
 feature vectors to occur on left hand side
CFeaturesrhs
 feature vectors to occur on right hand side
bool lhs_equals_rhs
 lhs
int32_t num_lhs
 number of feature vectors on left hand side
int32_t num_rhs
 number of feature vectors on right hand side
float64_t combined_kernel_weight
bool optimization_initialized
EOptimizationType opt_type
uint64_t properties
CKernelNormalizernormalizer

Constructor & Destructor Documentation

default constructor

Definition at line 52 of file WeightedDegreePositionStringKernel.cpp.

CWeightedDegreePositionStringKernel ( int32_t  size,
int32_t  degree,
int32_t  max_mismatch = 0,
int32_t  mkl_stepsize = 1 
)

constructor

Parameters:
sizecache size
degreedegree
max_mismatchmaximum mismatch
mkl_stepsizeMKL stepsize

Definition at line 59 of file WeightedDegreePositionStringKernel.cpp.

CWeightedDegreePositionStringKernel ( int32_t  size,
SGVector< float64_t weights,
int32_t  degree,
int32_t  max_mismatch,
SGVector< int32_t >  shifts,
int32_t  mkl_stepsize = 1 
)

constructor

Parameters:
sizecache size
weightsweights
degreedegree
max_mismatchmaximum mismatch
shiftsposition shifts
mkl_stepsizeMKL stepsize

Definition at line 76 of file WeightedDegreePositionStringKernel.cpp.

CWeightedDegreePositionStringKernel ( CStringFeatures< char > *  l,
CStringFeatures< char > *  r,
int32_t  degree 
)

constructor

Parameters:
lfeatures of left-hand side
rfeatures of right-hand side
degreedegree

Definition at line 100 of file WeightedDegreePositionStringKernel.cpp.

Definition at line 119 of file WeightedDegreePositionStringKernel.cpp.


Member Function Documentation

void add_example_to_single_tree ( int32_t  idx,
float64_t  weight,
int32_t  tree_num 
) [protected]

add example to single tree

Parameters:
idxindex
weightweight
tree_numwhich tree

Definition at line 695 of file WeightedDegreePositionStringKernel.cpp.

void add_example_to_tree ( int32_t  idx,
float64_t  weight 
) [protected, virtual]

add example to tree

Parameters:
idxindex
weightweight

Definition at line 644 of file WeightedDegreePositionStringKernel.cpp.

virtual void add_to_normal ( int32_t  idx,
float64_t  weight 
) [virtual]

add to normal

Parameters:
idxwhere to add
weightwhat to add

Reimplemented from CKernel.

Definition at line 210 of file WeightedDegreePositionStringKernel.h.

void build_gradient_parameter_dictionary ( CMap< TParameter *, CSGObject * > *  dict) [inherited]

Builds a dictionary of all parameters in SGObject as well of those of SGObjects that are parameters of this object. Dictionary maps parameters to the objects that own them.

Parameters:
dictdictionary of parameters to be built.

Definition at line 1156 of file SGObject.cpp.

void cache_kernel_row ( int32_t  x) [inherited]

cache kernel row

Parameters:
xx

Definition at line 291 of file Kernel.cpp.

void cache_multiple_kernel_rows ( int32_t *  key,
int32_t  varnum 
) [inherited]

cache multiple kernel rows

Parameters:
keykey
varnum

Definition at line 365 of file Kernel.cpp.

void cache_reset ( ) [inherited]

cache reset

Definition at line 444 of file Kernel.h.

void cleanup ( ) [virtual]

clean up kernel

Reimplemented from CKernel.

Definition at line 227 of file WeightedDegreePositionStringKernel.cpp.

void cleanup_POIM2 ( )

cleanup POIM2

Definition at line 1867 of file WeightedDegreePositionStringKernel.cpp.

virtual void clear_normal ( ) [virtual]

clear normal subkernel functionality

Reimplemented from CKernel.

Definition at line 184 of file WeightedDegreePositionStringKernel.h.

CSGObject * clone ( ) [virtual, inherited]

Creates a clone of the current object. This is done via recursively traversing all parameters, which corresponds to a deep copy. Calling equals on the cloned object always returns true although none of the memory of both objects overlaps.

Returns:
an identical copy of the given object, which is disjoint in memory. NULL if the clone fails. Note that the returned object is SG_REF'ed

Definition at line 1273 of file SGObject.cpp.

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

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

Implements CKernel.

Definition at line 608 of file WeightedDegreePositionStringKernel.cpp.

float64_t * compute_abs_weights ( int32_t &  len)

compute abs weights

Parameters:
lenlen
Returns:
computed abs weights

Definition at line 831 of file WeightedDegreePositionStringKernel.cpp.

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 
) [virtual]

compute batch

Parameters:
num_vecnumber of vectors
vec_idxvector index
targettarget
num_suppvecnumber of support vectors
IDXIDX
alphasalphas
factorfactor

Reimplemented from CKernel.

Definition at line 1230 of file WeightedDegreePositionStringKernel.cpp.

void * compute_batch_helper ( void *  p) [static]

helper for compute batch

Parameters:
pthread parameter

Definition at line 1172 of file WeightedDegreePositionStringKernel.cpp.

void compute_by_subkernel ( int32_t  idx,
float64_t subkernel_contrib 
) [virtual]

compute by subkernel

Parameters:
idxindex
subkernel_contribsubkernel contribution

Reimplemented from CKernel.

Definition at line 234 of file WeightedDegreePositionStringKernel.h.

float64_t compute_by_tree ( int32_t  idx) [virtual]

compute by tree

Parameters:
idxindex
Returns:
computed value

Definition at line 749 of file WeightedDegreePositionStringKernel.cpp.

void compute_by_tree ( int32_t  idx,
float64_t LevelContrib 
) [virtual]

compute by tree

Parameters:
idxindex
LevelContriblevel contribution

Definition at line 788 of file WeightedDegreePositionStringKernel.cpp.

char * compute_consensus ( int32_t &  num_feat,
int32_t  num_suppvec,
int32_t *  IDX,
float64_t alphas 
)

compute consensus string

Parameters:
num_featnumber of features
num_suppvecnumber of support vectors
IDXIDX
alphasalphas
Returns:
consensus string

Definition at line 1499 of file WeightedDegreePositionStringKernel.cpp.

virtual float64_t compute_optimized ( int32_t  idx) [virtual]

compute optimized

Parameters:
idxindex to compute
Returns:
optimized value at given index

Reimplemented from CKernel.

Definition at line 152 of file WeightedDegreePositionStringKernel.h.

float64_t * compute_POIM ( int32_t  max_degree,
int32_t &  num_feat,
int32_t &  num_sym,
float64_t poim_result,
int32_t  num_suppvec,
int32_t *  IDX,
float64_t alphas,
float64_t distrib 
)

compute POIM

Parameters:
max_degreemaximum degree
num_featnumber of features
num_symnumber of symbols
poim_resultpoim
num_suppvecnumber of support vectors
IDXIDX
alphasalphas
distribdistribution
Returns:
computed POIMs

Definition at line 1679 of file WeightedDegreePositionStringKernel.cpp.

void compute_POIM2 ( int32_t  max_degree,
CSVM svm 
)

compute POIM2

Parameters:
max_degreemaximum degree
svmSVM

Definition at line 1826 of file WeightedDegreePositionStringKernel.cpp.

int32_t compute_row_start ( int64_t  offs,
int32_t  n,
bool  symmetric 
) [protected, inherited]

compute row start offset for parallel kernel matrix computation

Parameters:
offsoffset
nnumber of columns
symmetricwhether matrix is symmetric

Definition at line 748 of file Kernel.h.

float64_t * compute_scoring ( int32_t  max_degree,
int32_t &  num_feat,
int32_t &  num_sym,
float64_t target,
int32_t  num_suppvec,
int32_t *  IDX,
float64_t weights 
)

compute positional scoring function, which assigns a weight per position, per symbol in the sequence

Parameters:
max_degreemaximum degree
num_featnumber of features
num_symnumber of symbols
targettarget
num_suppvecnumber of support vectors
IDXIDX
weightsweights
Returns:
computed scores

Definition at line 1343 of file WeightedDegreePositionStringKernel.cpp.

float64_t compute_with_mismatch ( char *  avec,
int32_t  alen,
char *  bvec,
int32_t  blen 
) [protected]

compute with mismatch

Parameters:
avecvector a
alenlength of vector a
bvecvector b
blenlength of vector b
Returns:
computed value

Definition at line 318 of file WeightedDegreePositionStringKernel.cpp.

float64_t compute_without_mismatch ( char *  avec,
int32_t  alen,
char *  bvec,
int32_t  blen 
) [protected]

compute without mismatch

Parameters:
avecvector a
alenlength of vector a
bvecvector b
blenlength of vector b
Returns:
computed value

Definition at line 398 of file WeightedDegreePositionStringKernel.cpp.

float64_t compute_without_mismatch_matrix ( char *  avec,
int32_t  alen,
char *  bvec,
int32_t  blen 
) [protected]

compute without mismatch matrix

Parameters:
avecvector a
alenlength of vector a
bvecvector b
blenlength of vector b
Returns:
computed value

Definition at line 464 of file WeightedDegreePositionStringKernel.cpp.

float64_t compute_without_mismatch_position_weights ( char *  avec,
float64_t posweights_lhs,
int32_t  alen,
char *  bvec,
float64_t posweights_rhs,
int32_t  blen 
) [protected]

compute without mismatch position weights

Parameters:
avecvector a
posweights_lhsposition weights left-hand side
alenlength of vector a
bvecvector b
posweights_rhsposition weights right-hand side
blenlength of vector b
Returns:
computed value

Definition at line 528 of file WeightedDegreePositionStringKernel.cpp.

void create_empty_tries ( ) [protected]

create emtpy tries

Definition at line 159 of file WeightedDegreePositionStringKernel.cpp.

virtual CSGObject* deep_copy ( ) const [virtual, inherited]

A deep copy. All the instance variables will also be copied.

Definition at line 126 of file SGObject.h.

bool delete_optimization ( ) [virtual]

delete optimization

Returns:
if deleting was successful

Reimplemented from CKernel.

Definition at line 293 of file WeightedDegreePositionStringKernel.cpp.

delete position weights

Returns:
if deleting was successful

Definition at line 473 of file WeightedDegreePositionStringKernel.h.

delete position weights left-hand side

Returns:
if deleting was successful

Definition at line 484 of file WeightedDegreePositionStringKernel.h.

delete position weights right-hand side

Returns:
if deleting was successful

Definition at line 495 of file WeightedDegreePositionStringKernel.h.

bool equals ( CSGObject other,
float64_t  accuracy = 0.0 
) [virtual, inherited]

Recursively compares the current SGObject to another one. Compares all registered numerical parameters, recursion upon complex (SGObject) parameters. Does not compare pointers!

May be overwritten but please do with care! Should not be necessary in most cases.

Parameters:
otherobject to compare with
accuracyaccuracy to use for comparison (optional)
Returns:
true if all parameters were equal, false if not

Definition at line 1177 of file SGObject.cpp.

float64_t * extract_w ( int32_t  max_degree,
int32_t &  num_feat,
int32_t &  num_sym,
float64_t w_result,
int32_t  num_suppvec,
int32_t *  IDX,
float64_t alphas 
)

extract w

Parameters:
max_degreemaximum degree
num_featnumber of features
num_symnumber of symbols
w_resultw
num_suppvecnumber of support vectors
IDXIDX
alphasalphas
Returns:
w

Definition at line 1616 of file WeightedDegreePositionStringKernel.cpp.

int32_t get_activenum_cache ( ) [inherited]

get activenum cache

Returns:
activecnum cache

Definition at line 456 of file Kernel.h.

int32_t get_cache_size ( ) [inherited]

return the size of the kernel cache

Returns:
size of kernel cache

Definition at line 440 of file Kernel.h.

get combined kernel weight

Returns:
combined kernel weight

Definition at line 644 of file Kernel.h.

int32_t get_degree ( )

get degree

Returns:
the degree

Definition at line 328 of file WeightedDegreePositionStringKernel.h.

float64_t* get_degree_weights ( int32_t &  d,
int32_t &  len 
)

get degree weights

Parameters:
ddegree weights will be stored here
lennumber of degree weights will be stored here

Definition at line 335 of file WeightedDegreePositionStringKernel.h.

virtual EFeatureClass get_feature_class ( ) [virtual, inherited]

return feature class the kernel can deal with

Returns:
feature class STRING

Implements CKernel.

Definition at line 69 of file StringKernel.h.

virtual EFeatureType get_feature_type ( ) [virtual, inherited]

return feature type the kernel can deal with

Returns:
templated feature type

Implements CKernel.

SGIO * get_global_io ( ) [inherited]

get the io object

Returns:
io object

Definition at line 174 of file SGObject.cpp.

Parallel * get_global_parallel ( ) [inherited]

get the parallel object

Returns:
parallel object

Definition at line 209 of file SGObject.cpp.

Version * get_global_version ( ) [inherited]

get the version object

Returns:
version object

Definition at line 222 of file SGObject.cpp.

bool get_is_initialized ( ) [inherited]

check if optimization is initialized

Returns:
if optimization is initialized

Definition at line 595 of file Kernel.h.

virtual SGVector<float64_t> get_kernel_col ( int32_t  j) [virtual, inherited]

get column j

Returns:
the jth column of the kernel matrix

Definition at line 259 of file Kernel.h.

SGVector<float64_t> get_kernel_diagonal ( SGVector< float64_t preallocated = SGVector<float64_t>()) [inherited]
Returns:
Vector with diagonal elements of the kernel matrix. Note that left- and right-handside features must be set and of equal size
Parameters:
preallocatedvector with space for results

Definition at line 225 of file Kernel.h.

template SGMatrix< float32_t > get_kernel_matrix< float32_t > ( ) [inherited]

get kernel matrix

Returns:
computed kernel matrix (needs to be cleaned up)

Definition at line 214 of file Kernel.h.

SGMatrix<T> get_kernel_matrix ( ) [inherited]

get kernel matrix (templated)

Returns:
the kernel matrix
template void * get_kernel_matrix_helper< float32_t > ( void *  p) [static, protected, inherited]

helper for computing the kernel matrix in a parallel way

Parameters:
pthread parameters

Definition at line 1011 of file Kernel.cpp.

virtual SGVector<float64_t> get_kernel_row ( int32_t  i) [virtual, inherited]

get row i

Returns:
the ith row of the kernel matrix

Definition at line 276 of file Kernel.h.

void get_kernel_row ( int32_t  docnum,
int32_t *  active2dnum,
float64_t buffer,
bool  full_line = false 
) [inherited]

get kernel row

Parameters:
docnumdocnum
active2dnumactive2dnum
bufferbuffer
full_linefull line

Definition at line 227 of file Kernel.cpp.

virtual EKernelType get_kernel_type ( ) [virtual]

return what type of kernel we are

Returns:
kernel type WEIGHTEDDEGREEPOS

Implements CStringKernel< char >.

Definition at line 105 of file WeightedDegreePositionStringKernel.h.

CFeatures* get_lhs ( ) [inherited]

get left-hand side of features used in kernel

Returns:
features of left-hand side

Definition at line 346 of file Kernel.h.

bool get_lhs_equals_rhs ( ) [inherited]

test whether features on lhs and rhs are the same

Returns:
true if features are the same

Definition at line 385 of file Kernel.h.

int32_t get_max_elems_cache ( ) [inherited]

get maximum elements in cache

Returns:
maximum elements in cache

Definition at line 450 of file Kernel.h.

int32_t get_max_mismatch ( )

get maximum mismatch

Returns:
maximum mismatch

Definition at line 322 of file WeightedDegreePositionStringKernel.h.

SGStringList< char > get_modelsel_names ( ) [inherited]
Returns:
vector of names of all parameters which are registered for model selection

Definition at line 1060 of file SGObject.cpp.

char * get_modsel_param_descr ( const char *  param_name) [inherited]

Returns description of a given parameter string, if it exists. SG_ERROR otherwise

Parameters:
param_namename of the parameter
Returns:
description of the parameter

Definition at line 1084 of file SGObject.cpp.

index_t get_modsel_param_index ( const char *  param_name) [inherited]

Returns index of model selection parameter with provided index

Parameters:
param_namename of model selection parameter
Returns:
index of model selection parameter with provided name, -1 if there is no such

Definition at line 1097 of file SGObject.cpp.

virtual const char* get_name ( ) const [virtual]

return the kernel's name

Returns:
name WeightedDegreePos

Reimplemented from CStringKernel< char >.

Definition at line 111 of file WeightedDegreePositionStringKernel.h.

CKernelNormalizer * get_normalizer ( ) [virtual, inherited]

obtain the current kernel normalizer

Returns:
the kernel normalizer

Definition at line 151 of file Kernel.cpp.

virtual int32_t get_num_subkernels ( ) [virtual]

get number of subkernels

Returns:
number of subkernels

Reimplemented from CKernel.

Definition at line 220 of file WeightedDegreePositionStringKernel.h.

virtual int32_t get_num_vec_lhs ( ) [virtual, inherited]

get number of vectors of lhs features

Returns:
number of vectors of left-hand side

Reimplemented in CCustomKernel.

Definition at line 358 of file Kernel.h.

virtual int32_t get_num_vec_rhs ( ) [virtual, inherited]

get number of vectors of rhs features

Returns:
number of vectors of right-hand side

Reimplemented in CCustomKernel.

Definition at line 367 of file Kernel.h.

get optimization type

Returns:
optimization type

Definition at line 583 of file Kernel.h.

virtual SGMatrix<float64_t> get_parameter_gradient ( const TParameter param,
index_t  index = -1 
) [virtual, inherited]

return derivative with respect to specified parameter

Parameters:
paramthe parameter
indexthe index of the element if parameter is a vector
Returns:
gradient with respect to parameter

Reimplemented in CCombinedKernel, CProductKernel, CGaussianKernel, CLinearARDKernel, and CGaussianARDKernel.

Definition at line 692 of file Kernel.h.

get POIM2

Returns:
poim

Definition at line 1861 of file WeightedDegreePositionStringKernel.cpp.

float64_t* get_position_weights ( int32_t &  len)

get position weights

Parameters:
lennumber of position weights will be stored here
Returns:
position weights

Definition at line 366 of file WeightedDegreePositionStringKernel.h.

CFeatures* get_rhs ( ) [inherited]

get right-hand side of features used in kernel

Returns:
features of right-hand side

Definition at line 352 of file Kernel.h.

const float64_t* get_subkernel_weights ( int32_t &  num_weights) [virtual]

get subkernel weights

Parameters:
num_weightsnumber of weights will be stored here
Returns:
subkernel weights

Reimplemented from CKernel.

Definition at line 251 of file WeightedDegreePositionStringKernel.h.

SGVector< float64_t > get_subkernel_weights ( ) [virtual, inherited]

get subkernel weights (swig compatible)

Returns:
subkernel weights

Reimplemented in CCombinedKernel.

Definition at line 865 of file Kernel.cpp.

float64_t* get_weights ( int32_t &  num_weights)

get weights

Parameters:
num_weightsnumber of weights will be stored here
Returns:
weights

Definition at line 347 of file WeightedDegreePositionStringKernel.h.

virtual bool has_features ( ) [virtual, inherited]

test whether features have been assigned to lhs and rhs

Returns:
true if features are assigned

Reimplemented in CCustomKernel, CCombinedKernel, and CProductKernel.

Definition at line 376 of file Kernel.h.

bool has_property ( EKernelProperty  p) [inherited]

check if kernel has given property

Parameters:
pkernel property
Returns:
if kernel has given property

Definition at line 565 of file Kernel.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 178 of file WeightedDegreePositionStringKernel.cpp.

initialize block weights

Returns:
if initialization was successful

Definition at line 1146 of file WeightedDegreePositionStringKernel.cpp.

initialize block weights constant

Returns:
if initialization was successful

Definition at line 1050 of file WeightedDegreePositionStringKernel.cpp.

initialize block weights cubic polynomial

Returns:
if initialization was successful

Definition at line 1095 of file WeightedDegreePositionStringKernel.cpp.

initialize block weights exponential

Returns:
if initialization was successful

Definition at line 1112 of file WeightedDegreePositionStringKernel.cpp.

initialize block weights from weighted degree

Returns:
if initialization was successful

Definition at line 1002 of file WeightedDegreePositionStringKernel.cpp.

initialize block weights from external weighted degree

Returns:
if initialization was successful

Definition at line 1022 of file WeightedDegreePositionStringKernel.cpp.

initialize block weights linear

Returns:
if initialization was successful

Definition at line 1064 of file WeightedDegreePositionStringKernel.cpp.

initialize block weights logarithmic

Returns:
if initialization was successful

Definition at line 1129 of file WeightedDegreePositionStringKernel.cpp.

initialize block weights squared polynomial

Returns:
if initialization was successful

Definition at line 1078 of file WeightedDegreePositionStringKernel.cpp.

bool init_normalizer ( ) [virtual, inherited]

initialize the current kernel normalizer

Returns:
if init was successful

Definition at line 157 of file Kernel.cpp.

virtual bool init_optimization ( int32_t  p_count,
int32_t *  IDX,
float64_t alphas 
) [virtual]

initialize optimization

Parameters:
p_countcount
IDXindex
alphasalphas
Returns:
if initializing was successful

Reimplemented from CKernel.

Definition at line 120 of file WeightedDegreePositionStringKernel.h.

bool init_optimization ( int32_t  count,
int32_t *  IDX,
float64_t alphas,
int32_t  tree_num,
int32_t  upto_tree = -1 
) [virtual]

initialize optimization do initialization for tree_num up to upto_tree, use tree_num=-1 to construct all trees

Parameters:
countcount
IDXIDX
alphasalphas
tree_numwhich tree
upto_treeup to this tree
Returns:
if initializing was successful

Definition at line 247 of file WeightedDegreePositionStringKernel.cpp.

bool init_optimization_svm ( CSVM svm) [inherited]

initialize optimization

Parameters:
svmsvm model
Returns:
if initializing was successful

Definition at line 895 of file Kernel.cpp.

bool is_generic ( EPrimitiveType *  generic) const [virtual, inherited]

If the SGSerializable is a class template then TRUE will be returned and GENERIC is set to the type of the generic.

Parameters:
genericset to the type of the generic if returning TRUE
Returns:
TRUE if a class template.

Definition at line 228 of file SGObject.cpp.

check if tree is initialized

Returns:
if tree is initialized

Definition at line 316 of file WeightedDegreePositionStringKernel.h.

float64_t kernel ( int32_t  idx_a,
int32_t  idx_b 
) [inherited]

get kernel function for lhs feature vector a and rhs feature vector b

Parameters:
idx_aindex of feature vector a
idx_bindex of feature vector b
Returns:
computed kernel function

Definition at line 201 of file Kernel.h.

int32_t kernel_cache_check ( int32_t  cacheidx) [inherited]

check if row at given index is cached

Parameters:
cacheidxindex in cache
Returns:
if row at given index is cached

Definition at line 531 of file Kernel.h.

void kernel_cache_cleanup ( ) [inherited]

cleanup kernel cache

Definition at line 556 of file Kernel.cpp.

void kernel_cache_init ( int32_t  size,
bool  regression_hack = false 
) [inherited]

initialize kernel cache

Parameters:
sizesize to initialize to
regression_hackif hack for regression shall be applied

Definition at line 170 of file Kernel.cpp.

void kernel_cache_reset_lru ( ) [inherited]

kernel cache reset lru

Definition at line 543 of file Kernel.cpp.

void kernel_cache_shrink ( int32_t  totdoc,
int32_t  num_shrink,
int32_t *  after 
) [inherited]

kernel cache shrink

Parameters:
totdoctotdoc
num_shrinknumber of shrink
afterafter

Definition at line 484 of file Kernel.cpp.

int32_t kernel_cache_space_available ( ) [inherited]

check if there is room for one more row in kernel cache

Returns:
if there is room for one more row in kernel cache

Definition at line 540 of file Kernel.h.

int32_t kernel_cache_touch ( int32_t  cacheidx) [inherited]

update lru time of item at given index to avoid removal from cache

Parameters:
cacheidxindex in cache
Returns:
if updating was successful

Definition at line 516 of file Kernel.h.

void list_kernel ( ) [inherited]

list kernel

Definition at line 697 of file Kernel.cpp.

void load ( CFile loader) [inherited]

load the kernel matrix

Parameters:
loaderFile object via which to load data

Definition at line 635 of file Kernel.cpp.

DynArray< TParameter * > * load_all_file_parameters ( int32_t  file_version,
int32_t  current_version,
CSerializableFile file,
const char *  prefix = "" 
) [inherited]

maps all parameters of this instance to the provided file version and loads all parameter data from the file into an array, which is sorted (basically calls load_file_parameter(...) for all parameters and puts all results into a sorted array)

Parameters:
file_versionparameter version of the file
current_versionversion from which mapping begins (you want to use Version::get_version_parameter() for this in most cases)
filefile to load from
prefixprefix for members
Returns:
(sorted) array of created TParameter instances with file data

Definition at line 633 of file SGObject.cpp.

DynArray< TParameter * > * load_file_parameters ( const SGParamInfo param_info,
int32_t  file_version,
CSerializableFile file,
const char *  prefix = "" 
) [inherited]

loads some specified parameters from a file with a specified version The provided parameter info has a version which is recursively mapped until the file parameter version is reached. Note that there may be possibly multiple parameters in the mapping, therefore, a set of TParameter instances is returned

Parameters:
param_infoinformation of parameter
file_versionparameter version of the file, must be <= provided parameter version
filefile to load from
prefixprefix for members
Returns:
new array with TParameter instances with the attached data

Definition at line 474 of file SGObject.cpp.

bool load_serializable ( CSerializableFile file,
const char *  prefix = "",
int32_t  param_version = Version::get_version_parameter() 
) [virtual, inherited]

Load this object from file. If it will fail (returning FALSE) then this object will contain inconsistent data and should not be used!

Parameters:
filewhere to load from
prefixprefix for members
param_version(optional) a parameter version different to (this is mainly for testing, better do not use)
Returns:
TRUE if done, otherwise FALSE

Definition at line 305 of file SGObject.cpp.

void load_serializable_post ( ) throw (ShogunException) [protected, virtual]

Can (optionally) be overridden to post-initialize some member variables which are not PARAMETER::ADD'ed. Make sure that at first the overridden method BASE_CLASS::LOAD_SERIALIZABLE_POST is called.

Exceptions:
ShogunExceptionWill be thrown if an error occurres.

Reimplemented from CKernel.

Definition at line 1878 of file WeightedDegreePositionStringKernel.cpp.

void load_serializable_pre ( ) throw (ShogunException) [protected, virtual, inherited]

Can (optionally) be overridden to pre-initialize some member variables which are not PARAMETER::ADD'ed. Make sure that at first the overridden method BASE_CLASS::LOAD_SERIALIZABLE_PRE is called.

Exceptions:
ShogunExceptionWill be thrown if an error occurres.

Reimplemented in CDynamicArray< T >, CDynamicArray< float64_t >, CDynamicArray< float32_t >, CDynamicArray< int32_t >, CDynamicArray< char >, CDynamicArray< bool >, and CDynamicObjectArray.

Definition at line 984 of file SGObject.cpp.

void map_parameters ( DynArray< TParameter * > *  param_base,
int32_t &  base_version,
DynArray< const SGParamInfo * > *  target_param_infos 
) [inherited]

Takes a set of TParameter instances (base) with a certain version and a set of target parameter infos and recursively maps the base level wise to the current version using CSGObject::migrate(...). The base is replaced. After this call, the base version containing parameters should be of same version/type as the initial target parameter infos. Note for this to work, the migrate methods and all the internal parameter mappings have to match

Parameters:
param_baseset of TParameter instances that are mapped to the provided target parameter infos
base_versionversion of the parameter base
target_param_infosset of SGParamInfo instances that specify the target parameter base

Definition at line 671 of file SGObject.cpp.

TParameter * migrate ( DynArray< TParameter * > *  param_base,
const SGParamInfo target 
) [protected, virtual, inherited]

creates a new TParameter instance, which contains migrated data from the version that is provided. The provided parameter data base is used for migration, this base is a collection of all parameter data of the previous version. Migration is done FROM the data in param_base TO the provided param info Migration is always one version step. Method has to be implemented in subclasses, if no match is found, base method has to be called.

If there is an element in the param_base which equals the target, a copy of the element is returned. This represents the case when nothing has changed and therefore, the migrate method is not overloaded in a subclass

Parameters:
param_baseset of TParameter instances to use for migration
targetparameter info for the resulting TParameter
Returns:
a new TParameter instance with migrated data from the base of the type which is specified by the target parameter

Definition at line 878 of file SGObject.cpp.

CKernel * obtain_from_generic ( CSGObject kernel) [static, inherited]

Obtains a kernel from a generic SGObject with error checking. Note that if passing NULL, result will be NULL

Parameters:
kernelObject to cast to CKernel, is *not* SG_REFed
Returns:
object casted to CKernel, NULL if not possible

Definition at line 881 of file Kernel.cpp.

void one_to_one_migration_prepare ( DynArray< TParameter * > *  param_base,
const SGParamInfo target,
TParameter *&  replacement,
TParameter *&  to_migrate,
char *  old_name = NULL 
) [protected, virtual, inherited]

This method prepares everything for a one-to-one parameter migration. One to one here means that only ONE element of the parameter base is needed for the migration (the one with the same name as the target). Data is allocated for the target (in the type as provided in the target SGParamInfo), and a corresponding new TParameter instance is written to replacement. The to_migrate pointer points to the single needed TParameter instance needed for migration. If a name change happened, the old name may be specified by old_name. In addition, the m_delete_data flag of to_migrate is set to true. So if you want to migrate data, the only thing to do after this call is converting the data in the m_parameter fields. If unsure how to use - have a look into an example for this. (base_migration_type_conversion.cpp for example)

Parameters:
param_baseset of TParameter instances to use for migration
targetparameter info for the resulting TParameter
replacement(used as output) here the TParameter instance which is returned by migration is created into
to_migratethe only source that is used for migration
old_namewith this parameter, a name change may be specified

Definition at line 818 of file SGObject.cpp.

void prepare_POIM2 ( SGMatrix< float64_t distrib)

prepare POIM2

Parameters:
distribdistribution

Definition at line 1815 of file WeightedDegreePositionStringKernel.cpp.

void print_modsel_params ( ) [inherited]

prints all parameter registered for model selection and their type

Definition at line 1036 of file SGObject.cpp.

void print_serializable ( const char *  prefix = "") [virtual, inherited]

prints registered parameters out

Parameters:
prefixprefix for members

Definition at line 240 of file SGObject.cpp.

void register_params ( ) [protected, virtual, inherited]

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 in CSpectrumMismatchRBFKernel, CSNPStringKernel, CANOVAKernel, CStringSubsequenceKernel, CGaussianMatchStringKernel, CGaussianShortRealKernel, CTensorProductPairKernel, CDistanceKernel, and CHistogramIntersectionKernel.

Definition at line 936 of file Kernel.cpp.

void remove_lhs ( ) [protected, virtual]

remove lhs from kernel

Reimplemented from CKernel.

Definition at line 148 of file WeightedDegreePositionStringKernel.cpp.

void remove_lhs_and_rhs ( ) [virtual, inherited]

remove lhs and rhs from kernel

Reimplemented in CCombinedKernel, and CProductKernel.

Definition at line 649 of file Kernel.cpp.

void remove_rhs ( ) [virtual, inherited]

takes all necessary steps if the rhs is removed from kernel

remove rhs from kernel

Reimplemented in CCombinedKernel, CCommUlongStringKernel, and CProductKernel.

Definition at line 682 of file Kernel.cpp.

void resize_kernel_cache ( KERNELCACHE_IDX  size,
bool  regression_hack = false 
) [inherited]

resize kernel cache

Parameters:
sizenew size
regression_hackhack for regression

Definition at line 85 of file Kernel.cpp.

void save ( CFile writer) [inherited]

save kernel matrix

Parameters:
writerFile object via which to save data

Definition at line 641 of file Kernel.cpp.

bool save_serializable ( CSerializableFile file,
const char *  prefix = "",
int32_t  param_version = Version::get_version_parameter() 
) [virtual, inherited]

Save this object to file.

Parameters:
filewhere to save the object; will be closed during returning if PREFIX is an empty string.
prefixprefix for members
param_version(optional) a parameter version different to (this is mainly for testing, better do not use)
Returns:
TRUE if done, otherwise FALSE

Definition at line 246 of file SGObject.cpp.

void save_serializable_post ( ) throw (ShogunException) [protected, virtual, inherited]

Can (optionally) be overridden to post-initialize some member variables which are not PARAMETER::ADD'ed. Make sure that at first the overridden method BASE_CLASS::SAVE_SERIALIZABLE_POST is called.

Exceptions:
ShogunExceptionWill be thrown if an error occurres.

Reimplemented from CSGObject.

Definition at line 928 of file Kernel.cpp.

void save_serializable_pre ( ) throw (ShogunException) [protected, virtual, inherited]

Can (optionally) be overridden to pre-initialize some member variables which are not PARAMETER::ADD'ed. Make sure that at first the overridden method BASE_CLASS::SAVE_SERIALIZABLE_PRE is called.

Exceptions:
ShogunExceptionWill be thrown if an error occurres.

Reimplemented from CSGObject.

Definition at line 920 of file Kernel.cpp.

void set_cache_size ( int32_t  size) [inherited]

set the size of the kernel cache

Parameters:
sizeof kernel cache

Definition at line 428 of file Kernel.h.

void set_combined_kernel_weight ( float64_t  nw) [inherited]

set combined kernel weight

Parameters:
nwnew combined kernel weight

Definition at line 650 of file Kernel.h.

void set_generic< complex128_t > ( ) [inherited]

set generic type to T

Definition at line 41 of file SGObject.cpp.

void set_global_io ( SGIO io) [inherited]

set the io object

Parameters:
ioio object to use

Definition at line 167 of file SGObject.cpp.

void set_global_parallel ( Parallel parallel) [inherited]

set the parallel object

Parameters:
parallelparallel object to use

Definition at line 180 of file SGObject.cpp.

void set_global_version ( Version version) [inherited]

set the version object

Parameters:
versionversion object to use

Definition at line 215 of file SGObject.cpp.

void set_is_initialized ( bool  p_init) [protected, inherited]

set is initialized

Parameters:
p_initif optimization shall be set to initialized

Definition at line 728 of file Kernel.h.

bool set_normalizer ( CKernelNormalizer normalizer) [virtual, inherited]

set the current kernel normalizer

Returns:
if successful

Reimplemented in CWeightedDegreeStringKernel.

Definition at line 139 of file Kernel.cpp.

virtual void set_optimization_type ( EOptimizationType  t) [virtual, inherited]

set optimization type

Parameters:
toptimization type to set

Reimplemented in CCombinedKernel.

Definition at line 589 of file Kernel.h.

void set_position_weights ( SGVector< float64_t pws) [virtual]

set position weights

Parameters:
pwsnew position weights
Returns:
if setting was successful

Definition at line 928 of file WeightedDegreePositionStringKernel.cpp.

bool set_position_weights_lhs ( float64_t pws,
int32_t  len,
int32_t  num 
)

set position weights for left-hand side

Parameters:
pwsnew position weights
lenlen
numnum
Returns:
if setting was successful

Definition at line 945 of file WeightedDegreePositionStringKernel.cpp.

bool set_position_weights_rhs ( float64_t pws,
int32_t  len,
int32_t  num 
)

set position weights for right-hand side

Parameters:
pwsnew position weights
lenlen
numnum
Returns:
if setting was successful

Definition at line 973 of file WeightedDegreePositionStringKernel.cpp.

void set_property ( EKernelProperty  p) [protected, inherited]

set property

Parameters:
pkernel property to set

Definition at line 710 of file Kernel.h.

void set_shifts ( SGVector< int32_t >  shifts)

set shifts

Parameters:
shiftsnew shifts

Definition at line 837 of file WeightedDegreePositionStringKernel.cpp.

virtual void set_subkernel_weights ( SGVector< float64_t w) [virtual]

set subkernel weights

Parameters:
wweights

Reimplemented from CKernel.

Definition at line 272 of file WeightedDegreePositionStringKernel.h.

void set_time ( int32_t  t) [inherited]

set the lru time

Parameters:
tthe time to use

Definition at line 506 of file Kernel.h.

bool set_wd_weights ( ) [virtual]

set wd weights

Returns:
if setting was successful

Definition at line 858 of file WeightedDegreePositionStringKernel.cpp.

bool set_weights ( SGMatrix< float64_t new_weights)

set weights

Parameters:
new_weightsnew weights

Definition at line 899 of file WeightedDegreePositionStringKernel.cpp.

virtual CSGObject* shallow_copy ( ) const [virtual, inherited]

A shallow copy. All the SGObject instance variables will be simply assigned and SG_REF-ed.

Reimplemented in CGaussianKernel.

Definition at line 117 of file SGObject.h.

void unset_generic ( ) [inherited]

unset generic type

this has to be called in classes specializing a template class

Definition at line 235 of file SGObject.cpp.

void unset_property ( EKernelProperty  p) [protected, inherited]

unset property

Parameters:
pkernel property to unset

Definition at line 719 of file Kernel.h.

bool update_parameter_hash ( ) [virtual, inherited]

Updates the hash of current parameter combination.

Returns:
bool if parameter combination has changed since last update.

Definition at line 187 of file SGObject.cpp.


Member Data Documentation

CAlphabet* alphabet [protected]

alphabet of features

Definition at line 776 of file WeightedDegreePositionStringKernel.h.

bool block_computation [protected]

if block computation is used

Definition at line 744 of file WeightedDegreePositionStringKernel.h.

float64_t* block_weights [protected]

(internal) block weights

Definition at line 747 of file WeightedDegreePositionStringKernel.h.

int32_t cache_size [protected, inherited]

cache_size in MB

Definition at line 876 of file Kernel.h.

float64_t combined_kernel_weight [protected, inherited]

combined kernel weight

Definition at line 901 of file Kernel.h.

int32_t degree [protected]

degree

Definition at line 727 of file WeightedDegreePositionStringKernel.h.

SGIO* io [inherited]

io

Definition at line 473 of file SGObject.h.

KERNEL_CACHE kernel_cache [protected, inherited]

kernel cache

Definition at line 880 of file Kernel.h.

KERNELCACHE_ELEM* kernel_matrix [protected, inherited]

this *COULD* store the whole kernel matrix usually not applicable / necessary to compute the whole matrix

Reimplemented in CSpectrumMismatchRBFKernel, and CSpectrumRBFKernel.

Definition at line 885 of file Kernel.h.

int32_t length [protected]

length

Definition at line 729 of file WeightedDegreePositionStringKernel.h.

CFeatures* lhs [protected, inherited]

feature vectors to occur on left hand side

Definition at line 888 of file Kernel.h.

bool lhs_equals_rhs [protected, inherited]

lhs

Definition at line 893 of file Kernel.h.

parameters wrt which we can compute gradients

Definition at line 488 of file SGObject.h.

uint32_t m_hash [inherited]

Hash of parameter values

Definition at line 494 of file SGObject.h.

model selection parameters

Definition at line 485 of file SGObject.h.

map for different parameter versions

Definition at line 491 of file SGObject.h.

Parameter* m_parameters [inherited]

parameters

Definition at line 482 of file SGObject.h.

float64_t* m_poim [protected]

temporary memory for the interface to the poim functions

Definition at line 766 of file WeightedDegreePositionStringKernel.h.

float64_t* m_poim_distrib [protected]

temporary memory for the interface to the poim functions

Definition at line 764 of file WeightedDegreePositionStringKernel.h.

int32_t m_poim_num_feat [protected]

length of string (==num_feat)

Definition at line 771 of file WeightedDegreePositionStringKernel.h.

int32_t m_poim_num_sym [protected]

number of symbols

Definition at line 769 of file WeightedDegreePositionStringKernel.h.

int32_t m_poim_result_len [protected]

total size of poim array

Definition at line 773 of file WeightedDegreePositionStringKernel.h.

int32_t max_mismatch [protected]

maximum mismatch

Definition at line 732 of file WeightedDegreePositionStringKernel.h.

int32_t max_shift [protected]

maximum shift

Definition at line 741 of file WeightedDegreePositionStringKernel.h.

int32_t mkl_stepsize [protected]

MKL stepsize

Definition at line 724 of file WeightedDegreePositionStringKernel.h.

CKernelNormalizer* normalizer [protected, inherited]

normalize the kernel(i,j) function based on this normalization function

Definition at line 915 of file Kernel.h.

int32_t num_lhs [protected, inherited]

number of feature vectors on left hand side

Definition at line 896 of file Kernel.h.

int32_t num_rhs [protected, inherited]

number of feature vectors on right hand side

Definition at line 898 of file Kernel.h.

EOptimizationType opt_type [protected, inherited]

optimization type (currently FASTBUTMEMHUNGRY and SLOWBUTMEMEFFICIENT)

Definition at line 908 of file Kernel.h.

bool optimization_initialized [protected, inherited]

if optimization is initialized

Definition at line 904 of file Kernel.h.

Parallel* parallel [inherited]

parallel

Definition at line 476 of file SGObject.h.

CTrie<POIMTrie> poim_tries [protected]

POIM tries

Definition at line 756 of file WeightedDegreePositionStringKernel.h.

bool* position_mask [protected]

position mask

Definition at line 719 of file WeightedDegreePositionStringKernel.h.

position weights

Definition at line 706 of file WeightedDegreePositionStringKernel.h.

int32_t position_weights_len [protected]

position weights len

Definition at line 708 of file WeightedDegreePositionStringKernel.h.

position weights left-hand side

Definition at line 711 of file WeightedDegreePositionStringKernel.h.

int32_t position_weights_lhs_len [protected]

position weights len

Definition at line 713 of file WeightedDegreePositionStringKernel.h.

position weights right-hand side

Definition at line 715 of file WeightedDegreePositionStringKernel.h.

int32_t position_weights_rhs_len [protected]

position weights len

Definition at line 717 of file WeightedDegreePositionStringKernel.h.

uint64_t properties [protected, inherited]

kernel properties

Definition at line 911 of file Kernel.h.

CFeatures* rhs [protected, inherited]

feature vectors to occur on right hand side

Definition at line 890 of file Kernel.h.

int32_t seq_length [protected]

length of sequence

Definition at line 734 of file WeightedDegreePositionStringKernel.h.

int32_t* shift [protected]

shifts

Definition at line 737 of file WeightedDegreePositionStringKernel.h.

int32_t shift_len [protected]

length of shifts

Definition at line 739 of file WeightedDegreePositionStringKernel.h.

bool tree_initialized [protected]

if tree is initialized

Definition at line 759 of file WeightedDegreePositionStringKernel.h.

CTrie<DNATrie> tries [protected]

tries

Definition at line 754 of file WeightedDegreePositionStringKernel.h.

EWDKernType type [protected]

WeightedDegree kernel type

Definition at line 749 of file WeightedDegreePositionStringKernel.h.

bool use_poim_tries [protected]

makes add_example_to_tree (ONLY!) use POIMTrie

Definition at line 761 of file WeightedDegreePositionStringKernel.h.

Version* version [inherited]

version

Definition at line 479 of file SGObject.h.

float64_t* weights [protected]

weights

Definition at line 699 of file WeightedDegreePositionStringKernel.h.

float64_t* weights_buffer [protected]

weights buffer

Definition at line 722 of file WeightedDegreePositionStringKernel.h.

int32_t weights_degree [protected]

degree

Definition at line 701 of file WeightedDegreePositionStringKernel.h.

int32_t weights_length [protected]

length

Definition at line 703 of file WeightedDegreePositionStringKernel.h.

int32_t which_degree [protected]

which degree

Definition at line 751 of file WeightedDegreePositionStringKernel.h.


The documentation for this class was generated from the following files:
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SHOGUN Machine Learning Toolbox - Documentation