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CWeightedDegreeStringKernel Class Reference

Detailed Description

The Weighted Degree String kernel.

The WD 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 $\beta_k$. It is defined as

\[ k({\bf x},{\bf x'})=\sum_{k=1}^d\beta_k\sum_{l=1}^{L-k+1}I({\bf u}_{k,l}({\bf x})={\bf u}_{k,l}({\bf x'})). \]

Here, ${\bf u}_{k,l}({\bf x})$ is the string of length k starting at position l of the sequence ${\bf x}$ and $I(\cdot)$ is the indicator function which evaluates to 1 when its argument is true and to 0 otherwise.

Definition at line 53 of file WeightedDegreeStringKernel.h.

Inheritance diagram for CWeightedDegreeStringKernel:
Inheritance graph
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List of all members.

Public Member Functions

 CWeightedDegreeStringKernel ()
 CWeightedDegreeStringKernel (int32_t degree, EWDKernType type=E_WD)
 CWeightedDegreeStringKernel (SGVector< float64_t > weights)
 CWeightedDegreeStringKernel (CStringFeatures< char > *l, CStringFeatures< char > *r, int32_t degree)
virtual ~CWeightedDegreeStringKernel ()
virtual bool init (CFeatures *l, CFeatures *r)
virtual void cleanup ()
EWDKernType get_type () const
virtual EKernelType get_kernel_type ()
virtual const char * get_name () const
virtual bool init_optimization (int32_t count, int32_t *IDX, float64_t *alphas)
virtual bool init_optimization (int32_t count, int32_t *IDX, float64_t *alphas, int32_t tree_num)
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)
virtual bool set_normalizer (CKernelNormalizer *normalizer_)
float64_tcompute_abs_weights (int32_t &len)
void compute_by_tree (int32_t idx, float64_t *LevelContrib)
bool is_tree_initialized ()
float64_tget_degree_weights (int32_t &d, int32_t &len)
float64_tget_weights (int32_t &num_weights)
float64_tget_position_weights (int32_t &len)
bool set_wd_weights_by_type (EWDKernType type)
void set_wd_weights (SGVector< float64_t > new_weights)
bool set_weights (SGMatrix< float64_t > new_weights)
bool set_position_weights (float64_t *pws, int32_t len)
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 set_max_mismatch (int32_t max)
int32_t get_max_mismatch () const
bool set_degree (int32_t deg)
int32_t get_degree () const
bool set_use_block_computation (bool block)
bool get_use_block_computation ()
bool set_mkl_stepsize (int32_t step)
int32_t get_mkl_stepsize ()
bool set_which_degree (int32_t which)
int32_t get_which_degree ()
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 ()
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 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 SGMatrix< float64_tget_parameter_gradient (TParameter *param, CSGObject *obj, 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_PARAMETER)
virtual bool load_serializable (CSerializableFile *file, const char *prefix="", int32_t param_version=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_parameter_dictionary (CMap< TParameter *, CSGObject * > &dict)

Static Public Member Functions

static void * compute_batch_helper (void *p)

Public Attributes

SGIOio
Parallelparallel
Versionversion
Parameterm_parameters
Parameterm_model_selection_parameters
ParameterMapm_parameter_map
uint32_t m_hash

Protected Member Functions

void create_empty_tries ()
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)
void add_example_to_tree_mismatch (int32_t idx, float64_t weight)
void add_example_to_single_tree_mismatch (int32_t idx, float64_t weight, int32_t tree_num)
float64_t compute_by_tree (int32_t idx)
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_using_block (char *avec, int32_t alen, char *bvec, int32_t blen)
virtual void remove_lhs ()
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 load_serializable_post () throw (ShogunException)
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)
virtual bool update_parameter_hash ()

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_tweights_buffer
int32_t mkl_stepsize
int32_t degree
int32_t length
int32_t max_mismatch
int32_t seq_length
bool initialized
bool block_computation
float64_tblock_weights
EWDKernType type
int32_t which_degree
CTrie< DNATrie > * tries
bool tree_initialized
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 48 of file WeightedDegreeStringKernel.cpp.

CWeightedDegreeStringKernel ( int32_t  degree,
EWDKernType  type = E_WD 
)

constructor

Parameters:
degreedegree
typeweighted degree kernel type

Definition at line 55 of file WeightedDegreeStringKernel.cpp.

constructor

Parameters:
weightskernel's weights

Definition at line 68 of file WeightedDegreeStringKernel.cpp.

CWeightedDegreeStringKernel ( 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 84 of file WeightedDegreeStringKernel.cpp.

Definition at line 96 of file WeightedDegreeStringKernel.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 435 of file WeightedDegreeStringKernel.cpp.

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

add example to single tree mismatch

Parameters:
idxindex
weightweight
tree_numwhich tree

Definition at line 486 of file WeightedDegreeStringKernel.cpp.

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

add example to tree

Parameters:
idxindex
weightweight

Definition at line 389 of file WeightedDegreeStringKernel.cpp.

void add_example_to_tree_mismatch ( int32_t  idx,
float64_t  weight 
) [protected]

add example to tree mismatch

Parameters:
idxindex
weightweight

Definition at line 460 of file WeightedDegreeStringKernel.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 212 of file WeightedDegreeStringKernel.h.

void build_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 1204 of file SGObject.cpp.

void cache_kernel_row ( int32_t  x) [inherited]

cache kernel row

Parameters:
xx

Definition at line 290 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 364 of file Kernel.cpp.

void cache_reset ( ) [inherited]

cache reset

Definition at line 527 of file Kernel.h.

void cleanup ( ) [virtual]

clean up kernel

Reimplemented from CKernel.

Definition at line 182 of file WeightedDegreeStringKernel.cpp.

virtual void clear_normal ( ) [virtual]

clear normal subkernel functionality

Reimplemented from CKernel.

Definition at line 194 of file WeightedDegreeStringKernel.h.

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 363 of file WeightedDegreeStringKernel.cpp.

float64_t * compute_abs_weights ( int32_t &  len)

compute abs weights

Parameters:
lenlen
Returns:
computed abs weights

Definition at line 565 of file WeightedDegreeStringKernel.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 862 of file WeightedDegreeStringKernel.cpp.

void * compute_batch_helper ( void *  p) [static]

helper for compute batch

Parameters:
pthread parameter

Definition at line 826 of file WeightedDegreeStringKernel.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 246 of file WeightedDegreeStringKernel.h.

void compute_by_tree ( int32_t  idx,
float64_t LevelContrib 
)

compute by tree

Parameters:
idxindex
LevelContriblevel contribution
Returns:
computed value

Definition at line 538 of file WeightedDegreeStringKernel.cpp.

float64_t compute_by_tree ( int32_t  idx) [protected]

compute by tree

Parameters:
idxindex
Returns:
computed value

Definition at line 514 of file WeightedDegreeStringKernel.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 161 of file WeightedDegreeStringKernel.h.

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 815 of file Kernel.h.

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

compute using block

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

Definition at line 290 of file WeightedDegreeStringKernel.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 262 of file WeightedDegreeStringKernel.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 316 of file WeightedDegreeStringKernel.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 339 of file WeightedDegreeStringKernel.cpp.

void create_empty_tries ( ) [protected]

create emtpy tries

Definition at line 127 of file WeightedDegreeStringKernel.cpp.

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

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

Definition at line 131 of file SGObject.h.

bool delete_optimization ( ) [virtual]

delete optimization

Returns:
if deleting was successful

Reimplemented from CKernel.

Definition at line 248 of file WeightedDegreeStringKernel.cpp.

delete position weights

Returns:
if deleting was successful

Definition at line 519 of file WeightedDegreeStringKernel.h.

int32_t get_activenum_cache ( ) [inherited]

get activenum cache

Returns:
activecnum cache

Definition at line 539 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 523 of file Kernel.h.

get combined kernel weight

Returns:
combined kernel weight

Definition at line 727 of file Kernel.h.

int32_t get_degree ( ) const

get degree

Returns:
degree

Definition at line 550 of file WeightedDegreeStringKernel.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 388 of file WeightedDegreeStringKernel.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 224 of file SGObject.cpp.

Parallel * get_global_parallel ( ) [inherited]

get the parallel object

Returns:
parallel object

Definition at line 259 of file SGObject.cpp.

Version * get_global_version ( ) [inherited]

get the version object

Returns:
version object

Definition at line 272 of file SGObject.cpp.

bool get_is_initialized ( ) [inherited]

check if optimization is initialized

Returns:
if optimization is initialized

Definition at line 678 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 248 of file Kernel.h.

get kernel matrix

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

Definition at line 238 of file Kernel.h.

SGMatrix<T> get_kernel_matrix ( ) [inherited]

get kernel matrix real

Returns:
the kernel matrix

Definition at line 280 of file Kernel.h.

static void* get_kernel_matrix_helper ( void *  p) [static, protected, inherited]

helper for computing the kernel matrix in a parallel way

Parameters:
pthread parameters

Definition at line 832 of file Kernel.h.

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 265 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 226 of file Kernel.cpp.

virtual EKernelType get_kernel_type ( ) [virtual]

return what type of kernel we are

Returns:
kernel type WEIGHTEDDEGREE

Implements CStringKernel< char >.

Definition at line 114 of file WeightedDegreeStringKernel.h.

CFeatures* get_lhs ( ) [inherited]

get left-hand side of features used in kernel

Returns:
features of left-hand side

Definition at line 429 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 468 of file Kernel.h.

int32_t get_max_elems_cache ( ) [inherited]

get maximum elements in cache

Returns:
maximum elements in cache

Definition at line 533 of file Kernel.h.

int32_t get_max_mismatch ( ) const

get maximum mismatch

Returns:
maximum mismatch

Definition at line 537 of file WeightedDegreeStringKernel.h.

int32_t get_mkl_stepsize ( )

get MKL step size

Returns:
MKL step size

Definition at line 586 of file WeightedDegreeStringKernel.h.

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

Definition at line 1108 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 1132 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 1145 of file SGObject.cpp.

virtual const char* get_name ( ) const [virtual]

return the kernel's name

Returns:
name WeightedDegree

Reimplemented from CStringKernel< char >.

Definition at line 120 of file WeightedDegreeStringKernel.h.

CKernelNormalizer * get_normalizer ( ) [virtual, inherited]

obtain the current kernel normalizer

Returns:
the kernel normalizer

Definition at line 150 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 230 of file WeightedDegreeStringKernel.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 441 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 450 of file Kernel.h.

get optimization type

Returns:
optimization type

Definition at line 666 of file Kernel.h.

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

return derivative with respect to specified parameter

Parameters:
paramthe parameter
objthe object that owns the 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 952 of file Kernel.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 423 of file WeightedDegreeStringKernel.h.

CFeatures* get_rhs ( ) [inherited]

get right-hand side of features used in kernel

Returns:
features of right-hand side

Definition at line 435 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 268 of file WeightedDegreeStringKernel.h.

EWDKernType get_type ( ) const

get WD kernel weighting type

Returns:
weighting type
See also:
EWDKernType

Definition at line 105 of file WeightedDegreeStringKernel.h.

check if block computation is performed

Returns:
if block computation is performed

Definition at line 567 of file WeightedDegreeStringKernel.h.

float64_t* get_weights ( int32_t &  num_weights)

get weights

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

Definition at line 400 of file WeightedDegreeStringKernel.h.

int32_t get_which_degree ( )

get which degree

Returns:
which degree

Definition at line 603 of file WeightedDegreeStringKernel.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 459 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 648 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 140 of file WeightedDegreeStringKernel.cpp.

initialize block weights

Returns:
if initialization was successful

Definition at line 801 of file WeightedDegreeStringKernel.cpp.

initialize block weights constant

Returns:
if initialization was successful

Definition at line 725 of file WeightedDegreeStringKernel.cpp.

initialize block weights cubic polynomial

Returns:
if initialization was successful

Definition at line 760 of file WeightedDegreeStringKernel.cpp.

initialize block weights exponential

Returns:
if initialization was successful

Definition at line 773 of file WeightedDegreeStringKernel.cpp.

initialize block weights from weighted degree

Returns:
if initialization was successful

Definition at line 684 of file WeightedDegreeStringKernel.cpp.

initialize block weights from external weighted degree

Returns:
if initialization was successful

Definition at line 701 of file WeightedDegreeStringKernel.cpp.

initialize block weights linear

Returns:
if initialization was successful

Definition at line 735 of file WeightedDegreeStringKernel.cpp.

initialize block weights logarithmic

Returns:
if initialization was successful

Definition at line 787 of file WeightedDegreeStringKernel.cpp.

initialize block weights squared polynomial

Returns:
if initialization was successful

Definition at line 746 of file WeightedDegreeStringKernel.cpp.

bool init_normalizer ( ) [virtual, inherited]

initialize the current kernel normalizer

Returns:
if init was successful

Definition at line 156 of file Kernel.cpp.

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

initialize optimization

Parameters:
countcount
IDXindex
alphasalphas
Returns:
if initializing was successful

Reimplemented from CKernel.

Definition at line 131 of file WeightedDegreeStringKernel.h.

bool init_optimization ( int32_t  count,
int32_t *  IDX,
float64_t alphas,
int32_t  tree_num 
) [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
Returns:
if initializing was successful

Definition at line 206 of file WeightedDegreeStringKernel.cpp.

bool init_optimization_svm ( CSVM svm) [inherited]

initialize optimization

Parameters:
svmsvm model
Returns:
if initializing was successful

Definition at line 865 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 278 of file SGObject.cpp.

check if tree is initialized

Returns:
if tree is initialized

Definition at line 381 of file WeightedDegreeStringKernel.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 225 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 614 of file Kernel.h.

void kernel_cache_cleanup ( ) [inherited]

cleanup kernel cache

Definition at line 552 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 169 of file Kernel.cpp.

void kernel_cache_reset_lru ( ) [inherited]

kernel cache reset lru

Definition at line 539 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 483 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 623 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 599 of file Kernel.h.

void list_kernel ( ) [inherited]

list kernel

Definition at line 691 of file Kernel.cpp.

void load ( CFile loader) [inherited]

load the kernel matrix

Parameters:
loaderFile object via which to load data

Definition at line 631 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_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 679 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 523 of file SGObject.cpp.

bool load_serializable ( CSerializableFile file,
const char *  prefix = "",
int32_t  param_version = 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

Reimplemented in CModelSelectionParameters.

Definition at line 354 of file SGObject.cpp.

void load_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::LOAD_SERIALIZABLE_POST is called.

Exceptions:
ShogunExceptionWill be thrown if an error occurres.

Reimplemented from CSGObject.

Reimplemented in CWeightedDegreePositionStringKernel, CGaussianKernel, CANOVAKernel, CInverseMultiQuadricKernel, CCircularKernel, and CExponentialKernel.

Definition at line 883 of file Kernel.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.

Definition at line 1028 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 717 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 923 of file SGObject.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 864 of file SGObject.cpp.

void print_modsel_params ( ) [inherited]

prints all parameter registered for model selection and their type

Definition at line 1084 of file SGObject.cpp.

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

prints registered parameters out

Parameters:
prefixprefix for members

Definition at line 290 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, CRegulatoryModulesStringKernel, CGaussianMatchStringKernel, CGaussianShortRealKernel, CTensorProductPairKernel, CDistanceKernel, and CHistogramIntersectionKernel.

Definition at line 906 of file Kernel.cpp.

void remove_lhs ( ) [protected, virtual]

remove lhs from kernel

Reimplemented from CKernel.

Definition at line 116 of file WeightedDegreeStringKernel.cpp.

void remove_lhs_and_rhs ( ) [virtual, inherited]

remove lhs and rhs from kernel

Reimplemented in CCombinedKernel, and CProductKernel.

Definition at line 645 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, CProductKernel, and CCommUlongStringKernel.

Definition at line 676 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 637 of file Kernel.cpp.

bool save_serializable ( CSerializableFile file,
const char *  prefix = "",
int32_t  param_version = 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

Reimplemented in CModelSelectionParameters.

Definition at line 296 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 898 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 890 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 511 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 733 of file Kernel.h.

bool set_degree ( int32_t  deg)

set degree

Parameters:
degnew degree
Returns:
if setting was successful

Definition at line 544 of file WeightedDegreeStringKernel.h.

void set_generic< floatmax_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 217 of file SGObject.cpp.

void set_global_parallel ( Parallel parallel) [inherited]

set the parallel object

Parameters:
parallelparallel object to use

Definition at line 230 of file SGObject.cpp.

void set_global_version ( Version version) [inherited]

set the version object

Parameters:
versionversion object to use

Definition at line 265 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 795 of file Kernel.h.

bool set_max_mismatch ( int32_t  max)

set maximum mismatch

Parameters:
maxnew maximum mismatch
Returns:
if setting was successful

Definition at line 966 of file WeightedDegreeStringKernel.cpp.

bool set_mkl_stepsize ( int32_t  step)

set MKL steps ize

Parameters:
stepnew step size
Returns:
if setting was successful

Definition at line 574 of file WeightedDegreeStringKernel.h.

virtual bool set_normalizer ( CKernelNormalizer normalizer_) [virtual]

set the current kernel normalizer

Returns:
if successful

Reimplemented from CKernel.

Definition at line 344 of file WeightedDegreeStringKernel.h.

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

set optimization type

Parameters:
toptimization type to set

Reimplemented in CCombinedKernel.

Definition at line 672 of file Kernel.h.

bool set_position_weights ( float64_t pws,
int32_t  len 
)

set position weights

Parameters:
pwsnew position weights
lennumber of position weights
Returns:
if setting was successful

Definition at line 654 of file WeightedDegreeStringKernel.cpp.

void set_property ( EKernelProperty  p) [protected, inherited]

set property

Parameters:
pkernel property to set

Definition at line 777 of file Kernel.h.

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

set subkernel weights

Parameters:
wweights

Reimplemented from CKernel.

Definition at line 293 of file WeightedDegreeStringKernel.h.

void set_time ( int32_t  t) [inherited]

set the lru time

Parameters:
tthe time to use

Definition at line 589 of file Kernel.h.

bool set_use_block_computation ( bool  block)

set if block computation shall be performed

Parameters:
blockif block computation shall be performed
Returns:
if setting was successful

Definition at line 557 of file WeightedDegreeStringKernel.h.

void set_wd_weights ( SGVector< float64_t new_weights)

set wd weights

Parameters:
new_weightsnew weights

Definition at line 440 of file WeightedDegreeStringKernel.h.

set wd weights

Parameters:
typeweighted degree kernel type
Returns:
if setting was successful

if we know a better weighting later on do a switch

Definition at line 571 of file WeightedDegreeStringKernel.cpp.

bool set_weights ( SGMatrix< float64_t new_weights)

set weights

Parameters:
new_weightsnew weights

Definition at line 624 of file WeightedDegreeStringKernel.cpp.

bool set_which_degree ( int32_t  which)

set which degree

Parameters:
whichwhich degree
Returns:
if setting was successful

Definition at line 593 of file WeightedDegreeStringKernel.h.

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 122 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 285 of file SGObject.cpp.

void unset_property ( EKernelProperty  p) [protected, inherited]

unset property

Parameters:
pkernel property to unset

Definition at line 786 of file Kernel.h.

bool update_parameter_hash ( ) [protected, virtual, inherited]

Updates the hash of current parameter combination.

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

Definition at line 237 of file SGObject.cpp.


Member Data Documentation

CAlphabet* alphabet [protected]

alphabet of features

Definition at line 759 of file WeightedDegreeStringKernel.h.

bool block_computation [protected]

if block computation is used

Definition at line 743 of file WeightedDegreeStringKernel.h.

float64_t* block_weights [protected]

(internal) block weights

Definition at line 746 of file WeightedDegreeStringKernel.h.

int32_t cache_size [protected, inherited]

cache_size in MB

Definition at line 991 of file Kernel.h.

float64_t combined_kernel_weight [protected, inherited]

combined kernel weight

Definition at line 1016 of file Kernel.h.

int32_t degree [protected]

degree

Definition at line 730 of file WeightedDegreeStringKernel.h.

bool initialized [protected]

if kernel is initialized

Definition at line 740 of file WeightedDegreeStringKernel.h.

SGIO* io [inherited]

io

Definition at line 462 of file SGObject.h.

KERNEL_CACHE kernel_cache [protected, inherited]

kernel cache

Definition at line 995 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 1000 of file Kernel.h.

int32_t length [protected]

length

Definition at line 732 of file WeightedDegreeStringKernel.h.

CFeatures* lhs [protected, inherited]

feature vectors to occur on left hand side

Definition at line 1003 of file Kernel.h.

bool lhs_equals_rhs [protected, inherited]

lhs

Definition at line 1008 of file Kernel.h.

uint32_t m_hash [inherited]

Hash of parameter values

Definition at line 480 of file SGObject.h.

model selection parameters

Definition at line 474 of file SGObject.h.

map for different parameter versions

Definition at line 477 of file SGObject.h.

Parameter* m_parameters [inherited]

parameters

Definition at line 471 of file SGObject.h.

int32_t max_mismatch [protected]

maximum mismatch

Definition at line 735 of file WeightedDegreeStringKernel.h.

int32_t mkl_stepsize [protected]

MKL step size

Definition at line 728 of file WeightedDegreeStringKernel.h.

CKernelNormalizer* normalizer [protected, inherited]

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

Definition at line 1030 of file Kernel.h.

int32_t num_lhs [protected, inherited]

number of feature vectors on left hand side

Definition at line 1011 of file Kernel.h.

int32_t num_rhs [protected, inherited]

number of feature vectors on right hand side

Definition at line 1013 of file Kernel.h.

EOptimizationType opt_type [protected, inherited]

optimization type (currently FASTBUTMEMHUNGRY and SLOWBUTMEMEFFICIENT)

Definition at line 1023 of file Kernel.h.

bool optimization_initialized [protected, inherited]

if optimization is initialized

Definition at line 1019 of file Kernel.h.

Parallel* parallel [inherited]

parallel

Definition at line 465 of file SGObject.h.

position weights

Definition at line 722 of file WeightedDegreeStringKernel.h.

int32_t position_weights_len [protected]

position weights

Definition at line 724 of file WeightedDegreeStringKernel.h.

uint64_t properties [protected, inherited]

kernel properties

Definition at line 1026 of file Kernel.h.

CFeatures* rhs [protected, inherited]

feature vectors to occur on right hand side

Definition at line 1005 of file Kernel.h.

int32_t seq_length [protected]

sequence length

Definition at line 737 of file WeightedDegreeStringKernel.h.

bool tree_initialized [protected]

if tree is initialized

Definition at line 756 of file WeightedDegreeStringKernel.h.

CTrie<DNATrie>* tries [protected]

tries

Definition at line 753 of file WeightedDegreeStringKernel.h.

EWDKernType type [protected]

WeightedDegree kernel type

Definition at line 748 of file WeightedDegreeStringKernel.h.

Version* version [inherited]

version

Definition at line 468 of file SGObject.h.

float64_t* weights [protected]

degree*length weights length must match seq_length if != 0

Definition at line 714 of file WeightedDegreeStringKernel.h.

float64_t* weights_buffer [protected]

weights buffer

Definition at line 726 of file WeightedDegreeStringKernel.h.

int32_t weights_degree [protected]

degree

Definition at line 716 of file WeightedDegreeStringKernel.h.

int32_t weights_length [protected]

length

Definition at line 718 of file WeightedDegreeStringKernel.h.

int32_t which_degree [protected]

which degree

Definition at line 750 of file WeightedDegreeStringKernel.h.


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