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CCombinedKernel Class Reference

Detailed Description

The Combined kernel is used to combine a number of kernels into a single CombinedKernel object by linear combination.

It keeps pointers to the added sub-kernels \(k_m({\bf x}, {\bf x'})\) and for each sub-kernel - a kernel specific weight \(\beta_m\).

It is especially useful to combine kernels working on different domains and to combine kernels looking at independent features and requires CCombinedFeatures to be used.

It is defined as:

\[ k_{combined}({\bf x}, {\bf x'}) = \sum_{m=1}^M \beta_m k_m({\bf x}, {\bf x'}) \]

Definition at line 49 of file CombinedKernel.h.

Inheritance diagram for CCombinedKernel:
Inheritance graph
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Public Member Functions

 CCombinedKernel (int32_t size=10, bool append_subkernel_weights=false)
 
virtual ~CCombinedKernel ()
 
virtual bool init (CFeatures *lhs, CFeatures *rhs)
 
virtual void cleanup ()
 
virtual EKernelType get_kernel_type ()
 
virtual EFeatureType get_feature_type ()
 
virtual EFeatureClass get_feature_class ()
 
virtual const char * get_name () const
 
void list_kernels ()
 
CKernelget_first_kernel ()
 
CKernelget_kernel (int32_t idx)
 
CKernelget_last_kernel ()
 
bool insert_kernel (CKernel *k, int32_t idx)
 
bool append_kernel (CKernel *k)
 
bool delete_kernel (int32_t idx)
 
bool get_append_subkernel_weights ()
 
int32_t get_num_subkernels ()
 
int32_t get_num_kernels ()
 
virtual bool has_features ()
 
virtual void remove_lhs ()
 
virtual void remove_rhs ()
 
virtual void remove_lhs_and_rhs ()
 
virtual bool init_optimization (int32_t count, int32_t *IDX, float64_t *weights)
 
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)
 
void emulate_compute_batch (CKernel *k, int32_t num_vec, int32_t *vec_idx, float64_t *target, int32_t num_suppvec, int32_t *IDX, float64_t *weights)
 
virtual void add_to_normal (int32_t idx, float64_t weight)
 
virtual void clear_normal ()
 
virtual void compute_by_subkernel (int32_t idx, float64_t *subkernel_contrib)
 
virtual const float64_tget_subkernel_weights (int32_t &num_weights)
 
virtual SGVector< float64_tget_subkernel_weights ()
 
virtual void set_subkernel_weights (SGVector< float64_t > weights)
 
virtual void set_optimization_type (EOptimizationType t)
 
bool precompute_subkernels ()
 
SGMatrix< float64_tget_parameter_gradient (const TParameter *param, index_t index=-1)
 
CDynamicObjectArrayget_array ()
 
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 float64_t sum_symmetric_block (index_t block_begin, index_t block_size, bool no_diag=true)
 
virtual float64_t sum_block (index_t block_begin_row, index_t block_begin_col, index_t block_size_row, index_t block_size_col, bool no_diag=false)
 
virtual SGVector< float64_trow_wise_sum_symmetric_block (index_t block_begin, index_t block_size, bool no_diag=true)
 
virtual SGMatrix< float64_trow_wise_sum_squared_sum_symmetric_block (index_t block_begin, index_t block_size, bool no_diag=true)
 
virtual SGVector< float64_trow_col_wise_sum_block (index_t block_begin_row, index_t block_begin_col, index_t block_size_row, index_t block_size_col, bool no_diag=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 ()
 
bool get_lhs_equals_rhs ()
 
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 ()
 
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_parameter_gradient_diagonal (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 ()
 
template<>
void set_generic ()
 
template<>
void set_generic ()
 
template<>
void set_generic ()
 
template<>
void set_generic ()
 
template<>
void set_generic ()
 
template<>
void set_generic ()
 
template<>
void set_generic ()
 
template<>
void set_generic ()
 
template<>
void set_generic ()
 
template<>
void set_generic ()
 
template<>
void set_generic ()
 
template<>
void set_generic ()
 
template<>
void set_generic ()
 
template<>
void set_generic ()
 
template<>
void set_generic ()
 
void unset_generic ()
 
virtual void print_serializable (const char *prefix="")
 
virtual bool save_serializable (CSerializableFile *file, const char *prefix="")
 
virtual bool load_serializable (CSerializableFile *file, const char *prefix="")
 
void set_global_io (SGIO *io)
 
SGIOget_global_io ()
 
void set_global_parallel (Parallel *parallel)
 
Parallelget_global_parallel ()
 
void set_global_version (Version *version)
 
Versionget_global_version ()
 
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 void update_parameter_hash ()
 
virtual bool parameter_hash_changed ()
 
virtual bool equals (CSGObject *other, float64_t accuracy=0.0, bool tolerant=false)
 
virtual CSGObjectclone ()
 

Static Public Member Functions

static void * compute_optimized_kernel_helper (void *p)
 
static void * compute_kernel_helper (void *p)
 
static CCombinedKernelobtain_from_generic (CKernel *kernel)
 
static CListcombine_kernels (CList *kernel_list)
 
static CKernelobtain_from_generic (CSGObject *kernel)
 

Public Attributes

SGIOio
 
Parallelparallel
 
Versionversion
 
Parameterm_parameters
 
Parameterm_model_selection_parameters
 
Parameterm_gradient_parameters
 
uint32_t m_hash
 

Protected Member Functions

virtual float64_t compute (int32_t x, int32_t y)
 
void adjust_num_lhs_rhs_initialized (CKernel *k)
 
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 void load_serializable_pre () throw (ShogunException)
 

Static Protected Member Functions

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

Protected Attributes

CDynamicObjectArraykernel_array
 
int32_t sv_count
 
int32_t * sv_idx
 
float64_tsv_weight
 
float64_tsubkernel_weights_buffer
 
bool append_subkernel_weights
 
bool initialized
 
int32_t cache_size
 cache_size in MB More...
 
KERNEL_CACHE kernel_cache
 kernel cache More...
 
KERNELCACHE_ELEMkernel_matrix
 
CFeatureslhs
 feature vectors to occur on left hand side More...
 
CFeaturesrhs
 feature vectors to occur on right hand side More...
 
bool lhs_equals_rhs
 lhs More...
 
int32_t num_lhs
 number of feature vectors on left hand side More...
 
int32_t num_rhs
 number of feature vectors on right hand side More...
 
float64_t combined_kernel_weight
 
bool optimization_initialized
 
EOptimizationType opt_type
 
uint64_t properties
 
CKernelNormalizernormalizer
 

Constructor & Destructor Documentation

CCombinedKernel ( int32_t  size = 10,
bool  append_subkernel_weights = false 
)

constructor

Parameters
sizecache size
append_subkernel_weightsif subkernel weights shall be appended

Definition at line 44 of file CombinedKernel.cpp.

~CCombinedKernel ( )
virtual

Definition at line 55 of file CombinedKernel.cpp.

Member Function Documentation

void add_to_normal ( int32_t  idx,
float64_t  weight 
)
virtual

add to normal vector

Parameters
idxwhere to add
weightwhat to add

Reimplemented from CKernel.

Definition at line 581 of file CombinedKernel.cpp.

void adjust_num_lhs_rhs_initialized ( CKernel k)
protected

adjust the variables num_lhs, num_rhs and initialized based on the kernel to be appended/inserted

Parameters
kkernel

Definition at line 415 of file CombinedKernel.h.

bool append_kernel ( CKernel k)

append kernel to the end of the array

Parameters
kkernel
Returns
if appending was successful

Definition at line 162 of file CombinedKernel.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 597 of file SGObject.cpp.

void cache_kernel_row ( int32_t  x)
inherited

cache kernel row

Parameters
xx

Definition at line 302 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 376 of file Kernel.cpp.

void cache_reset ( )
inherited

cache reset

Definition at line 602 of file Kernel.h.

void cleanup ( )
virtual

clean up kernel

Reimplemented from CKernel.

Definition at line 225 of file CombinedKernel.cpp.

void clear_normal ( )
virtual

clear normal vector

Reimplemented from CKernel.

Definition at line 592 of file CombinedKernel.cpp.

CSGObject * clone ( )
virtualinherited

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 714 of file SGObject.cpp.

CList * combine_kernels ( CList kernel_list)
static

Returns a list of all the different CombinedKernels produced by the cross-product between the kernel lists The returned list performs reference counting on the contained CombinedKernels.

Parameters
kernel_lista list of lists of kernels. Each sub-list must contain kernels of the same type
Returns
a list of CombinedKernels.

Definition at line 871 of file CombinedKernel.cpp.

float64_t compute ( int32_t  x,
int32_t  y 
)
protectedvirtual

compute kernel function

Parameters
xx
yy
Returns
computed kernel function

Implements CKernel.

Definition at line 256 of file CombinedKernel.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

computes output for a batch of examples in an optimized fashion (favorable if kernel supports it, i.e. has KP_BATCHEVALUATION. to the outputvector target (of length num_vec elements) the output for the examples enumerated in vec_idx are added. therefore make sure that it is initialized with ZERO. the following num_suppvec, IDX, alphas arguments are the number of support vectors, their indices and weights

Reimplemented from CKernel.

Definition at line 343 of file CombinedKernel.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 603 of file CombinedKernel.cpp.

void * compute_kernel_helper ( void *  p)
static

helper for compute kernel

Parameters
pthread parameter

Definition at line 387 of file CombinedKernel.cpp.

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 538 of file CombinedKernel.cpp.

void * compute_optimized_kernel_helper ( void *  p)
static

helper for compute optimized kernel

Parameters
pthread parameter

Definition at line 374 of file CombinedKernel.cpp.

int32_t compute_row_start ( int64_t  offs,
int32_t  n,
bool  symmetric 
)
protectedinherited

compute row start offset for parallel kernel matrix computation

Parameters
offsoffset
nnumber of columns
symmetricwhether matrix is symmetric

Definition at line 919 of file Kernel.h.

CSGObject * deep_copy ( ) const
virtualinherited

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

Definition at line 198 of file SGObject.cpp.

bool delete_kernel ( int32_t  idx)

delete kernel

Parameters
idxthe index of the kernel to delete
Returns
if deleting was successful

Definition at line 181 of file CombinedKernel.h.

bool delete_optimization ( )
virtual

delete optimization

Returns
if deleting was successful

Reimplemented from CKernel.

Definition at line 320 of file CombinedKernel.cpp.

void emulate_compute_batch ( CKernel k,
int32_t  num_vec,
int32_t *  vec_idx,
float64_t target,
int32_t  num_suppvec,
int32_t *  IDX,
float64_t weights 
)

emulates batch computation, via linadd optimization w^t x or even down to sum_i alpha_i K(x_i,x)

Parameters
kkernel
num_vecnumber of vectors
vec_idxvector index
targettarget
num_suppvecnumber of support vectors
IDXIDX
weightsweights

Definition at line 409 of file CombinedKernel.cpp.

bool equals ( CSGObject other,
float64_t  accuracy = 0.0,
bool  tolerant = false 
)
virtualinherited

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)
tolerantallows linient check on float equality (within accuracy)
Returns
true if all parameters were equal, false if not

Definition at line 618 of file SGObject.cpp.

int32_t get_activenum_cache ( )
inherited

get activenum cache

Returns
activecnum cache

Definition at line 614 of file Kernel.h.

bool get_append_subkernel_weights ( )

check if subkernel weights are appended

Returns
if subkernel weigths are appended

Definition at line 198 of file CombinedKernel.h.

CDynamicObjectArray* get_array ( )

Get the Kernel array

Returns
kernel array

Definition at line 384 of file CombinedKernel.h.

int32_t get_cache_size ( )
inherited

return the size of the kernel cache

Returns
size of kernel cache

Definition at line 598 of file Kernel.h.

float64_t get_combined_kernel_weight ( )
inherited

get combined kernel weight

Returns
combined kernel weight

Definition at line 802 of file Kernel.h.

virtual EFeatureClass get_feature_class ( )
virtual

return feature class the kernel can deal with

Returns
feature class COMBINED

Implements CKernel.

Definition at line 97 of file CombinedKernel.h.

virtual EFeatureType get_feature_type ( )
virtual

return feature type the kernel can deal with

Returns
feature type UNKNOWN

Implements CKernel.

Definition at line 88 of file CombinedKernel.h.

CKernel* get_first_kernel ( )

get first kernel

Returns
first kernel

Definition at line 115 of file CombinedKernel.h.

SGIO * get_global_io ( )
inherited

get the io object

Returns
io object

Definition at line 235 of file SGObject.cpp.

Parallel * get_global_parallel ( )
inherited

get the parallel object

Returns
parallel object

Definition at line 277 of file SGObject.cpp.

Version * get_global_version ( )
inherited

get the version object

Returns
version object

Definition at line 290 of file SGObject.cpp.

bool get_is_initialized ( )
inherited

check if optimization is initialized

Returns
if optimization is initialized

Definition at line 753 of file Kernel.h.

CKernel* get_kernel ( int32_t  idx)

get kernel

Parameters
idxindex of kernel
Returns
kernel at index idx

Definition at line 125 of file CombinedKernel.h.

virtual SGVector<float64_t> get_kernel_col ( int32_t  j)
virtualinherited

get column j

Returns
the jth column of the kernel matrix

Definition at line 262 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 230 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 219 of file Kernel.h.

SGMatrix< T > get_kernel_matrix ( )
inherited

get kernel matrix (templated)

Returns
the kernel matrix

Definition at line 1343 of file Kernel.cpp.

template void * get_kernel_matrix_helper< float32_t > ( void *  p)
staticprotectedinherited

helper for computing the kernel matrix in a parallel way

Parameters
pthread parameters

Definition at line 1292 of file Kernel.cpp.

virtual SGVector<float64_t> get_kernel_row ( int32_t  i)
virtualinherited

get row i

Returns
the ith row of the kernel matrix

Definition at line 279 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 238 of file Kernel.cpp.

virtual EKernelType get_kernel_type ( )
virtual

return what type of kernel we are

Returns
kernel type COMBINED

Implements CKernel.

Definition at line 79 of file CombinedKernel.h.

CKernel* get_last_kernel ( )

get last kernel

Returns
last kernel

Definition at line 134 of file CombinedKernel.h.

CFeatures* get_lhs ( )
inherited

get left-hand side of features used in kernel

Returns
features of left-hand side

Definition at line 504 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 543 of file Kernel.h.

int32_t get_max_elems_cache ( )
inherited

get maximum elements in cache

Returns
maximum elements in cache

Definition at line 608 of file Kernel.h.

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

Definition at line 498 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 522 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 535 of file SGObject.cpp.

virtual const char* get_name ( ) const
virtual

return the kernel's name

Returns
name Combined

Implements CSGObject.

Definition at line 106 of file CombinedKernel.h.

CKernelNormalizer * get_normalizer ( )
virtualinherited

obtain the current kernel normalizer

Returns
the kernel normalizer

Definition at line 162 of file Kernel.cpp.

int32_t get_num_kernels ( )

get number of contained kernels

Returns
number of contained kernels

Definition at line 229 of file CombinedKernel.h.

int32_t get_num_subkernels ( )
virtual

get number of subkernels

Returns
number of subkernels

Reimplemented from CKernel.

Definition at line 207 of file CombinedKernel.h.

virtual int32_t get_num_vec_lhs ( )
virtualinherited

get number of vectors of lhs features

Returns
number of vectors of left-hand side

Reimplemented in CCustomKernel.

Definition at line 516 of file Kernel.h.

virtual int32_t get_num_vec_rhs ( )
virtualinherited

get number of vectors of rhs features

Returns
number of vectors of right-hand side

Reimplemented in CCustomKernel.

Definition at line 525 of file Kernel.h.

EOptimizationType get_optimization_type ( )
inherited

get optimization type

Returns
optimization type

Definition at line 741 of file Kernel.h.

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

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 from CKernel.

Definition at line 784 of file CombinedKernel.cpp.

virtual SGVector<float64_t> get_parameter_gradient_diagonal ( const TParameter param,
index_t  index = -1 
)
virtualinherited

return diagonal part of derivative with respect to specified parameter

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

Definition at line 864 of file Kernel.h.

CFeatures* get_rhs ( )
inherited

get right-hand side of features used in kernel

Returns
features of right-hand side

Definition at line 510 of file Kernel.h.

const float64_t * get_subkernel_weights ( int32_t &  num_weights)
virtual

get subkernel weights

Parameters
num_weightswhere number of weights is stored
Returns
subkernel weights

Reimplemented from CKernel.

Definition at line 638 of file CombinedKernel.cpp.

SGVector< float64_t > get_subkernel_weights ( )
virtual

get subkernel weights (swig compatible)

Returns
subkernel weights

Reimplemented from CKernel.

Definition at line 682 of file CombinedKernel.cpp.

virtual bool has_features ( )
virtual

test whether features have been assigned to lhs and rhs

Returns
true if features are assigned

Reimplemented from CKernel.

Definition at line 238 of file CombinedKernel.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 723 of file Kernel.h.

bool init ( CFeatures lhs,
CFeatures rhs 
)
virtual

initialize kernel. Provided features have to be combined features. If they are not, all subkernels are tried to be initialised with the single same passed features objects

Parameters
lhsfeatures of left-hand side
rhsfeatures of right-hand side
Returns
if initializing was successful

Reimplemented from CKernel.

Definition at line 66 of file CombinedKernel.cpp.

bool init_normalizer ( )
virtualinherited

initialize the current kernel normalizer

Returns
if init was successful

Definition at line 168 of file Kernel.cpp.

bool init_optimization ( int32_t  count,
int32_t *  IDX,
float64_t weights 
)
virtual

initialize optimization

Parameters
countcount
IDXindex
weightsweights
Returns
if initializing was successful

Reimplemented from CKernel.

Definition at line 270 of file CombinedKernel.cpp.

bool init_optimization_svm ( CSVM svm)
inherited

initialize optimization

Parameters
svmsvm model
Returns
if initializing was successful

Definition at line 910 of file Kernel.cpp.

bool insert_kernel ( CKernel k,
int32_t  idx 
)

insert kernel at position idx idx must be < num_kernels

Parameters
kkernel
idxthe index of the position where the kernel should be added
Returns
if inserting was successful

Definition at line 146 of file CombinedKernel.h.

bool is_generic ( EPrimitiveType *  generic) const
virtualinherited

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 296 of file SGObject.cpp.

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 206 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 689 of file Kernel.h.

void kernel_cache_cleanup ( )
inherited

cleanup kernel cache

Definition at line 567 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 181 of file Kernel.cpp.

void kernel_cache_reset_lru ( )
inherited

kernel cache reset lru

Definition at line 554 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 495 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 698 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 674 of file Kernel.h.

void list_kernel ( )
inherited

list kernel

Definition at line 708 of file Kernel.cpp.

void list_kernels ( )

list kernels

Definition at line 242 of file CombinedKernel.cpp.

void load ( CFile loader)
inherited

load the kernel matrix

Parameters
loaderFile object via which to load data

Definition at line 646 of file Kernel.cpp.

bool load_serializable ( CSerializableFile file,
const char *  prefix = "" 
)
virtualinherited

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
Returns
TRUE if done, otherwise FALSE

Definition at line 369 of file SGObject.cpp.

void load_serializable_post ( )
throw (ShogunException
)
protectedvirtualinherited

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, CInverseMultiQuadricKernel, CCircularKernel, and CExponentialKernel.

Definition at line 928 of file Kernel.cpp.

void load_serializable_pre ( )
throw (ShogunException
)
protectedvirtualinherited

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 occurs.

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

Definition at line 421 of file SGObject.cpp.

CCombinedKernel * obtain_from_generic ( CKernel kernel)
static

Returns a casted version of the given kernel. Throws an error if parameter is not of class CombinedKernel. SG_REF's the returned kernel

Parameters
kernelkernel to cast to CombinedKernel
Returns
casted version of kernel.

Definition at line 858 of file CombinedKernel.cpp.

CKernel * obtain_from_generic ( CSGObject kernel)
staticinherited

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 896 of file Kernel.cpp.

bool parameter_hash_changed ( )
virtualinherited
Returns
whether parameter combination has changed since last update

Definition at line 262 of file SGObject.cpp.

bool precompute_subkernels ( )

precompute all sub-kernels

Definition at line 738 of file CombinedKernel.cpp.

void print_modsel_params ( )
inherited

prints all parameter registered for model selection and their type

Definition at line 474 of file SGObject.cpp.

void print_serializable ( const char *  prefix = "")
virtualinherited

prints registered parameters out

Parameters
prefixprefix for members

Definition at line 308 of file SGObject.cpp.

void register_params ( )
protectedvirtualinherited

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, CSubsequenceStringKernel, CGaussianMatchStringKernel, CGaussianShortRealKernel, CTensorProductPairKernel, CDistanceKernel, and CHistogramIntersectionKernel.

Definition at line 951 of file Kernel.cpp.

void remove_lhs ( )
virtual

remove lhs from kernel

Reimplemented from CKernel.

Definition at line 172 of file CombinedKernel.cpp.

void remove_lhs_and_rhs ( )
virtual

remove lhs and rhs from kernel

Reimplemented from CKernel.

Definition at line 206 of file CombinedKernel.cpp.

void remove_rhs ( )
virtual

remove rhs from kernel

Reimplemented from CKernel.

Definition at line 189 of file CombinedKernel.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.

SGVector< float64_t > row_col_wise_sum_block ( index_t  block_begin_row,
index_t  block_begin_col,
index_t  block_size_row,
index_t  block_size_col,
bool  no_diag = false 
)
virtualinherited

Computes row-wise/col-wise sum of kernel values. This method is useful while computing statistical estimation of mean/variance over kernel values but the kernel matrix is too huge to be fit inside memory.

Parameters
block_begin_rowthe row index at which the block starts
block_begin_colthe col index at which the block starts
block_size_rowthe number of rows in the block
block_size_colthe number of cols in the block

For Example, block_begin_row 0, block_begin_col 4 and block_size_row 5, block_size_col 6 represents the block that starts at index (0,4) in the kernel matrix and goes upto (0+5-1,4+6-1) i.e. (4,9) both inclusive

Parameters
no_diagif true (default is false), the diagonal elements are excluded from the row/col-wise sum, provided that block_size_row and block_size_col are same (i.e. the block is square). Otherwise, these are always added
Returns
a vector whose first block_size_row entries contain row-wise sum of kernel values computed as

\[ v[i]=\sum_{j}k(i+\text{block-begin-row}, j+\text{block-begin-col}) \]

and rest block_size_col entries col-wise sum of kernel values computed as

\[ v[\text{block-size-row}+j]=\sum_{i}k(i+\text{block-begin-row}, j+\text{block-begin-col}) \]

where \(i\in[0,\text{block-size-row}-1]\) and \(j\in[0,\text{block-size-col}-1]\)

Definition at line 1238 of file Kernel.cpp.

SGMatrix< float64_t > row_wise_sum_squared_sum_symmetric_block ( index_t  block_begin,
index_t  block_size,
bool  no_diag = true 
)
virtualinherited

Computes row-wise/col-wise sum and squared sum of kernel values from a symmetric part of the kernel matrix that always is supposed to contain the main upper diagonal. This method is useful while computing statistical estimation of mean/variance over kernel values but the kernel matrix is too huge to be fit inside memory.

Parameters
block_beginthe row and col index at which the block starts
block_sizethe number of rows and cols in the block

For Example, block_begin 4 and block_size 5 represents the block that starts at index (4,4) in the kernel matrix and goes upto (4+5-1,4+5-1) i.e. (8,8) both inclusive

Parameters
no_diagif true (default), the diagonal elements are excluded from the row/col-wise sum
Returns
a matrix whose first column contains the row-wise sum of kernel values computed as

\[ v_0[i]=\sum_{j}k(i+\text{block-begin}, j+\text{block-begin}) \]

and second column contains the row-wise sum of squared kernel values

\[ v_1[i]=\sum_{j}^k^2(i+\text{block-begin}, j+\text{block-begin}) \]

where \(i,j\in[0,\text{block-size}-1]\)

Definition at line 1179 of file Kernel.cpp.

SGVector< float64_t > row_wise_sum_symmetric_block ( index_t  block_begin,
index_t  block_size,
bool  no_diag = true 
)
virtualinherited

Computes row-wise/col-wise sum from a symmetric part of the kernel matrix that always is supposed to contain the main upper diagonal. This method is useful while computing statistical estimation of mean/variance over kernel values but the kernel matrix is too huge to be fit inside memory.

Parameters
block_beginthe row and col index at which the block starts
block_sizethe number of rows and cols in the block

For Example, block_begin 4 and block_size 5 represents the block that starts at index (4,4) in the kernel matrix and goes upto (4+5-1,4+5-1) i.e. (8,8) both inclusive

Parameters
no_diagif true (default), the diagonal elements are excluded from the row/col-wise sum
Returns
vector containing row-wise sum computed as

\[ v[i]=\sum_{j}k(i+\text{block-begin}, j+\text{block-begin}) \]

where \(i,j\in[0,\text{block-size}-1]\)

Definition at line 1125 of file Kernel.cpp.

void save ( CFile writer)
inherited

save kernel matrix

Parameters
writerFile object via which to save data

Definition at line 652 of file Kernel.cpp.

bool save_serializable ( CSerializableFile file,
const char *  prefix = "" 
)
virtualinherited

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
Returns
TRUE if done, otherwise FALSE

Definition at line 314 of file SGObject.cpp.

void save_serializable_post ( )
throw (ShogunException
)
protectedvirtualinherited

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 943 of file Kernel.cpp.

void save_serializable_pre ( )
throw (ShogunException
)
protectedvirtualinherited

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 935 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 586 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 808 of file Kernel.h.

void set_generic ( )
inherited

Definition at line 41 of file SGObject.cpp.

void set_generic ( )
inherited

Definition at line 46 of file SGObject.cpp.

void set_generic ( )
inherited

Definition at line 51 of file SGObject.cpp.

void set_generic ( )
inherited

Definition at line 56 of file SGObject.cpp.

void set_generic ( )
inherited

Definition at line 61 of file SGObject.cpp.

void set_generic ( )
inherited

Definition at line 66 of file SGObject.cpp.

void set_generic ( )
inherited

Definition at line 71 of file SGObject.cpp.

void set_generic ( )
inherited

Definition at line 76 of file SGObject.cpp.

void set_generic ( )
inherited

Definition at line 81 of file SGObject.cpp.

void set_generic ( )
inherited

Definition at line 86 of file SGObject.cpp.

void set_generic ( )
inherited

Definition at line 91 of file SGObject.cpp.

void set_generic ( )
inherited

Definition at line 96 of file SGObject.cpp.

void set_generic ( )
inherited

Definition at line 101 of file SGObject.cpp.

void set_generic ( )
inherited

Definition at line 106 of file SGObject.cpp.

void set_generic ( )
inherited

Definition at line 111 of file SGObject.cpp.

void set_generic ( )
inherited

set generic type to T

void set_global_io ( SGIO io)
inherited

set the io object

Parameters
ioio object to use

Definition at line 228 of file SGObject.cpp.

void set_global_parallel ( Parallel parallel)
inherited

set the parallel object

Parameters
parallelparallel object to use

Definition at line 241 of file SGObject.cpp.

void set_global_version ( Version version)
inherited

set the version object

Parameters
versionversion object to use

Definition at line 283 of file SGObject.cpp.

void set_is_initialized ( bool  p_init)
protectedinherited

set is initialized

Parameters
p_initif optimization shall be set to initialized

Definition at line 899 of file Kernel.h.

bool set_normalizer ( CKernelNormalizer normalizer)
virtualinherited

set the current kernel normalizer

Returns
if successful

Reimplemented in CWeightedDegreeStringKernel.

Definition at line 150 of file Kernel.cpp.

void set_optimization_type ( EOptimizationType  t)
virtual

set optimization type

Parameters
toptimization type

Reimplemented from CKernel.

Definition at line 725 of file CombinedKernel.cpp.

void set_property ( EKernelProperty  p)
protectedinherited

set property

Parameters
pkernel property to set

Definition at line 881 of file Kernel.h.

void set_subkernel_weights ( SGVector< float64_t weights)
virtual

set subkernel weights

Parameters
weightsnew subkernel weights

Reimplemented from CKernel.

Definition at line 694 of file CombinedKernel.cpp.

void set_time ( int32_t  t)
inherited

set the lru time

Parameters
tthe time to use

Definition at line 664 of file Kernel.h.

CSGObject * shallow_copy ( ) const
virtualinherited

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

Reimplemented in CGaussianKernel.

Definition at line 192 of file SGObject.cpp.

float64_t sum_block ( index_t  block_begin_row,
index_t  block_begin_col,
index_t  block_size_row,
index_t  block_size_col,
bool  no_diag = false 
)
virtualinherited

Computes sum of kernel values from a specified block. This method is useful while computing statistical estimation of mean/variance over kernel values but the kernel matrix is too huge to be fit inside memory.

Parameters
block_begin_rowthe row index at which the block starts
block_begin_colthe col index at which the block starts
block_size_rowthe number of rows in the block
block_size_colthe number of cols in the block

For example, block_begin_row 0, block_begin_col 4 and block_size_row 5, block_size_col 6 represents the block that starts at index (0,4) in the kernel matrix and goes upto (0+5-1,4+6-1) i.e. (4,9) both inclusive

Parameters
no_diagif true (default is false), the diagonal elements are excluded from the sum, provided that block_size_row and block_size_col are same (i.e. the block is square). Otherwise, these are always added
Returns
sum of kernel values within the block computed as

\[ \sum_{i}\sum_{j}k(i+\text{block-begin-row}, j+\text{block-begin-col}) \]

where \(i\in[0,\text{block-size-row}-1]\) and \(j\in[0,\text{block-size-col}-1]\)

Definition at line 1079 of file Kernel.cpp.

float64_t sum_symmetric_block ( index_t  block_begin,
index_t  block_size,
bool  no_diag = true 
)
virtualinherited

Computes sum from a symmetric part of the kernel matrix that always is supposed to contain the main upper diagonal. This method is useful while computing statistical estimation of mean/variance over kernel values but the kernel matrix is too huge to be fit inside memory.

Parameters
block_beginthe row and col index at which the block starts
block_sizethe number of rows and cols in the block

For example, block_begin 4 and block_size 5 represents the block that starts at index (4,4) in the kernel matrix and goes upto (4+5-1,4+5-1) i.e. (8,8) both inclusive

Parameters
no_diagif true (default), the diagonal elements are excluded from the sum
Returns
sum of kernel values within the block computed as

\[ \sum_{i}\sum_{j}k(i+\text{block-begin}, j+\text{block-begin}) \]

where \(i,j\in[0,\text{block-size}-1]\)

Definition at line 1026 of file Kernel.cpp.

void unset_generic ( )
inherited

unset generic type

this has to be called in classes specializing a template class

Definition at line 303 of file SGObject.cpp.

void unset_property ( EKernelProperty  p)
protectedinherited

unset property

Parameters
pkernel property to unset

Definition at line 890 of file Kernel.h.

void update_parameter_hash ( )
virtualinherited

Updates the hash of current parameter combination

Definition at line 248 of file SGObject.cpp.

Member Data Documentation

bool append_subkernel_weights
protected

if subkernel weights are appended

Definition at line 469 of file CombinedKernel.h.

int32_t cache_size
protectedinherited

cache_size in MB

Definition at line 1047 of file Kernel.h.

float64_t combined_kernel_weight
protectedinherited

combined kernel weight

Definition at line 1072 of file Kernel.h.

bool initialized
protected

whether kernel is ready to be used

Definition at line 471 of file CombinedKernel.h.

SGIO* io
inherited

io

Definition at line 369 of file SGObject.h.

CDynamicObjectArray* kernel_array
protected

list of kernels

Definition at line 459 of file CombinedKernel.h.

KERNEL_CACHE kernel_cache
protectedinherited

kernel cache

Definition at line 1051 of file Kernel.h.

KERNELCACHE_ELEM* kernel_matrix
protectedinherited

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

Definition at line 1056 of file Kernel.h.

CFeatures* lhs
protectedinherited

feature vectors to occur on left hand side

Definition at line 1059 of file Kernel.h.

bool lhs_equals_rhs
protectedinherited

lhs

Definition at line 1064 of file Kernel.h.

Parameter* m_gradient_parameters
inherited

parameters wrt which we can compute gradients

Definition at line 384 of file SGObject.h.

uint32_t m_hash
inherited

Hash of parameter values

Definition at line 387 of file SGObject.h.

Parameter* m_model_selection_parameters
inherited

model selection parameters

Definition at line 381 of file SGObject.h.

Parameter* m_parameters
inherited

parameters

Definition at line 378 of file SGObject.h.

CKernelNormalizer* normalizer
protectedinherited

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

Definition at line 1086 of file Kernel.h.

int32_t num_lhs
protectedinherited

number of feature vectors on left hand side

Definition at line 1067 of file Kernel.h.

int32_t num_rhs
protectedinherited

number of feature vectors on right hand side

Definition at line 1069 of file Kernel.h.

EOptimizationType opt_type
protectedinherited

optimization type (currently FASTBUTMEMHUNGRY and SLOWBUTMEMEFFICIENT)

Definition at line 1079 of file Kernel.h.

bool optimization_initialized
protectedinherited

if optimization is initialized

Definition at line 1075 of file Kernel.h.

Parallel* parallel
inherited

parallel

Definition at line 372 of file SGObject.h.

uint64_t properties
protectedinherited

kernel properties

Definition at line 1082 of file Kernel.h.

CFeatures* rhs
protectedinherited

feature vectors to occur on right hand side

Definition at line 1061 of file Kernel.h.

float64_t* subkernel_weights_buffer
protected

subkernel weights buffers

Definition at line 467 of file CombinedKernel.h.

int32_t sv_count
protected

support vector count

Definition at line 461 of file CombinedKernel.h.

int32_t* sv_idx
protected

support vector index

Definition at line 463 of file CombinedKernel.h.

float64_t* sv_weight
protected

support vector weights

Definition at line 465 of file CombinedKernel.h.

Version* version
inherited

version

Definition at line 375 of file SGObject.h.


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

SHOGUN Machine Learning Toolbox - Documentation