Detailed Description

MultiquadricKernel.

\[ K(x,x') = \sqrt{\| x - x' \|^2 +c^2} \]

Definition at line 30 of file MultiquadricKernel.h.

Inheritance diagram for CMultiquadricKernel:

Public Member Functions
	CMultiquadricKernel ()

	CMultiquadricKernel (int32_t cache, float64_t coef, CDistance *dist)

	CMultiquadricKernel (CFeatures l, CFeatures r, float64_t coef, CDistance *dist)

virtual bool	init (CFeatures l, CFeatures r)

virtual EKernelType	get_kernel_type ()

virtual EFeatureType	get_feature_type ()

virtual EFeatureClass	get_feature_class ()

virtual const char *	get_name () const

float64_t	get_coef ()

void	set_coef (float64_t value)

virtual	~CMultiquadricKernel ()

float64_t	kernel (int32_t idx_a, int32_t idx_b)

SGMatrix< float64_t >	get_kernel_matrix ()

template<class T >
SGMatrix< T >	get_kernel_matrix ()

SGVector< float64_t >	get_kernel_diagonal (SGVector< float64_t > preallocated=SGVector< float64_t >())

virtual SGVector< float64_t >	get_kernel_col (int32_t j)

virtual SGVector< float64_t >	get_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_t >	row_wise_sum_symmetric_block (index_t block_begin, index_t block_size, bool no_diag=true)

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

virtual 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)

virtual bool	set_normalizer (CKernelNormalizer *normalizer)

virtual CKernelNormalizer *	get_normalizer ()

virtual bool	init_normalizer ()

virtual void	cleanup ()

void	load (CFile *loader)

void	save (CFile *writer)

CFeatures *	get_lhs ()

CFeatures *	get_rhs ()

virtual int32_t	get_num_vec_lhs ()

virtual int32_t	get_num_vec_rhs ()

virtual bool	has_features ()

bool	get_lhs_equals_rhs ()

virtual void	remove_lhs_and_rhs ()

virtual void	remove_lhs ()

virtual void	remove_rhs ()
	takes all necessary steps if the rhs is removed from kernel More...

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)

virtual void	clear_normal ()

virtual void	add_to_normal (int32_t vector_idx, float64_t weight)

EOptimizationType	get_optimization_type ()

virtual void	set_optimization_type (EOptimizationType t)

bool	get_is_initialized ()

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

virtual bool	delete_optimization ()

bool	init_optimization_svm (CSVM *svm)

virtual float64_t	compute_optimized (int32_t vector_idx)

virtual void	compute_batch (int32_t num_vec, int32_t vec_idx, float64_t target, int32_t num_suppvec, int32_t IDX, float64_t alphas, float64_t factor=1.0)

float64_t	get_combined_kernel_weight ()

void	set_combined_kernel_weight (float64_t nw)

virtual int32_t	get_num_subkernels ()

virtual void	compute_by_subkernel (int32_t vector_idx, float64_t *subkernel_contrib)

virtual const float64_t *	get_subkernel_weights (int32_t &num_weights)

virtual SGVector< float64_t >	get_subkernel_weights ()

virtual void	set_subkernel_weights (SGVector< float64_t > weights)

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

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

virtual CSGObject *	shallow_copy () const

virtual CSGObject *	deep_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)

SGIO *	get_global_io ()

void	set_global_parallel (Parallel *parallel)

Parallel *	get_global_parallel ()

void	set_global_version (Version *version)

Version *	get_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)

bool	has (const std::string &name) const

template<typename T >
bool	has (const Tag< T > &tag) const

template<typename T , typename U = void>
bool	has (const std::string &name) const

template<typename T >
void	set (const Tag< T > &_tag, const T &value)

template<typename T , typename U = void>
void	set (const std::string &name, const T &value)

template<typename T >
T	get (const Tag< T > &_tag) const

template<typename T , typename U = void>
T	get (const std::string &name) const

virtual void	update_parameter_hash ()

virtual bool	parameter_hash_changed ()

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

virtual CSGObject *	clone ()

Static Public Member Functions
static CKernel *	obtain_from_generic (CSGObject *kernel)

Public Attributes
SGIO *	io

Parallel *	parallel

Version *	version

Parameter *	m_parameters

Parameter *	m_model_selection_parameters

Parameter *	m_gradient_parameters

uint32_t	m_hash

Protected Member Functions
virtual float64_t	compute (int32_t idx_a, int32_t idx_b)

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)

template<typename T >
void	register_param (Tag< T > &_tag, const T &value)

template<typename T >
void	register_param (const std::string &name, const T &value)

bool	clone_parameters (CSGObject *other)

Static Protected Member Functions
template<class T >
static void *	get_kernel_matrix_helper (void *p)

Protected Attributes
CDistance *	m_distance
	distance to be used More...

float64_t	m_coef
	theta parameter of kernel - coefficient More...

int32_t	cache_size
	cache_size in MB More...

KERNEL_CACHE	kernel_cache
	kernel cache More...

KERNELCACHE_ELEM *	kernel_matrix

CFeatures *	lhs
	feature vectors to occur on left hand side More...

CFeatures *	rhs
	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

CKernelNormalizer *	normalizer

Constructor & Destructor Documentation

CMultiquadricKernel ( )

default constructor

Definition at line 16 of file MultiquadricKernel.cpp.

CMultiquadricKernel	(	int32_t	cache,
		float64_t	coef,
		CDistance *	dist
	)

constructor

Parameters

cache	size of cache
coef	kernel parameter coef
dist	distance to be used

Definition at line 21 of file MultiquadricKernel.cpp.

CMultiquadricKernel	(	CFeatures *	l,
		CFeatures *	r,
		float64_t	coef,
		CDistance *	dist
	)

constructor

Parameters

l	features left-side
r	features right-side
coef	kernel parameter coef
dist	distance to be used

Definition at line 29 of file MultiquadricKernel.cpp.

~CMultiquadricKernel ( )

virtual

Definition at line 38 of file MultiquadricKernel.cpp.

Member Function Documentation

void add_to_normal	(	int32_t	vector_idx,
		float64_t	weight
	)

virtualinherited

add vector*factor to 'virtual' normal vector

Parameters

vector_idx	index
weight	weight

Reimplemented in CCombinedKernel, CWeightedDegreeStringKernel, CWeightedDegreePositionStringKernel, CCommUlongStringKernel, CCommWordStringKernel, CLinearKernel, CLinearStringKernel, and CWeightedCommWordStringKernel.

Definition at line 829 of file Kernel.cpp.

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

dict	dictionary of parameters to be built.

Definition at line 630 of file SGObject.cpp.

void cache_kernel_row ( int32_t x )

inherited

cache kernel row

Parameters

x x

Definition at line 300 of file Kernel.cpp.

void cache_multiple_kernel_rows	(	int32_t *	key,
		int32_t	varnum
	)

inherited

cache multiple kernel rows

Parameters

key	key
varnum

Definition at line 374 of file Kernel.cpp.

void cache_reset ( )

inherited

cache reset

Definition at line 603 of file kernel/Kernel.h.

void cleanup ( )

virtualinherited

clean up your kernel

base method only removes lhs and rhs overload to add further cleanup but make sure CKernel::cleanup() is called

Reimplemented in CWeightedDegreePositionStringKernel, CCustomKernel, CWeightedDegreeStringKernel, COligoStringKernel, CSubsequenceStringKernel, CPyramidChi2, CShiftInvariantKernel, CCommWordStringKernel, CSpectrumMismatchRBFKernel, CGaussianKernel, CWeightedCommWordStringKernel, CSalzbergWordStringKernel, CCommUlongStringKernel, CBesselKernel, CSNPStringKernel, CPolyKernel, CPolyMatchStringKernel, CPolyMatchWordStringKernel, CCombinedKernel, CSimpleLocalityImprovedStringKernel, CWaveletKernel, CExponentialKernel, CGaussianMatchStringKernel, CSpectrumRBFKernel, CFixedDegreeStringKernel, CSigmoidKernel, CSplineKernel, CHistogramWordStringKernel, CProductKernel, CLocalAlignmentStringKernel, CSparseSpatialSampleStringKernel, CLinearKernel, and CLinearStringKernel.

Definition at line 171 of file Kernel.cpp.

void clear_normal ( )

virtualinherited

for optimizable kernels, i.e. kernels where the weight vector can be computed explicitly (if it fits into memory)

Reimplemented in CCombinedKernel, CWeightedDegreeStringKernel, CWeightedDegreePositionStringKernel, CCommUlongStringKernel, CCommWordStringKernel, CLinearKernel, and CLinearStringKernel.

Definition at line 834 of file Kernel.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

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

Definition at line 729 of file SGObject.cpp.

bool clone_parameters ( CSGObject * other )

protectedinherited

Definition at line 754 of file SGObject.cpp.

float64_t compute	(	int32_t	idx_a,
		int32_t	idx_b
	)

protectedvirtual

compute kernel for specific feature vectors corresponding to [idx_a] of left-side and [idx_b] of right-side

Parameters

idx_a	left-side index
idx_b	right-side index

Returns: kernel value

Implements CKernel.

Definition at line 52 of file MultiquadricKernel.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`
	)

virtualinherited

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 in CCombinedKernel, CWeightedDegreeStringKernel, and CWeightedDegreePositionStringKernel.

Definition at line 822 of file Kernel.cpp.

void compute_by_subkernel	(	int32_t	vector_idx,
		float64_t *	subkernel_contrib
	)

virtualinherited

compute by subkernel

Parameters

vector_idx	index
subkernel_contrib	subkernel contribution

Reimplemented in CCombinedKernel, CWeightedDegreeStringKernel, and CWeightedDegreePositionStringKernel.

Definition at line 844 of file Kernel.cpp.

float64_t compute_optimized ( int32_t vector_idx )

virtualinherited

compute optimized

Parameters

vector_idx index to compute

Returns: optimized value at given index

Reimplemented in CCombinedKernel, CWeightedDegreeStringKernel, CWeightedDegreePositionStringKernel, CCommWordStringKernel, CCommUlongStringKernel, CLinearKernel, CLinearStringKernel, and CWeightedCommWordStringKernel.

Definition at line 816 of file Kernel.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

offs	offset
n	number of columns
symmetric	whether matrix is symmetric

Definition at line 920 of file kernel/Kernel.h.

CSGObject * deep_copy ( ) const

virtualinherited

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

Definition at line 231 of file SGObject.cpp.

bool delete_optimization ( )

virtualinherited

delete optimization

Returns: if deleting was successful

Reimplemented in CCombinedKernel, CWeightedDegreeStringKernel, CWeightedDegreePositionStringKernel, CCommWordStringKernel, CCommUlongStringKernel, CLinearKernel, and CLinearStringKernel.

Definition at line 810 of file Kernel.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

other	object to compare with
accuracy	accuracy to use for comparison (optional)
tolerant	allows linient check on float equality (within accuracy)

Returns: true if all parameters were equal, false if not

Definition at line 651 of file SGObject.cpp.

T get ( const Tag< T > & _tag ) const

inherited

Getter for a class parameter, identified by a Tag. Throws an exception if the class does not have such a parameter.

Parameters

_tag	name and type information of parameter

Returns: value of the parameter identified by the input tag

Definition at line 376 of file SGObject.h.

T get ( const std::string & name ) const

inherited

Getter for a class parameter, identified by a name. Throws an exception if the class does not have such a parameter.

Parameters

name	name of the parameter

Returns: value of the parameter corresponding to the input name and type

Definition at line 399 of file SGObject.h.

int32_t get_activenum_cache ( )

inherited

get activenum cache

Returns: activecnum cache

Definition at line 615 of file kernel/Kernel.h.

int32_t get_cache_size ( )

inherited

return the size of the kernel cache

Returns: size of kernel cache

Definition at line 599 of file kernel/Kernel.h.

float64_t get_coef ( )

getter for coef parameter

Returns: kernel parameter coefficient

Definition at line 81 of file MultiquadricKernel.h.

float64_t get_combined_kernel_weight ( )

inherited

get combined kernel weight

Returns: combined kernel weight

Definition at line 803 of file kernel/Kernel.h.

virtual EFeatureClass get_feature_class ( )

virtual

Returns: class of features

Implements CKernel.

Definition at line 71 of file MultiquadricKernel.h.

virtual EFeatureType get_feature_type ( )

virtual

Returns: type of features

Implements CKernel.

Definition at line 66 of file MultiquadricKernel.h.

SGIO * get_global_io ( )

inherited

get the io object

Returns: io object

Definition at line 268 of file SGObject.cpp.

Parallel * get_global_parallel ( )

inherited

get the parallel object

Returns: parallel object

Definition at line 310 of file SGObject.cpp.

Version * get_global_version ( )

inherited

get the version object

Returns: version object

Definition at line 323 of file SGObject.cpp.

bool get_is_initialized ( )

inherited

check if optimization is initialized

Returns: if optimization is initialized

Definition at line 754 of file kernel/Kernel.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 263 of file kernel/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

preallocated vector with space for results

Definition at line 231 of file kernel/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 220 of file kernel/Kernel.h.

SGMatrix< T > get_kernel_matrix ( )

inherited

get kernel matrix (templated)

Returns: the kernel matrix

Definition at line 1316 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

p	thread parameters

Definition at line 1265 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 280 of file kernel/Kernel.h.

void get_kernel_row	(	int32_t	docnum,
		int32_t *	active2dnum,
		float64_t *	buffer,
		bool	full_line = `false`
	)

inherited

get kernel row

Parameters

docnum	docnum
active2dnum	active2dnum
buffer	buffer
full_line	full line

Definition at line 236 of file Kernel.cpp.

virtual EKernelType get_kernel_type ( )

virtual

Returns: kernel type

Implements CKernel.

Definition at line 61 of file MultiquadricKernel.h.

CFeatures* get_lhs ( )

inherited

get left-hand side of features used in kernel

Returns: features of left-hand side

Definition at line 505 of file kernel/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 544 of file kernel/Kernel.h.

int32_t get_max_elems_cache ( )

inherited

get maximum elements in cache

Returns: maximum elements in cache

Definition at line 609 of file kernel/Kernel.h.

SGStringList< char > get_modelsel_names ( )

inherited

Returns: vector of names of all parameters which are registered for model selection

Definition at line 531 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_name name of the parameter

Returns: description of the parameter

Definition at line 555 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_name name of model selection parameter

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

Definition at line 568 of file SGObject.cpp.

virtual const char* get_name ( ) const

virtual

Returns: name of kernel

Implements CSGObject.

Definition at line 76 of file MultiquadricKernel.h.

CKernelNormalizer * get_normalizer ( )

virtualinherited

obtain the current kernel normalizer

Returns: the kernel normalizer

Definition at line 160 of file Kernel.cpp.

int32_t get_num_subkernels ( )

virtualinherited

get number of subkernels

Returns: number of subkernels

Reimplemented in CWeightedDegreeStringKernel, CWeightedDegreePositionStringKernel, CCombinedKernel, and CProductKernel.

Definition at line 839 of file Kernel.cpp.

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 517 of file kernel/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 526 of file kernel/Kernel.h.

EOptimizationType get_optimization_type ( )

inherited

get optimization type

Returns: optimization type

Definition at line 742 of file kernel/Kernel.h.

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

virtualinherited

return derivative with respect to specified parameter

Parameters

param	the parameter
index	the index of the element if parameter is a vector

Returns: gradient with respect to parameter

Reimplemented in CCombinedKernel, CExponentialARDKernel, CProductKernel, CGaussianARDKernel, CGaussianKernel, CPeriodicKernel, and CGaussianARDSparseKernel.

Definition at line 851 of file kernel/Kernel.h.

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

param	the parameter
index	the index of the element if parameter is a vector

Returns: diagonal part of gradient with respect to parameter

Reimplemented in CGaussianARDKernel, and CGaussianARDSparseKernel.

Definition at line 865 of file kernel/Kernel.h.

CFeatures* get_rhs ( )

inherited

get right-hand side of features used in kernel

Returns: features of right-hand side

Definition at line 511 of file kernel/Kernel.h.

const float64_t * get_subkernel_weights ( int32_t & num_weights )

virtualinherited

get subkernel weights

Parameters

num_weights number of weights will be stored here

Returns: subkernel weights

Reimplemented in CCombinedKernel, CWeightedDegreeStringKernel, and CWeightedDegreePositionStringKernel.

Definition at line 850 of file Kernel.cpp.

SGVector< float64_t > get_subkernel_weights ( )

virtualinherited

get subkernel weights (swig compatible)

Returns: subkernel weights

Reimplemented in CCombinedKernel.

Definition at line 856 of file Kernel.cpp.

bool has ( const std::string & name ) const

inherited

Checks if object has a class parameter identified by a name.

Parameters

name	name of the parameter

Returns: true if the parameter exists with the input name

Definition at line 299 of file SGObject.h.

bool has ( const Tag< T > & tag ) const

inherited

Checks if object has a class parameter identified by a Tag.

Parameters

tag	tag of the parameter containing name and type information

Returns: true if the parameter exists with the input tag

Definition at line 310 of file SGObject.h.

bool has ( const std::string & name ) const

inherited

Checks if a type exists for a class parameter identified by a name.

Parameters

name	name of the parameter

Returns: true if the parameter exists with the input name and type

Definition at line 321 of file SGObject.h.

virtual bool has_features ( )

virtualinherited

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 535 of file kernel/Kernel.h.

bool has_property ( EKernelProperty p )

inherited

check if kernel has given property

Parameters

p	kernel property

Returns: if kernel has given property

Definition at line 724 of file kernel/Kernel.h.

bool init	(	CFeatures *	l,
		CFeatures *	r
	)

virtual

initialize kernel with features

Parameters

l	features left-side
r	features right-side

Returns: true if successful

Reimplemented from CKernel.

Definition at line 44 of file MultiquadricKernel.cpp.

bool init_normalizer ( )

virtualinherited

initialize the current kernel normalizer

Returns: if init was successful

Definition at line 166 of file Kernel.cpp.

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

virtualinherited

initialize optimization

Parameters

count	count
IDX	index
weights	weights

Returns: if initializing was successful

Reimplemented in CCombinedKernel, CWeightedDegreeStringKernel, CWeightedDegreePositionStringKernel, CCommWordStringKernel, CCommUlongStringKernel, CLinearKernel, and CLinearStringKernel.

Definition at line 803 of file Kernel.cpp.

bool init_optimization_svm ( CSVM * svm )

inherited

initialize optimization

Parameters

svm svm model

Returns: if initializing was successful

Definition at line 886 of file Kernel.cpp.

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

generic set to the type of the generic if returning TRUE

Returns: TRUE if a class template.

Definition at line 329 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_a	index of feature vector a
idx_b	index of feature vector b

Returns: computed kernel function

Definition at line 207 of file kernel/Kernel.h.

int32_t kernel_cache_check ( int32_t cacheidx )

inherited

check if row at given index is cached

Parameters

cacheidx index in cache

Returns: if row at given index is cached

Definition at line 690 of file kernel/Kernel.h.

void kernel_cache_cleanup ( )

inherited

cleanup kernel cache

Definition at line 542 of file Kernel.cpp.

void kernel_cache_init	(	int32_t	size,
		bool	regression_hack = `false`
	)

inherited

initialize kernel cache

Parameters

size	size to initialize to
regression_hack	if hack for regression shall be applied

Definition at line 179 of file Kernel.cpp.

void kernel_cache_reset_lru ( )

inherited

kernel cache reset lru

Definition at line 529 of file Kernel.cpp.

void kernel_cache_shrink	(	int32_t	totdoc,
		int32_t	num_shrink,
		int32_t *	after
	)

inherited

kernel cache shrink

Parameters

totdoc	totdoc
num_shrink	number of shrink
after	after

Definition at line 470 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 699 of file kernel/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

cacheidx index in cache

Returns: if updating was successful

Definition at line 675 of file kernel/Kernel.h.

void list_kernel ( )

inherited

list kernel

Definition at line 683 of file Kernel.cpp.

void load ( CFile * loader )

inherited

load the kernel matrix

Parameters

loader File object via which to load data

Definition at line 621 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

file	where to load from
prefix	prefix for members

Returns: TRUE if done, otherwise FALSE

Definition at line 402 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

ShogunException Will be thrown if an error occurres.

Reimplemented from CSGObject.

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

Definition at line 904 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

ShogunException will 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 454 of file SGObject.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

kernel Object to cast to CKernel, is *not* SG_REFed

Returns: object casted to CKernel, NULL if not possible

Definition at line 872 of file Kernel.cpp.

bool parameter_hash_changed ( )

virtualinherited

Returns: whether parameter combination has changed since last update

Definition at line 295 of file SGObject.cpp.

void print_modsel_params ( )

inherited

prints all parameter registered for model selection and their type

Definition at line 507 of file SGObject.cpp.

void print_serializable ( const char * prefix = "" )

virtualinherited

prints registered parameters out

Parameters

prefix prefix for members

Definition at line 341 of file SGObject.cpp.

void register_param	(	Tag< T > &	_tag,
		const T &	value
	)

protectedinherited

Registers a class parameter which is identified by a tag. This enables the parameter to be modified by set() and retrieved by get(). Parameters can be registered in the constructor of the class.

Parameters

_tag	name and type information of parameter
value	value of the parameter

Definition at line 450 of file SGObject.h.

void register_param	(	const std::string &	name,
		const T &	value
	)

protectedinherited

Registers a class parameter which is identified by a name. This enables the parameter to be modified by set() and retrieved by get(). Parameters can be registered in the constructor of the class.

Parameters

name	name of the parameter
value	value of the parameter along with type information

Definition at line 463 of file SGObject.h.

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 927 of file Kernel.cpp.

void remove_lhs ( )

virtualinherited

remove lhs from kernel

Reimplemented in CWeightedDegreeStringKernel, CWeightedDegreePositionStringKernel, CCombinedKernel, CCommUlongStringKernel, and CProductKernel.

Definition at line 654 of file Kernel.cpp.

void remove_lhs_and_rhs ( )

virtualinherited

remove lhs and rhs from kernel

Reimplemented in CCombinedKernel, and CProductKernel.

Definition at line 635 of file Kernel.cpp.

void remove_rhs ( )

virtualinherited

takes all necessary steps if the rhs is removed from kernel

remove rhs from kernel

Reimplemented in CCombinedKernel, CCommUlongStringKernel, and CProductKernel.

Definition at line 668 of file Kernel.cpp.

void resize_kernel_cache	(	KERNELCACHE_IDX	size,
		bool	regression_hack = `false`
	)

inherited

resize kernel cache

Parameters

size	new size
regression_hack	hack for regression

Definition at line 83 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_row	the row index at which the block starts
block_begin_col	the col index at which the block starts
block_size_row	the number of rows in the block
block_size_col	the 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_diag if 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 \(j\in[0,\text{block-size-col}-1]\)

Reimplemented in CCustomKernel.

Definition at line 1211 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_begin	the row and col index at which the block starts
block_size	the 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_diag if 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 \(i,j\in[0,\text{block-size}-1]\)

Reimplemented in CCustomKernel.

Definition at line 1152 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_begin	the row and col index at which the block starts
block_size	the 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_diag if 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 \(i,j\in[0,\text{block-size}-1]\)

Reimplemented in CCustomKernel.

Definition at line 1098 of file Kernel.cpp.

void save ( CFile * writer )

inherited

save kernel matrix

Parameters

writer File object via which to save data

Definition at line 627 of file Kernel.cpp.

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

virtualinherited

Save this object to file.

Parameters

file	where to save the object; will be closed during returning if PREFIX is an empty string.
prefix	prefix for members

Returns: TRUE if done, otherwise FALSE

Definition at line 347 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

ShogunException Will be thrown if an error occurres.

Reimplemented from CSGObject.

Definition at line 919 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

ShogunException Will be thrown if an error occurres.

Reimplemented from CSGObject.

Definition at line 911 of file Kernel.cpp.

void set	(	const Tag< T > &	_tag,
		const T &	value
	)

inherited

Setter for a class parameter, identified by a Tag. Throws an exception if the class does not have such a parameter.

Parameters

_tag	name and type information of parameter
value	value of the parameter

Definition at line 337 of file SGObject.h.

void set	(	const std::string &	name,
		const T &	value
	)

inherited

Setter for a class parameter, identified by a name. Throws an exception if the class does not have such a parameter.

Parameters

name	name of the parameter
value	value of the parameter along with type information

Definition at line 363 of file SGObject.h.

void set_cache_size ( int32_t size )

inherited

set the size of the kernel cache

Parameters

size	of kernel cache

Definition at line 587 of file kernel/Kernel.h.

void set_coef ( float64_t value )

setter for coef parameter

Parameters

value kernel parameter coefficient

Definition at line 86 of file MultiquadricKernel.h.

void set_combined_kernel_weight ( float64_t nw )

inherited

set combined kernel weight

Parameters

nw	new combined kernel weight

Definition at line 809 of file kernel/Kernel.h.

void set_generic ( )

inherited

Definition at line 74 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 79 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 84 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 89 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 94 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 99 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 104 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 109 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 114 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 119 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 124 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 129 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 134 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 139 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 144 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

io	io object to use

Definition at line 261 of file SGObject.cpp.

void set_global_parallel ( Parallel * parallel )

inherited

set the parallel object

Parameters

parallel parallel object to use

Definition at line 274 of file SGObject.cpp.

void set_global_version ( Version * version )

inherited

set the version object

Parameters

version version object to use

Definition at line 316 of file SGObject.cpp.

void set_is_initialized ( bool p_init )

protectedinherited

set is initialized

Parameters

p_init if optimization shall be set to initialized

Definition at line 900 of file kernel/Kernel.h.

bool set_normalizer ( CKernelNormalizer * normalizer )

virtualinherited

set the current kernel normalizer

Returns: if successful

Reimplemented in CWeightedDegreeStringKernel.

Definition at line 148 of file Kernel.cpp.

virtual void set_optimization_type ( EOptimizationType t )

virtualinherited

set optimization type

Parameters

t	optimization type to set

Reimplemented in CCombinedKernel.

Definition at line 748 of file kernel/Kernel.h.

void set_property ( EKernelProperty p )

protectedinherited

set property

Parameters

p	kernel property to set

Definition at line 882 of file kernel/Kernel.h.

void set_subkernel_weights ( SGVector< float64_t > weights )

virtualinherited

set subkernel weights

Parameters

weights new subkernel weights

Reimplemented in CCombinedKernel, CWeightedDegreeStringKernel, and CWeightedDegreePositionStringKernel.

Definition at line 863 of file Kernel.cpp.

void set_time ( int32_t t )

inherited

set the lru time

Parameters

t	the time to use

Definition at line 665 of file kernel/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 225 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_row	the row index at which the block starts
block_begin_col	the col index at which the block starts
block_size_row	the number of rows in the block
block_size_col	the 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_diag if 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 \(j\in[0,\text{block-size-col}-1]\)

Reimplemented in CCustomKernel.

Definition at line 1053 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_begin	the row and col index at which the block starts
block_size	the 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_diag if 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 \(i,j\in[0,\text{block-size}-1]\)

Reimplemented in CCustomKernel.

Definition at line 1002 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 336 of file SGObject.cpp.

void unset_property ( EKernelProperty p )

protectedinherited

unset property

Parameters

p	kernel property to unset

Definition at line 891 of file kernel/Kernel.h.

void update_parameter_hash ( )

virtualinherited

Updates the hash of current parameter combination

Definition at line 281 of file SGObject.cpp.

Member Data Documentation

int32_t cache_size

protectedinherited

cache_size in MB

Definition at line 1048 of file kernel/Kernel.h.

float64_t combined_kernel_weight

protectedinherited

combined kernel weight

Definition at line 1073 of file kernel/Kernel.h.

SGIO* io

inherited

io

Definition at line 558 of file SGObject.h.

KERNEL_CACHE kernel_cache

protectedinherited

kernel cache

Definition at line 1052 of file kernel/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 1057 of file kernel/Kernel.h.

CFeatures* lhs

protectedinherited

feature vectors to occur on left hand side

Definition at line 1060 of file kernel/Kernel.h.

bool lhs_equals_rhs

protectedinherited

lhs

Definition at line 1065 of file kernel/Kernel.h.

float64_t m_coef

protected

theta parameter of kernel - coefficient

Definition at line 109 of file MultiquadricKernel.h.

CDistance* m_distance

protected

distance to be used

Definition at line 106 of file MultiquadricKernel.h.

Parameter* m_gradient_parameters

inherited

parameters wrt which we can compute gradients

Definition at line 573 of file SGObject.h.

uint32_t m_hash

inherited

Hash of parameter values

Definition at line 576 of file SGObject.h.

Parameter* m_model_selection_parameters

inherited

model selection parameters

Definition at line 570 of file SGObject.h.

Parameter* m_parameters

inherited

parameters

Definition at line 567 of file SGObject.h.

CKernelNormalizer* normalizer

protectedinherited

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

Definition at line 1087 of file kernel/Kernel.h.

int32_t num_lhs

protectedinherited

number of feature vectors on left hand side

Definition at line 1068 of file kernel/Kernel.h.

int32_t num_rhs

protectedinherited

number of feature vectors on right hand side

Definition at line 1070 of file kernel/Kernel.h.

EOptimizationType opt_type

protectedinherited

optimization type (currently FASTBUTMEMHUNGRY and SLOWBUTMEMEFFICIENT)

Definition at line 1080 of file kernel/Kernel.h.

bool optimization_initialized

protectedinherited

if optimization is initialized

Definition at line 1076 of file kernel/Kernel.h.

Parallel* parallel

inherited

parallel

Definition at line 561 of file SGObject.h.

uint64_t properties

protectedinherited

kernel properties

Definition at line 1083 of file kernel/Kernel.h.

CFeatures* rhs

protectedinherited

feature vectors to occur on right hand side

Definition at line 1062 of file kernel/Kernel.h.

Version* version

inherited

version

Definition at line 564 of file SGObject.h.

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

Detailed Description

Public Member Functions

Static Public Member Functions

Public Attributes

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation