SHOGUN
4.1.0
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The Weighted Degree String kernel.
The WD kernel of order d compares two sequences \({\bf x}\) and \({\bf x'}\) of length L by summing all contributions of k-mer matches of lengths \(k\in\{1,\dots,d\}\), weighted by coefficients \(\beta_k\). It is defined as
\[ k({\bf x},{\bf x'})=\sum_{k=1}^d\beta_k\sum_{l=1}^{L-k+1}I({\bf u}_{k,l}({\bf x})={\bf u}_{k,l}({\bf x'})). \]
Here, \({\bf u}_{k,l}({\bf x})\) is the string of length k starting at position l of the sequence \({\bf x}\) and \(I(\cdot)\) is the indicator function which evaluates to 1 when its argument is true and to 0 otherwise.
Definition at line 55 of file WeightedDegreeStringKernel.h.
Static Public Member Functions | |
static void * | compute_batch_helper (void *p) |
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 |
ParameterMap * | m_parameter_map |
uint32_t | m_hash |
Protected Member Functions | |
void | create_empty_tries () |
void | add_example_to_tree (int32_t idx, float64_t weight) |
void | add_example_to_single_tree (int32_t idx, float64_t weight, int32_t tree_num) |
void | add_example_to_tree_mismatch (int32_t idx, float64_t weight) |
void | add_example_to_single_tree_mismatch (int32_t idx, float64_t weight, int32_t tree_num) |
float64_t | compute_by_tree (int32_t idx) |
float64_t | compute (int32_t idx_a, int32_t idx_b) |
float64_t | compute_with_mismatch (char *avec, int32_t alen, char *bvec, int32_t blen) |
float64_t | compute_without_mismatch (char *avec, int32_t alen, char *bvec, int32_t blen) |
float64_t | compute_without_mismatch_matrix (char *avec, int32_t alen, char *bvec, int32_t blen) |
float64_t | compute_using_block (char *avec, int32_t alen, char *bvec, int32_t blen) |
virtual void | remove_lhs () |
void | set_property (EKernelProperty p) |
void | unset_property (EKernelProperty p) |
void | set_is_initialized (bool p_init) |
int32_t | compute_row_start (int64_t offs, int32_t n, bool symmetric) |
virtual void | load_serializable_post () throw (ShogunException) |
virtual void | save_serializable_pre () throw (ShogunException) |
virtual void | save_serializable_post () throw (ShogunException) |
virtual void | register_params () |
virtual TParameter * | migrate (DynArray< TParameter * > *param_base, const SGParamInfo *target) |
virtual void | one_to_one_migration_prepare (DynArray< TParameter * > *param_base, const SGParamInfo *target, TParameter *&replacement, TParameter *&to_migrate, char *old_name=NULL) |
virtual void | load_serializable_pre () throw (ShogunException) |
Static Protected Member Functions | |
template<class T > | |
static void * | get_kernel_matrix_helper (void *p) |
Protected Attributes | |
float64_t * | weights |
int32_t | weights_degree |
int32_t | weights_length |
float64_t * | position_weights |
int32_t | position_weights_len |
float64_t * | weights_buffer |
int32_t | mkl_stepsize |
int32_t | degree |
int32_t | length |
int32_t | max_mismatch |
int32_t | seq_length |
bool | initialized |
bool | block_computation |
float64_t * | block_weights |
EWDKernType | type |
int32_t | which_degree |
CTrie< DNATrie > * | tries |
bool | tree_initialized |
CAlphabet * | alphabet |
int32_t | cache_size |
cache_size in MB 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 |
default constructor
Definition at line 48 of file WeightedDegreeStringKernel.cpp.
CWeightedDegreeStringKernel | ( | int32_t | degree, |
EWDKernType | type = E_WD |
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) |
constructor
degree | degree |
type | weighted degree kernel type |
Definition at line 55 of file WeightedDegreeStringKernel.cpp.
CWeightedDegreeStringKernel | ( | SGVector< float64_t > | weights | ) |
constructor
weights | kernel's weights |
Definition at line 68 of file WeightedDegreeStringKernel.cpp.
CWeightedDegreeStringKernel | ( | CStringFeatures< char > * | l, |
CStringFeatures< char > * | r, | ||
int32_t | degree | ||
) |
constructor
l | features of left-hand side |
r | features of right-hand side |
degree | degree |
Definition at line 84 of file WeightedDegreeStringKernel.cpp.
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virtual |
Definition at line 96 of file WeightedDegreeStringKernel.cpp.
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protected |
add example to single tree
idx | index |
weight | weight |
tree_num | which tree |
Definition at line 435 of file WeightedDegreeStringKernel.cpp.
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add example to single tree mismatch
idx | index |
weight | weight |
tree_num | which tree |
Definition at line 486 of file WeightedDegreeStringKernel.cpp.
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protected |
add example to tree
idx | index |
weight | weight |
Definition at line 389 of file WeightedDegreeStringKernel.cpp.
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protected |
add example to tree mismatch
idx | index |
weight | weight |
Definition at line 460 of file WeightedDegreeStringKernel.cpp.
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add to normal
idx | where to add |
weight | what to add |
Reimplemented from CKernel.
Definition at line 214 of file WeightedDegreeStringKernel.h.
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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.
dict | dictionary of parameters to be built. |
Definition at line 1244 of file SGObject.cpp.
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clean up kernel
Reimplemented from CKernel.
Definition at line 182 of file WeightedDegreeStringKernel.cpp.
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clear normal subkernel functionality
Reimplemented from CKernel.
Definition at line 196 of file WeightedDegreeStringKernel.h.
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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.
Definition at line 1361 of file SGObject.cpp.
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protectedvirtual |
compute kernel function for features a and b idx_{a,b} denote the index of the feature vectors in the corresponding feature object
idx_a | index a |
idx_b | index b |
Implements CKernel.
Definition at line 363 of file WeightedDegreeStringKernel.cpp.
float64_t * compute_abs_weights | ( | int32_t & | len | ) |
compute abs weights
len | len |
Definition at line 565 of file WeightedDegreeStringKernel.cpp.
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virtual |
compute batch
num_vec | number of vectors |
vec_idx | vector index |
target | target |
num_suppvec | number of support vectors |
IDX | IDX |
alphas | alphas |
factor | factor |
Reimplemented from CKernel.
Definition at line 862 of file WeightedDegreeStringKernel.cpp.
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static |
helper for compute batch
p | thread parameter |
Definition at line 826 of file WeightedDegreeStringKernel.cpp.
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compute by subkernel
idx | index |
subkernel_contrib | subkernel contribution |
Reimplemented from CKernel.
Definition at line 248 of file WeightedDegreeStringKernel.h.
void compute_by_tree | ( | int32_t | idx, |
float64_t * | LevelContrib | ||
) |
compute by tree
idx | index |
LevelContrib | level contribution |
Definition at line 538 of file WeightedDegreeStringKernel.cpp.
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protected |
compute by tree
idx | index |
Definition at line 514 of file WeightedDegreeStringKernel.cpp.
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virtual |
compute optimized
idx | index to compute |
Reimplemented from CKernel.
Definition at line 163 of file WeightedDegreeStringKernel.h.
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protectedinherited |
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protected |
compute using block
avec | vector a |
alen | length of vector a |
bvec | vector b |
blen | length of vector b |
Definition at line 290 of file WeightedDegreeStringKernel.cpp.
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protected |
compute with mismatch
avec | vector a |
alen | length of vector a |
bvec | vector b |
blen | length of vector b |
Definition at line 262 of file WeightedDegreeStringKernel.cpp.
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protected |
compute without mismatch
avec | vector a |
alen | length of vector a |
bvec | vector b |
blen | length of vector b |
Definition at line 316 of file WeightedDegreeStringKernel.cpp.
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protected |
compute without mismatch matrix
avec | vector a |
alen | length of vector a |
bvec | vector b |
blen | length of vector b |
Definition at line 339 of file WeightedDegreeStringKernel.cpp.
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protected |
create emtpy tries
Definition at line 127 of file WeightedDegreeStringKernel.cpp.
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virtualinherited |
A deep copy. All the instance variables will also be copied.
Definition at line 200 of file SGObject.cpp.
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delete optimization
Reimplemented from CKernel.
Definition at line 248 of file WeightedDegreeStringKernel.cpp.
bool delete_position_weights | ( | ) |
delete position weights
Definition at line 521 of file WeightedDegreeStringKernel.h.
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.
other | object to compare with |
accuracy | accuracy to use for comparison (optional) |
tolerant | allows linient check on float equality (within accuracy) |
Definition at line 1265 of file SGObject.cpp.
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inherited |
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inherited |
int32_t get_degree | ( | ) | const |
float64_t* get_degree_weights | ( | int32_t & | d, |
int32_t & | len | ||
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get degree weights
d | degree weights will be stored here |
len | number of degree weights will be stored here |
Definition at line 390 of file WeightedDegreeStringKernel.h.
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virtualinherited |
return feature class the kernel can deal with
Implements CKernel.
Definition at line 71 of file StringKernel.h.
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virtualinherited |
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inherited |
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inherited |
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inherited |
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inherited |
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staticprotectedinherited |
helper for computing the kernel matrix in a parallel way
p | thread parameters |
Definition at line 803 of file Kernel.cpp.
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return what type of kernel we are
Implements CStringKernel< char >.
Definition at line 116 of file WeightedDegreeStringKernel.h.
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inherited |
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inherited |
int32_t get_max_mismatch | ( | ) | const |
get maximum mismatch
Definition at line 539 of file WeightedDegreeStringKernel.h.
int32_t get_mkl_stepsize | ( | ) |
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inherited |
Definition at line 1136 of file SGObject.cpp.
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inherited |
Returns description of a given parameter string, if it exists. SG_ERROR otherwise
param_name | name of the parameter |
Definition at line 1160 of file SGObject.cpp.
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inherited |
Returns index of model selection parameter with provided index
param_name | name of model selection parameter |
Definition at line 1173 of file SGObject.cpp.
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return the kernel's name
Reimplemented from CStringKernel< char >.
Definition at line 122 of file WeightedDegreeStringKernel.h.
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virtualinherited |
obtain the current kernel normalizer
Definition at line 147 of file Kernel.cpp.
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get number of subkernels
Reimplemented from CKernel.
Definition at line 232 of file WeightedDegreeStringKernel.h.
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virtualinherited |
get number of vectors of lhs features
Reimplemented in CCustomKernel.
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virtualinherited |
get number of vectors of rhs features
Reimplemented in CCustomKernel.
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inherited |
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return derivative with respect to specified parameter
param | the parameter |
index | the index of the element if parameter is a vector |
Reimplemented in CCombinedKernel, CProductKernel, CGaussianKernel, and CPeriodicKernel.
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virtualinherited |
float64_t* get_position_weights | ( | int32_t & | len | ) |
get position weights
len | number of position weights will be stored here |
Definition at line 425 of file WeightedDegreeStringKernel.h.
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virtual |
get subkernel weights
num_weights | number of weights will be stored here |
Reimplemented from CKernel.
Definition at line 270 of file WeightedDegreeStringKernel.h.
get subkernel weights (swig compatible)
Reimplemented in CCombinedKernel.
Definition at line 393 of file Kernel.cpp.
EWDKernType get_type | ( | ) | const |
get WD kernel weighting type
Definition at line 107 of file WeightedDegreeStringKernel.h.
bool get_use_block_computation | ( | ) |
check if block computation is performed
Definition at line 569 of file WeightedDegreeStringKernel.h.
float64_t* get_weights | ( | int32_t & | num_weights | ) |
get weights
num_weights | number of weights will be stored here |
Definition at line 402 of file WeightedDegreeStringKernel.h.
int32_t get_which_degree | ( | ) |
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virtualinherited |
test whether features have been assigned to lhs and rhs
Reimplemented in CCustomKernel, CCombinedKernel, and CProductKernel.
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initialize kernel
l | features of left-hand side |
r | features of right-hand side |
Reimplemented from CStringKernel< char >.
Definition at line 140 of file WeightedDegreeStringKernel.cpp.
bool init_block_weights | ( | ) |
initialize block weights
Definition at line 801 of file WeightedDegreeStringKernel.cpp.
bool init_block_weights_const | ( | ) |
initialize block weights constant
Definition at line 725 of file WeightedDegreeStringKernel.cpp.
bool init_block_weights_cubicpoly | ( | ) |
initialize block weights cubic polynomial
Definition at line 760 of file WeightedDegreeStringKernel.cpp.
bool init_block_weights_exp | ( | ) |
initialize block weights exponential
Definition at line 773 of file WeightedDegreeStringKernel.cpp.
bool init_block_weights_from_wd | ( | ) |
initialize block weights from weighted degree
Definition at line 684 of file WeightedDegreeStringKernel.cpp.
bool init_block_weights_from_wd_external | ( | ) |
initialize block weights from external weighted degree
Definition at line 701 of file WeightedDegreeStringKernel.cpp.
bool init_block_weights_linear | ( | ) |
initialize block weights linear
Definition at line 735 of file WeightedDegreeStringKernel.cpp.
bool init_block_weights_log | ( | ) |
initialize block weights logarithmic
Definition at line 787 of file WeightedDegreeStringKernel.cpp.
bool init_block_weights_sqpoly | ( | ) |
initialize block weights squared polynomial
Definition at line 746 of file WeightedDegreeStringKernel.cpp.
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initialize the current kernel normalizer
Definition at line 153 of file Kernel.cpp.
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initialize optimization
count | count |
IDX | index |
alphas | alphas |
Reimplemented from CKernel.
Definition at line 133 of file WeightedDegreeStringKernel.h.
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initialize optimization do initialization for tree_num up to upto_tree, use tree_num=-1 to construct all trees
count | count |
IDX | IDX |
alphas | alphas |
tree_num | which tree |
Definition at line 206 of file WeightedDegreeStringKernel.cpp.
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initialize optimization
svm | svm model |
Definition at line 423 of file Kernel.cpp.
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virtualinherited |
If the SGSerializable is a class template then TRUE will be returned and GENERIC is set to the type of the generic.
generic | set to the type of the generic if returning TRUE |
Definition at line 298 of file SGObject.cpp.
bool is_tree_initialized | ( | ) |
check if tree is initialized
Definition at line 383 of file WeightedDegreeStringKernel.h.
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inherited |
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list kernel
Definition at line 221 of file Kernel.cpp.
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load the kernel matrix
loader | File object via which to load data |
Definition at line 165 of file Kernel.cpp.
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inherited |
maps all parameters of this instance to the provided file version and loads all parameter data from the file into an array, which is sorted (basically calls load_file_parameter(...) for all parameters and puts all results into a sorted array)
file_version | parameter version of the file |
current_version | version from which mapping begins (you want to use Version::get_version_parameter() for this in most cases) |
file | file to load from |
prefix | prefix for members |
Definition at line 705 of file SGObject.cpp.
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loads some specified parameters from a file with a specified version The provided parameter info has a version which is recursively mapped until the file parameter version is reached. Note that there may be possibly multiple parameters in the mapping, therefore, a set of TParameter instances is returned
param_info | information of parameter |
file_version | parameter version of the file, must be <= provided parameter version |
file | file to load from |
prefix | prefix for members |
Definition at line 546 of file SGObject.cpp.
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virtualinherited |
Load this object from file. If it will fail (returning FALSE) then this object will contain inconsistent data and should not be used!
file | where to load from |
prefix | prefix for members |
param_version | (optional) a parameter version different to (this is mainly for testing, better do not use) |
Definition at line 375 of file SGObject.cpp.
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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.
ShogunException | Will be thrown if an error occurres. |
Reimplemented from CSGObject.
Reimplemented in CWeightedDegreePositionStringKernel, CGaussianKernel, CInverseMultiQuadricKernel, CCircularKernel, and CExponentialKernel.
Definition at line 441 of file Kernel.cpp.
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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.
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 1058 of file SGObject.cpp.
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inherited |
Takes a set of TParameter instances (base) with a certain version and a set of target parameter infos and recursively maps the base level wise to the current version using CSGObject::migrate(...). The base is replaced. After this call, the base version containing parameters should be of same version/type as the initial target parameter infos. Note for this to work, the migrate methods and all the internal parameter mappings have to match
param_base | set of TParameter instances that are mapped to the provided target parameter infos |
base_version | version of the parameter base |
target_param_infos | set of SGParamInfo instances that specify the target parameter base |
Definition at line 743 of file SGObject.cpp.
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protectedvirtualinherited |
creates a new TParameter instance, which contains migrated data from the version that is provided. The provided parameter data base is used for migration, this base is a collection of all parameter data of the previous version. Migration is done FROM the data in param_base TO the provided param info Migration is always one version step. Method has to be implemented in subclasses, if no match is found, base method has to be called.
If there is an element in the param_base which equals the target, a copy of the element is returned. This represents the case when nothing has changed and therefore, the migrate method is not overloaded in a subclass
param_base | set of TParameter instances to use for migration |
target | parameter info for the resulting TParameter |
Definition at line 950 of file SGObject.cpp.
Obtains a kernel from a generic SGObject with error checking. Note that if passing NULL, result will be NULL
kernel | Object to cast to CKernel, is not SG_REFed |
Definition at line 409 of file Kernel.cpp.
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protectedvirtualinherited |
This method prepares everything for a one-to-one parameter migration. One to one here means that only ONE element of the parameter base is needed for the migration (the one with the same name as the target). Data is allocated for the target (in the type as provided in the target SGParamInfo), and a corresponding new TParameter instance is written to replacement. The to_migrate pointer points to the single needed TParameter instance needed for migration. If a name change happened, the old name may be specified by old_name. In addition, the m_delete_data flag of to_migrate is set to true. So if you want to migrate data, the only thing to do after this call is converting the data in the m_parameter fields. If unsure how to use - have a look into an example for this. (base_migration_type_conversion.cpp for example)
param_base | set of TParameter instances to use for migration |
target | parameter info for the resulting TParameter |
replacement | (used as output) here the TParameter instance which is returned by migration is created into |
to_migrate | the only source that is used for migration |
old_name | with this parameter, a name change may be specified |
Definition at line 890 of file SGObject.cpp.
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virtualinherited |
Definition at line 264 of file SGObject.cpp.
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prints all parameter registered for model selection and their type
Definition at line 1112 of file SGObject.cpp.
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virtualinherited |
prints registered parameters out
prefix | prefix for members |
Definition at line 310 of file SGObject.cpp.
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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 464 of file Kernel.cpp.
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remove lhs from kernel
Reimplemented from CKernel.
Definition at line 116 of file WeightedDegreeStringKernel.cpp.
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virtualinherited |
remove lhs and rhs from kernel
Reimplemented in CCombinedKernel, and CProductKernel.
Definition at line 179 of file Kernel.cpp.
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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 208 of file Kernel.cpp.
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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.
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
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 |
\[ v[i]=\sum_{j}k(i+\text{block-begin-row}, j+\text{block-begin-col}) \]
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 749 of file Kernel.cpp.
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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.
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
no_diag | if true (default), the diagonal elements are excluded from the row/col-wise sum |
\[ v_0[i]=\sum_{j}k(i+\text{block-begin}, j+\text{block-begin}) \]
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 690 of file Kernel.cpp.
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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.
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
no_diag | if true (default), the diagonal elements are excluded from the row/col-wise sum |
\[ v[i]=\sum_{j}k(i+\text{block-begin}, j+\text{block-begin}) \]
where \(i,j\in[0,\text{block-size}-1]\)Definition at line 636 of file Kernel.cpp.
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save kernel matrix
writer | File object via which to save data |
Definition at line 171 of file Kernel.cpp.
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virtualinherited |
Save this object to file.
file | where to save the object; will be closed during returning if PREFIX is an empty string. |
prefix | prefix for members |
param_version | (optional) a parameter version different to (this is mainly for testing, better do not use) |
Definition at line 316 of file SGObject.cpp.
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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.
ShogunException | Will be thrown if an error occurres. |
Reimplemented from CSGObject.
Definition at line 456 of file Kernel.cpp.
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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.
ShogunException | Will be thrown if an error occurres. |
Reimplemented from CSGObject.
Definition at line 448 of file Kernel.cpp.
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inherited |
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bool set_degree | ( | int32_t | deg | ) |
set degree
deg | new degree |
Definition at line 546 of file WeightedDegreeStringKernel.h.
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Definition at line 42 of file SGObject.cpp.
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Definition at line 47 of file SGObject.cpp.
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Definition at line 52 of file SGObject.cpp.
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Definition at line 57 of file SGObject.cpp.
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Definition at line 62 of file SGObject.cpp.
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Definition at line 67 of file SGObject.cpp.
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Definition at line 72 of file SGObject.cpp.
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Definition at line 77 of file SGObject.cpp.
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Definition at line 82 of file SGObject.cpp.
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Definition at line 87 of file SGObject.cpp.
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Definition at line 92 of file SGObject.cpp.
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Definition at line 97 of file SGObject.cpp.
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Definition at line 102 of file SGObject.cpp.
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Definition at line 107 of file SGObject.cpp.
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Definition at line 112 of file SGObject.cpp.
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set generic type to T
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set the parallel object
parallel | parallel object to use |
Definition at line 243 of file SGObject.cpp.
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set the version object
version | version object to use |
Definition at line 285 of file SGObject.cpp.
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bool set_max_mismatch | ( | int32_t | max | ) |
set maximum mismatch
max | new maximum mismatch |
Definition at line 966 of file WeightedDegreeStringKernel.cpp.
bool set_mkl_stepsize | ( | int32_t | step | ) |
set MKL steps ize
step | new step size |
Definition at line 576 of file WeightedDegreeStringKernel.h.
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set the current kernel normalizer
Reimplemented from CKernel.
Definition at line 346 of file WeightedDegreeStringKernel.h.
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bool set_position_weights | ( | float64_t * | pws, |
int32_t | len | ||
) |
set position weights
pws | new position weights |
len | number of position weights |
Definition at line 654 of file WeightedDegreeStringKernel.cpp.
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set subkernel weights
w | weights |
Reimplemented from CKernel.
Definition at line 295 of file WeightedDegreeStringKernel.h.
bool set_use_block_computation | ( | bool | block | ) |
set if block computation shall be performed
block | if block computation shall be performed |
Definition at line 559 of file WeightedDegreeStringKernel.h.
set wd weights
new_weights | new weights |
Definition at line 442 of file WeightedDegreeStringKernel.h.
bool set_wd_weights_by_type | ( | EWDKernType | type | ) |
set wd weights
type | weighted degree kernel type |
if we know a better weighting later on do a switch
Definition at line 571 of file WeightedDegreeStringKernel.cpp.
set weights
new_weights | new weights |
Definition at line 624 of file WeightedDegreeStringKernel.cpp.
bool set_which_degree | ( | int32_t | which | ) |
set which degree
which | which degree |
Definition at line 595 of file WeightedDegreeStringKernel.h.
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A shallow copy. All the SGObject instance variables will be simply assigned and SG_REF-ed.
Reimplemented in CGaussianKernel.
Definition at line 194 of file SGObject.cpp.
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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.
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
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 |
\[ \sum_{i}\sum_{j}k(i+\text{block-begin-row}, j+\text{block-begin-col}) \]
where \(i\in[0,\text{block-size-row}-1]\) and \(j\in[0,\text{block-size-col}-1]\)Definition at line 590 of file Kernel.cpp.
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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.
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
no_diag | if true (default), the diagonal elements are excluded from the sum |
\[ \sum_{i}\sum_{j}k(i+\text{block-begin}, j+\text{block-begin}) \]
where \(i,j\in[0,\text{block-size}-1]\)Definition at line 537 of file Kernel.cpp.
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unset generic type
this has to be called in classes specializing a template class
Definition at line 305 of file SGObject.cpp.
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Updates the hash of current parameter combination
Definition at line 250 of file SGObject.cpp.
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alphabet of features
Definition at line 761 of file WeightedDegreeStringKernel.h.
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if block computation is used
Definition at line 745 of file WeightedDegreeStringKernel.h.
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(internal) block weights
Definition at line 748 of file WeightedDegreeStringKernel.h.
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degree
Definition at line 732 of file WeightedDegreeStringKernel.h.
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if kernel is initialized
Definition at line 742 of file WeightedDegreeStringKernel.h.
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io
Definition at line 496 of file SGObject.h.
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length
Definition at line 734 of file WeightedDegreeStringKernel.h.
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parameters wrt which we can compute gradients
Definition at line 511 of file SGObject.h.
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Hash of parameter values
Definition at line 517 of file SGObject.h.
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model selection parameters
Definition at line 508 of file SGObject.h.
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map for different parameter versions
Definition at line 514 of file SGObject.h.
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parameters
Definition at line 505 of file SGObject.h.
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maximum mismatch
Definition at line 737 of file WeightedDegreeStringKernel.h.
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MKL step size
Definition at line 730 of file WeightedDegreeStringKernel.h.
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parallel
Definition at line 499 of file SGObject.h.
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position weights
Definition at line 724 of file WeightedDegreeStringKernel.h.
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position weights
Definition at line 726 of file WeightedDegreeStringKernel.h.
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sequence length
Definition at line 739 of file WeightedDegreeStringKernel.h.
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if tree is initialized
Definition at line 758 of file WeightedDegreeStringKernel.h.
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tries
Definition at line 755 of file WeightedDegreeStringKernel.h.
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WeightedDegree kernel type
Definition at line 750 of file WeightedDegreeStringKernel.h.
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version
Definition at line 502 of file SGObject.h.
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degree*length weights length must match seq_length if != 0
Definition at line 716 of file WeightedDegreeStringKernel.h.
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weights buffer
Definition at line 728 of file WeightedDegreeStringKernel.h.
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degree
Definition at line 718 of file WeightedDegreeStringKernel.h.
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length
Definition at line 720 of file WeightedDegreeStringKernel.h.
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which degree
Definition at line 752 of file WeightedDegreeStringKernel.h.