SHOGUN
v3.2.0
|
The Weighted Degree String kernel.
The WD kernel of order d compares two sequences \({\bf x}\) and \({\bf x'}\) of length L by summing all contributions of k-mer matches of lengths \(k\in\{1,\dots,d\}\), weighted by coefficients \(\beta_k\). It is defined as
\[ k({\bf x},{\bf x'})=\sum_{k=1}^d\beta_k\sum_{l=1}^{L-k+1}I({\bf u}_{k,l}({\bf x})={\bf u}_{k,l}({\bf x'})). \]
Here, \({\bf u}_{k,l}({\bf x})\) is the string of length k starting at position l of the sequence \({\bf x}\) and \(I(\cdot)\) is the indicator function which evaluates to 1 when its argument is true and to 0 otherwise.
Definition at line 53 of file WeightedDegreeStringKernel.h.
default constructor
Definition at line 48 of file WeightedDegreeStringKernel.cpp.
CWeightedDegreeStringKernel | ( | int32_t | degree, |
EWDKernType | type = E_WD |
||
) |
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.
~CWeightedDegreeStringKernel | ( | ) | [virtual] |
Definition at line 96 of file WeightedDegreeStringKernel.cpp.
void add_example_to_single_tree | ( | int32_t | idx, |
float64_t | weight, | ||
int32_t | tree_num | ||
) | [protected] |
add example to single tree
idx | index |
weight | weight |
tree_num | which tree |
Definition at line 435 of file WeightedDegreeStringKernel.cpp.
void add_example_to_single_tree_mismatch | ( | int32_t | idx, |
float64_t | weight, | ||
int32_t | tree_num | ||
) | [protected] |
add example to single tree mismatch
idx | index |
weight | weight |
tree_num | which tree |
Definition at line 486 of file WeightedDegreeStringKernel.cpp.
void add_example_to_tree | ( | int32_t | idx, |
float64_t | weight | ||
) | [protected] |
add example to tree
idx | index |
weight | weight |
Definition at line 389 of file WeightedDegreeStringKernel.cpp.
void add_example_to_tree_mismatch | ( | int32_t | idx, |
float64_t | weight | ||
) | [protected] |
add example to tree mismatch
idx | index |
weight | weight |
Definition at line 460 of file WeightedDegreeStringKernel.cpp.
virtual void add_to_normal | ( | int32_t | idx, |
float64_t | weight | ||
) | [virtual] |
add to normal
idx | where to add |
weight | what to add |
Reimplemented from CKernel.
Definition at line 212 of file WeightedDegreeStringKernel.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.
dict | dictionary of parameters to be built. |
Definition at line 1156 of file SGObject.cpp.
void cache_kernel_row | ( | int32_t | x | ) | [inherited] |
void cache_multiple_kernel_rows | ( | int32_t * | key, |
int32_t | varnum | ||
) | [inherited] |
void cache_reset | ( | ) | [inherited] |
void cleanup | ( | ) | [virtual] |
clean up kernel
Reimplemented from CKernel.
Definition at line 182 of file WeightedDegreeStringKernel.cpp.
virtual void clear_normal | ( | ) | [virtual] |
clear normal subkernel functionality
Reimplemented from CKernel.
Definition at line 194 of file WeightedDegreeStringKernel.h.
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 1273 of file SGObject.cpp.
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.
void compute_batch | ( | int32_t | num_vec, |
int32_t * | vec_idx, | ||
float64_t * | target, | ||
int32_t | num_suppvec, | ||
int32_t * | IDX, | ||
float64_t * | alphas, | ||
float64_t | factor = 1.0 |
||
) | [virtual] |
compute batch
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.
void * compute_batch_helper | ( | void * | p | ) | [static] |
helper for compute batch
p | thread parameter |
Definition at line 826 of file WeightedDegreeStringKernel.cpp.
void compute_by_subkernel | ( | int32_t | idx, |
float64_t * | subkernel_contrib | ||
) | [virtual] |
compute by subkernel
idx | index |
subkernel_contrib | subkernel contribution |
Reimplemented from CKernel.
Definition at line 246 of file WeightedDegreeStringKernel.h.
void compute_by_tree | ( | int32_t | idx, |
float64_t * | LevelContrib | ||
) |
compute by tree
idx | index |
LevelContrib | level contribution |
Definition at line 538 of file WeightedDegreeStringKernel.cpp.
float64_t compute_by_tree | ( | int32_t | idx | ) | [protected] |
compute by tree
idx | index |
Definition at line 514 of file WeightedDegreeStringKernel.cpp.
virtual float64_t compute_optimized | ( | int32_t | idx | ) | [virtual] |
compute optimized
idx | index to compute |
Reimplemented from CKernel.
Definition at line 161 of file WeightedDegreeStringKernel.h.
int32_t compute_row_start | ( | int64_t | offs, |
int32_t | n, | ||
bool | symmetric | ||
) | [protected, inherited] |
float64_t compute_using_block | ( | char * | avec, |
int32_t | alen, | ||
char * | bvec, | ||
int32_t | blen | ||
) | [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.
float64_t compute_with_mismatch | ( | char * | avec, |
int32_t | alen, | ||
char * | bvec, | ||
int32_t | blen | ||
) | [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.
float64_t compute_without_mismatch | ( | char * | avec, |
int32_t | alen, | ||
char * | bvec, | ||
int32_t | blen | ||
) | [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.
float64_t compute_without_mismatch_matrix | ( | char * | avec, |
int32_t | alen, | ||
char * | bvec, | ||
int32_t | blen | ||
) | [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.
void create_empty_tries | ( | ) | [protected] |
create emtpy tries
Definition at line 127 of file WeightedDegreeStringKernel.cpp.
A deep copy. All the instance variables will also be copied.
Definition at line 126 of file SGObject.h.
bool delete_optimization | ( | ) | [virtual] |
delete optimization
Reimplemented from CKernel.
Definition at line 248 of file WeightedDegreeStringKernel.cpp.
bool delete_position_weights | ( | ) |
delete position weights
Definition at line 519 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) |
Definition at line 1177 of file SGObject.cpp.
int32_t get_activenum_cache | ( | ) | [inherited] |
int32_t get_cache_size | ( | ) | [inherited] |
float64_t get_combined_kernel_weight | ( | ) | [inherited] |
int32_t get_degree | ( | ) | const |
float64_t* get_degree_weights | ( | int32_t & | d, |
int32_t & | len | ||
) |
get degree weights
d | degree weights will be stored here |
len | number of degree weights will be stored here |
Definition at line 388 of file WeightedDegreeStringKernel.h.
virtual EFeatureClass get_feature_class | ( | ) | [virtual, inherited] |
return feature class the kernel can deal with
Implements CKernel.
Definition at line 69 of file StringKernel.h.
virtual EFeatureType get_feature_type | ( | ) | [virtual, inherited] |
SGIO * get_global_io | ( | ) | [inherited] |
Parallel * get_global_parallel | ( | ) | [inherited] |
Version * get_global_version | ( | ) | [inherited] |
bool get_is_initialized | ( | ) | [inherited] |
virtual SGVector<float64_t> get_kernel_col | ( | int32_t | j | ) | [virtual, inherited] |
template SGMatrix< float32_t > get_kernel_matrix< float32_t > | ( | ) | [inherited] |
SGMatrix<T> get_kernel_matrix | ( | ) | [inherited] |
get kernel matrix (templated)
template void * get_kernel_matrix_helper< float32_t > | ( | void * | p | ) | [static, protected, inherited] |
helper for computing the kernel matrix in a parallel way
p | thread parameters |
Definition at line 1011 of file Kernel.cpp.
virtual SGVector<float64_t> get_kernel_row | ( | int32_t | i | ) | [virtual, inherited] |
void get_kernel_row | ( | int32_t | docnum, |
int32_t * | active2dnum, | ||
float64_t * | buffer, | ||
bool | full_line = false |
||
) | [inherited] |
get kernel row
docnum | docnum |
active2dnum | active2dnum |
buffer | buffer |
full_line | full line |
Definition at line 227 of file Kernel.cpp.
virtual EKernelType get_kernel_type | ( | ) | [virtual] |
return what type of kernel we are
Implements CStringKernel< char >.
Definition at line 114 of file WeightedDegreeStringKernel.h.
bool get_lhs_equals_rhs | ( | ) | [inherited] |
int32_t get_max_elems_cache | ( | ) | [inherited] |
int32_t get_max_mismatch | ( | ) | const |
get maximum mismatch
Definition at line 537 of file WeightedDegreeStringKernel.h.
int32_t get_mkl_stepsize | ( | ) |
get MKL step size
Definition at line 586 of file WeightedDegreeStringKernel.h.
SGStringList< char > get_modelsel_names | ( | ) | [inherited] |
Definition at line 1060 of file SGObject.cpp.
char * get_modsel_param_descr | ( | const char * | param_name | ) | [inherited] |
Returns description of a given parameter string, if it exists. SG_ERROR otherwise
param_name | name of the parameter |
Definition at line 1084 of file SGObject.cpp.
index_t get_modsel_param_index | ( | const char * | param_name | ) | [inherited] |
Returns index of model selection parameter with provided index
param_name | name of model selection parameter |
Definition at line 1097 of file SGObject.cpp.
virtual const char* get_name | ( | ) | const [virtual] |
return the kernel's name
Reimplemented from CStringKernel< char >.
Definition at line 120 of file WeightedDegreeStringKernel.h.
CKernelNormalizer * get_normalizer | ( | ) | [virtual, inherited] |
obtain the current kernel normalizer
Definition at line 151 of file Kernel.cpp.
virtual int32_t get_num_subkernels | ( | ) | [virtual] |
get number of subkernels
Reimplemented from CKernel.
Definition at line 230 of file WeightedDegreeStringKernel.h.
virtual int32_t get_num_vec_lhs | ( | ) | [virtual, inherited] |
get number of vectors of lhs features
Reimplemented in CCustomKernel.
virtual int32_t get_num_vec_rhs | ( | ) | [virtual, inherited] |
get number of vectors of rhs features
Reimplemented in CCustomKernel.
EOptimizationType get_optimization_type | ( | ) | [inherited] |
virtual SGMatrix<float64_t> get_parameter_gradient | ( | const TParameter * | param, |
index_t | index = -1 |
||
) | [virtual, inherited] |
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, CLinearARDKernel, and CGaussianARDKernel.
float64_t* get_position_weights | ( | int32_t & | len | ) |
get position weights
len | number of position weights will be stored here |
Definition at line 423 of file WeightedDegreeStringKernel.h.
const float64_t* get_subkernel_weights | ( | int32_t & | num_weights | ) | [virtual] |
get subkernel weights
num_weights | number of weights will be stored here |
Reimplemented from CKernel.
Definition at line 268 of file WeightedDegreeStringKernel.h.
SGVector< float64_t > get_subkernel_weights | ( | ) | [virtual, inherited] |
get subkernel weights (swig compatible)
Reimplemented in CCombinedKernel.
Definition at line 865 of file Kernel.cpp.
EWDKernType get_type | ( | ) | const |
get WD kernel weighting type
Definition at line 105 of file WeightedDegreeStringKernel.h.
bool get_use_block_computation | ( | ) |
check if block computation is performed
Definition at line 567 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 400 of file WeightedDegreeStringKernel.h.
int32_t get_which_degree | ( | ) |
virtual bool has_features | ( | ) | [virtual, inherited] |
test whether features have been assigned to lhs and rhs
Reimplemented in CCustomKernel, CCombinedKernel, and CProductKernel.
bool has_property | ( | EKernelProperty | p | ) | [inherited] |
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.
bool init_normalizer | ( | ) | [virtual, inherited] |
initialize the current kernel normalizer
Definition at line 157 of file Kernel.cpp.
virtual bool init_optimization | ( | int32_t | count, |
int32_t * | IDX, | ||
float64_t * | alphas | ||
) | [virtual] |
initialize optimization
count | count |
IDX | index |
alphas | alphas |
Reimplemented from CKernel.
Definition at line 131 of file WeightedDegreeStringKernel.h.
bool init_optimization | ( | int32_t | count, |
int32_t * | IDX, | ||
float64_t * | alphas, | ||
int32_t | tree_num | ||
) | [virtual] |
initialize optimization do initialization for tree_num up to upto_tree, use tree_num=-1 to construct all trees
count | count |
IDX | IDX |
alphas | alphas |
tree_num | which tree |
Definition at line 206 of file WeightedDegreeStringKernel.cpp.
bool init_optimization_svm | ( | CSVM * | svm | ) | [inherited] |
initialize optimization
svm | svm model |
Definition at line 895 of file Kernel.cpp.
bool is_generic | ( | EPrimitiveType * | generic | ) | const [virtual, inherited] |
If the SGSerializable is a class template then TRUE will be returned and GENERIC is set to the type of the generic.
generic | set to the type of the generic if returning TRUE |
Definition at line 228 of file SGObject.cpp.
bool is_tree_initialized | ( | ) |
check if tree is initialized
Definition at line 381 of file WeightedDegreeStringKernel.h.
int32_t kernel_cache_check | ( | int32_t | cacheidx | ) | [inherited] |
void kernel_cache_cleanup | ( | ) | [inherited] |
cleanup kernel cache
Definition at line 556 of file Kernel.cpp.
void kernel_cache_init | ( | int32_t | size, |
bool | regression_hack = false |
||
) | [inherited] |
initialize kernel cache
size | size to initialize to |
regression_hack | if hack for regression shall be applied |
Definition at line 170 of file Kernel.cpp.
void kernel_cache_reset_lru | ( | ) | [inherited] |
kernel cache reset lru
Definition at line 543 of file Kernel.cpp.
void kernel_cache_shrink | ( | int32_t | totdoc, |
int32_t | num_shrink, | ||
int32_t * | after | ||
) | [inherited] |
kernel cache shrink
totdoc | totdoc |
num_shrink | number of shrink |
after | after |
Definition at line 484 of file Kernel.cpp.
int32_t kernel_cache_space_available | ( | ) | [inherited] |
int32_t kernel_cache_touch | ( | int32_t | cacheidx | ) | [inherited] |
void list_kernel | ( | ) | [inherited] |
list kernel
Definition at line 697 of file Kernel.cpp.
load the kernel matrix
loader | File object via which to load data |
Definition at line 635 of file Kernel.cpp.
DynArray< TParameter * > * load_all_file_parameters | ( | int32_t | file_version, |
int32_t | current_version, | ||
CSerializableFile * | file, | ||
const char * | prefix = "" |
||
) | [inherited] |
maps all parameters of this instance to the provided file version and loads all parameter data from the file into an array, which is sorted (basically calls load_file_parameter(...) for all parameters and puts all results into a sorted array)
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 633 of file SGObject.cpp.
DynArray< TParameter * > * load_file_parameters | ( | const SGParamInfo * | param_info, |
int32_t | file_version, | ||
CSerializableFile * | file, | ||
const char * | prefix = "" |
||
) | [inherited] |
loads some specified parameters from a file with a specified version The provided parameter info has a version which is recursively mapped until the file parameter version is reached. Note that there may be possibly multiple parameters in the mapping, therefore, a set of TParameter instances is returned
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 474 of file SGObject.cpp.
bool load_serializable | ( | CSerializableFile * | file, |
const char * | prefix = "" , |
||
int32_t | param_version = Version::get_version_parameter() |
||
) | [virtual, inherited] |
Load this object from file. If it will fail (returning FALSE) then this object will contain inconsistent data and should not be used!
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 305 of file SGObject.cpp.
void load_serializable_post | ( | ) | throw (ShogunException) [protected, virtual, inherited] |
Can (optionally) be overridden to post-initialize some member variables which are not PARAMETER::ADD'ed. Make sure that at first the overridden method BASE_CLASS::LOAD_SERIALIZABLE_POST is called.
ShogunException | Will be thrown if an error occurres. |
Reimplemented from CSGObject.
Reimplemented in CWeightedDegreePositionStringKernel, CGaussianKernel, CInverseMultiQuadricKernel, CCircularKernel, and CExponentialKernel.
Definition at line 913 of file Kernel.cpp.
void load_serializable_pre | ( | ) | throw (ShogunException) [protected, virtual, inherited] |
Can (optionally) be overridden to pre-initialize some member variables which are not PARAMETER::ADD'ed. Make sure that at first the overridden method BASE_CLASS::LOAD_SERIALIZABLE_PRE is called.
ShogunException | Will be thrown if an error occurres. |
Reimplemented in CDynamicArray< T >, CDynamicArray< float64_t >, CDynamicArray< float32_t >, CDynamicArray< int32_t >, CDynamicArray< char >, CDynamicArray< bool >, and CDynamicObjectArray.
Definition at line 984 of file SGObject.cpp.
void map_parameters | ( | DynArray< TParameter * > * | param_base, |
int32_t & | base_version, | ||
DynArray< const SGParamInfo * > * | target_param_infos | ||
) | [inherited] |
Takes a set of TParameter instances (base) with a certain version and a set of target parameter infos and recursively maps the base level wise to the current version using CSGObject::migrate(...). The base is replaced. After this call, the base version containing parameters should be of same version/type as the initial target parameter infos. Note for this to work, the migrate methods and all the internal parameter mappings have to match
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 671 of file SGObject.cpp.
TParameter * migrate | ( | DynArray< TParameter * > * | param_base, |
const SGParamInfo * | target | ||
) | [protected, virtual, inherited] |
creates a new TParameter instance, which contains migrated data from the version that is provided. The provided parameter data base is used for migration, this base is a collection of all parameter data of the previous version. Migration is done FROM the data in param_base TO the provided param info Migration is always one version step. Method has to be implemented in subclasses, if no match is found, base method has to be called.
If there is an element in the param_base which equals the target, a copy of the element is returned. This represents the case when nothing has changed and therefore, the migrate method is not overloaded in a subclass
param_base | set of TParameter instances to use for migration |
target | parameter info for the resulting TParameter |
Definition at line 878 of file SGObject.cpp.
CKernel * obtain_from_generic | ( | CSGObject * | kernel | ) | [static, inherited] |
Obtains a kernel from a generic SGObject with error checking. Note that if passing NULL, result will be NULL
kernel | Object to cast to CKernel, is *not* SG_REFed |
Definition at line 881 of file Kernel.cpp.
void one_to_one_migration_prepare | ( | DynArray< TParameter * > * | param_base, |
const SGParamInfo * | target, | ||
TParameter *& | replacement, | ||
TParameter *& | to_migrate, | ||
char * | old_name = NULL |
||
) | [protected, virtual, inherited] |
This method prepares everything for a one-to-one parameter migration. One to one here means that only ONE element of the parameter base is needed for the migration (the one with the same name as the target). Data is allocated for the target (in the type as provided in the target SGParamInfo), and a corresponding new TParameter instance is written to replacement. The to_migrate pointer points to the single needed TParameter instance needed for migration. If a name change happened, the old name may be specified by old_name. In addition, the m_delete_data flag of to_migrate is set to true. So if you want to migrate data, the only thing to do after this call is converting the data in the m_parameter fields. If unsure how to use - have a look into an example for this. (base_migration_type_conversion.cpp for example)
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 818 of file SGObject.cpp.
void print_modsel_params | ( | ) | [inherited] |
prints all parameter registered for model selection and their type
Definition at line 1036 of file SGObject.cpp.
void print_serializable | ( | const char * | prefix = "" | ) | [virtual, inherited] |
prints registered parameters out
prefix | prefix for members |
Definition at line 240 of file SGObject.cpp.
void register_params | ( | ) | [protected, virtual, inherited] |
Separate the function of parameter registration This can be the first stage of a *general* framework for cross-validation or other parameter-based operations
Reimplemented in CSpectrumMismatchRBFKernel, CSNPStringKernel, CANOVAKernel, CStringSubsequenceKernel, CGaussianMatchStringKernel, CGaussianShortRealKernel, CTensorProductPairKernel, CDistanceKernel, and CHistogramIntersectionKernel.
Definition at line 936 of file Kernel.cpp.
void remove_lhs | ( | ) | [protected, virtual] |
remove lhs from kernel
Reimplemented from CKernel.
Definition at line 116 of file WeightedDegreeStringKernel.cpp.
void remove_lhs_and_rhs | ( | ) | [virtual, inherited] |
remove lhs and rhs from kernel
Reimplemented in CCombinedKernel, and CProductKernel.
Definition at line 649 of file Kernel.cpp.
void remove_rhs | ( | ) | [virtual, inherited] |
takes all necessary steps if the rhs is removed from kernel
remove rhs from kernel
Reimplemented in CCombinedKernel, CCommUlongStringKernel, and CProductKernel.
Definition at line 682 of file Kernel.cpp.
void resize_kernel_cache | ( | KERNELCACHE_IDX | size, |
bool | regression_hack = false |
||
) | [inherited] |
resize kernel cache
size | new size |
regression_hack | hack for regression |
Definition at line 85 of file Kernel.cpp.
save kernel matrix
writer | File object via which to save data |
Definition at line 641 of file Kernel.cpp.
bool save_serializable | ( | CSerializableFile * | file, |
const char * | prefix = "" , |
||
int32_t | param_version = Version::get_version_parameter() |
||
) | [virtual, inherited] |
Save this object to file.
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 246 of file SGObject.cpp.
void save_serializable_post | ( | ) | throw (ShogunException) [protected, virtual, inherited] |
Can (optionally) be overridden to post-initialize some member variables which are not PARAMETER::ADD'ed. Make sure that at first the overridden method BASE_CLASS::SAVE_SERIALIZABLE_POST is called.
ShogunException | Will be thrown if an error occurres. |
Reimplemented from CSGObject.
Definition at line 928 of file Kernel.cpp.
void save_serializable_pre | ( | ) | throw (ShogunException) [protected, virtual, inherited] |
Can (optionally) be overridden to pre-initialize some member variables which are not PARAMETER::ADD'ed. Make sure that at first the overridden method BASE_CLASS::SAVE_SERIALIZABLE_PRE is called.
ShogunException | Will be thrown if an error occurres. |
Reimplemented from CSGObject.
Definition at line 920 of file Kernel.cpp.
void set_cache_size | ( | int32_t | size | ) | [inherited] |
void set_combined_kernel_weight | ( | float64_t | nw | ) | [inherited] |
bool set_degree | ( | int32_t | deg | ) |
set degree
deg | new degree |
Definition at line 544 of file WeightedDegreeStringKernel.h.
void set_generic< complex128_t > | ( | ) | [inherited] |
set generic type to T
Definition at line 41 of file SGObject.cpp.
void set_global_io | ( | SGIO * | io | ) | [inherited] |
void set_global_parallel | ( | Parallel * | parallel | ) | [inherited] |
set the parallel object
parallel | parallel object to use |
Definition at line 180 of file SGObject.cpp.
void set_global_version | ( | Version * | version | ) | [inherited] |
set the version object
version | version object to use |
Definition at line 215 of file SGObject.cpp.
void set_is_initialized | ( | bool | p_init | ) | [protected, inherited] |
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 574 of file WeightedDegreeStringKernel.h.
virtual bool set_normalizer | ( | CKernelNormalizer * | normalizer_ | ) | [virtual] |
set the current kernel normalizer
Reimplemented from CKernel.
Definition at line 344 of file WeightedDegreeStringKernel.h.
virtual void set_optimization_type | ( | EOptimizationType | t | ) | [virtual, inherited] |
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.
void set_property | ( | EKernelProperty | p | ) | [protected, inherited] |
virtual void set_subkernel_weights | ( | SGVector< float64_t > | w | ) | [virtual] |
set subkernel weights
w | weights |
Reimplemented from CKernel.
Definition at line 293 of file WeightedDegreeStringKernel.h.
void set_time | ( | int32_t | t | ) | [inherited] |
bool set_use_block_computation | ( | bool | block | ) |
set if block computation shall be performed
block | if block computation shall be performed |
Definition at line 557 of file WeightedDegreeStringKernel.h.
void set_wd_weights | ( | SGVector< float64_t > | new_weights | ) |
set wd weights
new_weights | new weights |
Definition at line 440 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.
bool set_weights | ( | SGMatrix< float64_t > | new_weights | ) |
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 593 of file WeightedDegreeStringKernel.h.
virtual CSGObject* shallow_copy | ( | ) | const [virtual, inherited] |
A shallow copy. All the SGObject instance variables will be simply assigned and SG_REF-ed.
Reimplemented in CGaussianKernel.
Definition at line 117 of file SGObject.h.
void unset_generic | ( | ) | [inherited] |
unset generic type
this has to be called in classes specializing a template class
Definition at line 235 of file SGObject.cpp.
void unset_property | ( | EKernelProperty | p | ) | [protected, inherited] |
bool update_parameter_hash | ( | ) | [virtual, inherited] |
Updates the hash of current parameter combination.
Definition at line 187 of file SGObject.cpp.
alphabet of features
Definition at line 759 of file WeightedDegreeStringKernel.h.
bool block_computation [protected] |
if block computation is used
Definition at line 743 of file WeightedDegreeStringKernel.h.
float64_t* block_weights [protected] |
(internal) block weights
Definition at line 746 of file WeightedDegreeStringKernel.h.
int32_t cache_size [protected, inherited] |
float64_t combined_kernel_weight [protected, inherited] |
int32_t degree [protected] |
degree
Definition at line 730 of file WeightedDegreeStringKernel.h.
bool initialized [protected] |
if kernel is initialized
Definition at line 740 of file WeightedDegreeStringKernel.h.
io
Definition at line 473 of file SGObject.h.
KERNEL_CACHE kernel_cache [protected, inherited] |
KERNELCACHE_ELEM* kernel_matrix [protected, inherited] |
this *COULD* store the whole kernel matrix usually not applicable / necessary to compute the whole matrix
Reimplemented in CSpectrumMismatchRBFKernel, and CSpectrumRBFKernel.
int32_t length [protected] |
length
Definition at line 732 of file WeightedDegreeStringKernel.h.
bool lhs_equals_rhs [protected, inherited] |
Parameter* m_gradient_parameters [inherited] |
parameters wrt which we can compute gradients
Definition at line 488 of file SGObject.h.
uint32_t m_hash [inherited] |
Hash of parameter values
Definition at line 494 of file SGObject.h.
Parameter* m_model_selection_parameters [inherited] |
model selection parameters
Definition at line 485 of file SGObject.h.
ParameterMap* m_parameter_map [inherited] |
map for different parameter versions
Definition at line 491 of file SGObject.h.
Parameter* m_parameters [inherited] |
parameters
Definition at line 482 of file SGObject.h.
int32_t max_mismatch [protected] |
maximum mismatch
Definition at line 735 of file WeightedDegreeStringKernel.h.
int32_t mkl_stepsize [protected] |
MKL step size
Definition at line 728 of file WeightedDegreeStringKernel.h.
CKernelNormalizer* normalizer [protected, inherited] |
int32_t num_lhs [protected, inherited] |
int32_t num_rhs [protected, inherited] |
EOptimizationType opt_type [protected, inherited] |
bool optimization_initialized [protected, inherited] |
parallel
Definition at line 476 of file SGObject.h.
float64_t* position_weights [protected] |
position weights
Definition at line 722 of file WeightedDegreeStringKernel.h.
int32_t position_weights_len [protected] |
position weights
Definition at line 724 of file WeightedDegreeStringKernel.h.
uint64_t properties [protected, inherited] |
int32_t seq_length [protected] |
sequence length
Definition at line 737 of file WeightedDegreeStringKernel.h.
bool tree_initialized [protected] |
if tree is initialized
Definition at line 756 of file WeightedDegreeStringKernel.h.
tries
Definition at line 753 of file WeightedDegreeStringKernel.h.
EWDKernType type [protected] |
WeightedDegree kernel type
Definition at line 748 of file WeightedDegreeStringKernel.h.
version
Definition at line 479 of file SGObject.h.
degree*length weights length must match seq_length if != 0
Definition at line 714 of file WeightedDegreeStringKernel.h.
float64_t* weights_buffer [protected] |
weights buffer
Definition at line 726 of file WeightedDegreeStringKernel.h.
int32_t weights_degree [protected] |
degree
Definition at line 716 of file WeightedDegreeStringKernel.h.
int32_t weights_length [protected] |
length
Definition at line 718 of file WeightedDegreeStringKernel.h.
int32_t which_degree [protected] |
which degree
Definition at line 750 of file WeightedDegreeStringKernel.h.