SHOGUN
v3.2.0
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The WeightedCommWordString kernel may be used to compute the weighted spectrum kernel (i.e. a spectrum kernel for 1 to K-mers, where each k-mer length is weighted by some coefficient \(\beta_k\)) from strings that have been mapped into unsigned 16bit integers.
These 16bit integers correspond to k-mers. To applicable in this kernel they need to be sorted (e.g. via the SortWordString pre-processor).
It basically uses the algorithm in the unix "comm" command (hence the name) to compute:
\[ k({\bf x},({\bf x'})= \sum_{k=1}^K\beta_k\Phi_k({\bf x})\cdot \Phi_k({\bf x'}) \]
where \(\Phi_k\) maps a sequence \({\bf x}\) that consists of letters in \(\Sigma\) to a feature vector of size \(|\Sigma|^k\). In this feature vector each entry denotes how often the k-mer appears in that \({\bf x}\).
Note that this representation is especially tuned to small alphabets (like the 2-bit alphabet DNA), for which it enables spectrum kernels of order 8.
For this kernel the linadd speedups are quite efficiently implemented using direct maps.
Definition at line 50 of file WeightedCommWordStringKernel.h.
Public Member Functions | |
CWeightedCommWordStringKernel () | |
CWeightedCommWordStringKernel (int32_t size, bool use_sign) | |
CWeightedCommWordStringKernel (CStringFeatures< uint16_t > *l, CStringFeatures< uint16_t > *r, bool use_sign=false, int32_t size=10) | |
virtual | ~CWeightedCommWordStringKernel () |
virtual bool | init (CFeatures *l, CFeatures *r) |
virtual void | cleanup () |
virtual float64_t | compute_optimized (int32_t idx) |
virtual void | add_to_normal (int32_t idx, float64_t weight) |
void | merge_normal () |
bool | set_wd_weights () |
bool | set_weights (SGVector< float64_t > weights) |
virtual EKernelType | get_kernel_type () |
virtual const char * | get_name () const |
virtual EFeatureType | get_feature_type () |
virtual float64_t * | compute_scoring (int32_t max_degree, int32_t &num_feat, int32_t &num_sym, float64_t *target, int32_t num_suppvec, int32_t *IDX, float64_t *alphas, bool do_init=true) |
virtual bool | init_dictionary (int32_t size) |
virtual bool | init_optimization (int32_t count, int32_t *IDX, float64_t *weights) |
virtual bool | delete_optimization () |
virtual void | clear_normal () |
void | get_dictionary (int32_t &dsize, float64_t *&dweights) |
char * | compute_consensus (int32_t &num_feat, int32_t num_suppvec, int32_t *IDX, float64_t *alphas) |
void | set_use_dict_diagonal_optimization (bool flag) |
bool | get_use_dict_diagonal_optimization () |
virtual EFeatureClass | get_feature_class () |
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) |
virtual bool | set_normalizer (CKernelNormalizer *normalizer) |
virtual CKernelNormalizer * | get_normalizer () |
virtual bool | init_normalizer () |
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 | list_kernel () |
bool | has_property (EKernelProperty p) |
EOptimizationType | get_optimization_type () |
virtual void | set_optimization_type (EOptimizationType t) |
bool | get_is_initialized () |
bool | init_optimization_svm (CSVM *svm) |
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 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="", int32_t param_version=Version::get_version_parameter()) |
virtual bool | load_serializable (CSerializableFile *file, const char *prefix="", int32_t param_version=Version::get_version_parameter()) |
DynArray< TParameter * > * | load_file_parameters (const SGParamInfo *param_info, int32_t file_version, CSerializableFile *file, const char *prefix="") |
DynArray< TParameter * > * | load_all_file_parameters (int32_t file_version, int32_t current_version, CSerializableFile *file, const char *prefix="") |
void | map_parameters (DynArray< TParameter *> *param_base, int32_t &base_version, DynArray< const SGParamInfo *> *target_param_infos) |
void | set_global_io (SGIO *io) |
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) |
virtual bool | update_parameter_hash () |
virtual bool | equals (CSGObject *other, float64_t accuracy=0.0) |
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 |
ParameterMap * | m_parameter_map |
uint32_t | m_hash |
Protected Member Functions | |
virtual float64_t | compute_helper (int32_t idx_a, int32_t idx_b, bool do_sort) |
virtual float64_t | compute (int32_t idx_a, int32_t idx_b) |
virtual float64_t | compute_diag (int32_t idx_a) |
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 | |
int32_t | degree |
float64_t * | weights |
int32_t | dictionary_size |
float64_t * | dictionary_weights |
bool | use_sign |
bool | use_dict_diagonal_optimization |
int32_t * | dict_diagonal_optimization |
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 18 of file WeightedCommWordStringKernel.cpp.
CWeightedCommWordStringKernel | ( | int32_t | size, |
bool | use_sign | ||
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constructor
size | cache size |
use_sign | if sign shall be used |
Definition at line 24 of file WeightedCommWordStringKernel.cpp.
CWeightedCommWordStringKernel | ( | CStringFeatures< uint16_t > * | l, |
CStringFeatures< uint16_t > * | r, | ||
bool | use_sign = false , |
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int32_t | size = 10 |
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) |
constructor
l | features of left-hand side |
r | features of right-hand side |
use_sign | if sign shall be used |
size | cache size |
Definition at line 32 of file WeightedCommWordStringKernel.cpp.
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virtual |
Definition at line 43 of file WeightedCommWordStringKernel.cpp.
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virtual |
add to normal
idx | where to add |
weight | what to add |
Reimplemented from CCommWordStringKernel.
Definition at line 191 of file WeightedCommWordStringKernel.cpp.
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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 1156 of file SGObject.cpp.
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virtual |
clean up kernel
Reimplemented from CCommWordStringKernel.
Definition at line 59 of file WeightedCommWordStringKernel.cpp.
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virtualinherited |
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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 1273 of file SGObject.cpp.
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protectedvirtualinherited |
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 215 of file CommWordStringKernel.h.
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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 344 of file Kernel.cpp.
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virtualinherited |
compute by subkernel
vector_idx | index |
subkernel_contrib | subkernel contribution |
Reimplemented in CCombinedKernel, CWeightedDegreeStringKernel, and CWeightedDegreePositionStringKernel.
Definition at line 366 of file Kernel.cpp.
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inherited |
compute consensus
num_feat | number of features |
num_suppvec | number of support vectors |
IDX | IDX |
alphas | alphas |
Definition at line 498 of file CommWordStringKernel.cpp.
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protectedvirtualinherited |
helper to compute only diagonal normalization for training
idx_a | index a |
Definition at line 85 of file CommWordStringKernel.cpp.
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protectedvirtual |
helper for compute
idx_a | index a |
idx_b | index b |
do_sort | if sorting shall be performed |
Reimplemented from CCommWordStringKernel.
Definition at line 96 of file WeightedCommWordStringKernel.cpp.
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virtual |
compute optimized
idx | index to compute |
Reimplemented from CCommWordStringKernel.
Definition at line 253 of file WeightedCommWordStringKernel.cpp.
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protectedinherited |
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virtual |
compute scoring
max_degree | maximum degree |
num_feat | number of features |
num_sym | number of symbols |
target | target |
num_suppvec | number of support vectors |
IDX | IDX |
alphas | alphas |
do_init | if initialization shall be performed |
Reimplemented from CCommWordStringKernel.
Definition at line 288 of file WeightedCommWordStringKernel.cpp.
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A deep copy. All the instance variables will also be copied.
Definition at line 126 of file SGObject.h.
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delete optimization
Reimplemented from CKernel.
Definition at line 318 of file CommWordStringKernel.cpp.
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.
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inherited |
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get dictionary
dsize | dictionary size will be stored in here |
dweights | dictionary weights will be stored in here |
Definition at line 153 of file CommWordStringKernel.h.
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return feature class the kernel can deal with
Implements CKernel.
Definition at line 69 of file StringKernel.h.
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virtual |
return feature type the kernel can deal with
Reimplemented from CCommWordStringKernel.
Definition at line 133 of file WeightedCommWordStringKernel.h.
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inherited |
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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 522 of file Kernel.cpp.
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return what type of kernel we are
Reimplemented from CCommWordStringKernel.
Definition at line 121 of file WeightedCommWordStringKernel.h.
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inherited |
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inherited |
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inherited |
Definition at line 1060 of file SGObject.cpp.
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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.
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Returns index of model selection parameter with provided index
param_name | name of model selection parameter |
Definition at line 1097 of file SGObject.cpp.
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return the kernel's name
Reimplemented from CCommWordStringKernel.
Definition at line 127 of file WeightedCommWordStringKernel.h.
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obtain the current kernel normalizer
Definition at line 136 of file Kernel.cpp.
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get number of subkernels
Reimplemented in CWeightedDegreeStringKernel, CWeightedDegreePositionStringKernel, CCombinedKernel, and CProductKernel.
Definition at line 361 of file Kernel.cpp.
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get number of vectors of lhs features
Reimplemented in CCustomKernel.
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get number of vectors of rhs features
Reimplemented in CCustomKernel.
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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, CLinearARDKernel, and CGaussianARDKernel.
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inherited |
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virtualinherited |
get subkernel weights
num_weights | number of weights will be stored here |
Reimplemented in CCombinedKernel, CWeightedDegreeStringKernel, and CWeightedDegreePositionStringKernel.
Definition at line 372 of file Kernel.cpp.
get subkernel weights (swig compatible)
Reimplemented in CCombinedKernel.
Definition at line 378 of file Kernel.cpp.
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get.use.dict.diagonal.optimization
Definition at line 201 of file CommWordStringKernel.h.
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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 CCommWordStringKernel.
Definition at line 48 of file WeightedCommWordStringKernel.cpp.
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virtualinherited |
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virtualinherited |
initialize the current kernel normalizer
Definition at line 142 of file Kernel.cpp.
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initialize optimization
count | count |
IDX | index |
weights | weights |
Reimplemented from CKernel.
Definition at line 292 of file CommWordStringKernel.cpp.
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inherited |
initialize optimization
svm | svm model |
Definition at line 408 of file Kernel.cpp.
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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.
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list kernel
Definition at line 210 of file Kernel.cpp.
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load the kernel matrix
loader | File object via which to load data |
Definition at line 154 of file Kernel.cpp.
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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.
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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 474 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 305 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 426 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 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.
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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.
void merge_normal | ( | ) |
merge normal
Definition at line 221 of file WeightedCommWordStringKernel.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 878 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 394 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 818 of file SGObject.cpp.
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prints all parameter registered for model selection and their type
Definition at line 1036 of file SGObject.cpp.
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virtualinherited |
prints registered parameters out
prefix | prefix for members |
Definition at line 240 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, CStringSubsequenceKernel, CGaussianMatchStringKernel, CGaussianShortRealKernel, CTensorProductPairKernel, CDistanceKernel, and CHistogramIntersectionKernel.
Definition at line 449 of file Kernel.cpp.
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virtualinherited |
remove lhs from kernel
Reimplemented in CWeightedDegreeStringKernel, CWeightedDegreePositionStringKernel, CCombinedKernel, CCommUlongStringKernel, and CProductKernel.
Definition at line 185 of file Kernel.cpp.
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virtualinherited |
remove lhs and rhs from kernel
Reimplemented in CCombinedKernel, and CProductKernel.
Definition at line 168 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 197 of file Kernel.cpp.
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save kernel matrix
writer | File object via which to save data |
Definition at line 160 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 246 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 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::SAVE_SERIALIZABLE_PRE is called.
ShogunException | Will be thrown if an error occurres. |
Reimplemented from CSGObject.
Definition at line 433 of file Kernel.cpp.
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Definition at line 41 of file SGObject.cpp.
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Definition at line 46 of file SGObject.cpp.
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Definition at line 51 of file SGObject.cpp.
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Definition at line 56 of file SGObject.cpp.
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Definition at line 61 of file SGObject.cpp.
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Definition at line 66 of file SGObject.cpp.
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Definition at line 71 of file SGObject.cpp.
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Definition at line 76 of file SGObject.cpp.
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Definition at line 81 of file SGObject.cpp.
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Definition at line 86 of file SGObject.cpp.
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Definition at line 91 of file SGObject.cpp.
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Definition at line 96 of file SGObject.cpp.
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Definition at line 101 of file SGObject.cpp.
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Definition at line 106 of file SGObject.cpp.
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Definition at line 111 of file SGObject.cpp.
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set generic type to T
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inherited |
set the parallel object
parallel | parallel object to use |
Definition at line 180 of file SGObject.cpp.
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inherited |
set the version object
version | version object to use |
Definition at line 215 of file SGObject.cpp.
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protectedinherited |
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virtualinherited |
set the current kernel normalizer
Reimplemented in CWeightedDegreeStringKernel.
Definition at line 124 of file Kernel.cpp.
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virtualinherited |
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protectedinherited |
set subkernel weights
weights | new subkernel weights |
Reimplemented in CCombinedKernel, CWeightedDegreeStringKernel, and CWeightedDegreePositionStringKernel.
Definition at line 385 of file Kernel.cpp.
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inherited |
set_use_dict_diagonal_optimization
flag | enable diagonal optimization |
Definition at line 192 of file CommWordStringKernel.h.
bool set_wd_weights | ( | ) |
set weighted degree weights
Definition at line 67 of file WeightedCommWordStringKernel.cpp.
set custom weights (swig compatible)
weights | weights |
Definition at line 85 of file WeightedCommWordStringKernel.cpp.
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virtualinherited |
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.
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inherited |
unset generic type
this has to be called in classes specializing a template class
Definition at line 235 of file SGObject.cpp.
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protectedinherited |
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virtualinherited |
Updates the hash of current parameter combination.
Definition at line 187 of file SGObject.cpp.
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protectedinherited |
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protected |
degree
Definition at line 167 of file WeightedCommWordStringKernel.h.
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protectedinherited |
array to hold counters for all strings
Definition at line 253 of file CommWordStringKernel.h.
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protectedinherited |
size of dictionary (number of possible strings)
Definition at line 242 of file CommWordStringKernel.h.
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protectedinherited |
dictionary weights - array to hold counters for all possible strings
Definition at line 245 of file CommWordStringKernel.h.
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inherited |
io
Definition at line 473 of file SGObject.h.
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protectedinherited |
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protectedinherited |
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inherited |
parameters wrt which we can compute gradients
Definition at line 488 of file SGObject.h.
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inherited |
Hash of parameter values
Definition at line 494 of file SGObject.h.
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inherited |
model selection parameters
Definition at line 485 of file SGObject.h.
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inherited |
map for different parameter versions
Definition at line 491 of file SGObject.h.
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inherited |
parameters
Definition at line 482 of file SGObject.h.
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protectedinherited |
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protectedinherited |
|
protectedinherited |
|
protectedinherited |
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protectedinherited |
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inherited |
parallel
Definition at line 476 of file SGObject.h.
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protectedinherited |
|
protectedinherited |
whether diagonal optimization shall be used
Definition at line 251 of file CommWordStringKernel.h.
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protectedinherited |
if sign shall be used
Definition at line 248 of file CommWordStringKernel.h.
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inherited |
version
Definition at line 479 of file SGObject.h.
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protected |
weights for each of the subkernels of degree 1...d
Definition at line 170 of file WeightedCommWordStringKernel.h.