SHOGUN
v3.0.0
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The standard Sigmoid kernel computed on dense real valued features.
Formally, it is computed as
\[ k({\bf x},{\bf x'})=\mbox{tanh}(\gamma {\bf x}\cdot{\bf x'}+c) \]
Definition at line 29 of file SigmoidKernel.h.
Public Member Functions | |
CSigmoidKernel () | |
CSigmoidKernel (int32_t size, float64_t gamma, float64_t coef0) | |
CSigmoidKernel (CDotFeatures *l, CDotFeatures *r, int32_t size, float64_t gamma, float64_t coef0) | |
virtual | ~CSigmoidKernel () |
virtual bool | init (CFeatures *l, CFeatures *r) |
virtual void | cleanup () |
virtual EKernelType | get_kernel_type () |
virtual const char * | get_name () const |
virtual EFeatureClass | get_feature_class () |
virtual EFeatureType | get_feature_type () |
float64_t | kernel (int32_t idx_a, int32_t idx_b) |
SGMatrix< float64_t > | get_kernel_matrix () |
template<class T > | |
SGMatrix< T > | get_kernel_matrix () |
SGVector< float64_t > | get_kernel_diagonal (SGVector< float64_t > preallocated=SGVector< float64_t >()) |
virtual SGVector< float64_t > | get_kernel_col (int32_t j) |
virtual SGVector< float64_t > | get_kernel_row (int32_t i) |
void | get_kernel_row (int32_t docnum, int32_t *active2dnum, float64_t *buffer, bool full_line=false) |
virtual 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 | |
void | set_cache_size (int32_t size) |
int32_t | get_cache_size () |
void | cache_reset () |
int32_t | get_max_elems_cache () |
int32_t | get_activenum_cache () |
void | cache_kernel_row (int32_t x) |
void | cache_multiple_kernel_rows (int32_t *key, int32_t varnum) |
void | kernel_cache_reset_lru () |
void | kernel_cache_shrink (int32_t totdoc, int32_t num_shrink, int32_t *after) |
void | resize_kernel_cache (KERNELCACHE_IDX size, bool regression_hack=false) |
void | set_time (int32_t t) |
int32_t | kernel_cache_touch (int32_t cacheidx) |
int32_t | kernel_cache_check (int32_t cacheidx) |
int32_t | kernel_cache_space_available () |
void | kernel_cache_init (int32_t size, bool regression_hack=false) |
void | kernel_cache_cleanup () |
void | list_kernel () |
bool | has_property (EKernelProperty p) |
virtual void | clear_normal () |
virtual void | add_to_normal (int32_t vector_idx, float64_t weight) |
EOptimizationType | get_optimization_type () |
virtual void | set_optimization_type (EOptimizationType t) |
bool | get_is_initialized () |
virtual bool | init_optimization (int32_t count, int32_t *IDX, float64_t *weights) |
virtual bool | delete_optimization () |
bool | init_optimization_svm (CSVM *svm) |
virtual float64_t | compute_optimized (int32_t vector_idx) |
virtual void | compute_batch (int32_t num_vec, int32_t *vec_idx, float64_t *target, int32_t num_suppvec, int32_t *IDX, float64_t *alphas, float64_t factor=1.0) |
float64_t | get_combined_kernel_weight () |
void | set_combined_kernel_weight (float64_t nw) |
virtual int32_t | get_num_subkernels () |
virtual void | compute_by_subkernel (int32_t vector_idx, float64_t *subkernel_contrib) |
virtual const float64_t * | get_subkernel_weights (int32_t &num_weights) |
virtual SGVector< float64_t > | get_subkernel_weights () |
virtual void | set_subkernel_weights (SGVector< float64_t > weights) |
virtual SGMatrix< float64_t > | get_parameter_gradient (const TParameter *param, index_t index=-1) |
virtual CSGObject * | shallow_copy () const |
virtual CSGObject * | deep_copy () const |
virtual bool | is_generic (EPrimitiveType *generic) const |
template<class T > | |
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 (int32_t idx_a, int32_t idx_b) |
void | set_property (EKernelProperty p) |
void | unset_property (EKernelProperty p) |
void | set_is_initialized (bool p_init) |
int32_t | compute_row_start (int64_t offs, int32_t n, bool symmetric) |
virtual void | load_serializable_post () throw (ShogunException) |
virtual void | save_serializable_pre () throw (ShogunException) |
virtual void | save_serializable_post () throw (ShogunException) |
virtual void | register_params () |
virtual 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 | gamma |
float64_t | coef0 |
int32_t | cache_size |
cache_size in MB | |
KERNEL_CACHE | kernel_cache |
kernel cache | |
KERNELCACHE_ELEM * | kernel_matrix |
CFeatures * | lhs |
feature vectors to occur on left hand side | |
CFeatures * | rhs |
feature vectors to occur on right hand side | |
bool | lhs_equals_rhs |
lhs | |
int32_t | num_lhs |
number of feature vectors on left hand side | |
int32_t | num_rhs |
number of feature vectors on right hand side | |
float64_t | combined_kernel_weight |
bool | optimization_initialized |
EOptimizationType | opt_type |
uint64_t | properties |
CKernelNormalizer * | normalizer |
CSigmoidKernel | ( | ) |
default constructor
Definition at line 17 of file SigmoidKernel.cpp.
CSigmoidKernel | ( | int32_t | size, |
float64_t | gamma, | ||
float64_t | coef0 | ||
) |
constructor
size | cache size |
gamma | gamma |
coef0 | coefficient 0 |
Definition at line 22 of file SigmoidKernel.cpp.
CSigmoidKernel | ( | CDotFeatures * | l, |
CDotFeatures * | r, | ||
int32_t | size, | ||
float64_t | gamma, | ||
float64_t | coef0 | ||
) |
constructor
l | features of left-hand side |
r | features of right-hand side |
size | cache size |
gamma | gamma |
coef0 | coefficient 0 |
Definition at line 31 of file SigmoidKernel.cpp.
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virtual |
Definition at line 43 of file SigmoidKernel.cpp.
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virtualinherited |
add vector*factor to 'virtual' normal vector
vector_idx | index |
weight | weight |
Reimplemented in CCombinedKernel, CWeightedDegreeStringKernel, CWeightedDegreePositionStringKernel, CCommUlongStringKernel, CCommWordStringKernel, CLinearKernel, CLinearStringKernel, and CWeightedCommWordStringKernel.
Definition at line 838 of file Kernel.cpp.
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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 1196 of file SGObject.cpp.
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for optimizable kernels, i.e. kernels where the weight vector can be computed explicitly (if it fits into memory)
Reimplemented in CCombinedKernel, CWeightedDegreeStringKernel, CWeightedDegreePositionStringKernel, CCommUlongStringKernel, CCommWordStringKernel, CLinearKernel, and CLinearStringKernel.
Definition at line 843 of file Kernel.cpp.
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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 1313 of file SGObject.cpp.
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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 |
Reimplemented from CDotKernel.
Definition at line 88 of file SigmoidKernel.h.
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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 831 of file Kernel.cpp.
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compute by subkernel
vector_idx | index |
subkernel_contrib | subkernel contribution |
Reimplemented in CCombinedKernel, CWeightedDegreeStringKernel, and CWeightedDegreePositionStringKernel.
Definition at line 853 of file Kernel.cpp.
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compute optimized
vector_idx | index to compute |
Reimplemented in CCombinedKernel, CWeightedDegreeStringKernel, CWeightedDegreePositionStringKernel, CCommWordStringKernel, CCommUlongStringKernel, CLinearKernel, CLinearStringKernel, and CWeightedCommWordStringKernel.
Definition at line 825 of file Kernel.cpp.
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A deep copy. All the instance variables will also be copied.
Definition at line 160 of file SGObject.h.
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delete optimization
Reimplemented in CCombinedKernel, CWeightedDegreeStringKernel, CWeightedDegreePositionStringKernel, CCommWordStringKernel, CCommUlongStringKernel, CLinearKernel, and CLinearStringKernel.
Definition at line 819 of file Kernel.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 1217 of file SGObject.cpp.
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return feature class the kernel can deal with
dot kernel returns unknown since features can be based on anything
Implements CKernel.
Reimplemented in CTensorProductPairKernel, CChi2Kernel, CAUCKernel, CANOVAKernel, CLinearARDKernel, and CWeightedDegreeRBFKernel.
Definition at line 86 of file DotKernel.h.
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return feature type the kernel can deal with
dot kernel returns unknown since features can be based on anything
Implements CKernel.
Reimplemented in CTensorProductPairKernel, CChi2Kernel, CAUCKernel, CLinearARDKernel, CANOVAKernel, and CWeightedDegreeRBFKernel.
Definition at line 94 of file DotKernel.h.
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get kernel matrix (templated)
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helper for computing the kernel matrix in a parallel way
p | thread parameters |
Definition at line 1011 of file Kernel.cpp.
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get kernel row
docnum | docnum |
active2dnum | active2dnum |
buffer | buffer |
full_line | full line |
Definition at line 229 of file Kernel.cpp.
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return what type of kernel we are
Implements CDotKernel.
Definition at line 71 of file SigmoidKernel.h.
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Definition at line 1100 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 1124 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 1137 of file SGObject.cpp.
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return the kernel's name
Reimplemented from CDotKernel.
Definition at line 77 of file SigmoidKernel.h.
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obtain the current kernel normalizer
Definition at line 153 of file Kernel.cpp.
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get number of subkernels
Reimplemented in CWeightedDegreeStringKernel, CWeightedDegreePositionStringKernel, CCombinedKernel, and CProductKernel.
Definition at line 848 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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get subkernel weights
num_weights | number of weights will be stored here |
Reimplemented in CCombinedKernel, CWeightedDegreeStringKernel, and CWeightedDegreePositionStringKernel.
Definition at line 859 of file Kernel.cpp.
get subkernel weights (swig compatible)
Reimplemented in CCombinedKernel.
Definition at line 865 of file Kernel.cpp.
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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 CDotKernel.
Definition at line 52 of file SigmoidKernel.cpp.
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initialize the current kernel normalizer
Definition at line 159 of file Kernel.cpp.
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initialize optimization
count | count |
IDX | index |
weights | weights |
Reimplemented in CCombinedKernel, CWeightedDegreeStringKernel, CWeightedDegreePositionStringKernel, CCommWordStringKernel, CCommUlongStringKernel, CLinearKernel, and CLinearStringKernel.
Definition at line 812 of file Kernel.cpp.
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initialize optimization
svm | svm model |
Definition at line 895 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 268 of file SGObject.cpp.
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cleanup kernel cache
Definition at line 556 of file Kernel.cpp.
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initialize kernel cache
size | size to initialize to |
regression_hack | if hack for regression shall be applied |
Definition at line 172 of file Kernel.cpp.
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kernel cache reset lru
Definition at line 543 of file Kernel.cpp.
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kernel cache shrink
totdoc | totdoc |
num_shrink | number of shrink |
after | after |
Definition at line 486 of file Kernel.cpp.
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list kernel
Definition at line 697 of file Kernel.cpp.
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load the kernel matrix
loader | File object via which to load data |
Definition at line 635 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 673 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 514 of file SGObject.cpp.
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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 345 of file SGObject.cpp.
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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.
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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 >, CDynamicArray< uint64_t >, and CDynamicObjectArray.
Definition at line 1024 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 711 of file SGObject.cpp.
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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 918 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 881 of file Kernel.cpp.
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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 858 of file SGObject.cpp.
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prints all parameter registered for model selection and their type
Definition at line 1076 of file SGObject.cpp.
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prints registered parameters out
prefix | prefix for members |
Definition at line 280 of file SGObject.cpp.
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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, CGaussianMatchStringKernel, CGaussianShortRealKernel, CTensorProductPairKernel, CDistanceKernel, and CHistogramIntersectionKernel.
Definition at line 936 of file Kernel.cpp.
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remove lhs from kernel
Reimplemented in CWeightedDegreeStringKernel, CWeightedDegreePositionStringKernel, CCombinedKernel, CCommUlongStringKernel, and CProductKernel.
Definition at line 668 of file Kernel.cpp.
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remove lhs and rhs from kernel
Reimplemented in CCombinedKernel, and CProductKernel.
Definition at line 649 of file Kernel.cpp.
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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.
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resize kernel cache
size | new size |
regression_hack | hack for regression |
Definition at line 85 of file Kernel.cpp.
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save kernel matrix
writer | File object via which to save data |
Definition at line 641 of file Kernel.cpp.
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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 286 of file SGObject.cpp.
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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.
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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.
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set generic type to T
Definition at line 41 of file SGObject.cpp.
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set the parallel object
parallel | parallel object to use |
Definition at line 220 of file SGObject.cpp.
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set the version object
version | version object to use |
Definition at line 255 of file SGObject.cpp.
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set the current kernel normalizer
Reimplemented in CWeightedDegreeStringKernel.
Definition at line 141 of file Kernel.cpp.
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set subkernel weights
weights | new subkernel weights |
Reimplemented in CCombinedKernel, CWeightedDegreeStringKernel, and CWeightedDegreePositionStringKernel.
Definition at line 872 of file Kernel.cpp.
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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 151 of file SGObject.h.
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unset generic type
this has to be called in classes specializing a template class
Definition at line 275 of file SGObject.cpp.
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Updates the hash of current parameter combination.
Definition at line 227 of file SGObject.cpp.
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coefficient 0
Definition at line 100 of file SigmoidKernel.h.
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gamma
Definition at line 98 of file SigmoidKernel.h.
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io
Definition at line 514 of file SGObject.h.
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parameters wrt which we can compute gradients
Definition at line 529 of file SGObject.h.
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Hash of parameter values
Definition at line 535 of file SGObject.h.
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model selection parameters
Definition at line 526 of file SGObject.h.
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map for different parameter versions
Definition at line 532 of file SGObject.h.
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parameters
Definition at line 523 of file SGObject.h.
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protectedinherited |
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protectedinherited |
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protectedinherited |
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protectedinherited |
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protectedinherited |
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inherited |
parallel
Definition at line 517 of file SGObject.h.
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protectedinherited |
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inherited |
version
Definition at line 520 of file SGObject.h.