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SHOGUN
v2.1.0
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SHOGUN
v2.1.0
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The Combined kernel is used to combine a number of kernels into a single CombinedKernel object by linear combination.
It keeps pointers to the added sub-kernels 
and for each sub-kernel - a kernel specific weight 
.
It is especially useful to combine kernels working on different domains and to combine kernels looking at independent features and requires CCombinedFeatures to be used.
It is defined as:
![\[ k_{combined}({\bf x}, {\bf x'}) = \sum_{m=1}^M \beta_m k_m({\bf x}, {\bf x'}) \]](form_114.png)
Definition at line 46 of file CombinedKernel.h.
Static Public Member Functions | |
| static void * | compute_optimized_kernel_helper (void *p) |
| static void * | compute_kernel_helper (void *p) |
| static CCombinedKernel * | obtain_from_generic (CKernel *kernel) |
| static CKernel * | obtain_from_generic (CSGObject *kernel) |
Public Attributes | |
| SGIO * | io |
| Parallel * | parallel |
| Version * | version |
| Parameter * | m_parameters |
| Parameter * | m_model_selection_parameters |
| ParameterMap * | m_parameter_map |
| uint32_t | m_hash |
Protected Member Functions | |
| virtual float64_t | compute (int32_t x, int32_t y) |
| void | adjust_num_lhs_rhs_initialized (CKernel *k) |
| 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 | |
| CList * | kernel_list |
| int32_t | sv_count |
| int32_t * | sv_idx |
| float64_t * | sv_weight |
| float64_t * | subkernel_weights_buffer |
| bool | append_subkernel_weights |
| bool | initialized |
| 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 |
| CCombinedKernel | ( | int32_t | size = 10, |
| bool | append_subkernel_weights = false |
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constructor
| size | cache size |
| append_subkernel_weights | if subkernel weights shall be appended |
Definition at line 44 of file CombinedKernel.cpp.
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Definition at line 55 of file CombinedKernel.cpp.
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add to normal vector
| idx | where to add |
| weight | what to add |
Reimplemented from CKernel.
Definition at line 603 of file CombinedKernel.cpp.
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adjust the variables num_lhs, num_rhs and initialized based on the kernel to be appended/inserted
| k | kernel |
Definition at line 419 of file CombinedKernel.h.
| bool append_kernel | ( | CKernel * | k | ) |
append kernel
| k | kernel |
Definition at line 192 of file CombinedKernel.h.
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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 1208 of file SGObject.cpp.
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compute kernel function
| x | x |
| y | y |
Implements CKernel.
Definition at line 267 of file CombinedKernel.cpp.
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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 from CKernel.
Definition at line 360 of file CombinedKernel.cpp.
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compute by subkernel
| idx | index |
| subkernel_contrib | subkernel contribution |
Reimplemented from CKernel.
Definition at line 631 of file CombinedKernel.cpp.
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helper for compute kernel
| p | thread parameter |
Definition at line 407 of file CombinedKernel.cpp.
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compute optimized
| idx | index to compute |
Reimplemented from CKernel.
Definition at line 558 of file CombinedKernel.cpp.
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helper for compute optimized kernel
| p | thread parameter |
Definition at line 394 of file CombinedKernel.cpp.
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A deep copy. All the instance variables will also be copied.
Definition at line 133 of file SGObject.h.
| bool delete_kernel | ( | ) |
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delete optimization
Reimplemented from CKernel.
Definition at line 334 of file CombinedKernel.cpp.
| void emulate_compute_batch | ( | CKernel * | k, |
| int32_t | num_vec, | ||
| int32_t * | vec_idx, | ||
| float64_t * | target, | ||
| int32_t | num_suppvec, | ||
| int32_t * | IDX, | ||
| float64_t * | weights | ||
| ) |
emulates batch computation, via linadd optimization w^t x or even down to sum_i alpha_i K(x_i,x)
| k | kernel |
| num_vec | number of vectors |
| vec_idx | vector index |
| target | target |
| num_suppvec | number of support vectors |
| IDX | IDX |
| weights | weights |
Definition at line 429 of file CombinedKernel.cpp.
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| bool get_append_subkernel_weights | ( | ) |
check if subkernel weights are appended
Definition at line 226 of file CombinedKernel.h.
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return feature class the kernel can deal with
Implements CKernel.
Definition at line 94 of file CombinedKernel.h.
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return feature type the kernel can deal with
Implements CKernel.
Definition at line 85 of file CombinedKernel.h.
| CKernel* get_first_kernel | ( | ) |
| CKernel* get_first_kernel | ( | CListElement *& | current | ) |
get first kernel
| current |
Definition at line 122 of file CombinedKernel.h.
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| CKernel* get_kernel | ( | int32_t | idx | ) |
get kernel
| idx | index of kernel |
Definition at line 132 of file CombinedKernel.h.
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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 CKernel.
Definition at line 76 of file CombinedKernel.h.
| CKernel* get_last_kernel | ( | ) |
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| CList* get_list | ( | ) |
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Definition at line 1113 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 1137 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 1150 of file SGObject.cpp.
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return the kernel's name
Implements CSGObject.
Definition at line 103 of file CombinedKernel.h.
| CKernel* get_next_kernel | ( | ) |
| CKernel* get_next_kernel | ( | CListElement *& | current | ) |
get next kernel multi-thread safe
| current |
Definition at line 166 of file CombinedKernel.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 from CKernel.
Definition at line 235 of file CombinedKernel.h.
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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 |
| obj | the object that owns the parameter |
| index | the index of the element if parameter is a vector |
Reimplemented from CKernel.
Definition at line 828 of file CombinedKernel.cpp.
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get subkernel weights
| num_weights | where number of weights is stored |
Reimplemented from CKernel.
Definition at line 670 of file CombinedKernel.cpp.
get subkernel weights (swig compatible)
Reimplemented from CKernel.
Definition at line 718 of file CombinedKernel.cpp.
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test whether features have been assigned to lhs and rhs
Reimplemented from CKernel.
Definition at line 259 of file CombinedKernel.h.
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initialize kernel. Provided features have to be combined features. If they are not, all subkernels are tried to be initialised with the single same passed features objects
| lhs | features of left-hand side |
| rhs | features of right-hand side |
Reimplemented from CKernel.
Definition at line 66 of file CombinedKernel.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 from CKernel.
Definition at line 283 of file CombinedKernel.cpp.
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initialize optimization
| svm | svm model |
Definition at line 892 of file Kernel.cpp.
| bool insert_kernel | ( | CKernel * | k | ) |
insert kernel
| k | kernel |
Definition at line 176 of file CombinedKernel.h.
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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 277 of file SGObject.cpp.
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cleanup kernel cache
Definition at line 555 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 542 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 696 of file Kernel.cpp.
| void list_kernels | ( | ) |
list kernels
Definition at line 249 of file CombinedKernel.cpp.
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load the kernel matrix
| loader | File object via which to load data |
Definition at line 634 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_PARAMETER for this in most cases) |
| file | file to load from |
| prefix | prefix for members |
Definition at line 682 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 523 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) |
Reimplemented in CModelSelectionParameters.
Definition at line 354 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, CANOVAKernel, CInverseMultiQuadricKernel, CCircularKernel, and CExponentialKernel.
Definition at line 910 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 1033 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 720 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 927 of file SGObject.cpp.
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Returns a casted version of the given kernel. Throws an error if parameter is not of class CombinedKernel. SG_REF's the returned kernel
| kernel | kernel to cast to CombinedKernel |
Definition at line 916 of file CombinedKernel.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 878 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 867 of file SGObject.cpp.
| bool precompute_subkernels | ( | ) |
precompute all sub-kernels
Definition at line 780 of file CombinedKernel.cpp.
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prints all parameter registered for model selection and their type
Definition at line 1089 of file SGObject.cpp.
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prints registered parameters out
| prefix | prefix for members |
Definition at line 289 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, CRegulatoryModulesStringKernel, CGaussianMatchStringKernel, CGaussianShortRealKernel, CTensorProductPairKernel, CDistanceKernel, and CHistogramIntersectionKernel.
Definition at line 933 of file Kernel.cpp.
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remove lhs from kernel
Reimplemented from CKernel.
Definition at line 171 of file CombinedKernel.cpp.
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remove lhs and rhs from kernel
Reimplemented from CKernel.
Definition at line 208 of file CombinedKernel.cpp.
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remove rhs from kernel
Reimplemented from CKernel.
Definition at line 191 of file CombinedKernel.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 640 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) |
Reimplemented in CModelSelectionParameters.
Definition at line 295 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 925 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 917 of file Kernel.cpp.
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set generic type to T
Definition at line 40 of file SGObject.cpp.
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set the parallel object
| parallel | parallel object to use |
Definition at line 229 of file SGObject.cpp.
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set the version object
| version | version object to use |
Definition at line 264 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 optimization type
| t | optimization type |
Reimplemented from CKernel.
Definition at line 765 of file CombinedKernel.cpp.
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set subkernel weights
| weights | new subkernel weights |
Reimplemented from CKernel.
Definition at line 730 of file CombinedKernel.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 124 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 284 of file SGObject.cpp.
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Updates the hash of current parameter combination.
Definition at line 236 of file SGObject.cpp.
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if subkernel weights are appended
Definition at line 473 of file CombinedKernel.h.
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whether kernel is ready to be used
Definition at line 475 of file CombinedKernel.h.
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io
Definition at line 465 of file SGObject.h.
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list of kernels
Definition at line 463 of file CombinedKernel.h.
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Hash of parameter values
Definition at line 483 of file SGObject.h.
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model selection parameters
Definition at line 477 of file SGObject.h.
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map for different parameter versions
Definition at line 480 of file SGObject.h.
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parameters
Definition at line 474 of file SGObject.h.
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parallel
Definition at line 468 of file SGObject.h.
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subkernel weights buffers
Definition at line 471 of file CombinedKernel.h.
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support vector count
Definition at line 465 of file CombinedKernel.h.
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support vector index
Definition at line 467 of file CombinedKernel.h.
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support vector weights
Definition at line 469 of file CombinedKernel.h.
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version
Definition at line 471 of file SGObject.h.