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SHOGUN
v3.0.0
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SHOGUN
v3.0.0
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Preprocessor PCACut performs principial component analysis on the input vectors and keeps only the n eigenvectors with eigenvalues above a certain threshold.
On preprocessing the stored covariance matrix is used to project vectors into eigenspace only returning vectors of reduced dimension n. Optional whitening is performed.
This is only useful if the dimensionality of the data is rather low, as the covariance matrix is of size num_feat*num_feat. Note that vectors don't have to have zero mean as it is substracted.
Public Member Functions | |
| CPCA (bool do_whitening=false, EPCAMode mode=FIXED_NUMBER, float64_t thresh=1e-6) | |
| virtual | ~CPCA () |
| virtual bool | init (CFeatures *features) |
| virtual void | cleanup () |
| virtual SGMatrix< float64_t > | apply_to_feature_matrix (CFeatures *features) |
| virtual SGVector< float64_t > | apply_to_feature_vector (SGVector< float64_t > vector) |
| SGMatrix< float64_t > | get_transformation_matrix () |
| SGVector< float64_t > | get_eigenvalues () |
| SGVector< float64_t > | get_mean () |
| virtual const char * | get_name () const |
| virtual EPreprocessorType | get_type () const |
| void | set_target_dim (int32_t dim) |
| int32_t | get_target_dim () const |
| void | set_distance (CDistance *distance) |
| CDistance * | get_distance () const |
| void | set_kernel (CKernel *kernel) |
| CKernel * | get_kernel () const |
| virtual EFeatureClass | get_feature_class () |
| return that we are dense features (just fixed size matrices) | |
| virtual EFeatureType | get_feature_type () |
| return feature type | |
| 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 () |
Public Attributes | |
| SGIO * | io |
| Parallel * | parallel |
| Version * | version |
| Parameter * | m_parameters |
| Parameter * | m_model_selection_parameters |
| Parameter * | m_gradient_parameters |
| ParameterMap * | m_parameter_map |
| uint32_t | m_hash |
Protected Member Functions | |
| void | init () |
| 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) |
| virtual void | load_serializable_post () throw (ShogunException) |
| virtual void | save_serializable_pre () throw (ShogunException) |
| virtual void | save_serializable_post () throw (ShogunException) |
Protected Attributes | |
| SGMatrix< float64_t > | m_transformation_matrix |
| int32_t | num_dim |
| int32_t | num_old_dim |
| SGVector< float64_t > | m_mean_vector |
| SGVector< float64_t > | m_eigenvalues_vector |
| bool | m_initialized |
| bool | m_whitening |
| EPCAMode | m_mode |
| float64_t | thresh |
| int32_t | m_target_dim |
| CDistance * | m_distance |
| CKernel * | m_kernel |
| CEmbeddingConverter * | m_converter |
| CPCA | ( | bool | do_whitening = false, |
| EPCAMode | mode = FIXED_NUMBER, |
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| float64_t | thresh = 1e-6 |
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apply preprocessor to feature matrix
| features | features |
Reimplemented from CDimensionReductionPreprocessor.
apply preprocessor to feature vector
| vector | feature vector |
Reimplemented from CDimensionReductionPreprocessor.
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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 1196 of file SGObject.cpp.
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virtual |
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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 1313 of file SGObject.cpp.
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virtualinherited |
A deep copy. All the instance variables will also be copied.
Definition at line 160 of file SGObject.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 1217 of file SGObject.cpp.
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inherited |
getter for distance
Definition at line 88 of file DimensionReductionPreprocessor.cpp.
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virtualinherited |
return that we are dense features (just fixed size matrices)
Implements CPreprocessor.
Reimplemented in CRandomFourierGaussPreproc.
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virtualinherited |
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inherited |
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inherited |
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inherited |
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inherited |
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inherited |
Definition at line 1100 of file SGObject.cpp.
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inherited |
Returns description of a given parameter string, if it exists. SG_ERROR otherwise
| param_name | name of the parameter |
Definition at line 1124 of file SGObject.cpp.
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inherited |
Returns index of model selection parameter with provided index
| param_name | name of model selection parameter |
Definition at line 1137 of file SGObject.cpp.
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virtual |
Reimplemented from CDimensionReductionPreprocessor.
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inherited |
getter for target dimension
Definition at line 76 of file DimensionReductionPreprocessor.cpp.
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virtual |
Reimplemented from CDimensionReductionPreprocessor.
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initialize preprocessor from features
| features |
Reimplemented from CDimensionReductionPreprocessor.
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protected |
default init
Reimplemented from CDimensionReductionPreprocessor.
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virtualinherited |
If the SGSerializable is a class template then TRUE will be returned and GENERIC is set to the type of the generic.
| generic | set to the type of the generic if returning TRUE |
Definition at line 268 of file SGObject.cpp.
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inherited |
maps all parameters of this instance to the provided file version and loads all parameter data from the file into an array, which is sorted (basically calls load_file_parameter(...) for all parameters and puts all results into a sorted array)
| file_version | parameter version of the file |
| current_version | version from which mapping begins (you want to use Version::get_version_parameter() for this in most cases) |
| file | file to load from |
| prefix | prefix for members |
Definition at line 673 of file SGObject.cpp.
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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 514 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 345 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 in CKernel, CWeightedDegreePositionStringKernel, CList, CAlphabet, CLinearHMM, CGaussianKernel, CInverseMultiQuadricKernel, CCircularKernel, and CExponentialKernel.
Definition at line 1029 of file SGObject.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 >, CDynamicArray< uint64_t >, and CDynamicObjectArray.
Definition at line 1024 of file SGObject.cpp.
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inherited |
Takes a set of TParameter instances (base) with a certain version and a set of target parameter infos and recursively maps the base level wise to the current version using CSGObject::migrate(...). The base is replaced. After this call, the base version containing parameters should be of same version/type as the initial target parameter infos. Note for this to work, the migrate methods and all the internal parameter mappings have to match
| param_base | set of TParameter instances that are mapped to the provided target parameter infos |
| base_version | version of the parameter base |
| target_param_infos | set of SGParamInfo instances that specify the target parameter base |
Definition at line 711 of file SGObject.cpp.
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protectedvirtualinherited |
creates a new TParameter instance, which contains migrated data from the version that is provided. The provided parameter data base is used for migration, this base is a collection of all parameter data of the previous version. Migration is done FROM the data in param_base TO the provided param info Migration is always one version step. Method has to be implemented in subclasses, if no match is found, base method has to be called.
If there is an element in the param_base which equals the target, a copy of the element is returned. This represents the case when nothing has changed and therefore, the migrate method is not overloaded in a subclass
| param_base | set of TParameter instances to use for migration |
| target | parameter info for the resulting TParameter |
Definition at line 918 of file SGObject.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 858 of file SGObject.cpp.
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inherited |
prints all parameter registered for model selection and their type
Definition at line 1076 of file SGObject.cpp.
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virtualinherited |
prints registered parameters out
| prefix | prefix for members |
Definition at line 280 of file SGObject.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 286 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 in CKernel.
Definition at line 1039 of file SGObject.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 in CKernel, CDynamicArray< T >, CDynamicArray< float64_t >, CDynamicArray< float32_t >, CDynamicArray< int32_t >, CDynamicArray< char >, CDynamicArray< bool >, CDynamicArray< uint64_t >, and CDynamicObjectArray.
Definition at line 1034 of file SGObject.cpp.
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setter for distance
| distance | distance to set |
Definition at line 81 of file DimensionReductionPreprocessor.cpp.
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inherited |
set generic type to T
Definition at line 41 of file SGObject.cpp.
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inherited |
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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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setter for kernel
| kernel | kernel to set |
Definition at line 94 of file DimensionReductionPreprocessor.cpp.
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inherited |
setter for target dimension
| dim | target dimension |
Definition at line 70 of file DimensionReductionPreprocessor.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 151 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 275 of file SGObject.cpp.
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virtualinherited |
Updates the hash of current parameter combination.
Definition at line 227 of file SGObject.cpp.
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inherited |
io
Definition at line 514 of file SGObject.h.
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protectedinherited |
embedding converter to be used
Definition at line 125 of file DimensionReductionPreprocessor.h.
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protectedinherited |
distance to be used
Definition at line 119 of file DimensionReductionPreprocessor.h.
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inherited |
parameters wrt which we can compute gradients
Definition at line 529 of file SGObject.h.
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inherited |
Hash of parameter values
Definition at line 535 of file SGObject.h.
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protectedinherited |
kernel to be used
Definition at line 122 of file DimensionReductionPreprocessor.h.
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inherited |
model selection parameters
Definition at line 526 of file SGObject.h.
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inherited |
map for different parameter versions
Definition at line 532 of file SGObject.h.
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inherited |
parameters
Definition at line 523 of file SGObject.h.
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protectedinherited |
target dim of dimensionality reduction preprocessor
Definition at line 116 of file DimensionReductionPreprocessor.h.
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inherited |
parallel
Definition at line 517 of file SGObject.h.
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version
Definition at line 520 of file SGObject.h.