SHOGUN
3.2.1
|
Preprocessor PCA performs principial component analysis on input feature vectors/matrices. When the init method in PCA is called with proper feature matrix X (with say N number of vectors and D feature dimension), a transformation matrix is computed and stored internally. This transformation matrix is then used to transform all D-dimensional feature vectors or feature matrices (with D feature dimensions) supplied via apply_to_feature_matrix or apply_to_feature_vector methods. This tranformation outputs the T-Dimensional approximation of all these input vectors and matrices (where T<=min(D,N)). The transformation matrix is essentially a DxT matrix, the columns of which correspond to the eigenvectors of the covariance matrix(XX') having top T eigenvalues.
This class provides 3 method options to compute the transformation matrix : EVD : Eigen Value Decomposition of Covariance Matrix ( \(XX^T\)) The covariance matrix \(XX^T\) is first formed internally and then its eigenvectors and eigenvalues are computed using QR decomposition of the matrix. The time complexity of this method is \(~10D^3\) and should be used when N > D.
SVD : Singular Value Decomposition of feature matrix X The transpose of feature matrix, \(X^T\), is decomposed using SVD. \(X^T = UDV^T\) The matrix V in this decomposition contains the required eigenvectors and the diagonal entries of the diagonal matrix D correspond to the non-negative eigenvalues. Eigenvalue, \(e_i\), is derived from a diagonal element, \(d_i\), using the formula \(e_i = \frac{\sqrt{d_i}}{N-1}\). The time complexity of this method is \(~14DN^2\) and should be used when N < D.
AUTO : This mode automagically chooses one of the above modes for the user based on whether N > D (chooses EVD) or N < D (chooses SVD).
This class provides 3 modes to determine the value of T :
FIXED_NUMBER : T is supplied by user directly using set_target_dims method
VARIANCE_EXPLAINED : The user supplies the fractional variance that he wants preserved in the target dimension T. From this supplied fractional variance (thresh), T is calculated as the smallest k such that the ratio of sum of largest k eigenvalues over total sum of all eigenvalues is greater than thresh.
THRESH : The user supplies a threshold. All eigenvectors with corresponding eigenvalue greater than the supplied threshold are chosen.
An option for whitening the transformation matrix is also given - do_whitening. Setting this option normalizes the eigenvectors (ie. the columns of transformation matrix) by dividing them with the square root of corresponding eigenvalues.
Note that vectors/matrices don't have to have zero mean as it is substracted within the class.
Public Member Functions | |
CPCA (bool do_whitening=false, EPCAMode mode=FIXED_NUMBER, float64_t thresh=1e-6, EPCAMethod method=AUTO, EPCAMemoryMode mem_mode=MEM_REALLOCATE) | |
CPCA (EPCAMethod method, bool do_whitening=false, EPCAMemoryMode mem=MEM_REALLOCATE) | |
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 |
EPCAMemoryMode | get_memory_mode () const |
void | set_memory_mode (EPCAMemoryMode e) |
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) More... | |
virtual EFeatureType | get_feature_type () |
return feature type More... | |
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 void | update_parameter_hash () |
virtual bool | parameter_hash_changed () |
virtual bool | equals (CSGObject *other, float64_t accuracy=0.0, bool tolerant=false) |
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 | m_thresh |
EPCAMemoryMode | m_mem_mode |
EPCAMethod | m_method |
int32_t | m_target_dim |
CDistance * | m_distance |
CKernel * | m_kernel |
CEmbeddingConverter * | m_converter |
CPCA | ( | bool | do_whitening = false , |
EPCAMode | mode = FIXED_NUMBER , |
||
float64_t | thresh = 1e-6 , |
||
EPCAMethod | method = AUTO , |
||
EPCAMemoryMode | mem_mode = MEM_REALLOCATE |
||
) |
standard constructor
do_whitening | normalize columns(eigenvectors) in transformation matrix |
mode | mode of pca : FIXED_NUMBER/VARIANCE_EXPLAINED/THRESHOLD |
thresh | threshold value for VARIANCE_EXPLAINED or THRESHOLD mode |
method | Matrix decomposition method used : SVD/EVD/AUTO[default] |
mem_mode | memory usage mode of PCA : MEM_REALLOCATE/MEM_IN_PLACE |
CPCA | ( | EPCAMethod | method, |
bool | do_whitening = false , |
||
EPCAMemoryMode | mem = MEM_REALLOCATE |
||
) |
apply preprocessor to feature matrix
features | features |
Reimplemented from CDimensionReductionPreprocessor.
apply preprocessor to feature vector
vector | feature vector |
Reimplemented from CDimensionReductionPreprocessor.
|
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 1174 of file SGObject.cpp.
|
virtual |
|
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 1291 of file SGObject.cpp.
|
virtualinherited |
A deep copy. All the instance variables will also be copied.
Definition at line 126 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) |
tolerant | allows linient check on float equality (within accuracy) |
Definition at line 1195 of file SGObject.cpp.
|
inherited |
getter for distance
Definition at line 88 of file DimensionReductionPreprocessor.cpp.
|
virtualinherited |
return that we are dense features (just fixed size matrices)
Implements CPreprocessor.
Reimplemented in CRandomFourierGaussPreproc.
|
virtualinherited |
|
inherited |
|
inherited |
|
inherited |
|
inherited |
EPCAMemoryMode get_memory_mode | ( | ) | const |
|
inherited |
Definition at line 1066 of file SGObject.cpp.
|
inherited |
Returns description of a given parameter string, if it exists. SG_ERROR otherwise
param_name | name of the parameter |
Definition at line 1090 of file SGObject.cpp.
|
inherited |
Returns index of model selection parameter with provided index
param_name | name of model selection parameter |
Definition at line 1103 of file SGObject.cpp.
|
virtual |
Reimplemented from CDimensionReductionPreprocessor.
|
inherited |
getter for target dimension
Definition at line 76 of file DimensionReductionPreprocessor.cpp.
|
virtual |
Reimplemented from CDimensionReductionPreprocessor.
|
virtual |
initialize preprocessor from features
features |
Reimplemented from CDimensionReductionPreprocessor.
|
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 234 of file SGObject.cpp.
|
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 639 of file SGObject.cpp.
|
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 480 of file SGObject.cpp.
|
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 311 of file SGObject.cpp.
|
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 CWeightedDegreePositionStringKernel, CKernel, CList, CAlphabet, CLinearHMM, CGaussianKernel, CInverseMultiQuadricKernel, CCircularKernel, and CExponentialKernel.
Definition at line 995 of file SGObject.cpp.
|
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 990 of file SGObject.cpp.
|
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 677 of file SGObject.cpp.
|
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 884 of file SGObject.cpp.
|
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 824 of file SGObject.cpp.
|
virtualinherited |
Definition at line 200 of file SGObject.cpp.
|
inherited |
prints all parameter registered for model selection and their type
Definition at line 1042 of file SGObject.cpp.
|
virtualinherited |
prints registered parameters out
prefix | prefix for members |
Definition at line 246 of file SGObject.cpp.
|
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 252 of file SGObject.cpp.
|
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 1005 of file SGObject.cpp.
|
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 >, and CDynamicObjectArray.
Definition at line 1000 of file SGObject.cpp.
|
inherited |
setter for distance
distance | distance to set |
Definition at line 81 of file DimensionReductionPreprocessor.cpp.
|
inherited |
Definition at line 41 of file SGObject.cpp.
|
inherited |
Definition at line 46 of file SGObject.cpp.
|
inherited |
Definition at line 51 of file SGObject.cpp.
|
inherited |
Definition at line 56 of file SGObject.cpp.
|
inherited |
Definition at line 61 of file SGObject.cpp.
|
inherited |
Definition at line 66 of file SGObject.cpp.
|
inherited |
Definition at line 71 of file SGObject.cpp.
|
inherited |
Definition at line 76 of file SGObject.cpp.
|
inherited |
Definition at line 81 of file SGObject.cpp.
|
inherited |
Definition at line 86 of file SGObject.cpp.
|
inherited |
Definition at line 91 of file SGObject.cpp.
|
inherited |
Definition at line 96 of file SGObject.cpp.
|
inherited |
Definition at line 101 of file SGObject.cpp.
|
inherited |
Definition at line 106 of file SGObject.cpp.
|
inherited |
Definition at line 111 of file SGObject.cpp.
|
inherited |
set generic type to T
|
inherited |
|
inherited |
set the parallel object
parallel | parallel object to use |
Definition at line 180 of file SGObject.cpp.
|
inherited |
set the version object
version | version object to use |
Definition at line 221 of file SGObject.cpp.
|
inherited |
setter for kernel
kernel | kernel to set |
Definition at line 94 of file DimensionReductionPreprocessor.cpp.
void set_memory_mode | ( | EPCAMemoryMode | e | ) |
|
inherited |
setter for target dimension
dim | target dimension |
Definition at line 70 of file DimensionReductionPreprocessor.cpp.
|
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.
|
inherited |
unset generic type
this has to be called in classes specializing a template class
Definition at line 241 of file SGObject.cpp.
|
virtualinherited |
Updates the hash of current parameter combination
Definition at line 187 of file SGObject.cpp.
|
inherited |
io
Definition at line 473 of file SGObject.h.
|
protectedinherited |
embedding converter to be used
Definition at line 125 of file DimensionReductionPreprocessor.h.
|
protectedinherited |
distance to be used
Definition at line 119 of file DimensionReductionPreprocessor.h.
|
inherited |
parameters wrt which we can compute gradients
Definition at line 488 of file SGObject.h.
|
inherited |
Hash of parameter values
Definition at line 494 of file SGObject.h.
|
protectedinherited |
kernel to be used
Definition at line 122 of file DimensionReductionPreprocessor.h.
|
protected |
|
protected |
|
inherited |
model selection parameters
Definition at line 485 of file SGObject.h.
|
inherited |
map for different parameter versions
Definition at line 491 of file SGObject.h.
|
inherited |
parameters
Definition at line 482 of file SGObject.h.
|
protectedinherited |
target dim of dimensionality reduction preprocessor
Definition at line 116 of file DimensionReductionPreprocessor.h.
|
inherited |
parallel
Definition at line 476 of file SGObject.h.
|
inherited |
version
Definition at line 479 of file SGObject.h.