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CPositionalPWM Class Reference

Detailed Description

Positional PWM.

Definition at line 22 of file PositionalPWM.h.

Inheritance diagram for CPositionalPWM:
Inheritance graph
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Public Member Functions

 CPositionalPWM ()
virtual ~CPositionalPWM ()
virtual bool train (CFeatures *data=NULL)
virtual int32_t get_num_model_parameters ()
virtual float64_t get_log_model_parameter (int32_t num_param)
virtual float64_t get_log_derivative (int32_t num_param, int32_t num_example)
virtual float64_t get_log_likelihood_example (int32_t num_example)
float64_t get_log_likelihood_window (uint8_t *window, int32_t len, float64_t pos)
virtual float64_t get_sigma ()
virtual void set_sigma (float64_t sigma)
virtual float64_t get_mean ()
virtual void set_mean (float64_t mean)
virtual void set_pwm (SGMatrix< float64_t > pwm)
virtual SGMatrix< float64_t > get_pwm () const
virtual SGMatrix< float64_t > get_w () const
virtual SGMatrix< float64_t > get_scoring (int32_t d)
void compute_w (int32_t num_pos)
void compute_scoring (int32_t max_degree)
virtual const char * get_name () const
virtual int32_t get_num_relevant_model_parameters ()
virtual float64_t get_log_likelihood_sample ()
virtual SGVector< float64_t > get_log_likelihood ()
virtual float64_t get_model_parameter (int32_t num_param)
virtual float64_t get_derivative (int32_t num_param, int32_t num_example)
virtual float64_t get_likelihood_example (int32_t num_example)
virtual void set_features (CFeatures *f)
virtual CFeatures * get_features ()
virtual void set_pseudo_count (float64_t pseudo)
virtual float64_t get_pseudo_count ()
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_PARAMETER)
virtual bool load_serializable (CSerializableFile *file, const char *prefix="", int32_t param_version=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_parameter_dictionary (CMap< TParameter *, CSGObject * > &dict)

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 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)
virtual bool update_parameter_hash ()

Protected Attributes

SGMatrix< float64_t > m_pwm
float64_t m_sigma
float64_t m_mean
SGMatrix< float64_t > m_w
SGVector< float64_t > m_poim
CFeatures * features
float64_t pseudo_count

Constructor & Destructor Documentation

CPositionalPWM ( )

default constructor

Definition at line 18 of file PositionalPWM.cpp.

~CPositionalPWM ( )
virtual

Definition at line 28 of file PositionalPWM.cpp.

Member Function Documentation

void build_parameter_dictionary ( CMap< TParameter *, CSGObject * > &  dict)
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.

Parameters
dictdictionary of parameters to be built.

Definition at line 1204 of file SGObject.cpp.

void compute_scoring ( int32_t  max_degree)

compute scoring

Parameters
max_degree

Definition at line 138 of file PositionalPWM.cpp.

void compute_w ( int32_t  num_pos)

compute w

Parameters
num_pos

Definition at line 99 of file PositionalPWM.cpp.

virtual CSGObject* deep_copy ( ) const
virtualinherited

A deep copy. All the instance variables will also be copied.

Definition at line 131 of file SGObject.h.

virtual float64_t get_derivative ( int32_t  num_param,
int32_t  num_example 
)
virtualinherited

get partial derivative of likelihood function

Parameters
num_parampartial derivative against which param
num_examplewhich example
Returns
derivative of likelihood function

Definition at line 129 of file Distribution.h.

virtual CFeatures* get_features ( )
virtualinherited

get feature vectors

Returns
feature vectors

Definition at line 160 of file Distribution.h.

SGIO * get_global_io ( )
inherited

get the io object

Returns
io object

Definition at line 224 of file SGObject.cpp.

Parallel * get_global_parallel ( )
inherited

get the parallel object

Returns
parallel object

Definition at line 259 of file SGObject.cpp.

Version * get_global_version ( )
inherited

get the version object

Returns
version object

Definition at line 272 of file SGObject.cpp.

virtual float64_t get_likelihood_example ( int32_t  num_example)
virtualinherited

compute likelihood for example

Parameters
num_examplewhich example
Returns
likelihood for example

Reimplemented in CGMM.

Definition at line 140 of file Distribution.h.

float64_t get_log_derivative ( int32_t  num_param,
int32_t  num_example 
)
virtual

get partial derivative of likelihood function (logarithmic)

Parameters
num_paramderivative against which param
num_examplewhich example
Returns
derivative of likelihood (logarithmic)

Implements CDistribution.

Definition at line 57 of file PositionalPWM.cpp.

SGVector< float64_t > get_log_likelihood ( )
virtualinherited

compute log likelihood for each example

Returns
log likelihood vector

Definition at line 37 of file Distribution.cpp.

float64_t get_log_likelihood_example ( int32_t  num_example)
virtual

compute log likelihood for example

abstract base method

Parameters
num_examplewhich example
Returns
log likelihood for example

Implements CDistribution.

Definition at line 63 of file PositionalPWM.cpp.

float64_t get_log_likelihood_sample ( )
virtualinherited

compute log likelihood for whole sample

Returns
log likelihood for whole sample

Definition at line 26 of file Distribution.cpp.

float64_t get_log_likelihood_window ( uint8_t *  window,
int32_t  len,
float64_t  pos 
)

get log likelihood window

Parameters
window
len
pos

Definition at line 87 of file PositionalPWM.cpp.

float64_t get_log_model_parameter ( int32_t  num_param)
virtual

get model parameter (logarithmic)

Returns
model parameter (logarithmic) if num_param < m_dim returns an element from the mean, else return an element from the covariance

Implements CDistribution.

Definition at line 43 of file PositionalPWM.cpp.

virtual float64_t get_mean ( )
virtual

get mean

Definition at line 94 of file PositionalPWM.h.

virtual float64_t get_model_parameter ( int32_t  num_param)
virtualinherited

get model parameter

Parameters
num_paramwhich param
Returns
model parameter

Definition at line 118 of file Distribution.h.

SGStringList< char > get_modelsel_names ( )
inherited
Returns
vector of names of all parameters which are registered for model selection

Definition at line 1108 of file SGObject.cpp.

char * get_modsel_param_descr ( const char *  param_name)
inherited

Returns description of a given parameter string, if it exists. SG_ERROR otherwise

Parameters
param_namename of the parameter
Returns
description of the parameter

Definition at line 1132 of file SGObject.cpp.

index_t get_modsel_param_index ( const char *  param_name)
inherited

Returns index of model selection parameter with provided index

Parameters
param_namename of model selection parameter
Returns
index of model selection parameter with provided name, -1 if there is no such

Definition at line 1145 of file SGObject.cpp.

virtual const char* get_name ( ) const
virtual
Returns
object name

Implements CSGObject.

Definition at line 154 of file PositionalPWM.h.

int32_t get_num_model_parameters ( )
virtual

get number of parameters in model

Returns
number of parameters in model

Implements CDistribution.

Definition at line 38 of file PositionalPWM.cpp.

int32_t get_num_relevant_model_parameters ( )
virtualinherited

get number of parameters in model that are relevant, i.e. > ALMOST_NEG_INFTY

Returns
number of relevant model parameters

Definition at line 50 of file Distribution.cpp.

virtual float64_t get_pseudo_count ( )
virtualinherited

get pseudo count

Returns
pseudo count

Definition at line 176 of file Distribution.h.

virtual SGMatrix<float64_t> get_pwm ( ) const
virtual

get pwm

Returns
current pwm

Definition at line 121 of file PositionalPWM.h.

SGMatrix< float64_t > get_scoring ( int32_t  d)
virtual

get poim u

Parameters
ddegree for which poim should be obtained
Returns
poim u

Definition at line 218 of file PositionalPWM.cpp.

virtual float64_t get_sigma ( )
virtual

get sigma

Definition at line 78 of file PositionalPWM.h.

virtual SGMatrix<float64_t> get_w ( ) const
virtual

get w

Returns
current w

Definition at line 130 of file PositionalPWM.h.

bool is_generic ( EPrimitiveType *  generic) const
virtualinherited

If the SGSerializable is a class template then TRUE will be returned and GENERIC is set to the type of the generic.

Parameters
genericset to the type of the generic if returning TRUE
Returns
TRUE if a class template.

Definition at line 278 of file SGObject.cpp.

DynArray< TParameter * > * load_all_file_parameters ( int32_t  file_version,
int32_t  current_version,
CSerializableFile *  file,
const char *  prefix = "" 
)
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)

Parameters
file_versionparameter version of the file
current_versionversion from which mapping begins (you want to use VERSION_PARAMETER for this in most cases)
filefile to load from
prefixprefix for members
Returns
(sorted) array of created TParameter instances with file data

Definition at line 679 of file SGObject.cpp.

DynArray< TParameter * > * load_file_parameters ( const SGParamInfo *  param_info,
int32_t  file_version,
CSerializableFile *  file,
const char *  prefix = "" 
)
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

Parameters
param_infoinformation of parameter
file_versionparameter version of the file, must be <= provided parameter version
filefile to load from
prefixprefix for members
Returns
new array with TParameter instances with the attached data

Definition at line 523 of file SGObject.cpp.

bool load_serializable ( CSerializableFile *  file,
const char *  prefix = "",
int32_t  param_version = VERSION_PARAMETER 
)
virtualinherited

Load this object from file. If it will fail (returning FALSE) then this object will contain inconsistent data and should not be used!

Parameters
filewhere to load from
prefixprefix for members
param_version(optional) a parameter version different to (this is mainly for testing, better do not use)
Returns
TRUE if done, otherwise FALSE

Reimplemented in CModelSelectionParameters.

Definition at line 354 of file SGObject.cpp.

void load_serializable_post ( ) throw (ShogunException)
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.

Exceptions
ShogunExceptionWill be thrown if an error occurres.

Reimplemented in CKernel, CWeightedDegreePositionStringKernel, CList, CAlphabet, CLinearHMM, CGaussianKernel, CANOVAKernel, CInverseMultiQuadricKernel, CCircularKernel, and CExponentialKernel.

Definition at line 1033 of file SGObject.cpp.

void load_serializable_pre ( ) throw (ShogunException)
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.

Exceptions
ShogunExceptionWill be thrown if an error occurres.

Definition at line 1028 of file SGObject.cpp.

void map_parameters ( DynArray< TParameter * > *  param_base,
int32_t &  base_version,
DynArray< const SGParamInfo * > *  target_param_infos 
)
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

Parameters
param_baseset of TParameter instances that are mapped to the provided target parameter infos
base_versionversion of the parameter base
target_param_infosset of SGParamInfo instances that specify the target parameter base

Definition at line 717 of file SGObject.cpp.

TParameter * migrate ( DynArray< TParameter * > *  param_base,
const SGParamInfo *  target 
)
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

Parameters
param_baseset of TParameter instances to use for migration
targetparameter info for the resulting TParameter
Returns
a new TParameter instance with migrated data from the base of the type which is specified by the target parameter

Definition at line 923 of file SGObject.cpp.

void one_to_one_migration_prepare ( DynArray< TParameter * > *  param_base,
const SGParamInfo *  target,
TParameter *&  replacement,
TParameter *&  to_migrate,
char *  old_name = NULL 
)
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)

Parameters
param_baseset of TParameter instances to use for migration
targetparameter info for the resulting TParameter
replacement(used as output) here the TParameter instance which is returned by migration is created into
to_migratethe only source that is used for migration
old_namewith this parameter, a name change may be specified

Definition at line 864 of file SGObject.cpp.

void print_modsel_params ( )
inherited

prints all parameter registered for model selection and their type

Definition at line 1084 of file SGObject.cpp.

void print_serializable ( const char *  prefix = "")
virtualinherited

prints registered parameters out

Parameters
prefixprefix for members

Definition at line 290 of file SGObject.cpp.

bool save_serializable ( CSerializableFile *  file,
const char *  prefix = "",
int32_t  param_version = VERSION_PARAMETER 
)
virtualinherited

Save this object to file.

Parameters
filewhere to save the object; will be closed during returning if PREFIX is an empty string.
prefixprefix for members
param_version(optional) a parameter version different to (this is mainly for testing, better do not use)
Returns
TRUE if done, otherwise FALSE

Reimplemented in CModelSelectionParameters.

Definition at line 296 of file SGObject.cpp.

void save_serializable_post ( ) throw (ShogunException)
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.

Exceptions
ShogunExceptionWill be thrown if an error occurres.

Reimplemented in CKernel.

Definition at line 1043 of file SGObject.cpp.

void save_serializable_pre ( ) throw (ShogunException)
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.

Exceptions
ShogunExceptionWill be thrown if an error occurres.

Reimplemented in CKernel.

Definition at line 1038 of file SGObject.cpp.

virtual void set_features ( CFeatures *  f)
virtualinherited

set feature vectors

Parameters
fnew feature vectors

Definition at line 149 of file Distribution.h.

void set_generic< floatmax_t > ( )
inherited

set generic type to T

Definition at line 41 of file SGObject.cpp.

void set_global_io ( SGIO *  io)
inherited

set the io object

Parameters
ioio object to use

Definition at line 217 of file SGObject.cpp.

void set_global_parallel ( Parallel *  parallel)
inherited

set the parallel object

Parameters
parallelparallel object to use

Definition at line 230 of file SGObject.cpp.

void set_global_version ( Version *  version)
inherited

set the version object

Parameters
versionversion object to use

Definition at line 265 of file SGObject.cpp.

virtual void set_mean ( float64_t  mean)
virtual

set mean

Parameters
meannew mean

Definition at line 103 of file PositionalPWM.h.

virtual void set_pseudo_count ( float64_t  pseudo)
virtualinherited

set pseudo count

Parameters
pseudonew pseudo count

Definition at line 170 of file Distribution.h.

virtual void set_pwm ( SGMatrix< float64_t >  pwm)
virtual

set pwm

Parameters
pwmnew pwm (values must be in logspace)

Definition at line 112 of file PositionalPWM.h.

virtual void set_sigma ( float64_t  sigma)
virtual

set sigma

Parameters
sigmanew sigma

Definition at line 87 of file PositionalPWM.h.

virtual CSGObject* shallow_copy ( ) const
virtualinherited

A shallow copy. All the SGObject instance variables will be simply assigned and SG_REF-ed.

Reimplemented in CGaussianKernel.

Definition at line 122 of file SGObject.h.

bool train ( CFeatures *  data = NULL)
virtual

learn distribution

Parameters
datatraining data
Returns
whether training was successful

Implements CDistribution.

Definition at line 32 of file PositionalPWM.cpp.

void unset_generic ( )
inherited

unset generic type

this has to be called in classes specializing a template class

Definition at line 285 of file SGObject.cpp.

bool update_parameter_hash ( )
protectedvirtualinherited

Updates the hash of current parameter combination.

Returns
bool if parameter combination has changed since last update.

Definition at line 237 of file SGObject.cpp.

Member Data Documentation

CFeatures* features
protectedinherited

feature vectors

Definition at line 180 of file Distribution.h.

SGIO* io
inherited

io

Definition at line 462 of file SGObject.h.

uint32_t m_hash
inherited

Hash of parameter values

Definition at line 480 of file SGObject.h.

float64_t m_mean
protected

mean

Definition at line 169 of file PositionalPWM.h.

Parameter* m_model_selection_parameters
inherited

model selection parameters

Definition at line 474 of file SGObject.h.

ParameterMap* m_parameter_map
inherited

map for different parameter versions

Definition at line 477 of file SGObject.h.

Parameter* m_parameters
inherited

parameters

Definition at line 471 of file SGObject.h.

SGVector<float64_t> m_poim
protected

poim

Definition at line 175 of file PositionalPWM.h.

SGMatrix<float64_t> m_pwm
protected

pwm

Definition at line 163 of file PositionalPWM.h.

float64_t m_sigma
protected

sigma

Definition at line 166 of file PositionalPWM.h.

SGMatrix<float64_t> m_w
protected

w

Definition at line 172 of file PositionalPWM.h.

Parallel* parallel
inherited

parallel

Definition at line 465 of file SGObject.h.

float64_t pseudo_count
protectedinherited

pseudo count

Definition at line 182 of file Distribution.h.

Version* version
inherited

version

Definition at line 468 of file SGObject.h.

The documentation for this class was generated from the following files:
SHOGUN Machine Learning Toolbox - Documentation