Detailed Description

Positional PWM.

Definition at line 27 of file PositionalPWM.h.

Inheritance diagram for CPositionalPWM:

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 SGVector< float64_t >	get_likelihood_for_all_examples ()

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 float64_t	update_params_em (float64_t *alpha_k, int32_t len)

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="")

virtual bool	load_serializable (CSerializableFile file, const char prefix="")

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 ()

Static Public Member Functions
static CDistribution *	obtain_from_generic (CSGObject *object)

Public Attributes
SGIO *	io

Parallel *	parallel

Version *	version

Parameter *	m_parameters

Parameter *	m_model_selection_parameters

Parameter *	m_gradient_parameters

uint32_t	m_hash

Protected Member Functions
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_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_gradient_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

dict	dictionary of parameters to be built.

Definition at line 597 of file SGObject.cpp.

CSGObject * clone ( )

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.

Returns: an identical copy of the given object, which is disjoint in memory. NULL if the clone fails. Note that the returned object is SG_REF'ed

Definition at line 714 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.

CSGObject * deep_copy ( ) const

virtualinherited

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

Definition at line 198 of file SGObject.cpp.

bool equals	(	CSGObject *	other,
		float64_t	accuracy = `0.0`,
		bool	tolerant = `false`
	)

virtualinherited

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.

Parameters

other	object to compare with
accuracy	accuracy to use for comparison (optional)
tolerant	allows linient check on float equality (within accuracy)

Returns: true if all parameters were equal, false if not

Definition at line 618 of file SGObject.cpp.

virtual float64_t get_derivative	(	int32_t	num_param,
		int32_t	num_example
	)

virtualinherited

get partial derivative of likelihood function

Parameters

num_param	partial derivative against which param
num_example	which example

Returns: derivative of likelihood function

Definition at line 134 of file Distribution.h.

virtual CFeatures* get_features ( )

virtualinherited

get feature vectors

Returns: feature vectors

Definition at line 171 of file Distribution.h.

SGIO * get_global_io ( )

inherited

get the io object

Returns: io object

Definition at line 235 of file SGObject.cpp.

Parallel * get_global_parallel ( )

inherited

get the parallel object

Returns: parallel object

Definition at line 277 of file SGObject.cpp.

Version * get_global_version ( )

inherited

get the version object

Returns: version object

Definition at line 290 of file SGObject.cpp.

virtual float64_t get_likelihood_example ( int32_t num_example )

virtualinherited

compute likelihood for example

Parameters

num_example which example

Returns: likelihood for example

Reimplemented in CGMM, and CLinearHMM.

Definition at line 145 of file Distribution.h.

SGVector< float64_t > get_likelihood_for_all_examples ( )

virtualinherited

compute likelihood for all vectors in sample

Returns: likelihood vector for all examples

Definition at line 65 of file Distribution.cpp.

float64_t get_log_derivative	(	int32_t	num_param,
		int32_t	num_example
	)

virtual

get partial derivative of likelihood function (logarithmic)

Parameters

num_param	derivative against which param
num_example	which 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 39 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_example which 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 28 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 99 of file PositionalPWM.h.

virtual float64_t get_model_parameter ( int32_t num_param )

virtualinherited

get model parameter

Parameters

num_param which param

Returns: model parameter

Definition at line 123 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 498 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_name name of the parameter

Returns: description of the parameter

Definition at line 522 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_name name of model selection parameter

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

Definition at line 535 of file SGObject.cpp.

virtual const char* get_name ( ) const

virtual

Returns: object name

Implements CSGObject.

Definition at line 159 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 52 of file Distribution.cpp.

virtual float64_t get_pseudo_count ( )

virtualinherited

get pseudo count

Returns: pseudo count

Definition at line 187 of file Distribution.h.

virtual SGMatrix<float64_t> get_pwm ( ) const

virtual

get pwm

Returns: current pwm

Definition at line 126 of file PositionalPWM.h.

SGMatrix< float64_t > get_scoring ( int32_t d )

virtual

get poim u

Parameters

d	degree 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 83 of file PositionalPWM.h.

virtual SGMatrix<float64_t> get_w ( ) const

virtual

get w

Returns: current w

Definition at line 135 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

generic set to the type of the generic if returning TRUE

Returns: TRUE if a class template.

Definition at line 296 of file SGObject.cpp.

bool load_serializable	(	CSerializableFile *	file,
		const char *	prefix = `""`
	)

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

file	where to load from
prefix	prefix for members

Returns: TRUE if done, otherwise FALSE

Definition at line 369 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

ShogunException will be thrown if an error occurs.

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

Definition at line 426 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

ShogunException will be thrown if an error occurs.

Reimplemented in CDynamicArray< T >, CDynamicArray< float64_t >, CDynamicArray< float32_t >, CDynamicArray< int32_t >, CDynamicArray< char >, CDynamicArray< bool >, and CDynamicObjectArray.

Definition at line 421 of file SGObject.cpp.

CDistribution * obtain_from_generic ( CSGObject * object )

staticinherited

obtain from generic

Parameters

object generic object

Returns: Distribution object

Definition at line 85 of file Distribution.cpp.

bool parameter_hash_changed ( )

virtualinherited

Returns: whether parameter combination has changed since last update

Definition at line 262 of file SGObject.cpp.

void print_modsel_params ( )

inherited

prints all parameter registered for model selection and their type

Definition at line 474 of file SGObject.cpp.

void print_serializable ( const char * prefix = "" )

virtualinherited

prints registered parameters out

Parameters

prefix prefix for members

Definition at line 308 of file SGObject.cpp.

bool save_serializable	(	CSerializableFile *	file,
		const char *	prefix = `""`
	)

virtualinherited

Save this object to file.

Parameters

file	where to save the object; will be closed during returning if PREFIX is an empty string.
prefix	prefix for members

Returns: TRUE if done, otherwise FALSE

Definition at line 314 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

ShogunException will be thrown if an error occurs.

Reimplemented in CKernel.

Definition at line 436 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

ShogunException will be thrown if an error occurs.

Reimplemented in CKernel, CDynamicArray< T >, CDynamicArray< float64_t >, CDynamicArray< float32_t >, CDynamicArray< int32_t >, CDynamicArray< char >, CDynamicArray< bool >, and CDynamicObjectArray.

Definition at line 431 of file SGObject.cpp.

virtual void set_features ( CFeatures * f )

virtualinherited

set feature vectors

Parameters

f	new feature vectors

Definition at line 160 of file Distribution.h.

void set_generic ( )

inherited

Definition at line 41 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 46 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 51 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 56 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 61 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 66 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 71 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 76 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 81 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 86 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 91 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 96 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 101 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 106 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 111 of file SGObject.cpp.

void set_generic ( )

inherited

set generic type to T

void set_global_io ( SGIO * io )

inherited

set the io object

Parameters

io	io object to use

Definition at line 228 of file SGObject.cpp.

void set_global_parallel ( Parallel * parallel )

inherited

set the parallel object

Parameters

parallel parallel object to use

Definition at line 241 of file SGObject.cpp.

void set_global_version ( Version * version )

inherited

set the version object

Parameters

version version object to use

Definition at line 283 of file SGObject.cpp.

virtual void set_mean ( float64_t mean )

virtual

set mean

Parameters

mean new mean

Definition at line 108 of file PositionalPWM.h.

virtual void set_pseudo_count ( float64_t pseudo )

virtualinherited

set pseudo count

Parameters

pseudo new pseudo count

Definition at line 181 of file Distribution.h.

virtual void set_pwm ( SGMatrix< float64_t > pwm )

virtual

set pwm

Parameters

pwm	new pwm (values must be in logspace)

Definition at line 117 of file PositionalPWM.h.

virtual void set_sigma ( float64_t sigma )

virtual

set sigma

Parameters

sigma new sigma

Definition at line 92 of file PositionalPWM.h.

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 192 of file SGObject.cpp.

bool train ( CFeatures * data = NULL )

virtual

learn distribution

Parameters

data	training 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 303 of file SGObject.cpp.

void update_parameter_hash ( )

virtualinherited

Updates the hash of current parameter combination

Definition at line 248 of file SGObject.cpp.

float64_t update_params_em	(	float64_t *	alpha_k,
		int32_t	len
	)

virtualinherited

update parameters in the em maximization step for mixture model of which this distribution is a part

abstract base method

Parameters

alpha_k	"belongingness" values of various data points
len	length of alpha_k array

Returns: sum of alpha_k values

Reimplemented in CGaussian.

Definition at line 78 of file Distribution.cpp.

Member Data Documentation

CFeatures* features

protectedinherited

feature vectors

Definition at line 209 of file Distribution.h.

SGIO* io

inherited

io

Definition at line 369 of file SGObject.h.

Parameter* m_gradient_parameters

inherited

parameters wrt which we can compute gradients

Definition at line 384 of file SGObject.h.

uint32_t m_hash

inherited

Hash of parameter values

Definition at line 387 of file SGObject.h.

float64_t m_mean

protected

mean

Definition at line 174 of file PositionalPWM.h.

Parameter* m_model_selection_parameters

inherited

model selection parameters

Definition at line 381 of file SGObject.h.

Parameter* m_parameters

inherited

parameters

Definition at line 378 of file SGObject.h.

SGVector<float64_t> m_poim

protected

poim

Definition at line 180 of file PositionalPWM.h.

SGMatrix<float64_t> m_pwm

protected

pwm

Definition at line 168 of file PositionalPWM.h.

float64_t m_sigma

protected

sigma

Definition at line 171 of file PositionalPWM.h.

SGMatrix<float64_t> m_w

protected

w

Definition at line 177 of file PositionalPWM.h.

Parallel* parallel

inherited

parallel

Definition at line 372 of file SGObject.h.

float64_t pseudo_count

protectedinherited

pseudo count

Definition at line 211 of file Distribution.h.

Version* version

inherited

version

Definition at line 375 of file SGObject.h.

The documentation for this class was generated from the following files:

Detailed Description

Public Member Functions

Static Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation