Detailed Description

Positional PWM.

Definition at line 22 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 ()
virtual SGMatrix< float64_t >	get_w ()
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
Public Member Functions inherited from CDistribution
	CDistribution ()
virtual	~CDistribution ()
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 ()
Public Member Functions inherited from CSGObject
	CSGObject ()
	CSGObject (const CSGObject &orig)
virtual	~CSGObject ()
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="")
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 ()
SGVector< char * >	get_modelsel_names ()
char *	get_modsel_param_descr (const char *param_name)
index_t	get_modsel_param_index (const char *param_name)

Protected Attributes
int32_t	m_pwm_rows
int32_t	m_pwm_cols
float64_t *	m_pwm
float64_t	m_sigma
float64_t	m_mean
int32_t	m_w_rows
int32_t	m_w_cols
float64_t *	m_w
int32_t	m_poim_len
float64_t *	m_poim
Protected Attributes inherited from CDistribution
CFeatures *	features
float64_t	pseudo_count

Additional Inherited Members
Public Attributes inherited from CSGObject
SGIO *	io
Parallel *	parallel
Version *	version
Parameter *	m_parameters
Parameter *	m_model_selection_parameters
Protected Member Functions inherited from CSGObject
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)

Constructor & Destructor Documentation

CPositionalPWM ( )

default constructor

Definition at line 18 of file PositionalPWM.cpp.

~CPositionalPWM ( )

virtual

Definition at line 27 of file PositionalPWM.cpp.

Member Function Documentation

void compute_scoring ( int32_t max_degree )

compute scoring

Parameters

max_degree

Definition at line 141 of file PositionalPWM.cpp.

void compute_w ( int32_t num_pos )

compute w

Parameters

num_pos

Definition at line 101 of file PositionalPWM.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 59 of file PositionalPWM.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 65 of file PositionalPWM.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 89 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 44 of file PositionalPWM.cpp.

virtual float64_t get_mean ( )

virtual

get mean

Definition at line 94 of file PositionalPWM.h.

virtual const char* get_name ( ) const

virtual

Returns: object name

Implements CSGObject.

Definition at line 156 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 39 of file PositionalPWM.cpp.

virtual SGMatrix<float64_t> get_pwm ( )

virtual

get pwm

Returns: current pwm

Definition at line 123 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 225 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 ( )

virtual

get w

Returns: current w

Definition at line 132 of file PositionalPWM.h.

virtual void set_mean ( float64_t mean )

virtual

set mean

Parameters

mean new mean

Definition at line 103 of file PositionalPWM.h.

virtual void set_pwm ( SGMatrix< float64_t > pwm )

virtual

set pwm

Parameters

pwm	new 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

sigma new sigma

Definition at line 87 of file PositionalPWM.h.

bool train ( CFeatures * data = NULL )

virtual

learn distribution

Parameters

data	training data

Returns: whether training was successful

Implements CDistribution.

Definition at line 33 of file PositionalPWM.cpp.

Member Data Documentation

float64_t m_mean

protected

mean

Definition at line 177 of file PositionalPWM.h.

float64_t* m_poim

protected

poim

Definition at line 192 of file PositionalPWM.h.

int32_t m_poim_len

protected

POIM len

Definition at line 189 of file PositionalPWM.h.

float64_t* m_pwm

protected

pwm

Definition at line 171 of file PositionalPWM.h.

int32_t m_pwm_cols

protected

pwm cols

Definition at line 168 of file PositionalPWM.h.

int32_t m_pwm_rows

protected

pwm rows

Definition at line 165 of file PositionalPWM.h.

float64_t m_sigma

protected

sigma

Definition at line 174 of file PositionalPWM.h.

float64_t* m_w

protected

w

Definition at line 186 of file PositionalPWM.h.

int32_t m_w_cols

protected

w cols

Definition at line 183 of file PositionalPWM.h.

int32_t m_w_rows

protected

w rows

Definition at line 180 of file PositionalPWM.h.

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

Detailed Description

Public Member Functions

Protected Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation