CGUIHMM Class Reference

Detailed Description

UI HMM (Hidden Markov Model)

Definition at line 26 of file GUIHMM.h.

Inheritance diagram for CGUIHMM:

Public Member Functions
	CGUIHMM ()
	CGUIHMM (CSGInterface *interface)
	~CGUIHMM ()
bool	new_hmm (int32_t n, int32_t m)
bool	load (char *filename)
bool	save (char *filename, bool is_binary=false)
bool	set_num_hmm_tables (char *param)
bool	baum_welch_train ()
bool	baum_welch_trans_train ()
bool	baum_welch_train_defined ()
bool	viterbi_train_defined ()
bool	viterbi_train ()
bool	linear_train (char align='l')
bool	linear_train_from_file (char *param)
bool	append_model (char *filename, int32_t base1=-1, int32_t base2=-1)
bool	add_states (int32_t num_states=1, float64_t value=0)
bool	set_hmm_as (char *target)
bool	set_pseudo (float64_t pseudo)
bool	convergence_criteria (int32_t num_iterations=100, float64_t epsilon=0.001)
bool	output_hmm ()
bool	output_hmm_defined ()
bool	best_path (int32_t from=0, int32_t to=100)
bool	normalize (bool keep_dead_states=false)
bool	save_path (char *filename, bool is_binary=false)
bool	save_likelihood (char *filename, bool is_binary=false)
bool	load_definitions (char *filename, bool do_init=false)
bool	set_max_dim (char *param)
bool	likelihood ()
bool	chop (float64_t value)
bool	relative_entropy (float64_t *&values, int32_t &len)
bool	entropy (float64_t *&values, int32_t &len)
bool	permutation_entropy (int32_t width=0, int32_t seq_num=-1)
CHMM *	get_pos ()
CHMM *	get_neg ()
CHMM *	get_test ()
void	set_current (CHMM *h)
CHMM *	get_current ()
float64_t	get_pseudo ()
CRegressionLabels *	classify (CRegressionLabels *output=NULL)
float64_t	classify_example (int32_t idx)
CRegressionLabels *	one_class_classify (CRegressionLabels *output=NULL)
CRegressionLabels *	linear_one_class_classify (CRegressionLabels *output=NULL)
float64_t	one_class_classify_example (int32_t idx)
virtual const char *	get_name () const
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)
bool	has (const std::string &name) const
template<typename T >
bool	has (const Tag< T > &tag) const
template<typename T , typename U = void>
bool	has (const std::string &name) const
template<typename T >
void	set (const Tag< T > &_tag, const T &value)
template<typename T , typename U = void>
void	set (const std::string &name, const T &value)
template<typename T >
T	get (const Tag< T > &_tag) const
template<typename T , typename U = void>
T	get (const std::string &name) const
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
uint32_t	m_hash

Protected Member Functions
bool	converge (float64_t x, float64_t y)
void	switch_model (CHMM **m1, CHMM **m2)
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)
template<typename T >
void	register_param (Tag< T > &_tag, const T &value)
template<typename T >
void	register_param (const std::string &name, const T &value)

Protected Attributes
CHMM *	working
CHMM *	pos
CHMM *	neg
CHMM *	test
float64_t	PSEUDO
int32_t	M
CSGInterface *	ui

Constructor & Destructor Documentation

CGUIHMM

(

)

constructor

Definition at line 30 of file GUIHMM.h.

CGUIHMM

(

CSGInterface *

interface

)

constructor

Parameters

interface

Definition at line 26 of file GUIHMM.cpp.

~CGUIHMM

(

)

destructor

Definition at line 39 of file GUIHMM.cpp.

Member Function Documentation

bool add_states	(	int32_t	num_states = 1,
		float64_t	value = 0
	)

add states to HMM

Definition at line 308 of file GUIHMM.cpp.

bool append_model	(	char *	filename,
		int32_t	base1 = -1,
		int32_t	base2 = -1
	)

append HMM/model for CmdlineInterface

Definition at line 254 of file GUIHMM.cpp.

bool baum_welch_train

(

)

train Baum-Welch

Definition at line 52 of file GUIHMM.cpp.

bool baum_welch_train_defined

(

)

train Baum-Welch defined

Definition at line 91 of file GUIHMM.cpp.

bool baum_welch_trans_train

(

)

train Baum-Welch trans

Definition at line 73 of file GUIHMM.cpp.

bool best_path	(	int32_t	from = 0,
		int32_t	to = 100
	)

print best path

Definition at line 535 of file GUIHMM.cpp.

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 630 of file SGObject.cpp.

bool chop

(

float64_t

value

)

chop HMM

Definition at line 499 of file GUIHMM.cpp.

CRegressionLabels * classify

(

CRegressionLabels *

output = NULL

)

classify

Parameters

output

Definition at line 149 of file GUIHMM.cpp.

float64_t classify_example

(

int32_t

idx

)

classify example

Parameters

idx

Definition at line 173 of file GUIHMM.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 747 of file SGObject.cpp.

bool converge ( float64_t  x, float64_t  y  )

protected

converge

Parameters

x
y

bool convergence_criteria	(	int32_t	num_iterations = 100,
		float64_t	epsilon = 0.001
	)

set convergence criteria

Definition at line 325 of file GUIHMM.cpp.

CSGObject * deep_copy ( ) const

virtualinherited

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

Definition at line 231 of file SGObject.cpp.

bool entropy	(	float64_t *&	values,
		int32_t &	len
	)

entropy

Parameters

values
len

Definition at line 599 of file GUIHMM.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 651 of file SGObject.cpp.

T get ( const Tag< T > &  _tag ) const

inherited

Getter for a class parameter, identified by a Tag. Throws an exception if the class does not have such a parameter.

Parameters

_tag	name and type information of parameter

Returns

value of the parameter identified by the input tag

Definition at line 367 of file SGObject.h.

T get ( const std::string &  name ) const

inherited

Getter for a class parameter, identified by a name. Throws an exception if the class does not have such a parameter.

Parameters

name	name of the parameter

Returns

value of the parameter corresponding to the input name and type

Definition at line 388 of file SGObject.h.

CHMM* get_current

(

)

get current

Definition at line 131 of file GUIHMM.h.

SGIO * get_global_io ( )

inherited

get the io object

Returns

io object

Definition at line 268 of file SGObject.cpp.

Parallel * get_global_parallel ( )

inherited

get the parallel object

Returns

parallel object

Definition at line 310 of file SGObject.cpp.

Version * get_global_version ( )

inherited

get the version object

Returns

version object

Definition at line 323 of file SGObject.cpp.

SGStringList< char > get_modelsel_names ( )

inherited

Returns

vector of names of all parameters which are registered for model selection

Definition at line 531 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 555 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 568 of file SGObject.cpp.

virtual const char* get_name ( ) const

virtual

Returns

object name

Implements CSGObject.

Definition at line 157 of file GUIHMM.h.

CHMM* get_neg

(

)

get neg

Definition at line 123 of file GUIHMM.h.

CHMM* get_pos

(

)

get pos

Definition at line 121 of file GUIHMM.h.

float64_t get_pseudo

(

)

get pseudo

Definition at line 133 of file GUIHMM.h.

CHMM* get_test

(

)

get test

Definition at line 125 of file GUIHMM.h.

bool has ( const std::string &  name ) const

inherited

Checks if object has a class parameter identified by a name.

Parameters

name	name of the parameter

Returns

true if the parameter exists with the input name

Definition at line 289 of file SGObject.h.

bool has ( const Tag< T > &  tag ) const

inherited

Checks if object has a class parameter identified by a Tag.

Parameters

tag	tag of the parameter containing name and type information

Returns

true if the parameter exists with the input tag

Definition at line 301 of file SGObject.h.

bool has ( const std::string &  name ) const

inherited

Checks if a type exists for a class parameter identified by a name.

Parameters

name	name of the parameter

Returns

true if the parameter exists with the input name and type

Definition at line 312 of file SGObject.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 329 of file SGObject.cpp.

bool likelihood

(

)

HMM likelihood

Definition at line 508 of file GUIHMM.cpp.

CRegressionLabels * linear_one_class_classify

(

CRegressionLabels *

output = NULL

)

linear one class classify

Parameters

output

Definition at line 213 of file GUIHMM.cpp.

bool linear_train

(

char

align = 'l'

)

linear train

Parameters

align

Definition at line 121 of file GUIHMM.cpp.

bool linear_train_from_file

(

char *

param

)

linear train from file

Parameters

param

bool load

(

char *

filename

)

load HMM from file

Definition at line 366 of file GUIHMM.cpp.

bool load_definitions	(	char *	filename,
		bool	do_init = false
	)

load definitions

Parameters

filename
do_init

Definition at line 416 of file GUIHMM.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 402 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 459 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 454 of file SGObject.cpp.

bool new_hmm	(	int32_t	n,
		int32_t	m
	)

create new HMM

Definition at line 44 of file GUIHMM.cpp.

bool normalize

(

bool

keep_dead_states = false

)

normalize

Parameters

keep_dead_states

Definition at line 555 of file GUIHMM.cpp.

CRegressionLabels * one_class_classify

(

CRegressionLabels *

output = NULL

)

one class classify

Parameters

output

Definition at line 191 of file GUIHMM.cpp.

float64_t one_class_classify_example

(

int32_t

idx

)

one class classfiy example

Parameters

idx

Definition at line 236 of file GUIHMM.cpp.

bool output_hmm

(

)

output HMM

Definition at line 517 of file GUIHMM.cpp.

bool output_hmm_defined

(

)

output HMM defined

Definition at line 526 of file GUIHMM.cpp.

bool parameter_hash_changed ( )

virtualinherited

Returns

whether parameter combination has changed since last update

Definition at line 295 of file SGObject.cpp.

bool permutation_entropy	(	int32_t	width = 0,
		int32_t	seq_num = -1
	)

define permutation entropy

Definition at line 624 of file GUIHMM.cpp.

void print_modsel_params ( )

inherited

prints all parameter registered for model selection and their type

Definition at line 507 of file SGObject.cpp.

void print_serializable ( const char *  prefix = "" )

virtualinherited

prints registered parameters out

Parameters

prefix

prefix for members

Definition at line 341 of file SGObject.cpp.

void register_param ( Tag< T > &  _tag, const T &  value  )

protectedinherited

Registers a class parameter which is identified by a tag. This enables the parameter to be modified by set() and retrieved by get(). Parameters can be registered in the constructor of the class.

Parameters

_tag	name and type information of parameter
value	value of the parameter

Definition at line 439 of file SGObject.h.

void register_param ( const std::string &  name, const T &  value  )

protectedinherited

Registers a class parameter which is identified by a name. This enables the parameter to be modified by set() and retrieved by get(). Parameters can be registered in the constructor of the class.

Parameters

name	name of the parameter
value	value of the parameter along with type information

Definition at line 452 of file SGObject.h.

bool relative_entropy	(	float64_t *&	values,
		int32_t &	len
	)

relative entropy

Parameters

values
len

Definition at line 564 of file GUIHMM.cpp.

bool save	(	char *	filename,
		bool	is_binary = false
	)

save HMM to file

Definition at line 389 of file GUIHMM.cpp.

bool save_likelihood	(	char *	filename,
		bool	is_binary = false
	)

save HMM likelihood to file

..future

Definition at line 438 of file GUIHMM.cpp.

bool save_path	(	char *	filename,
		bool	is_binary = false
	)

save path

Parameters

filename
is_binary

..future

Definition at line 467 of file GUIHMM.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 347 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 469 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 464 of file SGObject.cpp.

void set ( const Tag< T > &  _tag, const T &  value  )

inherited

Setter for a class parameter, identified by a Tag. Throws an exception if the class does not have such a parameter.

Parameters

_tag	name and type information of parameter
value	value of the parameter

Definition at line 328 of file SGObject.h.

void set ( const std::string &  name, const T &  value  )

inherited

Setter for a class parameter, identified by a name. Throws an exception if the class does not have such a parameter.

Parameters

name	name of the parameter
value	value of the parameter along with type information

Definition at line 354 of file SGObject.h.

void set_current

(

CHMM *

h

)

set current

Parameters

h

Definition at line 129 of file GUIHMM.h.

void set_generic ( )

inherited

Definition at line 74 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 79 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 84 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 89 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 94 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 99 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 104 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 109 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 114 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 119 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 124 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 129 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 134 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 139 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 144 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 261 of file SGObject.cpp.

void set_global_parallel ( Parallel *  parallel )

inherited

set the parallel object

Parameters

parallel

parallel object to use

Definition at line 274 of file SGObject.cpp.

void set_global_version ( Version *  version )

inherited

set the version object

Parameters

version

version object to use

Definition at line 316 of file SGObject.cpp.

bool set_hmm_as

(

char *

target

)

set HMM as POS/NEG/TEST

Definition at line 337 of file GUIHMM.cpp.

bool set_max_dim

(

char *

param

)

set max dim

Parameters

param

bool set_num_hmm_tables

(

char *

param

)

set num hmm tables

Parameters

param

bool set_pseudo

(

float64_t

pseudo

)

set HMM pseudo

Definition at line 318 of file GUIHMM.cpp.

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 225 of file SGObject.cpp.

void switch_model ( CHMM **  m1, CHMM **  m2  )

protected

switch model

Parameters

m1
m2

void unset_generic ( )

inherited

unset generic type

this has to be called in classes specializing a template class

Definition at line 336 of file SGObject.cpp.

void update_parameter_hash ( )

virtualinherited

Updates the hash of current parameter combination

Definition at line 281 of file SGObject.cpp.

bool viterbi_train

(

)

train Viterbi

Definition at line 101 of file GUIHMM.cpp.

bool viterbi_train_defined

(

)

train Viterbi defined

Definition at line 111 of file GUIHMM.cpp.

Member Data Documentation

SGIO* io

inherited

io

Definition at line 537 of file SGObject.h.

int32_t M

protected

M

Definition at line 184 of file GUIHMM.h.

Parameter* m_gradient_parameters

inherited

parameters wrt which we can compute gradients

Definition at line 552 of file SGObject.h.

uint32_t m_hash

inherited

Hash of parameter values

Definition at line 555 of file SGObject.h.

Parameter* m_model_selection_parameters

inherited

model selection parameters

Definition at line 549 of file SGObject.h.

Parameter* m_parameters

inherited

parameters

Definition at line 546 of file SGObject.h.

CHMM* neg

protected

neg

Definition at line 177 of file GUIHMM.h.

Parallel* parallel

inherited

parallel

Definition at line 540 of file SGObject.h.

CHMM* pos

protected

pos

Definition at line 175 of file GUIHMM.h.

float64_t PSEUDO

protected

pseudo

Definition at line 182 of file GUIHMM.h.

CHMM* test

protected

test

Definition at line 179 of file GUIHMM.h.

CSGInterface* ui

protected

ui

Definition at line 188 of file GUIHMM.h.

Version* version

inherited

version

Definition at line 543 of file SGObject.h.

CHMM* working

protected

working

Definition at line 172 of file GUIHMM.h.

---

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

• GUIHMM.h
• GUIHMM.cpp