SHOGUN  3.2.1
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Groups Pages
List of all members | Public Member Functions | Public Attributes | Protected Member Functions | Protected Attributes
CGUIHMM Class Reference

Detailed Description

UI HMM (Hidden Markov Model)

Definition at line 26 of file GUIHMM.h.

Inheritance diagram for CGUIHMM:
Inheritance graph
[legend]

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)
CHMMget_pos ()
CHMMget_neg ()
CHMMget_test ()
void set_current (CHMM *h)
CHMMget_current ()
float64_t get_pseudo ()
CRegressionLabelsclassify (CRegressionLabels *output=NULL)
float64_t classify_example (int32_t idx)
CRegressionLabelsone_class_classify (CRegressionLabels *output=NULL)
CRegressionLabelslinear_one_class_classify (CRegressionLabels *output=NULL)
float64_t one_class_classify_example (int32_t idx)
virtual const char * get_name () const
virtual CSGObjectshallow_copy () const
virtual CSGObjectdeep_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::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)
SGIOget_global_io ()
void set_global_parallel (Parallel *parallel)
Parallelget_global_parallel ()
void set_global_version (Version *version)
Versionget_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 CSGObjectclone ()

Public Attributes

SGIOio
Parallelparallel
Versionversion
Parameterm_parameters
Parameterm_model_selection_parameters
Parameterm_gradient_parameters
ParameterMapm_parameter_map
uint32_t m_hash

Protected Member Functions

bool converge (float64_t x, float64_t y)
void switch_model (CHMM **m1, CHMM **m2)
virtual TParametermigrate (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

CHMMworking
CHMMpos
CHMMneg
CHMMtest
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
dictdictionary of parameters to be built.

Definition at line 1185 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 1302 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 146 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
otherobject to compare with
accuracyaccuracy to use for comparison (optional)
tolerantallows linient check on float equality (within accuracy)
Returns
true if all parameters were equal, false if not

Definition at line 1206 of file SGObject.cpp.

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 183 of file SGObject.cpp.

Parallel * get_global_parallel ( )
inherited

get the parallel object

Returns
parallel object

Definition at line 224 of file SGObject.cpp.

Version * get_global_version ( )
inherited

get the version object

Returns
version object

Definition at line 237 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 1077 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 1101 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 1114 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 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 243 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.

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::get_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 648 of file SGObject.cpp.

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

load definitions

Parameters
filename
do_init

Definition at line 416 of file GUIHMM.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 489 of file SGObject.cpp.

bool load_serializable ( CSerializableFile file,
const char *  prefix = "",
int32_t  param_version = Version::get_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

Definition at line 320 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, CInverseMultiQuadricKernel, CCircularKernel, and CExponentialKernel.

Definition at line 1004 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.

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

Definition at line 999 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 686 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 893 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.

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 833 of file SGObject.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 209 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 1053 of file SGObject.cpp.

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

prints registered parameters out

Parameters
prefixprefix for members

Definition at line 255 of file SGObject.cpp.

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 = "",
int32_t  param_version = Version::get_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

Definition at line 261 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 1014 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, CDynamicArray< T >, CDynamicArray< float64_t >, CDynamicArray< float32_t >, CDynamicArray< int32_t >, CDynamicArray< char >, CDynamicArray< bool >, and CDynamicObjectArray.

Definition at line 1009 of file SGObject.cpp.

void set_current ( CHMM h)

set current

Parameters
h

Definition at line 129 of file GUIHMM.h.

void set_generic< complex128_t > ( )
inherited

set generic type to T

Definition at line 38 of file SGObject.cpp.

void set_global_io ( SGIO io)
inherited

set the io object

Parameters
ioio object to use

Definition at line 176 of file SGObject.cpp.

void set_global_parallel ( Parallel parallel)
inherited

set the parallel object

Parameters
parallelparallel object to use

Definition at line 189 of file SGObject.cpp.

void set_global_version ( Version version)
inherited

set the version object

Parameters
versionversion object to use

Definition at line 230 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 140 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 250 of file SGObject.cpp.

void update_parameter_hash ( )
virtualinherited

Updates the hash of current parameter combination

Definition at line 196 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 461 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 476 of file SGObject.h.

uint32_t m_hash
inherited

Hash of parameter values

Definition at line 482 of file SGObject.h.

Parameter* m_model_selection_parameters
inherited

model selection parameters

Definition at line 473 of file SGObject.h.

ParameterMap* m_parameter_map
inherited

map for different parameter versions

Definition at line 479 of file SGObject.h.

Parameter* m_parameters
inherited

parameters

Definition at line 470 of file SGObject.h.

CHMM* neg
protected

neg

Definition at line 177 of file GUIHMM.h.

Parallel* parallel
inherited

parallel

Definition at line 464 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 467 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:

SHOGUN Machine Learning Toolbox - Documentation