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CFactorGraph Class Reference

Detailed Description

Class CFactorGraph a factor graph is a structured input in general.

Definition at line 27 of file FactorGraph.h.

Inheritance diagram for CFactorGraph:
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Public Member Functions

 CFactorGraph ()
 
 CFactorGraph (const SGVector< int32_t > card)
 
 CFactorGraph (const CFactorGraph &fg)
 
 ~CFactorGraph ()
 
virtual const char * get_name () const
 
void add_factor (CFactor *factor)
 
void add_data_source (CFactorDataSource *datasource)
 
CDynamicObjectArrayget_factors () const
 
CDynamicObjectArrayget_factor_data_sources () const
 
int32_t get_num_factors () const
 
SGVector< int32_t > get_cardinalities () const
 
void set_cardinalities (SGVector< int32_t > cards)
 
void compute_energies ()
 
float64_t evaluate_energy (const SGVector< int32_t > state) const
 
float64_t evaluate_energy (const CFactorGraphObservation *obs) const
 
SGVector< float64_tevaluate_energies () const
 
CDisjointSetget_disjoint_set () const
 
int32_t get_num_edges () const
 
int32_t get_num_vars () const
 
void connect_components ()
 
bool is_acyclic_graph () const
 
bool is_connected_graph () const
 
bool is_tree_graph () const
 
virtual void loss_augmentation (CFactorGraphObservation *gt)
 
virtual void loss_augmentation (SGVector< int32_t > states_gt, SGVector< float64_t > loss=SGVector< float64_t >())
 
virtual CSGObjectshallow_copy () const
 
virtual CSGObjectdeep_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)
 
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
 
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

SGVector< int32_t > m_cardinalities
 
CDynamicObjectArraym_factors
 
CDynamicObjectArraym_datasources
 
CDisjointSetm_dset
 
bool m_has_cycle
 
int32_t m_num_edges
 

Constructor & Destructor Documentation

Definition at line 16 of file FactorGraph.cpp.

CFactorGraph ( const SGVector< int32_t >  card)

Constructor

Parameters
cardcardinalities of all the variables in the factor graph

Definition at line 25 of file FactorGraph.cpp.

CFactorGraph ( const CFactorGraph fg)

Copy constructor

Parameters
fga factor graph instance

Definition at line 33 of file FactorGraph.cpp.

deconstructor

Definition at line 46 of file FactorGraph.cpp.

Member Function Documentation

void add_data_source ( CFactorDataSource datasource)

add a data source

Parameters
datasourcea factor data source

Definition at line 105 of file FactorGraph.cpp.

void add_factor ( CFactor factor)

add a factor

Parameters
factora factor pointer

Definition at line 95 of file FactorGraph.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 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_energies ( )

compute energy tables in the factor graph

Definition at line 153 of file FactorGraph.cpp.

void connect_components ( )

connect graph nodes by performing union-find algorithm NOTE: make sure call this func before performing inference and other functions related to structure analysis

Definition at line 210 of file FactorGraph.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
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 618 of file SGObject.cpp.

SGVector< float64_t > evaluate_energies ( ) const
Returns
energy table for the graph

Definition at line 182 of file FactorGraph.cpp.

float64_t evaluate_energy ( const SGVector< int32_t >  state) const

evaluate energy given full assignment

Parameters
statean assignment

Definition at line 163 of file FactorGraph.cpp.

float64_t evaluate_energy ( const CFactorGraphObservation obs) const

evaluate energy for a given fully observed assignment

Parameters
obsfactor graph observation

Definition at line 177 of file FactorGraph.cpp.

SGVector< int32_t > get_cardinalities ( ) const
Returns
cardinalities

Definition at line 127 of file FactorGraph.cpp.

CDisjointSet * get_disjoint_set ( ) const
Returns
disjoint set

Definition at line 137 of file FactorGraph.cpp.

CDynamicObjectArray * get_factor_data_sources ( ) const
Returns
all the shared data

Definition at line 116 of file FactorGraph.cpp.

CDynamicObjectArray * get_factors ( ) const
Returns
all the factors

Definition at line 110 of file FactorGraph.cpp.

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.

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_namename 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_namename 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
class name

Implements CSGObject.

Definition at line 49 of file FactorGraph.h.

int32_t get_num_edges ( ) const
Returns
number of edges

Definition at line 143 of file FactorGraph.cpp.

int32_t get_num_factors ( ) const
Returns
number of factors

Definition at line 122 of file FactorGraph.cpp.

int32_t get_num_vars ( ) const
Returns
number of variable nodes

Definition at line 148 of file FactorGraph.cpp.

bool is_acyclic_graph ( ) const
Returns
is acyclic graph or not

Definition at line 247 of file FactorGraph.cpp.

bool is_connected_graph ( ) const
Returns
is connected graph or not

Definition at line 252 of file FactorGraph.cpp.

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 296 of file SGObject.cpp.

bool is_tree_graph ( ) const
Returns
is tree graph or not

Definition at line 257 of file FactorGraph.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
filewhere to load from
prefixprefix 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
ShogunExceptionwill 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
ShogunExceptionwill 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.

void loss_augmentation ( CFactorGraphObservation gt)
virtual

perform loss-augmentation

Parameters
gtan observation (states and loss weights are stored in it)

Definition at line 262 of file FactorGraph.cpp.

void loss_augmentation ( SGVector< int32_t >  states_gt,
SGVector< float64_t loss = SGVector<float64_t>() 
)
virtual

perform loss-augmentation

Parameters
states_gtground truth states
lossweighted loss for each variable

Definition at line 267 of file FactorGraph.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
prefixprefix 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
filewhere to save the object; will be closed during returning if PREFIX is an empty string.
prefixprefix 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
ShogunExceptionwill 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
ShogunExceptionwill 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.

void set_cardinalities ( SGVector< int32_t >  cards)

set cardinalities

Parameters
cardscardinalities of all variables

Definition at line 132 of file FactorGraph.cpp.

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
ioio object to use

Definition at line 228 of file SGObject.cpp.

void set_global_parallel ( Parallel parallel)
inherited

set the parallel object

Parameters
parallelparallel object to use

Definition at line 241 of file SGObject.cpp.

void set_global_version ( Version version)
inherited

set the version object

Parameters
versionversion object to use

Definition at line 283 of file SGObject.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 192 of file SGObject.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.

Member Data Documentation

SGIO* io
inherited

io

Definition at line 369 of file SGObject.h.

SGVector<int32_t> m_cardinalities
protected

cardinalities

Definition at line 148 of file FactorGraph.h.

CDynamicObjectArray* m_datasources
protected

added data sources

Definition at line 154 of file FactorGraph.h.

CDisjointSet* m_dset
protected

disjoint set

Definition at line 157 of file FactorGraph.h.

CDynamicObjectArray* m_factors
protected

added factors

Definition at line 151 of file FactorGraph.h.

Parameter* m_gradient_parameters
inherited

parameters wrt which we can compute gradients

Definition at line 384 of file SGObject.h.

bool m_has_cycle
protected

if has circle in the graph

Definition at line 160 of file FactorGraph.h.

uint32_t m_hash
inherited

Hash of parameter values

Definition at line 387 of file SGObject.h.

Parameter* m_model_selection_parameters
inherited

model selection parameters

Definition at line 381 of file SGObject.h.

int32_t m_num_edges
protected

number of edges

Definition at line 163 of file FactorGraph.h.

Parameter* m_parameters
inherited

parameters

Definition at line 378 of file SGObject.h.

Parallel* parallel
inherited

parallel

Definition at line 372 of file SGObject.h.

Version* version
inherited

version

Definition at line 375 of file SGObject.h.


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

SHOGUN Machine Learning Toolbox - Documentation