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CFactorGraph Class Reference

Detailed Description

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

Definition at line 25 of file FactorGraph.h.

Inheritance diagram for CFactorGraph:
Inheritance graph
[legend]

List of all members.

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 ()
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 bool update_parameter_hash ()
virtual bool equals (CSGObject *other, float64_t accuracy=0.0)
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

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

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 1156 of file SGObject.cpp.

CSGObject * clone ( ) [virtual, inherited]

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 1273 of file SGObject.cpp.

void compute_energies ( )

compute energy tables in the factor graph

Definition at line 153 of file FactorGraph.cpp.

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.

virtual CSGObject* deep_copy ( ) const [virtual, inherited]

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

Definition at line 126 of file SGObject.h.

bool equals ( CSGObject other,
float64_t  accuracy = 0.0 
) [virtual, inherited]

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

Definition at line 1177 of file SGObject.cpp.

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.

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.

Returns:
disjoint set

Definition at line 137 of file FactorGraph.cpp.

Returns:
all the shared data

Definition at line 116 of file FactorGraph.cpp.

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 174 of file SGObject.cpp.

Parallel * get_global_parallel ( ) [inherited]

get the parallel object

Returns:
parallel object

Definition at line 209 of file SGObject.cpp.

Version * get_global_version ( ) [inherited]

get the version object

Returns:
version object

Definition at line 222 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 1060 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 1084 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 1097 of file SGObject.cpp.

virtual const char* get_name ( ) const [virtual]
Returns:
class name

Implements CSGObject.

Definition at line 47 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 [virtual, inherited]

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 228 of file SGObject.cpp.

bool is_tree_graph ( ) const
Returns:
is tree graph or not

Definition at line 257 of file FactorGraph.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 633 of file SGObject.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 474 of file SGObject.cpp.

bool load_serializable ( CSerializableFile file,
const char *  prefix = "",
int32_t  param_version = Version::get_version_parameter() 
) [virtual, inherited]

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 305 of file SGObject.cpp.

void load_serializable_post ( ) throw (ShogunException) [protected, virtual, inherited]

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 989 of file SGObject.cpp.

void load_serializable_pre ( ) throw (ShogunException) [protected, virtual, inherited]

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 984 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.

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 671 of file SGObject.cpp.

TParameter * migrate ( DynArray< TParameter * > *  param_base,
const SGParamInfo target 
) [protected, virtual, inherited]

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 878 of file SGObject.cpp.

void one_to_one_migration_prepare ( DynArray< TParameter * > *  param_base,
const SGParamInfo target,
TParameter *&  replacement,
TParameter *&  to_migrate,
char *  old_name = NULL 
) [protected, virtual, inherited]

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 818 of file SGObject.cpp.

void print_modsel_params ( ) [inherited]

prints all parameter registered for model selection and their type

Definition at line 1036 of file SGObject.cpp.

void print_serializable ( const char *  prefix = "") [virtual, inherited]

prints registered parameters out

Parameters:
prefixprefix for members

Definition at line 240 of file SGObject.cpp.

bool save_serializable ( CSerializableFile file,
const char *  prefix = "",
int32_t  param_version = Version::get_version_parameter() 
) [virtual, inherited]

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 246 of file SGObject.cpp.

void save_serializable_post ( ) throw (ShogunException) [protected, virtual, inherited]

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 999 of file SGObject.cpp.

void save_serializable_pre ( ) throw (ShogunException) [protected, virtual, inherited]

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 994 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< complex128_t > ( ) [inherited]

set generic type to T

Definition at line 41 of file SGObject.cpp.

void set_global_io ( SGIO io) [inherited]

set the io object

Parameters:
ioio object to use

Definition at line 167 of file SGObject.cpp.

void set_global_parallel ( Parallel parallel) [inherited]

set the parallel object

Parameters:
parallelparallel object to use

Definition at line 180 of file SGObject.cpp.

void set_global_version ( Version version) [inherited]

set the version object

Parameters:
versionversion object to use

Definition at line 215 of file SGObject.cpp.

virtual CSGObject* shallow_copy ( ) const [virtual, inherited]

A shallow copy. All the SGObject instance variables will be simply assigned and SG_REF-ed.

Reimplemented in CGaussianKernel.

Definition at line 117 of file SGObject.h.

void unset_generic ( ) [inherited]

unset generic type

this has to be called in classes specializing a template class

Definition at line 235 of file SGObject.cpp.

bool update_parameter_hash ( ) [virtual, inherited]

Updates the hash of current parameter combination.

Returns:
bool if parameter combination has changed since last update.

Definition at line 187 of file SGObject.cpp.


Member Data Documentation

SGIO* io [inherited]

io

Definition at line 473 of file SGObject.h.

SGVector<int32_t> m_cardinalities [protected]

cardinalities

Definition at line 146 of file FactorGraph.h.

added data sources

Definition at line 152 of file FactorGraph.h.

CDisjointSet* m_dset [protected]

disjoint set

Definition at line 155 of file FactorGraph.h.

added factors

Definition at line 149 of file FactorGraph.h.

parameters wrt which we can compute gradients

Definition at line 488 of file SGObject.h.

bool m_has_cycle [protected]

if has circle in the graph

Definition at line 158 of file FactorGraph.h.

uint32_t m_hash [inherited]

Hash of parameter values

Definition at line 494 of file SGObject.h.

model selection parameters

Definition at line 485 of file SGObject.h.

int32_t m_num_edges [protected]

number of edges

Definition at line 161 of file FactorGraph.h.

map for different parameter versions

Definition at line 491 of file SGObject.h.

Parameter* m_parameters [inherited]

parameters

Definition at line 482 of file SGObject.h.

Parallel* parallel [inherited]

parallel

Definition at line 476 of file SGObject.h.

Version* version [inherited]

version

Definition at line 479 of file SGObject.h.


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