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CTwoStateModel Class Reference

Detailed Description

class CTwoStateModel class for the internal two-state representation used in the CHMSVMModel.

Definition at line 24 of file TwoStateModel.h.

Inheritance diagram for CTwoStateModel:
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Public Member Functions

 CTwoStateModel ()
virtual ~CTwoStateModel ()
virtual SGMatrix< float64_t > loss_matrix (CSequence *label_seq)
virtual float64_t loss (CSequence *label_seq_lhs, CSequence *label_seq_rhs)
virtual void reshape_emission_params (SGVector< float64_t > &emission_weights, SGVector< float64_t > w, int32_t num_feats, int32_t num_obs)
virtual void reshape_emission_params (CDynamicObjectArray *plif_matrix, SGVector< float64_t > w, int32_t num_feats, int32_t num_plif_nodes)
virtual void reshape_transmission_params (SGMatrix< float64_t > &transmission_weights, SGVector< float64_t > w)
virtual SGVector< int32_t > labels_to_states (CSequence *label_seq) const
virtual CSequence * states_to_labels (SGVector< int32_t > state_seq) const
virtual void weights_to_vector (SGVector< float64_t > &psi, SGMatrix< float64_t > transmission_weights, SGVector< float64_t > emission_weights, int32_t num_feats, int32_t num_obs) const
virtual SGVector< float64_t > weights_to_vector (SGMatrix< float64_t > transmission_weights, SGVector< float64_t > emission_weights, int32_t num_feats, int32_t num_obs) const
virtual SGVector< int32_t > get_monotonicity (int32_t num_free_states, int32_t num_feats) const
virtual const char * get_name () const
int32_t get_num_states () const
int32_t get_num_transmission_params () const
SGVector< float64_t > get_start_states () const
SGVector< float64_t > get_stop_states () const
virtual CSGObject * shallow_copy () const
virtual CSGObject * deep_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)
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)
virtual bool update_parameter_hash ()
virtual bool equals (CSGObject *other, float64_t accuracy=0.0)
virtual CSGObject * clone ()

Static Public Member Functions

static CHMSVMModel * simulate_data (int32_t num_exm, int32_t exm_len, int32_t num_features, int32_t num_noise_features)

Public Attributes

SGIO * io
Parallel * parallel
Version * version
Parameter * m_parameters
Parameter * m_model_selection_parameters
Parameter * m_gradient_parameters
ParameterMap * m_parameter_map
uint32_t m_hash

Protected Member Functions

virtual TParameter * migrate (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

int32_t m_num_states
int32_t m_num_transmission_params
SGMatrix< float64_t > m_state_loss_mat
SGVector< float64_t > m_p
SGVector< float64_t > m_q

Constructor & Destructor Documentation

CTwoStateModel ( )

default constructor

Definition at line 18 of file TwoStateModel.cpp.

~CTwoStateModel ( )
virtual

destructor

Definition at line 43 of file TwoStateModel.cpp.

Member Function Documentation

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 1196 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 1313 of file SGObject.cpp.

virtual CSGObject* deep_copy ( ) const
virtualinherited

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

Definition at line 160 of file SGObject.h.

bool equals ( CSGObject *  other,
float64_t  accuracy = 0.0 
)
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)
Returns
true if all parameters were equal, false if not

Definition at line 1217 of file SGObject.cpp.

SGIO * get_global_io ( )
inherited

get the io object

Returns
io object

Definition at line 214 of file SGObject.cpp.

Parallel * get_global_parallel ( )
inherited

get the parallel object

Returns
parallel object

Definition at line 249 of file SGObject.cpp.

Version * get_global_version ( )
inherited

get the version object

Returns
version object

Definition at line 262 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 1100 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 1124 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 1137 of file SGObject.cpp.

SGVector< int32_t > get_monotonicity ( int32_t  num_free_states,
int32_t  num_feats 
) const
virtual

specify monotonicity constraints for feature scoring functions. The elements of the vector returned can take one of three values:

see CStateModel::get_monotonicity

Parameters
num_free_statesnumber of states whose parameters are learnt
num_featsnumber of features
Returns
vector with monotonicity constraints of length num_feats times num_learnt_states

Reimplemented from CStateModel.

Definition at line 234 of file TwoStateModel.cpp.

virtual const char* get_name ( ) const
virtual
Returns
name of SGSerializable

Reimplemented from CStateModel.

Definition at line 172 of file TwoStateModel.h.

int32_t get_num_states ( ) const
inherited
Returns
number of states

Definition at line 24 of file StateModel.cpp.

int32_t get_num_transmission_params ( ) const
inherited
Returns
number of transmission parameters to be learnt

Definition at line 29 of file StateModel.cpp.

SGVector< float64_t > get_start_states ( ) const
inherited

return the distribution of start states, i.e. the specification of which states may appear in the start of a state sequence and which may not. The elements of the vector returned can take one out of two values:

  • -INFTY if the state is not allowed to be a start state
  • 0 otherwise

The distrubtion of start states m_p must be initialized in the constructor of CStateModel's child classes.

Returns
the distribution of start states m_p, vector of m_num_states elements

Definition at line 56 of file StateModel.cpp.

SGVector< float64_t > get_stop_states ( ) const
inherited

return the distribution of stop states, i.e. the specification of which states may appear in the end of a state sequence and which may not. The elements of the vector returned can take one out of two values:

  • -INFTY if the state is not allowed to be a stop state
  • 0 otherwise

The distrubtion of stop states m_q must be initialized in the constructor of CStateModel's child classes.

Returns
the distribution of start states m_p, vector of m_num_states elements

Definition at line 61 of file StateModel.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 268 of file SGObject.cpp.

SGVector< int32_t > labels_to_states ( CSequence *  label_seq) const
virtual

translates label sequence to state sequence

Parameters
label_seqlabel sequence
Returns
state sequence

Implements CStateModel.

Definition at line 75 of file TwoStateModel.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 673 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 514 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 345 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 1029 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 >, CDynamicArray< uint64_t >, and CDynamicObjectArray.

Definition at line 1024 of file SGObject.cpp.

float64_t loss ( CSequence *  label_seq_lhs,
CSequence *  label_seq_rhs 
)
virtual

computes the loss between two sequences of labels using the Hamming loss and the state loss matrix

Parameters
label_seq_lhsone label sequence
label_seq_rhsother label sequence
Returns
the Hamming loss

Implements CStateModel.

Definition at line 61 of file TwoStateModel.cpp.

SGMatrix< float64_t > loss_matrix ( CSequence *  label_seq)
virtual

computes a loss matrix with m_num_states rows and number of columns equal to the length of label_seq. This matrix can be added directly to the emission matrix used in Viterbi decoding during training to form the loss-augmented emission matrix

Parameters
label_seqlabel sequence (normally the true label sequence)
Returns
the loss matrix

Implements CStateModel.

Definition at line 47 of file TwoStateModel.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 711 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 918 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 
)
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 858 of file SGObject.cpp.

void print_modsel_params ( )
inherited

prints all parameter registered for model selection and their type

Definition at line 1076 of file SGObject.cpp.

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

prints registered parameters out

Parameters
prefixprefix for members

Definition at line 280 of file SGObject.cpp.

void reshape_emission_params ( SGVector< float64_t > &  emission_weights,
SGVector< float64_t >  w,
int32_t  num_feats,
int32_t  num_obs 
)
virtual

arranges the emission parameterss of the weight vector into a vector adding zero elements for the states whose parameters are not learnt. This vector is suitable to iterate through when constructing the emission matrix used in Viterbi decoding

Parameters
emission_weightsemission parameters outputted
wthe weight vector
num_featsnumber of features
num_obsnumber of emission scores per feature and state

Implements CStateModel.

Definition at line 120 of file TwoStateModel.cpp.

void reshape_emission_params ( CDynamicObjectArray *  plif_matrix,
SGVector< float64_t >  w,
int32_t  num_feats,
int32_t  num_plif_nodes 
)
virtual

arranges the emission parameters of the weight vector into a matrix of PLiFs adding zero elements for the states whose parameters are not learnt.

Parameters
plif_matrixmatrix of PLiFs outputted
wthe weight vector
num_featsnumber of features
num_plif_nodesnumber of nodes in the PLiFs

Implements CStateModel.

Definition at line 147 of file TwoStateModel.cpp.

void reshape_transmission_params ( SGMatrix< float64_t > &  transmission_weights,
SGVector< float64_t >  w 
)
virtual

arranges the transmission parameters of the weight vector into a matrix adding zero elements for the states whose parameters are not learnt. This matrix is suitable to iterate during Viterbi decoding

Parameters
transmission_weightstransmission parameters outputted
wthe weight vector

Implements CStateModel.

Definition at line 169 of file TwoStateModel.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 286 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 1039 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 >, CDynamicArray< uint64_t >, and CDynamicObjectArray.

Definition at line 1034 of file SGObject.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 207 of file SGObject.cpp.

void set_global_parallel ( Parallel *  parallel)
inherited

set the parallel object

Parameters
parallelparallel object to use

Definition at line 220 of file SGObject.cpp.

void set_global_version ( Version *  version)
inherited

set the version object

Parameters
versionversion object to use

Definition at line 255 of file SGObject.cpp.

virtual 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 151 of file SGObject.h.

CHMSVMModel * simulate_data ( int32_t  num_exm,
int32_t  exm_len,
int32_t  num_features,
int32_t  num_noise_features 
)
static

generates simulated data. The features are generated from the label sequence swapping some of the labels and adding noise

Parameters
num_exmnumber of sample pairs (sequence of features, sequence of labels) to generate
exm_lenlength of each sample sequence
num_featuresfeatures dimension
num_noise_featuresnumber of features to be pure noise
Returns
a model that contains the data simulated

Definition at line 249 of file TwoStateModel.cpp.

CSequence * states_to_labels ( SGVector< int32_t >  state_seq) const
virtual

translates state sequence to label sequence

Parameters
state_seqstate sequence
Returns
label sequence

Implements CStateModel.

Definition at line 98 of file TwoStateModel.cpp.

void unset_generic ( )
inherited

unset generic type

this has to be called in classes specializing a template class

Definition at line 275 of file SGObject.cpp.

bool update_parameter_hash ( )
virtualinherited

Updates the hash of current parameter combination.

Returns
bool if parameter combination has changed since last update.

Definition at line 227 of file SGObject.cpp.

void weights_to_vector ( SGVector< float64_t > &  psi,
SGMatrix< float64_t >  transmission_weights,
SGVector< float64_t >  emission_weights,
int32_t  num_feats,
int32_t  num_obs 
) const
virtual

reshapes the transition and emission weights into a vector (the joint feature vector so it will be possible to take the dot product with the weight vector). Version with the joint feature vector as parameter by reference

Parameters
psioutput vector
transmission_weightscounts of the state transitions for a state sequence
emission_weightscounts of the emission scores for a state sequence and a feature vector
num_featsnumber of features
num_obsnumber of emission scores per feature and state

Implements CStateModel.

Definition at line 193 of file TwoStateModel.cpp.

SGVector< float64_t > weights_to_vector ( SGMatrix< float64_t >  transmission_weights,
SGVector< float64_t >  emission_weights,
int32_t  num_feats,
int32_t  num_obs 
) const
virtual

reshapes the transition and emission weights into a vector (the joint feature vector so it will be possible to take the dot product with the weight vector). Version returning the joint feature vector

Parameters
transmission_weightscounts of the state transitions for a state sequence
emission_weightscounts of the emission scores for a state sequence and a feature vector
num_featsnumber of features
num_obsnumber of emission scores per feature and state
Returns
psi output vector

Implements CStateModel.

Definition at line 224 of file TwoStateModel.cpp.

Member Data Documentation

SGIO* io
inherited

io

Definition at line 514 of file SGObject.h.

Parameter* m_gradient_parameters
inherited

parameters wrt which we can compute gradients

Definition at line 529 of file SGObject.h.

uint32_t m_hash
inherited

Hash of parameter values

Definition at line 535 of file SGObject.h.

Parameter* m_model_selection_parameters
inherited

model selection parameters

Definition at line 526 of file SGObject.h.

int32_t m_num_states
protectedinherited

the number of states

Definition at line 217 of file StateModel.h.

int32_t m_num_transmission_params
protectedinherited

the number of transmission parameters

Definition at line 220 of file StateModel.h.

SGVector< float64_t > m_p
protectedinherited

the distribution of start states

Definition at line 226 of file StateModel.h.

ParameterMap* m_parameter_map
inherited

map for different parameter versions

Definition at line 532 of file SGObject.h.

Parameter* m_parameters
inherited

parameters

Definition at line 523 of file SGObject.h.

SGVector< float64_t > m_q
protectedinherited

the distribution of stop states

Definition at line 229 of file StateModel.h.

SGMatrix< float64_t > m_state_loss_mat
protectedinherited

state loss matrix, loss for every pair of states

Definition at line 223 of file StateModel.h.

Parallel* parallel
inherited

parallel

Definition at line 517 of file SGObject.h.

Version* version
inherited

version

Definition at line 520 of file SGObject.h.

The documentation for this class was generated from the following files:
SHOGUN Machine Learning Toolbox - Documentation