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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 26 of file TwoStateModel.h.

Inheritance diagram for CTwoStateModel:
Inheritance graph
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Public Member Functions

 CTwoStateModel ()
 
virtual ~CTwoStateModel ()
 
virtual SGMatrix< float64_tloss_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 CSequencestates_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_tweights_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_tget_start_states () const
 
SGVector< float64_tget_stop_states () const
 
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 ()
 

Static Public Member Functions

static CHMSVMModelsimulate_data (int32_t num_exm, int32_t exm_len, int32_t num_features, int32_t num_noise_features)
 

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

int32_t m_num_states
 
int32_t m_num_transmission_params
 
SGMatrix< float64_tm_state_loss_mat
 
SGVector< float64_tm_p
 
SGVector< float64_tm_q
 

Constructor & Destructor Documentation

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 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.

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.

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.

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 174 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 296 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.

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.

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.

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.

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 = "" 
)
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_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.

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 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.

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 369 of file SGObject.h.

Parameter* m_gradient_parameters
inherited

parameters wrt which we can compute gradients

Definition at line 384 of file SGObject.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_states
protectedinherited

the number of states

Definition at line 219 of file StateModel.h.

int32_t m_num_transmission_params
protectedinherited

the number of transmission parameters

Definition at line 222 of file StateModel.h.

SGVector< float64_t > m_p
protectedinherited

the distribution of start states

Definition at line 228 of file StateModel.h.

Parameter* m_parameters
inherited

parameters

Definition at line 378 of file SGObject.h.

SGVector< float64_t > m_q
protectedinherited

the distribution of stop states

Definition at line 231 of file StateModel.h.

SGMatrix< float64_t > m_state_loss_mat
protectedinherited

state loss matrix, loss for every pair of states

Definition at line 225 of file StateModel.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