Public Member Functions | Static Public Member Functions | Public Attributes | Protected Member Functions | Protected Attributes

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:
Inheritance graph
[legend]

List of all members.

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_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< 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 ()
void unset_generic ()
virtual void print_serializable (const char *prefix="")
virtual bool save_serializable (CSerializableFile *file, const char *prefix="", int32_t param_version=VERSION_PARAMETER)
virtual bool load_serializable (CSerializableFile *file, const char *prefix="", int32_t param_version=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_parameter_dictionary (CMap< TParameter *, CSGObject * > &dict)

Static Public Member Functions

static CHMSVMModelsimulate_two_state_data ()

Public Attributes

SGIOio
Parallelparallel
Versionversion
Parameterm_parameters
Parameterm_model_selection_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)
virtual bool update_parameter_hash ()

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

CTwoStateModel (  ) 

default constructor

Definition at line 17 of file TwoStateModel.cpp.

~CTwoStateModel (  )  [virtual]

destructor

Definition at line 42 of file TwoStateModel.cpp.


Member Function Documentation

void build_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:
dict dictionary of parameters to be built.

Definition at line 1201 of file SGObject.cpp.

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

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

Definition at line 131 of file SGObject.h.

SGIO * get_global_io (  )  [inherited]

get the io object

Returns:
io object

Definition at line 224 of file SGObject.cpp.

Parallel * get_global_parallel (  )  [inherited]

get the parallel object

Returns:
parallel object

Definition at line 259 of file SGObject.cpp.

Version * get_global_version (  )  [inherited]

get the version object

Returns:
version object

Definition at line 272 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 1108 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_name name of the parameter
Returns:
description of the parameter

Definition at line 1132 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_name name of model selection parameter
Returns:
index of model selection parameter with provided name, -1 if there is no such

Definition at line 1145 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_states number of states whose parameters are learnt
num_feats number of features
Returns:
vector with monotonicity constraints of length num_feats times num_learnt_states

Reimplemented from CStateModel.

Definition at line 201 of file TwoStateModel.cpp.

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

Reimplemented from CStateModel.

Definition at line 140 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 [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:
generic set to the type of the generic if returning TRUE
Returns:
TRUE if a class template.

Definition at line 278 of file SGObject.cpp.

SGVector< int32_t > labels_to_states ( CSequence label_seq  )  const [virtual]

translates label sequence to state sequence

Parameters:
label_seq label sequence
Returns:
state sequence

Implements CStateModel.

Definition at line 74 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_version parameter version of the file
current_version version from which mapping begins (you want to use VERSION_PARAMETER for this in most cases)
file file to load from
prefix prefix for members
Returns:
(sorted) array of created TParameter instances with file data

Definition at line 679 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_info information of parameter
file_version parameter version of the file, must be <= provided parameter version
file file to load from
prefix prefix for members
Returns:
new array with TParameter instances with the attached data

Definition at line 523 of file SGObject.cpp.

bool load_serializable ( CSerializableFile file,
const char *  prefix = "",
int32_t  param_version = 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:
file where to load from
prefix prefix 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

Reimplemented in CModelSelectionParameters.

Definition at line 354 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:
ShogunException Will be thrown if an error occurres.

Reimplemented in CLinearHMM, CAlphabet, CANOVAKernel, CCircularKernel, CExponentialKernel, CGaussianKernel, CInverseMultiQuadricKernel, CKernel, CWeightedDegreePositionStringKernel, and CList.

Definition at line 1033 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:
ShogunException Will be thrown if an error occurres.

Definition at line 1028 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_lhs one label sequence
label_seq_rhs other label sequence
Returns:
the Hamming loss

Implements CStateModel.

Definition at line 60 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_seq label sequence (normally the true label sequence)
Returns:
the loss matrix

Implements CStateModel.

Definition at line 46 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_base set of TParameter instances that are mapped to the provided target parameter infos
base_version version of the parameter base
target_param_infos set of SGParamInfo instances that specify the target parameter base

Definition at line 717 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_base set of TParameter instances to use for migration
target parameter 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 923 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_base set of TParameter instances to use for migration
target parameter info for the resulting TParameter
replacement (used as output) here the TParameter instance which is returned by migration is created into
to_migrate the only source that is used for migration
old_name with this parameter, a name change may be specified

Definition at line 864 of file SGObject.cpp.

void print_modsel_params (  )  [inherited]

prints all parameter registered for model selection and their type

Definition at line 1084 of file SGObject.cpp.

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

prints registered parameters out

Parameters:
prefix prefix for members

Definition at line 290 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_weights emission parameters outputted
w the weight vector
num_feats number of features
num_obs number of emission scores per feature and state

Implements CStateModel.

Definition at line 119 of file TwoStateModel.cpp.

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

arranges the tranmission parameterss 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_weights transmission parameters outputted
w the weight vector

Implements CStateModel.

Definition at line 146 of file TwoStateModel.cpp.

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

Save this object to file.

Parameters:
file where to save the object; will be closed during returning if PREFIX is an empty string.
prefix prefix 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

Reimplemented in CModelSelectionParameters.

Definition at line 296 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:
ShogunException Will be thrown if an error occurres.

Reimplemented in CKernel.

Definition at line 1043 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:
ShogunException Will be thrown if an error occurres.

Reimplemented in CKernel.

Definition at line 1038 of file SGObject.cpp.

void set_generic< floatmax_t > (  )  [inherited]

set generic type to T

void set_global_io ( SGIO io  )  [inherited]

set the io object

Parameters:
io io object to use

Definition at line 217 of file SGObject.cpp.

void set_global_parallel ( Parallel parallel  )  [inherited]

set the parallel object

Parameters:
parallel parallel object to use

Definition at line 230 of file SGObject.cpp.

void set_global_version ( Version version  )  [inherited]

set the version object

Parameters:
version version object to use

Definition at line 265 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 122 of file SGObject.h.

CHMSVMModel * simulate_two_state_data (  )  [static]

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

Returns:
a model that contains the data simulated

Definition at line 216 of file TwoStateModel.cpp.

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

translates state sequence to label sequence

Parameters:
state_seq state sequence
Returns:
label sequence

Implements CStateModel.

Definition at line 97 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 285 of file SGObject.cpp.

bool update_parameter_hash (  )  [protected, virtual, inherited]

Updates the hash of current parameter combination.

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

Definition at line 237 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)

Parameters:
psi output vector
transmission_weights counts of the state transitions for a state sequence
emission_weights counts of the emission scores for a state sequence and a feature vector
num_feats number of features
num_obs number of emission scores per feature and state

Implements CStateModel.

Definition at line 170 of file TwoStateModel.cpp.


Member Data Documentation

SGIO* io [inherited]

io

Definition at line 462 of file SGObject.h.

uint32_t m_hash [inherited]

Hash of parameter values

Definition at line 480 of file SGObject.h.

model selection parameters

Definition at line 474 of file SGObject.h.

int32_t m_num_states [protected, inherited]

the number of states

Definition at line 190 of file StateModel.h.

int32_t m_num_transmission_params [protected, inherited]

the number of transmission parameters

Definition at line 193 of file StateModel.h.

SGVector< float64_t > m_p [protected, inherited]

the distribution of start states

Definition at line 199 of file StateModel.h.

map for different parameter versions

Definition at line 477 of file SGObject.h.

Parameter* m_parameters [inherited]

parameters

Definition at line 471 of file SGObject.h.

SGVector< float64_t > m_q [protected, inherited]

the distribution of stop states

Definition at line 202 of file StateModel.h.

SGMatrix< float64_t > m_state_loss_mat [protected, inherited]

state loss matrix, loss for every pair of states

Definition at line 196 of file StateModel.h.

Parallel* parallel [inherited]

parallel

Definition at line 465 of file SGObject.h.

Version* version [inherited]

version

Definition at line 468 of file SGObject.h.


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