A pack of learning algorithms that can easily be used. More...

#include <BNLearner.h>

Inheritance diagram for gum::learning::BNLearner< GUM_SCALAR >:

Collaboration diagram for gum::learning::BNLearner< GUM_SCALAR >:

Public Types
enum class	ScoreType { AIC , BD , BDeu , BIC , fNML , K2 , LOG2LIKELIHOOD , MDL }
	an enumeration enabling to select easily the score we wish to use More...
enum class	ParamEstimatorType { ML }
	an enumeration to select the type of parameter estimation we shall apply More...
enum class	BNLearnerPriorType { NO_prior , SMOOTHING , DIRICHLET_FROM_DATABASE , DIRICHLET_FROM_BAYESNET , BDEU }
	an enumeration to select the prior More...
enum class	AlgoType { K2 , GREEDY_HILL_CLIMBING , LOCAL_SEARCH_WITH_TABU_LIST , MIIC , PC , FCI , EXTENDED_GREEDY_HILL_CLIMBING , GREEDY_THICK_THINNING }
	an enumeration to select easily the learning algorithm to use More...
enum class	ApproximationSchemeSTATE : char { Undefined , Continue , Epsilon , Rate , Limit , TimeLimit , Stopped }
	The different state of an approximation scheme. More...

Public Member Functions
BayesNet< GUM_SCALAR >	learnBN ()
	learn a Bayes Net from a file (must have read the db before)
BayesNet< GUM_SCALAR >	learnParameters (const DAG &dag, bool takeIntoAccountScore=true)
	learns a BN (its parameters) with the structure passed in argument
BayesNet< GUM_SCALAR >	learnParameters (const BayesNet< GUM_SCALAR > &bn, bool takeIntoAccountScore=true)
	learns a BN (its parameters) with the BN structure passed in argument, EM being initialized by this argument
BayesNet< GUM_SCALAR >	learnParameters (bool take_into_account_score=true)
	learns a BN (its parameters) when its structure is known
std::string	toString () const
std::vector< std::tuple< std::string, std::string, std::string > >	state () const
void	copyState (const BNLearner< GUM_SCALAR > &learner)
	copy the states of the BNLearner
BNLearner< GUM_SCALAR > &	setInitialDAG (const DAG &dag)
BNLearner< GUM_SCALAR > &	useEM (const double epsilon, const double noise=default_EM_noise)
	use The EM algorithm to learn parameters
BNLearner< GUM_SCALAR > &	useEMWithRateCriterion (const double epsilon, const double noise=default_EM_noise)
	use The EM algorithm to learn parameters with the rate stopping criterion
BNLearner< GUM_SCALAR > &	useEMWithDiffCriterion (const double epsilon, const double noise=default_EM_noise)
	use The EM algorithm to learn parameters with the diff stopping criterion
BNLearner< GUM_SCALAR > &	forbidEM ()
	prevent using the EM algorithm for parameter learning
BNLearner< GUM_SCALAR > &	EMsetEpsilon (const double eps)
	sets the stopping criterion of EM as being the minimal difference between two consecutive log-likelihoods
BNLearner< GUM_SCALAR > &	EMdisableEpsilon ()
	Disable the min log-likelihood diff stopping criterion.
BNLearner< GUM_SCALAR > &	EMenableEpsilon ()
	Enable the log-likelihood min diff stopping criterion in EM.
BNLearner< GUM_SCALAR > &	EMsetMinEpsilonRate (const double rate)
	sets the stopping criterion of EM as being the minimal log-likelihood's evolution rate
BNLearner< GUM_SCALAR > &	EMdisableMinEpsilonRate ()
	Disable the log-likelihood evolution rate stopping criterion.
BNLearner< GUM_SCALAR > &	EMenableMinEpsilonRate ()
	Enable the log-likelihood evolution rate stopping criterion.
BNLearner< GUM_SCALAR > &	EMsetMaxIter (const Size max)
	add a max iteration stopping criterion
BNLearner< GUM_SCALAR > &	EMdisableMaxIter ()
	Disable stopping criterion on max iterations.
BNLearner< GUM_SCALAR > &	EMenableMaxIter ()
	Enable stopping criterion on max iterations.
BNLearner< GUM_SCALAR > &	EMsetMaxTime (const double timeout)
	add a stopping criterion on timeout
BNLearner< GUM_SCALAR > &	EMdisableMaxTime ()
	Disable EM's timeout stopping criterion.
BNLearner< GUM_SCALAR > &	EMenableMaxTime ()
	enable EM's timeout stopping criterion
BNLearner< GUM_SCALAR > &	EMsetPeriodSize (const Size p)
	how many samples between 2 stoppings isEnabled
BNLearner< GUM_SCALAR > &	EMsetVerbosity (const bool v)
	sets or unsets EM's verbosity
BNLearner< GUM_SCALAR > &	useScoreAIC ()
BNLearner< GUM_SCALAR > &	useScoreBD ()
BNLearner< GUM_SCALAR > &	useScoreBDeu ()
BNLearner< GUM_SCALAR > &	useScoreBIC ()
BNLearner< GUM_SCALAR > &	useScoreK2 ()
BNLearner< GUM_SCALAR > &	useScoreLog2Likelihood ()
BNLearner< GUM_SCALAR > &	useNoPrior ()
BNLearner< GUM_SCALAR > &	useBDeuPrior (double weight=1.0)
BNLearner< GUM_SCALAR > &	useSmoothingPrior (double weight=1)
BNLearner< GUM_SCALAR > &	useDirichletPrior (std::string_view filename, double weight=1)
BNLearner< GUM_SCALAR > &	useDirichletPrior (const gum::BayesNet< GUM_SCALAR > &bn, double weight=1)
BNLearner< GUM_SCALAR > &	useGreedyHillClimbing ()
BNLearner< GUM_SCALAR > &	useExtendedGreedyHillClimbing ()
BNLearner< GUM_SCALAR > &	useGreedyThickThinning ()
BNLearner< GUM_SCALAR > &	setGreedyThickThinningReversals (bool allow)
bool	greedyThickThinningReversals () const
BNLearner< GUM_SCALAR > &	useLocalSearchWithTabuList (Size tabu_size=100, Size nb_decrease=2)
BNLearner< GUM_SCALAR > &	useK2 (const Sequence< NodeId > &order)
BNLearner< GUM_SCALAR > &	useK2 (const std::vector< NodeId > &order)
BNLearner< GUM_SCALAR > &	useMIIC ()
BNLearner< GUM_SCALAR > &	usePC ()
BNLearner< GUM_SCALAR > &	useFCI ()
BNLearner< GUM_SCALAR > &	useFCIChi2Test ()
BNLearner< GUM_SCALAR > &	useFCIG2Test ()
BNLearner< GUM_SCALAR > &	setFCIAlpha (double alpha)
BNLearner< GUM_SCALAR > &	setFCIMaxPathLength (Size max_len)
BNLearner< GUM_SCALAR > &	setFCIExhaustiveSepSet (bool exhaustive)
bool	fciExhaustiveSepSet () const
BNLearner< GUM_SCALAR > &	useChi2Test ()
BNLearner< GUM_SCALAR > &	useG2Test ()
BNLearner< GUM_SCALAR > &	setPCAlpha (double alpha)
BNLearner< GUM_SCALAR > &	setPCStable (bool stable)
BNLearner< GUM_SCALAR > &	setPCMaxCondSetSize (Size max_k)
BNLearner< GUM_SCALAR > &	setPCUnshieldedColliderSorted (bool sorted)
BNLearner< GUM_SCALAR > &	useNMLCorrection ()
BNLearner< GUM_SCALAR > &	useMDLCorrection ()
BNLearner< GUM_SCALAR > &	useNoCorrection ()
BNLearner< GUM_SCALAR > &	setMaxIndegree (Size max_indegree)
BNLearner< GUM_SCALAR > &	setSliceOrder (const NodeProperty< NodeId > &slice_order)
BNLearner< GUM_SCALAR > &	setSliceOrder (const std::vector< std::vector< std::string > > &slices)
BNLearner< GUM_SCALAR > &	setTotalOrder (const std::vector< std::string > &order)
BNLearner< GUM_SCALAR > &	setTotalOrder (const Sequence< NodeId > &order)
BNLearner< GUM_SCALAR > &	setForbiddenArcs (const ArcSet &set)
BNLearner< GUM_SCALAR > &	addForbiddenArc (const Arc &arc)
BNLearner< GUM_SCALAR > &	addForbiddenArc (NodeId tail, NodeId head)
BNLearner< GUM_SCALAR > &	addForbiddenArc (std::string_view tail, std::string_view head)
BNLearner< GUM_SCALAR > &	eraseForbiddenArc (const Arc &arc)
BNLearner< GUM_SCALAR > &	eraseForbiddenArc (NodeId tail, NodeId head)
BNLearner< GUM_SCALAR > &	eraseForbiddenArc (std::string_view tail, std::string_view head)
BNLearner< GUM_SCALAR > &	addMandatoryArc (const Arc &arc)
BNLearner< GUM_SCALAR > &	addMandatoryArc (NodeId tail, NodeId head)
BNLearner< GUM_SCALAR > &	addMandatoryArc (std::string_view tail, std::string_view head)
BNLearner< GUM_SCALAR > &	eraseMandatoryArc (const Arc &arc)
BNLearner< GUM_SCALAR > &	eraseMandatoryArc (NodeId tail, NodeId head)
BNLearner< GUM_SCALAR > &	eraseMandatoryArc (std::string_view tail, std::string_view head)
BNLearner< GUM_SCALAR > &	addPossibleEdge (const Edge &edge)
BNLearner< GUM_SCALAR > &	addPossibleEdge (NodeId tail, NodeId head)
BNLearner< GUM_SCALAR > &	addPossibleEdge (std::string_view tail, std::string_view head)
BNLearner< GUM_SCALAR > &	erasePossibleEdge (const Edge &edge)
BNLearner< GUM_SCALAR > &	erasePossibleEdge (NodeId tail, NodeId head)
BNLearner< GUM_SCALAR > &	erasePossibleEdge (std::string_view tail, std::string_view head)
BNLearner< GUM_SCALAR > &	setMandatoryArcs (const ArcSet &set)
BNLearner< GUM_SCALAR > &	setPossibleEdges (const EdgeSet &set)
BNLearner< GUM_SCALAR > &	setPossibleSkeleton (const UndiGraph &skeleton)
BNLearner< GUM_SCALAR > &	addNoParentNode (NodeId node)
BNLearner< GUM_SCALAR > &	addNoParentNode (std::string_view name)
BNLearner< GUM_SCALAR > &	eraseNoParentNode (NodeId node)
BNLearner< GUM_SCALAR > &	eraseNoParentNode (std::string_view name)
BNLearner< GUM_SCALAR > &	addNoChildrenNode (NodeId node)
BNLearner< GUM_SCALAR > &	addNoChildrenNode (std::string_view name)
BNLearner< GUM_SCALAR > &	eraseNoChildrenNode (NodeId node)
BNLearner< GUM_SCALAR > &	eraseNoChildrenNode (std::string_view name)
BNLearner< GUM_SCALAR > &	allowArcAdditions (bool allow)
BNLearner< GUM_SCALAR > &	allowArcDeletions (bool allow)
BNLearner< GUM_SCALAR > &	allowArcReversals (bool allow)
BNLearner< GUM_SCALAR > &	allowArcTriangleDeletions (bool allow)
bool	isConstraintBased () const
bool	isScoreBased () const
Size	EMPeriodSize () const
void	unsetTotalOrder ()
	removes the current total ordering constraint, if any
Constructors / Destructors
	BNLearner (std::string_view filename, const std::vector< std::string > &missingSymbols={"?"}, const bool induceTypes=true)
	default constructor
	BNLearner (const DatabaseTable &db)
	default constructor
	BNLearner (std::string_view filename, const gum::BayesNet< GUM_SCALAR > &src, const std::vector< std::string > &missing_symbols={"?"})
	Wrapper for BNLearner (filename,modalities,parse_database) using a bn to find those modalities and nodeids.
	BNLearner (const BNLearner &)
	copy constructor
	BNLearner (BNLearner &&)
	move constructor
	~BNLearner () override
	destructor
Operators
BNLearner &	operator= (const BNLearner &)
	copy operator
BNLearner &	operator= (BNLearner &&) noexcept
	move operator
Accessors / Modifiers
DAG	learnDAG ()
	learn a structure from a file (must have read the db before)
PDAG	learnPDAG ()
	learn a partial structure from a file (must have read the db before and must have selected miic)
PAG	learnPAG ()
	learn a PAG — only valid when useFCI() has been called
DAG	initialDAG ()
	returns the initial DAG structure
const std::vector< std::string > &	names () const
	returns the names of the variables in the database
const std::vector< std::size_t > &	domainSizes () const
	returns the domain sizes of the variables in the database
Size	domainSize (NodeId var) const
	learn a structure from a file (must have read the db before)
Size	domainSize (std::string_view var) const
	learn a structure from a file (must have read the db before)
NodeId	idFromName (std::string_view var_name) const
	returns the node id corresponding to a variable name
const DatabaseTable &	database () const
	returns the database used by the BNLearner
void	setDatabaseWeight (const double new_weight)
	assign a weight to all the rows of the learning database so that the sum of their weights is equal to new_weight
void	setRecordWeight (const std::size_t i, const double weight)
	sets the weight of the ith record of the database
double	recordWeight (const std::size_t i) const
	returns the weight of the ith record
double	databaseWeight () const
	returns the weight of the whole database
const std::string &	nameFromId (NodeId id) const
	returns the variable name corresponding to a given node id
void	useDatabaseRanges (const std::vector< std::pair< std::size_t, std::size_t > > &new_ranges)
	use a new set of database rows' ranges to perform learning
void	clearDatabaseRanges ()
	reset the ranges to the one range corresponding to the whole database
const std::vector< std::pair< std::size_t, std::size_t > > &	databaseRanges () const
	returns the current database rows' ranges used for learning
std::pair< std::size_t, std::size_t >	useCrossValidationFold (const std::size_t learning_fold, const std::size_t k_fold)
	sets the ranges of rows to be used for cross-validation learning
std::pair< double, double >	chi2 (NodeId id1, NodeId id2, const std::vector< NodeId > &knowing={})
	Return the <statistic,pvalue> pair for chi2 test in the database.
std::pair< double, double >	chi2 (std::string_view name1, std::string_view name2, const std::vector< std::string > &knowing={})
	Return the <statistic,pvalue> pair for the BNLearner.
std::pair< double, double >	G2 (NodeId id1, NodeId id2, const std::vector< NodeId > &knowing={})
	Return the <statistic,pvalue> pair for for G2 test in the database.
std::pair< double, double >	G2 (std::string_view name1, std::string_view name2, const std::vector< std::string > &knowing={})
	Return the <statistic,pvalue> pair for for G2 test in the database.
double	logLikelihood (const std::vector< NodeId > &vars, const std::vector< NodeId > &knowing={})
	Return the loglikelihood of vars in the base, conditioned by knowing for the BNLearner.
double	logLikelihood (const std::vector< std::string > &vars, const std::vector< std::string > &knowing={})
	Return the loglikelihood of vars in the base, conditioned by knowing for the BNLearner.
double	mutualInformation (NodeId id1, NodeId id2, const std::vector< NodeId > &knowing={})
	Return the mutual information of id1 and id2 in the base, conditioned by knowing for the BNLearner.
double	mutualInformation (std::string_view var1, std::string_view var2, const std::vector< std::string > &knowing={})
	Return the mutual information of var1 and var2 in the base, conditioned by knowing for the BNLearner.
double	correctedMutualInformation (NodeId id1, NodeId id2, const std::vector< NodeId > &knowing={})
	Return the mutual information of id1 and id2 in the base, conditioned by knowing for the BNLearner.
double	correctedMutualInformation (std::string_view var1, std::string_view var2, const std::vector< std::string > &knowing={})
	Return the mutual information of var1 and var2 in the base, conditioned by knowing for the BNLearner.
double	score (NodeId vars, const std::vector< NodeId > &knowing={})
	Return the value of the score currently in use by the BNLearner of a variable given a set of other variables.
double	score (std::string_view vars, const std::vector< std::string > &knowing={})
	Return the value of the score currently in use by the BNLearner of a variable given a set of other variables The score used is the one currently selected in the BNLearner.
std::vector< double >	rawPseudoCount (const std::vector< NodeId > &vars)
	Return the pseudo-counts of NodeIds vars in the base in a raw array.
std::vector< double >	rawPseudoCount (const std::vector< std::string > &vars)
	Return the pseudoconts of vars in the base in a raw array.
Size	nbCols () const
Size	nbRows () const
bool	isUsingEM () const
	indicates whether we use EM for parameter learning
EMApproximationScheme &	EM ()
	returns the EM parameter learning approximation scheme if EM is enabled
ApproximationSchemeSTATE	EMState () const
	returns the state of the last EM algorithm executed
std::string	EMStateMessage () const
	returns the state of the EM algorithm
bool	hasMissingValues () const
	returns true if the learner's database has missing values
Score selection
void	useScorefNML ()
	indicate that we wish to use a fNML score
void	useScoreMDL ()
	indicate that we wish to use a MDL score
a prior selection / parameterization
std::string	checkScorePriorCompatibility () const
	checks whether the current score and prior are compatible
MIIC parameterization and specific results
std::vector< Arc >	latentVariables () const
	get the list of arcs hiding latent variables
Accessors / Modifiers for adding constraints on learning
void	unsetSliceOrder ()
	removes the slice order constraint
Multithreading
void	setNumberOfThreads (Size nb) override
	sets the number max of threads that can be used
redistribute signals AND implementation of interface
IApproximationSchemeConfiguration
void	setCurrentApproximationScheme (const ApproximationScheme *approximationScheme)
	{@ /// distribute signals
void	distributeProgress (const ApproximationScheme *approximationScheme, Size pourcent, double error, double time)
	{@ /// distribute signals
void	distributeStop (const ApproximationScheme *approximationScheme, std::string_view message)
	distribute signals

void	setEpsilon (double eps) override
	Given that we approximate f(t), stopping criterion on \|f(t+1)-f(t)\| If the criterion was disabled it will be enabled.
double	epsilon () const override
	Get the value of epsilon.
void	disableEpsilon () override
	Disable stopping criterion on epsilon.
void	enableEpsilon () override
	Enable stopping criterion on epsilon.
bool	isEnabledEpsilon () const override

void	setMinEpsilonRate (double rate) override
	Given that we approximate f(t), stopping criterion on d/dt(\|f(t+1)-f(t)\|) If the criterion was disabled it will be enabled.
double	minEpsilonRate () const override
	Get the value of the minimal epsilon rate.
void	disableMinEpsilonRate () override
	Disable stopping criterion on epsilon rate.
void	enableMinEpsilonRate () override
	Enable stopping criterion on epsilon rate.
bool	isEnabledMinEpsilonRate () const override

void	setMaxIter (Size max) override
	stopping criterion on number of iterationsIf the criterion was disabled it will be enabled
Size	maxIter () const override
void	disableMaxIter () override
	Disable stopping criterion on max iterations.
void	enableMaxIter () override
	Enable stopping criterion on max iterations.
bool	isEnabledMaxIter () const override

void	setMaxTime (double timeout) override
	stopping criterion on timeout If the criterion was disabled it will be enabled
double	maxTime () const override
	returns the timeout (in seconds)
double	currentTime () const override
	get the current running time in second (double)
void	disableMaxTime () override
	Disable stopping criterion on timeout.
void	enableMaxTime () override
	stopping criterion on timeout If the criterion was disabled it will be enabled
bool	isEnabledMaxTime () const override

void	setPeriodSize (Size p) override
	how many samples between 2 stopping isEnableds
Size	periodSize () const override
	how many samples between 2 stopping isEnableds

void	setVerbosity (bool v) override
	verbosity
bool	verbosity () const override
	verbosity

ApproximationSchemeSTATE	stateApproximationScheme () const override
	history
Size	nbrIterations () const override
const std::vector< double > &	history () const override
EM approximation scheme for parameter learning
double	EMEpsilon () const
	Get the value of EM's min diff epsilon.
bool	EMisEnabledEpsilon () const
	return true if EM's stopping criterion is the log-likelihood min diff
double	EMMinEpsilonRate () const
	Get the value of the minimal log-likelihood evolution rate of EM.
bool	EMisEnabledMinEpsilonRate () const
Size	EMMaxIter () const
	return the max number of iterations criterion
bool	EMisEnabledMaxIter () const
double	EMMaxTime () const
	@brief returns EM's timeout (in milliseconds)
double	EMCurrentTime () const
	get the current running time in second (double)
bool	EMisEnabledMaxTime () const
bool	EMVerbosity () const
	returns the EM's verbosity status
ApproximationSchemeSTATE	EMStateApproximationScheme () const
	get the current state of EM
Size	EMnbrIterations () const
	returns the number of iterations performed by the last EM execution
const std::vector< double > &	EMHistory () const
	returns the history of the last EM execution
Getters and setters
std::string	messageApproximationScheme () const
	Returns the approximation scheme message.
Accessors/Modifiers
Size	getNumberOfThreads () const override
	returns the current max number of threads used by the class containing this ThreadNumberManager
bool	isGumNumberOfThreadsOverriden () const override
	indicates whether the class containing this ThreadNumberManager set its own number of threads

Public Attributes
Signaler< Size, double, double >	onProgress
	Progression, error and time.
Signaler< std::string_view >	onStop
	Criteria messageApproximationScheme.

Static Public Attributes
static constexpr double	default_EM_noise {0.1}
	the default noise amount added to CPTs during EM's initialization (see method useEM())

Protected Types
enum class	IndepTestType { Chi2 , G2 }
	independence test type for PC More...

Protected Member Functions
void	createPrior_ () override
	create the prior used for learning
PAG	learnPAG_ ()
PDAG	learnPDAG_ ()
void	_setPriorWeight_ (double weight)
	sets the prior weight
void	createScore_ ()
	create the score used for learning
ParamEstimator *	createParamEstimator_ (const DBRowGeneratorParser &parser, bool take_into_account_score=true)
	create the parameter estimator used for learning
DAG	learnDag_ ()
	returns the DAG learnt
MixedGraph	prepareSimpleMiic_ ()
	prepares the initial graph for Simple Miic
MixedGraph	prepareMiic_ ()
	prepares the initial graph for miic
MixedGraph	preparePC_ ()
	prepares the initial graph and independence test for PC
MixedGraph	prepareFCI_ ()
	prepares the initial graph and independence test for FCI
PriorType	getPriorType_ () const
	returns the type (as a string) of a given prior
void	createCorrectedMutualInformation_ ()
	create the Corrected Mutual Information instance for Miic

Static Protected Member Functions
static DatabaseTable	readFile_ (std::string_view filename, const std::vector< std::string > &missing_symbols)
	reads a file and returns a databaseVectInRam
static void	isCSVFileName_ (std::string_view filename)
	checks whether the extension of a CSV filename is correct

Protected Attributes
bool	inducedTypes_ {false}
	the policy for typing variables
ScoreType	scoreType_ {ScoreType::BDeu}
	the score selected for learning
Score *	score_ {nullptr}
	the score used
ParamEstimatorType	paramEstimatorType_ {ParamEstimatorType::ML}
	the type of the parameter estimator
bool	useEM_ {false}
	a Boolean indicating whether we should use EM for parameter learning or not
double	noiseEM_ {0.1}
	the noise factor (in (0,1)) used by EM for perturbing the CPT during init
CorrectedMutualInformation *	mutualInfo_ {nullptr}
	the selected correction for miic
BNLearnerPriorType	priorType_ {BNLearnerPriorType::NO_prior}
	the a priorselected for the score and parameters
Prior *	prior_ {nullptr}
	the prior used
NoPrior *	noPrior_ {nullptr}
double	priorWeight_ {1.0f}
	the weight of the prior
StructuralConstraintSliceOrder	constraintSliceOrder_
	the constraint for 2TBNs
StructuralConstraintTotalOrder	constraintTotalOrder_
	the total order ing constraint
StructuralConstraintIndegree	constraintIndegree_
	the constraint for indegrees
StructuralConstraintTabuList	constraintTabuList_
	the constraint for tabu lists
StructuralConstraintForbiddenArcs	constraintForbiddenArcs_
	the constraint on forbidden arcs
StructuralConstraintPossibleEdges	constraintPossibleEdges_
	the constraint on possible Edges
StructuralConstraintMandatoryArcs	constraintMandatoryArcs_
	the constraint on mandatory arcs
StructuralConstraintNoParentNodes	constraintNoParentNodes_
	the constraint on no parent nodes
StructuralConstraintNoChildrenNodes	constraintNoChildrenNodes_
	the constraint on no children nodes
AlgoType	selectedAlgo_ {AlgoType::MIIC}
	the selected learning algorithm
bool	allowArcAdditions_ {true}
	whether we allow or not arc additions during learning
bool	allowArcDeletions_ {true}
	whether we allow or not arc deletions during learning
bool	allowArcReversals_ {true}
	whether we allow or not arc reversals during learning
bool	allowArcTriangleDeletions_ {true}
	whether we allow or not arc deletions during learning
K2	algoK2_
	the K2 algorithm
SimpleMiic	algoSimpleMiic_
	the MIIC algorithm
Miic	algoMiic_
	the Constraint MIIC algorithm
CorrectedMutualInformation::KModeTypes	kmodeMiic_
	the penalty used in MIIC
gum::learning::PC	algoPC_
	the PC algorithm
IndepTestType	indepTestTypePC_ {IndepTestType::Chi2}
IndependenceTest *	indepTestPC_ {nullptr}
	owned independence test object for PC (rebuilt before each learn call)
double	alphaPc_ {0.05}
	PC parameters.
bool	stablePc_ {true}
Size	maxCondSetSizePc_ {Size(-1)}
bool	sortedUCPc_ {false}
gum::learning::FCI	algoFCI_
	the FCI algorithm
IndepTestType	indepTestTypeFCI_ {IndepTestType::Chi2}
	independence test type for FCI (reuses IndepTestType defined above)
IndependenceTest *	indepTestFCI_ {nullptr}
	owned independence test object for FCI (rebuilt before each learn call)
double	alphaFci_ {0.05}
	FCI parameters.
Size	maxPathLengthFci_ {Size(-1)}
bool	exhaustiveSepSetFci_ {false}
DAG2BNLearner	dag2BN_
	the parametric EM
GreedyHillClimbing	greedyHillClimbing_
	the greedy hill climbing algorithm
GreedyHillClimbing	extendedGreedyHillClimbing_
	the extended greedy hill climbing
GreedyThickThinning	greedyThickThinning_
	the greedy thick-thinning algorithm
LocalSearchWithTabuList	localSearchWithTabuList_
	the local search with tabu list algorithm
Database	scoreDatabase_
	the database to be used by the scores and parameter estimators
std::vector< std::pair< std::size_t, std::size_t > >	ranges_
	the set of rows' ranges within the database in which learning is done
Database *	priorDatabase_ {nullptr}
	the database used by the Dirichlet a priori
std::string	priorDbname_
	the filename for the Dirichlet a priori, if any
DAG	initialDag_
	an initial DAG given to learners
std::string	filename_ {"-"}
	the filename database
Size	nbDecreasingChanges_ {2}
const ApproximationScheme *	currentAlgorithm_ {nullptr}

Private Member Functions
NodeProperty< Sequence< std::string > >	_labelsFromBN_ (std::string_view filename, const BayesNet< GUM_SCALAR > &src)
	read the first line of a file to find column names
void	_checkDAGCompatibility_ (const DAG &dag)
	check that the database contains the nodes of the dag, else raise an exception
BayesNet< GUM_SCALAR >	_learnParameters_ (const DAG &dag, bool takeIntoAccountScore)
	learns a BN (its parameters) with the structure passed in argument using a single pass estimation (not EM)
std::pair< std::shared_ptr< ParamEstimator >, std::shared_ptr< ParamEstimator > >	_initializeEMParameterLearning_ (const DAG &dag, bool takeIntoAccountScore)
	initializes EM and returns a pair containing, first, a bootstrap estimator and, second, the EM estimator
BayesNet< GUM_SCALAR >	_learnParametersWithEM_ (const DAG &dag, bool takeIntoAccountScore)
	learns a BN (its parameters) with the structure passed in argument using the EM algorithm initialized by the BNLearner
BayesNet< GUM_SCALAR >	_learnParametersWithEM_ (const BayesNet< GUM_SCALAR > &bn, bool takeIntoAccountScore)
	learns a BN (its parameters) with the structure passed in argument using the EM algorithm initialized by the Bayes net passed in argument

Private Attributes
BayesNet< GUM_SCALAR >	_prior_bn_
Size	_nb_threads_ {0}
	the max number of threads used by the class

Detailed Description

template<GUM_Numeric GUM_SCALAR>
class gum::learning::BNLearner< GUM_SCALAR >

A pack of learning algorithms that can easily be used.

The pack currently contains K2, GreedyHillClimbing and LocalSearchWithTabuList

Definition at line 74 of file BNLearner.h.

Member Enumeration Documentation

◆ AlgoType

enum class gum::learning::IBNLearner::AlgoType

stronginherited

an enumeration to select easily the learning algorithm to use

Enumerator
K2
GREEDY_HILL_CLIMBING
LOCAL_SEARCH_WITH_TABU_LIST
MIIC
PC
FCI
EXTENDED_GREEDY_HILL_CLIMBING
GREEDY_THICK_THINNING

Definition at line 123 of file IBNLearner.h.

                        {
      K2,
      GREEDY_HILL_CLIMBING,
      LOCAL_SEARCH_WITH_TABU_LIST,
      MIIC,
      PC,
      FCI,
      EXTENDED_GREEDY_HILL_CLIMBING,
      GREEDY_THICK_THINNING
    };

◆ ApproximationSchemeSTATE

enum class gum::IApproximationSchemeConfiguration::ApproximationSchemeSTATE : char

stronginherited

The different state of an approximation scheme.

Enumerator
Undefined
Continue
Epsilon
Rate
Limit
TimeLimit
Stopped

Definition at line 87 of file IApproximationSchemeConfiguration.h.

                                        : char {
      Undefined,
      Continue,
      Epsilon,
      Rate,
      Limit,
      TimeLimit,
      Stopped
    };

◆ BNLearnerPriorType

enum class gum::learning::IBNLearner::BNLearnerPriorType

stronginherited

an enumeration to select the prior

Enumerator
NO_prior
SMOOTHING
DIRICHLET_FROM_DATABASE
DIRICHLET_FROM_BAYESNET
BDEU

Definition at line 114 of file IBNLearner.h.

                                  {
      NO_prior,
      SMOOTHING,
      DIRICHLET_FROM_DATABASE,
      DIRICHLET_FROM_BAYESNET,
      BDEU
    };

◆ IndepTestType

enum class gum::learning::IBNLearner::IndepTestType

strongprotectedinherited

independence test type for PC

Enumerator
Chi2
G2

Definition at line 1209 of file IBNLearner.h.

1209{ Chi2, G2 };

◆ ParamEstimatorType

enum class gum::learning::IBNLearner::ParamEstimatorType

stronginherited

an enumeration to select the type of parameter estimation we shall apply

Enumerator
ML

Definition at line 111 of file IBNLearner.h.

111{ ML };

◆ ScoreType

enum class gum::learning::IBNLearner::ScoreType

stronginherited

an enumeration enabling to select easily the score we wish to use

Enumerator
AIC
BD
BDeu
BIC
fNML
K2
LOG2LIKELIHOOD
MDL

Definition at line 107 of file IBNLearner.h.

107{ AIC, BD, BDeu, BIC, fNML, K2, LOG2LIKELIHOOD, MDL };

Constructor & Destructor Documentation

◆ BNLearner() [1/5]

template<GUM_Numeric GUM_SCALAR>

gum::learning::BNLearner< GUM_SCALAR >::BNLearner	(	std::string_view	filename,
		const std::vector< std::string > &	missingSymbols = {"?"},
		const bool	induceTypes = true )

default constructor

read the database file for the score / parameter estimation and var names

Parameters

filename	the name of a CSV file containing the dataset
missingSymbols	the set of symbols in the CSV that should be interpreted as missing values
induceTypes	By default, all the values in the dataset are interpreted as "labels", i.e., as categorical values. But if some columns of the dataset have only numerical values, it would certainly be better to tag them as corresponding to integer, range or continuous variables. By setting induceTypes to true, this is precisely what the BNLearner will do.

Referenced by BNLearner(), BNLearner(), addForbiddenArc(), addForbiddenArc(), addForbiddenArc(), addMandatoryArc(), addMandatoryArc(), addMandatoryArc(), addNoChildrenNode(), addNoChildrenNode(), addNoParentNode(), addNoParentNode(), addPossibleEdge(), addPossibleEdge(), addPossibleEdge(), allowArcAdditions(), allowArcDeletions(), allowArcReversals(), allowArcTriangleDeletions(), copyState(), EMdisableEpsilon(), EMdisableMaxIter(), EMdisableMaxTime(), EMdisableMinEpsilonRate(), EMenableEpsilon(), EMenableMaxIter(), EMenableMaxTime(), EMenableMinEpsilonRate(), EMsetEpsilon(), EMsetMaxIter(), EMsetMaxTime(), EMsetMinEpsilonRate(), EMsetPeriodSize(), EMsetVerbosity(), eraseForbiddenArc(), eraseForbiddenArc(), eraseForbiddenArc(), eraseMandatoryArc(), eraseMandatoryArc(), eraseMandatoryArc(), eraseNoChildrenNode(), eraseNoChildrenNode(), eraseNoParentNode(), eraseNoParentNode(), erasePossibleEdge(), erasePossibleEdge(), erasePossibleEdge(), forbidEM(), operator=(), operator=(), setFCIAlpha(), setFCIExhaustiveSepSet(), setFCIMaxPathLength(), setForbiddenArcs(), setGreedyThickThinningReversals(), setInitialDAG(), setMandatoryArcs(), setMaxIndegree(), setPCAlpha(), setPCMaxCondSetSize(), setPCStable(), setPCUnshieldedColliderSorted(), setPossibleEdges(), setPossibleSkeleton(), setSliceOrder(), setTotalOrder(), setTotalOrder(), useBDeuPrior(), useChi2Test(), useDirichletPrior(), useDirichletPrior(), useEM(), useEMWithDiffCriterion(), useEMWithRateCriterion(), useExtendedGreedyHillClimbing(), useFCI(), useFCIChi2Test(), useFCIG2Test(), useG2Test(), useGreedyHillClimbing(), useGreedyThickThinning(), useK2(), useK2(), useLocalSearchWithTabuList(), useMDLCorrection(), useMIIC(), useNMLCorrection(), useNoCorrection(), useNoPrior(), usePC(), useScoreAIC(), useScoreBD(), useScoreBDeu(), useScoreBIC(), useScoreK2(), useScoreLog2Likelihood(), and useSmoothingPrior().

◆ BNLearner() [2/5]

template<GUM_Numeric GUM_SCALAR>

gum::learning::BNLearner< GUM_SCALAR >::BNLearner ( const DatabaseTable & db )

default constructor

read the database file for the score / parameter estimation and var names

Parameters

db	an already initialized database table that is used to fill the Database

◆ BNLearner() [3/5]

template<GUM_Numeric GUM_SCALAR>

gum::learning::BNLearner< GUM_SCALAR >::BNLearner	(	std::string_view	filename,
		const gum::BayesNet< GUM_SCALAR > &	src,
		const std::vector< std::string > &	missing_symbols = {"?"} )

Wrapper for BNLearner (filename,modalities,parse_database) using a bn to find those modalities and nodeids.

◆ BNLearner() [4/5]

template<GUM_Numeric GUM_SCALAR>

gum::learning::BNLearner< GUM_SCALAR >::BNLearner ( const BNLearner< GUM_SCALAR > & )

copy constructor

References BNLearner().

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◆ BNLearner() [5/5]

template<GUM_Numeric GUM_SCALAR>

gum::learning::BNLearner< GUM_SCALAR >::BNLearner ( BNLearner< GUM_SCALAR > && )

move constructor

References BNLearner().

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◆ ~BNLearner()

template<GUM_Numeric GUM_SCALAR>

gum::learning::BNLearner< GUM_SCALAR >::~BNLearner ( )

override

destructor

Member Function Documentation

◆ _checkDAGCompatibility_()

template<GUM_Numeric GUM_SCALAR>

void gum::learning::BNLearner< GUM_SCALAR >::_checkDAGCompatibility_ ( const DAG & dag )

private

check that the database contains the nodes of the dag, else raise an exception

Exceptions

MissingVariableInDatabase if a variable of the BN is not found in the database.

Returns: nothing if all the nodes of the dag belong to the dataset

References _checkDAGCompatibility_().

Referenced by _checkDAGCompatibility_().

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◆ _initializeEMParameterLearning_()

template<GUM_Numeric GUM_SCALAR>

std::pair< std::shared_ptr< ParamEstimator >, std::shared_ptr< ParamEstimator > > gum::learning::BNLearner< GUM_SCALAR >::_initializeEMParameterLearning_	(	const DAG &	dag,
		bool	takeIntoAccountScore )

private

initializes EM and returns a pair containing, first, a bootstrap estimator and, second, the EM estimator

Parameters

dag the graphical structure of the BN learnt by EM

takeIntoAccountScore The dag passed in argument may have been learnt from a structure learning. In this case, if the score used to learn the structure has an implicit prior (like K2 which has a 1-smoothing prior), it is important to also take into account this implicit prior for parameter learning. By default, if a score exists, we will learn parameters by taking into account the prior specified by methods usePriorXXX () + the implicit prior of the score, else we just take into account the prior specified by usePriorXXX ()

Returns: a pair of estimators. The first one is used to fill the CPTs of the returned BN in order to initialize EM. It fills them using the database records without taking into account the missing values. The second estimator is the one used by all the subsequent iterations of the EM algorithm.

References _initializeEMParameterLearning_().

Referenced by _initializeEMParameterLearning_().

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◆ _labelsFromBN_()

template<GUM_Numeric GUM_SCALAR>

NodeProperty< Sequence< std::string > > gum::learning::BNLearner< GUM_SCALAR >::_labelsFromBN_	(	std::string_view	filename,
		const BayesNet< GUM_SCALAR > &	src )

private

read the first line of a file to find column names

References _labelsFromBN_().

Referenced by _labelsFromBN_().

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◆ _learnParameters_()

template<GUM_Numeric GUM_SCALAR>

BayesNet< GUM_SCALAR > gum::learning::BNLearner< GUM_SCALAR >::_learnParameters_	(	const DAG &	dag,
		bool	takeIntoAccountScore )

private

learns a BN (its parameters) with the structure passed in argument using a single pass estimation (not EM)

Parameters

dag the structure of the Bayesian network

takeIntoAccountScore The dag passed in argument may have been learnt from a structure learning. In this case, if the score used to learn the structure has an implicit prior (like K2 which has a 1-smoothing prior), it is important to also take into account this implicit prior for parameter learning. By default, if a score exists, we will learn parameters by taking into account the prior specified by methods usePriorXXX () + the implicit prior of the score, else we just take into account the prior specified by usePriorXXX ()

Exceptions

MissingVariableInDatabase	if a variable of the BN is not found in the database.
MissingValueInDatabase	if the database contains some missing values

References _learnParameters_().

Referenced by _learnParameters_().

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◆ _learnParametersWithEM_() [1/2]

template<GUM_Numeric GUM_SCALAR>

BayesNet< GUM_SCALAR > gum::learning::BNLearner< GUM_SCALAR >::_learnParametersWithEM_	(	const BayesNet< GUM_SCALAR > &	bn,
		bool	takeIntoAccountScore )

private

learns a BN (its parameters) with the structure passed in argument using the EM algorithm initialized by the Bayes net passed in argument

Parameters

bn the Bayesian network used to specify the graphical structure of the returned Bayes net and to initialize its CPTs before running EM. When a CPT is filled exclusively with only zeroes, then this one is initialized by the BNLearner using a specific estimator that does not take into account the missing values in the database

takeIntoAccountScore The dag passed in argument may have been learnt from a structure learning. In this case, if the score used to learn the structure has an implicit prior (like K2 which has a 1-smoothing prior), it is important to also take into account this implicit prior for parameter learning. By default, if a score exists, we will learn parameters by taking into account the prior specified by methods usePriorXXX () + the implicit prior of the score, else we just take into account the prior specified by usePriorXXX ()

Exceptions

MissingVariableInDatabase if a variable of the BN is not found in the database.

Warning: the EM algorithm initializes the parameters of the CPTs using those of the Bayes net passed in argument whenever those are not fully filled with zeroes, else the BNLearner initializes them using an estimator that does not take into account the missing values. If you wish the BNLearner to automatically initialize all the CPTs, use the method in which a DAG is passed in argument rather than a Bayes net.

References _learnParametersWithEM_().

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◆ _learnParametersWithEM_() [2/2]

template<GUM_Numeric GUM_SCALAR>

BayesNet< GUM_SCALAR > gum::learning::BNLearner< GUM_SCALAR >::_learnParametersWithEM_	(	const DAG &	dag,
		bool	takeIntoAccountScore )

private

learns a BN (its parameters) with the structure passed in argument using the EM algorithm initialized by the BNLearner

Parameters

dag the structure of the Bayesian network

takeIntoAccountScore The dag passed in argument may have been learnt from a structure learning. In this case, if the score used to learn the structure has an implicit prior (like K2 which has a 1-smoothing prior), it is important to also take into account this implicit prior for parameter learning. By default, if a score exists, we will learn parameters by taking into account the prior specified by methods usePriorXXX () + the implicit prior of the score, else we just take into account the prior specified by usePriorXXX ()

Exceptions

MissingVariableInDatabase if a variable of the BN is not found in the database.

Warning: the EM algorithm initializes the parameters of the CPTs by running a first estimator that does not take into account missing values. If you wish to initialize them yourself, use the method in which a Bayes net is passed in argument rather than a DAG.

References _learnParametersWithEM_().

Referenced by _learnParametersWithEM_(), and _learnParametersWithEM_().

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◆ _setPriorWeight_()

INLINE void gum::learning::IBNLearner::_setPriorWeight_ ( double weight )

protectedinherited

sets the prior weight

Definition at line 644 of file IBNLearner_inl.h.

                                                        {
    if (weight < 0) { GUM_ERROR(OutOfBounds, "the weight of the prior must be positive") }
 
    priorWeight_ = weight;
    checkScorePriorCompatibility();
  }

References checkScorePriorCompatibility(), GUM_ERROR, and priorWeight_.

Referenced by useBDeuPrior(), useDirichletPrior(), and useSmoothingPrior().

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◆ addForbiddenArc() [1/3]

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::addForbiddenArc ( const Arc & arc )

References BNLearner(), and addForbiddenArc().

Referenced by addForbiddenArc(), addForbiddenArc(), and addForbiddenArc().

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◆ addForbiddenArc() [2/3]

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::addForbiddenArc	(	NodeId	tail,
		NodeId	head )

References BNLearner(), and addForbiddenArc().

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◆ addForbiddenArc() [3/3]

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::addForbiddenArc	(	std::string_view	tail,
		std::string_view	head )

References BNLearner(), and addForbiddenArc().

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◆ addMandatoryArc() [1/3]

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::addMandatoryArc ( const Arc & arc )

References BNLearner(), and addMandatoryArc().

Referenced by addMandatoryArc(), addMandatoryArc(), and addMandatoryArc().

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◆ addMandatoryArc() [2/3]

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::addMandatoryArc	(	NodeId	tail,
		NodeId	head )

References BNLearner(), and addMandatoryArc().

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◆ addMandatoryArc() [3/3]

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::addMandatoryArc	(	std::string_view	tail,
		std::string_view	head )

References BNLearner(), and addMandatoryArc().

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◆ addNoChildrenNode() [1/2]

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::addNoChildrenNode ( NodeId node )

References BNLearner(), and addNoChildrenNode().

Referenced by addNoChildrenNode(), and addNoChildrenNode().

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◆ addNoChildrenNode() [2/2]

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::addNoChildrenNode ( std::string_view name )

References BNLearner(), and addNoChildrenNode().

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◆ addNoParentNode() [1/2]

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::addNoParentNode ( NodeId node )

References BNLearner(), and addNoParentNode().

Referenced by addNoParentNode(), and addNoParentNode().

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◆ addNoParentNode() [2/2]

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::addNoParentNode ( std::string_view name )

References BNLearner(), and addNoParentNode().

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◆ addPossibleEdge() [1/3]

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::addPossibleEdge ( const Edge & edge )

References BNLearner(), and addPossibleEdge().

Referenced by addPossibleEdge(), addPossibleEdge(), and addPossibleEdge().

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◆ addPossibleEdge() [2/3]

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::addPossibleEdge	(	NodeId	tail,
		NodeId	head )

References BNLearner(), and addPossibleEdge().

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◆ addPossibleEdge() [3/3]

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::addPossibleEdge	(	std::string_view	tail,
		std::string_view	head )

References BNLearner(), and addPossibleEdge().

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◆ allowArcAdditions()

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::allowArcAdditions ( bool allow )

References BNLearner(), and allowArcAdditions().

Referenced by allowArcAdditions().

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◆ allowArcDeletions()

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::allowArcDeletions ( bool allow )

References BNLearner(), and allowArcDeletions().

Referenced by allowArcDeletions().

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◆ allowArcReversals()

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::allowArcReversals ( bool allow )

References BNLearner(), and allowArcReversals().

Referenced by allowArcReversals().

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◆ allowArcTriangleDeletions()

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::allowArcTriangleDeletions ( bool allow )

References BNLearner(), and allowArcTriangleDeletions().

Referenced by allowArcTriangleDeletions().

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◆ checkScorePriorCompatibility()

std::string gum::learning::IBNLearner::checkScorePriorCompatibility ( ) const

inherited

checks whether the current score and prior are compatible

Returns: a non empty string if the prior is somehow compatible with the score.

Definition at line 1270 of file IBNLearner.cpp.

                                                           {
    if (this->isConstraintBased()) return "";
 
    const auto prior = getPriorType_();
 
    switch (scoreType_) {
      using enum gum::learning::IBNLearner::ScoreType;
      case AIC : return ScoreAIC::isPriorCompatible(prior, priorWeight_);
 
      case BD : return ScoreBD::isPriorCompatible(prior, priorWeight_);
 
      case BDeu : return ScoreBDeu::isPriorCompatible(prior, priorWeight_);
 
      case BIC : return ScoreBIC::isPriorCompatible(prior, priorWeight_);
 
      case fNML : return ScorefNML::isPriorCompatible(prior, priorWeight_);
 
      case K2 : return ScoreK2::isPriorCompatible(prior, priorWeight_);
 
      case LOG2LIKELIHOOD : return ScoreLog2Likelihood::isPriorCompatible(prior, priorWeight_);
 
      case MDL : return ScoreMDL::isPriorCompatible(prior, priorWeight_);
 
      default : return "IBNLearner does not support yet this score";
    }
  }

References AIC, BD, BDeu, BIC, fNML, getPriorType_(), isConstraintBased(), gum::learning::ScoreAIC::isPriorCompatible(), gum::learning::ScoreBD::isPriorCompatible(), gum::learning::ScoreBDeu::isPriorCompatible(), gum::learning::ScoreBIC::isPriorCompatible(), gum::learning::ScorefNML::isPriorCompatible(), gum::learning::ScoreK2::isPriorCompatible(), gum::learning::ScoreLog2Likelihood::isPriorCompatible(), LOG2LIKELIHOOD, MDL, priorWeight_, and scoreType_.

Referenced by _setPriorWeight_(), useBDeuPrior(), useDirichletPrior(), useNoPrior(), useScoreAIC(), useScoreBD(), useScoreBDeu(), useScoreBIC(), useScorefNML(), useScoreK2(), useScoreLog2Likelihood(), useScoreMDL(), and useSmoothingPrior().

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◆ chi2() [1/2]

std::pair< double, double > gum::learning::IBNLearner::chi2	(	NodeId	id1,
		NodeId	id2,
		const std::vector< NodeId > &	knowing = {} )

inherited

Return the <statistic,pvalue> pair for chi2 test in the database.

Parameters

id1	first variable
id2	second variable
knowing	list of observed variables

Returns: a std::pair<double,double>

Definition at line 1338 of file IBNLearner.cpp.

                                                                                             {
    createPrior_();
    gum::learning::IndepTestChi2 chi2score(scoreDatabase_.parser(), *prior_, databaseRanges());
 
    return chi2score.statistics(id1, id2, knowing);
  }

References createPrior_(), databaseRanges(), prior_, scoreDatabase_, and gum::learning::IndepTestChi2::statistics().

Referenced by chi2().

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◆ chi2() [2/2]

std::pair< double, double > gum::learning::IBNLearner::chi2	(	std::string_view	name1,
		std::string_view	name2,
		const std::vector< std::string > &	knowing = {} )

inherited

Return the <statistic,pvalue> pair for the BNLearner.

Parameters

id1	first variable
id2	second variable
knowing	list of observed variables

Returns: a std::pair<double,double>

Definition at line 1345 of file IBNLearner.cpp.

                                                                                      {
    std::vector< NodeId > knowingIds;
    std::transform(knowing.begin(),
                   knowing.end(),
                   std::back_inserter(knowingIds),
                   [this](const std::string& c) { return this->idFromName(c); });
    return chi2(idFromName(name1), idFromName(name2), knowingIds);
  }

References chi2(), and idFromName().

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◆ clearDatabaseRanges()

INLINE void gum::learning::IBNLearner::clearDatabaseRanges ( )

inherited

reset the ranges to the one range corresponding to the whole database

Definition at line 729 of file IBNLearner_inl.h.

729{ ranges_.clear(); }

gum::learning::IBNLearner::ranges_

std::vector< std::pair< std::size_t, std::size_t > > ranges_

the set of rows' ranges within the database in which learning is done

Definition IBNLearner.h:1254

References ranges_.

◆ copyState()

template<GUM_Numeric GUM_SCALAR>

void gum::learning::BNLearner< GUM_SCALAR >::copyState ( const BNLearner< GUM_SCALAR > & learner )

copy the states of the BNLearner

Warning: except the database ! just the configurations of the learner

References BNLearner(), and copyState().

Referenced by copyState().

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◆ correctedMutualInformation() [1/2]

double gum::learning::IBNLearner::correctedMutualInformation	(	NodeId	id1,
		NodeId	id2,
		const std::vector< NodeId > &	knowing = {} )

inherited

Return the mutual information of id1 and id2 in the base, conditioned by knowing for the BNLearner.

Warning: This function returns the mutual information corrected using defined correction (useNML, useMDL) and prior

Parameters

id1	nodeId
id2	nodeId
knowing	an optional vector of conditioning NodeIds

Returns: a double

Definition at line 1403 of file IBNLearner.cpp.

                                                                                    {
    createPrior_();
    gum::learning::CorrectedMutualInformation cmi(scoreDatabase_.parser(),
                                                  *prior_,
                                                  databaseRanges());
 
    switch (kmodeMiic_) {
      using enum gum::learning::CorrectedMutualInformation::KModeTypes;
      case MDL : cmi.useMDL(); break;
 
      case NML : cmi.useNML(); break;
 
      case NoCorr : cmi.useNoCorr(); break;
 
      default :
        GUM_ERROR(NotImplementedYet,
                  "The BNLearner's corrected mutual information class does "
                      << "not implement yet this correction : " << int(kmodeMiic_))
    }
    if (knowing.size() == (Size)0) return cmi.score(id1, id2) / scoreDatabase_.weight();
    else return cmi.score(id1, id2, knowing) / scoreDatabase_.weight();
  }

References createPrior_(), databaseRanges(), GUM_ERROR, kmodeMiic_, MDL, prior_, gum::learning::CorrectedMutualInformation::score(), scoreDatabase_, gum::learning::CorrectedMutualInformation::useMDL(), gum::learning::CorrectedMutualInformation::useNML(), and gum::learning::CorrectedMutualInformation::useNoCorr().

Referenced by correctedMutualInformation().

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◆ correctedMutualInformation() [2/2]

double gum::learning::IBNLearner::correctedMutualInformation	(	std::string_view	var1,
		std::string_view	var2,
		const std::vector< std::string > &	knowing = {} )

inherited

Return the mutual information of var1 and var2 in the base, conditioned by knowing for the BNLearner.

Warning: This function returns the mutual information corrected using defined correction (useNML, useMDL) and prior; This function returns the bare mutual information (without prior or correction)

Parameters

var1	name of a row
var2	name of a row
knowing	an optional vector of conditioning rows

Returns: a double

Definition at line 1428 of file IBNLearner.cpp.

                                                                                       {
    std::vector< NodeId > knowingIds;
 
    auto mapper = [this](const std::string& c) { return this->idFromName(c); };
 
    std::transform(knowing.begin(), knowing.end(), std::back_inserter(knowingIds), mapper);
 
    return correctedMutualInformation(this->idFromName(var1), this->idFromName(var2), knowingIds);
  }

References correctedMutualInformation(), and idFromName().

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◆ createCorrectedMutualInformation_()

void gum::learning::IBNLearner::createCorrectedMutualInformation_ ( )

protectedinherited

create the Corrected Mutual Information instance for Miic

Definition at line 966 of file IBNLearner.cpp.

                                                     {
    if (mutualInfo_ != nullptr) delete mutualInfo_;
 
    mutualInfo_ = new CorrectedMutualInformation(scoreDatabase_.parser(),
                                                 *noPrior_,
                                                 ranges_,
                                                 scoreDatabase_.nodeId2Columns());
    switch (kmodeMiic_) {
      using enum CorrectedMutualInformation::KModeTypes;
      case MDL : mutualInfo_->useMDL(); break;
      case NML : mutualInfo_->useNML(); break;
      case NoCorr : mutualInfo_->useNoCorr(); break;
      default :
        GUM_ERROR(NotImplementedYet,
                  "The BNLearner's corrected mutual information class does "
                      << "not implement yet this correction : " << int(kmodeMiic_))
    }
  }

References GUM_ERROR, kmodeMiic_, MDL, mutualInfo_, noPrior_, ranges_, and scoreDatabase_.

Referenced by prepareMiic_().

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◆ createParamEstimator_()

ParamEstimator * gum::learning::IBNLearner::createParamEstimator_	(	const DBRowGeneratorParser &	parser,
		bool	take_into_account_score = true )

protectedinherited

create the parameter estimator used for learning

Definition at line 544 of file IBNLearner.cpp.

                                                                                  {
    ParamEstimator* param_estimator = nullptr;
 
    // create the new estimator
    switch (paramEstimatorType_) {
      case ParamEstimatorType::ML :
        if (take_into_account_score && (score_ != nullptr)) {
          param_estimator = new ParamEstimatorML(parser,
                                                 *prior_,
                                                 score_->internalPrior(),
                                                 ranges_,
                                                 scoreDatabase_.nodeId2Columns());
        } else {
          param_estimator = new ParamEstimatorML(parser,
                                                 *prior_,
                                                 *noPrior_,
                                                 ranges_,
                                                 scoreDatabase_.nodeId2Columns());
        }
 
        break;
 
      default :
        GUM_ERROR(OperationNotAllowed,
                  "IBNLearner does not support " << "yet this parameter estimator")
    }
 
    // assign the number of threads
    param_estimator->setNumberOfThreads(
        this->isGumNumberOfThreadsOverriden() ? this->getNumberOfThreads() : 0);
 
    // assign the set of ranges
    param_estimator->setRanges(ranges_);
 
    return param_estimator;
  }

References gum::ThreadNumberManager::getNumberOfThreads(), GUM_ERROR, gum::ThreadNumberManager::isGumNumberOfThreadsOverriden(), ML, noPrior_, paramEstimatorType_, prior_, ranges_, score_, scoreDatabase_, gum::learning::ParamEstimator::setNumberOfThreads(), and gum::learning::ParamEstimator::setRanges().

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◆ createPrior_()

template<GUM_Numeric GUM_SCALAR>

void gum::learning::BNLearner< GUM_SCALAR >::createPrior_ ( )

overrideprotectedvirtual

create the prior used for learning

Implements gum::learning::IBNLearner.

References createPrior_().

Referenced by createPrior_().

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◆ createScore_()

void gum::learning::IBNLearner::createScore_ ( )

protectedinherited

create the score used for learning

Definition at line 471 of file IBNLearner.cpp.

                                {
    // first, save the old score, to be delete if everything is ok
    Score* old_score = score_;
 
    // create the new scoring function
    switch (scoreType_) {
      case ScoreType::AIC :
        score_ = new ScoreAIC(scoreDatabase_.parser(),
                              *prior_,
                              ranges_,
                              scoreDatabase_.nodeId2Columns());
        break;
 
      case ScoreType::BD :
        score_ = new ScoreBD(scoreDatabase_.parser(),
                             *prior_,
                             ranges_,
                             scoreDatabase_.nodeId2Columns());
        break;
 
      case ScoreType::BDeu :
        score_ = new ScoreBDeu(scoreDatabase_.parser(),
                               *prior_,
                               ranges_,
                               scoreDatabase_.nodeId2Columns());
        break;
 
      case ScoreType::BIC :
        score_ = new ScoreBIC(scoreDatabase_.parser(),
                              *prior_,
                              ranges_,
                              scoreDatabase_.nodeId2Columns());
        break;
 
      case ScoreType::fNML :
        score_ = new ScorefNML(scoreDatabase_.parser(),
                               *prior_,
                               ranges_,
                               scoreDatabase_.nodeId2Columns());
        break;
 
      case ScoreType::K2 :
        score_ = new ScoreK2(scoreDatabase_.parser(),
                             *prior_,
                             ranges_,
                             scoreDatabase_.nodeId2Columns());
        break;
 
      case ScoreType::LOG2LIKELIHOOD :
        score_ = new ScoreLog2Likelihood(scoreDatabase_.parser(),
                                         *prior_,
                                         ranges_,
                                         scoreDatabase_.nodeId2Columns());
        break;
 
      case ScoreType::MDL :
        score_ = new ScoreMDL(scoreDatabase_.parser(),
                              *prior_,
                              ranges_,
                              scoreDatabase_.nodeId2Columns());
        break;
 
      default : GUM_ERROR(OperationNotAllowed, "IBNLearner does not support yet this score")
    }
 
    // remove the old score, if any
    if (old_score != nullptr) delete old_score;
 
    // assign the number of threads
    score_->setNumberOfThreads(this->isGumNumberOfThreadsOverriden() ? this->getNumberOfThreads()
                                                                     : 0);
  }

References AIC, BD, BDeu, BIC, fNML, gum::ThreadNumberManager::getNumberOfThreads(), GUM_ERROR, gum::ThreadNumberManager::isGumNumberOfThreadsOverriden(), K2, LOG2LIKELIHOOD, MDL, prior_, ranges_, score_, scoreDatabase_, and scoreType_.

Referenced by learnDAG(), and score().

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◆ currentTime()

INLINE double gum::learning::IBNLearner::currentTime ( ) const

overridevirtualinherited

get the current running time in second (double)

Implements gum::IApproximationSchemeConfiguration.

Definition at line 890 of file IBNLearner_inl.h.

                                              {
    if (currentAlgorithm_ != nullptr) return currentAlgorithm_->currentTime();
    else GUM_ERROR(FatalError, "No chosen algorithm for learning")
  }

References currentAlgorithm_, and GUM_ERROR.

◆ database()

INLINE const DatabaseTable & gum::learning::IBNLearner::database ( ) const

inherited

returns the database used by the BNLearner

Definition at line 732 of file IBNLearner_inl.h.

                                                         {
    return scoreDatabase_.databaseTable();
  }

References scoreDatabase_.

Referenced by readFile_().

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◆ databaseRanges()

INLINE const std::vector< std::pair< std::size_t, std::size_t > > & gum::learning::IBNLearner::databaseRanges ( ) const

inherited

returns the current database rows' ranges used for learning

Returns: The method returns a vector of pairs [Xi,Yi) of indices of rows in the database. The learning is performed on these set of rows.

Warning: an empty set of ranges means the whole database.

Definition at line 724 of file IBNLearner_inl.h.

                                                {
    return ranges_;
  }

References ranges_.

Referenced by chi2(), correctedMutualInformation(), G2(), logLikelihood(), mutualInformation(), and rawPseudoCount().

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◆ databaseWeight()

INLINE double gum::learning::IBNLearner::databaseWeight ( ) const

inherited

returns the weight of the whole database

Definition at line 161 of file IBNLearner_inl.h.

161{ return scoreDatabase_.weight(); }

References scoreDatabase_.

◆ disableEpsilon()

INLINE void gum::learning::IBNLearner::disableEpsilon ( )

overridevirtualinherited

Disable stopping criterion on epsilon.

Implements gum::IApproximationSchemeConfiguration.

Definition at line 797 of file IBNLearner_inl.h.

                                         {
    algoK2_.approximationScheme().disableEpsilon();
    greedyHillClimbing_.disableEpsilon();
    localSearchWithTabuList_.disableEpsilon();
    dag2BN_.disableEpsilon();
  }

References algoK2_, dag2BN_, greedyHillClimbing_, and localSearchWithTabuList_.

◆ disableMaxIter()

INLINE void gum::learning::IBNLearner::disableMaxIter ( )

overridevirtualinherited

Disable stopping criterion on max iterations.

Implements gum::IApproximationSchemeConfiguration.

Definition at line 859 of file IBNLearner_inl.h.

                                         {
    algoK2_.approximationScheme().disableMaxIter();
    greedyHillClimbing_.disableMaxIter();
    localSearchWithTabuList_.disableMaxIter();
    dag2BN_.disableMaxIter();
  }

References algoK2_, dag2BN_, greedyHillClimbing_, and localSearchWithTabuList_.

◆ disableMaxTime()

INLINE void gum::learning::IBNLearner::disableMaxTime ( )

overridevirtualinherited

Disable stopping criterion on timeout.

Implements gum::IApproximationSchemeConfiguration.

Definition at line 895 of file IBNLearner_inl.h.

                                         {
    algoK2_.approximationScheme().disableMaxTime();
    greedyHillClimbing_.disableMaxTime();
    localSearchWithTabuList_.disableMaxTime();
    dag2BN_.disableMaxTime();
  }

References algoK2_, dag2BN_, greedyHillClimbing_, and localSearchWithTabuList_.

◆ disableMinEpsilonRate()

INLINE void gum::learning::IBNLearner::disableMinEpsilonRate ( )

overridevirtualinherited

Disable stopping criterion on epsilon rate.

Implements gum::IApproximationSchemeConfiguration.

Definition at line 828 of file IBNLearner_inl.h.

                                                {
    algoK2_.approximationScheme().disableMinEpsilonRate();
    greedyHillClimbing_.disableMinEpsilonRate();
    localSearchWithTabuList_.disableMinEpsilonRate();
    dag2BN_.disableMinEpsilonRate();
  }

References algoK2_, dag2BN_, greedyHillClimbing_, and localSearchWithTabuList_.

◆ distributeProgress()

INLINE void gum::learning::IBNLearner::distributeProgress	(	const ApproximationScheme *	approximationScheme,
		Size	pourcent,
		double	error,
		double	time )

inherited

{@ /// distribute signals

Definition at line 771 of file IBNLearner_inl.h.

                                                                              {
    setCurrentApproximationScheme(approximationScheme);
    if (onProgress.hasListener()) GUM_EMIT3(onProgress, pourcent, error, time);
  }

References GUM_EMIT3, gum::IApproximationSchemeConfiguration::onProgress, and setCurrentApproximationScheme().

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◆ distributeStop()

INLINE void gum::learning::IBNLearner::distributeStop	(	const ApproximationScheme *	approximationScheme,
		std::string_view	message )

inherited

distribute signals

Definition at line 779 of file IBNLearner_inl.h.

                                                                           {
    setCurrentApproximationScheme(approximationScheme);
    if (onStop.hasListener()) GUM_EMIT1(onStop, message);
  }

References GUM_EMIT1, gum::IApproximationSchemeConfiguration::onStop, and setCurrentApproximationScheme().

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◆ domainSize() [1/2]

INLINE Size gum::learning::IBNLearner::domainSize ( NodeId var ) const

inherited

learn a structure from a file (must have read the db before)

Definition at line 715 of file IBNLearner_inl.h.

715{ return scoreDatabase_.domainSizes()[var]; }

References scoreDatabase_.

◆ domainSize() [2/2]

INLINE Size gum::learning::IBNLearner::domainSize ( std::string_view var ) const

inherited

learn a structure from a file (must have read the db before)

Definition at line 718 of file IBNLearner_inl.h.

                                                             {
    return scoreDatabase_.domainSizes()[idFromName(var)];
  }

References idFromName(), and scoreDatabase_.

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◆ domainSizes()

INLINE const std::vector< std::size_t > & gum::learning::IBNLearner::domainSizes ( ) const

inherited

returns the domain sizes of the variables in the database

Definition at line 710 of file IBNLearner_inl.h.

                                                                     {
    return scoreDatabase_.domainSizes();
  }

References scoreDatabase_.

◆ EM()

INLINE EMApproximationScheme & gum::learning::IBNLearner::EM ( )

inherited

returns the EM parameter learning approximation scheme if EM is enabled

returns the EM parameter learning approximation scheme

Returns: returns the EM parameter learning approximation scheme if EM is enabled, else if raises a NotFound exception. The scheme can then be subsequently used to fine-tune the EM algorithm, e.g., by setting its max time or max number of iterations.

Exceptions

NotFound is raised if EM() is called while the EM algorithm has not been enabled by useEM(), useEMWithDiffCriterion() or useEMWithRateCriterion().

Definition at line 436 of file IBNLearner_inl.h.

                                               {
    if (useEM_) return dag2BN_;
    else GUM_ERROR(NotFound, "EM is currently forbidden. Please enable it with useEM()")
  }

References dag2BN_, GUM_ERROR, and useEM_.

◆ EMCurrentTime()

INLINE double gum::learning::IBNLearner::EMCurrentTime ( ) const

inherited

get the current running time in second (double)

Definition at line 992 of file IBNLearner_inl.h.

992{ return dag2BN_.currentTime(); }

References dag2BN_.

◆ EMdisableEpsilon()

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::EMdisableEpsilon ( )

Disable the min log-likelihood diff stopping criterion.

References BNLearner(), and EMdisableEpsilon().

Referenced by EMdisableEpsilon().

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◆ EMdisableMaxIter()

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::EMdisableMaxIter ( )

Disable stopping criterion on max iterations.

References BNLearner(), and EMdisableMaxIter().

Referenced by EMdisableMaxIter().

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◆ EMdisableMaxTime()

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::EMdisableMaxTime ( )

Disable EM's timeout stopping criterion.

References BNLearner(), and EMdisableMaxTime().

Referenced by EMdisableMaxTime().

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◆ EMdisableMinEpsilonRate()

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::EMdisableMinEpsilonRate ( )

Disable the log-likelihood evolution rate stopping criterion.

References BNLearner(), and EMdisableMinEpsilonRate().

Referenced by EMdisableMinEpsilonRate().

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◆ EMenableEpsilon()

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::EMenableEpsilon ( )

Enable the log-likelihood min diff stopping criterion in EM.

Warning: setting this stopping criterion disables the min rate criterion (if it was enabled)

References BNLearner(), and EMenableEpsilon().

Referenced by EMenableEpsilon().

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◆ EMenableMaxIter()

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::EMenableMaxIter ( )

Enable stopping criterion on max iterations.

References BNLearner(), and EMenableMaxIter().

Referenced by EMenableMaxIter().

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◆ EMenableMaxTime()

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::EMenableMaxTime ( )

enable EM's timeout stopping criterion

References BNLearner(), and EMenableMaxTime().

Referenced by EMenableMaxTime().

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◆ EMenableMinEpsilonRate()

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::EMenableMinEpsilonRate ( )

Enable the log-likelihood evolution rate stopping criterion.

Warning: setting this stopping criterion disables the min diff criterion (if it was enabled)

References BNLearner(), and EMenableMinEpsilonRate().

Referenced by EMenableMinEpsilonRate().

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◆ EMEpsilon()

INLINE double gum::learning::IBNLearner::EMEpsilon ( ) const

inherited

Get the value of EM's min diff epsilon.

Get the value of EM's min diff epsilon

Warning: Note that this value is not taken into account unless the min diff criterion is enabled

Definition at line 958 of file IBNLearner_inl.h.

958{ return dag2BN_.epsilon(); }

References dag2BN_.

◆ EMHistory()

INLINE const std::vector< double > & gum::learning::IBNLearner::EMHistory ( ) const

inherited

returns the history of the last EM execution

Warning: to activate the history recording, EM's verbosity must be set to true

Definition at line 1015 of file IBNLearner_inl.h.

1015{ return dag2BN_.history(); }

References dag2BN_.

◆ EMisEnabledEpsilon()

INLINE bool gum::learning::IBNLearner::EMisEnabledEpsilon ( ) const

inherited

return true if EM's stopping criterion is the log-likelihood min diff

Definition at line 964 of file IBNLearner_inl.h.

964{ return dag2BN_.isEnabledEpsilon(); }

References dag2BN_.

◆ EMisEnabledMaxIter()

INLINE bool gum::learning::IBNLearner::EMisEnabledMaxIter ( ) const

inherited

Returns: true if stopping criterion on max iterations is enabled, false otherwise

Definition at line 986 of file IBNLearner_inl.h.

986{ return dag2BN_.isEnabledMaxIter(); }

References dag2BN_.

◆ EMisEnabledMaxTime()

INLINE bool gum::learning::IBNLearner::EMisEnabledMaxTime ( ) const

inherited

Returns: true if stopping criterion on timeout is enabled, false otherwise

Definition at line 998 of file IBNLearner_inl.h.

998{ return dag2BN_.isEnabledMaxTime(); }

References dag2BN_.

◆ EMisEnabledMinEpsilonRate()

INLINE bool gum::learning::IBNLearner::EMisEnabledMinEpsilonRate ( ) const

inherited

Returns: true if EM's stopping criterion is the log-likelihood evolution rate

Definition at line 974 of file IBNLearner_inl.h.

                                                          {
    return dag2BN_.isEnabledMinEpsilonRate();
  }

References dag2BN_.

◆ EMMaxIter()

INLINE Size gum::learning::IBNLearner::EMMaxIter ( ) const

inherited

return the max number of iterations criterion

Warning: Note that this value is not taken into account unless the max iter criterion is enabled

Definition at line 980 of file IBNLearner_inl.h.

980{ return dag2BN_.maxIter(); }

References dag2BN_.

◆ EMMaxTime()

INLINE double gum::learning::IBNLearner::EMMaxTime ( ) const

inherited

@brief returns EM's timeout (in milliseconds)

Warning: Note that this value is not taken into account unless the max time criterion is enabled

Definition at line 990 of file IBNLearner_inl.h.

990{ return dag2BN_.maxTime(); }

References dag2BN_.

◆ EMMinEpsilonRate()

INLINE double gum::learning::IBNLearner::EMMinEpsilonRate ( ) const

inherited

Get the value of the minimal log-likelihood evolution rate of EM.

Warning: Note that this value is not taken into account unless the min rate criterion is enabled

Definition at line 968 of file IBNLearner_inl.h.

968{ return dag2BN_.minEpsilonRate(); }

References dag2BN_.

◆ EMnbrIterations()

INLINE Size gum::learning::IBNLearner::EMnbrIterations ( ) const

inherited

returns the number of iterations performed by the last EM execution

Definition at line 1013 of file IBNLearner_inl.h.

1013{ return dag2BN_.nbrIterations(); }

References dag2BN_.

◆ EMPeriodSize()

template<GUM_Numeric GUM_SCALAR>

INLINE Size gum::learning::IBNLearner::EMPeriodSize ( ) const

Definition at line 1569 of file IBNLearner_inl.h.

1002{ return dag2BN_.periodSize(); }

Referenced by EMsetPeriodSize().

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◆ EMsetEpsilon()

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::EMsetEpsilon ( const double eps )

sets the stopping criterion of EM as being the minimal difference between two consecutive log-likelihoods

Parameters

eps	the log-likelihood difference below which EM stops its iterations

Warning: setting this stopping criterion disables the min rate criterion (if it was enabled)

Exceptions

OutOfBounds if eps <= 0

References BNLearner(), and EMsetEpsilon().

Referenced by EMsetEpsilon().

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◆ EMsetMaxIter()

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::EMsetMaxIter ( const Size max )

add a max iteration stopping criterion

Parameters

max	the max number of iterations that EM is allowed to perform

Exceptions

OutOfBounds if max<=1

References BNLearner(), and EMsetMaxIter().

Referenced by EMsetMaxIter().

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◆ EMsetMaxTime()

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::EMsetMaxTime ( const double timeout )

add a stopping criterion on timeout

Parameters

timeout the timeout in milliseconds

Exceptions

OutOfBounds if timeout<=0.0

References BNLearner(), and EMsetMaxTime().

Referenced by EMsetMaxTime().

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◆ EMsetMinEpsilonRate()

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::EMsetMinEpsilonRate ( const double rate )

sets the stopping criterion of EM as being the minimal log-likelihood's evolution rate

Parameters

rate	the log-likelihood evolution rate below which EM stops its iterations

Warning: setting this stopping criterion disables the min diff criterion (if it was enabled)

Exceptions

OutOfBounds if rate<=0

References BNLearner(), and EMsetMinEpsilonRate().

Referenced by EMsetMinEpsilonRate().

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◆ EMsetPeriodSize()

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::EMsetPeriodSize ( const Size p )

how many samples between 2 stoppings isEnabled

Exceptions

OutOfBounds if p<1

References BNLearner(), gum::learning::IBNLearner::IBNLearner(), EMPeriodSize(), and EMsetPeriodSize().

Referenced by EMsetPeriodSize().

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◆ EMsetVerbosity()

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::EMsetVerbosity ( const bool v )

sets or unsets EM's verbosity

References BNLearner(), and EMsetVerbosity().

Referenced by EMsetVerbosity().

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◆ EMState()

INLINE IApproximationSchemeConfiguration::ApproximationSchemeSTATE gum::learning::IBNLearner::EMState ( ) const

inherited

returns the state of the last EM algorithm executed

Definition at line 442 of file IBNLearner_inl.h.

                                                                                             {
    if (useEM_) return dag2BN_.stateApproximationScheme();
    else return IApproximationSchemeConfiguration::ApproximationSchemeSTATE::Undefined;
  }

References dag2BN_, gum::IApproximationSchemeConfiguration::Undefined, and useEM_.

◆ EMStateApproximationScheme()

INLINE IApproximationSchemeConfiguration::ApproximationSchemeSTATE gum::learning::IBNLearner::EMStateApproximationScheme ( ) const

inherited

get the current state of EM

Definition at line 1009 of file IBNLearner_inl.h.

                                                      {
    return dag2BN_.stateApproximationScheme();
  }

References dag2BN_.

◆ EMStateMessage()

INLINE std::string gum::learning::IBNLearner::EMStateMessage ( ) const

inherited

returns the state of the EM algorithm

Definition at line 448 of file IBNLearner_inl.h.

                                                    {
    if (useEM_) return dag2BN_.messageApproximationScheme();
    else return "EM is currently forbidden. Please enable it with useEM()";
  }

References dag2BN_, and useEM_.

◆ EMVerbosity()

INLINE bool gum::learning::IBNLearner::EMVerbosity ( ) const

inherited

returns the EM's verbosity status

Definition at line 1006 of file IBNLearner_inl.h.

1006{ return dag2BN_.verbosity(); }

References dag2BN_.

◆ enableEpsilon()

INLINE void gum::learning::IBNLearner::enableEpsilon ( )

overridevirtualinherited

Enable stopping criterion on epsilon.

Implements gum::IApproximationSchemeConfiguration.

Definition at line 804 of file IBNLearner_inl.h.

                                        {
    algoK2_.approximationScheme().enableEpsilon();
    greedyHillClimbing_.enableEpsilon();
    localSearchWithTabuList_.enableEpsilon();
    dag2BN_.enableEpsilon();
  }

References algoK2_, dag2BN_, greedyHillClimbing_, and localSearchWithTabuList_.

◆ enableMaxIter()

INLINE void gum::learning::IBNLearner::enableMaxIter ( )

overridevirtualinherited

Enable stopping criterion on max iterations.

Implements gum::IApproximationSchemeConfiguration.

Definition at line 866 of file IBNLearner_inl.h.

                                        {
    algoK2_.approximationScheme().enableMaxIter();
    greedyHillClimbing_.enableMaxIter();
    localSearchWithTabuList_.enableMaxIter();
    dag2BN_.enableMaxIter();
  }

References algoK2_, dag2BN_, greedyHillClimbing_, and localSearchWithTabuList_.

◆ enableMaxTime()

INLINE void gum::learning::IBNLearner::enableMaxTime ( )

overridevirtualinherited

stopping criterion on timeout If the criterion was disabled it will be enabled

Exceptions

OutOfBounds if timeout<=0.0 timeout is time in second (double).

Implements gum::IApproximationSchemeConfiguration.

Definition at line 902 of file IBNLearner_inl.h.

                                        {
    algoK2_.approximationScheme().enableMaxTime();
    greedyHillClimbing_.enableMaxTime();
    localSearchWithTabuList_.enableMaxTime();
    dag2BN_.enableMaxTime();
  }

References algoK2_, dag2BN_, greedyHillClimbing_, and localSearchWithTabuList_.

◆ enableMinEpsilonRate()

INLINE void gum::learning::IBNLearner::enableMinEpsilonRate ( )

overridevirtualinherited

Enable stopping criterion on epsilon rate.

Implements gum::IApproximationSchemeConfiguration.

Definition at line 835 of file IBNLearner_inl.h.

                                               {
    algoK2_.approximationScheme().enableMinEpsilonRate();
    greedyHillClimbing_.enableMinEpsilonRate();
    localSearchWithTabuList_.enableMinEpsilonRate();
    dag2BN_.enableMinEpsilonRate();
  }

References algoK2_, dag2BN_, greedyHillClimbing_, and localSearchWithTabuList_.

◆ epsilon()

INLINE double gum::learning::IBNLearner::epsilon ( ) const

overridevirtualinherited

Get the value of epsilon.

Implements gum::IApproximationSchemeConfiguration.

Definition at line 792 of file IBNLearner_inl.h.

                                          {
    if (currentAlgorithm_ != nullptr) return currentAlgorithm_->epsilon();
    else GUM_ERROR(FatalError, "No chosen algorithm for learning")
  }

References currentAlgorithm_, and GUM_ERROR.

Referenced by gum::learning::BNLearner< GUM_SCALAR >::useEM(), useEM(), gum::learning::BNLearner< GUM_SCALAR >::useEMWithDiffCriterion(), useEMWithDiffCriterion(), gum::learning::BNLearner< GUM_SCALAR >::useEMWithRateCriterion(), and useEMWithRateCriterion().

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◆ eraseForbiddenArc() [1/3]

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::eraseForbiddenArc ( const Arc & arc )

References BNLearner(), and eraseForbiddenArc().

Referenced by eraseForbiddenArc(), eraseForbiddenArc(), and eraseForbiddenArc().

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◆ eraseForbiddenArc() [2/3]

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::eraseForbiddenArc	(	NodeId	tail,
		NodeId	head )

References BNLearner(), and eraseForbiddenArc().

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◆ eraseForbiddenArc() [3/3]

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::eraseForbiddenArc	(	std::string_view	tail,
		std::string_view	head )

References BNLearner(), and eraseForbiddenArc().

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◆ eraseMandatoryArc() [1/3]

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::eraseMandatoryArc ( const Arc & arc )

References BNLearner(), and eraseMandatoryArc().

Referenced by eraseMandatoryArc(), eraseMandatoryArc(), and eraseMandatoryArc().

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◆ eraseMandatoryArc() [2/3]

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::eraseMandatoryArc	(	NodeId	tail,
		NodeId	head )

References BNLearner(), and eraseMandatoryArc().

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◆ eraseMandatoryArc() [3/3]

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::eraseMandatoryArc	(	std::string_view	tail,
		std::string_view	head )

References BNLearner(), and eraseMandatoryArc().

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◆ eraseNoChildrenNode() [1/2]

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::eraseNoChildrenNode ( NodeId node )

References BNLearner(), and eraseNoChildrenNode().

Referenced by eraseNoChildrenNode(), and eraseNoChildrenNode().

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◆ eraseNoChildrenNode() [2/2]

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::eraseNoChildrenNode ( std::string_view name )

References BNLearner(), and eraseNoChildrenNode().

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◆ eraseNoParentNode() [1/2]

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::eraseNoParentNode ( NodeId node )

References BNLearner(), and eraseNoParentNode().

Referenced by eraseNoParentNode(), and eraseNoParentNode().

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◆ eraseNoParentNode() [2/2]

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::eraseNoParentNode ( std::string_view name )

References BNLearner(), and eraseNoParentNode().

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◆ erasePossibleEdge() [1/3]

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::erasePossibleEdge ( const Edge & edge )

References BNLearner(), and erasePossibleEdge().

Referenced by erasePossibleEdge(), erasePossibleEdge(), and erasePossibleEdge().

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◆ erasePossibleEdge() [2/3]

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::erasePossibleEdge	(	NodeId	tail,
		NodeId	head )

References BNLearner(), and erasePossibleEdge().

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◆ erasePossibleEdge() [3/3]

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::erasePossibleEdge	(	std::string_view	tail,
		std::string_view	head )

References BNLearner(), and erasePossibleEdge().

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◆ fciExhaustiveSepSet()

template<GUM_Numeric GUM_SCALAR>

bool gum::learning::BNLearner< GUM_SCALAR >::fciExhaustiveSepSet ( ) const

References fciExhaustiveSepSet().

Referenced by fciExhaustiveSepSet().

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◆ forbidEM()

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::forbidEM ( )

prevent using the EM algorithm for parameter learning

References BNLearner(), and forbidEM().

Referenced by forbidEM().

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◆ G2() [1/2]

std::pair< double, double > gum::learning::IBNLearner::G2	(	NodeId	id1,
		NodeId	id2,
		const std::vector< NodeId > &	knowing = {} )

inherited

Return the <statistic,pvalue> pair for for G2 test in the database.

Parameters

id1	first variable
id2	second variable
knowing	list of observed variables

Returns: a std::pair<double,double>

Definition at line 1357 of file IBNLearner.cpp.

                                                                                           {
    createPrior_();
    gum::learning::IndepTestG2 g2score(scoreDatabase_.parser(), *prior_, databaseRanges());
    return g2score.statistics(id1, id2, knowing);
  }

References createPrior_(), databaseRanges(), prior_, scoreDatabase_, and gum::learning::IndepTestG2::statistics().

Referenced by G2().

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◆ G2() [2/2]

std::pair< double, double > gum::learning::IBNLearner::G2	(	std::string_view	name1,
		std::string_view	name2,
		const std::vector< std::string > &	knowing = {} )

inherited

Return the <statistic,pvalue> pair for for G2 test in the database.

Parameters

id1	first variable
id2	second variable
knowing	list of observed variables

Returns: a std::pair<double,double>

Definition at line 1363 of file IBNLearner.cpp.

                                                                                    {
    std::vector< NodeId > knowingIds;
    std::transform(knowing.begin(),
                   knowing.end(),
                   std::back_inserter(knowingIds),
                   [this](const std::string& c) { return this->idFromName(c); });
    return G2(idFromName(name1), idFromName(name2), knowingIds);
  }

References G2(), and idFromName().

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◆ getNumberOfThreads()

Size gum::ThreadNumberManager::getNumberOfThreads ( ) const

nodiscardoverridevirtualinherited

returns the current max number of threads used by the class containing this ThreadNumberManager

Implements gum::IThreadNumberManager.

Referenced by gum::learning::IBNLearner::createParamEstimator_(), gum::learning::IBNLearner::createScore_(), gum::credal::InferenceEngine< GUM_SCALAR >::dispatchMarginalsToThreads_(), gum::credal::MultipleInferenceEngine< GUM_SCALAR, BNInferenceEngine >::expFusion_(), gum::ScheduledInference::scheduler(), and gum::credal::MultipleInferenceEngine< GUM_SCALAR, BNInferenceEngine >::verticesFusion_().

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◆ getPriorType_()

INLINE PriorType gum::learning::IBNLearner::getPriorType_ ( ) const

protectedinherited

returns the type (as a string) of a given prior

Definition at line 689 of file IBNLearner_inl.h.

                                                   {
    switch (priorType_) {
      using enum gum::learning::IBNLearner::BNLearnerPriorType;
      case NO_prior : return PriorType::NoPriorType;
      case SMOOTHING : return PriorType::SmoothingPriorType;
      case DIRICHLET_FROM_DATABASE :
      case DIRICHLET_FROM_BAYESNET : return PriorType::DirichletPriorType;
      case BDEU : return PriorType::BDeuPriorType;
      default :
        GUM_ERROR(OperationNotAllowed,
                  "IBNLearner getPriorType does "
                  "not support yet this prior")
    }
  }

References BDEU, gum::learning::BDeuPriorType, DIRICHLET_FROM_BAYESNET, DIRICHLET_FROM_DATABASE, gum::learning::DirichletPriorType, GUM_ERROR, NO_prior, gum::learning::NoPriorType, priorType_, SMOOTHING, and gum::learning::SmoothingPriorType.

Referenced by checkScorePriorCompatibility().

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◆ greedyThickThinningReversals()

template<GUM_Numeric GUM_SCALAR>

bool gum::learning::BNLearner< GUM_SCALAR >::greedyThickThinningReversals ( ) const

References greedyThickThinningReversals().

Referenced by greedyThickThinningReversals().

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◆ hasMissingValues()

INLINE bool gum::learning::IBNLearner::hasMissingValues ( ) const

inherited

returns true if the learner's database has missing values

Definition at line 467 of file IBNLearner_inl.h.

                                                 {
    return scoreDatabase_.databaseTable().hasMissingValues();
  }

References scoreDatabase_.

Referenced by rawPseudoCount().

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◆ history()

INLINE const std::vector< double > & gum::learning::IBNLearner::history ( ) const

overridevirtualinherited

Exceptions

OperationNotAllowed if scheme not performed or verbosity=false

Implements gum::IApproximationSchemeConfiguration.

Definition at line 949 of file IBNLearner_inl.h.

                                                              {
    if (currentAlgorithm_ != nullptr) return currentAlgorithm_->history();
    else GUM_ERROR(FatalError, "No chosen algorithm for learning")
  }

References currentAlgorithm_, and GUM_ERROR.

◆ idFromName()

INLINE NodeId gum::learning::IBNLearner::idFromName ( std::string_view var_name ) const

inherited

returns the node id corresponding to a variable name

Exceptions

MissingVariableInDatabase if a variable of the BN is not found in the database.

Definition at line 136 of file IBNLearner_inl.h.

                                                                    {
    return scoreDatabase_.idFromName(var_name);
  }

References scoreDatabase_.

Referenced by addForbiddenArc(), addMandatoryArc(), addNoChildrenNode(), addNoParentNode(), addPossibleEdge(), chi2(), correctedMutualInformation(), domainSize(), eraseForbiddenArc(), eraseMandatoryArc(), eraseNoChildrenNode(), eraseNoParentNode(), erasePossibleEdge(), G2(), logLikelihood(), mutualInformation(), rawPseudoCount(), score(), setSliceOrder(), and setTotalOrder().

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◆ initialDAG()

INLINE DAG gum::learning::IBNLearner::initialDAG ( )

inherited

returns the initial DAG structure

Definition at line 166 of file IBNLearner_inl.h.

166{ return initialDag_; }

gum::learning::IBNLearner::initialDag_

DAG initialDag_

an initial DAG given to learners

Definition IBNLearner.h:1263

References initialDag_.

◆ isConstraintBased()

template<GUM_Numeric GUM_SCALAR>

bool gum::learning::BNLearner< GUM_SCALAR >::isConstraintBased ( ) const

References isConstraintBased().

Referenced by isConstraintBased().

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◆ isCSVFileName_()

void gum::learning::IBNLearner::isCSVFileName_ ( std::string_view filename )

staticprotectedinherited

checks whether the extension of a CSV filename is correct

Definition at line 429 of file IBNLearner.cpp.

                                                         {
    // get the extension of the file
 
    if (auto filename_size = Size(filename.size()); filename_size < 4) {
      GUM_ERROR(FormatNotFound,
                "IBNLearner could not determine the "
                "file type of the database")
    }
 
    std::string extension(filename.substr(filename.size() - 4));
    std::transform(extension.begin(), extension.end(), extension.begin(), ::tolower);
 
    if (extension != ".csv") {
      GUM_ERROR(OperationNotAllowed, "IBNLearner does not support yet this type of database file")
    }
  }

References GUM_ERROR.

Referenced by gum::learning::IBNLearner::Database::Database(), gum::learning::IBNLearner::Database::Database(), and readFile_().

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◆ isEnabledEpsilon()

INLINE bool gum::learning::IBNLearner::isEnabledEpsilon ( ) const

overridevirtualinherited

Returns: true if stopping criterion on epsilon is enabled, false otherwise

Implements gum::IApproximationSchemeConfiguration.

Definition at line 811 of file IBNLearner_inl.h.

                                                 {
    if (currentAlgorithm_ != nullptr) return currentAlgorithm_->isEnabledEpsilon();
    else GUM_ERROR(FatalError, "No chosen algorithm for learning")
  }

References currentAlgorithm_, and GUM_ERROR.

◆ isEnabledMaxIter()

INLINE bool gum::learning::IBNLearner::isEnabledMaxIter ( ) const

overridevirtualinherited

Returns: true if stopping criterion on max iterations is enabled, false otherwise

Implements gum::IApproximationSchemeConfiguration.

Definition at line 873 of file IBNLearner_inl.h.

                                                 {
    if (currentAlgorithm_ != nullptr) return currentAlgorithm_->isEnabledMaxIter();
    else GUM_ERROR(FatalError, "No chosen algorithm for learning")
  }

References currentAlgorithm_, and GUM_ERROR.

◆ isEnabledMaxTime()

INLINE bool gum::learning::IBNLearner::isEnabledMaxTime ( ) const

overridevirtualinherited

Returns: true if stopping criterion on timeout is enabled, false otherwise

Implements gum::IApproximationSchemeConfiguration.

Definition at line 909 of file IBNLearner_inl.h.

                                                 {
    if (currentAlgorithm_ != nullptr) return currentAlgorithm_->isEnabledMaxTime();
    else GUM_ERROR(FatalError, "No chosen algorithm for learning")
  }

References currentAlgorithm_, and GUM_ERROR.

◆ isEnabledMinEpsilonRate()

INLINE bool gum::learning::IBNLearner::isEnabledMinEpsilonRate ( ) const

overridevirtualinherited

Returns: true if stopping criterion on epsilon rate is enabled, false otherwise

Implements gum::IApproximationSchemeConfiguration.

Definition at line 842 of file IBNLearner_inl.h.

                                                        {
    if (currentAlgorithm_ != nullptr) return currentAlgorithm_->isEnabledMinEpsilonRate();
    else GUM_ERROR(FatalError, "No chosen algorithm for learning")
  }

References currentAlgorithm_, and GUM_ERROR.

◆ isGumNumberOfThreadsOverriden()

bool gum::ThreadNumberManager::isGumNumberOfThreadsOverriden ( ) const

nodiscardoverridevirtualinherited

indicates whether the class containing this ThreadNumberManager set its own number of threads

Implements gum::IThreadNumberManager.

Referenced by gum::learning::IBNLearner::createParamEstimator_(), and gum::learning::IBNLearner::createScore_().

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◆ isScoreBased()

template<GUM_Numeric GUM_SCALAR>

bool gum::learning::BNLearner< GUM_SCALAR >::isScoreBased ( ) const

References isScoreBased().

Referenced by isScoreBased().

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◆ isUsingEM()

INLINE bool gum::learning::IBNLearner::isUsingEM ( ) const

inherited

indicates whether we use EM for parameter learning

Definition at line 433 of file IBNLearner_inl.h.

433{ return useEM_; }

References useEM_.

◆ latentVariables()

INLINE std::vector< Arc > gum::learning::IBNLearner::latentVariables ( ) const

inherited

get the list of arcs hiding latent variables

Exceptions

OperationNotAllowed when MIIC is not the selected algorithm

Definition at line 345 of file IBNLearner_inl.h.

                                                            {
    return algoMiic_.latentVariables();
  }

References algoMiic_.

◆ learnBN()

template<GUM_Numeric GUM_SCALAR>

BayesNet< GUM_SCALAR > gum::learning::BNLearner< GUM_SCALAR >::learnBN ( )

learn a Bayes Net from a file (must have read the db before)

References learnBN().

Referenced by learnBN().

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◆ learnDAG()

DAG gum::learning::IBNLearner::learnDAG ( )

inherited

learn a structure from a file (must have read the db before)

Definition at line 956 of file IBNLearner.cpp.

                           {
    createPrior_();
    createScore_();
    auto dag = learnDag_();
    for (const auto i: dag) {
      dag.setName(i, scoreDatabase_.databaseTable().variableName(i));
    }
    return dag;
  }

References createPrior_(), createScore_(), learnDag_(), and scoreDatabase_.

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◆ learnDag_()

DAG gum::learning::IBNLearner::learnDag_ ( )

protectedinherited

returns the DAG learnt

Definition at line 985 of file IBNLearner.cpp.

                            {
    // check that the database does not contain any missing value
    if (scoreDatabase_.databaseTable().hasMissingValues()
        || ((priorDatabase_ != nullptr)
            && (priorType_ == BNLearnerPriorType::DIRICHLET_FROM_DATABASE)
            && priorDatabase_->databaseTable().hasMissingValues())) {
      GUM_ERROR(MissingValueInDatabase,
                "For the moment, the BNLearner is unable to cope "
                "with missing values in databases")
    }
    // add the mandatory arcs to the initial dag and remove the forbidden ones
    // from the initial graph
    DAG init_graph = initialDag_;
 
    for (const auto& arc: constraintMandatoryArcs_.arcs()) {
      if (!init_graph.exists(arc.tail())) init_graph.addNodeWithId(arc.tail());
 
      if (!init_graph.exists(arc.head())) init_graph.addNodeWithId(arc.head());
 
      init_graph.addArc(arc.tail(), arc.head());
    }
 
    for (const auto& arc: constraintForbiddenArcs_.arcs())
      init_graph.eraseArc(arc);
 
 
    switch (selectedAlgo_) {
      // ========================================================================
      case AlgoType::PC : {
        BNLearnerListener listener(this, algoPC_);
        MixedGraph        mgraph = this->preparePC_();
        return algoPC_.learnDAG(mgraph);
      }
 
      // ========================================================================
      case AlgoType::FCI : {
        BNLearnerListener listener(this, algoFCI_);
        MixedGraph        mgraph = this->prepareFCI_();
        return algoFCI_.learnDAG(mgraph);
      }
 
      // ========================================================================
      case AlgoType::MIIC : {
        BNLearnerListener listener(this, algoMiic_);
        // create the mixedGraph and the corrected mutual information
        MixedGraph mgraph = this->prepareMiic_();
 
        algoMiic_.setMutualInformation(*mutualInfo_);
        return algoMiic_.learnDAG(mgraph);
      }
 
      // ========================================================================
      case AlgoType::GREEDY_HILL_CLIMBING : {
        BNLearnerListener listener(this, greedyHillClimbing_);
        StructuralConstraintSetStatic< StructuralConstraintMandatoryArcs,
                                       StructuralConstraintForbiddenArcs,
                                       StructuralConstraintPossibleEdges,
                                       StructuralConstraintSliceOrder,
                                       StructuralConstraintNoParentNodes,
                                       StructuralConstraintNoChildrenNodes,
                                       StructuralConstraintTotalOrder >
            invariable_constraints;
        static_cast< StructuralConstraintMandatoryArcs& >(invariable_constraints)
            = constraintMandatoryArcs_;
        static_cast< StructuralConstraintForbiddenArcs& >(invariable_constraints)
            = constraintForbiddenArcs_;
        static_cast< StructuralConstraintPossibleEdges& >(invariable_constraints)
            = constraintPossibleEdges_;
        static_cast< StructuralConstraintSliceOrder& >(invariable_constraints)
            = constraintSliceOrder_;
        static_cast< StructuralConstraintNoParentNodes& >(invariable_constraints)
            = constraintNoParentNodes_;
        static_cast< StructuralConstraintNoChildrenNodes& >(invariable_constraints)
            = constraintNoChildrenNodes_;
        static_cast< StructuralConstraintTotalOrder& >(invariable_constraints)
            = constraintTotalOrder_;
 
        StructuralConstraintSetStatic< StructuralConstraintIndegree, StructuralConstraintDAG >
            variable_constraints;
        static_cast< StructuralConstraintIndegree& >(variable_constraints) = constraintIndegree_;
 
        GraphChangesSelector4DiGraph selector(*score_,
                                              invariable_constraints,
                                              variable_constraints);
 
        // enforce that greedy hill climbing uses arc additions, deletions and reversals
        // and only these operations
        selector.useArcAdditions(true);
        selector.useArcDeletions(true);
        selector.useArcReversals(true);
        selector.useArcTriangleDeletions(false);
 
        return greedyHillClimbing_.learnStructure(selector, init_graph);
      }
 
      // ========================================================================
      case AlgoType::EXTENDED_GREEDY_HILL_CLIMBING : {
        BNLearnerListener listener(this, extendedGreedyHillClimbing_);
        StructuralConstraintSetStatic< StructuralConstraintMandatoryArcs,
                                       StructuralConstraintForbiddenArcs,
                                       StructuralConstraintPossibleEdges,
                                       StructuralConstraintNoParentNodes,
                                       StructuralConstraintNoChildrenNodes,
                                       StructuralConstraintSliceOrder,
                                       StructuralConstraintTotalOrder >
            invariable_constraints;
        static_cast< StructuralConstraintMandatoryArcs& >(invariable_constraints)
            = constraintMandatoryArcs_;
        static_cast< StructuralConstraintForbiddenArcs& >(invariable_constraints)
            = constraintForbiddenArcs_;
        static_cast< StructuralConstraintPossibleEdges& >(invariable_constraints)
            = constraintPossibleEdges_;
        static_cast< StructuralConstraintSliceOrder& >(invariable_constraints)
            = constraintSliceOrder_;
        static_cast< StructuralConstraintNoParentNodes& >(invariable_constraints)
            = constraintNoParentNodes_;
        static_cast< StructuralConstraintNoChildrenNodes& >(invariable_constraints)
            = constraintNoChildrenNodes_;
        static_cast< StructuralConstraintTotalOrder& >(invariable_constraints)
            = constraintTotalOrder_;
 
        StructuralConstraintSetStatic< StructuralConstraintIndegree, StructuralConstraintDAG >
            variable_constraints;
        static_cast< StructuralConstraintIndegree& >(variable_constraints) = constraintIndegree_;
 
        GraphChangesSelector4DiGraph selector(*score_,
                                              invariable_constraints,
                                              variable_constraints);
 
        selector.useArcAdditions(allowArcAdditions_);
        selector.useArcDeletions(allowArcDeletions_);
        selector.useArcReversals(allowArcReversals_);
        selector.useArcTriangleDeletions(allowArcTriangleDeletions_);
 
        return greedyHillClimbing_.learnStructure(selector, init_graph);
      }
 
      // ========================================================================
      case AlgoType::GREEDY_THICK_THINNING : {
        BNLearnerListener listener(this, greedyThickThinning_);
        StructuralConstraintSetStatic< StructuralConstraintMandatoryArcs,
                                       StructuralConstraintForbiddenArcs,
                                       StructuralConstraintPossibleEdges,
                                       StructuralConstraintSliceOrder,
                                       StructuralConstraintNoParentNodes,
                                       StructuralConstraintNoChildrenNodes,
                                       StructuralConstraintTotalOrder >
            invariable_constraints;
        static_cast< StructuralConstraintMandatoryArcs& >(invariable_constraints)
            = constraintMandatoryArcs_;
        static_cast< StructuralConstraintForbiddenArcs& >(invariable_constraints)
            = constraintForbiddenArcs_;
        static_cast< StructuralConstraintPossibleEdges& >(invariable_constraints)
            = constraintPossibleEdges_;
        static_cast< StructuralConstraintSliceOrder& >(invariable_constraints)
            = constraintSliceOrder_;
        static_cast< StructuralConstraintNoParentNodes& >(invariable_constraints)
            = constraintNoParentNodes_;
        static_cast< StructuralConstraintNoChildrenNodes& >(invariable_constraints)
            = constraintNoChildrenNodes_;
        static_cast< StructuralConstraintTotalOrder& >(invariable_constraints)
            = constraintTotalOrder_;
 
        StructuralConstraintSetStatic< StructuralConstraintIndegree, StructuralConstraintDAG >
            variable_constraints;
        static_cast< StructuralConstraintIndegree& >(variable_constraints) = constraintIndegree_;
 
        GraphChangesSelector4DiGraph selector(*score_,
                                              invariable_constraints,
                                              variable_constraints);
 
        return greedyThickThinning_.learnStructure(selector, init_graph);
      }
 
      // ========================================================================
      case AlgoType::LOCAL_SEARCH_WITH_TABU_LIST : {
        BNLearnerListener listener(this, localSearchWithTabuList_);
        StructuralConstraintSetStatic< StructuralConstraintMandatoryArcs,
                                       StructuralConstraintForbiddenArcs,
                                       StructuralConstraintPossibleEdges,
                                       StructuralConstraintSliceOrder,
                                       StructuralConstraintNoParentNodes,
                                       StructuralConstraintNoChildrenNodes,
                                       StructuralConstraintTotalOrder >
            invariable_constraints;
        static_cast< StructuralConstraintMandatoryArcs& >(invariable_constraints)
            = constraintMandatoryArcs_;
        static_cast< StructuralConstraintForbiddenArcs& >(invariable_constraints)
            = constraintForbiddenArcs_;
        static_cast< StructuralConstraintPossibleEdges& >(invariable_constraints)
            = constraintPossibleEdges_;
        static_cast< StructuralConstraintSliceOrder& >(invariable_constraints)
            = constraintSliceOrder_;
        static_cast< StructuralConstraintNoParentNodes& >(invariable_constraints)
            = constraintNoParentNodes_;
        static_cast< StructuralConstraintNoChildrenNodes& >(invariable_constraints)
            = constraintNoChildrenNodes_;
        static_cast< StructuralConstraintTotalOrder& >(invariable_constraints)
            = constraintTotalOrder_;
 
        StructuralConstraintSetStatic< StructuralConstraintTabuList,
                                       StructuralConstraintIndegree,
                                       StructuralConstraintDAG >
            variable_constraints;
        static_cast< StructuralConstraintTabuList& >(variable_constraints) = constraintTabuList_;
        static_cast< StructuralConstraintIndegree& >(variable_constraints) = constraintIndegree_;
 
        GraphChangesSelector4DiGraph selector(*score_,
                                              invariable_constraints,
                                              variable_constraints);
 
        selector.useArcAdditions(allowArcAdditions_);
        selector.useArcDeletions(allowArcDeletions_);
        selector.useArcReversals(allowArcReversals_);
        selector.useArcTriangleDeletions(allowArcTriangleDeletions_);
 
        return localSearchWithTabuList_.learnStructure(selector, init_graph);
      }
 
      // ========================================================================
      case AlgoType::K2 : {
        BNLearnerListener listener(this, algoK2_.approximationScheme());
        StructuralConstraintSetStatic< StructuralConstraintMandatoryArcs,
                                       StructuralConstraintForbiddenArcs,
                                       StructuralConstraintPossibleEdges,
                                       StructuralConstraintNoParentNodes,
                                       StructuralConstraintNoChildrenNodes,
                                       StructuralConstraintTotalOrder >
            invariable_constraints;
        static_cast< StructuralConstraintMandatoryArcs& >(invariable_constraints)
            = constraintMandatoryArcs_;
        static_cast< StructuralConstraintForbiddenArcs& >(invariable_constraints)
            = constraintForbiddenArcs_;
        static_cast< StructuralConstraintPossibleEdges& >(invariable_constraints)
            = constraintPossibleEdges_;
        static_cast< StructuralConstraintNoParentNodes& >(invariable_constraints)
            = constraintNoParentNodes_;
        static_cast< StructuralConstraintNoChildrenNodes& >(invariable_constraints)
            = constraintNoChildrenNodes_;
        static_cast< StructuralConstraintTotalOrder& >(invariable_constraints)
            = constraintTotalOrder_;
 
        // if some mandatory arcs are incompatible with the order, use a DAG
        // constraint instead of a DiGraph constraint to avoid cycles
        const ArcSet& mandatory_arcs
            = static_cast< StructuralConstraintMandatoryArcs& >(invariable_constraints).arcs();
        const Sequence< NodeId >& order            = algoK2_.order();
        bool                      order_compatible = true;
 
        for (const auto& arc: mandatory_arcs) {
          if (order.pos(arc.tail()) >= order.pos(arc.head())) {
            order_compatible = false;
            break;
          }
        }
 
        if (order_compatible) {
          StructuralConstraintSetStatic< StructuralConstraintIndegree, StructuralConstraintDiGraph >
              variable_constraints;
          static_cast< StructuralConstraintIndegree& >(variable_constraints) = constraintIndegree_;
 
          GraphChangesSelector4DiGraph selector(*score_,
                                                invariable_constraints,
                                                variable_constraints);
 
          return algoK2_.learnStructure(selector, init_graph);
        } else {
          StructuralConstraintSetStatic< StructuralConstraintIndegree, StructuralConstraintDAG >
              variable_constraints;
          static_cast< StructuralConstraintIndegree& >(variable_constraints) = constraintIndegree_;
 
          GraphChangesSelector4DiGraph selector(*score_,
                                                invariable_constraints,
                                                variable_constraints);
 
          return algoK2_.learnStructure(selector, init_graph);
        }
      }
    }
 
    GUM_ERROR(OperationNotAllowed,
              "the learnDAG method has not been implemented for this "
              "learning algorithm")
  }

Referenced by learnDAG().

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◆ learnPAG()

PAG gum::learning::IBNLearner::learnPAG ( )

inherited

learn a PAG — only valid when useFCI() has been called

Exceptions

OperationNotAllowed when FCI is not the selected algorithm

Definition at line 948 of file IBNLearner.cpp.

                           {
    auto pag = learnPAG_();
    for (const auto i: pag) {
      pag.setName(i, scoreDatabase_.databaseTable().variableName(i));
    }
    return pag;
  }

References learnPAG_(), and scoreDatabase_.

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◆ learnPAG_()

PAG gum::learning::IBNLearner::learnPAG_ ( )

protectedinherited

Definition at line 934 of file IBNLearner.cpp.

                            {
    if (selectedAlgo_ != AlgoType::FCI) {
      GUM_ERROR(OperationNotAllowed, "learnPAG() is only valid when using the FCI algorithm")
    }
    if (scoreDatabase_.databaseTable().hasMissingValues()) {
      GUM_ERROR(MissingValueInDatabase,
                "For the moment, the BNLearner is unable to learn "
                    << "structures with missing values in databases")
    }
    BNLearnerListener listener(this, algoFCI_);
    MixedGraph        mgraph = this->prepareFCI_();
    return algoFCI_.learnPAG(mgraph);
  }

References algoFCI_, FCI, GUM_ERROR, prepareFCI_(), scoreDatabase_, and selectedAlgo_.

Referenced by learnPAG().

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◆ learnParameters() [1/3]

template<GUM_Numeric GUM_SCALAR>

BayesNet< GUM_SCALAR > gum::learning::BNLearner< GUM_SCALAR >::learnParameters ( bool take_into_account_score = true )

learns a BN (its parameters) when its structure is known

Parameters

take_into_account_score The dag of the BN which was passed in argument to the BNLearner may have been learnt from a structure learning. In this case, if the score used to learn the structure has an implicit prior (like K2 which has a 1-smoothing prior), it is important to also take into account this implicit prior for parameter learning. By default, if a score exists, we will learn parameters by taking into account the prior specified by methods usePriorXXX () + the implicit prior of the score, else we just take into account the prior specified by usePriorXXX ()

Warning: if method useEM() has been executed, then the learning is performed using EM, else this is a standard (e.g. ML/MAP) learning

Exceptions

MissingVariableInDatabase	if a variable of the BN is not found in the database.
UnknownLabelInDatabase	if a label is found in the databast that do not correpond to the variable.
OperationNotAllowed	if EM is used but neither the min log-likelihood difference nor the min log-likelihood evolution rate have been selected as stopping criteria

References learnParameters().

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◆ learnParameters() [2/3]

template<GUM_Numeric GUM_SCALAR>

BayesNet< GUM_SCALAR > gum::learning::BNLearner< GUM_SCALAR >::learnParameters	(	const BayesNet< GUM_SCALAR > &	bn,
		bool	takeIntoAccountScore = true )

learns a BN (its parameters) with the BN structure passed in argument, EM being initialized by this argument

Parameters

bn the Bayesian network used to specify the graphical structure of the returned Bayes net and to initialize its CPTs before running EM. When a CPT is filled exclusively with only zeroes, then this one is initialized by the BNLearner using a specific estimator that does not take into account the missing values in the database

takeIntoAccountScore The dag passed in argument may have been learnt from a structure learning. In this case, if the score used to learn the structure has an implicit prior (like K2 which has a 1-smoothing prior), it is important to also take into account this implicit prior for parameter learning. By default, if a score exists, we will learn parameters by taking into account the prior specified by methods usePriorXXX () + the implicit prior of the score, else we just take into account the prior specified by usePriorXXX ()

Exceptions

MissingVariableInDatabase	if a variable of the BN is not found in the database.
OperationNotAllowed	if EM is used but no EM stopping criterion has been selected.

Warning: if method useEM() has been executed, then the learning is performed using EM, else this is a standard (e.g. ML/MAP) learning; the EM algorithm initializes the parameters of the CPTs using those of the Bayes net passed in argument whenever those are not fully filled with zeroes, else the BNLearner initializes them using an estimator that does not take into account the missing values. If you wish the BNLearner to automatically initialize all the CPTs, use the method in which a DAG is passed in argument rather than a Bayes net.

References learnParameters().

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◆ learnParameters() [3/3]

template<GUM_Numeric GUM_SCALAR>

BayesNet< GUM_SCALAR > gum::learning::BNLearner< GUM_SCALAR >::learnParameters	(	const DAG &	dag,
		bool	takeIntoAccountScore = true )

learns a BN (its parameters) with the structure passed in argument

Parameters

dag the structure of the Bayesian network

takeIntoAccountScore The dag passed in argument may have been learnt from a structure learning. In this case, if the score used to learn the structure has an implicit prior (like K2 which has a 1-smoothing prior), it is important to also take into account this implicit prior for parameter learning. By default, if a score exists, we will learn parameters by taking into account the prior specified by methods usePriorXXX () + the implicit prior of the score, else we just take into account the prior specified by usePriorXXX ()

Exceptions

MissingVariableInDatabase	if a variable of the BN is not found in the database.
MissingValueInDatabase	if the database contains some missing values and EM is not used for the learning.
OperationNotAllowed	if EM is used but no EM stopping criterion has been selected.

Warning: if method useEM() has been executed, then the learning is performed using EM, else this is a standard (e.g. ML/MAP) learning

References learnParameters().

Referenced by learnParameters(), learnParameters(), and learnParameters().

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◆ learnPDAG()

PDAG gum::learning::IBNLearner::learnPDAG ( )

inherited

learn a partial structure from a file (must have read the db before and must have selected miic)

Definition at line 926 of file IBNLearner.cpp.

                             {
    auto pdag = learnPDAG_();
    for (const auto i: pdag) {
      pdag.setName(i, scoreDatabase_.databaseTable().variableName(i));
    }
    return pdag;
  }

References learnPDAG_(), and scoreDatabase_.

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◆ learnPDAG_()

PDAG gum::learning::IBNLearner::learnPDAG_ ( )

protectedinherited

Definition at line 893 of file IBNLearner.cpp.

                              {
    if (selectedAlgo_ != AlgoType::MIIC && selectedAlgo_ != AlgoType::PC
        && selectedAlgo_ != AlgoType::FCI) {
      GUM_ERROR(OperationNotAllowed,
                "Score-based algorithms do not build PDAG. Please use a constraint-based "
                "algorithm instead")
    }
    // check that the database does not contain any missing value
    if (scoreDatabase_.databaseTable().hasMissingValues()) {
      GUM_ERROR(MissingValueInDatabase,
                "For the moment, the BNLearner is unable to learn "
                    << "structures with missing values in databases")
    }
 
    if (selectedAlgo_ == AlgoType::PC) {
      BNLearnerListener listener(this, algoPC_);
      MixedGraph        mgraph = this->preparePC_();
      return algoPC_.learnPDAG(mgraph);
    }
 
    if (selectedAlgo_ == AlgoType::FCI) {
      BNLearnerListener listener(this, algoFCI_);
      MixedGraph        mgraph = this->prepareFCI_();
      return algoFCI_.learnPDAG(mgraph);
    }
 
    BNLearnerListener listener(this, algoMiic_);
    // create the mixedGraph_constraint_MandatoryArcs.arcs
    MixedGraph mgraph = this->prepareMiic_();
    algoMiic_.setMutualInformation(*mutualInfo_);
    return algoMiic_.learnPDAG(mgraph);
  }

References algoFCI_, algoMiic_, algoPC_, FCI, GUM_ERROR, MIIC, mutualInfo_, PC, prepareFCI_(), prepareMiic_(), preparePC_(), scoreDatabase_, and selectedAlgo_.

Referenced by learnPDAG().

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◆ logLikelihood() [1/2]

double gum::learning::IBNLearner::logLikelihood	(	const std::vector< NodeId > &	vars,
		const std::vector< NodeId > &	knowing = {} )

inherited

Return the loglikelihood of vars in the base, conditioned by knowing for the BNLearner.

Parameters

vars	a vector of NodeIds
knowing	an optional vector of conditioning NodeIds

Returns: a double

Definition at line 1374 of file IBNLearner.cpp.

                                                                       {
    createPrior_();
    gum::learning::ScoreLog2Likelihood ll2score(scoreDatabase_.parser(), *prior_, databaseRanges());
 
    std::vector< NodeId > total(vars);
    total.insert(total.end(), knowing.begin(), knowing.end());
    double LLtotal = ll2score.score(IdCondSet(total, false, true));
    if (knowing.size() == (Size)0) {
      return LLtotal;
    } else {
      double LLknw = ll2score.score(IdCondSet(knowing, false, true));
      return LLtotal - LLknw;
    }
  }

References createPrior_(), databaseRanges(), prior_, gum::learning::ScoreLog2Likelihood::score(), and scoreDatabase_.

Referenced by logLikelihood().

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◆ logLikelihood() [2/2]

double gum::learning::IBNLearner::logLikelihood	(	const std::vector< std::string > &	vars,
		const std::vector< std::string > &	knowing = {} )

inherited

Return the loglikelihood of vars in the base, conditioned by knowing for the BNLearner.

Parameters

vars	a vector of name of rows
knowing	an optional vector of conditioning rows

Returns: a double

Definition at line 1390 of file IBNLearner.cpp.

                                                                          {
    std::vector< NodeId > ids;
    std::vector< NodeId > knowingIds;
 
    auto mapper = [this](const std::string& c) { return this->idFromName(c); };
 
    std::transform(vars.begin(), vars.end(), std::back_inserter(ids), mapper);
    std::transform(knowing.begin(), knowing.end(), std::back_inserter(knowingIds), mapper);
 
    return logLikelihood(ids, knowingIds);
  }

References idFromName(), and logLikelihood().

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◆ maxIter()

INLINE Size gum::learning::IBNLearner::maxIter ( ) const

overridevirtualinherited

Returns: the criterion on number of iterations

Implements gum::IApproximationSchemeConfiguration.

Definition at line 854 of file IBNLearner_inl.h.

                                        {
    if (currentAlgorithm_ != nullptr) return currentAlgorithm_->maxIter();
    else GUM_ERROR(FatalError, "No chosen algorithm for learning")
  }

References currentAlgorithm_, and GUM_ERROR.

◆ maxTime()

INLINE double gum::learning::IBNLearner::maxTime ( ) const

overridevirtualinherited

returns the timeout (in seconds)

Implements gum::IApproximationSchemeConfiguration.

Definition at line 885 of file IBNLearner_inl.h.

                                          {
    if (currentAlgorithm_ != nullptr) return currentAlgorithm_->maxTime();
    else GUM_ERROR(FatalError, "No chosen algorithm for learning")
  }

References currentAlgorithm_, and GUM_ERROR.

◆ messageApproximationScheme()

std::string gum::IApproximationSchemeConfiguration::messageApproximationScheme ( ) const

inherited

Returns the approximation scheme message.

Returns: Returns the approximation scheme message.

Definition at line 64 of file IApproximationSchemeConfiguration.cpp.

                                                                                {
    switch (stateApproximationScheme()) {
      case ApproximationSchemeSTATE::Continue : return "in progress";
 
      case ApproximationSchemeSTATE::Epsilon :
        return std::format("stopped with epsilon={}", epsilon());
 
      case ApproximationSchemeSTATE::Rate :
        return std::format("stopped with rate={}", minEpsilonRate());
 
      case ApproximationSchemeSTATE::Limit :
        return std::format("stopped with max iteration={}", maxIter());
 
      case ApproximationSchemeSTATE::TimeLimit :
        return std::format("stopped with timeout={}", maxTime());
 
      case ApproximationSchemeSTATE::Stopped : return "stopped on request";
 
      case ApproximationSchemeSTATE::Undefined : return "undefined state";
    }
    return {};
  }

References Continue, Epsilon, epsilon(), Limit, maxIter(), maxTime(), minEpsilonRate(), Rate, stateApproximationScheme(), Stopped, TimeLimit, and Undefined.

Referenced by gum::ApproximationScheme::continueApproximationScheme(), gum::credal::InferenceEngine< GUM_SCALAR >::getApproximationSchemeMsg(), and gum::credal::MultipleInferenceEngine< GUM_SCALAR, LazyPropagation< GUM_SCALAR > >::isEnabledMaxIter().

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◆ minEpsilonRate()

INLINE double gum::learning::IBNLearner::minEpsilonRate ( ) const

overridevirtualinherited

Get the value of the minimal epsilon rate.

Implements gum::IApproximationSchemeConfiguration.

Definition at line 823 of file IBNLearner_inl.h.

                                                 {
    if (currentAlgorithm_ != nullptr) return currentAlgorithm_->minEpsilonRate();
    else GUM_ERROR(FatalError, "No chosen algorithm for learning")
  }

References currentAlgorithm_, and GUM_ERROR.

◆ mutualInformation() [1/2]

double gum::learning::IBNLearner::mutualInformation	(	NodeId	id1,
		NodeId	id2,
		const std::vector< NodeId > &	knowing = {} )

inherited

Return the mutual information of id1 and id2 in the base, conditioned by knowing for the BNLearner.

Warning: This function returns the bare mutual information (without prior or correction)

Parameters

id1	nodeId
id2	nodeId
knowing	an optional vector of conditioning NodeIds

Returns: a double

Definition at line 1440 of file IBNLearner.cpp.

                                                                           {
    const auto prior = NoPrior(scoreDatabase_.databaseTable(), scoreDatabase_.nodeId2Columns());
    gum::learning::CorrectedMutualInformation cmi(scoreDatabase_.parser(), prior, databaseRanges());
    cmi.useNoCorr();
 
    if (knowing.size() == (Size)0) return cmi.score(id1, id2) / scoreDatabase_.weight();
    else return cmi.score(id1, id2, knowing) / scoreDatabase_.weight();
  }

References databaseRanges(), gum::learning::CorrectedMutualInformation::score(), scoreDatabase_, and gum::learning::CorrectedMutualInformation::useNoCorr().

Referenced by mutualInformation().

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◆ mutualInformation() [2/2]

double gum::learning::IBNLearner::mutualInformation	(	std::string_view	var1,
		std::string_view	var2,
		const std::vector< std::string > &	knowing = {} )

inherited

Return the mutual information of var1 and var2 in the base, conditioned by knowing for the BNLearner.

Warning: This function returns the bare mutual information (without prior or correction)

Parameters

var1	name of a row
var2	name of a row
knowing	an optional vector of conditioning rows

Returns: a double

Definition at line 1451 of file IBNLearner.cpp.

                                                                              {
    std::vector< NodeId > knowingIds;
 
    auto mapper = [this](const std::string& c) { return this->idFromName(c); };
 
    std::transform(knowing.begin(), knowing.end(), std::back_inserter(knowingIds), mapper);
 
    return mutualInformation(this->idFromName(var1), this->idFromName(var2), knowingIds);
  }

References idFromName(), and mutualInformation().

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◆ nameFromId()

INLINE const std::string & gum::learning::IBNLearner::nameFromId ( NodeId id ) const

inherited

returns the variable name corresponding to a given node id

Definition at line 141 of file IBNLearner_inl.h.

                                                                {
    return scoreDatabase_.nameFromId(id);
  }

References scoreDatabase_.

◆ names()

INLINE const std::vector< std::string > & gum::learning::IBNLearner::names ( ) const

inherited

returns the names of the variables in the database

Definition at line 705 of file IBNLearner_inl.h.

                                                               {
    return scoreDatabase_.names();
  }

References scoreDatabase_.

◆ nbCols()

INLINE Size gum::learning::IBNLearner::nbCols ( ) const

inherited

Returns: the number of cols in the database

Definition at line 736 of file IBNLearner_inl.h.

736{ return scoreDatabase_.domainSizes().size(); }

References scoreDatabase_.

◆ nbrIterations()

INLINE Size gum::learning::IBNLearner::nbrIterations ( ) const

overridevirtualinherited

Exceptions

OperationNotAllowed if scheme not performed

Implements gum::IApproximationSchemeConfiguration.

Definition at line 944 of file IBNLearner_inl.h.

                                              {
    if (currentAlgorithm_ != nullptr) return currentAlgorithm_->nbrIterations();
    else GUM_ERROR(FatalError, "No chosen algorithm for learning")
  }

References currentAlgorithm_, and GUM_ERROR.

◆ nbRows()

INLINE Size gum::learning::IBNLearner::nbRows ( ) const

inherited

Returns: the number of rows in the database

Definition at line 738 of file IBNLearner_inl.h.

738{ return scoreDatabase_.databaseTable().size(); }

References scoreDatabase_.

◆ operator=() [1/2]

template<GUM_Numeric GUM_SCALAR>

BNLearner & gum::learning::BNLearner< GUM_SCALAR >::operator= ( BNLearner< GUM_SCALAR > && )

noexcept

move operator

References BNLearner().

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◆ operator=() [2/2]

template<GUM_Numeric GUM_SCALAR>

BNLearner & gum::learning::BNLearner< GUM_SCALAR >::operator= ( const BNLearner< GUM_SCALAR > & )

copy operator

References BNLearner().

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◆ periodSize()

INLINE Size gum::learning::IBNLearner::periodSize ( ) const

overridevirtualinherited

how many samples between 2 stopping isEnableds

Exceptions

OutOfBounds if p<1

Implements gum::IApproximationSchemeConfiguration.

Definition at line 921 of file IBNLearner_inl.h.

                                           {
    if (currentAlgorithm_ != nullptr) return currentAlgorithm_->periodSize();
    else GUM_ERROR(FatalError, "No chosen algorithm for learning")
  }

References currentAlgorithm_, and GUM_ERROR.

◆ prepareFCI_()

MixedGraph gum::learning::IBNLearner::prepareFCI_ ( )

protectedinherited

prepares the initial graph and independence test for FCI

Definition at line 803 of file IBNLearner.cpp.

                                     {
    MixedGraph mgraph;
    DiGraph    forbiddenGraph;
    DAG        mandatoryGraph;
 
    for (Size i = 0; i < scoreDatabase_.databaseTable().nbVariables(); ++i) {
      mgraph.addNodeWithId(i);
      forbiddenGraph.addNodeWithId(i);
      mandatoryGraph.addNodeWithId(i);
    }
 
    const EdgeSet& possible_edges = constraintPossibleEdges_.edges();
    if (possible_edges.empty()) {
      for (const NodeId i: mgraph.nodes()) {
        for (NodeId j = 0; j < i; ++j) {
          mgraph.addEdge(j, i);
        }
      }
    } else {
      for (const auto& edge: possible_edges) {
        mgraph.addEdge(edge.first(), edge.second());
      }
    }
 
    for (const auto& arc: constraintMandatoryArcs_.arcs()) {
      mandatoryGraph.addArc(arc.tail(), arc.head());
      forbiddenGraph.addArc(arc.head(), arc.tail());
    }
    for (const auto& arc: constraintForbiddenArcs_.arcs()) {
      forbiddenGraph.addArc(arc.tail(), arc.head());
    }
 
    const gum::NodeProperty< gum::Size > sliceOrder = constraintSliceOrder_.sliceOrder();
    gum::NodeProperty< gum::Size >       copyOrder  = gum::HashTable(sliceOrder);
    for (const auto& [n1, r1]: sliceOrder) {
      for (const auto& [n2, r2]: copyOrder) {
        if (r1 > r2) {
          forbiddenGraph.addArc(n1, n2);
        } else if (r2 > r1) {
          forbiddenGraph.addArc(n2, n1);
        }
      }
      copyOrder.erase(n1);
    }
 
    const auto& totalOrder = constraintTotalOrder_.totalOrder();
    for (auto iter1 = totalOrder.begin(); iter1 != totalOrder.end(); ++iter1) {
      for (auto iter2 = iter1 + 1; iter2 != totalOrder.end(); ++iter2) {
        forbiddenGraph.addArc(*iter2, *iter1);
      }
    }
 
    for (const auto node: constraintNoParentNodes_.nodes()) {
      for (const auto node2: mgraph.nodes()) {
        if (node != node2) { forbiddenGraph.addArc(node2, node); }
      }
    }
    for (const auto node: constraintNoChildrenNodes_.nodes()) {
      for (const auto node2: mgraph.nodes()) {
        if (node != node2) { forbiddenGraph.addArc(node, node2); }
      }
    }
 
    if (indepTestFCI_) {
      delete indepTestFCI_;
      indepTestFCI_ = nullptr;
    }
    if (indepTestTypeFCI_ == IndepTestType::Chi2) {
      indepTestFCI_ = new IndepTestChi2(scoreDatabase_.parser(),
                                        *noPrior_,
                                        ranges_,
                                        scoreDatabase_.nodeId2Columns());
    } else {
      indepTestFCI_ = new IndepTestG2(scoreDatabase_.parser(),
                                      *noPrior_,
                                      ranges_,
                                      scoreDatabase_.nodeId2Columns());
    }
 
    algoFCI_.setMaxIndegree(constraintIndegree_.maxIndegree());
    algoFCI_.setMandatoryGraph(mandatoryGraph);
    algoFCI_.setForbiddenGraph(forbiddenGraph);
    algoFCI_.setIndependenceTest(*indepTestFCI_);
    algoFCI_.setAlpha(alphaFci_);
    algoFCI_.setMaxPathLength(maxPathLengthFci_);
    algoFCI_.setExhaustiveSepSet(exhaustiveSepSetFci_);
 
    return mgraph;
  }

References gum::DAG::addArc(), gum::DiGraph::addArc(), gum::UndiGraph::addEdge(), gum::NodeGraphPart::addNodeWithId(), algoFCI_, alphaFci_, Chi2, constraintForbiddenArcs_, constraintIndegree_, constraintMandatoryArcs_, constraintNoChildrenNodes_, constraintNoParentNodes_, constraintPossibleEdges_, constraintSliceOrder_, constraintTotalOrder_, gum::Set< Key >::empty(), exhaustiveSepSetFci_, indepTestFCI_, indepTestTypeFCI_, maxPathLengthFci_, gum::NodeGraphPart::nodes(), noPrior_, ranges_, and scoreDatabase_.

Referenced by learnDag_(), learnPAG_(), and learnPDAG_().

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◆ prepareMiic_()

MixedGraph gum::learning::IBNLearner::prepareMiic_ ( )

protectedinherited

prepares the initial graph for miic

Definition at line 611 of file IBNLearner.cpp.

                                      {
    // Initialize the mixed graph to the fully connected graph
    MixedGraph mgraph;
    DiGraph    forbiddenGraph;
    DAG        mandatoryGraph;
 
    // GUM_CHECKPOINT
    for (Size i = 0; i < scoreDatabase_.databaseTable().nbVariables(); ++i) {
      mgraph.addNodeWithId(i);
      forbiddenGraph.addNodeWithId(i);
      mandatoryGraph.addNodeWithId(i);
    }
 
    const EdgeSet& possible_edges = constraintPossibleEdges_.edges();
 
    if (possible_edges.empty()) {
      for (const NodeId i: mgraph.nodes()) {
        for (NodeId j = 0; j < i; ++j) {
          // contiguous nodeIds !
          mgraph.addEdge(j, i);
        }
      }
    } else {
      for (const auto& edge: possible_edges) {
        mgraph.addEdge(edge.first(), edge.second());
      }
    }
    // GUM_CHECKPOINT
 
    // translating the mandatory arcs for constraintMiic
    HashTable< std::pair< NodeId, NodeId >, char > initial_marks;
    const ArcSet&                                  mandatory_arcs = constraintMandatoryArcs_.arcs();
 
    // GUM_CHECKPOINT
    for (const auto& arc: mandatory_arcs) {
      mandatoryGraph.addArc(arc.tail(), arc.head());
      // MIIC's marks mechanism (orientationMiic_) handles the reverse direction;
      // adding it to forbiddenGraph would cause DuplicateElement (unlike preparePC_).
    }
 
    // GUM_CHECKPOINT
    //  translating the forbidden arcs for constraintMiic
    const ArcSet& forbidden_arcs = constraintForbiddenArcs_.arcs();
    for (const auto& arc: forbidden_arcs) {
      forbiddenGraph.addArc(arc.tail(), arc.head());
    }
 
    // GUM_CHECKPOINT
    const gum::NodeProperty< gum::Size > sliceOrder = constraintSliceOrder_.sliceOrder();
    gum::NodeProperty< gum::Size >       copyOrder  = gum::HashTable(sliceOrder);
    for (const auto& [n1, r1]: sliceOrder) {
      for (const auto& [n2, r2]: copyOrder) {
        if (r1 > r2) {
          forbiddenGraph.addArc(n1, n2);
          // initial_marks.insert({n1, n2}, '-');
        } else if (r2 > r1) {
          forbiddenGraph.addArc(n2, n1);
          // initial_marks.insert({n2, n1}, '-');
        }
      }
      copyOrder.erase(n1);
    }
 
    // GUM_CHECKPOINT
    const auto& totalOrder = constraintTotalOrder_.totalOrder();
    for (auto iter1 = totalOrder.begin(); iter1 != totalOrder.end(); ++iter1) {
      const auto node1 = *iter1;
      for (auto iter2 = iter1 + 1; iter2 != totalOrder.end(); ++iter2) {
        forbiddenGraph.addArc(*iter2, node1);
      }
    }
 
    for (const auto node: constraintNoParentNodes_.nodes()) {
      for (const auto node2: mgraph.nodes()) {
        if (node != node2) { forbiddenGraph.addArc(node2, node); }
      }
    }
 
    for (const auto node: constraintNoChildrenNodes_.nodes()) {
      for (const auto node2: mgraph.nodes()) {
        if (node != node2) { forbiddenGraph.addArc(node, node2); }
      }
    }
 
    // GUM_CHECKPOINT
    algoMiic_.setMaxIndegree(constraintIndegree_.maxIndegree());
    algoMiic_.addConstraints(initial_marks);
    algoMiic_.setMandatoryGraph(mandatoryGraph);
    algoMiic_.setForbiddenGraph(forbiddenGraph);
 
    // GUM_CHECKPOINT
    // create the mutual entropy object
    // if ( _mutual_info_ == nullptr) { this->useNMLCorrection(); }
    createCorrectedMutualInformation_();
 
    // GUM_CHECKPOINT
    return mgraph;
  }

References gum::DAG::addArc(), gum::DiGraph::addArc(), gum::UndiGraph::addEdge(), gum::NodeGraphPart::addNodeWithId(), algoMiic_, constraintForbiddenArcs_, constraintIndegree_, constraintMandatoryArcs_, constraintNoChildrenNodes_, constraintNoParentNodes_, constraintPossibleEdges_, constraintSliceOrder_, constraintTotalOrder_, createCorrectedMutualInformation_(), gum::Set< Key >::empty(), gum::NodeGraphPart::nodes(), and scoreDatabase_.

Referenced by learnDag_(), and learnPDAG_().

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◆ preparePC_()

MixedGraph gum::learning::IBNLearner::preparePC_ ( )

protectedinherited

prepares the initial graph and independence test for PC

Definition at line 710 of file IBNLearner.cpp.

                                    {
    MixedGraph mgraph;
    DiGraph    forbiddenGraph;
    DAG        mandatoryGraph;
 
    for (Size i = 0; i < scoreDatabase_.databaseTable().nbVariables(); ++i) {
      mgraph.addNodeWithId(i);
      forbiddenGraph.addNodeWithId(i);
      mandatoryGraph.addNodeWithId(i);
    }
 
    const EdgeSet& possible_edges = constraintPossibleEdges_.edges();
    if (possible_edges.empty()) {
      for (const NodeId i: mgraph.nodes()) {
        for (NodeId j = 0; j < i; ++j) {
          mgraph.addEdge(j, i);
        }
      }
    } else {
      for (const auto& edge: possible_edges) {
        mgraph.addEdge(edge.first(), edge.second());
      }
    }
 
    for (const auto& arc: constraintMandatoryArcs_.arcs()) {
      mandatoryGraph.addArc(arc.tail(), arc.head());
      forbiddenGraph.addArc(arc.head(), arc.tail());
    }
    for (const auto& arc: constraintForbiddenArcs_.arcs()) {
      forbiddenGraph.addArc(arc.tail(), arc.head());
    }
 
    const gum::NodeProperty< gum::Size > sliceOrder = constraintSliceOrder_.sliceOrder();
    gum::NodeProperty< gum::Size >       copyOrder  = gum::HashTable(sliceOrder);
    for (const auto& [n1, r1]: sliceOrder) {
      for (const auto& [n2, r2]: copyOrder) {
        if (r1 > r2) {
          forbiddenGraph.addArc(n1, n2);
        } else if (r2 > r1) {
          forbiddenGraph.addArc(n2, n1);
        }
      }
      copyOrder.erase(n1);
    }
 
    const auto& totalOrder = constraintTotalOrder_.totalOrder();
    for (auto iter1 = totalOrder.begin(); iter1 != totalOrder.end(); ++iter1) {
      for (auto iter2 = iter1 + 1; iter2 != totalOrder.end(); ++iter2) {
        forbiddenGraph.addArc(*iter2, *iter1);
      }
    }
 
    for (const auto node: constraintNoParentNodes_.nodes()) {
      for (const auto node2: mgraph.nodes()) {
        if (node != node2) { forbiddenGraph.addArc(node2, node); }
      }
    }
    for (const auto node: constraintNoChildrenNodes_.nodes()) {
      for (const auto node2: mgraph.nodes()) {
        if (node != node2) { forbiddenGraph.addArc(node, node2); }
      }
    }
 
    // build the independence test (owned by IBNLearner)
    if (indepTestPC_) {
      delete indepTestPC_;
      indepTestPC_ = nullptr;
    }
    if (indepTestTypePC_ == IndepTestType::Chi2) {
      indepTestPC_ = new IndepTestChi2(scoreDatabase_.parser(),
                                       *noPrior_,
                                       ranges_,
                                       scoreDatabase_.nodeId2Columns());
    } else {
      indepTestPC_ = new IndepTestG2(scoreDatabase_.parser(),
                                     *noPrior_,
                                     ranges_,
                                     scoreDatabase_.nodeId2Columns());
    }
 
    algoPC_.setMaxIndegree(constraintIndegree_.maxIndegree());
    algoPC_.setMandatoryGraph(mandatoryGraph);
    algoPC_.setForbiddenGraph(forbiddenGraph);
    algoPC_.setIndependenceTest(*indepTestPC_);
    algoPC_.setAlpha(alphaPc_);
    algoPC_.setStable(stablePc_);
    algoPC_.setMaxCondSetSize(maxCondSetSizePc_);
    algoPC_.setUCPriority(sortedUCPc_ ? gum::learning::PC::UCPriority::Sorted
                                      : gum::learning::PC::UCPriority::Standard);
 
    return mgraph;
  }

References gum::DAG::addArc(), gum::DiGraph::addArc(), gum::UndiGraph::addEdge(), gum::NodeGraphPart::addNodeWithId(), algoPC_, alphaPc_, Chi2, constraintForbiddenArcs_, constraintIndegree_, constraintMandatoryArcs_, constraintNoChildrenNodes_, constraintNoParentNodes_, constraintPossibleEdges_, constraintSliceOrder_, constraintTotalOrder_, gum::Set< Key >::empty(), indepTestPC_, indepTestTypePC_, maxCondSetSizePc_, gum::NodeGraphPart::nodes(), noPrior_, ranges_, scoreDatabase_, gum::learning::CIBasedLearning::Sorted, sortedUCPc_, stablePc_, and gum::learning::CIBasedLearning::Standard.

Referenced by learnDag_(), and learnPDAG_().

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◆ prepareSimpleMiic_()

MixedGraph gum::learning::IBNLearner::prepareSimpleMiic_ ( )

protectedinherited

prepares the initial graph for Simple Miic

◆ rawPseudoCount() [1/2]

std::vector< double > gum::learning::IBNLearner::rawPseudoCount ( const std::vector< NodeId > & vars )

inherited

Return the pseudo-counts of NodeIds vars in the base in a raw array.

Parameters

vars	a vector of

Returns: a std::vector<double> containing the contingency table

Definition at line 1481 of file IBNLearner.cpp.

                                                                                {
    if (this->hasMissingValues()) {
      GUM_ERROR(MissingValueInDatabase,
                "BNLearner cannot compute pseudo-counts with missing values in the database")
    }
    if (vars.empty()) {
      GUM_ERROR(OutOfBounds, "BNLearner::rawPseudoCount called with an empty vector of variables")
    }
    Tensor< double > res;
 
    createPrior_();
    gum::learning::PseudoCount count(scoreDatabase_.parser(), *prior_, databaseRanges());
    return count.get(vars);
  }

References createPrior_(), databaseRanges(), gum::learning::PseudoCount::get(), GUM_ERROR, hasMissingValues(), prior_, and scoreDatabase_.

Referenced by rawPseudoCount().

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◆ rawPseudoCount() [2/2]

std::vector< double > gum::learning::IBNLearner::rawPseudoCount ( const std::vector< std::string > & vars )

inherited

Return the pseudoconts of vars in the base in a raw array.

Parameters

vars	a vector of name

Returns: a std::vector<double> containing the contingency table

Definition at line 1496 of file IBNLearner.cpp.

                                                                                   {
    std::vector< NodeId > ids;
 
    auto mapper = [this](const std::string& c) { return this->idFromName(c); };
 
    std::transform(vars.begin(), vars.end(), std::back_inserter(ids), mapper);
    return rawPseudoCount(ids);
  }

References idFromName(), and rawPseudoCount().

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◆ readFile_()

DatabaseTable gum::learning::IBNLearner::readFile_	(	std::string_view	filename,
		const std::vector< std::string > &	missing_symbols )

staticprotectedinherited

reads a file and returns a databaseVectInRam

Definition at line 446 of file IBNLearner.cpp.

                                                                                     {
    // get the extension of the file
    isCSVFileName_(filename);
 
    DBInitializerFromCSV initializer{std::string(filename)};
 
    const auto&       var_names = initializer.variableNames();
    const std::size_t nb_vars   = var_names.size();
 
    DBTranslatorSet                translator_set;
    DBTranslator4LabelizedVariable translator(missing_symbols);
    for (std::size_t i = 0; i < nb_vars; ++i) {
      translator_set.insertTranslator(translator, i);
    }
 
    DatabaseTable database(missing_symbols, translator_set);
    database.setVariableNames(initializer.variableNames());
    initializer.fillDatabase(database);
 
    database.reorder();
 
    return database;
  }

References database(), gum::learning::IDBInitializer::fillDatabase(), gum::learning::DBTranslatorSet::insertTranslator(), isCSVFileName_(), and gum::learning::IDBInitializer::variableNames().

Referenced by gum::learning::IBNLearner::Database::Database().

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◆ recordWeight()

INLINE double gum::learning::IBNLearner::recordWeight ( const std::size_t i ) const

inherited

returns the weight of the ith record

Exceptions

OutOfBounds if i is outside the set of indices of the records

Definition at line 156 of file IBNLearner_inl.h.

                                                                {
    return scoreDatabase_.weight(i);
  }

References scoreDatabase_.

◆ score() [1/2]

double gum::learning::IBNLearner::score	(	NodeId	vars,
		const std::vector< NodeId > &	knowing = {} )

inherited

Return the value of the score currently in use by the BNLearner of a variable given a set of other variables.

Parameters

var	the NodeId of the LHS variable
knowing	an optional vector of conditioning variables, specified by their NodeIds

Returns: a double corresponding to the value of the score

Definition at line 1463 of file IBNLearner.cpp.

                                                                               {
    createPrior_();
    createScore_();
 
    return score_->score(var, knowing);
  }

References createPrior_(), createScore_(), and score_.

Referenced by score(), and useDatabaseRanges().

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◆ score() [2/2]

double gum::learning::IBNLearner::score	(	std::string_view	vars,
		const std::vector< std::string > &	knowing = {} )

inherited

Return the value of the score currently in use by the BNLearner of a variable given a set of other variables The score used is the one currently selected in the BNLearner.

Parameters

var	the name of the variable
knowing	an optional vector of conditioning variables, specified by their names

Returns: a double corresponding to the value of the score

Definition at line 1470 of file IBNLearner.cpp.

                                                                                    {
    auto mapper = [this](const std::string& c) { return this->idFromName(c); };
 
    const NodeId          id = this->idFromName(var);
    std::vector< NodeId > knowingIds;
    knowingIds.reserve(knowing.size());
    std::transform(knowing.begin(), knowing.end(), std::back_inserter(knowingIds), mapper);
 
    return score(id, knowingIds);
  }

References idFromName(), and score().

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◆ setCurrentApproximationScheme()

INLINE void gum::learning::IBNLearner::setCurrentApproximationScheme ( const ApproximationScheme * approximationScheme )

inherited

{@ /// distribute signals

Definition at line 767 of file IBNLearner_inl.h.

                                                                                              {
    currentAlgorithm_ = approximationScheme;
  }

References currentAlgorithm_.

Referenced by gum::learning::BNLearnerListener::BNLearnerListener(), distributeProgress(), and distributeStop().

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◆ setDatabaseWeight()

INLINE void gum::learning::IBNLearner::setDatabaseWeight ( const double new_weight )

inherited

assign a weight to all the rows of the learning database so that the sum of their weights is equal to new_weight

assign new weight to the rows of the learning database

Definition at line 146 of file IBNLearner_inl.h.

                                                                   {
    scoreDatabase_.setDatabaseWeight(new_weight);
  }

References scoreDatabase_.

◆ setEpsilon()

INLINE void gum::learning::IBNLearner::setEpsilon ( double eps )

overridevirtualinherited

Given that we approximate f(t), stopping criterion on |f(t+1)-f(t)| If the criterion was disabled it will be enabled.

Exceptions

OutOfBounds if eps<0

Implements gum::IApproximationSchemeConfiguration.

Definition at line 785 of file IBNLearner_inl.h.

                                               {
    algoK2_.approximationScheme().setEpsilon(eps);
    greedyHillClimbing_.setEpsilon(eps);
    localSearchWithTabuList_.setEpsilon(eps);
    dag2BN_.setEpsilon(eps);
  }

References algoK2_, dag2BN_, greedyHillClimbing_, and localSearchWithTabuList_.

◆ setFCIAlpha()

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::setFCIAlpha ( double alpha )

References BNLearner(), and setFCIAlpha().

Referenced by setFCIAlpha().

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◆ setFCIExhaustiveSepSet()

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::setFCIExhaustiveSepSet ( bool exhaustive )

References BNLearner(), and setFCIExhaustiveSepSet().

Referenced by setFCIExhaustiveSepSet().

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◆ setFCIMaxPathLength()

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::setFCIMaxPathLength ( Size max_len )

References BNLearner(), and setFCIMaxPathLength().

Referenced by setFCIMaxPathLength().

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◆ setForbiddenArcs()

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::setForbiddenArcs ( const ArcSet & set )

References BNLearner(), and setForbiddenArcs().

Referenced by setForbiddenArcs().

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◆ setGreedyThickThinningReversals()

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::setGreedyThickThinningReversals ( bool allow )

References BNLearner(), and setGreedyThickThinningReversals().

Referenced by setGreedyThickThinningReversals().

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◆ setInitialDAG()

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::setInitialDAG ( const DAG & dag )

References BNLearner(), and setInitialDAG().

Referenced by setInitialDAG().

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◆ setMandatoryArcs()

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::setMandatoryArcs ( const ArcSet & set )

References BNLearner(), and setMandatoryArcs().

Referenced by setMandatoryArcs().

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◆ setMaxIndegree()

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::setMaxIndegree ( Size max_indegree )

References BNLearner(), and setMaxIndegree().

Referenced by setMaxIndegree().

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◆ setMaxIter()

INLINE void gum::learning::IBNLearner::setMaxIter ( Size max )

overridevirtualinherited

stopping criterion on number of iterationsIf the criterion was disabled it will be enabled

Parameters

max	The maximum number of iterations

Exceptions

OutOfBounds if max<=1

Implements gum::IApproximationSchemeConfiguration.

Definition at line 847 of file IBNLearner_inl.h.

                                             {
    algoK2_.approximationScheme().setMaxIter(max);
    greedyHillClimbing_.setMaxIter(max);
    localSearchWithTabuList_.setMaxIter(max);
    dag2BN_.setMaxIter(max);
  }

References algoK2_, dag2BN_, greedyHillClimbing_, and localSearchWithTabuList_.

◆ setMaxTime()

INLINE void gum::learning::IBNLearner::setMaxTime ( double timeout )

overridevirtualinherited

stopping criterion on timeout If the criterion was disabled it will be enabled

Exceptions

OutOfBounds if timeout<=0.0 timeout is time in second (double).

Implements gum::IApproximationSchemeConfiguration.

Definition at line 878 of file IBNLearner_inl.h.

                                                   {
    algoK2_.approximationScheme().setMaxTime(timeout);
    greedyHillClimbing_.setMaxTime(timeout);
    localSearchWithTabuList_.setMaxTime(timeout);
    dag2BN_.setMaxTime(timeout);
  }

References algoK2_, dag2BN_, greedyHillClimbing_, and localSearchWithTabuList_.

◆ setMinEpsilonRate()

INLINE void gum::learning::IBNLearner::setMinEpsilonRate ( double rate )

overridevirtualinherited

Given that we approximate f(t), stopping criterion on d/dt(|f(t+1)-f(t)|) If the criterion was disabled it will be enabled.

Exceptions

OutOfBounds if rate<0

Implements gum::IApproximationSchemeConfiguration.

Definition at line 816 of file IBNLearner_inl.h.

                                                       {
    algoK2_.approximationScheme().setMinEpsilonRate(rate);
    greedyHillClimbing_.setMinEpsilonRate(rate);
    localSearchWithTabuList_.setMinEpsilonRate(rate);
    dag2BN_.setMinEpsilonRate(rate);
  }

References algoK2_, dag2BN_, greedyHillClimbing_, and localSearchWithTabuList_.

◆ setNumberOfThreads()

INLINE void gum::learning::IBNLearner::setNumberOfThreads ( Size nb )

overridevirtualinherited

sets the number max of threads that can be used

Parameters

nb	the number max of threads to be used. If this number is set to 0, then it is defaulted to aGrUM's max number of threads

Implements gum::IThreadNumberManager.

Definition at line 741 of file IBNLearner_inl.h.

                                                    {
    ThreadNumberManager::setNumberOfThreads(nb);
    if (score_ != nullptr) score_->setNumberOfThreads(nb);
  }

References score_, and gum::ThreadNumberManager::setNumberOfThreads().

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◆ setPCAlpha()

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::setPCAlpha ( double alpha )

References BNLearner(), and setPCAlpha().

Referenced by setPCAlpha().

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◆ setPCMaxCondSetSize()

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::setPCMaxCondSetSize ( Size max_k )

References BNLearner(), and setPCMaxCondSetSize().

Referenced by setPCMaxCondSetSize().

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◆ setPCStable()

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::setPCStable ( bool stable )

References BNLearner(), and setPCStable().

Referenced by setPCStable().

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◆ setPCUnshieldedColliderSorted()

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::setPCUnshieldedColliderSorted ( bool sorted )

References BNLearner(), and setPCUnshieldedColliderSorted().

Referenced by setPCUnshieldedColliderSorted().

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◆ setPeriodSize()

INLINE void gum::learning::IBNLearner::setPeriodSize ( Size p )

overridevirtualinherited

how many samples between 2 stopping isEnableds

Exceptions

OutOfBounds if p<1

Implements gum::IApproximationSchemeConfiguration.

Definition at line 914 of file IBNLearner_inl.h.

                                              {
    algoK2_.approximationScheme().setPeriodSize(p);
    greedyHillClimbing_.setPeriodSize(p);
    localSearchWithTabuList_.setPeriodSize(p);
    dag2BN_.setPeriodSize(p);
  }

References algoK2_, dag2BN_, greedyHillClimbing_, and localSearchWithTabuList_.

◆ setPossibleEdges()

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::setPossibleEdges ( const EdgeSet & set )

References BNLearner(), and setPossibleEdges().

Referenced by setPossibleEdges().

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◆ setPossibleSkeleton()

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::setPossibleSkeleton ( const UndiGraph & skeleton )

References BNLearner(), and setPossibleSkeleton().

Referenced by setPossibleSkeleton().

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◆ setRecordWeight()

INLINE void gum::learning::IBNLearner::setRecordWeight	(	const std::size_t	i,
		const double	weight )

inherited

sets the weight of the ith record of the database

assign new weight to the ith row of the learning database

Exceptions

OutOfBounds if i is outside the set of indices of the records or if the weight is negative

Definition at line 151 of file IBNLearner_inl.h.

                                                                                    {
    scoreDatabase_.setWeight(i, new_weight);
  }

References scoreDatabase_.

◆ setSliceOrder() [1/2]

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::setSliceOrder ( const NodeProperty< NodeId > & slice_order )

References BNLearner(), and setSliceOrder().

Referenced by setSliceOrder(), and setSliceOrder().

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◆ setSliceOrder() [2/2]

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::setSliceOrder ( const std::vector< std::vector< std::string > > & slices )

References setSliceOrder().

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◆ setTotalOrder() [1/2]

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::setTotalOrder ( const Sequence< NodeId > & order )

References BNLearner(), and setTotalOrder().

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◆ setTotalOrder() [2/2]

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::setTotalOrder ( const std::vector< std::string > & order )

References BNLearner(), and setTotalOrder().

Referenced by setTotalOrder(), and setTotalOrder().

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◆ setVerbosity()

INLINE void gum::learning::IBNLearner::setVerbosity ( bool v )

overridevirtualinherited

verbosity

Implements gum::IApproximationSchemeConfiguration.

Definition at line 926 of file IBNLearner_inl.h.

                                             {
    algoK2_.approximationScheme().setVerbosity(v);
    greedyHillClimbing_.setVerbosity(v);
    localSearchWithTabuList_.setVerbosity(v);
    dag2BN_.setVerbosity(v);
  }

References algoK2_, dag2BN_, greedyHillClimbing_, and localSearchWithTabuList_.

◆ state()

template<GUM_Numeric GUM_SCALAR>

std::vector< std::tuple< std::string, std::string, std::string > > gum::learning::BNLearner< GUM_SCALAR >::state ( ) const

Returns: a representation of the state of the learner in the form vector<key,value,comment>

References state().

Referenced by state().

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◆ stateApproximationScheme()

INLINE IApproximationSchemeConfiguration::ApproximationSchemeSTATE gum::learning::IBNLearner::stateApproximationScheme ( ) const

overridevirtualinherited

history

Implements gum::IApproximationSchemeConfiguration.

Definition at line 939 of file IBNLearner_inl.h.

                                                    {
    if (currentAlgorithm_ != nullptr) return currentAlgorithm_->stateApproximationScheme();
    else GUM_ERROR(FatalError, "No chosen algorithm for learning")
  }

References currentAlgorithm_, and GUM_ERROR.

◆ toString()

template<GUM_Numeric GUM_SCALAR>

std::string gum::learning::BNLearner< GUM_SCALAR >::toString ( ) const

Returns: Returns a string representation of this BNLearner's current features.

References toString().

Referenced by toString().

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◆ unsetSliceOrder()

INLINE void gum::learning::IBNLearner::unsetSliceOrder ( )

inherited

removes the slice order constraint

The methd is useful if you had previously added a slice order constraint and you do not want to use it anymore

Definition at line 624 of file IBNLearner_inl.h.

624{ setSliceOrder(NodeProperty< NodeId >()); }

gum::learning::IBNLearner::setSliceOrder

void setSliceOrder(const NodeProperty< NodeId > &slice_order)

sets a partial order on the nodes

Definition IBNLearner_inl.h:608

References setSliceOrder().

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◆ unsetTotalOrder()

INLINE void gum::learning::IBNLearner::unsetTotalOrder ( )

inherited

removes the current total ordering constraint, if any

Definition at line 641 of file IBNLearner_inl.h.

641{ setTotalOrder(Sequence< NodeId >()); }

gum::learning::IBNLearner::setTotalOrder

void setTotalOrder(const Sequence< NodeId > &order)

sets a total order over some nodes

Definition IBNLearner_inl.h:627

References setTotalOrder().

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◆ useBDeuPrior()

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::useBDeuPrior ( double weight = 1.0 )

References BNLearner(), and useBDeuPrior().

Referenced by useBDeuPrior().

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◆ useChi2Test()

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::useChi2Test ( )

References BNLearner(), and useChi2Test().

Referenced by useChi2Test().

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◆ useCrossValidationFold()

std::pair< std::size_t, std::size_t > gum::learning::IBNLearner::useCrossValidationFold	(	const std::size_t	learning_fold,
		const std::size_t	k_fold )

inherited

sets the ranges of rows to be used for cross-validation learning

When applied on (x,k), the method indicates to the subsequent learnings that they should be performed on the xth fold in a k-fold cross-validation context. For instance, if a database has 1000 rows, and if we perform a 10-fold cross-validation, then, the first learning fold (learning_fold=0) corresponds to rows interval [100,1000) and the test dataset corresponds to [0,100). The second learning fold (learning_fold=1) is [0,100) U [200,1000) and the corresponding test dataset is [100,200).

Parameters

learning_fold	a number indicating the set of rows used for learning. If N denotes the size of the database, and k_fold represents the number of folds in the cross validation, then the set of rows used for testing is [learning_fold * N / k_fold, (learning_fold+1) * N / k_fold) and the learning database is the complement in the database
k_fold	the value of "k" in k-fold cross validation

Returns: a pair [x,y) of rows' indices that corresponds to the indices of rows in the original database that constitute the test dataset

Exceptions

OutOfBounds is raised if k_fold is equal to 0 or learning_fold is greater than or eqal to k_fold, or if k_fold is greater than or equal to the size of the database.

Definition at line 1299 of file IBNLearner.cpp.

                                                                 {
    if (k_fold == 0) { GUM_ERROR(OutOfBounds, "K-fold cross validation with k=0 is forbidden") }
 
    if (learning_fold >= k_fold) {
      GUM_ERROR(OutOfBounds,
                "In " << k_fold << "-fold cross validation, the learning "
                      << "fold should be strictly lower than " << k_fold
                      << " but, here, it is equal to " << learning_fold)
    }
 
    const std::size_t db_size = scoreDatabase_.databaseTable().nbRows();
    if (k_fold >= db_size) {
      GUM_ERROR(OutOfBounds,
                "In " << k_fold << "-fold cross validation, the database's "
                      << "size should be strictly greater than " << k_fold
                      << " but, here, the database has only " << db_size << "rows")
    }
 
    // create the ranges of rows of the test database
    const std::size_t foldSize   = db_size / k_fold;
    const std::size_t unfold_deb = learning_fold * foldSize;
    const std::size_t unfold_end = unfold_deb + foldSize;
 
    ranges_.clear();
    if (learning_fold == std::size_t(0)) {
      ranges_.push_back(std::pair< std::size_t, std::size_t >(unfold_end, db_size));
    } else {
      ranges_.push_back(std::pair< std::size_t, std::size_t >(std::size_t(0), unfold_deb));
 
      if (learning_fold != k_fold - 1) {
        ranges_.push_back(std::pair< std::size_t, std::size_t >(unfold_end, db_size));
      }
    }
 
    return std::pair< std::size_t, std::size_t >(unfold_deb, unfold_end);
  }

References GUM_ERROR, ranges_, and scoreDatabase_.

◆ useDatabaseRanges()

void gum::learning::IBNLearner::useDatabaseRanges ( const std::vector< std::pair< std::size_t, std::size_t > > & new_ranges )

inherited

use a new set of database rows' ranges to perform learning

Parameters

ranges a set of pairs {(X1,Y1),...,(Xn,Yn)} of database's rows indices. The subsequent learnings are then performed only on the union of the rows [Xi,Yi), i in {1,...,n}. This is useful, e.g, when performing cross validation tasks, in which part of the database should be ignored. An empty set of ranges is equivalent to an interval [X,Y) ranging over the whole database.

Definition at line 1506 of file IBNLearner.cpp.

                                                                      {
    // use a score to detect whether the ranges are ok
    ScoreLog2Likelihood score(scoreDatabase_.parser(), *noPrior_);
    score.setRanges(new_ranges);
    ranges_ = score.ranges();
  }

References noPrior_, ranges_, score(), and scoreDatabase_.

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◆ useDirichletPrior() [1/2]

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::useDirichletPrior	(	const gum::BayesNet< GUM_SCALAR > &	bn,
		double	weight = 1 )

References BNLearner(), and useDirichletPrior().

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◆ useDirichletPrior() [2/2]

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::useDirichletPrior	(	std::string_view	filename,
		double	weight = 1 )

References BNLearner(), and useDirichletPrior().

Referenced by useDirichletPrior(), and useDirichletPrior().

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◆ useEM()

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::useEM	(	const double	epsilon,
		const double	noise = default_EM_noise )

use The EM algorithm to learn parameters

This is essentially an alias for Method useEMWithRateCriterion().

Parameters

epsilon	sets the approximation stopping criterion: EM stops whenever the absolute value of the relative difference between two consecutive log-likelihoods drops below epsilon. Note that epsilon=0 is considered as a directive to not use EM. However, if you wish to forbid the use of EM, prefer executing Method forbidEM() rather than useEM(0) as it is more unequivocal.
noise	When EM starts, it initializes all the CPTs of the Bayes net. EM adds a noise to these CPTs by mixing their values with some random noise. The formula used is, up to some normalizing constant: new_cpt = (1-noise) * cpt + noise * random_cpt(). Of course, noise must belong to interval [0,1].

Returns: the BNLearner (so that we can chains the calls to useXXX() methods)

Warning: if epsilon=0, EM is not used

Exceptions

OutOfBounds is raised if epsilon is strictly negative or if noise does not belong to interval [0,1].

References BNLearner(), gum::learning::IBNLearner::default_EM_noise, gum::learning::IBNLearner::epsilon(), and useEM().

Referenced by useEM().

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◆ useEMWithDiffCriterion()

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::useEMWithDiffCriterion	(	const double	epsilon,
		const double	noise = default_EM_noise )

use The EM algorithm to learn parameters with the diff stopping criterion

Parameters

epsilon	epsilon sets the approximation stopping criterion: EM stops whenever the difference between two consecutive log-likelihoods drops below epsilon. Note that, for using EM, epsilon should be strictly positive.
noise	When EM starts, it initializes all the CPTs of the Bayes net. EM adds a noise to these CPTs by mixing their values with some random noise. The formula used is, up to some normalizing constant: new_cpt = (1-noise) * cpt + noise * random_cpt(). Of course, noise must belong to interval [0,1].

Returns: the BNLearner (so that we can chains the calls to useXXX() methods)

Exceptions

OutOfBounds is raised if epsilon is not strictly positive or if noise does not belong to interval [0,1].

References BNLearner(), gum::learning::IBNLearner::default_EM_noise, gum::learning::IBNLearner::epsilon(), and useEMWithDiffCriterion().

Referenced by useEMWithDiffCriterion().

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◆ useEMWithRateCriterion()

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::useEMWithRateCriterion	(	const double	epsilon,
		const double	noise = default_EM_noise )

use The EM algorithm to learn parameters with the rate stopping criterion

Parameters

epsilon	epsilon sets the approximation stopping criterion: EM stops whenever the absolute value of the relative difference between two consecutive log-likelihoods drops below epsilon. Note that, for using EM, epsilon should be strictly positive.
max_nb_iter	the maximum number of EM iterations allowed. If equal to 0, this stopping criterion is unused.
noise	When EM starts, it initializes all the CPTs of the Bayes net. EM adds a noise to these CPTs by mixing their values with some random noise. The formula used is, up to some normalizing constant: new_cpt = (1-noise) * cpt + noise * random_cpt(). Of course, noise must belong to interval [0,1].

Returns: the BNLearner (so that we can chains the calls to useXXX() methods)

Exceptions

OutOfBounds is raised if epsilon is not strictly positive or if noise does not belong to interval [0,1].

References BNLearner(), gum::learning::IBNLearner::default_EM_noise, gum::learning::IBNLearner::epsilon(), and useEMWithRateCriterion().

Referenced by useEMWithRateCriterion().

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◆ useExtendedGreedyHillClimbing()

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::useExtendedGreedyHillClimbing ( )

References BNLearner(), and useExtendedGreedyHillClimbing().

Referenced by useExtendedGreedyHillClimbing().

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◆ useFCI()

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::useFCI ( )

References BNLearner(), and useFCI().

Referenced by useFCI().

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◆ useFCIChi2Test()

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::useFCIChi2Test ( )

References BNLearner(), and useFCIChi2Test().

Referenced by useFCIChi2Test().

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◆ useFCIG2Test()

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::useFCIG2Test ( )

References BNLearner(), and useFCIG2Test().

Referenced by useFCIG2Test().

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◆ useG2Test()

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::useG2Test ( )

References BNLearner(), and useG2Test().

Referenced by useG2Test().

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◆ useGreedyHillClimbing()

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::useGreedyHillClimbing ( )

References BNLearner(), and useGreedyHillClimbing().

Referenced by useGreedyHillClimbing().

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◆ useGreedyThickThinning()

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::useGreedyThickThinning ( )

References BNLearner(), and useGreedyThickThinning().

Referenced by useGreedyThickThinning().

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◆ useK2() [1/2]

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::useK2 ( const Sequence< NodeId > & order )

References BNLearner(), and useK2().

Referenced by useK2(), and useK2().

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◆ useK2() [2/2]

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::useK2 ( const std::vector< NodeId > & order )

References BNLearner(), and useK2().

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◆ useLocalSearchWithTabuList()

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::useLocalSearchWithTabuList	(	Size	tabu_size = 100,
		Size	nb_decrease = 2 )

References BNLearner(), and useLocalSearchWithTabuList().

Referenced by useLocalSearchWithTabuList().

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◆ useMDLCorrection()

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::useMDLCorrection ( )

References BNLearner(), and useMDLCorrection().

Referenced by useMDLCorrection().

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◆ useMIIC()

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::useMIIC ( )

References BNLearner(), and useMIIC().

Referenced by useMIIC().

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◆ useNMLCorrection()

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::useNMLCorrection ( )

References BNLearner(), and useNMLCorrection().

Referenced by useNMLCorrection().

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◆ useNoCorrection()

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::useNoCorrection ( )

References BNLearner(), and useNoCorrection().

Referenced by useNoCorrection().

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◆ useNoPrior()

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::useNoPrior ( )

References BNLearner(), and useNoPrior().

Referenced by useNoPrior().

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◆ usePC()

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::usePC ( )

References BNLearner(), and usePC().

Referenced by usePC().

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◆ useScoreAIC()

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::useScoreAIC ( )

References BNLearner(), and useScoreAIC().

Referenced by useScoreAIC().

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◆ useScoreBD()

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::useScoreBD ( )

References BNLearner(), and useScoreBD().

Referenced by useScoreBD().

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◆ useScoreBDeu()

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::useScoreBDeu ( )

References BNLearner(), and useScoreBDeu().

Referenced by useScoreBDeu().

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◆ useScoreBIC()

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::useScoreBIC ( )

References BNLearner(), and useScoreBIC().

Referenced by useScoreBIC().

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◆ useScorefNML()

INLINE void gum::learning::IBNLearner::useScorefNML ( )

inherited

indicate that we wish to use a fNML score

Definition at line 193 of file IBNLearner_inl.h.

                                       {
    scoreType_ = ScoreType::fNML;
    checkScorePriorCompatibility();
  }

References checkScorePriorCompatibility(), fNML, and scoreType_.

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◆ useScoreK2()

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::useScoreK2 ( )

References BNLearner(), and useScoreK2().

Referenced by useScoreK2().

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◆ useScoreLog2Likelihood()

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::useScoreLog2Likelihood ( )

References BNLearner(), and useScoreLog2Likelihood().

Referenced by useScoreLog2Likelihood().

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◆ useScoreMDL()

INLINE void gum::learning::IBNLearner::useScoreMDL ( )

inherited

indicate that we wish to use a MDL score

Definition at line 211 of file IBNLearner_inl.h.

                                      {
    scoreType_ = ScoreType::MDL;
    checkScorePriorCompatibility();
  }

References checkScorePriorCompatibility(), MDL, and scoreType_.

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◆ useSmoothingPrior()

template<GUM_Numeric GUM_SCALAR>

BNLearner< GUM_SCALAR > & gum::learning::BNLearner< GUM_SCALAR >::useSmoothingPrior ( double weight = 1 )

References BNLearner(), and useSmoothingPrior().

Referenced by useSmoothingPrior().

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◆ verbosity()

INLINE bool gum::learning::IBNLearner::verbosity ( ) const

overridevirtualinherited

verbosity

Implements gum::IApproximationSchemeConfiguration.

Definition at line 933 of file IBNLearner_inl.h.

                                          {
    if (currentAlgorithm_ != nullptr) return currentAlgorithm_->verbosity();
    else GUM_ERROR(FatalError, "No chosen algorithm for learning")
  }

References currentAlgorithm_, and GUM_ERROR.

Member Data Documentation

◆ _nb_threads_

Size gum::ThreadNumberManager::_nb_threads_ {0}

privateinherited

the max number of threads used by the class

Definition at line 126 of file threadNumberManager.h.

126{0};

◆ _prior_bn_

template<GUM_Numeric GUM_SCALAR>

BayesNet< GUM_SCALAR > gum::learning::BNLearner< GUM_SCALAR >::_prior_bn_

private

Definition at line 542 of file BNLearner.h.

◆ algoFCI_

gum::learning::FCI gum::learning::IBNLearner::algoFCI_

protectedinherited

the FCI algorithm

Definition at line 1222 of file IBNLearner.h.

Referenced by learnDag_(), learnPAG_(), learnPDAG_(), and prepareFCI_().

◆ algoK2_

K2 gum::learning::IBNLearner::algoK2_

protectedinherited

the K2 algorithm

Definition at line 1193 of file IBNLearner.h.

Referenced by IBNLearner(), IBNLearner(), disableEpsilon(), disableMaxIter(), disableMaxTime(), disableMinEpsilonRate(), enableEpsilon(), enableMaxIter(), enableMaxTime(), enableMinEpsilonRate(), learnDag_(), operator=(), operator=(), setEpsilon(), setMaxIter(), setMaxTime(), setMinEpsilonRate(), setPeriodSize(), setVerbosity(), useK2(), and useK2().

◆ algoMiic_

Miic gum::learning::IBNLearner::algoMiic_

protectedinherited

the Constraint MIIC algorithm

Definition at line 1199 of file IBNLearner.h.

Referenced by IBNLearner(), IBNLearner(), latentVariables(), learnDag_(), learnPDAG_(), operator=(), operator=(), and prepareMiic_().

◆ algoPC_

gum::learning::PC gum::learning::IBNLearner::algoPC_

protectedinherited

the PC algorithm

Definition at line 1206 of file IBNLearner.h.

Referenced by learnDag_(), learnPDAG_(), and preparePC_().

◆ algoSimpleMiic_

SimpleMiic gum::learning::IBNLearner::algoSimpleMiic_

protectedinherited

the MIIC algorithm

Definition at line 1196 of file IBNLearner.h.

Referenced by IBNLearner(), IBNLearner(), operator=(), and operator=().

◆ allowArcAdditions_

bool gum::learning::IBNLearner::allowArcAdditions_ {true}

protectedinherited

whether we allow or not arc additions during learning

Definition at line 1181 of file IBNLearner.h.

1181{true};

Referenced by allowArcAdditions(), and learnDag_().

◆ allowArcDeletions_

bool gum::learning::IBNLearner::allowArcDeletions_ {true}

protectedinherited

whether we allow or not arc deletions during learning

Definition at line 1184 of file IBNLearner.h.

1184{true};

Referenced by allowArcDeletions(), and learnDag_().

◆ allowArcReversals_

bool gum::learning::IBNLearner::allowArcReversals_ {true}

protectedinherited

whether we allow or not arc reversals during learning

Definition at line 1187 of file IBNLearner.h.

1187{true};

Referenced by allowArcReversals(), and learnDag_().

◆ allowArcTriangleDeletions_

bool gum::learning::IBNLearner::allowArcTriangleDeletions_ {true}

protectedinherited

whether we allow or not arc deletions during learning

Definition at line 1190 of file IBNLearner.h.

1190{true};

Referenced by allowArcTriangleDeletions(), and learnDag_().

◆ alphaFci_

double gum::learning::IBNLearner::alphaFci_ {0.05}

protectedinherited

FCI parameters.

Definition at line 1231 of file IBNLearner.h.

1231{0.05};

Referenced by prepareFCI_(), and setFCIAlpha().

◆ alphaPc_

double gum::learning::IBNLearner::alphaPc_ {0.05}

protectedinherited

PC parameters.

Definition at line 1216 of file IBNLearner.h.

1216{0.05};

Referenced by preparePC_(), and setPCAlpha().

◆ constraintForbiddenArcs_

StructuralConstraintForbiddenArcs gum::learning::IBNLearner::constraintForbiddenArcs_

protectedinherited

the constraint on forbidden arcs

Definition at line 1163 of file IBNLearner.h.

Referenced by IBNLearner(), IBNLearner(), addForbiddenArc(), eraseForbiddenArc(), learnDag_(), operator=(), operator=(), prepareFCI_(), prepareMiic_(), preparePC_(), and setForbiddenArcs().

◆ constraintIndegree_

StructuralConstraintIndegree gum::learning::IBNLearner::constraintIndegree_

protectedinherited

the constraint for indegrees

Definition at line 1157 of file IBNLearner.h.

Referenced by IBNLearner(), IBNLearner(), learnDag_(), operator=(), operator=(), prepareFCI_(), prepareMiic_(), preparePC_(), and setMaxIndegree().

◆ constraintMandatoryArcs_

StructuralConstraintMandatoryArcs gum::learning::IBNLearner::constraintMandatoryArcs_

protectedinherited

the constraint on mandatory arcs

Definition at line 1169 of file IBNLearner.h.

Referenced by IBNLearner(), IBNLearner(), addMandatoryArc(), eraseMandatoryArc(), learnDag_(), operator=(), operator=(), prepareFCI_(), prepareMiic_(), preparePC_(), and setMandatoryArcs().

◆ constraintNoChildrenNodes_

StructuralConstraintNoChildrenNodes gum::learning::IBNLearner::constraintNoChildrenNodes_

protectedinherited

the constraint on no children nodes

Definition at line 1175 of file IBNLearner.h.

Referenced by IBNLearner(), IBNLearner(), addNoChildrenNode(), eraseNoChildrenNode(), learnDag_(), operator=(), operator=(), prepareFCI_(), prepareMiic_(), and preparePC_().

◆ constraintNoParentNodes_

StructuralConstraintNoParentNodes gum::learning::IBNLearner::constraintNoParentNodes_

protectedinherited

the constraint on no parent nodes

Definition at line 1172 of file IBNLearner.h.

Referenced by IBNLearner(), IBNLearner(), addNoParentNode(), eraseNoParentNode(), learnDag_(), operator=(), operator=(), prepareFCI_(), prepareMiic_(), and preparePC_().

◆ constraintPossibleEdges_

StructuralConstraintPossibleEdges gum::learning::IBNLearner::constraintPossibleEdges_

protectedinherited

the constraint on possible Edges

Definition at line 1166 of file IBNLearner.h.

Referenced by addPossibleEdge(), erasePossibleEdge(), learnDag_(), prepareFCI_(), prepareMiic_(), preparePC_(), and setPossibleEdges().

◆ constraintSliceOrder_

StructuralConstraintSliceOrder gum::learning::IBNLearner::constraintSliceOrder_

protectedinherited

the constraint for 2TBNs

Definition at line 1151 of file IBNLearner.h.

Referenced by IBNLearner(), IBNLearner(), learnDag_(), operator=(), operator=(), prepareFCI_(), prepareMiic_(), preparePC_(), and setSliceOrder().

◆ constraintTabuList_

StructuralConstraintTabuList gum::learning::IBNLearner::constraintTabuList_

protectedinherited

the constraint for tabu lists

Definition at line 1160 of file IBNLearner.h.

Referenced by IBNLearner(), IBNLearner(), learnDag_(), operator=(), operator=(), and useLocalSearchWithTabuList().

◆ constraintTotalOrder_

StructuralConstraintTotalOrder gum::learning::IBNLearner::constraintTotalOrder_

protectedinherited

the total order ing constraint

Definition at line 1154 of file IBNLearner.h.

Referenced by learnDag_(), prepareFCI_(), prepareMiic_(), preparePC_(), and setTotalOrder().

◆ currentAlgorithm_

const ApproximationScheme* gum::learning::IBNLearner::currentAlgorithm_ {nullptr}

protectedinherited

Definition at line 1272 of file IBNLearner.h.

1272{nullptr};

Referenced by currentTime(), epsilon(), history(), isEnabledEpsilon(), isEnabledMaxIter(), isEnabledMaxTime(), isEnabledMinEpsilonRate(), maxIter(), maxTime(), minEpsilonRate(), nbrIterations(), operator=(), operator=(), periodSize(), setCurrentApproximationScheme(), stateApproximationScheme(), and verbosity().

◆ dag2BN_

DAG2BNLearner gum::learning::IBNLearner::dag2BN_

protectedinherited

the parametric EM

Definition at line 1236 of file IBNLearner.h.

Referenced by IBNLearner(), IBNLearner(), disableEpsilon(), disableMaxIter(), disableMaxTime(), disableMinEpsilonRate(), EM(), EMCurrentTime(), EMdisableEpsilon(), EMdisableMaxIter(), EMdisableMaxTime(), EMdisableMinEpsilonRate(), EMenableEpsilon(), EMenableMaxIter(), EMenableMaxTime(), EMenableMinEpsilonRate(), EMEpsilon(), EMHistory(), EMisEnabledEpsilon(), EMisEnabledMaxIter(), EMisEnabledMaxTime(), EMisEnabledMinEpsilonRate(), EMMaxIter(), EMMaxTime(), EMMinEpsilonRate(), EMnbrIterations(), EMPeriodSize(), EMsetEpsilon(), EMsetMaxIter(), EMsetMaxTime(), EMsetMinEpsilonRate(), EMsetPeriodSize(), EMsetVerbosity(), EMState(), EMStateApproximationScheme(), EMStateMessage(), EMVerbosity(), enableEpsilon(), enableMaxIter(), enableMaxTime(), enableMinEpsilonRate(), operator=(), operator=(), setEpsilon(), setMaxIter(), setMaxTime(), setMinEpsilonRate(), setPeriodSize(), setVerbosity(), useEM(), and useEMWithDiffCriterion().

◆ default_EM_noise

double gum::learning::IBNLearner::default_EM_noise {0.1}

staticconstexprinherited

the default noise amount added to CPTs during EM's initialization (see method useEM())

Definition at line 135 of file IBNLearner.h.

135{0.1};

Referenced by gum::learning::BNLearner< GUM_SCALAR >::useEM(), gum::learning::BNLearner< GUM_SCALAR >::useEMWithDiffCriterion(), and gum::learning::BNLearner< GUM_SCALAR >::useEMWithRateCriterion().

◆ exhaustiveSepSetFci_

bool gum::learning::IBNLearner::exhaustiveSepSetFci_ {false}

protectedinherited

Definition at line 1233 of file IBNLearner.h.

1233{false};

Referenced by fciExhaustiveSepSet(), prepareFCI_(), and setFCIExhaustiveSepSet().

◆ extendedGreedyHillClimbing_

GreedyHillClimbing gum::learning::IBNLearner::extendedGreedyHillClimbing_

protectedinherited

the extended greedy hill climbing

Definition at line 1242 of file IBNLearner.h.

Referenced by learnDag_().

◆ filename_

std::string gum::learning::IBNLearner::filename_ {"-"}

protectedinherited

the filename database

Definition at line 1266 of file IBNLearner.h.

1266{"-"};

Referenced by IBNLearner(), IBNLearner(), IBNLearner(), IBNLearner(), operator=(), and operator=().

◆ greedyHillClimbing_

GreedyHillClimbing gum::learning::IBNLearner::greedyHillClimbing_

protectedinherited

the greedy hill climbing algorithm

Definition at line 1239 of file IBNLearner.h.

Referenced by IBNLearner(), IBNLearner(), disableEpsilon(), disableMaxIter(), disableMaxTime(), disableMinEpsilonRate(), enableEpsilon(), enableMaxIter(), enableMaxTime(), enableMinEpsilonRate(), learnDag_(), operator=(), operator=(), setEpsilon(), setMaxIter(), setMaxTime(), setMinEpsilonRate(), setPeriodSize(), and setVerbosity().

◆ greedyThickThinning_

GreedyThickThinning gum::learning::IBNLearner::greedyThickThinning_

protectedinherited

the greedy thick-thinning algorithm

Definition at line 1245 of file IBNLearner.h.

Referenced by greedyThickThinningReversals(), learnDag_(), and setGreedyThickThinningReversals().

◆ indepTestFCI_

IndependenceTest* gum::learning::IBNLearner::indepTestFCI_ {nullptr}

protectedinherited

owned independence test object for FCI (rebuilt before each learn call)

Definition at line 1228 of file IBNLearner.h.

1228{nullptr};

Referenced by ~IBNLearner(), and prepareFCI_().

◆ indepTestPC_

IndependenceTest* gum::learning::IBNLearner::indepTestPC_ {nullptr}

protectedinherited

owned independence test object for PC (rebuilt before each learn call)

Definition at line 1213 of file IBNLearner.h.

1213{nullptr};

Referenced by ~IBNLearner(), and preparePC_().

◆ indepTestTypeFCI_

IndepTestType gum::learning::IBNLearner::indepTestTypeFCI_ {IndepTestType::Chi2}

protectedinherited

independence test type for FCI (reuses IndepTestType defined above)

Definition at line 1225 of file IBNLearner.h.

1225{IndepTestType::Chi2};

Referenced by prepareFCI_(), useFCIChi2Test(), and useFCIG2Test().

◆ indepTestTypePC_

IndepTestType gum::learning::IBNLearner::indepTestTypePC_ {IndepTestType::Chi2}

protectedinherited

Definition at line 1210 of file IBNLearner.h.

1210{IndepTestType::Chi2};

Referenced by preparePC_(), useChi2Test(), and useG2Test().

◆ inducedTypes_

bool gum::learning::IBNLearner::inducedTypes_ {false}

protectedinherited

the policy for typing variables

Definition at line 1119 of file IBNLearner.h.

1119{false};

Referenced by IBNLearner(), IBNLearner(), IBNLearner(), and IBNLearner().

◆ initialDag_

DAG gum::learning::IBNLearner::initialDag_

protectedinherited

an initial DAG given to learners

Definition at line 1263 of file IBNLearner.h.

Referenced by IBNLearner(), IBNLearner(), initialDAG(), learnDag_(), operator=(), operator=(), and setInitialDAG().

◆ kmodeMiic_

CorrectedMutualInformation::KModeTypes gum::learning::IBNLearner::kmodeMiic_

protectedinherited

Initial value:

{

CorrectedMutualInformation::KModeTypes::MDL}

gum::learning::CorrectedMutualInformation::KModeTypes::MDL

@ MDL

Definition correctedMutualInformation.h:298

the penalty used in MIIC

Definition at line 1202 of file IBNLearner.h.

1202 {

1203 CorrectedMutualInformation::KModeTypes::MDL};

Referenced by IBNLearner(), IBNLearner(), correctedMutualInformation(), createCorrectedMutualInformation_(), operator=(), operator=(), useMDLCorrection(), useNMLCorrection(), and useNoCorrection().

◆ localSearchWithTabuList_

LocalSearchWithTabuList gum::learning::IBNLearner::localSearchWithTabuList_

protectedinherited

the local search with tabu list algorithm

Definition at line 1248 of file IBNLearner.h.

Referenced by IBNLearner(), IBNLearner(), disableEpsilon(), disableMaxIter(), disableMaxTime(), disableMinEpsilonRate(), enableEpsilon(), enableMaxIter(), enableMaxTime(), enableMinEpsilonRate(), learnDag_(), operator=(), operator=(), setEpsilon(), setMaxIter(), setMaxTime(), setMinEpsilonRate(), setPeriodSize(), setVerbosity(), and useLocalSearchWithTabuList().

◆ maxCondSetSizePc_

Size gum::learning::IBNLearner::maxCondSetSizePc_ {Size(-1)}

protectedinherited

Definition at line 1218 of file IBNLearner.h.

1218{Size(-1)};

Referenced by preparePC_(), and setPCMaxCondSetSize().

◆ maxPathLengthFci_

Size gum::learning::IBNLearner::maxPathLengthFci_ {Size(-1)}

protectedinherited

Definition at line 1232 of file IBNLearner.h.

1232{Size(-1)};

Referenced by prepareFCI_(), and setFCIMaxPathLength().

◆ mutualInfo_

CorrectedMutualInformation* gum::learning::IBNLearner::mutualInfo_ {nullptr}

protectedinherited

the selected correction for miic

Definition at line 1137 of file IBNLearner.h.

1137{nullptr};

Referenced by ~IBNLearner(), createCorrectedMutualInformation_(), learnDag_(), learnPDAG_(), operator=(), and operator=().

◆ nbDecreasingChanges_

Size gum::learning::IBNLearner::nbDecreasingChanges_ {2}

protectedinherited

Definition at line 1269 of file IBNLearner.h.

1269{2};

Referenced by IBNLearner(), IBNLearner(), operator=(), operator=(), and useLocalSearchWithTabuList().

◆ noiseEM_

double gum::learning::IBNLearner::noiseEM_ {0.1}

protectedinherited

the noise factor (in (0,1)) used by EM for perturbing the CPT during init

Definition at line 1134 of file IBNLearner.h.

1134{0.1};

Referenced by IBNLearner(), IBNLearner(), operator=(), operator=(), useEM(), and useEMWithDiffCriterion().

◆ noPrior_

NoPrior* gum::learning::IBNLearner::noPrior_ {nullptr}

protectedinherited

Definition at line 1145 of file IBNLearner.h.

1145{nullptr};

Referenced by IBNLearner(), IBNLearner(), IBNLearner(), IBNLearner(), IBNLearner(), ~IBNLearner(), createCorrectedMutualInformation_(), createParamEstimator_(), prepareFCI_(), preparePC_(), and useDatabaseRanges().

◆ onProgress

Signaler< Size, double, double > gum::IApproximationSchemeConfiguration::onProgress

inherited

Progression, error and time.

Definition at line 81 of file IApproximationSchemeConfiguration.h.

Referenced by gum::ApproximationScheme::continueApproximationScheme(), gum::learning::IBNLearner::distributeProgress(), gum::learning::Miic::initiation_(), gum::learning::SimpleMiic::initiation_(), gum::learning::Miic::iteration_(), gum::learning::SimpleMiic::iteration_(), gum::learning::SimpleMiic::orientationLatents_(), gum::learning::Miic::orientationMiic_(), and gum::learning::SimpleMiic::orientationMiic_().

◆ onStop

Signaler< std::string_view > gum::IApproximationSchemeConfiguration::onStop

inherited

Criteria messageApproximationScheme.

Definition at line 84 of file IApproximationSchemeConfiguration.h.

Referenced by gum::learning::IBNLearner::distributeStop().

◆ paramEstimatorType_

ParamEstimatorType gum::learning::IBNLearner::paramEstimatorType_ {ParamEstimatorType::ML}

protectedinherited

the type of the parameter estimator

Definition at line 1128 of file IBNLearner.h.

1128{ParamEstimatorType::ML};

Referenced by IBNLearner(), IBNLearner(), createParamEstimator_(), operator=(), and operator=().

◆ prior_

Prior* gum::learning::IBNLearner::prior_ {nullptr}

protectedinherited

the prior used

Definition at line 1143 of file IBNLearner.h.

1143{nullptr};

Referenced by ~IBNLearner(), chi2(), correctedMutualInformation(), createParamEstimator_(), createScore_(), G2(), logLikelihood(), operator=(), operator=(), and rawPseudoCount().

◆ priorDatabase_

Database* gum::learning::IBNLearner::priorDatabase_ {nullptr}

protectedinherited

the database used by the Dirichlet a priori

Definition at line 1257 of file IBNLearner.h.

1257{nullptr};

Referenced by ~IBNLearner(), learnDag_(), operator=(), and operator=().

◆ priorDbname_

std::string gum::learning::IBNLearner::priorDbname_

protectedinherited

the filename for the Dirichlet a priori, if any

Definition at line 1260 of file IBNLearner.h.

Referenced by IBNLearner(), IBNLearner(), operator=(), operator=(), and useDirichletPrior().

◆ priorType_

BNLearnerPriorType gum::learning::IBNLearner::priorType_ {BNLearnerPriorType::NO_prior}

protectedinherited

the a priorselected for the score and parameters

Definition at line 1140 of file IBNLearner.h.

1140{BNLearnerPriorType::NO_prior};

Referenced by IBNLearner(), IBNLearner(), getPriorType_(), learnDag_(), operator=(), operator=(), useBDeuPrior(), useDirichletPrior(), useNoPrior(), and useSmoothingPrior().

◆ priorWeight_

double gum::learning::IBNLearner::priorWeight_ {1.0f}

protectedinherited

the weight of the prior

Definition at line 1148 of file IBNLearner.h.

1148{1.0f};

Referenced by IBNLearner(), IBNLearner(), _setPriorWeight_(), checkScorePriorCompatibility(), operator=(), and operator=().

◆ ranges_

std::vector< std::pair< std::size_t, std::size_t > > gum::learning::IBNLearner::ranges_

protectedinherited

the set of rows' ranges within the database in which learning is done

Definition at line 1254 of file IBNLearner.h.

Referenced by IBNLearner(), IBNLearner(), clearDatabaseRanges(), createCorrectedMutualInformation_(), createParamEstimator_(), createScore_(), databaseRanges(), operator=(), operator=(), prepareFCI_(), preparePC_(), useCrossValidationFold(), and useDatabaseRanges().

◆ score_

Score* gum::learning::IBNLearner::score_ {nullptr}

protectedinherited

the score used

Definition at line 1125 of file IBNLearner.h.

1125{nullptr};

Referenced by ~IBNLearner(), createParamEstimator_(), createScore_(), learnDag_(), operator=(), operator=(), score(), and setNumberOfThreads().

◆ scoreDatabase_

Database gum::learning::IBNLearner::scoreDatabase_

protectedinherited

the database to be used by the scores and parameter estimators

Definition at line 1251 of file IBNLearner.h.

Referenced by IBNLearner(), IBNLearner(), IBNLearner(), IBNLearner(), IBNLearner(), chi2(), correctedMutualInformation(), createCorrectedMutualInformation_(), createParamEstimator_(), createScore_(), database(), databaseWeight(), domainSize(), domainSize(), domainSizes(), G2(), hasMissingValues(), idFromName(), learnDAG(), learnDag_(), learnPAG(), learnPAG_(), learnPDAG(), learnPDAG_(), logLikelihood(), mutualInformation(), nameFromId(), names(), nbCols(), nbRows(), operator=(), operator=(), prepareFCI_(), prepareMiic_(), preparePC_(), rawPseudoCount(), recordWeight(), setDatabaseWeight(), setRecordWeight(), useCrossValidationFold(), and useDatabaseRanges().

◆ scoreType_

ScoreType gum::learning::IBNLearner::scoreType_ {ScoreType::BDeu}

protectedinherited

the score selected for learning

Definition at line 1122 of file IBNLearner.h.

1122{ScoreType::BDeu};

Referenced by IBNLearner(), IBNLearner(), checkScorePriorCompatibility(), createScore_(), operator=(), operator=(), useScoreAIC(), useScoreBD(), useScoreBDeu(), useScoreBIC(), useScorefNML(), useScoreK2(), useScoreLog2Likelihood(), and useScoreMDL().

◆ selectedAlgo_

AlgoType gum::learning::IBNLearner::selectedAlgo_ {AlgoType::MIIC}

protectedinherited

the selected learning algorithm

Definition at line 1178 of file IBNLearner.h.

1178{AlgoType::MIIC};

Referenced by IBNLearner(), IBNLearner(), fciExhaustiveSepSet(), isConstraintBased(), learnDag_(), learnPAG_(), learnPDAG_(), operator=(), operator=(), setFCIAlpha(), setFCIExhaustiveSepSet(), setFCIMaxPathLength(), setPCAlpha(), setPCMaxCondSetSize(), setPCStable(), setPCUnshieldedColliderSorted(), useChi2Test(), useExtendedGreedyHillClimbing(), useFCI(), useFCIChi2Test(), useFCIG2Test(), useG2Test(), useGreedyHillClimbing(), useGreedyThickThinning(), useK2(), useK2(), useLocalSearchWithTabuList(), useMIIC(), and usePC().

◆ sortedUCPc_

bool gum::learning::IBNLearner::sortedUCPc_ {false}

protectedinherited

Definition at line 1219 of file IBNLearner.h.

1219{false};

Referenced by preparePC_(), and setPCUnshieldedColliderSorted().

◆ stablePc_

bool gum::learning::IBNLearner::stablePc_ {true}

protectedinherited

Definition at line 1217 of file IBNLearner.h.

1217{true};

Referenced by preparePC_(), and setPCStable().

◆ useEM_

bool gum::learning::IBNLearner::useEM_ {false}

protectedinherited

a Boolean indicating whether we should use EM for parameter learning or not

Definition at line 1131 of file IBNLearner.h.

1131{false};

Referenced by IBNLearner(), IBNLearner(), EM(), EMState(), EMStateMessage(), forbidEM(), isUsingEM(), operator=(), operator=(), useEM(), and useEMWithDiffCriterion().

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

agrum/BN/learning/BNLearner.h

Public Types

Public Member Functions

Public Attributes

Static Public Attributes

Protected Types

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Detailed Description

Member Enumeration Documentation

◆ AlgoType

◆ ApproximationSchemeSTATE

◆ BNLearnerPriorType

◆ IndepTestType

◆ ParamEstimatorType

◆ ScoreType

Constructor & Destructor Documentation

◆ BNLearner() [1/5]

◆ BNLearner() [2/5]

◆ BNLearner() [3/5]

◆ BNLearner() [4/5]

◆ BNLearner() [5/5]

◆ ~BNLearner()

Member Function Documentation

◆ _checkDAGCompatibility_()

◆ _initializeEMParameterLearning_()

◆ _labelsFromBN_()

◆ _learnParameters_()

◆ _learnParametersWithEM_() [1/2]

◆ _learnParametersWithEM_() [2/2]

◆ _setPriorWeight_()

◆ addForbiddenArc() [1/3]

◆ addForbiddenArc() [2/3]

◆ addForbiddenArc() [3/3]

◆ addMandatoryArc() [1/3]

◆ addMandatoryArc() [2/3]

◆ addMandatoryArc() [3/3]

◆ addNoChildrenNode() [1/2]

◆ addNoChildrenNode() [2/2]

◆ addNoParentNode() [1/2]

◆ addNoParentNode() [2/2]

◆ addPossibleEdge() [1/3]

◆ addPossibleEdge() [2/3]

◆ addPossibleEdge() [3/3]

◆ allowArcAdditions()

◆ allowArcDeletions()

◆ allowArcReversals()

◆ allowArcTriangleDeletions()

◆ checkScorePriorCompatibility()

◆ chi2() [1/2]

◆ chi2() [2/2]

◆ clearDatabaseRanges()

◆ copyState()

◆ correctedMutualInformation() [1/2]

◆ correctedMutualInformation() [2/2]

◆ createCorrectedMutualInformation_()

◆ createParamEstimator_()

◆ createPrior_()

◆ createScore_()

◆ currentTime()

◆ database()

◆ databaseRanges()

◆ databaseWeight()

◆ disableEpsilon()

◆ disableMaxIter()

◆ disableMaxTime()

◆ disableMinEpsilonRate()

◆ distributeProgress()

◆ distributeStop()

◆ domainSize() [1/2]

◆ domainSize() [2/2]

◆ domainSizes()

◆ EM()

◆ EMCurrentTime()

◆ EMdisableEpsilon()

◆ EMdisableMaxIter()

◆ EMdisableMaxTime()

◆ EMdisableMinEpsilonRate()