BNLearner.h

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/**
 *
 *   Copyright (c) 2005-2021 by Pierre-Henri WUILLEMIN(@LIP6) & Christophe GONZALES(@AMU)
 *   info_at_agrum_dot_org
 *
 *  This library is free software: you can redistribute it and/or modify
 *  it under the terms of the GNU Lesser General Public License as published by
 *  the Free Software Foundation, either version 3 of the License, or
 *  (at your option) any later version.
 *
 *  This library is distributed in the hope that it will be useful,
 *  but WITHOUT ANY WARRANTY; without even the implied warranty of
 *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *  GNU Lesser General Public License for more details.
 *
 *  You should have received a copy of the GNU Lesser General Public License
 *  along with this library.  If not, see <http://www.gnu.org/licenses/>.
 *
 */


/** @file
 * @brief A basic pack of learning algorithms that can easily be used
 *
 * The pack currently contains K2, GreedyHillClimbing and
 *LocalSearchWithTabuList
 *
 * @author Christophe GONZALES(@AMU) and Pierre-Henri WUILLEMIN(@LIP6)
 */
#ifndef GUM_LEARNING_BN_LEARNER_H
#define GUM_LEARNING_BN_LEARNER_H

#include <sstream>
#include <algorithm>
#include <vector>

#include <agrum/BN/BayesNet.h>
#include <agrum/agrum.h>
#include <agrum/tools/core/bijection.h>
#include <agrum/tools/core/sequence.h>
#include <agrum/tools/graphs/DAG.h>

#include <agrum/BN/learning/BNLearnUtils/genericBNLearner.h>

namespace gum {

  namespace learning {

    class BNLearnerListener;

    /** @class BNLearner
     * @brief A pack of learning algorithms that can easily be used
     *
     * The pack currently contains K2, GreedyHillClimbing and
     * LocalSearchWithTabuList
     * @ingroup learning_group
     */
    template < typename GUM_SCALAR >
    class BNLearner: public genericBNLearner {
      public:
      // ##########################################################################
      /// @name Constructors / Destructors
      // ##########################################################################
      /// @{

      /// default constructor
      /**
       * read the database file for the score / parameter estimation and var
       * names
       */
      BNLearner(const std::string&                filename,
                const std::vector< std::string >& missing_symbols = {"?"});

      BNLearner(const DatabaseTable<>& db);

      /**
       * @brief Read the database file for the score / parameter estimation and
       * var names.
       *
       * If modalities = { 1 -> {True, False, Big} }, then the node of id 1 in
       * the BN will have 3 modalities, the first one being True, the second
       * one being False, and the third bein Big.
       *
       * A parsing of the database will allow to determine which ones are
       * really necessary and will keep them in the order specified by the user
       * (NodeProperty modalities). If parse_database is set to false (the
       * default), then the modalities specified by the user will be considered
       * as being exactly those of the variables of the BN (as a consequence,
       * if we find other values in the database, an exception will be raised
       * during learning).
       *
       * @param filename The file to learn from.
       * @param modalities indicate for some nodes (not necessarily all the
       * nodes of the BN) which modalities they should have and in which order
       * these modalities should be stored into the nodes.
       * @param parse_database if true, the modalities specified by the user
       * will be considered as a superset of the modalities of the variables.
       */
      /*
      BNLearner(const std::string&                             filename,
                const NodeProperty< Sequence< std::string > >& modalities );
      */


      /**
       * Wrapper for BNLearner (filename,modalities,parse_database) using a bn
       * to find those modalities and nodeids.
       **/
      BNLearner(const std::string&                 filename,
                const gum::BayesNet< GUM_SCALAR >& src,
                const std::vector< std::string >&  missing_symbols = {"?"});

      /// copy constructor
      BNLearner(const BNLearner&);

      /// move constructor
      BNLearner(BNLearner&&);

      /// destructor
      virtual ~BNLearner();

      /// @}

      // ##########################################################################
      /// @name Operators
      // ##########################################################################
      /// @{

      /// copy operator
      BNLearner& operator=(const BNLearner&);

      /// move operator
      BNLearner& operator=(BNLearner&&);

      /// @}

      /// learn a Bayes Net from a file (must have read the db before)
      BayesNet< GUM_SCALAR > learnBN();

      /// learns a BN (its parameters) when its structure is known
      /**
       * @param dag the structure of the Bayesian network
       * @param 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 apriori (like K2 which has a
       * 1-smoothing apriori), it is important to also take into account this
       * implicit apriori for parameter learning. By default, if a score
       * exists, we will learn parameters by taking into account the apriori
       * specified by methods useAprioriXXX () + the implicit apriori of the
       * score, else we just take into account the apriori specified by
       * useAprioriXXX () */
      BayesNet< GUM_SCALAR > learnParameters(const DAG& dag, bool takeIntoAccountScore = true);

      // learns a BN (its parameters) when its structure is known
      /** @param 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 apriori (like K2 which has a
       * 1-smoothing apriori), it is important to also take into account this
       * implicit apriori for parameter learning. By default, if a score
       * exists, we will learn parameters by taking into account the apriori
       * specified by methods useAprioriXXX () + the implicit apriori of the
       * score, else we just take into account the apriori specified by
       * useAprioriXXX ()
       * @throw MissingVariableInDatabase if a variable of the BN is not found
       * in the database.
       * @throw UnknownLabelInDatabase if a label is found in the databast that
       * do not correpond to the variable.
       */
      BayesNet< GUM_SCALAR > learnParameters(bool take_into_account_score = true);

      private:
      /// read the first line of a file to find column names
      NodeProperty< Sequence< std::string > > _labelsFromBN_(const std::string&            filename,
                                                             const BayesNet< GUM_SCALAR >& src);
    };

  } /* namespace learning */

} /* namespace gum */

/// always include templated methods
#include <agrum/BN/learning/BNLearner_tpl.h>

#endif /* GUM_LEARNING_BN_LEARNER_H */