pyAgrum-nightly 2.3.0.9.dev202512061764412981__cp310-abi3-macosx_11_0_arm64.whl

pyagrum/skbn/bnclassifier.py

@@ -0,0 +1,1014 @@
+############################################################################
+#   This file is part of the aGrUM/pyAgrum library.                        #
+#                                                                          #
+#   Copyright (c) 2005-2025 by                                             #
+#       - Pierre-Henri WUILLEMIN(_at_LIP6)                                 #
+#       - Christophe GONZALES(_at_AMU)                                     #
+#                                                                          #
+#   The aGrUM/pyAgrum library is free software; you can redistribute it    #
+#   and/or modify it under the terms of either :                           #
+#                                                                          #
+#    - 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,                              #
+#    - the MIT license (MIT),                                              #
+#    - or both in dual license, as here.                                   #
+#                                                                          #
+#   (see https://agrum.gitlab.io/articles/dual-licenses-lgplv3mit.html)    #
+#                                                                          #
+#   This aGrUM/pyAgrum library is distributed in the hope that it will be  #
+#   useful, but WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,          #
+#   INCLUDING BUT NOT LIMITED TO THE WARRANTIES MERCHANTABILITY or FITNESS #
+#   FOR A PARTICULAR PURPOSE  AND NONINFRINGEMENT. IN NO EVENT SHALL THE   #
+#   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER #
+#   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,        #
+#   ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR  #
+#   OTHER DEALINGS IN THE SOFTWARE.                                        #
+#                                                                          #
+#   See LICENCES for more details.                                         #
+#                                                                          #
+#   SPDX-FileCopyrightText: Copyright 2005-2025                            #
+#       - Pierre-Henri WUILLEMIN(_at_LIP6)                                 #
+#       - Christophe GONZALES(_at_AMU)                                     #
+#   SPDX-License-Identifier: LGPL-3.0-or-later OR MIT                      #
+#                                                                          #
+#   Contact  : info_at_agrum_dot_org                                       #
+#   homepage : http://agrum.gitlab.io                                      #
+#   gitlab   : https://gitlab.com/agrumery/agrum                           #
+#                                                                          #
+############################################################################
+
+from typing import List, Union
+
+import pandas
+import numpy
+import os
+import tempfile
+import warnings
+
+import sklearn
+
+import pyagrum as gum
+from pyagrum.lib.discreteTypeProcessor import DiscreteTypeProcessor
+from pyagrum.lib.discreteTypeProcessor import check_int
+
+from ._utils import _ImplementPrior as IPrior
+from ._utils import _CalculateThreshold as CThreshold
+from ._utils import _DFNames as DFNames
+from ._utils import _createCSVfromNDArrays as CSV
+
+from ._MBCalcul import compileMarkovBlanket
+from ._MBCalcul import (
+  _calcul_proba_for_binary_class,
+  _calcul_most_probable_for_nary_class,
+  _calcul_proba_for_nary_class,
+)
+
+from ._learningMethods import _fitStandard as BN_fitStandard
+from ._learningMethods import _fitNaiveBayes as BN_fitNaiveBayes
+from ._learningMethods import _fitTAN as BN_fitTAN
+from ._learningMethods import _fitChowLiu as BN_fitChowLiu
+
+
+class BNClassifier(sklearn.base.BaseEstimator, sklearn.base.ClassifierMixin):
+  """
+  Represents a (scikit-learn compliant) classifier which uses a BN to classify. A BNClassifier is build using
+
+   - a Bayesian network,
+   - a database and a learning algorithm and parameters
+   - the use of DiscreteTypeProcessor to discretize with different algorithms some variables.
+
+  The classifier can be used to predict the class of new data.
+
+  Warnings
+  --------
+  This class can be pickled. However, the state of this class is only the classifier itself,
+  not the parameter used to train it.
+
+
+  Parameters
+  ----------
+            learningMethod: str
+                A string designating which learning algorithm we want to use. Possible values are: Chow-Liu, NaiveBayes,
+                TAN, MIIC + (MDL ou NML), GHC, Tabu.
+                GHC designates Greedy Hill Climbing.
+                MIIC designates Multivariate Information based Inductive Causation
+                TAN designates Tree-augmented NaiveBayes
+                Tabu designated Tabu list searching
+
+            prior: str
+                A string designating the type of a priorsmoothing we want to use. Possible values are Smoothing,
+                BDeu, Dirichlet and NoPrior .
+                Note: if using Dirichlet smoothing DirichletCsv cannot be set to none
+                By default (when prior is None) : a smoothing(0.01) is applied.
+
+            scoringType: str
+                A string designating the scoring method we want to use. Since scoring is used while constructing the
+                network and not when learning its parameters, the scoring will be ignored if using a learning algorithm
+                with a fixed network structure such as Chow-Liu, TAN or NaiveBayes.
+                possible values are:  AIC, BIC, BD, BDeu, K2, Log2
+                AIC means Akaike information criterion
+                BIC means Bayesian Information criterion
+                BD means Bayesian-Dirichlet scoring
+                BDeu means Bayesian-Dirichlet equivalent uniform
+                Log2 means log2 likelihood ratio test
+
+            constraints: dict()
+                A dictionary designating the constraints that we want to put on the structure of the Bayesian network.
+                Ignored if using a learning algorithm where the structure is fixed such as TAN or NaiveBayes.
+                the keys of the dictionary should be the strings "PossibleEdges" , "MandatoryArcs" and  "ForbiddenArcs".
+                The format of the values should be a tuple of strings (tail,head) which designates the string arc from
+                tail to head. For example if we put the value ("x0"."y") in MandatoryArcs the network will surely have
+                an arc going from x0 to y.
+
+                Note: PossibleEdge allows between nodes x and y allows for either (x,y) or (y,x) (or none of them)
+                to be added to the Bayesian network, while the others are not symmetric.
+
+            priorWeight: double
+                The weight used for a prior.
+
+            possibleSkeleton: pyagrum.undigraph
+                An undirected graph that serves as a possible skeleton for the Bayesian network
+
+            DirichletCsv: str
+                the file name of the csv file we want to use for the dirichlet prior. Will be ignored if prior is not
+                set to Dirichlet.
+
+            discretizationStrategy: str
+                sets the default method of discretization for this discretizer. This method will be used if the user has
+                not specified another method for that specific variable using the setDiscretizationParameters method
+                possible values are: 'quantile', 'uniform', 'kmeans', 'NML', 'CAIM' and 'MDLP'
+
+            discretizationNbBins: str or int
+                sets the number of bins if the method used is quantile, kmeans, uniform. In this case this parameter can
+                also be set to the string 'elbowMethod' so that the best number of bins is found automatically.
+                If the method used is NML, this parameter sets the maximum number of bins up to which the NML
+                algorithm searches for the optimal number of bins. In this case this parameter must be an int
+                If any other discretization method is used, this parameter is ignored.
+
+            discretizationThreshold: int or float
+                When using default parameters a variable will be treated as continuous only if it has more unique values
+                than this number (if the number is an int greater than 1).
+                If the number is a float between 0 and 1, we will test if the proportion of unique values is bigger than
+                this number.
+                For instance, if you have entered 0.95, the variable will be treated as continuous only if more than 95%
+                of its values are unique.
+
+            usePR: bool
+                indicates if the threshold to choose is Prevision-Recall curve's threshold or ROC's threshold by
+                default.
+                ROC curves should be used when there are roughly equal numbers of observations for each class.
+                Precision-Recall curves should be used when there is a moderate to large class imbalance especially for
+                the target's class.
+
+    beta: float
+        if you choose the Precision-Recall curve's threshold, the F-beta score is maximized. By default, beta=1
+        to have the F1 score. A value inferior of 1 will give more weight to precision. A value superior of 1
+        will give more weight to recall. For example, beta = 0.5 makes precision twice as important as recall,
+        while beta = 2 does the opposite.
+
+            significant_digit:
+                number of significant digits when computing probabilities
+  """
+
+  def __init__(
+    self,
+    learningMethod="MIIC",
+    prior=None,
+    scoringType="BIC",
+    constraints=None,
+    priorWeight=1,
+    possibleSkeleton=None,
+    DirichletCsv=None,
+    discretizationStrategy="quantile",
+    discretizationNbBins=5,
+    discretizationThreshold=25,
+    usePR=False,
+    beta=1,
+    significant_digit=10,
+  ):
+    """
+    Parameters
+    ----------
+            learningMethod: str
+                A string designating which type of learning we want to use. Possible values are: Chow-Liu, NaiveBayes,
+                TAN, MIIC + (MDL ou NML), GHC, Tabu.
+                GHC designates Greedy Hill Climbing.
+                MIIC designates Multivariate Information based Inductive Causation
+                TAN designates Tree-augmented NaiveBayes
+                Tabu designated Tabu list searching
+
+            prior: str
+                A string designating the type of prior we want to use. Possible values are Smoothing, BDeu ,
+                Dirichlet and NoPrior.
+                Note: if using Dirichlet smoothing DirichletCsv cannot be set to none
+
+            scoringType: str
+                A string designating the type of scoring we want to use. Since scoring is used while constructing the
+                network and not when learning its parameters, the scoring will be ignored if using a learning algorithm
+                with a fixed network structure such as Chow-Liu, TAN or NaiveBayes.
+                possible values are:  AIC, BIC, BD, BDeu, K2, Log2
+                AIC means Akaike information criterion
+                BIC means Bayesian Information criterion
+                BD means Bayesian-Dirichlet scoring
+                BDeu means Bayesian-Dirichlet equivalent uniform
+                Log2 means log2 likelihood ratio test
+
+            constraints: dict()
+                A dictionary designating the constraints that we want to put on the structure of the Bayesian network.
+                Ignored if using a learning algorithm where the structure is fixed such as TAN or NaiveBayes.
+                the keys of the dictionary should be the strings "PossibleEdges" , "MandatoryArcs" and  "ForbiddenArcs".
+                The format of the values should be a tuple of strings (tail,head) which designates the string arc from
+                tail to head. For example if we put the value ("x0"."y") in MandatoryArcs the network will surely have
+                an arc going from x0 to y.
+                Note: PossibleEdges allows for both (tail,head) and (head,tail) to be added to the Bayesian network,
+                while the others are not symmetric.
+
+            priorWeight: double
+                The weight used for a prior.
+
+            possibleSkeleton: pyagrum.undigraph
+                An undirected graph that serves as a possible skeleton for the Bayesian network
+
+            DirichletCsv: str
+                the file name of the csv file we want to use for the dirichlet prior. Will be ignored if prior is not
+                set to Dirichlet.
+
+            discretizationStrategy: str
+                sets the default method of discretization for this discretizer. This method will be used if the user has
+                not specified another method for that specific variable using the setDiscretizationParameters method
+                possible values are: 'quantile', 'uniform', 'kmeans', 'NML', 'CAIM' and 'MDLP'
+
+            discretizationNbBins: str or int
+                sets the number of bins if the method used is quantile, kmeans, uniform. In this case this parameter can
+                also be set to the string 'elbowMethod' so that the best number of bins is found automatically.
+                If the method used is NML, this parameter sets the the maximum number of bins up to which the NML
+                algorithm searches for the optimal number of bins. In this case this parameter must be an int
+                If any other discetization method is used, this parameter is ignored.
+
+            discretizationThreshold: int or float
+                When using default parameters a variable will be treated as continuous only if it has more unique values
+                than this number (if the number is an int greater than 1).
+                If the number is a float between 0 and 1, we will test if the proportion of unique values is bigger than
+                this number.
+                For instance, if you have entered 0.95, the variable will be treated as continouus only if more than 95%
+                of its values are unique.
+
+            usePR: bool
+                indicates if the threshold to choose is Prevision-Recall curve's threshold or ROC's threshold by
+                default.
+                ROC curves should be used when there are roughly equal numbers of observations for each class.
+                Precision-Recall curves should be used when there is a moderate to large class imbalance especially for
+                the target's class.
+
+            significant_digit:
+                number of significant digits when computing probabilities
+    """
+
+    # The method of learning used
+    self.learningMethod = learningMethod
+
+    # An object used to stock the learner object from pyagrum
+    self.learner = None
+
+    # Used to stock the Bayesian network learned
+    self.bn = None
+
+    # The threshold used for predicting the class. THe algorithm calculates the probability of a certain class, the
+    # classifier designates it as that class only if the probability is higher than the threshold.
+    # The ROC curve is used to calculate the optimal threshold
+    self.threshold = 0.5
+    self.usePR = usePR
+    self.beta = beta
+
+    # the type of prior used
+    self.prior = prior
+
+    # the weight used for the a prior
+    self.priorWeight = priorWeight
+
+    # the type of scoring used
+    self.scoringType = scoringType
+
+    # the constraints forced onto the structure of the Bayesian network
+    self.constraints = constraints
+
+    self.possibleSkeleton = possibleSkeleton
+
+    self.DirichletCsv = DirichletCsv
+
+    self.MarkovBlanket = None
+
+    self.significant_digit = significant_digit
+
+    self.discretizationNbBins = discretizationNbBins
+    self.discretizationStrategy = discretizationStrategy
+    self.discretizationThreshold = discretizationThreshold
+    self.type_processor = DiscreteTypeProcessor(
+      defaultDiscretizationMethod=discretizationStrategy,
+      defaultNumberOfBins=discretizationNbBins,
+      discretizationThreshold=discretizationThreshold,
+    )
+
+    # boolean that tells us whether this classifier is obtained from an already trained model (using the function
+    # fromTrainedModel) or not
+    self.fromModel = False
+
+    self.label = "1.0"
+
+    # the name of the target variable
+    self.target = "y"
+
+    # the type of the target variable
+    self.targetType = None
+    self.isBinaryClassifier = None
+
+    # dict(str:int)
+    # The keys of this dictionary are the names of the variables. The value associated to each name is
+    # the index of the variable.
+    self.variableNameIndexDictionary = None
+
+  def fit(self, X=None, y=None, data=None, targetName=None):
+    """
+    Fits the model to the training data provided. The two possible uses of this function are `fit(X,y)`
+    and `fit(data=...,targetName=...)`. Any other combination will raise a ValueError
+
+    Parameters
+    ----------
+        X: {array-like, sparse matrix} of shape (n_samples, n_features)
+            training data. Warning: Raises ValueError if either data or targetname is not None. Raises ValueError
+            if y is None.
+        y: array-like of shape (n_samples)
+            Target values. Warning: Raises ValueError if either data or targetname is not None. Raises ValueError
+            if X is None
+        data: Union[str,pandas.DataFrame]
+            the source of training data : csv filename or pandas.DataFrame. targetName is mandatory to find the class
+            in this source.
+        targetName: str
+            specifies the name of the targetVariable in the csv file. Warning: Raises ValueError if either X or y is
+            not None. Raises ValueError if data is None.
+    """
+    if data is None:
+      if targetName is not None:
+        raise ValueError(
+          "This function should be used either as fit(X,y) or fit(data=...,targetName=...). You have set "
+          "data to None, but have entered a targetName"
+        )
+      if X is None or y is None:
+        raise ValueError(
+          "This function should be used either as fit(X,y) or fit(data=...,targetName=...). You have not "
+          "entered a data source (filename or pandas.DataFrame) and not specified the X and y matrices"
+          " that should be used"
+        )
+    else:
+      if targetName is None:
+        raise ValueError(
+          "This function should be used either as fit(X,y) or fit(data=...,targetName=...). The name of the "
+          "target must be specified if using this function with data  containing a csv filename or a pandas.DataFrame."
+        )
+      if X is not None or y is not None:
+        raise ValueError(
+          "This function should be used either as fit(X,y) or fit(data=...,targetName=...). You can not give "
+          "a data and the X and y matrices at the same time."
+        )
+      if isinstance(data, str):
+        X, y = self.XYfromCSV(data, True, targetName)
+      else:  # pandas.DataFrame
+        y = data[targetName]
+        X = data.drop(targetName, axis=1)
+
+    self.fromModel = False
+    variableNames = None
+    self.type_processor.clear()
+
+    if isinstance(y, pandas.DataFrame):  # type(y) == pandas.DataFrame:
+      self.target = y.columns.tolist()[0]
+      if check_int(self.target):
+        self.target = "Y"
+    elif type(y) is pandas.core.series.Series:
+      self.target = y.name
+    else:
+      self.target = "y"
+
+    if isinstance(X, pandas.DataFrame):  # type(X) == pandas.DataFrame:
+      variableNames = [f"X{x}" if check_int(x) else x for x in X.columns]
+
+    # verifies the shape of the two arrays
+    X, y = sklearn.utils.check_X_y(X, y, dtype=None, accept_sparse=True)
+
+    d = X.shape[1]
+
+    if variableNames is None:
+      variableNames = ["x" + str(i) for i in range(d)]
+
+    self.variableNameIndexDictionary = dict()
+
+    for i in range(d):
+      self.variableNameIndexDictionary[variableNames[i]] = i
+
+    self.targetType = y.dtype
+
+    possibleValuesY = numpy.unique(y)
+
+    if len(possibleValuesY) == 1:
+      raise ValueError("There is only 1 possible values for Y in the data provided")
+    if len(possibleValuesY) > 10:
+      warnings.warn(
+        f"A classifier with too many possible values for Y (here : {possibleValuesY})"
+        "in the data provided is not meaningfull ("
+        "please use regression methods instead)."
+      )
+
+    self.isBinaryClassifier = len(possibleValuesY) == 2
+
+    self.bn = gum.BayesNet("Template")
+
+    is_int_varY = True
+    min_vY = max_vY = None
+    for value in possibleValuesY:
+      if not check_int(value):
+        is_int_varY = False
+        break
+      else:
+        v = int(value)
+        if min_vY is None or min_vY > v:
+          min_vY = v
+        if max_vY is None or max_vY < v:
+          max_vY = v
+
+    if is_int_varY:
+      if len(possibleValuesY) == max_vY - min_vY + 1:  # no hole in the list of int
+        var = gum.RangeVariable(self.target, self.target, min_vY, max_vY)
+      else:
+        var = gum.IntegerVariable(self.target, self.target, [int(v) for v in possibleValuesY])
+    else:
+      var = gum.LabelizedVariable(self.target, self.target, [str(v) for v in possibleValuesY])
+    self.bn.add(var)
+
+    for i in range(d):
+      var = self.type_processor._createVariable(variableNames[i], X[:, i], y, possibleValuesY)
+      self.bn.add(var)
+
+    csvfile = tempfile.NamedTemporaryFile(delete=False)
+    tmpfilename = csvfile.name
+    csvfilename = tmpfilename + ".csv"
+    csvfile.close()
+
+    CSV(X, y, self.target, self.variableNameIndexDictionary, csvfilename)
+
+    self.learner = gum.BNLearner(csvfilename, self.bn)
+
+    IPrior(self.prior, self.learner, self.priorWeight, self.DirichletCsv)
+
+    if self.learningMethod == "NaiveBayes":
+      self.bn = BN_fitNaiveBayes(X, y, self.bn, self.learner, variableNames, self.target, self.constraints)
+    elif self.learningMethod == "TAN":
+      self.bn = BN_fitTAN(X, y, self.bn, self.learner, variableNames, self.target)
+    elif self.learningMethod == "Chow-Liu":
+      self.bn = BN_fitChowLiu(X, y, self.bn, self.learner, variableNames, self.target)
+    else:
+      self.bn = BN_fitStandard(
+        X, y, self.learner, self.learningMethod, self.possibleSkeleton, self.scoringType, self.constraints
+      )
+
+    self.label = self.bn.variableFromName(self.target).labels()[1]
+
+    self.MarkovBlanket = compileMarkovBlanket(self.bn, self.target)
+
+    if self.isBinaryClassifier:
+      self.threshold = CThreshold(
+        self.MarkovBlanket, self.target, csvfilename, self.usePR, self.beta, self.significant_digit
+      )
+
+    os.remove(csvfilename)
+    os.remove(tmpfilename)
+
+  def fromTrainedModel(self, bn, targetAttribute, targetModality="", copy=False, threshold=0.5, variableList=None):
+    """
+    parameters:
+        bn: pyagrum.BayesNet
+            The Bayesian network we want to use for this classifier
+        targetAttribute: str
+            the attribute that will be the target in this classifier
+        targetModality: str
+            If this is a binary classifier we have to specify which modality we are looking at if the target
+            attribute has more than 2 possible values
+            if !="", a binary classifier is created.
+            if =="", a classifier is created that can be non-binary depending on the number of modalities
+            for targetAttribute. If binary, the second one is taken as targetModality.
+        copy: bool
+            Indicates whether we want to put a copy of bn in the classifier, or bn itself.
+        threshold: double
+            The classification threshold. If the probability that the target modality is true is larger than this
+            threshold we predict that modality
+        variableList: list(str)
+            A list of strings. variableList[i] is the name of the variable that has the index i. We use this information
+            when calling predict to know which column corresponds to which variable.
+            If this list is set to none, then we use the order in which the variables were added to the network.
+
+    returns:
+        void
+
+    Creates a BN classifier from an already trained pyAgrum Bayesian network
+    """
+
+    self.fromModel = True
+
+    # the set of the names of all the variables in the Bayesian network
+    namesSet = set(bn.names())
+
+    # The target specified must be a variable in the Bayesian network
+    if targetAttribute not in namesSet:
+      raise ValueError("the target variable does not appear in the Bayesian network")
+
+    self.target = targetAttribute
+
+    self.learner = None
+
+    if copy:
+      self.bn = gum.BayesNet(bn)
+    else:
+      self.bn = bn
+
+    self.threshold = threshold
+
+    self.MarkovBlanket = compileMarkovBlanket(self.bn, self.target)
+
+    self.variableNameIndexDictionary = dict()
+    # if the user specified an order for the variables then we use this order
+    if variableList is not None:
+      if len(namesSet) - 1 != len(variableList):
+        raise ValueError("variableList should include all variables in the Bayesian network except the target")
+
+      i = 0
+      for name in variableList:
+        if name not in namesSet:
+          raise ValueError("variableList includes a name that does not appear in the Bayesian network")
+        self.variableNameIndexDictionary[name] = i
+        i = i + 1
+
+    # if the user didn't specify an order we use the order that the variables were added in
+    else:
+      variableList = bn.names()
+      i = 0
+      for name in variableList:
+        if name == self.target:
+          continue
+        self.variableNameIndexDictionary[name] = i
+        i = i + 1
+
+    if targetModality != "":
+      self.isBinaryClassifier = True
+      self.label = targetModality
+    else:
+      if self.bn.variableFromName(self.target).domainSize() == 2:
+        self.isBinaryClassifier = True
+        self.label = self.bn.variableFromName(self.target).labels()[1]  # we take the label 1 as targetModality
+      else:
+        self.isBinaryClassifier = False
+
+    def changeVariableName(self, oldName, newName):
+      """
+      Changes the name of a variable inside the Bayesian network
+
+      Parameters
+      ----------
+            oldName: str
+                the old name of the variable
+            newName: str
+                the new name of the variable
+      """
+      if oldName == self.target:
+        self.bn.changeVariableName(oldName, newName)
+        self.target = newName
+        self.MarkovBlanket.changeVariableName(oldName, newName)
+        return
+
+      if oldName not in self.variableNameIndexDictionary:
+        raise ValueError("The oldName you have specified is not a name of a variable in the Bayesian network")
+      index = self.variableNameIndexDictionary.pop(oldName)
+
+      self.variableNameIndexDictionary[newName] = index
+
+      self.bn.changeVariableName(oldName, newName)
+
+      if oldName in self.MarkovBlanket.names():
+        self.MarkovBlanket.changeVariableName(oldName, newName)
+
+  # ------------------method Markov Blanket and predict---------------------
+
+  def predict(self, X, with_labels=True):
+    """
+    Predicts the most likely class for each row of input data, with bn's Markov Blanket
+
+    Parameters
+    ----------
+        X: str,{array-like, sparse matrix} of shape (n_samples, n_features) or str
+            test data, can be either dataFrame, matrix or name of a csv file
+        with_labels: bool
+            tells us whether the csv includes the labels themselves or their indexes.
+    returns:
+        y: array-like of shape (n_samples,)
+            Predicted classes
+    """
+    if isinstance(X, str):
+      X, _ = self.XYfromCSV(X, target=self.target)
+
+    if isinstance(X, pandas.DataFrame):  # type(X) == pandas.DataFrame:
+      dictName = DFNames(X)
+    else:
+      dictName = self.variableNameIndexDictionary
+
+    if self.fromModel:
+      X = sklearn.utils.check_array(X, dtype="str", ensure_2d=False)
+    else:
+      X = sklearn.utils.check_array(X, dtype=None, ensure_2d=False)
+
+    if self.isBinaryClassifier:
+      returned_list = self._binary_predict(X, dictName)
+    else:
+      returned_list = self._nary_predict(X, dictName, with_labels)
+
+    returned_list = numpy.array(returned_list)
+    if not self.fromModel:
+      if self.targetType == "bool":
+        returned_list = returned_list == "True"
+      elif numpy.issubdtype(self.targetType, numpy.number):
+        returned_list = returned_list.astype("float")
+
+    return returned_list
+
+  def _nary_predict(self, X, dictName, with_labels) -> Union[List[str], List[int]]:
+    """
+    For a classifier, predicts the most likely class for each row of input data, with bn's Markov Blanket
+
+    Parameters
+    ----------
+    X: {array-like, sparse matrix} of shape (n_samples, n_features) or str
+            test data, can be either dataFrame, matrix or name of a csv file
+      the data
+    dictName: Dict[str,int]
+      dictionary of the name of a variable and his column in the database
+    with_labels: bool
+      whether `data` contains the labels themselves or their ids.
+
+    Returns
+    -------
+    array-like of shape (n_samples,)
+      the list of predictions as idLabel or label name.
+    """
+    returned_list = []
+    I = self.MarkovBlanket.completeInstantiation()
+    I.erase(self.target)
+    for x in X:
+      vals, _ = _calcul_most_probable_for_nary_class(x, I, dictName, self.MarkovBlanket, self.target)
+      if with_labels:
+        returned_list.append(self.MarkovBlanket.variable(self.target).label(vals[0][0][self.target]))
+      else:
+        returned_list.append(vals[0][0][self.target])
+
+    return returned_list
+
+  def _binary_predict(self, X, dictName) -> Union[List[str], List[bool]]:
+    """
+    For a binary classifier, predicts the most likely class for each row of input data, with bn's Markov Blanket
+
+    Parameters
+    ----------
+    X: {array-like, sparse matrix} of shape (n_samples, n_features) or str
+            test data, can be either dataFrame, matrix or name of a csv file
+      the datas
+    dictName: Dict[str,int]
+      dictionary of the name of a variable and his column in the database
+
+    Returns
+    -------
+    array-like of shape (n_samples,)
+      the list of predictions
+    """
+    returned_list = []
+    # list of other labels of the target
+    labels = [
+      self.bn.variable(self.target).label(i)
+      for i in range(self.bn.variable(self.target).domainSize())
+      if self.bn.variable(self.target).label(i) != self.label
+    ]
+
+    # negative value to add to the list returned
+    label0 = labels[0]
+    # label of the target
+    label1 = self.label
+    # Instantiation use to apply values of the database
+    I = self.MarkovBlanket.completeInstantiation()
+    # read through database's ligns
+    for x in X:
+      res = round(
+        _calcul_proba_for_binary_class(x, label1, labels, I, dictName, self.MarkovBlanket, self.target),
+        self.significant_digit,
+      )
+
+      if res >= self.threshold:  # Positive value predicted
+        if self.fromModel:
+          returned_list.append(True)
+        else:
+          returned_list.append(label1)
+      else:  # Negative value predicted
+        if self.fromModel:
+          returned_list.append(False)
+        else:
+          returned_list.append(label0)
+
+    return returned_list
+
+  # ------------------interaction with sklearn, pour ROC et Precision-Recall ---------------------
+
+  def predict_proba(self, X):
+    """
+    Predicts the probability of classes for each row of input data, with bn's Markov Blanket
+
+    Parameters
+    ----------
+    X: str or {array-like, sparse matrix} of shape (n_samples, n_features) or str
+            test data, can be either dataFrame, matrix or name of a csv file
+
+    Returns
+    -------
+    array-like of shape (n_samples,)
+      Predicted probability for each classes
+    """
+    # dictionary of the name of a variable and his column in the database
+    dictName = self.variableNameIndexDictionary
+
+    if isinstance(X, pandas.DataFrame):  # type(X) == pandas.DataFrame:
+      dictName = DFNames(X)
+      vals = X.to_numpy()
+    elif isinstance(X, str):
+      vals, _ = self.XYfromCSV(X, target=self.target)
+      dictName = DFNames(vals)
+      vals = vals.to_numpy()
+    else:
+      vals = X
+
+    if self.fromModel:
+      vals = sklearn.utils.check_array(vals, dtype="str", ensure_2d=False)
+    else:
+      sklearn.utils.check_array(vals, dtype=None, ensure_2d=False)
+
+    returned_list = []
+
+    # label of the target
+    label1 = self.label
+    # list of other labels of the target
+    labels = [
+      self.bn.variable(self.target).label(i)
+      for i in range(self.bn.variable(self.target).domainSize())
+      if self.bn.variable(self.target).label(i) != self.label
+    ]
+
+    # Instantiation use to apply values of the database
+    I = self.MarkovBlanket.completeInstantiation()
+
+    # read through database's ligns
+    if self.isBinaryClassifier:
+      for x in vals:
+        res = round(
+          _calcul_proba_for_binary_class(x, label1, labels, I, dictName, self.MarkovBlanket, self.target),
+          self.significant_digit,
+        )
+        returned_list.append([1 - res, res])
+    else:
+      local_inst = gum.Instantiation(I)
+      local_inst.erase(self.target)
+      for x in vals:
+        returned_list.append(
+          _calcul_proba_for_nary_class(x, local_inst, dictName, self.MarkovBlanket, self.target).tolist()
+        )
+
+    return numpy.array(returned_list)
+
+  # ------------------ BNClassifier compatible from pyagrum to sklearn ---------------------
+
+  def XYfromCSV(self, filename, with_labels=True, target=None):
+    """
+    Reads the data from a csv file and separates it into an X matrix and a y column vector.
+
+    Parameters
+    ----------
+    filename: str
+        the name of the csv file
+    with_labels: bool
+        tells us whether the csv includes the labels themselves or their indexes.
+    target: str or None
+        The name of the column that will be put in the dataframe y. If target is None, we use the target that is
+        already specified in the classifier
+
+    Returns
+    -------
+    Tuple(pandas.Dataframe,pandas.Dataframe)
+        Matrix X containing the data,Column-vector containing the class for each data vector in X
+    """
+    if self.fromModel:
+      dataframe = pandas.read_csv(filename, dtype="str")
+    else:
+      dataframe = pandas.read_csv(filename)
+
+    if target is None:
+      target = self.target
+    y = dataframe[target]
+    X = dataframe.drop(target, axis=1)
+
+    if not with_labels:
+      variableList = X.columns.tolist()
+      targetVariable = self.bn.variableFromName(target)
+      for index in range(len(variableList)):
+        variableList[index] = self.bn.variableFromName(variableList[index])
+      for row in X:
+        for i in range(len(row)):
+          row[i] = variableList[i].labels(row[i])
+      if self.fromModel:
+        if self.isBinaryClassifier:
+          labelIndex = 0
+          labelList = targetVariable.labels()
+          while labelIndex < len(labelList):
+            if labelList[labelIndex] == self.label:
+              break
+            labelIndex += 1
+          y = y == labelIndex
+      else:
+        for index in range(len(y)):
+          y[index] = targetVariable(y[index])
+
+    elif self.fromModel:
+      y = y.astype("str")
+      if self.isBinaryClassifier:
+        y = y == self.label
+
+    return X, y
+
+  def preparedData(self, X=None, y=None, data=None):
+    """
+    Given an X and a y (or a data source : filename or pandas.DataFrame),
+    returns a pandas.Dataframe with the prepared (especially discretized) values of the base
+
+    Parameters
+    ----------
+        X: {array-like, sparse matrix} of shape (n_samples, n_features)
+            training data. Warning: Raises ValueError if either filename or targetname is not None. Raises ValueError
+            if y is None.
+        y: array-like of shape (n_samples)
+            Target values. Warning: Raises ValueError if either filename or targetname is not None. Raises ValueError
+            if X is None
+        data: Union[str,pandas.DataFrame]
+            specifies the csv file or the DataFrame where the data values are located. Warning: Raises ValueError
+            if either X or y is not None.
+
+    Returns
+    -------
+      pandas.Dataframe
+    """
+    if self.variableNameIndexDictionary is None:
+      raise ValueError("First, you need to fit a model !")
+
+    targetName = self.target
+    if data is None:
+      if X is None or y is None:
+        raise ValueError(
+          "This function should be used either as preparedData(X,y) or preparedData(data=...). You have not "
+          "entered a csv file name and not specified the X and y matrices that should be used"
+        )
+    else:
+      if targetName is None:
+        raise ValueError(
+          "This function should be used either as preparedData(X,y) or preparedData(data=...). The name of the "
+          "target must be specified if using this function with a csv file."
+        )
+      if X is not None or y is not None:
+        raise ValueError(
+          "This function should be used either as preparedData(X,y) or preparedData(data=...). You have entered "
+          "a data source and the X and y matrices at the same time."
+        )
+
+      if isinstance(data, str):
+        X, y = self.XYfromCSV(data, True, targetName)
+      else:  # pandas.DataFrame
+        y = data[targetName]
+        X = data.drop(targetName, axis=1)
+
+    def bestTypedVal(v, idx):
+      if v.varType() == gum.VarType_DISCRETIZED:
+        return v.label(idx)
+      elif v.varType() == gum.VarType_INTEGER:
+        return int(v.numerical(idx))
+      elif v.varType() == gum.VarType_LABELIZED:
+        return v.label(idx)
+      elif v.varType() == gum.VarType_RANGE:
+        return int(v.numerical(idx))
+      elif v.varType() == gum.VarType_NUMERICAL:
+        return float(v.numerical(idx))
+      else:
+        raise gum.NotFound("This type of variable does not exist yet.")
+
+    reverse = {v: k for k, v in self.variableNameIndexDictionary.items()}
+    if isinstance(X, pandas.DataFrame):  # to be sure of the name of the columns
+      X = X.rename(columns=reverse)
+    varY = self.bn.variable(self.target)
+    df = pandas.DataFrame([], columns=[reverse[k] for k in range(len(reverse))] + [self.target])
+
+    for n in range(len(X)):
+      ligne = []
+      for k in range(len(reverse)):
+        if isinstance(X, pandas.DataFrame):
+          val = X[reverse[k]][n]
+        else:  # np.array
+          val = X[n][k]
+        var = self.bn.variable(reverse[k])
+        ligne.append(bestTypedVal(var, var[str(val)]))
+
+      ligne.append(bestTypedVal(varY, varY[str(y[n])]))
+      df.loc[len(df)] = ligne
+
+    return df
+
+  def __getstate__(self):
+    """
+    Returns the state of the object (used for pickling)
+
+    Warnings
+    --------
+    This method is used for pickling and should not be called directly.
+    Note that the "learning side" of the BNClassifier is not in the state which focus on the classifier itself.
+
+    Returns
+    -------
+    the state as a dictionary.
+    """
+    return {
+      "bn": self.bn,
+      "target": self.target,
+      "targetType": self.targetType,
+      "label": self.label,
+      "fromModel": self.fromModel,
+      "threshold": self.threshold,
+      "variableNameIndexDictionary": self.variableNameIndexDictionary,
+      "params": self.get_params(),
+      "discretizer": self.type_processor,
+    }
+
+  def __setstate__(self, state):
+    """
+    Sets the state of the object (used for pickling)
+
+    Warnings
+    --------
+    This method is used for pickling and should not be called directly.
+    Note that the "learning side" of the BNClassifier is not in the state which focus on the classifier itself.
+
+    Parameters
+    ----------
+    state : dict
+      the state of the object as a dictionary
+
+    Returns
+    -------
+      self
+    """
+    self.__init__()
+    self.fromTrainedModel(bn=state["bn"], targetAttribute=state["target"], targetModality=state["label"], copy=False)
+    self.targetType = state["targetType"]
+    self.fromModel = state["fromModel"]
+    self.threshold = state["threshold"]
+    self.variableNameIndexDictionary = state["variableNameIndexDictionary"]
+    self.set_params(**state["params"])
+    self.discertizer = state["discretizer"]
+    return self
+
+  def showROC_PR(self, data, *, beta=1, save_fig=False, show_progress=False, bgcolor=None):
+    """
+    Use the `pyagrum.lib.bn2roc` tools to create ROC and Precision-Recall curve
+
+    Parameters
+    ----------
+    data: str | dataframe
+        a csv filename or a DataFrame
+    beta : float
+        the value of beta for the F-beta score
+    save_fig : bool
+        whether the graph should be saved
+    show_progress : bool
+        indicates if the resulting curve must be printed
+    bgcolor: str
+        HTML background color for the figure (default: None if transparent)
+    """
+    import pyagrum.lib.bn2roc as bn2roc
+
+    bn2roc.showROC_PR(
+      self.bn,
+      data,
+      self.target,
+      self.label,
+      beta=beta,
+      significant_digits=self.significant_digit,
+      save_fig=save_fig,
+      show_progress=show_progress,
+      bgcolor=bgcolor,
+    )