Updated Docs

main_package/classes/estimators/fam_score_calculator.py

@@ -27,7 +27,7 @@ import structure_graph.conditional_intensity_matrix as cim_class
 
 class FamScoreCalculator:
     """
-    Has the task of calculating the FamScore of a node
+    Has the task of calculating the FamScore of a node by using a Bayesian score function
     """
 
     def __init__(self):
@@ -38,16 +38,20 @@ class FamScoreCalculator:
 
     def marginal_likelihood_theta(self,
                         cims: cim_class.ConditionalIntensityMatrix,
-                        alpha_xu: float = 1,
+                        alpha_xu: float,
-                        alpha_xxu: float = 1):
+                        alpha_xxu: float):
         """
-        calculate the FamScore value of the node identified by the label node_id
+        Calculate the FamScore value of the node identified by the label node_id
-        Parameters:
+
-            cims: np.array with all the node's cims,
+        :param cims: np.array with all the node's cims
-            alpha_xu: hyperparameter over the CTBN’s q parameters
+        :type cims: np.array
-            alpha_xxu: hyperparameter over the CTBN’s theta parameters
+        :param alpha_xu: hyperparameter over the CTBN’s q parameters, default to 0.1
-        Returns:
+        :type alpha_xu: float
-            the value of the marginal likelihood over theta
+        :param alpha_xxu: distribuited hyperparameter over the CTBN’s theta parameters
+        :type alpha_xxu: float
+
+        :return: the value of the marginal likelihood over theta
+        :rtype: float
         """
         return np.sum(
                         [self.variable_cim_xu_marginal_likelihood_theta(cim,
@@ -57,16 +61,20 @@ class FamScoreCalculator:
 
     def variable_cim_xu_marginal_likelihood_theta(self,
                         cim: cim_class.ConditionalIntensityMatrix,
-                        alpha_xu: float = 1,
+                        alpha_xu: float,
-                        alpha_xxu: float = 1):
+                        alpha_xxu: float):
         """
-        calculate the value of the marginal likelihood over theta given a cim
+        Calculate the value of the marginal likelihood over theta given a cim
-        Parameters:
+
-            cim: A conditional_intensity_matrix object with the sufficient statistics,
+        :param cim: A conditional_intensity_matrix object with the sufficient statistics
-            alpha_xu: hyperparameter over the CTBN’s q parameters
+        :type cim: class:'ConditionalIntensityMatrix'
-            alpha_xxu: hyperparameter over the CTBN’s theta parameters
+        :param alpha_xu: hyperparameter over the CTBN’s q parameters, default to 0.1
-        Returns:
+        :type alpha_xu: float
-            the value of the marginal likelihood over theta
+        :param alpha_xxu: distribuited hyperparameter over the CTBN’s theta parameters
+        :type alpha_xxu: float
+
+        :return: the value of the marginal likelihood over theta
+        :rtype: float
         """
 
         'get cim length'
@@ -84,18 +92,21 @@ class FamScoreCalculator:
     def single_cim_xu_marginal_likelihood_theta(self,
                     index: int,
                     cim: cim_class.ConditionalIntensityMatrix,
-                    alpha_xu: float = 1,
+                    alpha_xu: float,
-                    alpha_xxu: float = 1):
+                    alpha_xxu: float):
         """
-        calculate the marginal likelihood on q of the node when assumes a specif value
+        Calculate the marginal likelihood on q of the node when assumes a specif value
         and a specif parents's assignment
-        Parameters:
+
-            index: current x instance's index
+        :param cim: A conditional_intensity_matrix object with the sufficient statistics
-            cim: A conditional_intensity_matrix object with the sufficient statistics,
+        :type cim: class:'ConditionalIntensityMatrix'
-            alpha_xu: hyperparameter over the CTBN’s q parameters
+        :param alpha_xu: hyperparameter over the CTBN’s q parameters
-            alpha_xxu: hyperparameter over the CTBN’s theta parameters
+        :type alpha_xu: float
-        Returns:
+        :param alpha_xxu: distribuited hyperparameter over the CTBN’s theta parameters
-            the marginal likelihood of the node when assumes a specif value
+        :type alpha_xxu: float
+
+        :return: the value of the marginal likelihood over theta when the node assumes a specif value
+        :rtype: float
         """
 
         values = list(range(len(cim._state_residence_times)))
@@ -118,12 +129,16 @@ class FamScoreCalculator:
                                                 M_xxu_suff_stats: float,
                                                 alpha_xxu: float=1):
         """
-        calculate the second part of the marginal likelihood over theta formula
+        Calculate the second part of the marginal likelihood over theta formula
-        Parameters:
+        
-            M_xxu_suff_stats: value of the suffucient statistic M[xx'|u]
+
-            alpha_xxu: hyperparameter over the CTBN’s theta parameters
+        :param M_xxu_suff_stats: value of the suffucient statistic M[xx'|u]
-        Returns:
+        :type M_xxu_suff_stats: float
-            the marginal likelihood of the node when assumes a specif value
+        :param alpha_xxu: distribuited hyperparameter over the CTBN’s theta parameters
+        :type alpha_xxu: float
+
+        :return: the value of the marginal likelihood over theta when the node assumes a specif value
+        :rtype: float
         """
         return loggamma(alpha_xxu+M_xxu_suff_stats) - loggamma(alpha_xxu)
 
@@ -133,32 +148,42 @@ class FamScoreCalculator:
 
     def marginal_likelihood_q(self,
                         cims: np.array,
-                        tau_xu: float=1,
+                        tau_xu: float=0.1,
                         alpha_xu: float=1):
         """
-        calculate the value of the marginal likelihood over q of the node identified by the label node_id
+        Calculate the value of the marginal likelihood over q of the node identified by the label node_id
-        Parameters:
+        
-            cims: np.array with all the node's cims,
+        :param cims: np.array with all the node's cims
-            tau_xu: hyperparameter over the CTBN’s q parameters
+        :type cims: np.array
-            alpha_xu: hyperparameter over the CTBN’s q parameters
+        :param tau_xu: hyperparameter over the CTBN’s q parameters
-        Returns:
+        :type tau_xu: float
-            the value of the marginal likelihood over q
+        :param alpha_xu: hyperparameter over the CTBN’s q parameters
+        :type alpha_xu: float
+
+
+        :return: the value of the marginal likelihood over q
+        :rtype: float
         """
 
         return np.sum([self.variable_cim_xu_marginal_likelihood_q(cim, tau_xu, alpha_xu) for cim in cims])
 
     def variable_cim_xu_marginal_likelihood_q(self,
                         cim: cim_class.ConditionalIntensityMatrix,
-                        tau_xu: float=1,
+                        tau_xu: float=0.1,
                         alpha_xu: float=1):
         """
-        calculate the value of the marginal likelihood over q given a cim
+        Calculate the value of the marginal likelihood over q given a cim
-        Parameters:
+        
-            cim: A conditional_intensity_matrix object with the sufficient statistics,
+        :param cim: A conditional_intensity_matrix object with the sufficient statistics
-            tau_xu: hyperparameter over the CTBN’s q parameters
+        :type cim: class:'ConditionalIntensityMatrix'
-            alpha_xu: hyperparameter over the CTBN’s q parameters
+        :param tau_xu: hyperparameter over the CTBN’s q parameters
-        Returns:
+        :type tau_xu: float
-            the value of the marginal likelihood over q
+        :param alpha_xu: hyperparameter over the CTBN’s q parameters
+        :type alpha_xu: float
+
+
+        :return: the value of the marginal likelihood over q
+        :rtype: float
         """
 
         'get cim length'
@@ -177,18 +202,26 @@ class FamScoreCalculator:
     def single_cim_xu_marginal_likelihood_q(self,
                         M_xu_suff_stats: float,
                         T_xu_suff_stats: float,
-                        tau_xu: float=1,
+                        tau_xu: float=0.1,
                         alpha_xu: float=1):
         """
-        calculate the marginal likelihood on q of the node when assumes a specif value
+        Calculate the marginal likelihood on q of the node when assumes a specif value
         and a specif parents's assignment
-        Parameters:
+        
-            M_xu_suff_stats: value of the suffucient statistic M[x|u]
+        :param M_xu_suff_stats: value of the suffucient statistic M[x|u]
-            T_xu_suff_stats: value of the suffucient statistic T[x|u]
+        :type M_xxu_suff_stats: float
-            tau_xu: hyperparameter over the CTBN’s q parameters
+        :param T_xu_suff_stats: value of the suffucient statistic T[x|u]
-            alpha_xu: hyperparameter over the CTBN’s q parameters
+        :type T_xu_suff_stats: float
-        Returns:
+        :param cim: A conditional_intensity_matrix object with the sufficient statistics
-            the marginal likelihood of the node when assumes a specif value
+        :type cim: class:'ConditionalIntensityMatrix'
+        :param tau_xu: hyperparameter over the CTBN’s q parameters
+        :type tau_xu: float
+        :param alpha_xu: hyperparameter over the CTBN’s q parameters
+        :type alpha_xu: float
+
+
+        :return: the value of the marginal likelihood of the node when assumes a specif value
+        :rtype: float
         """
         return (
                 loggamma(alpha_xu + M_xu_suff_stats + 1) + 
@@ -210,13 +243,19 @@ class FamScoreCalculator:
                 tau_xu: float=0.1,
                 alpha_xu: float=1):
         """
-        calculate the FamScore value of the node identified by the label node_id
+        Calculate the FamScore value of the node
-        Parameters:
+        
-            cims: np.array with all the node's cims,
+        
-            tau_xu: hyperparameter over the CTBN’s q parameters
+        :param cims: np.array with all the node's cims
-            alpha_xu: hyperparameter over the CTBN’s q parameters
+        :type cims: np.array
-        Returns:
+        :param tau_xu: hyperparameter over the CTBN’s q parameters, default to 0.1
-            the FamScore value of the node
+        :type tau_xu: float, optional
+        :param alpha_xu: hyperparameter over the CTBN’s q parameters, default to 1
+        :type alpha_xu: float, optional
+
+
+        :return: the FamScore value of the node
+        :rtype: float
         """
         #print("------")
         #print(self.marginal_likelihood_q(cims,

main_package/classes/estimators/parameters_estimator.py

@@ -9,42 +9,41 @@ import structure_graph.sets_of_cims_container as acims
 
 
 class ParametersEstimator:
-    """
+    """Has the task of computing the cims of particular node given the trajectories and the net structure
-    Has the task of computing the cims of particular node given the trajectories in samplepath and the net structure
+    in the graph ``_net_graph``.
-    in the graph net_graph
+
-
+    :param trajectories:  the trajectories
-    :sample_path: the container of the trajectories
+    :type trajectories: Trajectory
-    :net_graph: the net structure
+    :param net_graph: the net structure
-    :single_set_of_cims: the set of cims object that will hold the cims of the node
+    :type net_graph: NetworkGraph
+    :_single_set_of_cims: the set of cims object that will hold the cims of the node
     """
 
     def __init__(self, sample_path: sp.SamplePath, net_graph: ng.NetworkGraph):
+        """Constructor Method
+        """
         self.sample_path = sample_path
         self.net_graph = net_graph
         self.sets_of_cims_struct = None
         self.single_set_of_cims = None
 
     def fast_init(self, node_id: str):
-        """
+        """Initializes all the necessary structures for the parameters estimation for the node ``node_id``.
-        Initializes all the necessary structures for the parameters estimation.
 
-        Parameters:
+        :param node_id: the node label
-            node_id: the node label
+        :type node_id: string
-        Returns:
-            void
         """
         p_vals = self.net_graph.aggregated_info_about_nodes_parents[2]
         node_states_number = self.net_graph.get_states_number(node_id)
         self.single_set_of_cims = sofc.SetOfCims(node_id, p_vals, node_states_number, self.net_graph.p_combs)
 
     def compute_parameters_for_node(self, node_id: str) -> sofc.SetOfCims:
-        """
+        """Compute the CIMS of the node identified by the label ``node_id``.
-        Compute the CIMS of the node identified by the label node_id
 
-        Parameters:
+        :param node_id: the node label
-            node_id: the node label
+        :type node_id: string
-        Returns:
+        :return: A SetOfCims object filled with the computed CIMS
-            A setOfCims object filled with the computed CIMS
+        :rtype: SetOfCims
         """
         node_indx = self.net_graph.get_node_indx(node_id)
         state_res_times = self.single_set_of_cims._state_residence_times
@@ -65,18 +64,20 @@ class ParametersEstimator:
 
     def compute_state_res_time_for_node(self, node_indx: int, times: np.ndarray, trajectory: np.ndarray,
                                         cols_filter: np.ndarray, scalar_indexes_struct: np.ndarray, T: np.ndarray):
-        """
+        """Compute the state residence times for a node and fill the matrix ``T`` with the results
-        Compute the state residence times for a node and fill the matrix T with the results
+
-
+        :param node_indx: the index of the node
-        Parameters:
+        :type node_indx: int
-            node_indx: the index of the node
+        :param times: the times deltas vector
-            times: the times deltas vector
+        :type times: numpy.array
-            trajectory: the trajectory
+        :param trajectory: the trajectory
-            cols_filter: the columns filtering structure
+        :type trajectory: numpy.ndArray
-            scalar_indexes_struct: the indexing structure
+        :param cols_filter: the columns filtering structure
-            T: the state residence times vectors
+        :type cols_filter: numpy.array
-        Returns:
+        :param scalar_indexes_struct: the indexing structure
-            void
+        :type scalar_indexes_struct: numpy.array
+        :param T: the state residence times vectors
+        :type T: numpy.ndArray
         """
         T[:] = np.bincount(np.sum(trajectory[:, cols_filter] * scalar_indexes_struct / scalar_indexes_struct[0], axis=1)
                            .astype(np.int), \
@@ -84,18 +85,18 @@ class ParametersEstimator:
                            minlength=scalar_indexes_struct[-1]).reshape(-1, T.shape[1])
 
     def compute_state_transitions_for_a_node(self, node_indx, trajectory, cols_filter, scalar_indexing, M):
-        """
+        """Compute the state residence times for a node and fill the matrices ``M`` with the results.
-        Compute the state residence times for a node and fill the matrices M with the results
+
-
+        :param node_indx: the index of the node
-        Parameters:
+        :type node_indx: int
-            node_indx: the index of the node
+        :param trajectory: the trajectory
-            times: the times deltas vector
+        :type trajectory: numpy.ndArray
-            trajectory: the trajectory
+        :param cols_filter: the columns filtering structure
-            cols_filter: the columns filtering structure
+        :type cols_filter: numpy.array
-            scalar_indexes: the indexing structure
+        :param scalar_indexing: the indexing structure
-            M: the state transition matrices
+        :type scalar_indexing: numpy.array
-        Returns:
+        :param M: the state transitions matrices
-            void
+        :type M: numpy.ndArray
         """
         diag_indices = np.array([x * M.shape[1] + x % M.shape[1] for x in range(M.shape[0] * M.shape[1])],
                                 dtype=np.int64)

main_package/classes/estimators/structure_constraint_based_estimator.py

@@ -255,7 +255,7 @@ class StructureConstraintBasedEstimator(se.StructureEstimator):
         return set(itertools.chain.from_iterable(list_edges_partial))
 
         
-    @timing_write
+    @timing
     def estimate_structure(self,disable_multiprocessing:bool=False):
         return self.ctpc_algorithm(disable_multiprocessing=disable_multiprocessing)
 

main_package/classes/estimators/structure_estimator.py

@@ -24,13 +24,11 @@ class StructureEstimator(ABC):
     """
     Has the task of estimating the network structure given the trajectories in samplepath.
 
-    :sample_path: the sample_path object containing the trajectories and the real structure
+    :param sample_path: the _sample_path object containing the trajectories and the real structure
+    :type sample_path: SamplePath
+    :param known_edges: List of known edges
+    :type known_edges: List
 
-    :nodes: the nodes labels
-    :nodes_vals: the nodes cardinalities
-    :nodes_indxs: the nodes indexes
-    :complete_graph: the complete directed graph built using the nodes labels in nodes
-    :cache: the cache object
     """
 
     def __init__(self, sample_path: sp.SamplePath, known_edges: typing.List = None):

main_package/classes/estimators/structure_score_based_estimator.py

@@ -42,6 +42,15 @@ class StructureScoreBasedEstimator(se.StructureEstimator):
     Has the task of estimating the network structure given the trajectories in samplepath by
     using a score based approach.
 
+    :param sample_path: the _sample_path object containing the trajectories and the real structure
+    :type sample_path: SamplePath
+    :param tau_xu: hyperparameter over the CTBN’s q parameters, default to 0.1
+    :type tau_xu: float, optional
+    :param alpha_xu: hyperparameter over the CTBN’s q parameters, default to 1
+    :type alpha_xu: float, optional
+    :param known_edges: List of known edges, default to []
+    :type known_edges: List, optional
+
     """
 
     def __init__(self, sample_path: sp.SamplePath, tau_xu:int=0.1, alpha_xu:int = 1,known_edges: typing.List= []):
@@ -50,24 +59,27 @@ class StructureScoreBasedEstimator(se.StructureEstimator):
         self.alpha_xu=alpha_xu
 
 
-    @timing_write
+    @timing
     def estimate_structure(self, max_parents:int = None, iterations_number:int= 40,
                          patience:int = None, tabu_length:int = None, tabu_rules_duration:int = None,
-                         optimizer: str = 'hill',disable_multiprocessing:bool= False ):
+                         optimizer: str = 'tabu',disable_multiprocessing:bool= False ):
         """
         Compute the score-based algorithm to find the optimal structure
 
-        Parameters:
+        :param max_parents: maximum number of parents for each variable. If None, disabled, default to None
-            max_parents: maximum number of parents for each variable. If None, disabled
+        :type max_parents: int, optional
-            iterations_number: maximum number of optimization algorithm's iteration
+        :param iterations_number: maximum number of optimization algorithm's iteration, default to 40
-            patience: number of iteration without any improvement before to stop the search.If None, disabled
+        :type iterations_number: int, optional
-            tabu_length: maximum lenght of the data structures used in the optimization process
+        :param patience: number of iteration without any improvement before to stop the search.If None, disabled, default to None
-            tabu_rules_duration: number of iterations in which each rule keeps its value 
+        :type patience: int, optional
-            optimzer: name of the optimizer algorithm. Possible values: 'hill' (Hill climbing),'tabu' (tabu search)
+        :param tabu_length: maximum lenght of the data structures used in the optimization process, default to None
-            disable_multiprocessing: true if you desire to disable the multiprocessing operations
+        :type tabu_length: int, optional
-        Returns:
+        :param tabu_rules_duration: number of iterations in which each rule keeps its value, default to None
-            void
+        :type tabu_rules_duration: int, optional
-
+        :param optimizer: name of the optimizer algorithm. Possible values: 'hill' (Hill climbing),'tabu' (tabu search), defualt to 'tabu'
+        :type optimizer: string, optional
+        :param disable_multiprocessing: true if you desire to disable the multiprocessing operations, default to False
+        :type disable_multiprocessing: Boolean, optional
         """
         'Save the true edges structure in tuples'
         true_edges = copy.deepcopy(self._sample_path.structure.edges)
@@ -160,16 +172,24 @@ class StructureScoreBasedEstimator(se.StructureEstimator):
                             optimizer:str = 'hill' ):
         """
         Use the FamScore of a node in order to find the best parent nodes
-        Parameters:
+        
-            node_id: current node's id
+        :param node_id: current node's id
-            max_parents: maximum number of parents for each variable. If None, disabled
+        :type node_id: string
-            iterations_number: maximum number of optimization algorithm's iteration
+        :param max_parents: maximum number of parents for each variable. If None, disabled, default to None
-            patience: number of iteration without any improvement before to stop the search.If None, disabled
+        :type max_parents: int, optional
-            tabu_length: maximum lenght of the data structures used in the optimization process
+        :param iterations_number: maximum number of optimization algorithm's iteration, default to 40
-            tabu_rules_duration: number of iterations in which each rule keeps its value 
+        :type iterations_number: int, optional
-            optimzer: name of the optimizer algorithm. Possible values: 'hill' (Hill climbing),'tabu' (tabu search)
+        :param patience: number of iteration without any improvement before to stop the search.If None, disabled, default to None
-        Returns:
+        :type patience: int, optional
-            A list of the best edges for the currente node
+        :param tabu_length: maximum lenght of the data structures used in the optimization process, default to None
+        :type tabu_length: int, optional
+        :param tabu_rules_duration: number of iterations in which each rule keeps its value, default to None
+        :type tabu_rules_duration: int, optional
+        :param optimizer: name of the optimizer algorithm. Possible values: 'hill' (Hill climbing),'tabu' (tabu search), defualt to 'tabu'
+        :type optimizer: string, optional
+
+        :return: A list of the best edges for the currente node
+        :rtype: List
         """
 
         "choose the optimizer algotithm"
@@ -195,14 +215,19 @@ class StructureScoreBasedEstimator(se.StructureEstimator):
 
     
     def get_score_from_graph(self,
-                            graph: ng.NetworkGraph,node_id:str):
+                            graph: ng.NetworkGraph,
+                            node_id:str):
         """
-        Use the FamScore of a node in order to find the best parent nodes
+        Get the FamScore of a node 
-        Parameters:
+        
-           node_id: current node's id
+        :param node_id: current node's id
-           graph: current graph to be computed 
+        :type node_id: string
-        Returns:
+        :param graph: current graph to be computed
-            The FamSCore for this graph structure
+        :type graph: class:'NetworkGraph'
+
+
+        :return: The FamSCore for this graph structure
+        :rtype: float
         """
 
         'inizialize the graph for a single node'

main_package/classes/optimizers/constraint_based_optimizer.py

@@ -22,7 +22,16 @@ import structure_graph.network_graph as ng
 
 class ConstraintBasedOptimizer(Optimizer):
     """
-    Optimizer class that implement Hill Climbing Search
+    Optimizer class that implement a CTPC Algorithm
+    
+
+    :param node_id: current node's id
+    :type node_id: string
+    :param structure_estimator: a structure estimator object with the information about the net
+    :type structure_estimator: class:'StructureEstimator' 
+    :param tot_vars_count: number of variables in the dataset
+    :type tot_vars_count: int
+
     
     """
     def __init__(self,
@@ -31,8 +40,7 @@ class ConstraintBasedOptimizer(Optimizer):
                 tot_vars_count:int
                 ):
         """
-        Compute Optimization process for a structure_estimator
+        Constructor
-
         """
         super().__init__(node_id, structure_estimator)
         self.tot_vars_count = tot_vars_count
@@ -41,13 +49,10 @@ class ConstraintBasedOptimizer(Optimizer):
 
     def optimize_structure(self):
         """
-        Compute Optimization process for a structure_estimator
+        Compute Optimization process for a structure_estimator by using a CTPC Algorithm
-
-        Parameters:
-
-        Returns:
-            the estimated structure for the node
 
+        :return: the estimated structure for the node
+        :rtype: List
         """
         print("##################TESTING VAR################", self.node_id)
 

main_package/classes/optimizers/hill_climbing_search.py

@@ -22,6 +22,20 @@ class HillClimbing(Optimizer):
     """
     Optimizer class that implement Hill Climbing Search
     
+
+    :param node_id: current node's id
+    :type node_id: string
+    :param structure_estimator: a structure estimator object with the information about the net
+    :type structure_estimator: class:'StructureEstimator' 
+    :param max_parents: maximum number of parents for each variable. If None, disabled, default to None
+    :type max_parents: int, optional
+    :param iterations_number: maximum number of optimization algorithm's iteration, default to 40
+    :type iterations_number: int, optional
+    :param patience: number of iteration without any improvement before to stop the search.If None, disabled, default to None
+    :type patience: int, optional
+
+
+    
     """
     def __init__(self,
                 node_id:str,
@@ -31,16 +45,7 @@ class HillClimbing(Optimizer):
                 patience:int = None
                 ):
         """
-        Compute Optimization process for a structure_estimator
+        Constructor
-
-        Parameters:
-            node_id: the node label
-            structure_estimator: a structure estimator object with the information about the net
-            max_parents: maximum number of parents for each variable. If None, disabled
-            iterations_number: maximum number of optimization algorithm's iteration
-            patience: number of iteration without any improvement before to stop the search.If None, disabled
-
-
         """
         super().__init__(node_id, structure_estimator)
         self.max_parents = max_parents
@@ -51,13 +56,10 @@ class HillClimbing(Optimizer):
 
     def optimize_structure(self) -> typing.List:
         """
-        Compute Optimization process for a structure_estimator
+        Compute Optimization process for a structure_estimator by using a Hill Climbing Algorithm
-
-        Parameters:
-
-        Returns:
-            the estimated structure for the node
 
+        :return: the estimated structure for the node
+        :rtype: List
         """
 
         #'Create the graph for the single node'

main_package/classes/optimizers/optimizer.py

@@ -17,6 +17,11 @@ from estimators import structure_estimator as se
 class Optimizer(abc.ABC):
     """
     Interface class for all the optimizer's child classes
+
+    :param node_id: the node label
+    :type node_id: string
+    :param structure_estimator: A structureEstimator Object to predict the structure
+    :type structure_estimator: class:'StructureEstimator'
     
     """
 
@@ -30,10 +35,7 @@ class Optimizer(abc.ABC):
         """
         Compute Optimization process for a structure_estimator
 
-        Parameters:
+        :return: the estimated structure for the node
-
+        :rtype: List
-        Returns:
-            the estimated structure for the node
-
         """
     pass

main_package/classes/optimizers/tabu_search.py

@@ -22,7 +22,24 @@ import queue
 
 class TabuSearch(Optimizer):
     """
-    Optimizer class that implement Hill Climbing Search
+    Optimizer class that implement Tabu Search
+
+
+    :param node_id: current node's id
+    :type node_id: string
+    :param structure_estimator: a structure estimator object with the information about the net
+    :type structure_estimator: class:'StructureEstimator' 
+    :param max_parents: maximum number of parents for each variable. If None, disabled, default to None
+    :type max_parents: int, optional
+    :param iterations_number: maximum number of optimization algorithm's iteration, default to 40
+    :type iterations_number: int, optional
+    :param patience: number of iteration without any improvement before to stop the search.If None, disabled, default to None
+    :type patience: int, optional
+    :param tabu_length: maximum lenght of the data structures used in the optimization process, default to None
+    :type tabu_length: int, optional
+    :param tabu_rules_duration: number of iterations in which each rule keeps its value, default to None
+    :type tabu_rules_duration: int, optional
+
     
     """
     def __init__(self,
@@ -35,17 +52,7 @@ class TabuSearch(Optimizer):
                 tabu_rules_duration = None
                 ):
         """
-        Compute Optimization process for a structure_estimator
+        Constructor
-
-        Parameters:
-            node_id: the node label
-            structure_estimator: a structure estimator object with the information about the net
-            max_parents: maximum number of parents for each variable. If None, disabled
-            iterations_number: maximum number of optimization algorithm's iteration
-            patience: number of iteration without any improvement before to stop the search.If None, disabled
-            tabu_length: maximum lenght of the data structures used in the optimization process
-            tabu_rules_duration: number of iterations in which each rule keeps its value 
-
         """
         super().__init__(node_id, structure_estimator)
         self.max_parents = max_parents
@@ -57,13 +64,10 @@ class TabuSearch(Optimizer):
 
     def optimize_structure(self) -> typing.List:
         """
-        Compute Optimization process for a structure_estimator
+        Compute Optimization process for a structure_estimator by using a Hill Climbing Algorithm
-
-        Parameters:
-
-        Returns:
-            the estimated structure for the node
 
+        :return: the estimated structure for the node
+        :rtype: List
         """
         print(f"tabu search is processing the structure of {self.node_id}")
 

main_package/classes/structure_graph/conditional_intensity_matrix.py

@@ -4,27 +4,25 @@ import sys
 sys.path.append('../')
 
 class ConditionalIntensityMatrix:
-    """
+    """Abstracts the Conditional Intesity matrix of a node as aggregation of the state residence times vector
-    Abstracts the Conditional Intesity matrix of a node as aggregation of the state residence times vector
     and state transition matrix and the actual CIM matrix.
 
-    :_state_residence_times: state residence times vector
+    :param state_residence_times: state residence times vector
-    :_state_transition_matrix: the transitions count matrix
+    :type state_residence_times: numpy.array
+    :param state_transition_matrix: the transitions count matrix
+    :type state_transition_matrix: numpy.ndArray
     :_cim: the actual cim of the node
     """
     def __init__(self, state_residence_times: np.array, state_transition_matrix: np.array):
+        """Constructor Method
+        """
         self._state_residence_times = state_residence_times
         self._state_transition_matrix = state_transition_matrix
         self._cim = self.state_transition_matrix.astype(np.float64)
 
     def compute_cim_coefficients(self):
-        """
+        """Compute the coefficients of the matrix _cim by using the following equality q_xx' = M[x, x'] / T[x].
-        Compute the coefficients of the matrix _cim by using the following equality q_xx' = M[x, x'] / T[x]
+        The class member ``_cim`` will contain the computed cim
-
-        Parameters:
-            void
-        Returns:
-            void
         """
         np.fill_diagonal(self._cim, self._cim.diagonal() * -1)
         self._cim = ((self._cim.T + 1) / (self._state_residence_times + 1)).T

main_package/classes/utility/cache.py

@@ -7,26 +7,29 @@ import structure_graph.set_of_cims as sofc
 
 
 class Cache:
-    """
+    """This class acts as a cache of ``SetOfCims`` objects for a node.
-    This class has the role of a cache for SetOfCIMS of a test node that have been already computed during the ctpc algorithm.
 
-    :list_of_sets_of_parents: a list of Sets of the parents to which the cim in cache at SAME index is related
+    :_list_of_sets_of_parents: a list of ``Sets`` objects of the parents to which the cim in cache at SAME
-    :actual_cache: a list of setOfCims objects
+        index is related
+    :_actual_cache: a list of setOfCims objects
     """
 
     def __init__(self):
+        """Constructor Method
+        """
         self.list_of_sets_of_parents = []
         self.actual_cache = []
 
     def find(self, parents_comb: typing.Set): #typing.Union[typing.Set, str]
         """
-        Tries to find in cache given the symbolic parents combination parents_comb the SetOfCims related to that parents_comb.
+        Tries to find in cache given the symbolic parents combination ``parents_comb`` the ``SetOfCims``
-        Parameters:
+        related to that ``parents_comb``.
-            parents_comb: the parents related to that SetOfCims
-        Returns:
-            A SetOfCims object if the parents_comb index is found in list_of_sets_of_parents.
-            None otherwise.
 
+        :param parents_comb: the parents related to that ``SetOfCims``
+        :type parents_comb: Set
+        :return: A ``SetOfCims`` object if the ``parents_comb`` index is found in ``_list_of_sets_of_parents``.
+            None otherwise.
+        :rtype: SetOfCims
         """
         try:
             #print("Cache State:", self.list_of_sets_of_indxs)
@@ -38,28 +41,20 @@ class Cache:
             return None
 
     def put(self, parents_comb: typing.Union[typing.Set, str], socim: sofc.SetOfCims):
-        """
+        """Place in cache the ``SetOfCims`` object, and the related symbolic index ``parents_comb`` in
-        Place in cache the SetOfCims object, and the related sybolyc index parents_comb in list_of_sets_of_parents
+        ``_list_of_sets_of_parents``.
-
-        Parameters:
-            parents_comb: the symbolic set index
-            socim: the related SetOfCims object
 
-        Returns:
+        :param parents_comb: the symbolic set index
-            void
+        :type parents_comb: Set
+        :param socim: the related SetOfCims object
+        :type socim: SetOfCims
         """
         #print("Putting in cache:", parents_comb)
         self.list_of_sets_of_parents.append(parents_comb)
         self.actual_cache.append(socim)
 
     def clear(self):
-        """
+        """Clear the contents both of ``_actual_cache`` and ``_list_of_sets_of_parents``.
-        Clear the contents of both caches.
-
-        Parameters:
-            void
-        Returns:
-            void
         """
         del self.list_of_sets_of_parents[:]
         del self.actual_cache[:]