Started with score based implementation

.gitignore

@@ -1,4 +1,5 @@
 __pycache__
 .vscode
 **/__pycache__
-**/data
+**/data
+**/results_data

main_package/classes/fam_score_calculator.py

@@ -0,0 +1,121 @@
+
+import itertools
+import json
+import typing
+
+import networkx as nx
+import numpy as np
+from networkx.readwrite import json_graph
+
+from math import log
+
+from scipy.special import gamma
+from random import choice
+
+import set_of_cims as soCims 
+import network_graph as net_graph
+import conditional_intensity_matrix as cim_class
+
+
+'''
+TODO: Parlare dell'idea di ciclare sulle cim senza filtrare
+TODO: Parlare di gamma in scipy e math(overflow) 
+TODO: Problema warning overflow
+'''
+
+class FamScoreCalculator:
+    """
+    Has the task of calculate the FamScore of a node
+    """
+
+    def __init__(self):
+        pass
+
+    def marginal_likelihood_theta(self, 
+                            node_id: str, 
+                            set_of_cims: soCims.SetOfCims,
+                            graph:net_graph.NetworkGraph):
+        """
+       calculate the value of the marginal likelihood over theta of the node identified by the label node_id
+        Parameters:
+            node_id: the label of the node
+        Returns:
+            the value of the marginal likelihood over theta
+        """
+        return 2
+
+    def marginal_likelihood_q(self,
+                        cims: np.array,
+                        tau_xu:float = 1,
+                        alpha_xu:float = 1):
+        """
+        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,
+            tau_xu: hyperparameter over the CTBN’s q parameters
+            alpha_xu: hyperparameter over the CTBN’s q parameters
+        Returns:
+            the value of the marginal likelihood over q
+        """
+        return np.prod([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,
+                        alpha_xu:float = 1):
+        'get cim length'
+        values=len(cim.state_residence_times) 
+
+        'compute the marginal likelihood for the current cim'
+        return np.prod([
+                    self.single_cim_xu_marginal_likelihood_q(
+                                                cim.state_transition_matrix[index,index],
+                                                cim.state_residence_times[index],
+                                                tau_xu,
+                                                alpha_xu)
+                    for index in range(values)])    
+
+
+    def single_cim_xu_marginal_likelihood_q(self,
+                        M_suff_stats:float,
+                        T_suff_stats:float,
+                        tau_xu:float = 1,
+                        alpha_xu:float = 1):
+        """
+        calculate the marginal likelihood of the node when assumes a specif value
+        and a specif parents's assignment 
+        Parameters:
+            cims: np.array with all the node's cims,
+            tau_xu: hyperparameter over the CTBN’s q parameters
+            alpha_xu: hyperparameter over the CTBN’s q parameters
+        Returns:
+            the marginal likelihood of the node when assumes a specif value
+        """
+        print(M_suff_stats)
+        return  (gamma(alpha_xu + M_suff_stats + 1)* (tau_xu**(alpha_xu+1))) \
+                / \
+                (gamma(alpha_xu + 1)*((tau_xu + T_suff_stats)**(alpha_xu + M_suff_stats + 1)))
+
+
+    def get_fam_score(self,
+                cims: np.array,
+                tau_xu:float = 1,
+                alpha_xu:float = 1,
+                alpha_xxu:float = 1):
+        """
+        calculate the FamScore value of the node identified by the label node_id
+        Parameters:
+            cims: np.array with all the node's cims,
+            tau_xu: hyperparameter over the CTBN’s q parameters
+            alpha_xu: hyperparameter over the CTBN’s q parameters
+            alpha_xxu: hyperparameter over the CTBN’s theta parameters
+        Returns:
+            the FamScore value of the node
+        """
+        return log(
+                    self.marginal_likelihood_q(cims,tau_xu,alpha_xu)
+                ) \
+                + \
+                log(
+                    self.marginal_likelihood_theta(cims,tau_xu,alpha_xu,alpha_xxu)
+                    )

main_package/classes/parameters_estimator.py

@@ -14,7 +14,7 @@ class ParametersEstimator:
 
     :sample_path: the container of the trajectories
     :net_graph: the net structure
-    :single_srt_of_cims: the set of cims object that will hold the cims of the node
+    :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):

main_package/classes/structure_estimator.py

@@ -302,7 +302,7 @@ class StructureEstimator:
         name = self.sample_path.importer.file_path.rsplit('/',1)[-1]
         #print(name)
         name = 'results_' + name
-        with open(name, 'w') as f:
+        with open(name, 'w+') as f:
             json.dump(res, f)
 
 

main_package/classes/structure_score_based_estimator.py

@@ -0,0 +1,168 @@
+
+import itertools
+import json
+import typing
+
+import networkx as nx
+import numpy as np
+from networkx.readwrite import json_graph
+
+from random import choice
+
+import cache as ch
+import conditional_intensity_matrix as condim
+import network_graph as ng
+import parameters_estimator as pe
+import sample_path as sp
+import structure as st
+import fam_score_calculator as fam_score
+
+
+'''
+#TODO: Insert maximum number of parents
+#TODO: Evaluate if it's better to start from a complete or an empty graph 
+#TODO: Create a parent class StructureEstimator and Two Subclasses (Score-Based and Constraint-Based)
+'''
+
+class StructureScoreBasedEstimator:
+    """
+    Has the task of estimating the network structure given the trajectories in samplepath by
+    using a score based approach.
+
+    :sample_path: the sample_path object containing the trajectories and the real structure
+
+    :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):
+        self.sample_path = sample_path
+        self.nodes = np.array(self.sample_path.structure.nodes_labels)
+        self.nodes_vals = self.sample_path.structure.nodes_values
+        self.nodes_indxs = self.sample_path.structure.nodes_indexes
+        self.complete_graph = self.build_complete_graph(self.sample_path.structure.nodes_labels)
+        self.cache = ch.Cache()
+
+    def build_complete_graph(self, node_ids: typing.List):
+        """
+        Builds a complete directed graph (no self loops) given the nodes labels in the list node_ids:
+
+        Parameters:
+            node_ids: the list of nodes labels
+        Returns:
+            a complete Digraph Object
+        """
+        complete_graph = nx.DiGraph()
+        complete_graph.add_nodes_from(node_ids)
+        complete_graph.add_edges_from(itertools.permutations(node_ids, 2))
+        return complete_graph
+
+
+
+    def estimate_structure(self):
+        """
+        Compute the score-based algorithm to find the optimal structure
+
+        Parameters:
+           node_id: the label of the node
+        Returns:
+            void
+
+        """
+        estimate_parents = self.estimate_parents
+        'Estimate the best parents for each node'
+        #[estimate_parents(n) for n in self.nodes]
+        estimate_parents('X')
+    
+    def estimate_parents(self,node_id:str):
+        """
+        Use the FamScore of a node in order to find the best parent nodes
+
+        Parameters:
+            void
+        Returns:
+            void
+
+        """
+        'Create the graph for the single node'
+        graph = ng.NetworkGraph(self.sample_path.structure)
+        'inizialize the graph for a single node'
+        graph.fast_init(node_id)
+
+        params_estimation = pe.ParametersEstimator(self.sample_path, graph)
+
+        'Inizialize and compute parameters for node'
+        params_estimation.fast_init(node_id)
+        SoCims = params_estimation.compute_parameters_for_node(node_id)
+
+        'Get the node\'s parents list'
+        parents = graph.get_parents_by_id(node_id)
+
+        values = graph.get_states_number(parents[0])
+
+        print(f" actual_cims {len(SoCims.actual_cims)} padri {len(parents)} ")
+
+        fam_score_obj = fam_score.FamScoreCalculator()
+
+        score = fam_score_obj.get_fam_score(SoCims.actual_cims)
+        
+        '''mask = np.array([True,True])
+
+        cims = SoCims.filter_cims_with_mask(mask,[1,1])
+
+       # print(f"-----{len(SoCims.transition_matrices)}-------")
+        print(f"{cims[0].state_transition_matrix}")
+
+        cims = SoCims.filter_cims_with_mask(mask,[0,0])
+
+        print(f"---parents {len(parents)}---------")
+        print(f"{cims[0].state_transition_matrix}")
+        '''
+
+       
+        
+
+
+    def generate_possible_sub_sets_of_size(self, u: typing.List, size: int, parent_label: str):
+        """
+        Creates a list containing all possible subsets of the list u of size size,
+        that do not contains a the node identified by parent_label.
+
+        Parameters:
+            u: the list of nodes
+            size: the size of the subsets
+            parent_label: the nodes to exclude in the subsets generation
+        Returns:
+            a Map Object containing a list of lists
+
+        """
+        list_without_test_parent = u[:]
+        list_without_test_parent.remove(parent_label)
+        return map(list, itertools.combinations(list_without_test_parent, size))
+
+    def save_results(self):
+        """
+        Save the estimated Structure to a .json file
+
+        Parameters:
+            void
+        Returns:
+            void
+        """
+        res = json_graph.node_link_data(self.complete_graph)
+        name = self.sample_path.importer.file_path.rsplit('/',1)[-1]
+        #print(name)
+        name = 'results_' + name
+        with open(name, 'w+') as f:
+            json.dump(res, f)
+
+
+    def remove_diagonal_elements(self, matrix):
+        m = matrix.shape[0]
+        strided = np.lib.stride_tricks.as_strided
+        s0, s1 = matrix.strides
+        return strided(matrix.ravel()[1:], shape=(m - 1, m), strides=(s0 + s1, s1)).reshape(m, -1)
+

main_package/tests/test_sets_of_cims_container.py

@@ -14,6 +14,7 @@ class TestSetsOfCimsContainer(unittest.TestCase):
         cls.parents_states_list = [[], [3], [3, 3]]
 
     def test_init(self):
+        #TODO: Fix this initialization
         c1 = scc.SetsOfCimsContainer(self.variables, self.states_per_node, self.parents_states_list)
         self.assertEqual(len(c1.sets_of_cims), len(self.variables))
         for set_of_cims in c1.sets_of_cims:

main_package/tests/test_structure_score_based_estimator.py

@@ -0,0 +1,63 @@
+import sys
+sys.path.append("../classes/")
+import glob
+import math
+import os
+import unittest
+
+import networkx as nx
+import numpy as np
+import psutil
+from line_profiler import LineProfiler
+
+import cache as ch
+import sample_path as sp
+import structure_score_based_estimator as se
+import json_importer as ji
+
+
+
+class TestStructureScoreBasedEstimator(unittest.TestCase):
+
+    @classmethod
+    def setUpClass(cls):
+        cls.read_files = glob.glob(os.path.join('../data', "*.json"))
+        cls.importer = ji.JsonImporter(cls.read_files[0], 'samples', 'dyn.str', 'variables', 'Time', 'Name')
+        cls.s1 = sp.SamplePath(cls.importer)
+        cls.s1.build_trajectories()
+        cls.s1.build_structure()
+
+
+
+
+    def test_esecuzione(self):
+        se1 = se.StructureScoreBasedEstimator(self.s1)
+        se1.estimate_structure()
+
+if __name__ == '__main__':
+    unittest.main()
+
+    '''
+
+        def test_init(self):
+        exp_alfa = 0.1
+        chi_alfa = 0.1
+        se1 = se.StructureScoreBasedEstimator(self.s1)
+        self.assertEqual(self.s1, se1.sample_path)
+        self.assertTrue(np.array_equal(se1.nodes, np.array(self.s1.structure.nodes_labels)))
+        self.assertTrue(np.array_equal(se1.nodes_indxs, self.s1.structure.nodes_indexes))
+        self.assertTrue(np.array_equal(se1.nodes_vals, self.s1.structure.nodes_values))
+        self.assertIsInstance(se1.complete_graph, nx.DiGraph)
+        self.assertIsInstance(se1.cache, ch.Cache)
+
+    def test_build_complete_graph(self):
+        nodes_numb = len(self.s1.structure.nodes_labels)
+        se1 = se.StructureScoreBasedEstimator(self.s1)
+        cg = se1.build_complete_graph(self.s1.structure.nodes_labels)
+        self.assertEqual(len(cg.edges), nodes_numb*(nodes_numb - 1))
+        ''for node in self.s1.structure.nodes_labels:
+            no_self_loops = self.s1.structure.nodes_labels[:]
+            no_self_loops.remove(node)
+            for n2 in no_self_loops:
+                self.assertIn((node, n2), cg.edges)''
+    '''