Add removable_edges_matrix to StructureEstimator

PyCTBN/classes/structure_estimator.py

@@ -36,7 +36,8 @@ class StructureEstimator(object):
     :_cache: the Cache object
     """
 
-    def __init__(self, sample_path: SamplePath, exp_test_alfa: float, chi_test_alfa: float):
+    def __init__(self, sample_path: SamplePath, exp_test_alfa: float, chi_test_alfa: float,
+                 thumb_threshold:int = 25, known_edges: typing.List = None):
         """Constructor Method
         """
         self._sample_path = sample_path
@@ -46,6 +47,8 @@ class StructureEstimator(object):
         self._complete_graph = StructureEstimator.build_complete_graph(self._sample_path.structure.nodes_labels)
         self._exp_test_sign = exp_test_alfa
         self._chi_test_alfa = chi_test_alfa
+        self._thumb_threshold = thumb_threshold
+        self._removable_edges_matrix = self.build_removable_edges_matrix(known_edges)
         self._cache = Cache()
 
     @staticmethod
@@ -62,8 +65,18 @@ class StructureEstimator(object):
         complete_graph.add_edges_from(itertools.permutations(node_ids, 2))
         return complete_graph
 
+    def build_removable_edges_matrix(self, known_edges: typing.List):
+        tot_vars_count = self._sample_path.total_variables_count
+        complete_adj_matrix = np.full((tot_vars_count, tot_vars_count), True)
+        if known_edges:
+            for edge in known_edges:
+                i = self._sample_path.structure.get_node_indx(edge[0])
+                j = self._sample_path.structure.get_node_indx(edge[1])
+                complete_adj_matrix[i][j] = False
+        return complete_adj_matrix
+
     def complete_test(self, test_parent: str, test_child: str, parent_set: typing.List, child_states_numb: int,
-                      tot_vars_count: int) -> bool:
+                      tot_vars_count: int, parent_indx, child_indx) -> bool:
         """Performs a complete independence test on the directed graphs G1 = {test_child U parent_set}
         G2 = {G1 U test_parent} (added as an additional parent of the test_child).
         Generates all the necessary structures and datas to perform the tests.
@@ -117,16 +130,21 @@ class StructureEstimator(object):
             p2.fast_init(test_child)
             sofc1 = p2.compute_parameters_for_node(test_child)
             self._cache.put(set(p_set), sofc1)
-
+        thumb_value = 0.0
+        if child_states_numb > 2:
+            parent_val = self._sample_path.structure.get_states_number(test_parent)
+            bool_mask_vals = np.isin(self._nodes, parent_set)
+            parents_vals = self._nodes_vals[bool_mask_vals]
+            thumb_value = self.compute_thumb_value(parent_val, child_states_numb, parents_vals)
         for cim1, p_comb in zip(sofc1.actual_cims, sofc1.p_combs):
             cond_cims = sofc2.filter_cims_with_mask(cims_filter, p_comb)
             for cim2 in cond_cims:
-                if not self.independence_test(child_states_numb, cim1, cim2):
+                if not self.independence_test(child_states_numb, cim1, cim2, thumb_value, parent_indx, child_indx):
                     return False
         return True
 
     def independence_test(self, child_states_numb: int, cim1: ConditionalIntensityMatrix,
-                          cim2: ConditionalIntensityMatrix) -> bool:
+                          cim2: ConditionalIntensityMatrix, thumb_value: float, parent_indx, child_indx) -> bool:
         """Compute the actual independence test using two cims.
         It is performed first the exponential test and if the null hypothesis is not rejected,
         it is performed also the chi_test.
@@ -146,6 +164,10 @@ class StructureEstimator(object):
         r2s = M2.diagonal()
         C1 = cim1.cim
         C2 = cim2.cim
+        if child_states_numb > 2:
+            if (np.sum(np.diagonal(M1)) / thumb_value) < self._thumb_threshold:
+                self._removable_edges_matrix[parent_indx][child_indx] = False
+                return False
         F_stats = C2.diagonal() / C1.diagonal()
         exp_alfa = self._exp_test_sign
         for val in range(0, child_states_numb):
@@ -165,6 +187,14 @@ class StructureEstimator(object):
                 return False
         return True
 
+
+    def compute_thumb_value(self, parent_val, child_val, parent_set_vals):
+        df = (child_val - 1) ** 2
+        df = df * parent_val
+        for v in parent_set_vals:
+            df = df * v
+        return df
+
     def one_iteration_of_CTPC_algorithm(self, var_id: str) -> None:
         """Performs an iteration of the CTPC algorithm using the node ``var_id`` as ``test_child``.
 
@@ -179,10 +209,13 @@ class StructureEstimator(object):
             parent_indx = 0
             while parent_indx < len(u):
                 removed = False
-                S = StructureEstimator.generate_possible_sub_sets_of_size(u, b, u[parent_indx])
                 test_parent = u[parent_indx]
+                i = self._sample_path.structure.get_node_indx(test_parent)
+                j = self._sample_path.structure.get_node_indx(var_id)
+                if self._removable_edges_matrix[i][j]:
+                    S = StructureEstimator.generate_possible_sub_sets_of_size(u, b, test_parent)
                     for parents_set in S:
-                    if self.complete_test(test_parent, var_id, parents_set, child_states_numb, tot_vars_count):
+                        if self.complete_test(test_parent, var_id, parents_set, child_states_numb, tot_vars_count, i, j):
                             self._complete_graph.remove_edge(test_parent, var_id)
                             u.remove(test_parent)
                             removed = True
@@ -263,7 +296,7 @@ class StructureEstimator(object):
         edges_colors = ['red' if edge in spurious_edges else 'black' for edge in self._complete_graph.edges]
         graph_to_draw.add_edges_from(spurious_edges)
         graph_to_draw.add_edges_from(non_spurious_edges)
-        pos = nx.spring_layout(graph_to_draw, k=5, scale=3)
+        pos = nx.spring_layout(graph_to_draw, k=0.5*1/np.sqrt(len(graph_to_draw.nodes())), iterations=50,scale=10)
         options = {
             "node_size": 2000,
             "node_color": "white",

PyCTBN/tests/original_ctpc_algorithm.py

@@ -242,27 +242,12 @@ class OriginalCTPCAlgorithm(AbstractImporter):
                                 dtype=np.int64)
         #print(diag_indices)
         T_filter = np.array([child_id, *parents_id], dtype=np.int) + 1
-        #print("TFilter",T_filter)
-        #print("TVector", T_vector)
-        #print("Trajectories", trajectories)
-        #print("Actual TVect",T_vector / T_vector[0])
-        #print("Masked COlumns", trajectories[:, T_filter])  # Colonne non shiftate dei values
-        #print("Masked Multiplied COlumns",trajectories[:, T_filter] * (T_vector / T_vector[0]) )
-        #print("Summing",np.sum(trajectories[:, T_filter] * (T_vector / T_vector[0]), axis=1))
-        #print("Deltas",trajectories[:, int(trajectories.shape[1] / 2)]) # i delta times
         assert np.sum(trajectories[:, T_filter] * (T_vector / T_vector[0]), axis=1).size == \
                trajectories[:, int(trajectories.shape[1] / 2)].size
         #print(T_vector[-1])
         T[:] = np.bincount(np.sum(trajectories[:, T_filter] * T_vector / T_vector[0], axis=1).astype(np.int), \
                            trajectories[:, int(trajectories.shape[1] / 2)], minlength=T_vector[-1]).reshape(-1,
                                                                                                             T.shape[1])
-        #print("Shape", T.shape[1])
-        #print(np.bincount(np.sum(trajectories[:, T_filter] * T_vector / T_vector[0], axis=1).astype(np.int), \
-                           #trajectories[:, int(trajectories.shape[1] / 2)], minlength=T_vector[-1]))
-        ###### Transitions #######
-
-        #print("Shifted Node column", trajectories[:, int(trajectories.shape[1] / 2) + 1 + child_id].astype(np.int))
-        #print("Step 2", trajectories[:, int(trajectories.shape[1] / 2) + 1 + child_id].astype(np.int) >= 0)
         trj_tmp = trajectories[trajectories[:, int(trajectories.shape[1] / 2) + 1 + child_id].astype(np.int) >= 0]
         #print("Trj Temp", trj_tmp)
 
@@ -270,13 +255,6 @@ class OriginalCTPCAlgorithm(AbstractImporter):
         M_filter = np.array([child_id, child_id, *parents_id], dtype=np.int) + 1
         #print("MFilter", M_filter)
         M_filter[0] += int(trj_tmp.shape[1] / 2)
-        #print("MFilter", M_filter)
-        #print("MVector", M_vector)
-        #print("Division", M_vector / M_vector[0])
-        #print("Masked Traj temp", (trj_tmp[:, M_filter]))
-        #print("Masked Multiplied Traj temp", trj_tmp[:, M_filter] * M_vector / M_vector[0])
-        #print("Summing", np.sum(trj_tmp[:, M_filter] * M_vector / M_vector[0], axis=1))
-        #print(M.shape[2])
 
         M[:] = np.bincount(np.sum(trj_tmp[:, M_filter] * M_vector / M_vector[0], axis=1).astype(np.int), \
                            minlength=M_vector[-1]).reshape(-1, M.shape[1], M.shape[2])
@@ -390,6 +368,7 @@ class OriginalCTPCAlgorithm(AbstractImporter):
 
         #print("C2:", CIM_from)
 
+
         if self.variables.loc[to_var, "Value"] > 2:
             df = (self.variables.loc[to_var, "Value"] - 1) ** 2
             df = df * (self.variables.loc[from_var, "Value"])

PyCTBN/tests/performance_comparisons.py

@@ -5,7 +5,7 @@ import numpy as np
 import pandas as pd
 import networkx as nx
 import timeit
-import psutil
+#import psutil
 
 from ..classes.sample_path import SamplePath
 from ..classes.structure_estimator import StructureEstimator
@@ -66,9 +66,9 @@ class PerformanceComparisons(unittest.TestCase):
             self.aux_build_importer(0)
             se1 = StructureEstimator(self.s1, 0.1, 0.1)
             se1.ctpc_algorithm()
-            current_process = psutil.Process(os.getpid())
+            #current_process = psutil.Process(os.getpid())
-            mem = current_process.memory_info().rss
+            #mem = current_process.memory_info().rss
-            self.memory_usages.append((mem / 10 ** 6))
+            #self.memory_usages.append((mem / 10 ** 6))
         self.save_memory_usage_data(self.memory_usages)
 
     def aux_build_importer(self, indx):

PyCTBN/tests/test_structure_estimator.py

@@ -50,6 +50,17 @@ class TestStructureEstimator(unittest.TestCase):
             no_self_loops.remove(node)
             for n2 in no_self_loops:
                 self.assertIn((node, n2), cg.edges)
+        #se1.save_plot_estimated_structure_graph()
+
+    def test_build_removable_edges_matrix(self):
+        exp_alfa = 0.1
+        chi_alfa = 0.1
+        known_edges = self.s1.structure.edges[0:2]
+        se1 = StructureEstimator(self.s1, exp_alfa, chi_alfa, known_edges)
+        for edge in known_edges:
+            i = self.s1.structure.get_node_indx(edge[0])
+            j = self.s1.structure.get_node_indx(edge[1])
+            self.assertFalse(se1._removable_edges_matrix[i][j])
 
     def test_generate_possible_sub_sets_of_size(self):
         exp_alfa = 0.1
@@ -67,7 +78,8 @@ class TestStructureEstimator(unittest.TestCase):
                     self.assertFalse(node in sset)
 
     def test_time(self):
-        se1 = StructureEstimator(self.s1, 0.1, 0.1)
+        known_edges = [self.s1.structure.edges[0]]
+        se1 = StructureEstimator(self.s1, 0.1, 0.1, 25, known_edges)
         exec_time = timeit.timeit(se1.ctpc_algorithm, number=1)
         print("Execution Time: ", exec_time)
         for ed in self.s1.structure.edges: