fixed bug of parsing and em

eelxpeng · Sep 18, 2018 · f30ddcd · f30ddcd
1 parent 5eec490
commit f30ddcd
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Showing 3 changed files with 19 additions and 16 deletions.
diff --git a/pyltm/io/bifparser.py b/pyltm/io/bifparser.py
@@ -60,7 +60,7 @@ def parse(self, filename):
         self.net = None
         for inst in tree.children:
             self.read_tree(inst)
-        print(str(self.net))
+
         return self.net
 
     def read_tree(self, t):

diff --git a/pyltm/learner/em_framework.py b/pyltm/learner/em_framework.py
@@ -28,17 +28,18 @@ def initializeSufficientStatistics(self, batch_size):
         ctp = NaturalCliqueTreePropagation(self._model)
         ctp.initializePotentials()
         tree = ctp.cliqueTree()
-        sufficientStatistics = [None]*len(tree.nodes)
-        batchSufficientStatistics = [None]*len(tree.nodes)
-        for i in range(len(tree.nodes)):
-            if isinstance(tree.nodes[i], DiscreteClique):
-                sufficientStatistics[i] = DiscreteCliqueSufficientStatistics(tree.nodes[i], batch_size)
-                batchSufficientStatistics[i] = DiscreteCliqueSufficientStatistics(tree.nodes[i], batch_size)
-            elif isinstance(tree.nodes[i], MixedClique):
-                sufficientStatistics[i] = MixedCliqueSufficientStatistics(tree.nodes[i], batch_size)
-                batchSufficientStatistics[i] = MixedCliqueSufficientStatistics(tree.nodes[i], batch_size)
+        cliques = tree.cliques
+        sufficientStatistics = [None]*len(cliques)
+        batchSufficientStatistics = [None]*len(cliques)
+        for i in range(len(cliques)):
+            if isinstance(cliques[i], DiscreteClique):
+                sufficientStatistics[i] = DiscreteCliqueSufficientStatistics(cliques[i], batch_size)
+                batchSufficientStatistics[i] = DiscreteCliqueSufficientStatistics(cliques[i], batch_size)
+            elif isinstance(cliques[i], MixedClique):
+                sufficientStatistics[i] = MixedCliqueSufficientStatistics(cliques[i], batch_size)
+                batchSufficientStatistics[i] = MixedCliqueSufficientStatistics(cliques[i], batch_size)
             else:
-                raise ValueError("invalid clique type")
+                raise Exception("unknown type of clique")
         return sufficientStatistics, batchSufficientStatistics
 
     def reset(self):
@@ -51,6 +52,9 @@ def stepwise_e_step(self, data, varNames):
         varNames: list of string
         '''
         ctp = NaturalCliqueTreePropagation(self._model)
+        tree = ctp.cliqueTree()
+        cliques = tree.cliques
+
         # set up evidence
         datacase = ContinuousDatacase.create(varNames)
         datacase.synchronize(self._model)
@@ -61,15 +65,14 @@ def stepwise_e_step(self, data, varNames):
             ctp.use(evidence)
             ctp.propagate()
 
-            for j in range(len(ctp.cliqueTree().nodes)):
-                self.batchSufficientStatistics[j].add(ctp.cliqueTree().nodes[j].potential)
+            for j in range(len(cliques)):
+                self.batchSufficientStatistics[j].add(cliques[j].potential)
 
         # construct variable to statisticMap
         variableStatisticMap = dict()
-        tree = ctp.cliqueTree()
         for node in self._model.nodes:
             clique = tree.getClique(node.variable)
-            index = tree.nodes.index(clique)
+            index = cliques.index(clique)
             variableStatisticMap[node.variable] = (self.sufficientStatistics[index], self.batchSufficientStatistics[index])
         return variableStatisticMap
 

diff --git a/pyltm/model/potential/cptpotential.py b/pyltm/model/potential/cptpotential.py
@@ -184,7 +184,7 @@ def divide(self, other):
         if isinstance(other, float) or isinstance(other, int):
             self._parameter.prob[:] = self._parameter.prob / other
         else:
-            self._parameter.prob[:] = self._parameter.prob / other._parameter.prob
+            self._parameter.prob[:] = self._parameter.prob / np.maximum(other._parameter.prob, 1e-10)
 
     @property
     def parameter(self):