decrease the time required to find an elimination order

packages/CLPBN/clpbn/bp/ElimGraph.cpp

@@ -54,16 +54,20 @@ VarIds
 ElimGraph::getEliminatingOrder (const VarIds& exclude)
 {
   VarIds elimOrder;
-  marked_.resize (nodes_.size(), false);
+  unmarked_.reserve (nodes_.size());
-  for (unsigned i = 0; i < exclude.size(); i++) {
+  for (unsigned i = 0; i < nodes_.size(); i++) {
-    assert (getEgNode (exclude[i]));
+    if (Util::contains (exclude, nodes_[i]->varId()) == false) {
-    EgNode* node = getEgNode (exclude[i]);
+      unmarked_.insert (nodes_[i]);
-    marked_[*node] = true;
+    }
   }
   unsigned nVarsToEliminate = nodes_.size() - exclude.size();
   for (unsigned i = 0; i < nVarsToEliminate; i++) {
     EgNode* node = getLowestCostNode();
-    marked_[*node] = true;
+    unmarked_.remove (node);
+    const EGNeighs& neighs = node->neighbors();
+    for (unsigned j = 0; j < neighs.size(); j++) {
+      neighs[j]->removeNeighbor (node);
+    }
     elimOrder.push_back (node->varId());
     connectAllNeighbors (node);
   }
@@ -77,7 +81,7 @@ ElimGraph::print (void) const
 {
   for (unsigned i = 0; i < nodes_.size(); i++) {
     cout << "node " << nodes_[i]->label() << " neighs:" ;
-    vector<EgNode*> neighs = nodes_[i]->neighbors();
+    EGNeighs neighs = nodes_[i]->neighbors();
     for (unsigned j = 0; j < neighs.size(); j++) {
       cout << "  " << neighs[j]->label();
     }
@@ -120,7 +124,7 @@ ElimGraph::exportToGraphViz (
   }
 
   for (unsigned i = 0; i < nodes_.size(); i++) {
-    vector<EgNode*> neighs = nodes_[i]->neighbors();
+    EGNeighs neighs = nodes_[i]->neighbors();
     for (unsigned j = 0; j < neighs.size(); j++) {
       out << '"' << nodes_[i]->label() << '"' << " -- " ;
       out << '"' << neighs[j]->label() << '"' << endl;
@@ -171,118 +175,44 @@ ElimGraph::getLowestCostNode (void) const
 {
   EgNode* bestNode = 0;
   unsigned minCost = std::numeric_limits<unsigned>::max();
-  for (unsigned i = 0; i < nodes_.size(); i++) {
-    if (marked_[i]) continue;
   unsigned cost = 0;
+  EGNeighs::const_iterator it;
   switch (elimHeuristic) {
-      case MIN_NEIGHBORS:
+    case MIN_NEIGHBORS: {
-        cost = getNeighborsCost (nodes_[i]);
+      for (it = unmarked_.begin(); it != unmarked_.end(); ++ it) {
+        cost = getNeighborsCost (*it);
+        if (cost < minCost) {
+          bestNode = *it;
+          minCost  = cost;
+        }
+      }}
       break;
     case MIN_WEIGHT:
-        cost = getWeightCost (nodes_[i]);
+      //cost = getWeightCost (unmarked_[i]);
       break;
     case MIN_FILL:
-        cost = getFillCost (nodes_[i]);
+      //cost = getFillCost (unmarked_[i]);
       break;
     case WEIGHTED_MIN_FILL:
-        cost = getWeightedFillCost (nodes_[i]);
+      //cost = getWeightedFillCost (unmarked_[i]);
       break;
     default:
       assert (false);
   }
-    if (cost < minCost) {
-      bestNode = nodes_[i];
-      minCost  = cost;
-    }
-  }
   assert (bestNode);
   return bestNode;
 }
 
 
 
-unsigned
-ElimGraph::getNeighborsCost (const EgNode* n) const
-{
-  unsigned cost = 0;
-  const vector<EgNode*>& neighs = n->neighbors();
-  for (unsigned i = 0; i < neighs.size(); i++) {
-    if (marked_[*neighs[i]] == false) {
-      cost ++;
-    }
-  }
-  return cost;
-}
-
-
-
-unsigned
-ElimGraph::getWeightCost (const EgNode* n) const
-{
-  unsigned cost = 1;
-  const vector<EgNode*>& neighs = n->neighbors();
-  for (unsigned i = 0; i < neighs.size(); i++) {
-    if (marked_[*neighs[i]] == false) {
-      cost *= neighs[i]->range();
-    }
-  }
-  return cost;
-}
-
-
-
-unsigned
-ElimGraph::getFillCost (const EgNode* n) const
-{
-  unsigned cost = 0;
-  const vector<EgNode*>& neighs = n->neighbors();
-  if (neighs.size() > 0) {
-    for (unsigned i = 0; i < neighs.size() - 1; i++) {
-      if (marked_[*neighs[i]] == true) continue;
-      for (unsigned j = i+1; j < neighs.size(); j++) {
-        if (marked_[*neighs[j]] == true) continue;
-        if (!neighbors (neighs[i], neighs[j])) {
-          cost ++;
-        }
-      }
-    }
-  }
-  return cost;
-}
-
-
-
-unsigned
-ElimGraph::getWeightedFillCost (const EgNode* n) const
-{
-  unsigned cost = 0;
-  const vector<EgNode*>& neighs = n->neighbors();
-  if (neighs.size() > 0) {
-    for (unsigned i = 0; i < neighs.size() - 1; i++) {
-      if (marked_[*neighs[i]] == true) continue;
-      for (unsigned j = i+1; j < neighs.size(); j++) {
-        if (marked_[*neighs[j]] == true) continue;
-        if (!neighbors (neighs[i], neighs[j])) {
-          cost += neighs[i]->range() * neighs[j]->range();
-        }
-      }
-    }
-  }
-  return cost;
-}
-
-
-
 void
 ElimGraph::connectAllNeighbors (const EgNode* n)
 {
-  const vector<EgNode*>& neighs = n->neighbors();
+  const EGNeighs& neighs = n->neighbors();
   if (neighs.size() > 0) {
     for (unsigned i = 0; i < neighs.size() - 1; i++) {
-      if (marked_[*neighs[i]] == true) continue;
       for (unsigned j = i+1; j < neighs.size(); j++) {
-        if (marked_[*neighs[j]] == true) continue;
+        if ( ! neighbors (neighs[i], neighs[j])) {
-        if (!neighbors (neighs[i], neighs[j])) {
           addEdge (neighs[i], neighs[j]);
         }
       }
@@ -290,17 +220,3 @@ ElimGraph::connectAllNeighbors (const EgNode* n)
   }
 }
 
-
-
-bool
-ElimGraph::neighbors (const EgNode* n1, const EgNode* n2) const
-{
-  const vector<EgNode*>& neighs = n1->neighbors();
-  for (unsigned i = 0; i < neighs.size(); i++) {
-    if (neighs[i] == n2) {
-      return true;
-    }
-  }
-  return false;
-}
-

packages/CLPBN/clpbn/bp/ElimGraph.h

@@ -4,8 +4,10 @@
 #include "unordered_map"
 
 #include "FactorGraph.h"
+#include "TinySet.h"
 #include "Horus.h"
 
+
 using namespace std;
 
 enum ElimHeuristic 
@@ -17,17 +19,26 @@ enum ElimHeuristic
 };
 
 
+class EgNode;
+
+typedef TinySet<EgNode*> EGNeighs;
+
+
 class EgNode : public Var
 {
   public:
     EgNode (VarId vid, unsigned range) : Var (vid, range) { }
 
-    void addNeighbor (EgNode* n) { neighs_.push_back (n);  }
+    void addNeighbor (EgNode* n) { neighs_.insert (n);  }
 
-    const vector<EgNode*>& neighbors (void) const { return neighs_; }
+    void removeNeighbor (EgNode* n) { neighs_.remove (n); }
+
+    bool isNeighbor (EgNode* n) const { return neighs_.contains (n); }
+
+    const EGNeighs& neighbors (void) const { return neighs_; }
 
   private:
-    vector<EgNode*>  neighs_;
+    EGNeighs neighs_;
 };
 
 
@@ -58,25 +69,68 @@ class ElimGraph
       n2->addNeighbor (n1);
     }
 
+    unsigned getNeighborsCost (const EgNode* n) const
+    {
+      return n->neighbors().size();
+    }
+
+    unsigned getWeightCost (const EgNode* n) const
+    {
+      unsigned cost = 1;
+      const EGNeighs& neighs = n->neighbors();
+      for (unsigned i = 0; i < neighs.size(); i++) {
+        cost *= neighs[i]->range();
+      }
+      return cost;
+    }
+
+    unsigned getFillCost (const EgNode* n) const
+    {
+      unsigned cost = 0;
+      const EGNeighs& neighs = n->neighbors();
+      if (neighs.size() > 0) {
+        for (unsigned i = 0; i < neighs.size() - 1; i++) {
+          for (unsigned j = i + 1; j < neighs.size(); j++) {
+            if ( ! neighbors (neighs[i], neighs[j])) {
+              cost ++;
+            }
+         }
+       }
+     }
+     return cost;
+   }
+
+    unsigned getWeightedFillCost (const EgNode* n) const
+    {
+      unsigned cost = 0;
+      const EGNeighs& neighs = n->neighbors();
+      if (neighs.size() > 0) {
+        for (unsigned i = 0; i < neighs.size() - 1; i++) {
+          for (unsigned j = i+1; j < neighs.size(); j++) {
+            if ( ! neighbors (neighs[i], neighs[j])) {
+              cost += neighs[i]->range() * neighs[j]->range();
+            }
+          }
+        }
+      }
+      return cost;
+    }
+
+    bool neighbors (EgNode* n1, EgNode* n2) const
+    {
+      return n1->isNeighbor (n2);
+    }
+
     void addNode (EgNode*);
 
     EgNode* getEgNode (VarId) const;
+
     EgNode* getLowestCostNode (void) const;
 
-    unsigned getNeighborsCost (const EgNode*) const;
-
-    unsigned getWeightCost (const EgNode*) const;
-
-    unsigned getFillCost (const EgNode*) const;
-
-    unsigned getWeightedFillCost (const EgNode*) const;
-
     void connectAllNeighbors (const EgNode*);
 
-    bool neighbors (const EgNode*, const EgNode*) const;
-
     vector<EgNode*> nodes_;
-    vector<bool>    marked_;
+    TinySet<EgNode*> unmarked_;
     unordered_map<VarId, EgNode*> varMap_;
 };
 

packages/CLPBN/clpbn/bp/TODO

@@ -5,4 +5,8 @@
 - Consider using hashs instead of vectors of colors to calculate the groups in
   counting bp
 - use more psize_t instead of unsigned for looping through params
+- Find a way to decrease the time required to find an
+  elimination order for variable elimination
+- Add a sequential elimination heuristic
+