rework the examples and erase the city network in the old format

packages/CLPBN/clpbn/bp/BpSolver.cpp

@@ -132,8 +132,8 @@ BpSolver::runSolver (void)
   while (!converged() && nIters_ < BpOptions::maxIter) {
     nIters_ ++;
     if (Constants::DEBUG >= 2) {
-      Util::printHeader (" Iteration " + nIters_);
+      Util::printHeader (string ("Iteration ") + Util::toString (nIters_));
-      cout << endl;
+      // cout << endl;
     }
     switch (BpOptions::schedule) {
      case BpOptions::Schedule::SEQ_RANDOM:
@@ -468,6 +468,9 @@ BpSolver::converged (void)
         if (Constants::DEBUG == 0) break;
       }
     }
+    if (Constants::DEBUG >= 2) {
+      cout << endl;
+    }
   }
   return converged;
 }

packages/CLPBN/clpbn/bp/CFactorGraph.cpp

@@ -263,21 +263,22 @@ CFactorGraph::getGroundFactorGraph (void) const
       fg->addEdge (static_cast<VarNode*> (myGroundVars[j]), fn);
     }
   }
+  fg->print();
   return fg;
 }
 
 
 
 unsigned
-CFactorGraph::getGroundEdgeCount (
+CFactorGraph::getEdgeCount (
     const FacCluster* fc,
     const VarCluster* vc) const
 {
-  const FacNodes& clusterGroundFactors = fc->getGroundFactors();
-  VarNode* varNode = vc->getGroundVarNodes()[0];
   unsigned count = 0;
+  VarId vid = vc->getGroundVarNodes().front()->varId();
+  const FacNodes& clusterGroundFactors = fc->getGroundFactors();
   for (unsigned i = 0; i < clusterGroundFactors.size(); i++) {
-    if (clusterGroundFactors[i]->factor().indexOf (varNode->varId()) != -1) {
+    if (clusterGroundFactors[i]->factor().contains (vid)) {
       count ++;
     }
   }

packages/CLPBN/clpbn/bp/CFactorGraph.h

@@ -186,7 +186,7 @@ class CFactorGraph
 
     FactorGraph* getGroundFactorGraph (void) const;
 
-    unsigned getGroundEdgeCount (const FacCluster*, const VarCluster*) const;
+    unsigned getEdgeCount (const FacCluster*, const VarCluster*) const;
  
     static bool checkForIdenticalFactors;
  

packages/CLPBN/clpbn/bp/CbpSolver.cpp

@@ -99,7 +99,7 @@ CbpSolver::createLinks (void)
   for (unsigned i = 0; i < fcs.size(); i++) {
     const VarClusters& vcs = fcs[i]->getVarClusters();
     for (unsigned j = 0; j < vcs.size(); j++) {
-      unsigned c = cfg_->getGroundEdgeCount (fcs[i], vcs[j]);
+      unsigned c = cfg_->getEdgeCount (fcs[i], vcs[j]);
       links_.push_back (new CbpSolverLink (
           fcs[i]->getRepresentativeFactor(),
           vcs[j]->getRepresentativeVariable(), c));

packages/CLPBN/clpbn/bp/ConstraintTree.cpp

@@ -43,6 +43,14 @@ CTNode::removeChild (CTNode* child)
 
 
 
+void
+CTNode::removeChilds (void)
+{
+  childs_.clear();
+}
+
+
+
 void
 CTNode::removeAndDeleteChild (CTNode* child)
 {
@@ -897,19 +905,19 @@ ConstraintTree::getNodesAtLevel (unsigned level) const
 void
 ConstraintTree::swapLogVar (LogVar X)
 {
+  TupleSet before = tupleSet();
   LogVars::iterator it = 
       std::find (logVars_.begin(),logVars_.end(), X);
   assert (it != logVars_.end());
   unsigned pos = std::distance (logVars_.begin(), it);
-
   const CTNodes& nodes = getNodesAtLevel (pos);
   for (unsigned i = 0; i < nodes.size(); i++) {
-    const CTNodes childs = nodes[i]->childs();
+    CTNodes childsCopy = nodes[i]->childs();
-    for (unsigned j = 0; j < childs.size(); j++) {
+    nodes[i]->removeChilds();
-       nodes[i]->removeChild (childs[j]);
+    for (unsigned j = 0; j < childsCopy.size(); j++) {
-       const CTNodes grandsons = childs[j]->childs();
+       const CTNodes grandsons = childsCopy[j]->childs();
        for (unsigned k = 0; k < grandsons.size(); k++) {
-         CTNode* childCopy = new CTNode (*childs[j]);
+         CTNode* childCopy = new CTNode (*childsCopy[j]);
          const CTNodes greatGrandsons = grandsons[k]->childs();
          for (unsigned t = 0; t < greatGrandsons.size(); t++) {
            grandsons[k]->removeChild (greatGrandsons[t]);
@@ -920,10 +928,9 @@ ConstraintTree::swapLogVar (LogVar X)
          grandsons[k]->setLevel (grandsons[k]->level() - 1);
          nodes[i]->addChild (grandsons[k], false);
        }
-       delete childs[j];
+       delete childsCopy[j];
     }
   }
-
   std::swap (logVars_[pos], logVars_[pos + 1]);
 }
 

packages/CLPBN/clpbn/bp/ConstraintTree.h

@@ -50,6 +50,8 @@ class CTNode
 
     void removeChild (CTNode*);
 
+    void removeChilds (void);
+
     void removeAndDeleteChild (CTNode*);
 
     void removeAndDeleteAllChilds (void);

packages/CLPBN/clpbn/bp/FoveSolver.cpp

@@ -455,7 +455,7 @@ FoveSolver::absorveEvidence (
     }
     pfList.add (newPfs);
   }
-  if (Constants::DEBUG > 1 && obsFormulas.empty() == false) {
+  if (Constants::DEBUG >= 2 && obsFormulas.empty() == false) {
     Util::printAsteriskLine();
     cout << "AFTER EVIDENCE ABSORVED" << endl;
     for (unsigned i = 0; i < obsFormulas.size(); i++) {
@@ -493,7 +493,7 @@ FoveSolver::runSolver (const Grounds& query)
   shatterAgainstQuery (query);
   runWeakBayesBall (query);
   while (true) {
-    if (Constants::DEBUG > 1) {
+    if (Constants::DEBUG >= 2) {
       Util::printDashedLine();
       pfList_.print();
       LiftedOperator::printValidOps (pfList_, query);
@@ -502,7 +502,7 @@ FoveSolver::runSolver (const Grounds& query)
     if (op == 0) {
       break;
     }
-    if (Constants::DEBUG > 1) {
+    if (Constants::DEBUG >= 2) {
       cout << "best operation: " << op->toString() << endl;
     }
     op->apply();
@@ -594,7 +594,7 @@ FoveSolver::runWeakBayesBall (const Grounds& query)
     }
   }
 
-  if (Constants::DEBUG > 1) {
+  if (Constants::DEBUG >= 2) {
     Util::printHeader ("REQUIRED PARFACTORS");
     pfList_.print();
   }
@@ -605,15 +605,16 @@ FoveSolver::runWeakBayesBall (const Grounds& query)
 void
 FoveSolver::shatterAgainstQuery (const Grounds& query)
 {
-  return ;
   for (unsigned i = 0; i < query.size(); i++) {
     if (query[i].isAtom()) {
       continue;
     }
+    bool found = false;
     Parfactors newPfs;
     ParfactorList::iterator it = pfList_.begin();
     while (it != pfList_.end()) {
       if ((*it)->containsGround (query[i])) {
+        found = true;
         std::pair<ConstraintTree*, ConstraintTree*> split = 
             (*it)->constr()->split (query[i].args(), query[i].arity());
         ConstraintTree* commCt = split.first;
@@ -629,9 +630,14 @@ FoveSolver::shatterAgainstQuery (const Grounds& query)
         ++ it;
       }
     }
+    if (found == false) {
+      cerr << "error: could not find a parfactor with ground " ;
+      cerr << "`" << query[i] << "'" << endl;
+      exit (0);	
+    }
     pfList_.add (newPfs);
   }
-  if (Constants::DEBUG > 1) {
+  if (Constants::DEBUG >= 2) {
     cout << endl;
     Util::printAsteriskLine();
     cout << "SHATTERED AGAINST THE QUERY" << endl;

packages/CLPBN/clpbn/bp/Horus.h

@@ -16,15 +16,15 @@ class Factor;
 class VarNode;
 class FacNode;
 
-typedef vector<double>       Params;
+typedef vector<double>    Params;
-typedef unsigned             VarId;
+typedef unsigned          VarId;
-typedef vector<VarId>        VarIds;
+typedef vector<VarId>     VarIds;
-typedef vector<Var*>         Vars;
+typedef vector<Var*>      Vars;
-typedef vector<VarNode*>     VarNodes;
+typedef vector<VarNode*>  VarNodes;
-typedef vector<FacNode*>     FacNodes;
+typedef vector<FacNode*>  FacNodes;
-typedef vector<Factor*>      Factors;
+typedef vector<Factor*>   Factors;
-typedef vector<string>       States;
+typedef vector<string>    States;
-typedef vector<unsigned>     Ranges;
+typedef vector<unsigned>  Ranges;
 
 
 enum InfAlgorithms
@@ -47,7 +47,7 @@ extern InfAlgorithms infAlgorithm;
 namespace Constants {
 
 // level of debug information
-const unsigned DEBUG = 1;
+const unsigned DEBUG = 5;
 
 const int NO_EVIDENCE = -1;
 

packages/CLPBN/clpbn/bp/HorusYap.cpp

@@ -64,20 +64,17 @@ int createLiftedNetwork (void)
   }
 
   // LiftedUtils::printSymbolDictionary();
-  if (Constants::DEBUG > 1) {
+  if (Constants::DEBUG > 2) {
     // Util::printHeader ("INITIAL PARFACTORS");
     // for (unsigned i = 0; i < parfactors.size(); i++) {
     //  parfactors[i]->print();
-    //  cout << endl;
     // }
-    // parfactors[0]->countConvert (LogVar (0));
-    //parfactors[1]->fullExpand (LogVar (1));
-    Util::printHeader ("SHATTERED PARFACTORS");
   }
 
   ParfactorList* pfList = new ParfactorList (parfactors);
 
-  if (Constants::DEBUG > 1) {
+  if (Constants::DEBUG >= 2) {
+    Util::printHeader ("SHATTERED PARFACTORS");
     pfList->print();
   }
 
@@ -257,7 +254,8 @@ Params
 readParameters (YAP_Term paramL)
 {
   Params params;
-  while (paramL!= YAP_TermNil()) {
+  assert (YAP_IsPairTerm (paramL));
+  while (paramL != YAP_TermNil()) {
     params.push_back ((double) YAP_FloatOfTerm (YAP_HeadOfTerm (paramL)));
     paramL = YAP_TailOfTerm (paramL);
   }

packages/CLPBN/clpbn/bp/Parfactor.cpp

@@ -528,11 +528,13 @@ Parfactor::print (bool printParams) const
     cout << args_[i];
   }
   cout << endl;
-  vector<string> groups;
+  if (args_[0].group() != Util::maxUnsigned()) {
-  for (unsigned i = 0; i < args_.size(); i++) {
+    vector<string> groups;
-    groups.push_back (string ("g") + Util::toString (args_[i].group()));
+    for (unsigned i = 0; i < args_.size(); i++) {
+      groups.push_back (string ("g") + Util::toString (args_[i].group()));
+    }
+    cout << "Groups:    " << groups  << endl;
   }
-  cout << "Groups:    " << groups  << endl;
   cout << "LogVars:   " << constr_->logVarSet()  << endl;
   cout << "Ranges:    " << ranges_ << endl;
   if (printParams == false) {

packages/CLPBN/clpbn/bp/ParfactorList.cpp

@@ -116,7 +116,6 @@ ParfactorList::print (void) const
   list<Parfactor*>::const_iterator it;
   for (it = pfList_.begin(); it != pfList_.end(); ++it) {
     (*it)->print();
-    cout << endl;
   }
 }
 
@@ -219,7 +218,7 @@ ParfactorList::shatter (
   ProbFormula& f1 = g1->argument (fIdx1);
   ProbFormula& f2 = g2->argument (fIdx2);
   // cout << endl;
-  // Util::printDashLine();
+  // Util::printDashedLine();
   // cout << "-> SHATTERING (#" << g1 << ", #" << g2 << ")" << endl;
   // g1->print();
   // cout << "-> WITH" << endl;
@@ -228,7 +227,7 @@ ParfactorList::shatter (
   // cout << g1->constr()->tupleSet (f1.logVars()) << endl;
   // cout << "-> ON: " << f2 << "|" ;
   // cout << g2->constr()->tupleSet (f2.logVars()) << endl;
-  // Util::printDashLine();
+  // Util::printDashedLine();
   if (f1.isAtom()) {
     unsigned group = (f1.group() < f2.group()) ? f1.group() : f2.group();
     f1.setGroup (group);
@@ -265,18 +264,19 @@ ParfactorList::shatter (
   assert (commCt1->tupleSet (f1.arity()) == 
           commCt2->tupleSet (f2.arity()));
 
-  // stringstream ss1; ss1 << "" << count << "_A.dot" ;
+   // unsigned static count = 0; count ++;
-  // stringstream ss2; ss2 << "" << count << "_B.dot" ;
+   // stringstream ss1; ss1 << "" << count << "_A.dot" ;
-  // stringstream ss3; ss3 << "" << count << "_A_comm.dot" ;
+   // stringstream ss2; ss2 << "" << count << "_B.dot" ;
-  // stringstream ss4; ss4 << "" << count << "_A_excl.dot" ;
+   // stringstream ss3; ss3 << "" << count << "_A_comm.dot" ;
-  // stringstream ss5; ss5 << "" << count << "_B_comm.dot" ;
+   // stringstream ss4; ss4 << "" << count << "_A_excl.dot" ;
-  // stringstream ss6; ss6 << "" << count << "_B_excl.dot" ;
+   // stringstream ss5; ss5 << "" << count << "_B_comm.dot" ;
-  // ct1->exportToGraphViz     (ss1.str().c_str(), true);
+   // stringstream ss6; ss6 << "" << count << "_B_excl.dot" ;
-  // ct2->exportToGraphViz     (ss2.str().c_str(), true);
+   // g1->constr()->exportToGraphViz (ss1.str().c_str(), true);
-  // commCt1->exportToGraphViz (ss3.str().c_str(), true);
+   // g2->constr()->exportToGraphViz (ss2.str().c_str(), true);
-  // exclCt1->exportToGraphViz (ss4.str().c_str(), true);
+   // commCt1->exportToGraphViz (ss3.str().c_str(), true);
-  // commCt2->exportToGraphViz (ss5.str().c_str(), true);
+   // exclCt1->exportToGraphViz (ss4.str().c_str(), true);
-  // exclCt2->exportToGraphViz (ss6.str().c_str(), true);
+   // commCt2->exportToGraphViz (ss5.str().c_str(), true);
+   // exclCt2->exportToGraphViz (ss6.str().c_str(), true);
 
   if (exclCt1->empty() && exclCt2->empty()) {
     unsigned group = (f1.group() < f2.group())

packages/CLPBN/clpbn/bp/TODO

@@ -1,5 +1,4 @@
 TODO
-
+ - add a way to calculate combinations and factorials with large numbers
- - add way to calculate combinations and factorials with large numbers
  - refactor sumOut in parfactor -> is really ugly code
  - Indexer: start receiving ranges as constant reference

packages/CLPBN/clpbn/bp/Util.cpp

@@ -155,7 +155,8 @@ getStateLines (const Vars& vars)
 
 
 
-void printHeader (string header, std::ostream& os)
+void
+printHeader (string header, std::ostream& os)
 {
   printAsteriskLine (os);
   os << header << endl;
@@ -164,7 +165,8 @@ void printHeader (string header, std::ostream& os)
 
 
 
-void printSubHeader (string header, std::ostream& os)
+void
+printSubHeader (string header, std::ostream& os)
 {
   printDashedLine (os);
   os << header << endl;
@@ -173,7 +175,8 @@ void printSubHeader (string header, std::ostream& os)
 
 
 
-void printAsteriskLine (std::ostream& os)
+void
+printAsteriskLine (std::ostream& os)
 {
   os << "********************************" ;
   os << "********************************" ;
@@ -182,7 +185,8 @@ void printAsteriskLine (std::ostream& os)
 
 
 
-void printDashedLine (std::ostream& os)
+void
+printDashedLine (std::ostream& os)
 {
   os << "--------------------------------" ;
   os << "--------------------------------" ;
@@ -382,13 +386,13 @@ Statistics::writeStatistics (const char* fileName)
 
 void
 Statistics::updateCompressingStatistics (
-    unsigned nGroundVars,
+    unsigned nrGroundVars,
-    unsigned nGroundFactors,
+    unsigned nrGroundFactors,
-    unsigned nClusterVars, 
+    unsigned nrClusterVars, 
-    unsigned nClusterFactors,
+    unsigned nrClusterFactors,
-    unsigned nWithoutNeighs) {
+    unsigned nrNeighborless) {
-  compressInfo_.push_back (CompressInfo (nGroundVars, nGroundFactors,
+  compressInfo_.push_back (CompressInfo (nrGroundVars, nrGroundFactors,
-      nClusterVars, nClusterFactors, nWithoutNeighs));
+      nrClusterVars, nrClusterFactors, nrNeighborless));
 }
 
 
@@ -460,17 +464,17 @@ Statistics::getStatisticString (void)
     ss3 << "Ground   Cluster   Ground    Cluster   Neighborless" << endl;
     ss3 << "Vars     Vars      Factors   Factors   Vars"         << endl;
     for (unsigned i = 0; i < compressInfo_.size(); i++) {
-      ss3 << setw (9) << compressInfo_[i].nGroundVars;
+      ss3 << setw (9)  << compressInfo_[i].nrGroundVars;
-      ss3 << setw (10) << compressInfo_[i].nClusterVars;
+      ss3 << setw (10) << compressInfo_[i].nrClusterVars;
-      ss3 << setw (10) << compressInfo_[i].nGroundFactors;
+      ss3 << setw (10) << compressInfo_[i].nrGroundFactors;
-      ss3 << setw (10) << compressInfo_[i].nClusterFactors;
+      ss3 << setw (10) << compressInfo_[i].nrClusterFactors;
-      ss3 << setw (10) << compressInfo_[i].nWithoutNeighs;
+      ss3 << setw (10) << compressInfo_[i].nrNeighborless;
       ss3 << endl;
-      c1 += compressInfo_[i].nGroundVars - compressInfo_[i].nWithoutNeighs;
+      c1 += compressInfo_[i].nrGroundVars - compressInfo_[i].nrNeighborless;
-      c2 += compressInfo_[i].nClusterVars;
+      c2 += compressInfo_[i].nrClusterVars;
-      c3 += compressInfo_[i].nGroundFactors - compressInfo_[i].nWithoutNeighs;
+      c3 += compressInfo_[i].nrGroundFactors - compressInfo_[i].nrNeighborless;
-      c4 += compressInfo_[i].nClusterFactors;
+      c4 += compressInfo_[i].nrClusterFactors;
-      if (compressInfo_[i].nWithoutNeighs != 0) {
+      if (compressInfo_[i].nrNeighborless != 0) {
         c2 --;
         c4 --;
       } 

packages/CLPBN/clpbn/bp/Util.h

@@ -332,17 +332,17 @@ struct CompressInfo
 { 
   CompressInfo (unsigned a, unsigned b, unsigned c, unsigned d, unsigned e)
   {
-    nGroundVars     = a; 
+    nrGroundVars     = a; 
-    nGroundFactors  = b; 
+    nrGroundFactors  = b; 
-    nClusterVars    = c;
+    nrClusterVars    = c;
-    nClusterFactors = d;
+    nrClusterFactors = d;
-    nWithoutNeighs  = e;
+    nrNeighborless   = e;
   }
-  unsigned nGroundVars;
+  unsigned nrGroundVars;
-  unsigned nGroundFactors;
+  unsigned nrGroundFactors;
-  unsigned nClusterVars;
+  unsigned nrClusterVars;
-  unsigned nClusterFactors;
+  unsigned nrClusterFactors;
-  unsigned nWithoutNeighs;
+  unsigned nrNeighborless;
 };
 
 

packages/CLPBN/clpbn/bp/benchmarks/city/bp_tests.sh

@@ -1,10 +1,10 @@
 #!/bin/bash
 
-cp ~/bin/yap ~/bin/town_bnbp
+cp ~/bin/yap ~/bin/town_bp
-YAP=~/bin/town_bnbp
+YAP=~/bin/town_bp
 
 #OUT_FILE_NAME=results`date "+ %H:%M:%S %d-%m-%Y"`.log
-OUT_FILE_NAME=bnbp.log
+OUT_FILE_NAME=bp.log
 rm -f $OUT_FILE_NAME
 rm -f ignore.$OUT_FILE_NAME
 
@@ -38,13 +38,13 @@ function run_all_graphs
   echo "results for solver $2" >> $OUT_FILE_NAME
   echo "*******************************************************************" >> "$OUT_FILE_NAME"
   run_solver  town_1000     $1  town_1000     $3  $4  $5
-  run_solver  town_5000     $1  town_5000     $3  $4  $5
+  #run_solver  town_5000     $1  town_5000     $3  $4  $5
-  run_solver  town_10000    $1  town_10000    $3  $4  $5
+  #run_solver  town_10000    $1  town_10000    $3  $4  $5
-  run_solver  town_50000    $1  town_50000    $3  $4  $5
+  #run_solver  town_50000    $1  town_50000    $3  $4  $5
-  run_solver  town_100000   $1  town_100000   $3  $4  $5
+  #run_solver  town_100000   $1  town_100000   $3  $4  $5
-  run_solver  town_500000   $1  town_500000   $3  $4  $5
+  #run_solver  town_500000   $1  town_500000   $3  $4  $5
-  run_solver  town_1000000  $1  town_1000000  $3  $4  $5
+  #run_solver  town_1000000  $1  town_1000000  $3  $4  $5
 }
 
-run_all_graphs  bp     "bn_bp(seq_fixed)              "  bn_bp  seq_fixed
+run_all_graphs  bp     "bp(seq_fixed)       z          "  bp   seq_fixed
 

packages/CLPBN/clpbn/bp/benchmarks/city/city_generator.sh

@@ -0,0 +1,37 @@
+#!/home/tiago/bin/yap -L --
+
+
+:- initialization(main).
+
+
+main :-
+    unix(argv([H])),
+    generate_town(H).
+
+
+generate_town(N) :-
+    atomic_concat(['city_', N, '.yap'], FileName),
+    open(FileName, 'write', S),
+    atom_number(N, N2),
+    generate_people(S, N2, 4),
+    write(S, '\n'),
+    generate_query(S, N2, 4),
+    write(S, '\n'),
+    close(S).
+
+
+generate_people(S, N, Counting) :-
+    Counting > N, !.
+generate_people(S, N, Counting) :-
+    format(S, 'people(p~w, nyc).~n', [Counting]),
+    Counting1 is Counting + 1,
+    generate_people(S, N, Counting1).
+
+
+generate_query(S, N, Counting) :- 
+    Counting > N, !.
+generate_query(S, N, Counting) :- !,
+    format(S, 'ev(descn(p~w, t)).~n', [Counting]),
+    Counting1 is Counting + 1,
+    generate_query(S, N, Counting1).
+

packages/CLPBN/clpbn/bp/benchmarks/city/parschema.yap

@@ -1,21 +0,0 @@
-
-bayes conservative_city(C)::[y,n] ; cons_table(C) ; [city(C)].
-
-bayes gender(P)::[m,f] ; gender_table(P) ; [people(P,_)].
-
-bayes hair_color(P)::[t,f] , conservative_city(C) ; hair_color_table(P) ; [people(P,C)].
-
-bayes car_color(P)::[t,f] , hair_color(P) ; car_color_table(P); [people(P,_)].
-
-bayes height(P)::[t,f] , gender(P) ; height_table(P) ; [people(P,_)].
-
-bayes shoe_size(P):[t,f] , height(P) ; shoe_size_table(P); [people(P,_)].
-
-bayes guilty(P)::[y,n] ; guilty_table(P) ; [people(P,_)].
-
-bayes descn(P)::[t,f] , car_color(P), hair_color(P), height(P), guilty(P) ; descn_table(P) ; [people(P,_)].
-
-bayes witness(C)::[t,f] , descn(Joe) , descn(P2) ; wit_table ; [city(C), Joe=joe, P2=p2].
-
-:- ensure_loaded(tables).
-

packages/CLPBN/clpbn/bp/benchmarks/city/schema.yap

@@ -1,65 +0,0 @@
-
-conservative_city(City, Cons) :-
-	cons_table(City, ConsDist),
-	{ Cons = conservative_city(City) with p([y,n], ConsDist) }.
-
-
-gender(X, Gender) :-
-	gender_table(X, GenderDist),
-	{ Gender = gender(X) with p([m,f], GenderDist) }.
-
-
-hair_color(X, Color) :-
-	lives(X, City),
-	conservative_city(City, Cons),
-	hair_color_table(X,ColorTable),
-	{ Color = hair_color(X) with
-		p([t,f], ColorTable,[Cons]) }.
-
-
-car_color(X, Color) :-
-	hair_color(X, HColor),
-	car_color_table(X,CColorTable),
-	{ Color = car_color(X) with
-		p([t,f], CColorTable,[HColor]) }.
-
-
-height(X, Height) :-
-	gender(X, Gender),
-	height_table(X,HeightTable),
-	{ Height = height(X) with
-		p([t,f], HeightTable,[Gender]) }.
-
-
-shoe_size(X, Shoesize) :-
-	height(X, Height),
-	shoe_size_table(X,ShoesizeTable),
-	{ Shoesize = shoe_size(X) with
-		p([t,f], ShoesizeTable,[Height]) }.
-
-
-guilty(X, Guilt) :-
-	guilty_table(X, GuiltDist),
-	{ Guilt = guilty(X) with p([y,n], GuiltDist) }.
-
-
-descn(X, Descn) :-
-	car_color(X, Car),
-	hair_color(X, Hair),
-	height(X, Height),
-	guilty(X, Guilt),
-	descn_table(X, DescTable),
-	{ Descn = descn(X) with
-		p([t,f], DescTable,[Car,Hair,Height,Guilt]) }.
-
-
-witness(City, Witness) :-
-	descn(joe, DescnJ),
-	descn(p2, Descn2),
-	wit_table(WitTable),
-	{ Witness = witness(City) with
-		p([t,f], WitTable,[DescnJ, Descn2]) }.
-
-
-:- ensure_loaded(tables).
-

packages/CLPBN/clpbn/bp/benchmarks/city/tables.yap

@@ -1,46 +0,0 @@
-
-cons_table(amsterdam, [0.2, 0.8]) :- !.
-cons_table(_, [0.8, 0.2]).
-
-
-gender_table(_, [0.55, 0.44]).
-
-
-hair_color_table(_,
-     /* conservative_city */
-     /* y     n   */
-      [ 0.05, 0.1,
-        0.95, 0.9 ]).
-    
-
-car_color_table(_,
-     /* t    f */
-      [ 0.9, 0.2,
-        0.1, 0.8 ]).
-	
-
-height_table(_,
-     /* m    f */
-      [ 0.6, 0.4,
-        0.4, 0.6 ]).
-	
-
-shoe_size_table(_,
-     /* t    f */
-      [ 0.9, 0.1,
-        0.1, 0.9 ]).
-
-
-guilty_table(_, [0.23, 0.77]).
-
-
-descn_table(_,
-     /* color, hair, height, guilt */
-     /* ttttt  tttf  ttft  ttff  tfttt tftf  tfft  tfff  ttttt fttf  ftft  ftff  ffttt fftf  ffft  ffff */
-      [ 0.99,  0.5,  0.23, 0.88, 0.41, 0.3, 0.76, 0.87, 0.44, 0.43, 0.29, 0.72, 0.33, 0.91, 0.95, 0.92,
-        0.01,  0.5,  0.77, 0.12, 0.59, 0.7, 0.24, 0.13, 0.56, 0.57, 0.61, 0.28, 0.77, 0.09, 0.05, 0.08]).
-
-
-wit_table([0.2, 0.45, 0.24, 0.34,
-           0.8, 0.55, 0.76, 0.66]).
-

packages/CLPBN/clpbn/bp/benchmarks/city/town_10_new.yap

@@ -1,47 +0,0 @@
-:- source.
-:- style_check(all).
-:- yap_flag(unknown,error).
-:- yap_flag(write_strings,on).
-:- use_module(library(clpbn)).
-%:- set_clpbn_flag(solver, bp).
-
-:- set_clpbn_flag(solver,fove).
-
-:- [-parschema].
-
-run_query(Guilty) :- 
-    guilty(joe, Guilty),
-    witness(nyc, t).
-    %runall(X, ev(X)).
-
-
-runall(G, Wrapper) :-
-    findall(G, Wrapper, L),
-    execute_all(L).
-
-
-execute_all([]).
-execute_all(G.L) :-
-    call(G),
-    execute_all(L).
-
-
-%ev(descn(p2, t)).
-%ev(descn(p3, t)).
-
-
-city(nyc).
-city(oporto).
-
-people(joe,nyc).
-people(p2,nyc).
-people(p3,nyc).
-%people(p4,nyc).
-%people(p5,nyc).
-%people(p6,nyc).
-%people(p7,nyc).
-%people(p8,nyc).
-%people(p9,nyc).
-
-
-

packages/CLPBN/clpbn/bp/benchmarks/city/town_3.yap

@@ -1,29 +0,0 @@
-:- source.
-:- style_check(all).
-:- yap_flag(unknown,error).
-:- yap_flag(write_strings,on).
-:- use_module(library(clpbn)).
-:- set_clpbn_flag(solver, bp).
-:- [-schema].
-
-lives(_joe, nyc).
-
-run_query(Guilty) :- 
-	guilty(joe, Guilty),
-	witness(nyc, t),
-	runall(X, ev(X)).
-
-
-runall(G, Wrapper) :-
-	findall(G, Wrapper, L),
-	execute_all(L).
-
-
-execute_all([]).
-execute_all(G.L) :-
-	call(G),
-	execute_all(L).
-
-
-ev(descn(p2, t)).
-ev(descn(p3, t)).

packages/CLPBN/clpbn/bp/benchmarks/city/town_generator.sh

@@ -1,59 +0,0 @@
-#!/home/tiago/bin/yap -L --
-
-/* 
-Steps:
-1. generate N facts lives(I, nyc), 0 <= I < N.
-2. generate evidence on descn for N people, *** except for 1 ***
-3. Run query ?- guilty(joe, Guilty), witness(joe, t), descn(2,t), descn(3, f), descn(4, f) ...
-*/
-
-:- initialization(main).
-
-
-main :-
-	unix(argv([H])),
-	generate_town(H).
-
-
-generate_town(N) :-
-	atomic_concat(['town_', N, '.yap'], FileName),
-	open(FileName, 'write', S),
-	write(S, ':- source.\n'),
-	write(S, ':- style_check(all).\n'),
-	write(S, ':- yap_flag(unknown,error).\n'),
-	write(S, ':- yap_flag(write_strings,on).\n'),
-	write(S, ':- use_module(library(clpbn)).\n'),
-	write(S, ':- set_clpbn_flag(solver, bp).\n'),
-	write(S, ':- [-schema].\n\n'),
-	write(S, 'lives(_joe, nyc).\n'),
-    atom_number(N, N2),
-	generate_people(S, N2, 2),
-	write(S, '\nrun_query(Guilty) :- \n'),
-	write(S, '\tguilty(joe, Guilty),\n'),
-	write(S, '\twitness(nyc, t),\n'),
-	write(S, '\trunall(X, ev(X)).\n\n\n'),
-	write(S, 'runall(G, Wrapper) :-\n'),
-	write(S, '\tfindall(G, Wrapper, L),\n'),
-	write(S, '\texecute_all(L).\n\n\n'),
-	write(S, 'execute_all([]).\n'),
-	write(S, 'execute_all(G.L) :-\n'),
-	write(S, '\tcall(G),\n'),
-	write(S, '\texecute_all(L).\n\n\n'),
-	generate_query(S, N2, 2),
-	close(S).
-
-
-generate_people(_, N, Counting1) :- !.
-generate_people(S, N, Counting) :-
-	format(S, 'lives(p~w, nyc).~n', [Counting]),
-	Counting1 is Counting + 1,
-	generate_people(S, N, Counting1).
-
-
-generate_query(S, N, Counting) :- 
-	Counting > N, !.
-generate_query(S, N, Counting) :- !,
-	format(S, 'ev(descn(p~w, t)).~n', [Counting]),
-	Counting1 is Counting + 1,
-	generate_query(S, N, Counting1).
-

packages/CLPBN/clpbn/bp/examples/allopstest.yap

@@ -1,18 +0,0 @@
-
-:- use_module(library(pfl)).
-
-:- set_clpbn_flag(solver,fove).
-
-
-c(x1,y1,z1).
-c(x1,y1,z2).
-c(x2,y2,z1).
-c(x3,y2,z1).
-
-bayes p(X)::[t,f] ; [0.2, 0.4] ; [c(X,_,_)].
-
-bayes q(Y)::[t,f] ; [0.5, 0.6] ; [c(_,Y,_)].
-
-bayes s(Z)::[t,f] , p(X) , q(Y) ; [0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8] ; [c(X,Y,Z)].
-
-% bayes series::[t,f] , attends(X) ; [0.5, 0.6, 0.7, 0.8] ; [c(X,_)].

packages/CLPBN/clpbn/bp/examples/cbp_example.uai

@@ -1,3 +1,5 @@
+# example in counting belief propagation paper
+
 MARKOV
 3
 2 2 2
@@ -5,7 +7,6 @@ MARKOV
 2 0 1
 2 2 1
 
-
 4
   1.2 1.4 2.0 0.4
 

packages/CLPBN/clpbn/bp/examples/city.yap

@@ -0,0 +1,98 @@
+:- use_module(library(pfl)).
+
+:- set_pfl_flag(solver,fove).
+%:- set_pfl_flag(solver,bp), clpbn_horus:set_horus_flag(inf_alg,ve).
+%:- set_pfl_flag(solver,bp), clpbn_horus:set_horus_flag(inf_alg,bp).
+%:- set_pfl_flag(solver,bp), clpbn_horus:set_horus_flag(inf_alg,cbp).
+
+
+people(joe,nyc).
+people(p2, nyc).
+people(p3, nyc).
+
+
+ev(descn(p2, t)).
+ev(descn(p3, t)).
+
+
+:- [city_7].
+
+
+bayes city_conservativeness(C)::[y,n] ; cons_table(C) ; [people(_,C)].
+
+bayes gender(P)::[m,f] ; gender_table(P) ; [people(P,_)].
+
+bayes hair_color(P)::[t,f] , city_conservativeness(C) ; hair_color_table(P) ; [people(P,C)].
+
+bayes car_color(P)::[t,f] , hair_color(P) ; car_color_table(P); [people(P,_)].
+
+bayes height(P)::[t,f] , gender(P) ; height_table(P) ; [people(P,_)].
+
+bayes shoe_size(P):[t,f] , height(P) ; shoe_size_table(P); [people(P,_)].
+
+bayes guilty(P)::[y,n] ; guilty_table(P) ; [people(P,_)].
+
+bayes descn(P)::[t,f] , car_color(P), hair_color(P), height(P), guilty(P) ; descn_table(P) ; [people(P,_)].
+
+bayes witness(C)::[t,f] , descn(Joe) , descn(P2) ; wit_table ; [people(_,C), Joe=joe, P2=p2].
+
+
+cons_table(amsterdam, [0.2, 0.8]) :- !.
+cons_table(_, [0.8, 0.2]).
+
+
+gender_table(_, [0.55, 0.44]).
+
+
+hair_color_table(_,
+     /* conservative_city */
+     /* y     n   */
+      [ 0.05, 0.1,
+        0.95, 0.9 ]).
+    
+
+car_color_table(_,
+     /* t    f */
+      [ 0.9, 0.2,
+        0.1, 0.8 ]).
+	
+
+height_table(_,
+     /* m    f */
+      [ 0.6, 0.4,
+        0.4, 0.6 ]).
+	
+
+shoe_size_table(_,
+     /* t    f */
+      [ 0.9, 0.1,
+        0.1, 0.9 ]).
+
+
+guilty_table(_, [0.23, 0.77]).
+
+
+descn_table(_,
+     /* color, hair, height, guilt */
+     /* ttttt  tttf  ttft  ttff  tfttt tftf  tfft  tfff  ttttt fttf  ftft  ftff  ffttt fftf  ffft  ffff */
+      [ 0.99,  0.5,  0.23, 0.88, 0.41, 0.3, 0.76, 0.87, 0.44, 0.43, 0.29, 0.72, 0.33, 0.91, 0.95, 0.92,
+        0.01,  0.5,  0.77, 0.12, 0.59, 0.7, 0.24, 0.13, 0.56, 0.57, 0.61, 0.28, 0.77, 0.09, 0.05, 0.08]).
+
+
+wit_table([0.2, 0.45, 0.24, 0.34,
+           0.8, 0.55, 0.76, 0.66]).
+
+
+runall(G, Wrapper) :-
+	findall(G, Wrapper, L),
+	execute_all(L).
+
+
+execute_all([]).
+execute_all(G.L) :-
+	call(G),
+	execute_all(L).
+
+
+?- witness(nyc, t), runall(X, ev(X)), guilty(joe, Guilty).
+

packages/CLPBN/clpbn/bp/examples/comp_workshops.yap

@@ -1,9 +1,9 @@
-
 :- use_module(library(pfl)).
 
-%:- set_clpbn_flag(solver,ve).
+:- set_pfl_flag(solver,fove).
-%:- set_clpbn_flag(solver,bp), clpbn_bp:set_horus_flag(inf_alg,ve).
+%:- set_pfl_flag(solver,bp), clpbn_horus:set_horus_flag(inf_alg,ve).
-:- set_clpbn_flag(solver,fove).
+%:- set_pfl_flag(solver,bp), clpbn_horus:set_horus_flag(inf_alg,bp).
+%:- set_pfl_flag(solver,bp), clpbn_horus:set_horus_flag(inf_alg,cbp).
 
 c(p1,w1).
 c(p1,w2).
@@ -25,8 +25,5 @@ markov attends(P)::[t,f] , hot(W)::[t,f] ; [0.1, 0.2, 0.3, 0.4] ; [c(P,W)].
 
 markov attends(P)::[t,f], series::[t,f] ; [0.5, 0.6, 0.7, 0.8] ; [c(P,_)].
 
-:- clpbn_horus:set_horus_flag(use_logarithms,true).
-
 ?- series(X).
 
-

packages/CLPBN/clpbn/bp/examples/fail.yap

@@ -2,7 +2,9 @@
 :- use_module(library(pfl)).
 
 :- set_pfl_flag(solver,fove).
-%:- set_pfl_flag(solver,fove).
+%:- set_pfl_flag(solver,bp), clpbn_horus:set_horus_flag(inf_alg,ve).
+%:- set_pfl_flag(solver,bp), clpbn_horus:set_horus_flag(inf_alg,bp).
+%:- set_pfl_flag(solver,bp), clpbn_horus:set_horus_flag(inf_alg,cbp).
 
 
 t(ann).
@@ -10,10 +12,10 @@ t(dave).
 
 % p(ann,t).
 
-bayes p(X)::[t,f] ; [0.1, 0.3] ; [t(X)].
+markov p(X)::[t,f] ; [0.1, 0.3] ; [t(X)].
 
 % use standard Prolog queries: provide evidence first.
 
-?- p(dave,t), p(ann,X).
+?- p(ann,t), p(ann,X).
 % ?- p(ann,X).
 

packages/CLPBN/clpbn/bp/examples/smokers.yap

@@ -1,39 +1,23 @@
-
 :- use_module(library(pfl)).
 
-%:- set_pfl_flag(solver,ve).
+:- set_pfl_flag(solver,fove).
-:- set_pfl_flag(solver,bp), clpbn_horus:set_horus_flag(inf_alg,ve).
+%:- set_pfl_flag(solver,bp), clpbn_horus:set_horus_flag(inf_alg,ve).
-% :- set_pfl_flag(solver,fove).
+%:- set_pfl_flag(solver,bp), clpbn_horus:set_horus_flag(inf_alg,bp).
+%:- set_pfl_flag(solver,bp), clpbn_horus:set_horus_flag(inf_alg,cbp).
 
 :- yap_flag(write_strings, off).
 
+
 friends(P1, P2) :-
-	person(P1),
+    person(P1),
-	person(P2),
+    person(P2),
-	P1 \= P2.
+    P1 \= P2.
 
-person(john).
+person @ 3.
-person(maggie).
-%person(harry).
-%person(bill).
-%person(matt).
-%person(diana).
-%person(bob).
-%person(dick).
-%person(burr).
-%person(ann).
-
-% person @ 2.
 
 markov smokes(P)::[t,f] , cancer(P)::[t,f] ; [0.1, 0.2, 0.3, 0.4] ; [person(P)].
 
 markov friend(P1,P2)::[t,f], smokes(P1)::[t,f], smokes(P2)::[t,f] ; [0.5, 0.6, 0.7, 0.8, 0.5, 0.6, 0.7, 0.8] ; [friends(P1, P2)].
 
-% ?- smokes(person_0, t), smokes(person_1, t), friend(person_0, person_1, F).
+?- smokes(person_1, t), smokes(person_2, f), friend(person_1, person_2, X).
-
-% ?- smokes(john, t), smokes(maggie, f), friend(john, maggie, X).
-
-?- smokes(john, t), friend(john, maggie, X).
-
-% ?- friend(john, maggie, X).
 

packages/CLPBN/clpbn/bp/examples/smokers_2.fg

@@ -1,120 +0,0 @@
-14
-
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-2 
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-1 1.000000
-
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-
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-

packages/CLPBN/clpbn/bp/examples/smokers_3.fg

@@ -1,239 +0,0 @@
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-

packages/CLPBN/clpbn/bp/examples/smokers_4.fg

@@ -1,398 +0,0 @@
-44
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packages/CLPBN/clpbn/bp/examples/workshop_attrs.yap

@@ -1,9 +1,9 @@
-
 :- use_module(library(pfl)).
 
-%:- set_clpbn_flag(solver,ve).
+:- set_pfl_flag(solver,fove).
-%:- set_clpbn_flag(solver,bp), clpbn_bp:set_horus_flag(inf_alg,ve).
+%:- set_pfl_flag(solver,bp), clpbn_horus:set_horus_flag(inf_alg,ve).
-:- set_clpbn_flag(solver,fove).
+%:- set_pfl_flag(solver,bp), clpbn_horus:set_horus_flag(inf_alg,bp).
+%:- set_pfl_flag(solver,bp), clpbn_horus:set_horus_flag(inf_alg,cbp).
 
 c(p1).
 c(p2).
@@ -26,7 +26,5 @@ markov attends(P)::[t,f] , attr6::[t,f] ; [0.1, 0.2, 0.3, 0.4] ; [c(P)].
 
 markov attends(P)::[t,f], series::[t,f] ; [0.5, 0.6, 0.7, 0.8] ; [c(P)].
 
-%:- clpbn_horus:set_horus_flag(use_logarithms,true).
-
 ?- series(X).
 

packages/CLPBN/clpbn/fove.yap

@@ -50,7 +50,7 @@ init_fove_solver(_, AllAttVars, _, fove(ParfactorList, DistIds)) :-
   get_dist_ids(Parfactors, DistIds0),
   sort(DistIds0, DistIds),
   get_observed_vars(AllAttVars, ObservedVars),
-  writeln(factors:Parfactors:'\n'),
+  writeln(parfactors:Parfactors:'\n'),
   writeln(evidence:ObservedVars:'\n'),
   create_lifted_network(Parfactors,ObservedVars,ParfactorList).
 
@@ -139,11 +139,11 @@ get_dists_parameters([Id|Ids], [dist(Id, Params)|DistsInfo]) :-
 
 
 run_fove_solver(QueryVarsAtts, Solutions, fove(ParfactorList, DistIds)) :-
-  get_dists_parameters(DistIds, DistsParams),
-  writeln(distParams:DistsParams),
-  set_parfactors_params(ParfactorList, DistsParams),
   get_query_vars(QueryVarsAtts, QueryVars),
   writeln(queryVars:QueryVars), writeln(''),
+  get_dists_parameters(DistIds, DistsParams),
+  writeln(dists:DistsParams), writeln(''),
+  set_parfactors_params(ParfactorList, DistsParams),
   run_lifted_solver(ParfactorList, QueryVars, Solutions).
 
 

packages/CLPBN/clpbn/horus.yap

@@ -28,10 +28,8 @@ warning :-
 :- catch(load_foreign_files([horus], [], init_predicates), _, patch_things_up) -> true ; warning.
 
 
-
+:- set_horus_flag(inf_alg, ve).
-%:- set_horus_flag(inf_alg, ve).
+%:- set_horus_flag(inf_alg, bp).
-:- set_horus_flag(inf_alg, bn_bp).
-%:- set_horus_flag(inf_alg, fg_bp).
 %: -set_horus_flag(inf_alg, cbp).
 
 :- set_horus_flag(schedule, seq_fixed).

packages/CLPBN/pfl.yap

@@ -145,7 +145,7 @@ add_evidence(Sk,Var) :-
 
 get_pfl_parameters(Id,Out) :-
 	factor(_Type,Id,_FList,_FV,Phi,_Constraints),
-	writeln(factor(_Type,Id,_FList,_FV,_Phi,_Constraints)),
+	%writeln(factor(_Type,Id,_FList,_FV,_Phi,_Constraints)),
 	( is_list(Phi) -> Out = Phi ; call(user:Phi, Out) ).