diff --git a/packages/CLPBN/clpbn/bp/BayesBall.cpp b/packages/CLPBN/clpbn/bp/BayesBall.cpp index d39679ea0..820c215fc 100644 --- a/packages/CLPBN/clpbn/bp/BayesBall.cpp +++ b/packages/CLPBN/clpbn/bp/BayesBall.cpp @@ -60,7 +60,7 @@ BayesBall::getMinimalFactorGraph (const VarIds& queryIds) void BayesBall::constructGraph (FactorGraph* fg) const { - const FgFacSet& facNodes = fg_.getFactorNodes(); + const FactorNodes& facNodes = fg_.factorNodes(); for (unsigned i = 0; i < facNodes.size(); i++) { const DAGraphNode* n = dag_.getNode ( facNodes[i]->factor()->argument (0)); diff --git a/packages/CLPBN/clpbn/bp/BayesBall.h b/packages/CLPBN/clpbn/bp/BayesBall.h index 3d4a36b61..42032410b 100644 --- a/packages/CLPBN/clpbn/bp/BayesBall.h +++ b/packages/CLPBN/clpbn/bp/BayesBall.h @@ -6,11 +6,9 @@ #include #include -#include "GraphicalModel.h" -#include "Horus.h" - #include "FactorGraph.h" #include "BayesNet.h" +#include "Horus.h" using namespace std; diff --git a/packages/CLPBN/clpbn/bp/BayesNet.h b/packages/CLPBN/clpbn/bp/BayesNet.h index eb78d4179..d3e96e450 100644 --- a/packages/CLPBN/clpbn/bp/BayesNet.h +++ b/packages/CLPBN/clpbn/bp/BayesNet.h @@ -6,19 +6,19 @@ #include #include -#include "GraphicalModel.h" +#include "Var.h" #include "Horus.h" using namespace std; -class VarNode; +class Var; -class DAGraphNode : public VarNode +class DAGraphNode : public Var { public: - DAGraphNode (VarNode* vn) : VarNode (vn) , visited_(false), + DAGraphNode (Var* v) : Var (v) , visited_(false), markedOnTop_(false), markedOnBottom_(false) { } const vector& childs (void) const { return childs_; } diff --git a/packages/CLPBN/clpbn/bp/CFactorGraph.cpp b/packages/CLPBN/clpbn/bp/CFactorGraph.cpp index c1fec9625..b28f13427 100644 --- a/packages/CLPBN/clpbn/bp/CFactorGraph.cpp +++ b/packages/CLPBN/clpbn/bp/CFactorGraph.cpp @@ -10,14 +10,14 @@ CFactorGraph::CFactorGraph (const FactorGraph& fg) groundFg_ = &fg; freeColor_ = 0; - const FgVarSet& varNodes = fg.getVarNodes(); + const VarNodes& varNodes = fg.varNodes(); varSignatures_.reserve (varNodes.size()); for (unsigned i = 0; i < varNodes.size(); i++) { unsigned c = (varNodes[i]->neighbors().size() * 2) + 1; varSignatures_.push_back (Signature (c)); } - const FgFacSet& facNodes = fg.getFactorNodes(); + const FactorNodes& facNodes = fg.factorNodes(); factorSignatures_.reserve (facNodes.size()); for (unsigned i = 0; i < facNodes.size(); i++) { unsigned c = facNodes[i]->neighbors().size() + 1; @@ -49,7 +49,7 @@ CFactorGraph::setInitialColors (void) { // create the initial variable colors VarColorMap colorMap; - const FgVarSet& varNodes = groundFg_->getVarNodes(); + const VarNodes& varNodes = groundFg_->varNodes(); for (unsigned i = 0; i < varNodes.size(); i++) { unsigned dsize = varNodes[i]->range(); VarColorMap::iterator it = colorMap.find (dsize); @@ -70,7 +70,7 @@ CFactorGraph::setInitialColors (void) setColor (varNodes[i], stateColors[idx]); } - const FgFacSet& facNodes = groundFg_->getFactorNodes(); + const FactorNodes& facNodes = groundFg_->factorNodes(); if (checkForIdenticalFactors) { unsigned groupCount = 1; for (unsigned i = 0; i < facNodes.size(); i++) { @@ -114,8 +114,8 @@ CFactorGraph::createGroups (void) FacSignMap factorGroups; unsigned nIters = 0; bool groupsHaveChanged = true; - const FgVarSet& varNodes = groundFg_->getVarNodes(); - const FgFacSet& facNodes = groundFg_->getFactorNodes(); + const VarNodes& varNodes = groundFg_->varNodes(); + const FactorNodes& facNodes = groundFg_->factorNodes(); while (groupsHaveChanged || nIters == 1) { nIters ++; @@ -127,14 +127,14 @@ CFactorGraph::createGroups (void) const Signature& signature = getSignature (facNodes[i]); FacSignMap::iterator it = factorGroups.find (signature); if (it == factorGroups.end()) { - it = factorGroups.insert (make_pair (signature, FgFacSet())).first; + it = factorGroups.insert (make_pair (signature, FactorNodes())).first; } it->second.push_back (facNodes[i]); } for (FacSignMap::iterator it = factorGroups.begin(); it != factorGroups.end(); it++) { Color newColor = getFreeColor(); - FgFacSet& groupMembers = it->second; + FactorNodes& groupMembers = it->second; for (unsigned i = 0; i < groupMembers.size(); i++) { setColor (groupMembers[i], newColor); } @@ -147,14 +147,14 @@ CFactorGraph::createGroups (void) const Signature& signature = getSignature (varNodes[i]); VarSignMap::iterator it = varGroups.find (signature); if (it == varGroups.end()) { - it = varGroups.insert (make_pair (signature, FgVarSet())).first; + it = varGroups.insert (make_pair (signature, VarNodes())).first; } it->second.push_back (varNodes[i]); } for (VarSignMap::iterator it = varGroups.begin(); it != varGroups.end(); it++) { Color newColor = getFreeColor(); - FgVarSet& groupMembers = it->second; + VarNodes& groupMembers = it->second; for (unsigned i = 0; i < groupMembers.size(); i++) { setColor (groupMembers[i], newColor); } @@ -177,7 +177,7 @@ CFactorGraph::createClusters ( varClusters_.reserve (varGroups.size()); for (VarSignMap::const_iterator it = varGroups.begin(); it != varGroups.end(); it++) { - const FgVarSet& groupVars = it->second; + const VarNodes& groupVars = it->second; VarCluster* vc = new VarCluster (groupVars); for (unsigned i = 0; i < groupVars.size(); i++) { vid2VarCluster_.insert (make_pair (groupVars[i]->varId(), vc)); @@ -188,8 +188,8 @@ CFactorGraph::createClusters ( facClusters_.reserve (factorGroups.size()); for (FacSignMap::const_iterator it = factorGroups.begin(); it != factorGroups.end(); it++) { - FgFacNode* groupFactor = it->second[0]; - const FgVarSet& neighs = groupFactor->neighbors(); + FactorNode* groupFactor = it->second[0]; + const VarNodes& neighs = groupFactor->neighbors(); VarClusterSet varClusters; varClusters.reserve (neighs.size()); for (unsigned i = 0; i < neighs.size(); i++) { @@ -203,11 +203,11 @@ CFactorGraph::createClusters ( const Signature& -CFactorGraph::getSignature (const FgVarNode* varNode) +CFactorGraph::getSignature (const VarNode* varNode) { Signature& sign = varSignatures_[varNode->getIndex()]; vector::iterator it = sign.colors.begin(); - const FgFacSet& neighs = varNode->neighbors(); + const FactorNodes& neighs = varNode->neighbors(); for (unsigned i = 0; i < neighs.size(); i++) { *it = getColor (neighs[i]); it ++; @@ -221,11 +221,11 @@ CFactorGraph::getSignature (const FgVarNode* varNode) const Signature& -CFactorGraph::getSignature (const FgFacNode* facNode) +CFactorGraph::getSignature (const FactorNode* facNode) { Signature& sign = factorSignatures_[facNode->getIndex()]; vector::iterator it = sign.colors.begin(); - const FgVarSet& neighs = facNode->neighbors(); + const VarNodes& neighs = facNode->neighbors(); for (unsigned i = 0; i < neighs.size(); i++) { *it = getColor (neighs[i]); it ++; @@ -241,27 +241,27 @@ CFactorGraph::getCompressedFactorGraph (void) { FactorGraph* fg = new FactorGraph(); for (unsigned i = 0; i < varClusters_.size(); i++) { - FgVarNode* var = varClusters_[i]->getGroundFgVarNodes()[0]; - FgVarNode* newVar = new FgVarNode (var); + VarNode* var = varClusters_[i]->getGroundVarNodes()[0]; + VarNode* newVar = new VarNode (var); varClusters_[i]->setRepresentativeVariable (newVar); fg->addVariable (newVar); } for (unsigned i = 0; i < facClusters_.size(); i++) { const VarClusterSet& myVarClusters = facClusters_[i]->getVarClusters(); - VarNodes myGroundVars; + Vars myGroundVars; myGroundVars.reserve (myVarClusters.size()); for (unsigned j = 0; j < myVarClusters.size(); j++) { - FgVarNode* v = myVarClusters[j]->getRepresentativeVariable(); + VarNode* v = myVarClusters[j]->getRepresentativeVariable(); myGroundVars.push_back (v); } Factor* newFactor = new Factor (myGroundVars, facClusters_[i]->getGroundFactors()[0]->params()); - FgFacNode* fn = new FgFacNode (newFactor); + FactorNode* fn = new FactorNode (newFactor); facClusters_[i]->setRepresentativeFactor (fn); fg->addFactor (fn); for (unsigned j = 0; j < myGroundVars.size(); j++) { - fg->addEdge (fn, static_cast (myGroundVars[j])); + fg->addEdge (fn, static_cast (myGroundVars[j])); } } fg->setIndexes(); @@ -275,17 +275,17 @@ CFactorGraph::getGroundEdgeCount ( const FacCluster* fc, const VarCluster* vc) const { - const FgFacSet& clusterGroundFactors = fc->getGroundFactors(); - FgVarNode* varNode = vc->getGroundFgVarNodes()[0]; + const FactorNodes& clusterGroundFactors = fc->getGroundFactors(); + VarNode* varNode = vc->getGroundVarNodes()[0]; unsigned count = 0; for (unsigned i = 0; i < clusterGroundFactors.size(); i++) { if (clusterGroundFactors[i]->factor()->indexOf (varNode->varId()) != -1) { count ++; } } - // CFgVarSet vars = vc->getGroundFgVarNodes(); + // CVarNodes vars = vc->getGroundVarNodes(); // for (unsigned i = 1; i < vars.size(); i++) { - // FgVarNode* var = vc->getGroundFgVarNodes()[i]; + // VarNode* var = vc->getGroundVarNodes()[i]; // unsigned count2 = 0; // for (unsigned i = 0; i < clusterGroundFactors.size(); i++) { // if (clusterGroundFactors[i]->getPosition (var) != -1) { @@ -308,7 +308,7 @@ CFactorGraph::printGroups ( cout << "variable groups:" << endl; for (VarSignMap::const_iterator it = varGroups.begin(); it != varGroups.end(); it++) { - const FgVarSet& groupMembers = it->second; + const VarNodes& groupMembers = it->second; if (groupMembers.size() > 0) { cout << count << ": " ; for (unsigned i = 0; i < groupMembers.size(); i++) { @@ -323,7 +323,7 @@ CFactorGraph::printGroups ( cout << endl << "factor groups:" << endl; for (FacSignMap::const_iterator it = factorGroups.begin(); it != factorGroups.end(); it++) { - const FgFacSet& groupMembers = it->second; + const FactorNodes& groupMembers = it->second; if (groupMembers.size() > 0) { cout << ++count << ": " ; for (unsigned i = 0; i < groupMembers.size(); i++) { diff --git a/packages/CLPBN/clpbn/bp/CFactorGraph.h b/packages/CLPBN/clpbn/bp/CFactorGraph.h index 426f13ff3..a46714c37 100644 --- a/packages/CLPBN/clpbn/bp/CFactorGraph.h +++ b/packages/CLPBN/clpbn/bp/CFactorGraph.h @@ -25,8 +25,8 @@ typedef unordered_map VarId2VarCluster; typedef vector VarClusterSet; typedef vector FacClusterSet; -typedef unordered_map VarSignMap; -typedef unordered_map FacSignMap; +typedef unordered_map VarSignMap; +typedef unordered_map FacSignMap; @@ -87,7 +87,7 @@ struct SignatureHash class VarCluster { public: - VarCluster (const FgVarSet& vs) + VarCluster (const VarNodes& vs) { for (unsigned i = 0; i < vs.size(); i++) { groundVars_.push_back (vs[i]); @@ -104,21 +104,21 @@ class VarCluster return facClusters_; } - FgVarNode* getRepresentativeVariable (void) const { return representVar_; } - void setRepresentativeVariable (FgVarNode* v) { representVar_ = v; } - const FgVarSet& getGroundFgVarNodes (void) const { return groundVars_; } + VarNode* getRepresentativeVariable (void) const { return representVar_; } + void setRepresentativeVariable (VarNode* v) { representVar_ = v; } + const VarNodes& getGroundVarNodes (void) const { return groundVars_; } private: - FgVarSet groundVars_; + VarNodes groundVars_; FacClusterSet facClusters_; - FgVarNode* representVar_; + VarNode* representVar_; }; class FacCluster { public: - FacCluster (const FgFacSet& groundFactors, const VarClusterSet& vcs) + FacCluster (const FactorNodes& groundFactors, const VarClusterSet& vcs) { groundFactors_ = groundFactors; varClusters_ = vcs; @@ -132,7 +132,7 @@ class FacCluster return varClusters_; } - bool containsGround (const FgFacNode* fn) + bool containsGround (const FactorNode* fn) { for (unsigned i = 0; i < groundFactors_.size(); i++) { if (groundFactors_[i] == fn) { @@ -142,26 +142,26 @@ class FacCluster return false; } - FgFacNode* getRepresentativeFactor (void) const + FactorNode* getRepresentativeFactor (void) const { return representFactor_; } - void setRepresentativeFactor (FgFacNode* fn) + void setRepresentativeFactor (FactorNode* fn) { representFactor_ = fn; } - const FgFacSet& getGroundFactors (void) const + const FactorNodes& getGroundFactors (void) const { return groundFactors_; } private: - FgFacSet groundFactors_; + FactorNodes groundFactors_; VarClusterSet varClusters_; - FgFacNode* representFactor_; + FactorNode* representFactor_; }; @@ -176,7 +176,7 @@ class CFactorGraph const FacClusterSet& getFacClusters (void) { return facClusters_; } - FgVarNode* getEquivalentVariable (VarId vid) + VarNode* getEquivalentVariable (VarId vid) { VarCluster* vc = vid2VarCluster_.find (vid)->second; return vc->getRepresentativeVariable(); @@ -195,20 +195,20 @@ class CFactorGraph return freeColor_ - 1; } - Color getColor (const FgVarNode* vn) const + Color getColor (const VarNode* vn) const { return varColors_[vn->getIndex()]; } - Color getColor (const FgFacNode* fn) const { + Color getColor (const FactorNode* fn) const { return factorColors_[fn->getIndex()]; } - void setColor (const FgVarNode* vn, Color c) + void setColor (const VarNode* vn, Color c) { varColors_[vn->getIndex()] = c; } - void setColor (const FgFacNode* fn, Color c) + void setColor (const FactorNode* fn, Color c) { factorColors_[fn->getIndex()] = c; } @@ -224,9 +224,9 @@ class CFactorGraph void createClusters (const VarSignMap&, const FacSignMap&); - const Signature& getSignature (const FgVarNode*); + const Signature& getSignature (const VarNode*); - const Signature& getSignature (const FgFacNode*); + const Signature& getSignature (const FactorNode*); void printGroups (const VarSignMap&, const FacSignMap&) const; diff --git a/packages/CLPBN/clpbn/bp/CbpSolver.cpp b/packages/CLPBN/clpbn/bp/CbpSolver.cpp index 3b8ecb787..b342d24c4 100644 --- a/packages/CLPBN/clpbn/bp/CbpSolver.cpp +++ b/packages/CLPBN/clpbn/bp/CbpSolver.cpp @@ -17,7 +17,7 @@ Params CbpSolver::getPosterioriOf (VarId vid) { assert (lfg_->getEquivalentVariable (vid)); - FgVarNode* var = lfg_->getEquivalentVariable (vid); + VarNode* var = lfg_->getEquivalentVariable (vid); Params probs; if (var->hasEvidence()) { probs.resize (var->range(), LogAware::noEvidence()); @@ -52,7 +52,7 @@ CbpSolver::getJointDistributionOf (const VarIds& jointVarIds) for (unsigned i = 0; i < jointVarIds.size(); i++) { eqVarIds.push_back (lfg_->getEquivalentVariable (jointVarIds[i])->varId()); } - return FgBpSolver::getJointDistributionOf (eqVarIds); + return BpSolver::getJointDistributionOf (eqVarIds); } @@ -63,12 +63,12 @@ CbpSolver::initializeSolver (void) { unsigned nGroundVars, nGroundFacs, nWithoutNeighs; if (Constants::COLLECT_STATS) { - nGroundVars = factorGraph_->getVarNodes().size(); - nGroundFacs = factorGraph_->getFactorNodes().size(); - const FgVarSet& vars = factorGraph_->getVarNodes(); + nGroundVars = factorGraph_->varNodes().size(); + nGroundFacs = factorGraph_->factorNodes().size(); + const VarNodes& vars = factorGraph_->varNodes(); nWithoutNeighs = 0; for (unsigned i = 0; i < vars.size(); i++) { - const FgFacSet& factors = vars[i]->neighbors(); + const FactorNodes& factors = vars[i]->neighbors(); if (factors.size() == 1 && factors[0]->neighbors().size() == 1) { nWithoutNeighs ++; } @@ -78,23 +78,23 @@ CbpSolver::initializeSolver (void) lfg_ = new CFactorGraph (*factorGraph_); // cout << "Uncompressed Factor Graph" << endl; - // factorGraph_->printGraphicalModel(); + // factorGraph_->print(); // factorGraph_->exportToGraphViz ("uncompressed_fg.dot"); factorGraph_ = lfg_->getCompressedFactorGraph(); if (Constants::COLLECT_STATS) { - unsigned nClusterVars = factorGraph_->getVarNodes().size(); - unsigned nClusterFacs = factorGraph_->getFactorNodes().size(); + unsigned nClusterVars = factorGraph_->varNodes().size(); + unsigned nClusterFacs = factorGraph_->factorNodes().size(); Statistics::updateCompressingStatistics (nGroundVars, nGroundFacs, nClusterVars, nClusterFacs, nWithoutNeighs); } // cout << "Compressed Factor Graph" << endl; - // factorGraph_->printGraphicalModel(); + // factorGraph_->print(); // factorGraph_->exportToGraphViz ("compressed_fg.dot"); // abort(); - FgBpSolver::initializeSolver(); + BpSolver::initializeSolver(); } @@ -154,7 +154,7 @@ CbpSolver::maxResidualSchedule (void) linkMap_.find (link)->second = sortedOrder_.insert (link); // update the messages that depend on message source --> destin - const FgFacSet& factorNeighbors = link->getVariable()->neighbors(); + const FactorNodes& factorNeighbors = link->getVariable()->neighbors(); for (unsigned i = 0; i < factorNeighbors.size(); i++) { const SpLinkSet& links = ninf(factorNeighbors[i])->getLinks(); for (unsigned j = 0; j < links.size(); j++) { @@ -192,8 +192,8 @@ Params CbpSolver::getVar2FactorMsg (const SpLink* link) const { Params msg; - const FgVarNode* src = link->getVariable(); - const FgFacNode* dst = link->getFactor(); + const VarNode* src = link->getVariable(); + const FactorNode* dst = link->getFactor(); const CbpSolverLink* l = static_cast (link); if (src->hasEvidence()) { msg.resize (src->range(), LogAware::noEvidence()); diff --git a/packages/CLPBN/clpbn/bp/CbpSolver.h b/packages/CLPBN/clpbn/bp/CbpSolver.h index d57e7e149..bed535bd9 100644 --- a/packages/CLPBN/clpbn/bp/CbpSolver.h +++ b/packages/CLPBN/clpbn/bp/CbpSolver.h @@ -1,7 +1,7 @@ #ifndef HORUS_CBP_H #define HORUS_CBP_H -#include "FgBpSolver.h" +#include "BpSolver.h" #include "CFactorGraph.h" class Factor; @@ -9,7 +9,7 @@ class Factor; class CbpSolverLink : public SpLink { public: - CbpSolverLink (FgFacNode* fn, FgVarNode* vn, unsigned c) : SpLink (fn, vn) + CbpSolverLink (FactorNode* fn, VarNode* vn, unsigned c) : SpLink (fn, vn) { edgeCount_ = c; poweredMsg_.resize (vn->range(), LogAware::one()); @@ -34,10 +34,10 @@ class CbpSolverLink : public SpLink -class CbpSolver : public FgBpSolver +class CbpSolver : public BpSolver { public: - CbpSolver (FactorGraph& fg) : FgBpSolver (fg) { } + CbpSolver (FactorGraph& fg) : BpSolver (fg) { } ~CbpSolver (void); diff --git a/packages/CLPBN/clpbn/bp/ElimGraph.h b/packages/CLPBN/clpbn/bp/ElimGraph.h index b79b4cb6a..05e17c8d4 100644 --- a/packages/CLPBN/clpbn/bp/ElimGraph.h +++ b/packages/CLPBN/clpbn/bp/ElimGraph.h @@ -17,10 +17,10 @@ enum ElimHeuristic }; -class EgNode : public VarNode +class EgNode : public Var { public: - EgNode (VarId vid, unsigned range) : VarNode (vid, range) { } + EgNode (VarId vid, unsigned range) : Var (vid, range) { } void addNeighbor (EgNode* n) { neighs_.push_back (n); } diff --git a/packages/CLPBN/clpbn/bp/Factor.cpp b/packages/CLPBN/clpbn/bp/Factor.cpp index 3099afba6..498f9d338 100644 --- a/packages/CLPBN/clpbn/bp/Factor.cpp +++ b/packages/CLPBN/clpbn/bp/Factor.cpp @@ -29,7 +29,7 @@ Factor::Factor (VarId vid, unsigned range) -Factor::Factor (const VarNodes& vars) +Factor::Factor (const Vars& vars) { int nrParams = 1; for (unsigned i = 0; i < vars.size(); i++) { @@ -60,7 +60,7 @@ Factor::Factor ( Factor::Factor ( - const VarNodes& vars, + const Vars& vars, const Params& params, unsigned distId) { @@ -267,7 +267,7 @@ Factor::getLabel (void) const ss << "f(" ; for (unsigned i = 0; i < args_.size(); i++) { if (i != 0) ss << "," ; - ss << VarNode (args_[i], ranges_[i]).label(); + ss << Var (args_[i], ranges_[i]).label(); } ss << ")" ; return ss.str(); @@ -278,9 +278,9 @@ Factor::getLabel (void) const void Factor::print (void) const { - VarNodes vars; + Vars vars; for (unsigned i = 0; i < args_.size(); i++) { - vars.push_back (new VarNode (args_[i], ranges_[i])); + vars.push_back (new Var (args_[i], ranges_[i])); } vector jointStrings = Util::getJointStateStrings (vars); for (unsigned i = 0; i < params_.size(); i++) { diff --git a/packages/CLPBN/clpbn/bp/Factor.h b/packages/CLPBN/clpbn/bp/Factor.h index cc138825d..21979f0f2 100644 --- a/packages/CLPBN/clpbn/bp/Factor.h +++ b/packages/CLPBN/clpbn/bp/Factor.h @@ -3,7 +3,7 @@ #include -#include "VarNode.h" +#include "Var.h" #include "Indexer.h" #include "Util.h" @@ -260,11 +260,11 @@ class Factor : public TFactor Factor (VarId, unsigned); - Factor (const VarNodes&); + Factor (const Vars&); Factor (VarId, unsigned, const Params&); - Factor (const VarNodes&, const Params&, + Factor (const Vars&, const Params&, unsigned = Util::maxUnsigned()); Factor (const VarIds&, const Ranges&, const Params&, diff --git a/packages/CLPBN/clpbn/bp/FactorGraph.cpp b/packages/CLPBN/clpbn/bp/FactorGraph.cpp index a457ab26f..3c8f8f2e6 100644 --- a/packages/CLPBN/clpbn/bp/FactorGraph.cpp +++ b/packages/CLPBN/clpbn/bp/FactorGraph.cpp @@ -18,17 +18,17 @@ bool FactorGraph::orderFactorVariables = false; FactorGraph::FactorGraph (const FactorGraph& fg) { - const FgVarSet& vars = fg.getVarNodes(); + const VarNodes& vars = fg.varNodes(); for (unsigned i = 0; i < vars.size(); i++) { - FgVarNode* varNode = new FgVarNode (vars[i]); + VarNode* varNode = new VarNode (vars[i]); addVariable (varNode); } - const FgFacSet& facs = fg.getFactorNodes(); + const FactorNodes& facs = fg.factorNodes(); for (unsigned i = 0; i < facs.size(); i++) { - FgFacNode* facNode = new FgFacNode (facs[i]); + FactorNode* facNode = new FactorNode (facs[i]); addFactor (facNode); - const FgVarSet& neighs = facs[i]->neighbors(); + const VarNodes& neighs = facs[i]->neighbors(); for (unsigned j = 0; j < neighs.size(); j++) { addEdge (facNode, varNodes_[neighs[j]->getIndex()]); } @@ -68,7 +68,7 @@ FactorGraph::readFromUaiFormat (const char* fileName) while (is.peek() == '#' || is.peek() == '\n') getline (is, line); for (unsigned i = 0; i < nVars; i++) { - addVariable (new FgVarNode (i, domainSizes[i])); + addVariable (new VarNode (i, domainSizes[i])); } unsigned nFactors; @@ -77,21 +77,21 @@ FactorGraph::readFromUaiFormat (const char* fileName) while (is.peek() == '#' || is.peek() == '\n') getline (is, line); unsigned nFactorVars; is >> nFactorVars; - VarNodes neighs; + Vars neighs; for (unsigned j = 0; j < nFactorVars; j++) { unsigned vid; is >> vid; - FgVarNode* neigh = getFgVarNode (vid); + VarNode* neigh = getVarNode (vid); if (!neigh) { cerr << "error: invalid variable identifier (" << vid << ")" << endl; abort(); } neighs.push_back (neigh); } - FgFacNode* fn = new FgFacNode (new Factor (neighs)); + FactorNode* fn = new FactorNode (new Factor (neighs)); addFactor (fn); for (unsigned j = 0; j < neighs.size(); j++) { - addEdge (fn, static_cast (neighs[j])); + addEdge (fn, static_cast (neighs[j])); } } @@ -162,15 +162,15 @@ FactorGraph::readFromLibDaiFormat (const char* fileName) vids.push_back (vid); } - VarNodes neighs; + Vars neighs; unsigned nParams = 1; for (unsigned j = 0; j < nVars; j++) { unsigned dsize; while ((is.peek()) == '#') getline (is, line); is >> dsize; - FgVarNode* var = getFgVarNode (vids[j]); + VarNode* var = getVarNode (vids[j]); if (var == 0) { - var = new FgVarNode (vids[j], dsize); + var = new VarNode (vids[j], dsize); addVariable (var); } else { if (var->range() != dsize) { @@ -199,10 +199,10 @@ FactorGraph::readFromLibDaiFormat (const char* fileName) if (Globals::logDomain) { Util::toLog (params); } - FgFacNode* fn = new FgFacNode (new Factor (neighs, params)); + FactorNode* fn = new FactorNode (new Factor (neighs, params)); addFactor (fn); for (unsigned j = 0; j < neighs.size(); j++) { - addEdge (fn, static_cast (neighs[j])); + addEdge (fn, static_cast (neighs[j])); } } is.close(); @@ -224,7 +224,7 @@ FactorGraph::~FactorGraph (void) void -FactorGraph::addVariable (FgVarNode* vn) +FactorGraph::addVariable (VarNode* vn) { varNodes_.push_back (vn); vn->setIndex (varNodes_.size() - 1); @@ -234,7 +234,7 @@ FactorGraph::addVariable (FgVarNode* vn) void -FactorGraph::addFactor (FgFacNode* fn) +FactorGraph::addFactor (FactorNode* fn) { facNodes_.push_back (fn); fn->setIndex (facNodes_.size() - 1); @@ -245,7 +245,7 @@ FactorGraph::addFactor (FgFacNode* fn) void FactorGraph::addFactor (const Factor& factor) { - FgFacNode* fn = new FgFacNode (factor); + FactorNode* fn = new FactorNode (factor); addFactor (fn); const VarIds& vids = factor.arguments(); for (unsigned i = 0; i < vids.size(); i++) { @@ -257,7 +257,7 @@ FactorGraph::addFactor (const Factor& factor) } } if (found == false) { - FgVarNode* vn = new FgVarNode (vids[i], factor.range (i)); + VarNode* vn = new VarNode (vids[i], factor.range (i)); addVariable (vn); addEdge (vn, fn); } @@ -267,7 +267,7 @@ FactorGraph::addFactor (const Factor& factor) void -FactorGraph::addEdge (FgVarNode* vn, FgFacNode* fn) +FactorGraph::addEdge (VarNode* vn, FactorNode* fn) { vn->addNeighbor (fn); fn->addNeighbor (vn); @@ -276,7 +276,7 @@ FactorGraph::addEdge (FgVarNode* vn, FgFacNode* fn) void -FactorGraph::addEdge (FgFacNode* fn, FgVarNode* vn) +FactorGraph::addEdge (FactorNode* fn, VarNode* vn) { fn->addNeighbor (vn); vn->addNeighbor (fn); @@ -284,28 +284,6 @@ FactorGraph::addEdge (FgFacNode* fn, FgVarNode* vn) -VarNode* -FactorGraph::getVariableNode (VarId vid) const -{ - FgVarNode* vn = getFgVarNode (vid); - assert (vn); - return vn; -} - - - -VarNodes -FactorGraph::getVariableNodes (void) const -{ - VarNodes vars; - for (unsigned i = 0; i < varNodes_.size(); i++) { - vars.push_back (varNodes_[i]); - } - return vars; -} - - - bool FactorGraph::isTree (void) const { @@ -348,7 +326,7 @@ FactorGraph::setIndexes (void) void -FactorGraph::printGraphicalModel (void) const +FactorGraph::print (void) const { for (unsigned i = 0; i < varNodes_.size(); i++) { cout << "var id = " << varNodes_[i]->varId() << endl; @@ -390,7 +368,7 @@ FactorGraph::exportToGraphViz (const char* fileName) const out << "\"" << ", shape=box]" << endl; } for (unsigned i = 0; i < facNodes_.size(); i++) { - const FgVarSet& myVars = facNodes_[i]->neighbors(); + const VarNodes& myVars = facNodes_[i]->neighbors(); for (unsigned j = 0; j < myVars.size(); j++) { out << '"' << facNodes_[i]->getLabel() << '"' ; out << " -- " ; @@ -422,7 +400,7 @@ FactorGraph::exportToUaiFormat (const char* fileName) const out << facNodes_.size() << endl; for (unsigned i = 0; i < facNodes_.size(); i++) { - const FgVarSet& factorVars = facNodes_[i]->neighbors(); + const VarNodes& factorVars = facNodes_[i]->neighbors(); out << factorVars.size(); for (unsigned j = 0; j < factorVars.size(); j++) { out << " " << factorVars[j]->getIndex(); @@ -458,7 +436,7 @@ FactorGraph::exportToLibDaiFormat (const char* fileName) const } out << facNodes_.size() << endl << endl; for (unsigned i = 0; i < facNodes_.size(); i++) { - const FgVarSet& factorVars = facNodes_[i]->neighbors(); + const VarNodes& factorVars = facNodes_[i]->neighbors(); out << factorVars.size() << endl; for (int j = factorVars.size() - 1; j >= 0; j--) { out << factorVars[j]->varId() << " " ; @@ -503,13 +481,13 @@ FactorGraph::containsCycle (void) const bool FactorGraph::containsCycle ( - const FgVarNode* v, - const FgFacNode* p, + const VarNode* v, + const FactorNode* p, vector& visitedVars, vector& visitedFactors) const { visitedVars[v->getIndex()] = true; - const FgFacSet& adjacencies = v->neighbors(); + const FactorNodes& adjacencies = v->neighbors(); for (unsigned i = 0; i < adjacencies.size(); i++) { int w = adjacencies[i]->getIndex(); if (!visitedFactors[w]) { @@ -528,13 +506,13 @@ FactorGraph::containsCycle ( bool FactorGraph::containsCycle ( - const FgFacNode* v, - const FgVarNode* p, + const FactorNode* v, + const VarNode* p, vector& visitedVars, vector& visitedFactors) const { visitedFactors[v->getIndex()] = true; - const FgVarSet& adjacencies = v->neighbors(); + const VarNodes& adjacencies = v->neighbors(); for (unsigned i = 0; i < adjacencies.size(); i++) { int w = adjacencies[i]->getIndex(); if (!visitedVars[w]) { diff --git a/packages/CLPBN/clpbn/bp/FactorGraph.h b/packages/CLPBN/clpbn/bp/FactorGraph.h index c120a9edd..3929eb728 100644 --- a/packages/CLPBN/clpbn/bp/FactorGraph.h +++ b/packages/CLPBN/clpbn/bp/FactorGraph.h @@ -4,52 +4,51 @@ #include #include "Factor.h" -#include "GraphicalModel.h" #include "BayesNet.h" #include "Horus.h" using namespace std; -class FgFacNode; +class FactorNode; -class FgVarNode : public VarNode +class VarNode : public Var { public: - FgVarNode (VarId varId, unsigned nrStates) : VarNode (varId, nrStates) { } + VarNode (VarId varId, unsigned nrStates) : Var (varId, nrStates) { } - FgVarNode (const VarNode* v) : VarNode (v) { } + VarNode (const Var* v) : Var (v) { } - void addNeighbor (FgFacNode* fn) { neighs_.push_back (fn); } + void addNeighbor (FactorNode* fn) { neighs_.push_back (fn); } - const FgFacSet& neighbors (void) const { return neighs_; } + const FactorNodes& neighbors (void) const { return neighs_; } private: - DISALLOW_COPY_AND_ASSIGN (FgVarNode); + DISALLOW_COPY_AND_ASSIGN (VarNode); - FgFacSet neighs_; + FactorNodes neighs_; }; -class FgFacNode +class FactorNode { public: - FgFacNode (const FgFacNode* fn) + FactorNode (const FactorNode* fn) { factor_ = new Factor (*fn->factor()); index_ = -1; } - FgFacNode (Factor* f) : factor_(new Factor(*f)), index_(-1) { } + FactorNode (Factor* f) : factor_(new Factor(*f)), index_(-1) { } - FgFacNode (const Factor& f) : factor_(new Factor (f)), index_(-1) { } + FactorNode (const Factor& f) : factor_(new Factor (f)), index_(-1) { } Factor* factor() const { return factor_; } - void addNeighbor (FgVarNode* vn) { neighs_.push_back (vn); } + void addNeighbor (VarNode* vn) { neighs_.push_back (vn); } - const FgVarSet& neighbors (void) const { return neighs_; } + const VarNodes& neighbors (void) const { return neighs_; } int getIndex (void) const { @@ -73,24 +72,24 @@ class FgFacNode } private: - DISALLOW_COPY_AND_ASSIGN (FgFacNode); + DISALLOW_COPY_AND_ASSIGN (FactorNode); Factor* factor_; - FgVarSet neighs_; + VarNodes neighs_; int index_; }; struct CompVarId { - bool operator() (const VarNode* vn1, const VarNode* vn2) const + bool operator() (const Var* v1, const Var* v2) const { - return vn1->varId() < vn2->varId(); + return v1->varId() < v2->varId(); } }; -class FactorGraph : public GraphicalModel +class FactorGraph { public: FactorGraph (void) { } @@ -99,15 +98,15 @@ class FactorGraph : public GraphicalModel ~FactorGraph (void); - const FgVarSet& getVarNodes (void) const { return varNodes_; } + const VarNodes& varNodes (void) const { return varNodes_; } - const FgFacSet& getFactorNodes (void) const { return facNodes_; } + const FactorNodes& factorNodes (void) const { return facNodes_; } void setFromBayesNetwork (void) { fromBayesNet_ = true; } bool isFromBayesNetwork (void) const { return fromBayesNet_ ; } - FgVarNode* getFgVarNode (VarId vid) const + VarNode* getVarNode (VarId vid) const { IndexMap::const_iterator it = varMap_.find (vid); return (it != varMap_.end()) ? varNodes_[it->second] : 0; @@ -117,19 +116,15 @@ class FactorGraph : public GraphicalModel void readFromLibDaiFormat (const char*); - void addVariable (FgVarNode*); + void addVariable (VarNode*); - void addFactor (FgFacNode*); + void addFactor (FactorNode*); void addFactor (const Factor& factor); - void addEdge (FgVarNode*, FgFacNode*); + void addEdge (VarNode*, FactorNode*); - void addEdge (FgFacNode*, FgVarNode*); - - VarNode* getVariableNode (unsigned) const; - - VarNodes getVariableNodes (void) const; + void addEdge (FactorNode*, VarNode*); bool isTree (void) const; @@ -137,7 +132,7 @@ class FactorGraph : public GraphicalModel void setIndexes (void); - void printGraphicalModel (void) const; + void print (void) const; void exportToGraphViz (const char*) const; @@ -152,14 +147,14 @@ class FactorGraph : public GraphicalModel bool containsCycle (void) const; - bool containsCycle (const FgVarNode*, const FgFacNode*, + bool containsCycle (const VarNode*, const FactorNode*, vector&, vector&) const; - bool containsCycle (const FgFacNode*, const FgVarNode*, + bool containsCycle (const FactorNode*, const VarNode*, vector&, vector&) const; - FgVarSet varNodes_; - FgFacSet facNodes_; + VarNodes varNodes_; + FactorNodes facNodes_; bool fromBayesNet_; DAGraph structure_; diff --git a/packages/CLPBN/clpbn/bp/FgBpSolver.cpp b/packages/CLPBN/clpbn/bp/FgBpSolver.cpp deleted file mode 100644 index 9999a21c9..000000000 --- a/packages/CLPBN/clpbn/bp/FgBpSolver.cpp +++ /dev/null @@ -1,496 +0,0 @@ -#include -#include - -#include - -#include - -#include "FgBpSolver.h" -#include "FactorGraph.h" -#include "Factor.h" -#include "Indexer.h" -#include "Horus.h" - - -FgBpSolver::FgBpSolver (const FactorGraph& fg) : Solver (&fg) -{ - factorGraph_ = &fg; -} - - - -FgBpSolver::~FgBpSolver (void) -{ - for (unsigned i = 0; i < varsI_.size(); i++) { - delete varsI_[i]; - } - for (unsigned i = 0; i < facsI_.size(); i++) { - delete facsI_[i]; - } - for (unsigned i = 0; i < links_.size(); i++) { - delete links_[i]; - } -} - - - -void -FgBpSolver::runSolver (void) -{ - clock_t start; - if (Constants::COLLECT_STATS) { - start = clock(); - } - runLoopySolver(); - if (Constants::DEBUG >= 2) { - cout << endl; - if (nIters_ < BpOptions::maxIter) { - cout << "Sum-Product converged in " ; - cout << nIters_ << " iterations" << endl; - } else { - cout << "The maximum number of iterations was hit, terminating..." ; - cout << endl; - } - } - unsigned size = factorGraph_->getVarNodes().size(); - if (Constants::COLLECT_STATS) { - unsigned nIters = 0; - bool loopy = factorGraph_->isTree() == false; - if (loopy) nIters = nIters_; - double time = (double (clock() - start)) / CLOCKS_PER_SEC; - Statistics::updateStatistics (size, loopy, nIters, time); - } -} - - - -Params -FgBpSolver::getPosterioriOf (VarId vid) -{ - assert (factorGraph_->getFgVarNode (vid)); - FgVarNode* var = factorGraph_->getFgVarNode (vid); - Params probs; - if (var->hasEvidence()) { - probs.resize (var->range(), LogAware::noEvidence()); - probs[var->getEvidence()] = LogAware::withEvidence(); - } else { - probs.resize (var->range(), LogAware::multIdenty()); - const SpLinkSet& links = ninf(var)->getLinks(); - if (Globals::logDomain) { - for (unsigned i = 0; i < links.size(); i++) { - Util::add (probs, links[i]->getMessage()); - } - LogAware::normalize (probs); - Util::fromLog (probs); - } else { - for (unsigned i = 0; i < links.size(); i++) { - Util::multiply (probs, links[i]->getMessage()); - } - LogAware::normalize (probs); - } - } - return probs; -} - - - -Params -FgBpSolver::getJointDistributionOf (const VarIds& jointVarIds) -{ - int idx = -1; - FgVarNode* vn = factorGraph_->getFgVarNode (jointVarIds[0]); - const FgFacSet& factorNodes = vn->neighbors(); - for (unsigned i = 0; i < factorNodes.size(); i++) { - if (factorNodes[i]->factor()->contains (jointVarIds)) { - idx = i; - break; - } - } - if (idx == -1) { - return getJointByConditioning (jointVarIds); - } else { - Factor res (*factorNodes[idx]->factor()); - const SpLinkSet& links = ninf(factorNodes[idx])->getLinks(); - for (unsigned i = 0; i < links.size(); i++) { - Factor msg (links[i]->getVariable()->varId(), - links[i]->getVariable()->range(), - getVar2FactorMsg (links[i])); - res.multiply (msg); - } - res.sumOutAllExcept (jointVarIds); - res.reorderArguments (jointVarIds); - res.normalize(); - Params jointDist = res.params(); - if (Globals::logDomain) { - Util::fromLog (jointDist); - } - return jointDist; - } -} - - - -void -FgBpSolver::runLoopySolver (void) -{ - initializeSolver(); - nIters_ = 0; - - while (!converged() && nIters_ < BpOptions::maxIter) { - - nIters_ ++; - if (Constants::DEBUG >= 2) { - Util::printHeader (" Iteration " + nIters_); - cout << endl; - } - - switch (BpOptions::schedule) { - case BpOptions::Schedule::SEQ_RANDOM: - random_shuffle (links_.begin(), links_.end()); - // no break - - case BpOptions::Schedule::SEQ_FIXED: - for (unsigned i = 0; i < links_.size(); i++) { - calculateAndUpdateMessage (links_[i]); - } - break; - - case BpOptions::Schedule::PARALLEL: - for (unsigned i = 0; i < links_.size(); i++) { - calculateMessage (links_[i]); - } - for (unsigned i = 0; i < links_.size(); i++) { - updateMessage(links_[i]); - } - break; - - case BpOptions::Schedule::MAX_RESIDUAL: - maxResidualSchedule(); - break; - } - if (Constants::DEBUG >= 2) { - cout << endl; - } - } -} - - - -void -FgBpSolver::initializeSolver (void) -{ - const FgVarSet& varNodes = factorGraph_->getVarNodes(); - for (unsigned i = 0; i < varsI_.size(); i++) { - delete varsI_[i]; - } - varsI_.reserve (varNodes.size()); - for (unsigned i = 0; i < varNodes.size(); i++) { - varsI_.push_back (new SPNodeInfo()); - } - - const FgFacSet& facNodes = factorGraph_->getFactorNodes(); - for (unsigned i = 0; i < facsI_.size(); i++) { - delete facsI_[i]; - } - facsI_.reserve (facNodes.size()); - for (unsigned i = 0; i < facNodes.size(); i++) { - facsI_.push_back (new SPNodeInfo()); - } - - for (unsigned i = 0; i < links_.size(); i++) { - delete links_[i]; - } - createLinks(); - - for (unsigned i = 0; i < links_.size(); i++) { - FgFacNode* src = links_[i]->getFactor(); - FgVarNode* dst = links_[i]->getVariable(); - ninf (dst)->addSpLink (links_[i]); - ninf (src)->addSpLink (links_[i]); - } -} - - - -void -FgBpSolver::createLinks (void) -{ - const FgFacSet& facNodes = factorGraph_->getFactorNodes(); - for (unsigned i = 0; i < facNodes.size(); i++) { - const FgVarSet& neighbors = facNodes[i]->neighbors(); - for (unsigned j = 0; j < neighbors.size(); j++) { - links_.push_back (new SpLink (facNodes[i], neighbors[j])); - } - } -} - - - -bool -FgBpSolver::converged (void) -{ - if (links_.size() == 0) { - return true; - } - if (nIters_ == 0 || nIters_ == 1) { - return false; - } - bool converged = true; - if (BpOptions::schedule == BpOptions::Schedule::MAX_RESIDUAL) { - double maxResidual = (*(sortedOrder_.begin()))->getResidual(); - if (maxResidual > BpOptions::accuracy) { - converged = false; - } else { - converged = true; - } - } else { - for (unsigned i = 0; i < links_.size(); i++) { - double residual = links_[i]->getResidual(); - if (Constants::DEBUG >= 2) { - cout << links_[i]->toString() + " residual = " << residual << endl; - } - if (residual > BpOptions::accuracy) { - converged = false; - if (Constants::DEBUG == 0) break; - } - } - } - return converged; -} - - - -void -FgBpSolver::maxResidualSchedule (void) -{ - if (nIters_ == 1) { - for (unsigned i = 0; i < links_.size(); i++) { - calculateMessage (links_[i]); - SortedOrder::iterator it = sortedOrder_.insert (links_[i]); - linkMap_.insert (make_pair (links_[i], it)); - } - return; - } - - for (unsigned c = 0; c < links_.size(); c++) { - if (Constants::DEBUG >= 2) { - cout << "current residuals:" << endl; - for (SortedOrder::iterator it = sortedOrder_.begin(); - it != sortedOrder_.end(); it ++) { - cout << " " << setw (30) << left << (*it)->toString(); - cout << "residual = " << (*it)->getResidual() << endl; - } - } - - SortedOrder::iterator it = sortedOrder_.begin(); - SpLink* link = *it; - if (link->getResidual() < BpOptions::accuracy) { - return; - } - updateMessage (link); - link->clearResidual(); - sortedOrder_.erase (it); - linkMap_.find (link)->second = sortedOrder_.insert (link); - - // update the messages that depend on message source --> destin - const FgFacSet& factorNeighbors = link->getVariable()->neighbors(); - for (unsigned i = 0; i < factorNeighbors.size(); i++) { - if (factorNeighbors[i] != link->getFactor()) { - const SpLinkSet& links = ninf(factorNeighbors[i])->getLinks(); - for (unsigned j = 0; j < links.size(); j++) { - if (links[j]->getVariable() != link->getVariable()) { - calculateMessage (links[j]); - SpLinkMap::iterator iter = linkMap_.find (links[j]); - sortedOrder_.erase (iter->second); - iter->second = sortedOrder_.insert (links[j]); - } - } - } - } - if (Constants::DEBUG >= 2) { - Util::printDashedLine(); - } - } -} - - - -void -FgBpSolver::calculateFactor2VariableMsg (SpLink* link) const -{ - const FgFacNode* src = link->getFactor(); - const FgVarNode* dst = link->getVariable(); - const SpLinkSet& links = ninf(src)->getLinks(); - // calculate the product of messages that were sent - // to factor `src', except from var `dst' - unsigned msgSize = 1; - for (unsigned i = 0; i < links.size(); i++) { - msgSize *= links[i]->getVariable()->range(); - } - unsigned repetitions = 1; - Params msgProduct (msgSize, LogAware::multIdenty()); - if (Globals::logDomain) { - for (int i = links.size() - 1; i >= 0; i--) { - if (links[i]->getVariable() != dst) { - Util::add (msgProduct, getVar2FactorMsg (links[i]), repetitions); - repetitions *= links[i]->getVariable()->range(); - } else { - unsigned ds = links[i]->getVariable()->range(); - Util::add (msgProduct, Params (ds, 1.0), repetitions); - repetitions *= ds; - } - } - } else { - for (int i = links.size() - 1; i >= 0; i--) { - if (links[i]->getVariable() != dst) { - if (Constants::DEBUG >= 5) { - cout << " message from " << links[i]->getVariable()->label(); - cout << ": " << endl; - } - Util::multiply (msgProduct, getVar2FactorMsg (links[i]), repetitions); - repetitions *= links[i]->getVariable()->range(); - } else { - unsigned ds = links[i]->getVariable()->range(); - Util::multiply (msgProduct, Params (ds, 1.0), repetitions); - repetitions *= ds; - } - } - } - - Factor result (src->factor()->arguments(), - src->factor()->ranges(), - msgProduct); - result.multiply (*(src->factor())); - if (Constants::DEBUG >= 5) { - cout << " message product: " << msgProduct << endl; - cout << " original factor: " << src->params() << endl; - cout << " factor product: " << result.params() << endl; - } - result.sumOutAllExcept (dst->varId()); - if (Constants::DEBUG >= 5) { - cout << " marginalized: " ; - cout << result.params() << endl; - } - const Params& resultParams = result.params(); - Params& message = link->getNextMessage(); - for (unsigned i = 0; i < resultParams.size(); i++) { - message[i] = resultParams[i]; - } - LogAware::normalize (message); - if (Constants::DEBUG >= 5) { - cout << " curr msg: " << link->getMessage() << endl; - cout << " next msg: " << message << endl; - } -} - - - -Params -FgBpSolver::getVar2FactorMsg (const SpLink* link) const -{ - const FgVarNode* src = link->getVariable(); - const FgFacNode* dst = link->getFactor(); - Params msg; - if (src->hasEvidence()) { - msg.resize (src->range(), LogAware::noEvidence()); - msg[src->getEvidence()] = LogAware::withEvidence(); - if (Constants::DEBUG >= 5) { - cout << msg; - } - } else { - msg.resize (src->range(), LogAware::one()); - } - if (Constants::DEBUG >= 5) { - cout << msg; - } - const SpLinkSet& links = ninf (src)->getLinks(); - if (Globals::logDomain) { - for (unsigned i = 0; i < links.size(); i++) { - if (links[i]->getFactor() != dst) { - Util::add (msg, links[i]->getMessage()); - } - } - } else { - for (unsigned i = 0; i < links.size(); i++) { - if (links[i]->getFactor() != dst) { - Util::multiply (msg, links[i]->getMessage()); - if (Constants::DEBUG >= 5) { - cout << " x " << links[i]->getMessage(); - } - } - } - } - if (Constants::DEBUG >= 5) { - cout << " = " << msg; - } - return msg; -} - - - -Params -FgBpSolver::getJointByConditioning (const VarIds& jointVarIds) const -{ - FgVarSet jointVars; - for (unsigned i = 0; i < jointVarIds.size(); i++) { - assert (factorGraph_->getFgVarNode (jointVarIds[i])); - jointVars.push_back (factorGraph_->getFgVarNode (jointVarIds[i])); - } - - FactorGraph* fg = new FactorGraph (*factorGraph_); - FgBpSolver solver (*fg); - solver.runSolver(); - Params prevBeliefs = solver.getPosterioriOf (jointVarIds[0]); - - VarIds observedVids = {jointVars[0]->varId()}; - - for (unsigned i = 1; i < jointVarIds.size(); i++) { - assert (jointVars[i]->hasEvidence() == false); - Params newBeliefs; - VarNodes observedVars; - for (unsigned j = 0; j < observedVids.size(); j++) { - observedVars.push_back (fg->getFgVarNode (observedVids[j])); - } - StatesIndexer idx (observedVars, false); - while (idx.valid()) { - for (unsigned j = 0; j < observedVars.size(); j++) { - observedVars[j]->setEvidence (idx[j]); - } - ++ idx; - FgBpSolver solver (*fg); - solver.runSolver(); - Params beliefs = solver.getPosterioriOf (jointVarIds[i]); - for (unsigned k = 0; k < beliefs.size(); k++) { - newBeliefs.push_back (beliefs[k]); - } - } - - int count = -1; - for (unsigned j = 0; j < newBeliefs.size(); j++) { - if (j % jointVars[i]->range() == 0) { - count ++; - } - newBeliefs[j] *= prevBeliefs[count]; - } - prevBeliefs = newBeliefs; - observedVids.push_back (jointVars[i]->varId()); - } - return prevBeliefs; -} - - - -void -FgBpSolver::printLinkInformation (void) const -{ - for (unsigned i = 0; i < links_.size(); i++) { - SpLink* l = links_[i]; - cout << l->toString() << ":" << endl; - cout << " curr msg = " ; - cout << l->getMessage() << endl; - cout << " next msg = " ; - cout << l->getNextMessage() << endl; - cout << " residual = " << l->getResidual() << endl; - } -} - diff --git a/packages/CLPBN/clpbn/bp/FgBpSolver.h b/packages/CLPBN/clpbn/bp/FgBpSolver.h deleted file mode 100644 index e57f2ca1d..000000000 --- a/packages/CLPBN/clpbn/bp/FgBpSolver.h +++ /dev/null @@ -1,186 +0,0 @@ -#ifndef HORUS_FGBPSOLVER_H -#define HORUS_FGBPSOLVER_H - -#include -#include -#include - -#include "Solver.h" -#include "Factor.h" -#include "FactorGraph.h" -#include "Util.h" - -using namespace std; - - -class SpLink -{ - public: - SpLink (FgFacNode* fn, FgVarNode* vn) - { - fac_ = fn; - var_ = vn; - v1_.resize (vn->range(), LogAware::tl (1.0 / vn->range())); - v2_.resize (vn->range(), LogAware::tl (1.0 / vn->range())); - currMsg_ = &v1_; - nextMsg_ = &v2_; - msgSended_ = false; - residual_ = 0.0; - } - - virtual ~SpLink (void) { }; - - FgFacNode* getFactor (void) const { return fac_; } - - FgVarNode* getVariable (void) const { return var_; } - - const Params& getMessage (void) const { return *currMsg_; } - - Params& getNextMessage (void) { return *nextMsg_; } - - bool messageWasSended (void) const { return msgSended_; } - - double getResidual (void) const { return residual_; } - - void clearResidual (void) { residual_ = 0.0; } - - void updateResidual (void) - { - residual_ = LogAware::getMaxNorm (v1_,v2_); - } - - virtual void updateMessage (void) - { - swap (currMsg_, nextMsg_); - msgSended_ = true; - } - - string toString (void) const - { - stringstream ss; - ss << fac_->getLabel(); - ss << " -- " ; - ss << var_->label(); - return ss.str(); - } - - protected: - FgFacNode* fac_; - FgVarNode* var_; - Params v1_; - Params v2_; - Params* currMsg_; - Params* nextMsg_; - bool msgSended_; - double residual_; -}; - -typedef vector SpLinkSet; - - -class SPNodeInfo -{ - public: - void addSpLink (SpLink* link) { links_.push_back (link); } - const SpLinkSet& getLinks (void) { return links_; } - private: - SpLinkSet links_; -}; - - -class FgBpSolver : public Solver -{ - public: - FgBpSolver (const FactorGraph&); - - virtual ~FgBpSolver (void); - - void runSolver (void); - - virtual Params getPosterioriOf (VarId); - - virtual Params getJointDistributionOf (const VarIds&); - - protected: - virtual void initializeSolver (void); - - virtual void createLinks (void); - - virtual void maxResidualSchedule (void); - - virtual void calculateFactor2VariableMsg (SpLink*) const; - - virtual Params getVar2FactorMsg (const SpLink*) const; - - virtual Params getJointByConditioning (const VarIds&) const; - - virtual void printLinkInformation (void) const; - - SPNodeInfo* ninf (const FgVarNode* var) const - { - return varsI_[var->getIndex()]; - } - - SPNodeInfo* ninf (const FgFacNode* fac) const - { - return facsI_[fac->getIndex()]; - } - - void calculateAndUpdateMessage (SpLink* link, bool calcResidual = true) - { - if (Constants::DEBUG >= 3) { - cout << "calculating & updating " << link->toString() << endl; - } - calculateFactor2VariableMsg (link); - if (calcResidual) { - link->updateResidual(); - } - link->updateMessage(); - } - - void calculateMessage (SpLink* link, bool calcResidual = true) - { - if (Constants::DEBUG >= 3) { - cout << "calculating " << link->toString() << endl; - } - calculateFactor2VariableMsg (link); - if (calcResidual) { - link->updateResidual(); - } - } - - void updateMessage (SpLink* link) - { - link->updateMessage(); - if (Constants::DEBUG >= 3) { - cout << "updating " << link->toString() << endl; - } - } - - struct CompareResidual - { - inline bool operator() (const SpLink* link1, const SpLink* link2) - { - return link1->getResidual() > link2->getResidual(); - } - }; - - SpLinkSet links_; - unsigned nIters_; - vector varsI_; - vector facsI_; - const FactorGraph* factorGraph_; - - typedef multiset SortedOrder; - SortedOrder sortedOrder_; - - typedef unordered_map SpLinkMap; - SpLinkMap linkMap_; - - private: - void runLoopySolver (void); - bool converged (void); -}; - -#endif // HORUS_FGBPSOLVER_H - diff --git a/packages/CLPBN/clpbn/bp/GraphicalModel.h b/packages/CLPBN/clpbn/bp/GraphicalModel.h deleted file mode 100644 index e0d427b75..000000000 --- a/packages/CLPBN/clpbn/bp/GraphicalModel.h +++ /dev/null @@ -1,64 +0,0 @@ -#ifndef HORUS_GRAPHICALMODEL_H -#define HORUS_GRAPHICALMODEL_H - -#include - -#include - -#include - -#include "VarNode.h" -#include "Util.h" -#include "Horus.h" - -using namespace std; - - -struct VarInfo -{ - VarInfo (string l, const States& sts) : label(l), states(sts) { } - string label; - States states; -}; - - -class GraphicalModel -{ - public: - virtual ~GraphicalModel (void) { }; - - virtual VarNode* getVariableNode (VarId) const = 0; - - virtual VarNodes getVariableNodes (void) const = 0; - - virtual void printGraphicalModel (void) const = 0; - - static void addVariableInformation ( - VarId vid, string label, const States& states) - { - assert (Util::contains (varsInfo_, vid) == false); - varsInfo_.insert (make_pair (vid, VarInfo (label, states))); - } - - static VarInfo getVarInformation (VarId vid) - { - assert (Util::contains (varsInfo_, vid)); - return varsInfo_.find (vid)->second; - } - - static bool variablesHaveInformation (void) - { - return varsInfo_.size() != 0; - } - - static void clearVariablesInformation (void) - { - varsInfo_.clear(); - } - - private: - static unordered_map varsInfo_; -}; - -#endif // HORUS_GRAPHICALMODEL_H - diff --git a/packages/CLPBN/clpbn/bp/Horus.h b/packages/CLPBN/clpbn/bp/Horus.h index c38a9fd53..7b92c6e5a 100644 --- a/packages/CLPBN/clpbn/bp/Horus.h +++ b/packages/CLPBN/clpbn/bp/Horus.h @@ -11,30 +11,27 @@ using namespace std; -class VarNode; -class BayesNode; -class FgVarNode; -class FgFacNode; +class Var; class Factor; +class VarNode; +class FactorNode; typedef vector Params; typedef unsigned VarId; typedef vector VarIds; +typedef vector Vars; typedef vector VarNodes; -typedef vector BnNodeSet; -typedef vector FgVarSet; -typedef vector FgFacSet; -typedef vector FactorSet; +typedef vector FactorNodes; +typedef vector Factors; typedef vector States; typedef vector Ranges; enum InfAlgorithms { - VE, // variable elimination - BN_BP, // bayesian network belief propagation - FG_BP, // factor graph belief propagation - CBP // counting bp solver + VE, // variable elimination + BP, // belief propagation + CBP // counting belief propagation }; diff --git a/packages/CLPBN/clpbn/bp/HorusCli.cpp b/packages/CLPBN/clpbn/bp/HorusCli.cpp index 1d0f76b52..1e0389823 100644 --- a/packages/CLPBN/clpbn/bp/HorusCli.cpp +++ b/packages/CLPBN/clpbn/bp/HorusCli.cpp @@ -5,13 +5,13 @@ #include "FactorGraph.h" #include "VarElimSolver.h" -#include "FgBpSolver.h" +#include "BpSolver.h" #include "CbpSolver.h" using namespace std; void processArguments (FactorGraph&, int, const char* []); -void runSolver (Solver*, const VarNodes&); +void runSolver (Solver*, const VarIds&); const string USAGE = "usage: \ ./hcli FILE [VARIABLE | OBSERVED_VARIABLE=EVIDENCE]..." ; @@ -48,7 +48,7 @@ main (int argc, const char* argv[]) void processArguments (FactorGraph& fg, int argc, const char* argv[]) { - VarNodes queryVars; + VarIds queryIds; for (int i = 2; i < argc; i++) { const string& arg = argv[i]; if (arg.find ('=') == std::string::npos) { @@ -62,9 +62,9 @@ processArguments (FactorGraph& fg, int argc, const char* argv[]) stringstream ss; ss << arg; ss >> vid; - VarNode* queryVar = fg.getFgVarNode (vid); + VarNode* queryVar = fg.getVarNode (vid); if (queryVar) { - queryVars.push_back (queryVar); + queryIds.push_back (vid); } else { cerr << "error: there isn't a variable with " ; cerr << "`" << vid << "' as id" ; @@ -93,7 +93,7 @@ processArguments (FactorGraph& fg, int argc, const char* argv[]) stringstream ss; ss << arg.substr (0, pos); ss >> vid; - VarNode* var = fg.getFgVarNode (vid); + VarNode* var = fg.getVarNode (vid); if (var) { if (!Util::isInteger (arg.substr (pos + 1))) { cerr << "error: `" << arg.substr (pos + 1) << "' " ; @@ -127,8 +127,8 @@ processArguments (FactorGraph& fg, int argc, const char* argv[]) case InfAlgorithms::VE: solver = new VarElimSolver (fg); break; - case InfAlgorithms::FG_BP: - solver = new FgBpSolver (fg); + case InfAlgorithms::BP: + solver = new BpSolver (fg); break; case InfAlgorithms::CBP: solver = new CbpSolver (fg); @@ -136,27 +136,23 @@ processArguments (FactorGraph& fg, int argc, const char* argv[]) default: assert (false); } - runSolver (solver, queryVars); + runSolver (solver, queryIds); } void -runSolver (Solver* solver, const VarNodes& queryVars) +runSolver (Solver* solver, const VarIds& queryIds) { - VarIds vids; - for (unsigned i = 0; i < queryVars.size(); i++) { - vids.push_back (queryVars[i]->varId()); - } - if (queryVars.size() == 0) { + if (queryIds.size() == 0) { solver->runSolver(); solver->printAllPosterioris(); - } else if (queryVars.size() == 1) { + } else if (queryIds.size() == 1) { solver->runSolver(); - solver->printPosterioriOf (vids[0]); + solver->printPosterioriOf (queryIds[0]); } else { solver->runSolver(); - solver->printJointDistributionOf (vids); + solver->printJointDistributionOf (queryIds); } delete solver; } diff --git a/packages/CLPBN/clpbn/bp/HorusYap.cpp b/packages/CLPBN/clpbn/bp/HorusYap.cpp index 3e84b0a07..9384c10b5 100644 --- a/packages/CLPBN/clpbn/bp/HorusYap.cpp +++ b/packages/CLPBN/clpbn/bp/HorusYap.cpp @@ -11,7 +11,7 @@ #include "FactorGraph.h" #include "FoveSolver.h" #include "VarElimSolver.h" -#include "FgBpSolver.h" +#include "BpSolver.h" #include "CbpSolver.h" #include "ElimGraph.h" #include "BayesBall.h" @@ -241,8 +241,8 @@ createGroundNetwork (void) unsigned vid = (unsigned) YAP_IntOfTerm ((YAP_ArgOfTerm (1, evTerm))); unsigned ev = (unsigned) YAP_IntOfTerm ((YAP_ArgOfTerm (2, evTerm))); cout << vid << " == " << ev << endl; - assert (fg->getFgVarNode (vid)); - fg->getFgVarNode (vid)->setEvidence (ev); + assert (fg->getVarNode (vid)); + fg->getVarNode (vid)->setEvidence (ev); evidenceList = YAP_TailOfTerm (evidenceList); } @@ -348,7 +348,6 @@ runGroundSolver (void) taskList = YAP_TailOfTerm (taskList); } - fg->printGraphicalModel(); vector results; if (Globals::infAlgorithm == InfAlgorithms::VE) { runVeSolver (fg, tasks, results); @@ -414,8 +413,8 @@ void runBpSolver ( mfg = BayesBall::getMinimalFactorGraph ( *fg, VarIds (vids.begin(),vids.end())); } - if (Globals::infAlgorithm == InfAlgorithms::FG_BP) { - solver = new FgBpSolver (*mfg); + if (Globals::infAlgorithm == InfAlgorithms::BP) { + solver = new BpSolver (*mfg); } else if (Globals::infAlgorithm == InfAlgorithms::CBP) { CFactorGraph::checkForIdenticalFactors = false; solver = new CbpSolver (*mfg); @@ -494,7 +493,7 @@ setBayesNetParams (void) int setExtraVarsInfo (void) { - GraphicalModel::clearVariablesInformation(); + Var::clearVariablesInformation(); YAP_Term varsInfoL = YAP_ARG2; while (varsInfoL != YAP_TermNil()) { YAP_Term head = YAP_HeadOfTerm (varsInfoL); @@ -507,7 +506,7 @@ setExtraVarsInfo (void) states.push_back ((char*) YAP_AtomName (atom)); statesL = YAP_TailOfTerm (statesL); } - GraphicalModel::addVariableInformation (vid, + Var::addVariableInformation (vid, (char*) YAP_AtomName (label), states); varsInfoL = YAP_TailOfTerm (varsInfoL); } @@ -524,10 +523,8 @@ setHorusFlag (void) string value ((char*) YAP_AtomName (YAP_AtomOfTerm (YAP_ARG2))); if ( value == "ve") { Globals::infAlgorithm = InfAlgorithms::VE; - } else if (value == "bn_bp") { - Globals::infAlgorithm = InfAlgorithms::BN_BP; - } else if (value == "fg_bp") { - Globals::infAlgorithm = InfAlgorithms::FG_BP; + } else if (value == "bp") { + Globals::infAlgorithm = InfAlgorithms::BP; } else if (value == "cbp") { Globals::infAlgorithm = InfAlgorithms::CBP; } else { diff --git a/packages/CLPBN/clpbn/bp/Indexer.h b/packages/CLPBN/clpbn/bp/Indexer.h index ded5a1fea..3ebe53f94 100644 --- a/packages/CLPBN/clpbn/bp/Indexer.h +++ b/packages/CLPBN/clpbn/bp/Indexer.h @@ -8,7 +8,7 @@ #include #include -#include "VarNode.h" +#include "Var.h" #include "Util.h" @@ -31,7 +31,7 @@ class StatesIndexer } } - StatesIndexer (const VarNodes& vars, bool calcOffsets = true) + StatesIndexer (const Vars& vars, bool calcOffsets = true) { size_ = 1; indices_.resize (vars.size(), 0); diff --git a/packages/CLPBN/clpbn/bp/Makefile.in b/packages/CLPBN/clpbn/bp/Makefile.in index efa8c5b7d..4cb384f62 100644 --- a/packages/CLPBN/clpbn/bp/Makefile.in +++ b/packages/CLPBN/clpbn/bp/Makefile.in @@ -45,7 +45,6 @@ CWD=$(PWD) HEADERS = \ - $(srcdir)/GraphicalModel.h \ $(srcdir)/BayesNet.h \ $(srcdir)/BayesBall.h \ $(srcdir)/ElimGraph.h \ @@ -55,10 +54,10 @@ HEADERS = \ $(srcdir)/ConstraintTree.h \ $(srcdir)/Solver.h \ $(srcdir)/VarElimSolver.h \ - $(srcdir)/FgBpSolver.h \ + $(srcdir)/BpSolver.h \ $(srcdir)/CbpSolver.h \ $(srcdir)/FoveSolver.h \ - $(srcdir)/VarNode.h \ + $(srcdir)/Var.h \ $(srcdir)/Indexer.h \ $(srcdir)/Parfactor.h \ $(srcdir)/ProbFormula.h \ @@ -77,10 +76,10 @@ CPP_SOURCES = \ $(srcdir)/Factor.cpp \ $(srcdir)/CFactorGraph.cpp \ $(srcdir)/ConstraintTree.cpp \ - $(srcdir)/VarNode.cpp \ + $(srcdir)/Var.cpp \ $(srcdir)/Solver.cpp \ $(srcdir)/VarElimSolver.cpp \ - $(srcdir)/FgBpSolver.cpp \ + $(srcdir)/BpSolver.cpp \ $(srcdir)/CbpSolver.cpp \ $(srcdir)/FoveSolver.cpp \ $(srcdir)/Parfactor.cpp \ @@ -100,10 +99,10 @@ OBJS = \ Factor.o \ CFactorGraph.o \ ConstraintTree.o \ - VarNode.o \ + Var.o \ Solver.o \ VarElimSolver.o \ - FgBpSolver.o \ + BpSolver.o \ CbpSolver.o \ FoveSolver.o \ Parfactor.o \ @@ -122,10 +121,10 @@ HCLI_OBJS = \ Factor.o \ CFactorGraph.o \ ConstraintTree.o \ - VarNode.o \ + Var.o \ Solver.o \ VarElimSolver.o \ - FgBpSolver.o \ + BpSolver.o \ CbpSolver.o \ FoveSolver.o \ Parfactor.o \ diff --git a/packages/CLPBN/clpbn/bp/Solver.cpp b/packages/CLPBN/clpbn/bp/Solver.cpp index 65a46238f..1fa57e9ee 100644 --- a/packages/CLPBN/clpbn/bp/Solver.cpp +++ b/packages/CLPBN/clpbn/bp/Solver.cpp @@ -5,7 +5,7 @@ void Solver::printAllPosterioris (void) { - const VarNodes& vars = gm_->getVariableNodes(); + const VarNodes& vars = fg_.varNodes(); for (unsigned i = 0; i < vars.size(); i++) { printPosterioriOf (vars[i]->varId()); } @@ -16,11 +16,11 @@ Solver::printAllPosterioris (void) void Solver::printPosterioriOf (VarId vid) { - VarNode* var = gm_->getVariableNode (vid); + VarNode* vn = fg_.getVarNode (vid); const Params& posterioriDist = getPosterioriOf (vid); - const States& states = var->states(); + const States& states = vn->states(); for (unsigned i = 0; i < states.size(); i++) { - cout << "P(" << var->label() << "=" << states[i] << ") = " ; + cout << "P(" << vn->label() << "=" << states[i] << ") = " ; cout << setprecision (Constants::PRECISION) << posterioriDist[i]; cout << endl; } @@ -32,12 +32,12 @@ Solver::printPosterioriOf (VarId vid) void Solver::printJointDistributionOf (const VarIds& vids) { - VarNodes vars; + Vars vars; VarIds vidsWithoutEvidence; for (unsigned i = 0; i < vids.size(); i++) { - VarNode* var = gm_->getVariableNode (vids[i]); - if (var->hasEvidence() == false) { - vars.push_back (var); + VarNode* vn = fg_.getVarNode (vids[i]); + if (vn->hasEvidence() == false) { + vars.push_back (vn); vidsWithoutEvidence.push_back (vids[i]); } } diff --git a/packages/CLPBN/clpbn/bp/Solver.h b/packages/CLPBN/clpbn/bp/Solver.h index e4351ab3d..826f25e0d 100644 --- a/packages/CLPBN/clpbn/bp/Solver.h +++ b/packages/CLPBN/clpbn/bp/Solver.h @@ -3,15 +3,16 @@ #include -#include "GraphicalModel.h" -#include "VarNode.h" +#include "Var.h" +#include "FactorGraph.h" + using namespace std; class Solver { public: - Solver (const GraphicalModel* gm) : gm_(gm) { } + Solver (const FactorGraph& fg) : fg_(fg) { } virtual ~Solver() { } // ensure that subclass destructor is called @@ -28,7 +29,7 @@ class Solver void printJointDistributionOf (const VarIds& vids); private: - const GraphicalModel* gm_; + const FactorGraph& fg_; }; #endif // HORUS_SOLVER_H diff --git a/packages/CLPBN/clpbn/bp/Util.cpp b/packages/CLPBN/clpbn/bp/Util.cpp index 2a5c15100..7a3d4f2a2 100644 --- a/packages/CLPBN/clpbn/bp/Util.cpp +++ b/packages/CLPBN/clpbn/bp/Util.cpp @@ -5,7 +5,6 @@ #include "Util.h" #include "Indexer.h" -#include "GraphicalModel.h" namespace Globals { @@ -25,12 +24,11 @@ Schedule schedule = BpOptions::Schedule::SEQ_FIXED; //Schedule schedule = BpOptions::Schedule::SEQ_RANDOM; //Schedule schedule = BpOptions::Schedule::PARALLEL; //Schedule schedule = BpOptions::Schedule::MAX_RESIDUAL; -double accuracy = 0.0001; -unsigned maxIter = 1000; +double accuracy = 0.0001; +unsigned maxIter = 1000; } -unordered_map GraphicalModel::varsInfo_; vector Statistics::netInfo_; vector Statistics::compressInfo_; @@ -139,7 +137,7 @@ parametersToString (const Params& v, unsigned precision) vector -getJointStateStrings (const VarNodes& vars) +getJointStateStrings (const Vars& vars) { StatesIndexer idx (vars); vector jointStrings; @@ -401,10 +399,9 @@ Statistics::getStatisticString (void) stringstream ss2, ss3, ss4, ss1; ss1 << "running mode: " ; switch (Globals::infAlgorithm) { - case InfAlgorithms::VE: ss1 << "ve" << endl; break; - case InfAlgorithms::BN_BP: ss1 << "bn_bp" << endl; break; - case InfAlgorithms::FG_BP: ss1 << "fg_bp" << endl; break; - case InfAlgorithms::CBP: ss1 << "cbp" << endl; break; + case InfAlgorithms::VE: ss1 << "ve" << endl; break; + case InfAlgorithms::BP: ss1 << "bp" << endl; break; + case InfAlgorithms::CBP: ss1 << "cbp" << endl; break; } ss1 << "message schedule: " ; switch (BpOptions::schedule) { diff --git a/packages/CLPBN/clpbn/bp/Util.h b/packages/CLPBN/clpbn/bp/Util.h index 1d2f01a41..4e053dab2 100644 --- a/packages/CLPBN/clpbn/bp/Util.h +++ b/packages/CLPBN/clpbn/bp/Util.h @@ -62,7 +62,7 @@ bool isInteger (const string&); string parametersToString (const Params&, unsigned = Constants::PRECISION); -vector getJointStateStrings (const VarNodes&); +vector getJointStateStrings (const Vars&); void printHeader (string, std::ostream& os = std::cout); diff --git a/packages/CLPBN/clpbn/bp/VarElimSolver.cpp b/packages/CLPBN/clpbn/bp/VarElimSolver.cpp index 3a20bb9f3..c12019eb9 100644 --- a/packages/CLPBN/clpbn/bp/VarElimSolver.cpp +++ b/packages/CLPBN/clpbn/bp/VarElimSolver.cpp @@ -6,7 +6,7 @@ #include "Util.h" -VarElimSolver::VarElimSolver (const FactorGraph& fg) : Solver (&fg) +VarElimSolver::VarElimSolver (const FactorGraph& fg) : Solver (fg) { factorGraph_ = &fg; } @@ -23,8 +23,8 @@ VarElimSolver::~VarElimSolver (void) Params VarElimSolver::getPosterioriOf (VarId vid) { - assert (factorGraph_->getFgVarNode (vid)); - FgVarNode* vn = factorGraph_->getFgVarNode (vid); + assert (factorGraph_->getVarNode (vid)); + VarNode* vn = factorGraph_->getVarNode (vid); if (vn->hasEvidence()) { Params params (vn->range(), 0.0); params[vn->getEvidence()] = 1.0; @@ -57,11 +57,11 @@ VarElimSolver::getJointDistributionOf (const VarIds& vids) void VarElimSolver::createFactorList (void) { - const FgFacSet& factorNodes = factorGraph_->getFactorNodes(); + const FactorNodes& factorNodes = factorGraph_->factorNodes(); factorList_.reserve (factorNodes.size() * 2); for (unsigned i = 0; i < factorNodes.size(); i++) { factorList_.push_back (new Factor (*factorNodes[i]->factor())); - const FgVarSet& neighs = factorNodes[i]->neighbors(); + const VarNodes& neighs = factorNodes[i]->neighbors(); for (unsigned j = 0; j < neighs.size(); j++) { unordered_map >::iterator it = varFactors_.find (neighs[j]->varId()); @@ -79,7 +79,7 @@ VarElimSolver::createFactorList (void) void VarElimSolver::absorveEvidence (void) { - const FgVarSet& varNodes = factorGraph_->getVarNodes(); + const VarNodes& varNodes = factorGraph_->varNodes(); for (unsigned i = 0; i < varNodes.size(); i++) { if (varNodes[i]->hasEvidence()) { const vector& idxs = @@ -126,7 +126,7 @@ VarElimSolver::processFactorList (const VarIds& vids) VarIds unobservedVids; for (unsigned i = 0; i < vids.size(); i++) { - if (factorGraph_->getFgVarNode (vids[i])->hasEvidence() == false) { + if (factorGraph_->getVarNode (vids[i])->hasEvidence() == false) { unobservedVids.push_back (vids[i]); } } diff --git a/packages/CLPBN/clpbn/bp/VarNode.cpp b/packages/CLPBN/clpbn/bp/VarNode.cpp deleted file mode 100644 index 2bda87c13..000000000 --- a/packages/CLPBN/clpbn/bp/VarNode.cpp +++ /dev/null @@ -1,100 +0,0 @@ -#include -#include - -#include "VarNode.h" -#include "GraphicalModel.h" - -using namespace std; - - -VarNode::VarNode (const VarNode* v) -{ - varId_ = v->varId(); - range_ = v->range(); - evidence_ = v->getEvidence(); - index_ = std::numeric_limits::max(); -} - - - -VarNode::VarNode (VarId varId, unsigned range, int evidence) -{ - assert (range != 0); - assert (evidence < (int) range); - varId_ = varId; - range_ = range; - evidence_ = evidence; - index_ = std::numeric_limits::max(); -} - - - -bool -VarNode::isValidState (int stateIndex) -{ - return stateIndex >= 0 && stateIndex < (int) range_; -} - - - -bool -VarNode::isValidState (const string& stateName) -{ - States states = GraphicalModel::getVarInformation (varId_).states; - return Util::contains (states, stateName); -} - - - -void -VarNode::setEvidence (int ev) -{ - assert (ev < (int) range_); - evidence_ = ev; -} - - - -void -VarNode::setEvidence (const string& ev) -{ - States states = GraphicalModel::getVarInformation (varId_).states; - for (unsigned i = 0; i < states.size(); i++) { - if (states[i] == ev) { - evidence_ = i; - return; - } - } - assert (false); -} - - - -string -VarNode::label (void) const -{ - if (GraphicalModel::variablesHaveInformation()) { - return GraphicalModel::getVarInformation (varId_).label; - } - stringstream ss; - ss << "x" << varId_; - return ss.str(); -} - - - -States -VarNode::states (void) const -{ - if (GraphicalModel::variablesHaveInformation()) { - return GraphicalModel::getVarInformation (varId_).states; - } - States states; - for (unsigned i = 0; i < range_; i++) { - stringstream ss; - ss << i ; - states.push_back (ss.str()); - } - return states; -} - diff --git a/packages/CLPBN/clpbn/bp/VarNode.h b/packages/CLPBN/clpbn/bp/VarNode.h deleted file mode 100644 index e208f13ab..000000000 --- a/packages/CLPBN/clpbn/bp/VarNode.h +++ /dev/null @@ -1,71 +0,0 @@ -#ifndef HORUS_VARNODE_H -#define HORUS_VARNODE_H - -#include - -#include - -#include "Horus.h" - -using namespace std; - -class VarNode -{ - public: - VarNode (const VarNode*); - - VarNode (VarId, unsigned, int = Constants::NO_EVIDENCE); - - virtual ~VarNode (void) { }; - - unsigned varId (void) const { return varId_; } - - unsigned range (void) const { return range_; } - - int getEvidence (void) const { return evidence_; } - - unsigned getIndex (void) const { return index_; } - - void setIndex (unsigned idx) { index_ = idx; } - - operator unsigned () const { return index_; } - - bool hasEvidence (void) const - { - return evidence_ != Constants::NO_EVIDENCE; - } - - bool operator== (const VarNode& var) const - { - assert (!(varId_ == var.varId() && range_ != var.range())); - return varId_ == var.varId(); - } - - bool operator!= (const VarNode& var) const - { - assert (!(varId_ == var.varId() && range_ != var.range())); - return varId_ != var.varId(); - } - - bool isValidState (int); - - bool isValidState (const string&); - - void setEvidence (int); - - void setEvidence (const string&); - - string label (void) const; - - States states (void) const; - - private: - VarId varId_; - unsigned range_; - int evidence_; - unsigned index_; - -}; - -#endif // BP_VARNODE_H - diff --git a/packages/CLPBN/clpbn/bp/benchmarks/city/fg_bp_tests.sh b/packages/CLPBN/clpbn/bp/benchmarks/city/fg_bp_tests.sh deleted file mode 100755 index 9c478e1be..000000000 --- a/packages/CLPBN/clpbn/bp/benchmarks/city/fg_bp_tests.sh +++ /dev/null @@ -1,50 +0,0 @@ -#!/bin/bash - -cp ~/bin/yap ~/bin/town_fgbp -YAP=~/bin/town_fgbp - -#OUT_FILE_NAME=results`date "+ %H:%M:%S %d-%m-%Y"`.log -OUT_FILE_NAME=fb_bp.log -rm -f $OUT_FILE_NAME -rm -f ignore.$OUT_FILE_NAME - - -function run_solver -{ -if [ $2 = bp ] -then - extra_flag1=clpbn_horus:set_horus_flag\(inf_alg,$4\) - extra_flag2=clpbn_horus:set_horus_flag\(schedule,$5\) -else - extra_flag1=true - extra_flag2=true -fi -/usr/bin/time -o $OUT_FILE_NAME -a -f "real:%E\tuser:%U\tsys:%S" $YAP << EOF >> $OUT_FILE_NAME 2>> ignore.$OUT_FILE_NAME -[$1]. -clpbn:set_clpbn_flag(solver,$2), - clpbn_horus:set_horus_flag(use_logarithms, true), - $extra_flag1, $extra_flag2, - run_query(_R), - open("$OUT_FILE_NAME", 'append',S), - format(S, '$3: ~15+ ',[]), - close(S). -EOF -} - - -function run_all_graphs -{ - echo "*******************************************************************" >> "$OUT_FILE_NAME" - 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_10000 $1 town_10000 $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_500000 $1 town_500000 $3 $4 $5 - #run_solver town_1000000 $1 town_1000000 $3 $4 $5 -} - -run_all_graphs bp "fg_bp(seq_fixed) " fg_bp seq_fixed - diff --git a/packages/CLPBN/clpbn/bp/benchmarks/school/run_school_tests.sh b/packages/CLPBN/clpbn/bp/benchmarks/school/run_school_tests.sh index 123c29468..716c03a34 100755 --- a/packages/CLPBN/clpbn/bp/benchmarks/school/run_school_tests.sh +++ b/packages/CLPBN/clpbn/bp/benchmarks/school/run_school_tests.sh @@ -9,7 +9,7 @@ OUT_FILE_NAME=results.log rm -f $OUT_FILE_NAME rm -f ignore.$OUT_FILE_NAME -# yap -g "['../../../../examples/School/sch32'], [missing5], use_module(library(clpbn/learning/em)), graph(L), clpbn:set_clpbn_flag(em_solver,bp), clpbn_horus:set_horus_flag(inf_alg,fg_bp), statistics(runtime, _), em(L,0.01,10,_,Lik), statistics(runtime, [T,_])." +# yap -g "['../../../../examples/School/sch32'], [missing5], use_module(library(clpbn/learning/em)), graph(L), clpbn:set_clpbn_flag(em_solver,bp), clpbn_horus:set_horus_flag(inf_alg, bp), statistics(runtime, _), em(L,0.01,10,_,Lik), statistics(runtime, [T,_])." function run_solver { @@ -58,24 +58,21 @@ function run_all_graphs } -#run_all_graphs bp "hve(min_neighbors) " ve min_neighbors -#run_all_graphs bp "bn_bp(seq_fixed) " bn_bp seq_fixed -run_all_graphs bp "fg_bp(seq_fixed) " fg_bp seq_fixed -#run_all_graphs bp "cbp(seq_fixed) " cbp seq_fixed +#run_all_graphs bp "hve(min_neighbors) " ve min_neighbors +#run_all_graphs bp "bp(seq_fixed) " bp seq_fixed +#run_all_graphs bp "cbp(seq_fixed) " cbp seq_fixed exit -run_all_graphs bp "hve(min_neighbors) " ve min_neighbors -run_all_graphs bp "hve(min_weight) " ve min_weight -run_all_graphs bp "hve(min_fill) " ve min_fill -run_all_graphs bp "hve(w_min_fill) " ve weighted_min_fill -run_all_graphs bp "bn_bp(seq_fixed) " bn_bp seq_fixed -run_all_graphs bp "bn_bp(max_residual) " bn_bp max_residual -run_all_graphs bp "fg_bp(seq_fixed) " fg_bp seq_fixed -run_all_graphs bp "fg_bp(max_residual) " fg_bp max_residual -run_all_graphs bp "cbp(seq_fixed) " cbp seq_fixed -run_all_graphs bp "cbp(max_residual) " cbp max_residual -run_all_graphs gibbs "gibbs " +run_all_graphs bp "hve(min_neighbors) " ve min_neighbors +run_all_graphs bp "hve(min_weight) " ve min_weight +run_all_graphs bp "hve(min_fill) " ve min_fill +run_all_graphs bp "hve(w_min_fill) " ve weighted_min_fill +run_all_graphs bp "bp(seq_fixed) " bp seq_fixed +run_all_graphs bp "bp(max_residual) " bp max_residual +run_all_graphs bp "cbp(seq_fixed) " cbp seq_fixed +run_all_graphs bp "cbp(max_residual) " cbp max_residual +run_all_graphs gibbs "gibbs " echo "************************************************************************" >> "$OUT_FILE_NAME" echo "results for solver ve" >> "$OUT_FILE_NAME" echo "************************************************************************" >> "$OUT_FILE_NAME" diff --git a/packages/CLPBN/clpbn/bp/examples/burglary-alarm.xml b/packages/CLPBN/clpbn/bp/examples/burglary-alarm.xml deleted file mode 100644 index 0c737444f..000000000 --- a/packages/CLPBN/clpbn/bp/examples/burglary-alarm.xml +++ /dev/null @@ -1,81 +0,0 @@ - - - - - - - -Simple Loop - - - B - b1 - b2 - - - - E - e1 - e2 - - - - A - a1 - a2 - - - - J - j1 - j2 - - - - M - m1 - m2 - - - - B - .001 .999
- - - - E - .002 .998
- - - - A - B - E - .95 .05 .94 .06 .29 .71 .001 .999
- - - - J - A - .9 .1 .05 .95
- - - - M - A - .7 .3 .01 .99
- - - - - diff --git a/packages/CLPBN/clpbn/bp/examples/burglary-alarm.yap b/packages/CLPBN/clpbn/bp/examples/burglary-alarm.yap index 4d43f021c..52f9800ec 100644 --- a/packages/CLPBN/clpbn/bp/examples/burglary-alarm.yap +++ b/packages/CLPBN/clpbn/bp/examples/burglary-alarm.yap @@ -3,7 +3,7 @@ %:- set_pfl_flag(solver,ve). :- 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,fg_bp). +%:- set_pfl_flag(solver,bp), clpbn_horus:set_horus_flag(inf_alg,bp). %:- set_pfl_flag(solver,fove). % :- yap_flag(write_strings, off).