From 6986e8c0d7eafadea36846124457a392ebec549f Mon Sep 17 00:00:00 2001 From: Tiago Gomes Date: Mon, 9 Apr 2012 15:40:51 +0100 Subject: [PATCH] Improvements Factor nodes now contain a factor object instead of a pointer. Refactor the way .fg and .uai formats are readed. --- packages/CLPBN/clpbn/bp.yap | 102 +++------ packages/CLPBN/clpbn/bp/BayesBall.cpp | 8 +- packages/CLPBN/clpbn/bp/BayesNet.h | 2 +- packages/CLPBN/clpbn/bp/BpSolver.cpp | 15 +- packages/CLPBN/clpbn/bp/BpSolver.h | 2 +- packages/CLPBN/clpbn/bp/CFactorGraph.cpp | 33 ++- packages/CLPBN/clpbn/bp/FactorGraph.cpp | 256 ++++++++++------------ packages/CLPBN/clpbn/bp/FactorGraph.h | 49 ++--- packages/CLPBN/clpbn/bp/HorusCli.cpp | 5 +- packages/CLPBN/clpbn/bp/HorusYap.cpp | 40 ++-- packages/CLPBN/clpbn/bp/Util.cpp | 4 +- packages/CLPBN/clpbn/bp/Util.h | 2 +- packages/CLPBN/clpbn/bp/Var.cpp | 12 +- packages/CLPBN/clpbn/bp/Var.h | 8 +- packages/CLPBN/clpbn/bp/VarElimSolver.cpp | 3 +- packages/CLPBN/clpbn/horus.yap | 2 +- 16 files changed, 233 insertions(+), 310 deletions(-) diff --git a/packages/CLPBN/clpbn/bp.yap b/packages/CLPBN/clpbn/bp.yap index 07bf7cba3..656cab075 100644 --- a/packages/CLPBN/clpbn/bp.yap +++ b/packages/CLPBN/clpbn/bp.yap @@ -40,7 +40,6 @@ get_pfl_parameters/2 ]). -% :- use_module(library(clpbn/horus)). :- use_module(library(lists)). @@ -53,45 +52,42 @@ [create_ground_network/4, set_bayes_net_params/2, run_ground_solver/3, - set_extra_vars_info/2, + set_vars_information/2, free_ground_network/1 ]). -call_bp_ground(QueryKeys, AllKeys, Factors, Evidence, Solutions) :- +call_bp_ground(QueryKeys, AllKeys, Factors, Evidence, Output) :- b_hash_new(Hash0), keys_to_ids(AllKeys, 0, Hash0, Hash), - %InvMap =.. [view|AllKeys], - list_of_keys_to_ids(QueryKeys, Hash, QueryIds), - evidence_to_ids(Evidence, Hash, EvIds), - factors_to_ids(Factors, Hash, FactorIds), get_factors_type(Factors, Type), + evidence_to_ids(Evidence, Hash, EvidenceIds), + factors_to_ids(Factors, Hash, FactorIds), writeln(type:Type), writeln(''), writeln(allKeys:AllKeys), writeln(''), - %writeln(allKeysIds:Hash), writeln(''), - writeln(queryKeys:QueryKeys), writeln(''), - writeln(queryIds:QueryIds), writeln(''), writeln(factors:Factors), writeln(''), writeln(factorIds:FactorIds), writeln(''), writeln(evidence:Evidence), writeln(''), - writeln(evIds:EvIds), - create_ground_network(Type, FactorIds, EvIds, Network), - run_ground_fixme_solver(ground(Network,Hash), QueryKeys, Solutions). - %free_graphical_model(Network). + writeln(evidenceIds:EvidenceIds), writeln(''), + create_ground_network(Type, FactorIds, EvidenceIds, Network), + %get_vars_information(AllKeys, StatesNames), + %set_vars_information(AllKeys, StatesNames), + run_solver(ground(Network,Hash), QueryKeys, Solutions), + writeln(answer:Solutions), + %clpbn_bind_vals([QueryKeys], Solutions, Output). + free_ground_network(Network). -run_ground_fixme_solver(ground(Network,Hash), QueryKeys, Solutions) :- +run_solver(ground(Network,Hash), QueryKeys, Solutions) :- %get_dists_parameters(DistIds, DistsParams), %set_bayes_net_params(Network, DistsParams), - %vars_to_ids(QueryVars, QueryVarsIds), + list_of_keys_to_ids(QueryKeys, Hash, QueryIds), + writeln(queryKeys:QueryKeys), writeln(''), + writeln(queryIds:QueryIds), writeln(''), list_of_keys_to_ids(QueryKeys, Hash, QueryIds), run_ground_solver(Network, [QueryIds], Solutions). -get_factors_type([f(bayes, _, _)|_], bayes) :- ! . -get_factors_type([f(markov, _, _)|_], markov) :- ! . - - keys_to_ids([], _, Hash, Hash). keys_to_ids([Key|AllKeys], I0, Hash0, Hash) :- b_hash_insert(Hash0, Key, I0, HashI), @@ -99,27 +95,16 @@ keys_to_ids([Key|AllKeys], I0, Hash0, Hash) :- keys_to_ids(AllKeys, I, HashI, Hash). +get_factors_type([f(bayes, _, _)|_], bayes) :- ! . +get_factors_type([f(markov, _, _)|_], markov) :- ! . + + list_of_keys_to_ids([], _, []). list_of_keys_to_ids([Key|QueryKeys], Hash, [Id|QueryIds]) :- b_hash_lookup(Key, Id, Hash), list_of_keys_to_ids(QueryKeys, Hash, QueryIds). -evidence_to_ids([], _, []). -evidence_to_ids([Key=Ev|QueryKeys], Hash, [Id=Ev|QueryIds]) :- - b_hash_lookup(Key, Id, Hash), - evidence_to_ids(QueryKeys, Hash, QueryIds). - - - -%evidence_to_ids([], _, [], []). -%evidence_to_ids([Key=V|QueryKeys], Hash, [Id=V|QueryIds], [Id=Name|QueryNames]) :- -% b_hash_lookup(Key, Id, Hash), -% pfl:skolem(Key,Dom), -% nth0(V, Dom, Name), -% evidence_to_ids(QueryKeys, Hash, QueryIds, QueryNames). - - factors_to_ids([], _, []). factors_to_ids([f(_, Keys, CPT)|Fs], Hash, [f(Ids, Ranges, CPT, DistId)|NFs]) :- list_of_keys_to_ids(Keys, Hash, Ids), @@ -135,6 +120,22 @@ get_ranges(K.Ks, Range.Rs) :- !, get_ranges(Ks, Rs). +evidence_to_ids([], _, []). +evidence_to_ids([Key=Ev|QueryKeys], Hash, [Id=Ev|QueryIds]) :- + b_hash_lookup(Key, Id, Hash), + evidence_to_ids(QueryKeys, Hash, QueryIds). + + +get_vars_information([], []). +get_vars_information(Key.QueryKeys, Domain.StatesNames) :- + pfl:skolem(Key, Domain), + get_vars_information(QueryKeys, StatesNames). + + +finalize_bp_solver(bp(Network, _)) :- + free_ground_network(Network). + + bp([[]],_,_) :- !. bp([QueryVars], AllVars, Output) :- init_bp_solver(_, AllVars, _, Network), @@ -144,53 +145,22 @@ bp([QueryVars], AllVars, Output) :- init_bp_solver(_, AllVars0, _, bp(BayesNet, DistIds)) :- - %writeln('init_bp_solver'), %check_for_agg_vars(AllVars0, AllVars), - %writeln('clpbn_vars:'), print_clpbn_vars(AllVars), get_vars_info(AllVars, VarsInfo, DistIds0), sort(DistIds0, DistIds), create_ground_network(VarsInfo, BayesNet), - %get_extra_vars_info(AllVars, ExtraVarsInfo), - %set_extra_vars_info(BayesNet, ExtraVarsInfo), - %writeln(extravarsinfo:ExtraVarsInfo), true. run_bp_solver(QueryVars, Solutions, bp(Network, DistIds)) :- - %writeln('-> run_bp_solver'), get_dists_parameters(DistIds, DistsParams), set_bayes_net_params(Network, DistsParams), vars_to_ids(QueryVars, QueryVarsIds), run_ground_solver(Network, QueryVarsIds, Solutions). -finalize_bp_solver(bp(Network, _)) :- - free_ground_network(Network). - - -get_extra_vars_info([], []). -get_extra_vars_info([V|Vs], [v(VarId, Label, Domain)|VarsInfo]) :- - get_atts(V, [id(VarId)]), !, - clpbn:get_atts(V, [key(Key), dist(DistId, _)]), - term_to_atom(Key, Label), - get_dist_domain(DistId, Domain0), - numbers_to_atoms(Domain0, Domain), - get_extra_vars_info(Vs, VarsInfo). -get_extra_vars_info([_|Vs], VarsInfo) :- - get_extra_vars_info(Vs, VarsInfo). - - get_dists_parameters([],[]). get_dists_parameters([Id|Ids], [dist(Id, Params)|DistsInfo]) :- get_dist_params(Id, Params), get_dists_parameters(Ids, DistsInfo). - -numbers_to_atoms([], []). -numbers_to_atoms([Atom|L0], [Atom|L]) :- - atom(Atom), !, - numbers_to_atoms(L0, L). -numbers_to_atoms([Number|L0], [Atom|L]) :- - number_atom(Number, Atom), - numbers_to_atoms(L0, L). - diff --git a/packages/CLPBN/clpbn/bp/BayesBall.cpp b/packages/CLPBN/clpbn/bp/BayesBall.cpp index 820c215fc..4d5616874 100644 --- a/packages/CLPBN/clpbn/bp/BayesBall.cpp +++ b/packages/CLPBN/clpbn/bp/BayesBall.cpp @@ -63,12 +63,12 @@ BayesBall::constructGraph (FactorGraph* fg) const const FactorNodes& facNodes = fg_.factorNodes(); for (unsigned i = 0; i < facNodes.size(); i++) { const DAGraphNode* n = dag_.getNode ( - facNodes[i]->factor()->argument (0)); + facNodes[i]->factor().argument (0)); if (n->isMarkedOnTop()) { - fg->addFactor (Factor (*(facNodes[i]->factor()))); + fg->addFactor (Factor (facNodes[i]->factor())); } else if (n->hasEvidence() && n->isVisited()) { - VarIds varIds = { facNodes[i]->factor()->argument (0) }; - Ranges ranges = { facNodes[i]->factor()->range (0) }; + VarIds varIds = { facNodes[i]->factor().argument (0) }; + Ranges ranges = { facNodes[i]->factor().range (0) }; Params params (ranges[0], LogAware::noEvidence()); params[n->getEvidence()] = LogAware::withEvidence(); fg->addFactor (Factor (varIds, ranges, params)); diff --git a/packages/CLPBN/clpbn/bp/BayesNet.h b/packages/CLPBN/clpbn/bp/BayesNet.h index d3e96e450..bd6977ff5 100644 --- a/packages/CLPBN/clpbn/bp/BayesNet.h +++ b/packages/CLPBN/clpbn/bp/BayesNet.h @@ -84,5 +84,5 @@ class DAGraph unordered_map varMap_; }; - #endif // HORUS_BAYESNET_H + diff --git a/packages/CLPBN/clpbn/bp/BpSolver.cpp b/packages/CLPBN/clpbn/bp/BpSolver.cpp index d746d2db3..5722fe957 100644 --- a/packages/CLPBN/clpbn/bp/BpSolver.cpp +++ b/packages/CLPBN/clpbn/bp/BpSolver.cpp @@ -101,7 +101,7 @@ BpSolver::getJointDistributionOf (const VarIds& jointVarIds) VarNode* vn = factorGraph_->getVarNode (jointVarIds[0]); const FactorNodes& factorNodes = vn->neighbors(); for (unsigned i = 0; i < factorNodes.size(); i++) { - if (factorNodes[i]->factor()->contains (jointVarIds)) { + if (factorNodes[i]->factor().contains (jointVarIds)) { idx = i; break; } @@ -109,7 +109,7 @@ BpSolver::getJointDistributionOf (const VarIds& jointVarIds) if (idx == -1) { return getJointByConditioning (jointVarIds); } else { - Factor res (*factorNodes[idx]->factor()); + 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(), @@ -316,9 +316,9 @@ BpSolver::maxResidualSchedule (void) void -BpSolver::calculateFactor2VariableMsg (SpLink* link) const +BpSolver::calculateFactor2VariableMsg (SpLink* link) { - const FactorNode* src = link->getFactor(); + FactorNode* src = link->getFactor(); const VarNode* dst = link->getVariable(); const SpLinkSet& links = ninf(src)->getLinks(); // calculate the product of messages that were sent @@ -357,10 +357,9 @@ BpSolver::calculateFactor2VariableMsg (SpLink* link) const } } - Factor result (src->factor()->arguments(), - src->factor()->ranges(), - msgProduct); - result.multiply (*(src->factor())); + 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; diff --git a/packages/CLPBN/clpbn/bp/BpSolver.h b/packages/CLPBN/clpbn/bp/BpSolver.h index 13fc6243d..c76ccc928 100644 --- a/packages/CLPBN/clpbn/bp/BpSolver.h +++ b/packages/CLPBN/clpbn/bp/BpSolver.h @@ -108,7 +108,7 @@ class BpSolver : public Solver virtual void maxResidualSchedule (void); - virtual void calculateFactor2VariableMsg (SpLink*) const; + virtual void calculateFactor2VariableMsg (SpLink*); virtual Params getVar2FactorMsg (const SpLink*) const; diff --git a/packages/CLPBN/clpbn/bp/CFactorGraph.cpp b/packages/CLPBN/clpbn/bp/CFactorGraph.cpp index b28f13427..30dec03b7 100644 --- a/packages/CLPBN/clpbn/bp/CFactorGraph.cpp +++ b/packages/CLPBN/clpbn/bp/CFactorGraph.cpp @@ -74,20 +74,20 @@ CFactorGraph::setInitialColors (void) if (checkForIdenticalFactors) { unsigned groupCount = 1; for (unsigned i = 0; i < facNodes.size(); i++) { - Factor* f1 = facNodes[i]->factor(); - if (f1->distId() != Util::maxUnsigned()) { + Factor& f1 = facNodes[i]->factor(); + if (f1.distId() != Util::maxUnsigned()) { continue; } - f1->setDistId (groupCount); + f1.setDistId (groupCount); for (unsigned j = i + 1; j < facNodes.size(); j++) { - Factor* f2 = facNodes[j]->factor(); - if (f2->distId() != Util::maxUnsigned()) { + Factor& f2 = facNodes[j]->factor(); + if (f2.distId() != Util::maxUnsigned()) { continue; } - if (f1->size() == f2->size() && - f1->ranges() == f2->ranges() && - f1->params() == f2->params()) { - f2->setDistId (groupCount); + if (f1.size() == f2.size() && + f1.ranges() == f2.ranges() && + f1.params() == f2.params()) { + f2.setDistId (groupCount); } } groupCount ++; @@ -96,7 +96,7 @@ CFactorGraph::setInitialColors (void) // create the initial factor colors DistColorMap distColors; for (unsigned i = 0; i < facNodes.size(); i++) { - unsigned distId = facNodes[i]->factor()->distId(); + unsigned distId = facNodes[i]->factor().distId(); DistColorMap::iterator it = distColors.find (distId); if (it == distColors.end()) { it = distColors.insert (make_pair (distId, getFreeColor())).first; @@ -211,7 +211,7 @@ CFactorGraph::getSignature (const VarNode* varNode) for (unsigned i = 0; i < neighs.size(); i++) { *it = getColor (neighs[i]); it ++; - *it = neighs[i]->factor()->indexOf (varNode->varId()); + *it = neighs[i]->factor().indexOf (varNode->varId()); it ++; } *it = getColor (varNode); @@ -244,7 +244,7 @@ CFactorGraph::getCompressedFactorGraph (void) VarNode* var = varClusters_[i]->getGroundVarNodes()[0]; VarNode* newVar = new VarNode (var); varClusters_[i]->setRepresentativeVariable (newVar); - fg->addVariable (newVar); + fg->addVarNode (newVar); } for (unsigned i = 0; i < facClusters_.size(); i++) { @@ -255,11 +255,10 @@ CFactorGraph::getCompressedFactorGraph (void) VarNode* v = myVarClusters[j]->getRepresentativeVariable(); myGroundVars.push_back (v); } - Factor* newFactor = new Factor (myGroundVars, - facClusters_[i]->getGroundFactors()[0]->params()); - FactorNode* fn = new FactorNode (newFactor); + FactorNode* fn = new FactorNode (Factor (myGroundVars, + facClusters_[i]->getGroundFactors()[0]->params())); facClusters_[i]->setRepresentativeFactor (fn); - fg->addFactor (fn); + fg->addFactorNode (fn); for (unsigned j = 0; j < myGroundVars.size(); j++) { fg->addEdge (fn, static_cast (myGroundVars[j])); } @@ -279,7 +278,7 @@ CFactorGraph::getGroundEdgeCount ( VarNode* varNode = vc->getGroundVarNodes()[0]; unsigned count = 0; for (unsigned i = 0; i < clusterGroundFactors.size(); i++) { - if (clusterGroundFactors[i]->factor()->indexOf (varNode->varId()) != -1) { + if (clusterGroundFactors[i]->factor().indexOf (varNode->varId()) != -1) { count ++; } } diff --git a/packages/CLPBN/clpbn/bp/FactorGraph.cpp b/packages/CLPBN/clpbn/bp/FactorGraph.cpp index 3c8f8f2e6..de8748aa3 100644 --- a/packages/CLPBN/clpbn/bp/FactorGraph.cpp +++ b/packages/CLPBN/clpbn/bp/FactorGraph.cpp @@ -18,21 +18,20 @@ bool FactorGraph::orderFactorVariables = false; FactorGraph::FactorGraph (const FactorGraph& fg) { - const VarNodes& vars = fg.varNodes(); - for (unsigned i = 0; i < vars.size(); i++) { - VarNode* varNode = new VarNode (vars[i]); - addVariable (varNode); + const VarNodes& varNodes = fg.varNodes(); + for (unsigned i = 0; i < varNodes.size(); i++) { + addVarNode (new VarNode (varNodes[i])); } - - const FactorNodes& facs = fg.factorNodes(); - for (unsigned i = 0; i < facs.size(); i++) { - FactorNode* facNode = new FactorNode (facs[i]); - addFactor (facNode); - const VarNodes& neighs = facs[i]->neighbors(); + const FactorNodes& facNodes = fg.factorNodes(); + for (unsigned i = 0; i < facNodes.size(); i++) { + FactorNode* facNode = new FactorNode (facNodes[i]->factor()); + addFactorNode (facNode); + const VarNodes& neighs = facNodes[i]->neighbors(); for (unsigned j = 0; j < neighs.size(); j++) { addEdge (facNode, varNodes_[neighs[j]->getIndex()]); } } + setIndexes(); } @@ -40,82 +39,70 @@ FactorGraph::FactorGraph (const FactorGraph& fg) void FactorGraph::readFromUaiFormat (const char* fileName) { - ifstream is (fileName); + ifstream is (fileName); if (!is.is_open()) { cerr << "error: cannot read from file " + std::string (fileName) << endl; abort(); } - + ignoreLines (is); string line; - while (is.peek() == '#' || is.peek() == '\n') getline (is, line); getline (is, line); if (line != "MARKOV") { cerr << "error: the network must be a MARKOV network " << endl; abort(); } - - while (is.peek() == '#' || is.peek() == '\n') getline (is, line); - unsigned nVars; - is >> nVars; - - while (is.peek() == '#' || is.peek() == '\n') getline (is, line); - vector domainSizes (nVars); - for (unsigned i = 0; i < nVars; i++) { - unsigned ds; - is >> ds; - domainSizes[i] = ds; + // read the number of vars + ignoreLines (is); + unsigned nrVars; + is >> nrVars; + // read the range of each var + ignoreLines (is); + Ranges ranges (nrVars); + for (unsigned i = 0; i < nrVars; i++) { + is >> ranges[i]; } - - while (is.peek() == '#' || is.peek() == '\n') getline (is, line); - for (unsigned i = 0; i < nVars; i++) { - addVariable (new VarNode (i, domainSizes[i])); - } - - unsigned nFactors; - is >> nFactors; - for (unsigned i = 0; i < nFactors; i++) { - while (is.peek() == '#' || is.peek() == '\n') getline (is, line); - unsigned nFactorVars; - is >> nFactorVars; - Vars neighs; - for (unsigned j = 0; j < nFactorVars; j++) { - unsigned vid; + unsigned nrFactors; + unsigned nrArgs; + unsigned vid; + is >> nrFactors; + vector factorVarIds; + vector factorRanges; + for (unsigned i = 0; i < nrFactors; i++) { + ignoreLines (is); + is >> nrArgs; + factorVarIds.push_back ({ }); + factorRanges.push_back ({ }); + for (unsigned j = 0; j < nrArgs; j++) { is >> vid; - VarNode* neigh = getVarNode (vid); - if (!neigh) { - cerr << "error: invalid variable identifier (" << vid << ")" << endl; + if (vid >= ranges.size()) { + cerr << "error: invalid variable identifier `" << vid << "'" << endl; + cerr << "identifiers must be between 0 and " << ranges.size() - 1 ; + cerr << endl; abort(); } - neighs.push_back (neigh); - } - FactorNode* fn = new FactorNode (new Factor (neighs)); - addFactor (fn); - for (unsigned j = 0; j < neighs.size(); j++) { - addEdge (fn, static_cast (neighs[j])); + factorVarIds.back().push_back (vid); + factorRanges.back().push_back (ranges[vid]); } } - - for (unsigned i = 0; i < nFactors; i++) { - while (is.peek() == '#' || is.peek() == '\n') getline (is, line); - unsigned nParams; - is >> nParams; - if (facNodes_[i]->params().size() != nParams) { - cerr << "error: invalid number of parameters for factor " ; - cerr << facNodes_[i]->getLabel() ; - cerr << ", expected: " << facNodes_[i]->params().size(); - cerr << ", given: " << nParams << endl; + // read the parameters + unsigned nrParams; + for (unsigned i = 0; i < nrFactors; i++) { + ignoreLines (is); + is >> nrParams; + if (nrParams != Util::expectedSize (factorRanges[i])) { + cerr << "error: invalid number of parameters for factor nº " << i ; + cerr << ", expected: " << Util::expectedSize (factorRanges[i]); + cerr << ", given: " << nrParams << endl; abort(); } - Params params (nParams); - for (unsigned j = 0; j < nParams; j++) { - double param; - is >> param; - params[j] = param; + Params params (nrParams); + for (unsigned j = 0; j < nrParams; j++) { + is >> params[j]; } if (Globals::logDomain) { Util::toLog (params); } - facNodes_[i]->factor()->setParams (params); + addFactor (Factor (factorVarIds[i], factorRanges[i], params)); } is.close(); setIndexes(); @@ -131,79 +118,51 @@ FactorGraph::readFromLibDaiFormat (const char* fileName) cerr << "error: cannot read from file " + std::string (fileName) << endl; abort(); } - - string line; - unsigned nFactors; - - while ((is.peek()) == '#') getline (is, line); - is >> nFactors; - - if (is.fail()) { - cerr << "error: cannot read the number of factors" << endl; - abort(); - } - - getline (is, line); - if (is.fail() || line.size() > 0) { - cerr << "error: cannot read the number of factors" << endl; - abort(); - } - - for (unsigned i = 0; i < nFactors; i++) { - unsigned nVars; - while ((is.peek()) == '#') getline (is, line); - - is >> nVars; + ignoreLines (is); + unsigned nrFactors; + unsigned nrArgs; + VarId vid; + is >> nrFactors; + for (unsigned i = 0; i < nrFactors; i++) { + ignoreLines (is); + // read the factor arguments + is >> nrArgs; VarIds vids; - for (unsigned j = 0; j < nVars; j++) { - VarId vid; - while ((is.peek()) == '#') getline (is, line); + for (unsigned j = 0; j < nrArgs; j++) { + ignoreLines (is); is >> vid; vids.push_back (vid); } - - Vars neighs; - unsigned nParams = 1; - for (unsigned j = 0; j < nVars; j++) { - unsigned dsize; - while ((is.peek()) == '#') getline (is, line); - is >> dsize; + // read ranges + Ranges ranges (nrArgs); + for (unsigned j = 0; j < nrArgs; j++) { + ignoreLines (is); + is >> ranges[j]; VarNode* var = getVarNode (vids[j]); - if (var == 0) { - var = new VarNode (vids[j], dsize); - addVariable (var); - } else { - if (var->range() != dsize) { - cerr << "error: variable `" << vids[j] << "' appears in two or " ; - cerr << "more factors with different domain sizes" << endl; - } + if (var != 0 && ranges[j] != var->range()) { + cerr << "error: variable `" << vids[j] << "' appears in two or " ; + cerr << "more factors with a different range" << endl; } - neighs.push_back (var); - nParams *= var->range(); } - Params params (nParams, 0); + // read parameters + ignoreLines (is); unsigned nNonzeros; - while ((is.peek()) == '#') getline (is, line); is >> nNonzeros; - + Params params (Util::expectedSize (ranges), 0); for (unsigned j = 0; j < nNonzeros; j++) { + ignoreLines (is); unsigned index; - double val; - while ((is.peek()) == '#') getline (is, line); is >> index; - while ((is.peek()) == '#') getline (is, line); + ignoreLines (is); + double val; is >> val; params[index] = val; } - reverse (neighs.begin(), neighs.end()); + reverse (vids.begin(), vids.end()); if (Globals::logDomain) { Util::toLog (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])); - } + addFactor (Factor (vids, ranges, params)); } is.close(); setIndexes(); @@ -223,30 +182,11 @@ FactorGraph::~FactorGraph (void) -void -FactorGraph::addVariable (VarNode* vn) -{ - varNodes_.push_back (vn); - vn->setIndex (varNodes_.size() - 1); - varMap_.insert (make_pair (vn->varId(), varNodes_.size() - 1)); -} - - - -void -FactorGraph::addFactor (FactorNode* fn) -{ - facNodes_.push_back (fn); - fn->setIndex (facNodes_.size() - 1); -} - - - void FactorGraph::addFactor (const Factor& factor) { FactorNode* fn = new FactorNode (factor); - addFactor (fn); + addFactorNode (fn); const VarIds& vids = factor.arguments(); for (unsigned i = 0; i < vids.size(); i++) { bool found = false; @@ -258,7 +198,7 @@ FactorGraph::addFactor (const Factor& factor) } if (found == false) { VarNode* vn = new VarNode (vids[i], factor.range (i)); - addVariable (vn); + addVarNode (vn); addEdge (vn, fn); } } @@ -266,6 +206,25 @@ FactorGraph::addFactor (const Factor& factor) +void +FactorGraph::addVarNode (VarNode* vn) +{ + varNodes_.push_back (vn); + vn->setIndex (varNodes_.size() - 1); + varMap_.insert (make_pair (vn->varId(), varNodes_.size() - 1)); +} + + + +void +FactorGraph::addFactorNode (FactorNode* fn) +{ + facNodes_.push_back (fn); + fn->setIndex (facNodes_.size() - 1); +} + + + void FactorGraph::addEdge (VarNode* vn, FactorNode* fn) { @@ -301,7 +260,7 @@ FactorGraph::getStructure (void) structure_.addNode (new DAGraphNode (varNodes_[i])); } for (unsigned i = 0; i < facNodes_.size(); i++) { - const VarIds& vids = facNodes_[i]->factor()->arguments(); + const VarIds& vids = facNodes_[i]->factor().arguments(); for (unsigned j = 1; j < vids.size(); j++) { structure_.addEdge (vids[j], vids[0]); } @@ -340,7 +299,7 @@ FactorGraph::print (void) const cout << endl << endl; } for (unsigned i = 0; i < facNodes_.size(); i++) { - facNodes_[i]->factor()->print(); + facNodes_[i]->factor().print(); } } @@ -446,7 +405,7 @@ FactorGraph::exportToLibDaiFormat (const char* fileName) const out << factorVars[j]->range() << " " ; } out << endl; - Params params = facNodes_[i]->factor()->params(); + Params params = facNodes_[i]->factor().params(); if (Globals::logDomain) { Util::fromLog (params); } @@ -461,6 +420,17 @@ FactorGraph::exportToLibDaiFormat (const char* fileName) const +void +FactorGraph::ignoreLines (std::ifstream& is) const +{ + string ignoreStr; + while (is.peek() == '#' || is.peek() == '\n') { + getline (is, ignoreStr); + } +} + + + bool FactorGraph::containsCycle (void) const { diff --git a/packages/CLPBN/clpbn/bp/FactorGraph.h b/packages/CLPBN/clpbn/bp/FactorGraph.h index 3929eb728..17c0657ff 100644 --- a/packages/CLPBN/clpbn/bp/FactorGraph.h +++ b/packages/CLPBN/clpbn/bp/FactorGraph.h @@ -34,47 +34,28 @@ class VarNode : public Var class FactorNode { public: - FactorNode (const FactorNode* fn) - { - factor_ = new Factor (*fn->factor()); - index_ = -1; - } + FactorNode (const Factor& f) : factor_(f), index_(-1) { } - FactorNode (Factor* f) : factor_(new Factor(*f)), index_(-1) { } + const Factor& factor (void) const { return factor_; } - FactorNode (const Factor& f) : factor_(new Factor (f)), index_(-1) { } - - Factor* factor() const { return factor_; } + Factor& factor (void) { return factor_; } void addNeighbor (VarNode* vn) { neighs_.push_back (vn); } - const VarNodes& neighbors (void) const { return neighs_; } + const VarNodes& neighbors (void) const { return neighs_; } - int getIndex (void) const - { - assert (index_ != -1); - return index_; - } + int getIndex (void) const { return index_; } - void setIndex (int index) - { - index_ = index; - } + void setIndex (int index) { index_ = index; } - const Params& params (void) const - { - return factor_->params(); - } + const Params& params (void) const { return factor_.params(); } - string getLabel (void) - { - return factor_->getLabel(); - } + string getLabel (void) { return factor_.getLabel(); } private: DISALLOW_COPY_AND_ASSIGN (FactorNode); - Factor* factor_; + Factor factor_; VarNodes neighs_; int index_; }; @@ -116,12 +97,12 @@ class FactorGraph void readFromLibDaiFormat (const char*); - void addVariable (VarNode*); - - void addFactor (FactorNode*); - void addFactor (const Factor& factor); + void addVarNode (VarNode*); + + void addFactorNode (FactorNode*); + void addEdge (VarNode*, FactorNode*); void addEdge (FactorNode*, VarNode*); @@ -145,6 +126,8 @@ class FactorGraph private: // DISALLOW_COPY_AND_ASSIGN (FactorGraph); + void ignoreLines (std::ifstream&) const; + bool containsCycle (void) const; bool containsCycle (const VarNode*, const FactorNode*, @@ -153,7 +136,7 @@ class FactorGraph bool containsCycle (const FactorNode*, const VarNode*, vector&, vector&) const; - VarNodes varNodes_; + VarNodes varNodes_; FactorNodes facNodes_; bool fromBayesNet_; diff --git a/packages/CLPBN/clpbn/bp/HorusCli.cpp b/packages/CLPBN/clpbn/bp/HorusCli.cpp index 1e0389823..75f25215b 100644 --- a/packages/CLPBN/clpbn/bp/HorusCli.cpp +++ b/packages/CLPBN/clpbn/bp/HorusCli.cpp @@ -31,15 +31,16 @@ main (int argc, const char* argv[]) FactorGraph fg; if (extension == "uai") { fg.readFromUaiFormat (argv[1]); - processArguments (fg, argc, argv); } else if (extension == "fg") { fg.readFromLibDaiFormat (argv[1]); - processArguments (fg, argc, argv); } else { cerr << "error: the graphical model must be defined either " ; cerr << "in a UAI or libDAI file" << endl; exit (0); } + fg.print(); + assert (false); + processArguments (fg, argc, argv); return 0; } diff --git a/packages/CLPBN/clpbn/bp/HorusYap.cpp b/packages/CLPBN/clpbn/bp/HorusYap.cpp index 9384c10b5..18d0680e8 100644 --- a/packages/CLPBN/clpbn/bp/HorusYap.cpp +++ b/packages/CLPBN/clpbn/bp/HorusYap.cpp @@ -214,8 +214,6 @@ createGroundNetwork (void) { FactorGraph* fg = new FactorGraph();; string factorsType ((char*) YAP_AtomName (YAP_AtomOfTerm (YAP_ARG1))); - cout << "factors type: '" << factorsType << "'" << endl; - YAP_Term factorList = YAP_ARG2; while (factorList != YAP_TermNil()) { YAP_Term factor = YAP_HeadOfTerm (factorList); @@ -240,7 +238,6 @@ createGroundNetwork (void) YAP_Term evTerm = YAP_HeadOfTerm (evidenceList); unsigned vid = (unsigned) YAP_IntOfTerm ((YAP_ArgOfTerm (1, evTerm))); unsigned ev = (unsigned) YAP_IntOfTerm ((YAP_ArgOfTerm (2, evTerm))); - cout << vid << " == " << ev << endl; assert (fg->getVarNode (vid)); fg->getVarNode (vid)->setEvidence (ev); evidenceList = YAP_TailOfTerm (evidenceList); @@ -354,7 +351,7 @@ runGroundSolver (void) } else { runBpSolver (fg, tasks, results); } - cout << "results: " << results << endl; + YAP_Term list = YAP_TermNil(); for (int i = results.size() - 1; i >= 0; i--) { const Params& beliefs = results[i]; @@ -491,24 +488,29 @@ setBayesNetParams (void) int -setExtraVarsInfo (void) +setVarsInformation (void) { - Var::clearVariablesInformation(); - YAP_Term varsInfoL = YAP_ARG2; - while (varsInfoL != YAP_TermNil()) { - YAP_Term head = YAP_HeadOfTerm (varsInfoL); - VarId vid = YAP_IntOfTerm (YAP_ArgOfTerm (1, head)); - YAP_Atom label = YAP_AtomOfTerm (YAP_ArgOfTerm (2, head)); - YAP_Term statesL = YAP_ArgOfTerm (3, head); + Var::clearVarsInfo(); + YAP_Term labelsL = YAP_ARG1; + vector labels; + while (labelsL != YAP_TermNil()) { + YAP_Atom atom = YAP_AtomOfTerm (YAP_HeadOfTerm (labelsL)); + labels.push_back ((char*) YAP_AtomName (atom)); + labelsL = YAP_TailOfTerm (labelsL); + } + unsigned count = 0; + YAP_Term stateNamesL = YAP_ARG2; + while (stateNamesL != YAP_TermNil()) { States states; - while (statesL != YAP_TermNil()) { - YAP_Atom atom = YAP_AtomOfTerm (YAP_HeadOfTerm (statesL)); + YAP_Term namesL = YAP_HeadOfTerm (stateNamesL); + while (namesL != YAP_TermNil()) { + YAP_Atom atom = YAP_AtomOfTerm (YAP_HeadOfTerm (namesL)); states.push_back ((char*) YAP_AtomName (atom)); - statesL = YAP_TailOfTerm (statesL); + namesL = YAP_TailOfTerm (namesL); } - Var::addVariableInformation (vid, - (char*) YAP_AtomName (label), states); - varsInfoL = YAP_TailOfTerm (varsInfoL); + Var::addVarInfo (count, labels[count], states); + count ++; + stateNamesL = YAP_TailOfTerm (stateNamesL); } return TRUE; } @@ -627,7 +629,7 @@ init_predicates (void) YAP_UserCPredicate ("run_ground_solver", runGroundSolver, 3); YAP_UserCPredicate ("set_parfactors_params", setParfactorsParams, 2); YAP_UserCPredicate ("set_bayes_net_params", setBayesNetParams, 2); - YAP_UserCPredicate ("set_extra_vars_info", setExtraVarsInfo, 2); + YAP_UserCPredicate ("set_vars_information", setVarsInformation, 2); YAP_UserCPredicate ("set_horus_flag", setHorusFlag, 2); YAP_UserCPredicate ("free_parfactors", freeParfactors, 1); YAP_UserCPredicate ("free_ground_network", freeGroundNetwork, 1); diff --git a/packages/CLPBN/clpbn/bp/Util.cpp b/packages/CLPBN/clpbn/bp/Util.cpp index 7a3d4f2a2..1c3d6c441 100644 --- a/packages/CLPBN/clpbn/bp/Util.cpp +++ b/packages/CLPBN/clpbn/bp/Util.cpp @@ -366,12 +366,12 @@ Statistics::printStatistics (void) void -Statistics::writeStatisticsToFile (const char* fileName) +Statistics::writeStatistics (const char* fileName) { ofstream out (fileName); if (!out.is_open()) { cerr << "error: cannot open file to write at " ; - cerr << "Statistics::writeStatisticsToFile()" << endl; + cerr << "Statistics::writeStats()" << endl; abort(); } out << getStatisticString(); diff --git a/packages/CLPBN/clpbn/bp/Util.h b/packages/CLPBN/clpbn/bp/Util.h index 4e053dab2..e7af16311 100644 --- a/packages/CLPBN/clpbn/bp/Util.h +++ b/packages/CLPBN/clpbn/bp/Util.h @@ -359,7 +359,7 @@ class Statistics static void printStatistics (void); - static void writeStatisticsToFile (const char*); + static void writeStatistics (const char*); static void updateCompressingStatistics ( unsigned, unsigned, unsigned, unsigned, unsigned); diff --git a/packages/CLPBN/clpbn/bp/Var.cpp b/packages/CLPBN/clpbn/bp/Var.cpp index c359e0747..b786a302d 100644 --- a/packages/CLPBN/clpbn/bp/Var.cpp +++ b/packages/CLPBN/clpbn/bp/Var.cpp @@ -42,7 +42,7 @@ Var::isValidState (int stateIndex) bool Var::isValidState (const string& stateName) { - States states = Var::getVarInformation (varId_).states; + States states = Var::getVarInfo (varId_).states; return Util::contains (states, stateName); } @@ -60,7 +60,7 @@ Var::setEvidence (int ev) void Var::setEvidence (const string& ev) { - States states = Var::getVarInformation (varId_).states; + States states = Var::getVarInfo (varId_).states; for (unsigned i = 0; i < states.size(); i++) { if (states[i] == ev) { evidence_ = i; @@ -75,8 +75,8 @@ Var::setEvidence (const string& ev) string Var::label (void) const { - if (Var::variablesHaveInformation()) { - return Var::getVarInformation (varId_).label; + if (Var::varsHaveInfo()) { + return Var::getVarInfo (varId_).label; } stringstream ss; ss << "x" << varId_; @@ -88,8 +88,8 @@ Var::label (void) const States Var::states (void) const { - if (Var::variablesHaveInformation()) { - return Var::getVarInformation (varId_).states; + if (Var::varsHaveInfo()) { + return Var::getVarInfo (varId_).states; } States states; for (unsigned i = 0; i < range_; i++) { diff --git a/packages/CLPBN/clpbn/bp/Var.h b/packages/CLPBN/clpbn/bp/Var.h index e3ae62e19..ce759330b 100644 --- a/packages/CLPBN/clpbn/bp/Var.h +++ b/packages/CLPBN/clpbn/bp/Var.h @@ -71,25 +71,25 @@ class Var States states (void) const; - static void addVariableInformation ( + static void addVarInfo ( 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) + static VarInfo getVarInfo (VarId vid) { assert (Util::contains (varsInfo_, vid)); return varsInfo_.find (vid)->second; } - static bool variablesHaveInformation (void) + static bool varsHaveInfo (void) { return varsInfo_.size() != 0; } - static void clearVariablesInformation (void) + static void clearVarsInfo (void) { varsInfo_.clear(); } diff --git a/packages/CLPBN/clpbn/bp/VarElimSolver.cpp b/packages/CLPBN/clpbn/bp/VarElimSolver.cpp index c12019eb9..beb89b21e 100644 --- a/packages/CLPBN/clpbn/bp/VarElimSolver.cpp +++ b/packages/CLPBN/clpbn/bp/VarElimSolver.cpp @@ -60,7 +60,7 @@ VarElimSolver::createFactorList (void) 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())); + factorList_.push_back (new Factor (factorNodes[i]->factor())); // FIXME const VarNodes& neighs = factorNodes[i]->neighbors(); for (unsigned j = 0; j < neighs.size(); j++) { unordered_map >::iterator it @@ -95,7 +95,6 @@ VarElimSolver::absorveEvidence (void) } } } - printActiveFactors(); } diff --git a/packages/CLPBN/clpbn/horus.yap b/packages/CLPBN/clpbn/horus.yap index 37c5109a0..80e791e13 100644 --- a/packages/CLPBN/clpbn/horus.yap +++ b/packages/CLPBN/clpbn/horus.yap @@ -12,7 +12,7 @@ set_bayes_net_params/2, run_lifted_solver/3, run_ground_solver/3, - set_extra_vars_info/2, + set_vars_information/2, set_horus_flag/2, free_parfactors/1, free_ground_network/1