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This commit is contained in:
Tiago Gomes 2012-12-21 15:20:28 +00:00
parent 4b901d26d7
commit d8c5725b2e
52 changed files with 0 additions and 14293 deletions
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84
packages/CLPBN/horus2/BayesBall.cpp
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#include <cstdlib>
#include <cassert>
#include <iostream>
#include <fstream>
#include <sstream>
#include "BayesBall.h"
#include "Util.h"
FactorGraph*
BayesBall::getMinimalFactorGraph (const VarIds& queryIds)
{
assert (fg_.bayesianFactors());
Scheduling scheduling;
for (size_t i = 0; i < queryIds.size(); i++) {
assert (dag_.getNode (queryIds[i]));
BBNode* n = dag_.getNode (queryIds[i]);
scheduling.push (ScheduleInfo (n, false, true));
}
while (!scheduling.empty()) {
ScheduleInfo& sch = scheduling.front();
BBNode* n = sch.node;
n->setAsVisited();
if (n->hasEvidence() == false && sch.visitedFromChild) {
if (n->isMarkedOnTop() == false) {
n->markOnTop();
scheduleParents (n, scheduling);
}
if (n->isMarkedOnBottom() == false) {
n->markOnBottom();
scheduleChilds (n, scheduling);
}
}
if (sch.visitedFromParent) {
if (n->hasEvidence() && n->isMarkedOnTop() == false) {
n->markOnTop();
scheduleParents (n, scheduling);
}
if (n->hasEvidence() == false && n->isMarkedOnBottom() == false) {
n->markOnBottom();
scheduleChilds (n, scheduling);
}
}
scheduling.pop();
}
FactorGraph* fg = new FactorGraph();
constructGraph (fg);
return fg;
}
void
BayesBall::constructGraph (FactorGraph* fg) const
{
const FacNodes& facNodes = fg_.facNodes();
for (size_t i = 0; i < facNodes.size(); i++) {
const BBNode* n = dag_.getNode (
facNodes[i]->factor().argument (0));
if (n->isMarkedOnTop()) {
fg->addFactor (facNodes[i]->factor());
} else if (n->hasEvidence() && n->isVisited()) {
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));
}
}
const VarNodes& varNodes = fg_.varNodes();
for (size_t i = 0; i < varNodes.size(); i++) {
if (varNodes[i]->hasEvidence()) {
VarNode* vn = fg->getVarNode (varNodes[i]->varId());
if (vn) {
vn->setEvidence (varNodes[i]->getEvidence());
}
}
}
}

85
packages/CLPBN/horus2/BayesBall.h
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#ifndef HORUS_BAYESBALL_H
#define HORUS_BAYESBALL_H
#include <vector>
#include <queue>
#include <list>
#include <map>
#include "FactorGraph.h"
#include "BayesBallGraph.h"
#include "Horus.h"
using namespace std;
struct ScheduleInfo
{
ScheduleInfo (BBNode* n, bool vfp, bool vfc) :
node(n), visitedFromParent(vfp), visitedFromChild(vfc) { }
BBNode* node;
bool visitedFromParent;
bool visitedFromChild;
};
typedef queue<ScheduleInfo, list<ScheduleInfo>> Scheduling;
class BayesBall
{
public:
BayesBall (FactorGraph& fg)
: fg_(fg) , dag_(fg.getStructure())
{
dag_.clear();
}
FactorGraph* getMinimalFactorGraph (const VarIds&);
static FactorGraph* getMinimalFactorGraph (FactorGraph& fg, VarIds vids)
{
BayesBall bb (fg);
return bb.getMinimalFactorGraph (vids);
}
private:
void constructGraph (FactorGraph* fg) const;
void scheduleParents (const BBNode* n, Scheduling& sch) const;
void scheduleChilds (const BBNode* n, Scheduling& sch) const;
FactorGraph& fg_;
BayesBallGraph& dag_;
};
inline void
BayesBall::scheduleParents (const BBNode* n, Scheduling& sch) const
{
const vector<BBNode*>& ps = n->parents();
for (vector<BBNode*>::const_iterator it = ps.begin();
it != ps.end(); ++it) {
sch.push (ScheduleInfo (*it, false, true));
}
}
inline void
BayesBall::scheduleChilds (const BBNode* n, Scheduling& sch) const
{
const vector<BBNode*>& cs = n->childs();
for (vector<BBNode*>::const_iterator it = cs.begin();
it != cs.end(); ++it) {
sch.push (ScheduleInfo (*it, true, false));
}
}
#endif // HORUS_BAYESBALL_H

106
packages/CLPBN/horus2/BayesBallGraph.cpp
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#include <cstdlib>
#include <cassert>
#include <iostream>
#include <fstream>
#include <sstream>
#include "BayesBallGraph.h"
#include "Util.h"
void
BayesBallGraph::addNode (BBNode* n)
{
assert (Util::contains (varMap_, n->varId()) == false);
nodes_.push_back (n);
varMap_[n->varId()] = n;
}
void
BayesBallGraph::addEdge (VarId vid1, VarId vid2)
{
unordered_map<VarId, BBNode*>::iterator it1;
unordered_map<VarId, BBNode*>::iterator it2;
it1 = varMap_.find (vid1);
it2 = varMap_.find (vid2);
assert (it1 != varMap_.end());
assert (it2 != varMap_.end());
it1->second->addChild (it2->second);
it2->second->addParent (it1->second);
}
const BBNode*
BayesBallGraph::getNode (VarId vid) const
{
unordered_map<VarId, BBNode*>::const_iterator it;
it = varMap_.find (vid);
return it != varMap_.end() ? it->second : 0;
}
BBNode*
BayesBallGraph::getNode (VarId vid)
{
unordered_map<VarId, BBNode*>::const_iterator it;
it = varMap_.find (vid);
return it != varMap_.end() ? it->second : 0;
}
void
BayesBallGraph::setIndexes (void)
{
for (size_t i = 0; i < nodes_.size(); i++) {
nodes_[i]->setIndex (i);
}
}
void
BayesBallGraph::clear (void)
{
for (size_t i = 0; i < nodes_.size(); i++) {
nodes_[i]->clear();
}
}
void
BayesBallGraph::exportToGraphViz (const char* fileName)
{
ofstream out (fileName);
if (!out.is_open()) {
cerr << "Error: couldn't open file '" << fileName << "'." ;
return;
}
out << "digraph {" << endl;
out << "ranksep=1" << endl;
for (size_t i = 0; i < nodes_.size(); i++) {
out << nodes_[i]->varId() ;
out << " [" ;
out << "label=\"" << nodes_[i]->label() << "\"" ;
if (nodes_[i]->hasEvidence()) {
out << ",style=filled, fillcolor=yellow" ;
}
out << "]" << endl;
}
for (size_t i = 0; i < nodes_.size(); i++) {
const vector<BBNode*>& childs = nodes_[i]->childs();
for (size_t j = 0; j < childs.size(); j++) {
out << nodes_[i]->varId() << " -> " << childs[j]->varId();
out << " [style=bold]" << endl ;
}
}
out << "}" << endl;
out.close();
}

84
packages/CLPBN/horus2/BayesBallGraph.h
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#ifndef HORUS_BAYESBALLGRAPH_H
#define HORUS_BAYESBALLGRAPH_H
#include <vector>
#include <queue>
#include <list>
#include <map>
#include "Var.h"
#include "Horus.h"
using namespace std;
class BBNode : public Var
{
public:
BBNode (Var* v) : Var (v) , visited_(false),
markedOnTop_(false), markedOnBottom_(false) { }
const vector<BBNode*>& childs (void) const { return childs_; }
vector<BBNode*>& childs (void) { return childs_; }
const vector<BBNode*>& parents (void) const { return parents_; }
vector<BBNode*>& parents (void) { return parents_; }
void addParent (BBNode* p) { parents_.push_back (p); }
void addChild (BBNode* c) { childs_.push_back (c); }
bool isVisited (void) const { return visited_; }
void setAsVisited (void) { visited_ = true; }
bool isMarkedOnTop (void) const { return markedOnTop_; }
void markOnTop (void) { markedOnTop_ = true; }
bool isMarkedOnBottom (void) const { return markedOnBottom_; }
void markOnBottom (void) { markedOnBottom_ = true; }
void clear (void) { visited_ = markedOnTop_ = markedOnBottom_ = false; }
private:
bool visited_;
bool markedOnTop_;
bool markedOnBottom_;
vector<BBNode*> childs_;
vector<BBNode*> parents_;
};
class BayesBallGraph
{
public:
BayesBallGraph (void) { }
void addNode (BBNode* n);
void addEdge (VarId vid1, VarId vid2);
const BBNode* getNode (VarId vid) const;
BBNode* getNode (VarId vid);
bool empty (void) const { return nodes_.empty(); }
void setIndexes (void);
void clear (void);
void exportToGraphViz (const char*);
private:
vector<BBNode*> nodes_;
unordered_map<VarId, BBNode*> varMap_;
};
#endif // HORUS_BAYESBALLGRAPH_H

471
packages/CLPBN/horus2/BeliefProp.cpp
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#include <cassert>
#include <limits>
#include <algorithm>
#include <iostream>
#include "BeliefProp.h"
#include "FactorGraph.h"
#include "Factor.h"
#include "Indexer.h"
#include "Horus.h"
BeliefProp::BeliefProp (const FactorGraph& fg) : GroundSolver (fg)
{
runned_ = false;
}
BeliefProp::~BeliefProp (void)
{
for (size_t i = 0; i < varsI_.size(); i++) {
delete varsI_[i];
}
for (size_t i = 0; i < facsI_.size(); i++) {
delete facsI_[i];
}
for (size_t i = 0; i < links_.size(); i++) {
delete links_[i];
}
}
Params
BeliefProp::solveQuery (VarIds queryVids)
{
assert (queryVids.empty() == false);
return queryVids.size() == 1
? getPosterioriOf (queryVids[0])
: getJointDistributionOf (queryVids);
}
void
BeliefProp::printSolverFlags (void) const
{
stringstream ss;
ss << "belief propagation [" ;
ss << "schedule=" ;
typedef BpOptions::Schedule Sch;
switch (BpOptions::schedule) {
case Sch::SEQ_FIXED: ss << "seq_fixed"; break;
case Sch::SEQ_RANDOM: ss << "seq_random"; break;
case Sch::PARALLEL: ss << "parallel"; break;
case Sch::MAX_RESIDUAL: ss << "max_residual"; break;
}
ss << ",max_iter=" << Util::toString (BpOptions::maxIter);
ss << ",accuracy=" << Util::toString (BpOptions::accuracy);
ss << ",log_domain=" << Util::toString (Globals::logDomain);
ss << "]" ;
cout << ss.str() << endl;
}
Params
BeliefProp::getPosterioriOf (VarId vid)
{
if (runned_ == false) {
runSolver();
}
assert (fg.getVarNode (vid));
VarNode* var = fg.getVarNode (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 BpLinks& links = ninf(var)->getLinks();
if (Globals::logDomain) {
for (size_t i = 0; i < links.size(); i++) {
probs += links[i]->message();
}
LogAware::normalize (probs);
Util::exp (probs);
} else {
for (size_t i = 0; i < links.size(); i++) {
probs *= links[i]->message();
}
LogAware::normalize (probs);
}
}
return probs;
}
Params
BeliefProp::getJointDistributionOf (const VarIds& jointVarIds)
{
if (runned_ == false) {
runSolver();
}
VarNode* vn = fg.getVarNode (jointVarIds[0]);
const FacNodes& facNodes = vn->neighbors();
size_t idx = facNodes.size();
for (size_t i = 0; i < facNodes.size(); i++) {
if (facNodes[i]->factor().contains (jointVarIds)) {
idx = i;
break;
}
}
if (idx == facNodes.size()) {
return getJointByConditioning (jointVarIds);
}
return getFactorJoint (facNodes[idx], jointVarIds);
}
Params
BeliefProp::getFactorJoint (
FacNode* fn,
const VarIds& jointVarIds)
{
if (runned_ == false) {
runSolver();
}
Factor res (fn->factor());
const BpLinks& links = ninf(fn)->getLinks();
for (size_t i = 0; i < links.size(); i++) {
Factor msg ({links[i]->varNode()->varId()},
{links[i]->varNode()->range()},
getVarToFactorMsg (links[i]));
res.multiply (msg);
}
res.sumOutAllExcept (jointVarIds);
res.reorderArguments (jointVarIds);
res.normalize();
Params jointDist = res.params();
if (Globals::logDomain) {
Util::exp (jointDist);
}
return jointDist;
}
void
BeliefProp::runSolver (void)
{
initializeSolver();
nIters_ = 0;
while (!converged() && nIters_ < BpOptions::maxIter) {
nIters_ ++;
if (Globals::verbosity > 1) {
Util::printHeader (string ("Iteration ") + Util::toString (nIters_));
}
switch (BpOptions::schedule) {
case BpOptions::Schedule::SEQ_RANDOM:
std::random_shuffle (links_.begin(), links_.end());
// no break
case BpOptions::Schedule::SEQ_FIXED:
for (size_t i = 0; i < links_.size(); i++) {
calculateAndUpdateMessage (links_[i]);
}
break;
case BpOptions::Schedule::PARALLEL:
for (size_t i = 0; i < links_.size(); i++) {
calculateMessage (links_[i]);
}
for (size_t i = 0; i < links_.size(); i++) {
updateMessage(links_[i]);
}
break;
case BpOptions::Schedule::MAX_RESIDUAL:
maxResidualSchedule();
break;
}
}
if (Globals::verbosity > 0) {
if (nIters_ < BpOptions::maxIter) {
cout << "Belief propagation converged in " ;
cout << nIters_ << " iterations" << endl;
} else {
cout << "The maximum number of iterations was hit, terminating..." ;
cout << endl;
}
cout << endl;
}
runned_ = true;
}
void
BeliefProp::createLinks (void)
{
const FacNodes& facNodes = fg.facNodes();
for (size_t i = 0; i < facNodes.size(); i++) {
const VarNodes& neighbors = facNodes[i]->neighbors();
for (size_t j = 0; j < neighbors.size(); j++) {
links_.push_back (new BpLink (facNodes[i], neighbors[j]));
}
}
}
void
BeliefProp::maxResidualSchedule (void)
{
if (nIters_ == 1) {
for (size_t 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 (size_t c = 0; c < links_.size(); c++) {
if (Globals::verbosity > 1) {
cout << "current residuals:" << endl;
for (SortedOrder::iterator it = sortedOrder_.begin();
it != sortedOrder_.end(); ++it) {
cout << " " << setw (30) << left << (*it)->toString();
cout << "residual = " << (*it)->residual() << endl;
}
}
SortedOrder::iterator it = sortedOrder_.begin();
BpLink* link = *it;
if (link->residual() < 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 FacNodes& factorNeighbors = link->varNode()->neighbors();
for (size_t i = 0; i < factorNeighbors.size(); i++) {
if (factorNeighbors[i] != link->facNode()) {
const BpLinks& links = ninf(factorNeighbors[i])->getLinks();
for (size_t j = 0; j < links.size(); j++) {
if (links[j]->varNode() != link->varNode()) {
calculateMessage (links[j]);
BpLinkMap::iterator iter = linkMap_.find (links[j]);
sortedOrder_.erase (iter->second);
iter->second = sortedOrder_.insert (links[j]);
}
}
}
}
if (Globals::verbosity > 1) {
Util::printDashedLine();
}
}
}
void
BeliefProp::calcFactorToVarMsg (BpLink* link)
{
FacNode* src = link->facNode();
const VarNode* dst = link->varNode();
const BpLinks& links = ninf(src)->getLinks();
// calculate the product of messages that were sent
// to factor `src', except from var `dst'
unsigned reps = 1;
unsigned msgSize = Util::sizeExpected (src->factor().ranges());
Params msgProduct (msgSize, LogAware::multIdenty());
if (Globals::logDomain) {
for (size_t i = links.size(); i-- > 0; ) {
if (links[i]->varNode() != dst) {
if (Constants::SHOW_BP_CALCS) {
cout << " message from " << links[i]->varNode()->label();
cout << ": " ;
}
Util::apply_n_times (msgProduct, getVarToFactorMsg (links[i]),
reps, std::plus<double>());
if (Constants::SHOW_BP_CALCS) {
cout << endl;
}
}
reps *= links[i]->varNode()->range();
}
} else {
for (size_t i = links.size(); i-- > 0; ) {
if (links[i]->varNode() != dst) {
if (Constants::SHOW_BP_CALCS) {
cout << " message from " << links[i]->varNode()->label();
cout << ": " ;
}
Util::apply_n_times (msgProduct, getVarToFactorMsg (links[i]),
reps, std::multiplies<double>());
if (Constants::SHOW_BP_CALCS) {
cout << endl;
}
}
reps *= links[i]->varNode()->range();
}
}
Factor result (src->factor().arguments(),
src->factor().ranges(), msgProduct);
result.multiply (src->factor());
if (Constants::SHOW_BP_CALCS) {
cout << " message product: " << msgProduct << endl;
cout << " original factor: " << src->factor().params() << endl;
cout << " factor product: " << result.params() << endl;
}
result.sumOutAllExcept (dst->varId());
if (Constants::SHOW_BP_CALCS) {
cout << " marginalized: " << result.params() << endl;
}
link->nextMessage() = result.params();
LogAware::normalize (link->nextMessage());
if (Constants::SHOW_BP_CALCS) {
cout << " curr msg: " << link->message() << endl;
cout << " next msg: " << link->nextMessage() << endl;
}
}
Params
BeliefProp::getVarToFactorMsg (const BpLink* link) const
{
const VarNode* src = link->varNode();
Params msg;
if (src->hasEvidence()) {
msg.resize (src->range(), LogAware::noEvidence());
msg[src->getEvidence()] = LogAware::withEvidence();
} else {
msg.resize (src->range(), LogAware::one());
}
if (Constants::SHOW_BP_CALCS) {
cout << msg;
}
BpLinks::const_iterator it;
const BpLinks& links = ninf (src)->getLinks();
if (Globals::logDomain) {
for (it = links.begin(); it != links.end(); ++it) {
if (*it != link) {
msg += (*it)->message();
}
if (Constants::SHOW_BP_CALCS) {
cout << " x " << (*it)->message();
}
}
} else {
for (it = links.begin(); it != links.end(); ++it) {
if (*it != link) {
msg *= (*it)->message();
}
if (Constants::SHOW_BP_CALCS) {
cout << " x " << (*it)->message();
}
}
}
if (Constants::SHOW_BP_CALCS) {
cout << " = " << msg;
}
return msg;
}
Params
BeliefProp::getJointByConditioning (const VarIds& jointVarIds) const
{
return GroundSolver::getJointByConditioning (
GroundSolverType::BP, fg, jointVarIds);
}
void
BeliefProp::initializeSolver (void)
{
const VarNodes& varNodes = fg.varNodes();
varsI_.reserve (varNodes.size());
for (size_t i = 0; i < varNodes.size(); i++) {
varsI_.push_back (new SPNodeInfo());
}
const FacNodes& facNodes = fg.facNodes();
facsI_.reserve (facNodes.size());
for (size_t i = 0; i < facNodes.size(); i++) {
facsI_.push_back (new SPNodeInfo());
}
createLinks();
for (size_t i = 0; i < links_.size(); i++) {
FacNode* src = links_[i]->facNode();
VarNode* dst = links_[i]->varNode();
ninf (dst)->addBpLink (links_[i]);
ninf (src)->addBpLink (links_[i]);
}
}
bool
BeliefProp::converged (void)
{
if (links_.size() == 0) {
return true;
}
if (nIters_ == 0) {
return false;
}
if (Globals::verbosity > 2) {
cout << endl;
}
if (nIters_ == 1) {
if (Globals::verbosity > 1) {
cout << "no residuals" << endl << endl;
}
return false;
}
bool converged = true;
if (BpOptions::schedule == BpOptions::Schedule::MAX_RESIDUAL) {
double maxResidual = (*(sortedOrder_.begin()))->residual();
if (maxResidual > BpOptions::accuracy) {
converged = false;
} else {
converged = true;
}
} else {
for (size_t i = 0; i < links_.size(); i++) {
double residual = links_[i]->residual();
if (Globals::verbosity > 1) {
cout << links_[i]->toString() + " residual = " << residual << endl;
}
if (residual > BpOptions::accuracy) {
converged = false;
if (Globals::verbosity < 2) {
break;
}
}
}
if (Globals::verbosity > 1) {
cout << endl;
}
}
return converged;
}
void
BeliefProp::printLinkInformation (void) const
{
for (size_t i = 0; i < links_.size(); i++) {
BpLink* l = links_[i];
cout << l->toString() << ":" << endl;
cout << " curr msg = " ;
cout << l->message() << endl;
cout << " next msg = " ;
cout << l->nextMessage() << endl;
cout << " residual = " << l->residual() << endl;
}
}

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packages/CLPBN/horus2/BeliefProp.h
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#ifndef HORUS_BELIEFPROP_H
#define HORUS_BELIEFPROP_H
#include <set>
#include <vector>
#include <sstream>
#include "GroundSolver.h"
#include "Factor.h"
#include "FactorGraph.h"
#include "Util.h"
using namespace std;
class BpLink
{
public:
BpLink (FacNode* fn, VarNode* vn)
{
fac_ = fn;
var_ = vn;
v1_.resize (vn->range(), LogAware::log (1.0 / vn->range()));
v2_.resize (vn->range(), LogAware::log (1.0 / vn->range()));
currMsg_ = &v1_;
nextMsg_ = &v2_;
residual_ = 0.0;
}
virtual ~BpLink (void) { };
FacNode* facNode (void) const { return fac_; }
VarNode* varNode (void) const { return var_; }
const Params& message (void) const { return *currMsg_; }
Params& nextMessage (void) { return *nextMsg_; }
double residual (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_);
}
string toString (void) const
{
stringstream ss;
ss << fac_->getLabel();
ss << " -- " ;
ss << var_->label();
return ss.str();
}
protected:
FacNode* fac_;
VarNode* var_;
Params v1_;
Params v2_;
Params* currMsg_;
Params* nextMsg_;
double residual_;
};
typedef vector<BpLink*> BpLinks;
class SPNodeInfo
{
public:
void addBpLink (BpLink* link) { links_.push_back (link); }
const BpLinks& getLinks (void) { return links_; }
private:
BpLinks links_;
};
class BeliefProp : public GroundSolver
{
public:
BeliefProp (const FactorGraph&);
virtual ~BeliefProp (void);
Params solveQuery (VarIds);
virtual void printSolverFlags (void) const;
virtual Params getPosterioriOf (VarId);
virtual Params getJointDistributionOf (const VarIds&);
protected:
void runSolver (void);
virtual void createLinks (void);
virtual void maxResidualSchedule (void);
virtual void calcFactorToVarMsg (BpLink*);
virtual Params getVarToFactorMsg (const BpLink*) const;
virtual Params getJointByConditioning (const VarIds&) const;
public:
Params getFactorJoint (FacNode* fn, const VarIds&);
protected:
SPNodeInfo* ninf (const VarNode* var) const
{
return varsI_[var->getIndex()];
}
SPNodeInfo* ninf (const FacNode* fac) const
{
return facsI_[fac->getIndex()];
}
void calculateAndUpdateMessage (BpLink* link, bool calcResidual = true)
{
if (Globals::verbosity > 2) {
cout << "calculating & updating " << link->toString() << endl;
}
calcFactorToVarMsg (link);
if (calcResidual) {
link->updateResidual();
}
link->updateMessage();
}
void calculateMessage (BpLink* link, bool calcResidual = true)
{
if (Globals::verbosity > 2) {
cout << "calculating " << link->toString() << endl;
}
calcFactorToVarMsg (link);
if (calcResidual) {
link->updateResidual();
}
}
void updateMessage (BpLink* link)
{
link->updateMessage();
if (Globals::verbosity > 2) {
cout << "updating " << link->toString() << endl;
}
}
struct CompareResidual
{
inline bool operator() (const BpLink* link1, const BpLink* link2)
{
return link1->residual() > link2->residual();
}
};
BpLinks links_;
unsigned nIters_;
vector<SPNodeInfo*> varsI_;
vector<SPNodeInfo*> facsI_;
bool runned_;
typedef multiset<BpLink*, CompareResidual> SortedOrder;
SortedOrder sortedOrder_;
typedef unordered_map<BpLink*, SortedOrder::iterator> BpLinkMap;
BpLinkMap linkMap_;
private:
void initializeSolver (void);
bool converged (void);
virtual void printLinkInformation (void) const;
};
#endif // HORUS_BELIEFPROP_H

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#ifndef HORUS_CONSTRAINTTREE_H
#define HORUS_CONSTRAINTTREE_H
#include <cassert>
#include <algorithm>
#include <iostream>
#include <sstream>
#include "TinySet.h"
#include "LiftedUtils.h"
using namespace std;
class CTNode;
typedef vector<CTNode*> CTNodes;
class ConstraintTree;
typedef vector<ConstraintTree*> ConstraintTrees;
class CTNode
{
public:
struct CompareSymbol
{
bool operator() (const CTNode* n1, const CTNode* n2) const
{
return n1->symbol() < n2->symbol();
}
};
private:
typedef TinySet<CTNode*, CompareSymbol> CTChilds_;
public:
CTNode (const CTNode& n, const CTChilds_& chs = CTChilds_())
: symbol_(n.symbol()), childs_(chs), level_(n.level()) { }
CTNode (Symbol s, unsigned l, const CTChilds_& chs = CTChilds_())
: symbol_(s), childs_(chs), level_(l) { }
unsigned level (void) const { return level_; }
void setLevel (unsigned level) { level_ = level; }
Symbol symbol (void) const { return symbol_; }
void setSymbol (const Symbol s) { symbol_ = s; }
public:
CTChilds_& childs (void) { return childs_; }
const CTChilds_& childs (void) const { return childs_; }
size_t nrChilds (void) const { return childs_.size(); }
bool isRoot (void) const { return level_ == 0; }
bool isLeaf (void) const { return childs_.empty(); }
CTChilds_::iterator findSymbol (Symbol symb)
{
CTNode tmp (symb, 0);
return childs_.find (&tmp);
}
void mergeSubtree (CTNode*, bool = true);
void removeChild (CTNode*);
void removeChilds (void);
void removeAndDeleteChild (CTNode*);
void removeAndDeleteAllChilds (void);
SymbolSet childSymbols (void) const;
static CTNode* copySubtree (const CTNode*);
static void deleteSubtree (CTNode*);
private:
void updateChildLevels (CTNode*, unsigned);
Symbol symbol_;
CTChilds_ childs_;
unsigned level_;
};
ostream& operator<< (ostream &out, const CTNode&);
typedef TinySet<CTNode*, CTNode::CompareSymbol> CTChilds;
class ConstraintTree
{
public:
ConstraintTree (unsigned);
ConstraintTree (const LogVars&);
ConstraintTree (const LogVars&, const Tuples&);
ConstraintTree (vector<vector<string>> names);
ConstraintTree (const ConstraintTree&);
ConstraintTree (const CTChilds& rootChilds, const LogVars& logVars)
: root_(new CTNode (0, 0, rootChilds)),
logVars_(logVars),
logVarSet_(logVars) { }
~ConstraintTree (void);
CTNode* root (void) const { return root_; }
bool empty (void) const { return root_->childs().empty(); }
const LogVars& logVars (void) const
{
assert (LogVarSet (logVars_) == logVarSet_);
return logVars_;
}
const LogVarSet& logVarSet (void) const
{
assert (LogVarSet (logVars_) == logVarSet_);
return logVarSet_;
}
size_t nrLogVars (void) const
{
return logVars_.size();
assert (LogVarSet (logVars_) == logVarSet_);
}
void addTuple (const Tuple&);
bool containsTuple (const Tuple&);
void moveToTop (const LogVars&);
void moveToBottom (const LogVars&);
void join (ConstraintTree*, bool oneTwoOne = false);
unsigned getLevel (LogVar) const;
void rename (LogVar, LogVar);
void applySubstitution (const Substitution&);
void project (const LogVarSet&);
ConstraintTree projectedCopy (const LogVarSet&);
void remove (const LogVarSet&);
bool isSingleton (LogVar);
LogVarSet singletons (void);
TupleSet tupleSet (unsigned = 0) const;
TupleSet tupleSet (const LogVars&);
unsigned size (void) const;
unsigned nrSymbols (LogVar);
void exportToGraphViz (const char*, bool = false) const;
bool isCountNormalized (const LogVarSet&);
unsigned getConditionalCount (const LogVarSet&);
TinySet<unsigned> getConditionalCounts (const LogVarSet&);
bool isCartesianProduct (const LogVarSet&);
std::pair<ConstraintTree*, ConstraintTree*> split (const Tuple&);
std::pair<ConstraintTree*, ConstraintTree*> split (
const LogVars&, ConstraintTree*, const LogVars&);
ConstraintTrees countNormalize (const LogVarSet&);
ConstraintTrees jointCountNormalize (
ConstraintTree*, ConstraintTree*, LogVar, LogVar, LogVar);
LogVars expand (LogVar);
ConstraintTrees ground (LogVar);
void cloneLogVar (LogVar, LogVar);
ConstraintTree& operator= (const ConstraintTree& ct);
private:
unsigned countTuples (const CTNode*) const;
CTNodes getNodesBelow (CTNode*) const;
CTNodes getNodesAtLevel (unsigned) const;
unsigned nrNodes (const CTNode* n) const;
void appendOnBottom (CTNode* n1, const CTChilds&);
void swapLogVar (LogVar);
bool join (CTNode*, const Tuple&, size_t, CTNode*);
void getTuples (CTNode*, Tuples, unsigned, Tuples&, CTNodes&) const;
vector<std::pair<CTNode*, unsigned>> countNormalize (
const CTNode*, unsigned);
static void split (
CTNode*, CTNode*, CTChilds&, CTChilds&, unsigned);
CTNode* root_;
LogVars logVars_;
LogVarSet logVarSet_;
};
#endif // HORUS_CONSTRAINTTREE_H

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#include "CountingBp.h"
#include "WeightedBp.h"
bool CountingBp::checkForIdenticalFactors = true;
CountingBp::CountingBp (const FactorGraph& fg)
: GroundSolver (fg), freeColor_(0)
{
findIdenticalFactors();
setInitialColors();
createGroups();
compressedFg_ = getCompressedFactorGraph();
solver_ = new WeightedBp (*compressedFg_, getWeights());
}
CountingBp::~CountingBp (void)
{
delete solver_;
delete compressedFg_;
for (size_t i = 0; i < varClusters_.size(); i++) {
delete varClusters_[i];
}
for (size_t i = 0; i < facClusters_.size(); i++) {
delete facClusters_[i];
}
}
void
CountingBp::printSolverFlags (void) const
{
stringstream ss;
ss << "counting bp [" ;
ss << "schedule=" ;
typedef BpOptions::Schedule Sch;
switch (BpOptions::schedule) {
case Sch::SEQ_FIXED: ss << "seq_fixed"; break;
case Sch::SEQ_RANDOM: ss << "seq_random"; break;
case Sch::PARALLEL: ss << "parallel"; break;
case Sch::MAX_RESIDUAL: ss << "max_residual"; break;
}
ss << ",max_iter=" << BpOptions::maxIter;
ss << ",accuracy=" << BpOptions::accuracy;
ss << ",log_domain=" << Util::toString (Globals::logDomain);
ss << ",chkif=" <<
Util::toString (CountingBp::checkForIdenticalFactors);
ss << "]" ;
cout << ss.str() << endl;
}
Params
CountingBp::solveQuery (VarIds queryVids)
{
assert (queryVids.empty() == false);
Params res;
if (queryVids.size() == 1) {
res = solver_->getPosterioriOf (getRepresentative (queryVids[0]));
} else {
VarNode* vn = fg.getVarNode (queryVids[0]);
const FacNodes& facNodes = vn->neighbors();
size_t idx = facNodes.size();
for (size_t i = 0; i < facNodes.size(); i++) {
if (facNodes[i]->factor().contains (queryVids)) {
idx = i;
break;
}
cout << endl;
}
if (idx == facNodes.size()) {
res = GroundSolver::getJointByConditioning (
GroundSolverType::CBP, fg, queryVids);
} else {
VarIds reprArgs;
for (size_t i = 0; i < queryVids.size(); i++) {
reprArgs.push_back (getRepresentative (queryVids[i]));
}
FacNode* reprFac = getRepresentative (facNodes[idx]);
assert (reprFac != 0);
res = solver_->getFactorJoint (reprFac, reprArgs);
}
}
return res;
}
void
CountingBp::findIdenticalFactors()
{
const FacNodes& facNodes = fg.facNodes();
if (checkForIdenticalFactors == false ||
facNodes.size() == 1) {
return;
}
for (size_t i = 0; i < facNodes.size(); i++) {
facNodes[i]->factor().setDistId (Util::maxUnsigned());
}
unsigned groupCount = 1;
for (size_t i = 0; i < facNodes.size() - 1; i++) {
Factor& f1 = facNodes[i]->factor();
if (f1.distId() != Util::maxUnsigned()) {
continue;
}
f1.setDistId (groupCount);
for (size_t j = i + 1; j < facNodes.size(); j++) {
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);
}
}
groupCount ++;
}
}
void
CountingBp::setInitialColors (void)
{
varColors_.resize (fg.nrVarNodes());
facColors_.resize (fg.nrFacNodes());
// create the initial variable colors
VarColorMap colorMap;
const VarNodes& varNodes = fg.varNodes();
for (size_t i = 0; i < varNodes.size(); i++) {
unsigned range = varNodes[i]->range();
VarColorMap::iterator it = colorMap.find (range);
if (it == colorMap.end()) {
it = colorMap.insert (make_pair (
range, Colors (range + 1, -1))).first;
}
unsigned idx = varNodes[i]->hasEvidence()
? varNodes[i]->getEvidence()
: range;
Colors& stateColors = it->second;
if (stateColors[idx] == -1) {
stateColors[idx] = getNewColor();
}
setColor (varNodes[i], stateColors[idx]);
}
const FacNodes& facNodes = fg.facNodes();
// create the initial factor colors
DistColorMap distColors;
for (size_t i = 0; i < facNodes.size(); i++) {
unsigned distId = facNodes[i]->factor().distId();
DistColorMap::iterator it = distColors.find (distId);
if (it == distColors.end()) {
it = distColors.insert (make_pair (distId, getNewColor())).first;
}
setColor (facNodes[i], it->second);
}
}
void
CountingBp::createGroups (void)
{
VarSignMap varGroups;
FacSignMap facGroups;
unsigned nIters = 0;
bool groupsHaveChanged = true;
const VarNodes& varNodes = fg.varNodes();
const FacNodes& facNodes = fg.facNodes();
while (groupsHaveChanged || nIters == 1) {
nIters ++;
// set a new color to the variables with the same signature
size_t prevVarGroupsSize = varGroups.size();
varGroups.clear();
for (size_t i = 0; i < varNodes.size(); i++) {
const VarSignature& signature = getSignature (varNodes[i]);
VarSignMap::iterator it = varGroups.find (signature);
if (it == varGroups.end()) {
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 = getNewColor();
VarNodes& groupMembers = it->second;
for (size_t i = 0; i < groupMembers.size(); i++) {
setColor (groupMembers[i], newColor);
}
}
size_t prevFactorGroupsSize = facGroups.size();
facGroups.clear();
// set a new color to the factors with the same signature
for (size_t i = 0; i < facNodes.size(); i++) {
const FacSignature& signature = getSignature (facNodes[i]);
FacSignMap::iterator it = facGroups.find (signature);
if (it == facGroups.end()) {
it = facGroups.insert (make_pair (signature, FacNodes())).first;
}
it->second.push_back (facNodes[i]);
}
for (FacSignMap::iterator it = facGroups.begin();
it != facGroups.end(); ++it) {
Color newColor = getNewColor();
FacNodes& groupMembers = it->second;
for (size_t i = 0; i < groupMembers.size(); i++) {
setColor (groupMembers[i], newColor);
}
}
groupsHaveChanged = prevVarGroupsSize != varGroups.size()
|| prevFactorGroupsSize != facGroups.size();
}
// printGroups (varGroups, facGroups);
createClusters (varGroups, facGroups);
}
void
CountingBp::createClusters (
const VarSignMap& varGroups,
const FacSignMap& facGroups)
{
varClusters_.reserve (varGroups.size());
for (VarSignMap::const_iterator it = varGroups.begin();
it != varGroups.end(); ++it) {
const VarNodes& groupVars = it->second;
VarCluster* vc = new VarCluster (groupVars);
for (size_t i = 0; i < groupVars.size(); i++) {
varClusterMap_.insert (make_pair (groupVars[i]->varId(), vc));
}
varClusters_.push_back (vc);
}
facClusters_.reserve (facGroups.size());
for (FacSignMap::const_iterator it = facGroups.begin();
it != facGroups.end(); ++it) {
FacNode* groupFactor = it->second[0];
const VarNodes& neighs = groupFactor->neighbors();
VarClusters varClusters;
varClusters.reserve (neighs.size());
for (size_t i = 0; i < neighs.size(); i++) {
VarId vid = neighs[i]->varId();
varClusters.push_back (varClusterMap_.find (vid)->second);
}
facClusters_.push_back (new FacCluster (it->second, varClusters));
}
}
VarSignature
CountingBp::getSignature (const VarNode* varNode)
{
const FacNodes& neighs = varNode->neighbors();
VarSignature sign;
sign.reserve (neighs.size() + 1);
for (size_t i = 0; i < neighs.size(); i++) {
sign.push_back (make_pair (
getColor (neighs[i]),
neighs[i]->factor().indexOf (varNode->varId())));
}
std::sort (sign.begin(), sign.end());
sign.push_back (make_pair (getColor (varNode), 0));
return sign;
}
FacSignature
CountingBp::getSignature (const FacNode* facNode)
{
const VarNodes& neighs = facNode->neighbors();
FacSignature sign;
sign.reserve (neighs.size() + 1);
for (size_t i = 0; i < neighs.size(); i++) {
sign.push_back (getColor (neighs[i]));
}
sign.push_back (getColor (facNode));
return sign;
}
VarId
CountingBp::getRepresentative (VarId vid)
{
assert (Util::contains (varClusterMap_, vid));
VarCluster* vc = varClusterMap_.find (vid)->second;
return vc->representative()->varId();
}
FacNode*
CountingBp::getRepresentative (FacNode* fn)
{
for (size_t i = 0; i < facClusters_.size(); i++) {
if (Util::contains (facClusters_[i]->members(), fn)) {
return facClusters_[i]->representative();
}
}
return 0;
}
FactorGraph*
CountingBp::getCompressedFactorGraph (void)
{
FactorGraph* fg = new FactorGraph();
for (size_t i = 0; i < varClusters_.size(); i++) {
VarNode* newVar = new VarNode (varClusters_[i]->first());
varClusters_[i]->setRepresentative (newVar);
fg->addVarNode (newVar);
}
for (size_t i = 0; i < facClusters_.size(); i++) {
Vars vars;
const VarClusters& clusters = facClusters_[i]->varClusters();
for (size_t j = 0; j < clusters.size(); j++) {
vars.push_back (clusters[j]->representative());
}
const Factor& groundFac = facClusters_[i]->first()->factor();
FacNode* fn = new FacNode (Factor (
vars, groundFac.params(), groundFac.distId()));
facClusters_[i]->setRepresentative (fn);
fg->addFacNode (fn);
for (size_t j = 0; j < vars.size(); j++) {
fg->addEdge (static_cast<VarNode*> (vars[j]), fn);
}
}
return fg;
}
vector<vector<unsigned>>
CountingBp::getWeights (void) const
{
vector<vector<unsigned>> weights;
weights.reserve (facClusters_.size());
for (size_t i = 0; i < facClusters_.size(); i++) {
const VarClusters& neighs = facClusters_[i]->varClusters();
weights.push_back ({ });
weights.back().reserve (neighs.size());
for (size_t j = 0; j < neighs.size(); j++) {
weights.back().push_back (getWeight (
facClusters_[i], neighs[j], j));
}
}
return weights;
}
unsigned
CountingBp::getWeight (
const FacCluster* fc,
const VarCluster* vc,
size_t index) const
{
unsigned weight = 0;
VarId reprVid = vc->representative()->varId();
VarNode* groundVar = fg.getVarNode (reprVid);
const FacNodes& neighs = groundVar->neighbors();
for (size_t i = 0; i < neighs.size(); i++) {
FacNodes::const_iterator it;
it = std::find (fc->members().begin(), fc->members().end(), neighs[i]);
if (it != fc->members().end() &&
(*it)->factor().indexOf (reprVid) == index) {
weight ++;
}
}
return weight;
}
void
CountingBp::printGroups (
const VarSignMap& varGroups,
const FacSignMap& facGroups) const
{
unsigned count = 1;
cout << "variable groups:" << endl;
for (VarSignMap::const_iterator it = varGroups.begin();
it != varGroups.end(); ++it) {
const VarNodes& groupMembers = it->second;
if (groupMembers.size() > 0) {
cout << count << ": " ;
for (size_t i = 0; i < groupMembers.size(); i++) {
cout << groupMembers[i]->label() << " " ;
}
count ++;
cout << endl;
}
}
count = 1;
cout << endl << "factor groups:" << endl;
for (FacSignMap::const_iterator it = facGroups.begin();
it != facGroups.end(); ++it) {
const FacNodes& groupMembers = it->second;
if (groupMembers.size() > 0) {
cout << ++count << ": " ;
for (size_t i = 0; i < groupMembers.size(); i++) {
cout << groupMembers[i]->getLabel() << " " ;
}
count ++;
cout << endl;
}
}
}

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#ifndef HORUS_COUNTINGBP_H
#define HORUS_COUNTINGBP_H
#include <unordered_map>
#include "GroundSolver.h"
#include "FactorGraph.h"
#include "Util.h"
#include "Horus.h"
class VarCluster;
class FacCluster;
class WeightedBp;
typedef long Color;
typedef vector<Color> Colors;
typedef vector<std::pair<Color,unsigned>> VarSignature;
typedef vector<Color> FacSignature;
typedef unordered_map<unsigned, Color> DistColorMap;
typedef unordered_map<unsigned, Colors> VarColorMap;
typedef unordered_map<VarSignature, VarNodes> VarSignMap;
typedef unordered_map<FacSignature, FacNodes> FacSignMap;
typedef unordered_map<VarId, VarCluster*> VarClusterMap;
typedef vector<VarCluster*> VarClusters;
typedef vector<FacCluster*> FacClusters;
template <class T>
inline size_t hash_combine (size_t seed, const T& v)
{
return seed ^ (hash<T>()(v) + 0x9e3779b9 + (seed << 6) + (seed >> 2));
}
namespace std {
template <typename T1, typename T2> struct hash<std::pair<T1,T2>>
{
size_t operator() (const std::pair<T1,T2>& p) const
{
return hash_combine (std::hash<T1>()(p.first), p.second);
}
};
template <typename T> struct hash<std::vector<T>>
{
size_t operator() (const std::vector<T>& vec) const
{
size_t h = 0;
typename vector<T>::const_iterator first = vec.begin();
typename vector<T>::const_iterator last = vec.end();
for (; first != last; ++first) {
h = hash_combine (h, *first);
}
return h;
}
};
}
class VarCluster
{
public:
VarCluster (const VarNodes& vs) : members_(vs) { }
const VarNode* first (void) const { return members_.front(); }
const VarNodes& members (void) const { return members_; }
VarNode* representative (void) const { return repr_; }
void setRepresentative (VarNode* vn) { repr_ = vn; }
private:
VarNodes members_;
VarNode* repr_;
};
class FacCluster
{
public:
FacCluster (const FacNodes& fcs, const VarClusters& vcs)
: members_(fcs), varClusters_(vcs) { }
const FacNode* first (void) const { return members_.front(); }
const FacNodes& members (void) const { return members_; }
FacNode* representative (void) const { return repr_; }
void setRepresentative (FacNode* fn) { repr_ = fn; }
VarClusters& varClusters (void) { return varClusters_; }
private:
FacNodes members_;
FacNode* repr_;
VarClusters varClusters_;
};
class CountingBp : public GroundSolver
{
public:
CountingBp (const FactorGraph& fg);
~CountingBp (void);
void printSolverFlags (void) const;
Params solveQuery (VarIds);
static bool checkForIdenticalFactors;
private:
Color getNewColor (void)
{
++ freeColor_;
return freeColor_ - 1;
}
Color getColor (const VarNode* vn) const
{
return varColors_[vn->getIndex()];
}
Color getColor (const FacNode* fn) const
{
return facColors_[fn->getIndex()];
}
void setColor (const VarNode* vn, Color c)
{
varColors_[vn->getIndex()] = c;
}
void setColor (const FacNode* fn, Color c)
{
facColors_[fn->getIndex()] = c;
}
void findIdenticalFactors (void);
void setInitialColors (void);
void createGroups (void);
void createClusters (const VarSignMap&, const FacSignMap&);
VarSignature getSignature (const VarNode*);
FacSignature getSignature (const FacNode*);
void printGroups (const VarSignMap&, const FacSignMap&) const;
VarId getRepresentative (VarId vid);
FacNode* getRepresentative (FacNode*);
FactorGraph* getCompressedFactorGraph (void);
vector<vector<unsigned>> getWeights (void) const;
unsigned getWeight (const FacCluster*,
const VarCluster*, size_t index) const;
Color freeColor_;
Colors varColors_;
Colors facColors_;
VarClusters varClusters_;
FacClusters facClusters_;
VarClusterMap varClusterMap_;
const FactorGraph* compressedFg_;
WeightedBp* solver_;
};
#endif // HORUS_COUNTINGBP_H

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packages/CLPBN/horus2/ElimGraph.cpp
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#include <limits>
#include <fstream>
#include "ElimGraph.h"
ElimHeuristic ElimGraph::elimHeuristic = MIN_NEIGHBORS;
ElimGraph::ElimGraph (const vector<Factor*>& factors)
{
for (size_t i = 0; i < factors.size(); i++) {
if (factors[i] == 0) { // if contained just one var with evidence
continue;
}
const VarIds& vids = factors[i]->arguments();
for (size_t j = 0; j < vids.size() - 1; j++) {
EgNode* n1 = getEgNode (vids[j]);
if (n1 == 0) {
n1 = new EgNode (vids[j], factors[i]->range (j));
addNode (n1);
}
for (size_t k = j + 1; k < vids.size(); k++) {
EgNode* n2 = getEgNode (vids[k]);
if (n2 == 0) {
n2 = new EgNode (vids[k], factors[i]->range (k));
addNode (n2);
}
if (neighbors (n1, n2) == false) {
addEdge (n1, n2);
}
}
}
if (vids.size() == 1) {
if (getEgNode (vids[0]) == 0) {
addNode (new EgNode (vids[0], factors[i]->range (0)));
}
}
}
}
ElimGraph::~ElimGraph (void)
{
for (size_t i = 0; i < nodes_.size(); i++) {
delete nodes_[i];
}
}
VarIds
ElimGraph::getEliminatingOrder (const VarIds& exclude)
{
VarIds elimOrder;
unmarked_.reserve (nodes_.size());
for (size_t i = 0; i < nodes_.size(); i++) {
if (Util::contains (exclude, nodes_[i]->varId()) == false) {
unmarked_.insert (nodes_[i]);
}
}
size_t nrVarsToEliminate = nodes_.size() - exclude.size();
for (size_t i = 0; i < nrVarsToEliminate; i++) {
EgNode* node = getLowestCostNode();
unmarked_.remove (node);
const EGNeighs& neighs = node->neighbors();
for (size_t j = 0; j < neighs.size(); j++) {
neighs[j]->removeNeighbor (node);
}
elimOrder.push_back (node->varId());
connectAllNeighbors (node);
}
return elimOrder;
}
void
ElimGraph::print (void) const
{
for (size_t i = 0; i < nodes_.size(); i++) {
cout << "node " << nodes_[i]->label() << " neighs:" ;
EGNeighs neighs = nodes_[i]->neighbors();
for (size_t j = 0; j < neighs.size(); j++) {
cout << " " << neighs[j]->label();
}
cout << endl;
}
}
void
ElimGraph::exportToGraphViz (
const char* fileName,
bool showNeighborless,
const VarIds& highlightVarIds) const
{
ofstream out (fileName);
if (!out.is_open()) {
cerr << "Error: couldn't open file '" << fileName << "'." ;
return;
}
out << "strict graph {" << endl;
for (size_t i = 0; i < nodes_.size(); i++) {
if (showNeighborless || nodes_[i]->neighbors().size() != 0) {
out << '"' << nodes_[i]->label() << '"' << endl;
}
}
for (size_t i = 0; i < highlightVarIds.size(); i++) {
EgNode* node =getEgNode (highlightVarIds[i]);
if (node) {
out << '"' << node->label() << '"' ;
out << " [shape=box3d]" << endl;
} else {
cerr << "Error: invalid variable id: " << highlightVarIds[i] << "." ;
cerr << endl;
exit (EXIT_FAILURE);
}
}
for (size_t i = 0; i < nodes_.size(); i++) {
EGNeighs neighs = nodes_[i]->neighbors();
for (size_t j = 0; j < neighs.size(); j++) {
out << '"' << nodes_[i]->label() << '"' << " -- " ;
out << '"' << neighs[j]->label() << '"' << endl;
}
}
out << "}" << endl;
out.close();
}
VarIds
ElimGraph::getEliminationOrder (
const Factors& factors,
VarIds excludedVids)
{
if (elimHeuristic == ElimHeuristic::SEQUENTIAL) {
VarIds allVids;
Factors::const_iterator first = factors.begin();
Factors::const_iterator end = factors.end();
for (; first != end; ++first) {
Util::addToVector (allVids, (*first)->arguments());
}
TinySet<VarId> elimOrder (allVids);
elimOrder -= TinySet<VarId> (excludedVids);
return elimOrder.elements();
}
ElimGraph graph (factors);
return graph.getEliminatingOrder (excludedVids);
}
void
ElimGraph::addNode (EgNode* n)
{
nodes_.push_back (n);
n->setIndex (nodes_.size() - 1);
varMap_.insert (make_pair (n->varId(), n));
}
EgNode*
ElimGraph::getEgNode (VarId vid) const
{
unordered_map<VarId, EgNode*>::const_iterator it;
it = varMap_.find (vid);
return (it != varMap_.end()) ? it->second : 0;
}
EgNode*
ElimGraph::getLowestCostNode (void) const
{
EgNode* bestNode = 0;
unsigned minCost = std::numeric_limits<unsigned>::max();
EGNeighs::const_iterator it;
switch (elimHeuristic) {
case MIN_NEIGHBORS: {
for (it = unmarked_.begin(); it != unmarked_.end(); ++ it) {
unsigned cost = getNeighborsCost (*it);
if (cost < minCost) {
bestNode = *it;
minCost = cost;
}
}}
break;
case MIN_WEIGHT: {
for (it = unmarked_.begin(); it != unmarked_.end(); ++ it) {
unsigned cost = getWeightCost (*it);
if (cost < minCost) {
bestNode = *it;
minCost = cost;
}
}}
break;
case MIN_FILL: {
for (it = unmarked_.begin(); it != unmarked_.end(); ++ it) {
unsigned cost = getFillCost (*it);
if (cost < minCost) {
bestNode = *it;
minCost = cost;
}
}}
break;
case WEIGHTED_MIN_FILL: {
for (it = unmarked_.begin(); it != unmarked_.end(); ++ it) {
unsigned cost = getWeightedFillCost (*it);
if (cost < minCost) {
bestNode = *it;
minCost = cost;
}
}}
break;
default:
assert (false);
}
assert (bestNode);
return bestNode;
}
void
ElimGraph::connectAllNeighbors (const EgNode* n)
{
const EGNeighs& neighs = n->neighbors();
if (neighs.size() > 0) {
for (size_t i = 0; i < neighs.size() - 1; i++) {
for (size_t j = i + 1; j < neighs.size(); j++) {
if ( ! neighbors (neighs[i], neighs[j])) {
addEdge (neighs[i], neighs[j]);
}
}
}
}
}

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#ifndef HORUS_ELIMGRAPH_H
#define HORUS_ELIMGRAPH_H
#include "unordered_map"
#include "FactorGraph.h"
#include "TinySet.h"
#include "Horus.h"
using namespace std;
enum ElimHeuristic
{
SEQUENTIAL,
MIN_NEIGHBORS,
MIN_WEIGHT,
MIN_FILL,
WEIGHTED_MIN_FILL
};
class EgNode;
typedef TinySet<EgNode*> EGNeighs;
class EgNode : public Var
{
public:
EgNode (VarId vid, unsigned range) : Var (vid, range) { }
void addNeighbor (EgNode* n) { neighs_.insert (n); }
void removeNeighbor (EgNode* n) { neighs_.remove (n); }
bool isNeighbor (EgNode* n) const { return neighs_.contains (n); }
const EGNeighs& neighbors (void) const { return neighs_; }
private:
EGNeighs neighs_;
};
class ElimGraph
{
public:
ElimGraph (const Factors&);
~ElimGraph (void);
VarIds getEliminatingOrder (const VarIds&);
void print (void) const;
void exportToGraphViz (const char*, bool = true,
const VarIds& = VarIds()) const;
static VarIds getEliminationOrder (const Factors&, VarIds);
static ElimHeuristic elimHeuristic;
private:
void addEdge (EgNode* n1, EgNode* n2)
{
assert (n1 != n2);
n1->addNeighbor (n2);
n2->addNeighbor (n1);
}
unsigned getNeighborsCost (const EgNode* n) const
{
return n->neighbors().size();
}
unsigned getWeightCost (const EgNode* n) const
{
unsigned cost = 1;
const EGNeighs& neighs = n->neighbors();
for (size_t i = 0; i < neighs.size(); i++) {
cost *= neighs[i]->range();
}
return cost;
}
unsigned getFillCost (const EgNode* n) const
{
unsigned cost = 0;
const EGNeighs& neighs = n->neighbors();
if (neighs.size() > 0) {
for (size_t i = 0; i < neighs.size() - 1; i++) {
for (size_t j = i + 1; j < neighs.size(); j++) {
if ( ! neighbors (neighs[i], neighs[j])) {
cost ++;
}
}
}
}
return cost;
}
unsigned getWeightedFillCost (const EgNode* n) const
{
unsigned cost = 0;
const EGNeighs& neighs = n->neighbors();
if (neighs.size() > 0) {
for (size_t i = 0; i < neighs.size() - 1; i++) {
for (size_t j = i + 1; j < neighs.size(); j++) {
if ( ! neighbors (neighs[i], neighs[j])) {
cost += neighs[i]->range() * neighs[j]->range();
}
}
}
}
return cost;
}
bool neighbors (EgNode* n1, EgNode* n2) const
{
return n1->isNeighbor (n2);
}
void addNode (EgNode*);
EgNode* getEgNode (VarId) const;
EgNode* getLowestCostNode (void) const;
void connectAllNeighbors (const EgNode*);
vector<EgNode*> nodes_;
TinySet<EgNode*> unmarked_;
unordered_map<VarId, EgNode*> varMap_;
};
#endif // HORUS_ELIMGRAPH_H

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#include <cstdlib>
#include <cassert>
#include <algorithm>
#include <iostream>
#include <sstream>
#include "Factor.h"
#include "Indexer.h"
Factor::Factor (const Factor& g)
{
clone (g);
}
Factor::Factor (
const VarIds& vids,
const Ranges& ranges,
const Params& params,
unsigned distId)
{
args_ = vids;
ranges_ = ranges;
params_ = params;
distId_ = distId;
assert (params_.size() == Util::sizeExpected (ranges_));
}
Factor::Factor (
const Vars& vars,
const Params& params,
unsigned distId)
{
for (size_t i = 0; i < vars.size(); i++) {
args_.push_back (vars[i]->varId());
ranges_.push_back (vars[i]->range());
}
params_ = params;
distId_ = distId;
assert (params_.size() == Util::sizeExpected (ranges_));
}
void
Factor::sumOut (VarId vid)
{
if (vid == args_.front() && ranges_.front() == 2) {
// optimization
sumOutFirstVariable();
} else if (vid == args_.back() && ranges_.back() == 2) {
// optimization
sumOutLastVariable();
} else {
assert (indexOf (vid) != args_.size());
sumOutIndex (indexOf (vid));
}
}
void
Factor::sumOutAllExcept (VarId vid)
{
assert (indexOf (vid) != args_.size());
sumOutAllExceptIndex (indexOf (vid));
}
void
Factor::sumOutAllExcept (const VarIds& vids)
{
vector<bool> mask (args_.size(), false);
for (unsigned i = 0; i < vids.size(); i++) {
assert (indexOf (vids[i]) != args_.size());
mask[indexOf (vids[i])] = true;
}
sumOutArgs (mask);
}
void
Factor::sumOutAllExceptIndex (size_t idx)
{
assert (idx < args_.size());
vector<bool> mask (args_.size(), false);
mask[idx] = true;
sumOutArgs (mask);
}
void
Factor::multiply (Factor& g)
{
if (args_.size() == 0) {
clone (g);
return;
}
TFactor<VarId>::multiply (g);
}
string
Factor::getLabel (void) const
{
stringstream ss;
ss << "f(" ;
for (size_t i = 0; i < args_.size(); i++) {
if (i != 0) ss << "," ;
ss << Var (args_[i], ranges_[i]).label();
}
ss << ")" ;
return ss.str();
}
void
Factor::print (void) const
{
Vars vars;
for (size_t i = 0; i < args_.size(); i++) {
vars.push_back (new Var (args_[i], ranges_[i]));
}
vector<string> jointStrings = Util::getStateLines (vars);
for (size_t i = 0; i < params_.size(); i++) {
// cout << "[" << distId_ << "] " ;
cout << "f(" << jointStrings[i] << ")" ;
cout << " = " << params_[i] << endl;
}
cout << endl;
for (size_t i = 0; i < vars.size(); i++) {
delete vars[i];
}
}
void
Factor::sumOutFirstVariable (void)
{
size_t sep = params_.size() / 2;
if (Globals::logDomain) {
std::transform (
params_.begin(), params_.begin() + sep,
params_.begin() + sep, params_.begin(),
Util::logSum);
} else {
std::transform (
params_.begin(), params_.begin() + sep,
params_.begin() + sep, params_.begin(),
std::plus<double>());
}
params_.resize (sep);
args_.erase (args_.begin());
ranges_.erase (ranges_.begin());
}
void
Factor::sumOutLastVariable (void)
{
Params::iterator first1 = params_.begin();
Params::iterator first2 = params_.begin();
Params::iterator last = params_.end();
if (Globals::logDomain) {
while (first2 != last) {
// the arguments can be swaped, but that is ok
*first1++ = Util::logSum (*first2++, *first2++);
}
} else {
while (first2 != last) {
*first1++ = (*first2++) + (*first2++);
}
}
params_.resize (params_.size() / 2);
args_.pop_back();
ranges_.pop_back();
}
void
Factor::sumOutArgs (const vector<bool>& mask)
{
assert (mask.size() == args_.size());
size_t new_size = 1;
Ranges oldRanges = ranges_;
args_.clear();
ranges_.clear();
for (unsigned i = 0; i < mask.size(); i++) {
if (mask[i]) {
new_size *= ranges_[i];
args_.push_back (args_[i]);
ranges_.push_back (ranges_[i]);
}
}
Params newps (new_size, LogAware::addIdenty());
Params::const_iterator first = params_.begin();
Params::const_iterator last = params_.end();
MapIndexer indexer (oldRanges, mask);
if (Globals::logDomain) {
while (first != last) {
newps[indexer] = Util::logSum (newps[indexer], *first++);
++ indexer;
}
} else {
while (first != last) {
newps[indexer] += *first++;
++ indexer;
}
}
params_ = newps;
}
void
Factor::clone (const Factor& g)
{
args_ = g.arguments();
ranges_ = g.ranges();
params_ = g.params();
distId_ = g.distId();
}

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#ifndef HORUS_FACTOR_H
#define HORUS_FACTOR_H
#include <vector>
#include "Var.h"
#include "Indexer.h"
#include "Util.h"
using namespace std;
template <typename T>
class TFactor
{
public:
const vector<T>& arguments (void) const { return args_; }
vector<T>& arguments (void) { return args_; }
const Ranges& ranges (void) const { return ranges_; }
const Params& params (void) const { return params_; }
Params& params (void) { return params_; }
size_t nrArguments (void) const { return args_.size(); }
size_t size (void) const { return params_.size(); }
unsigned distId (void) const { return distId_; }
void setDistId (unsigned id) { distId_ = id; }
void normalize (void) { LogAware::normalize (params_); }
void randomize (void)
{
for (size_t i = 0; i < params_.size(); ++i) {
params_[i] = (double) std::rand() / RAND_MAX;
}
}
void setParams (const Params& newParams)
{
params_ = newParams;
assert (params_.size() == Util::sizeExpected (ranges_));
}
size_t indexOf (const T& t) const
{
return Util::indexOf (args_, t);
}
const T& argument (size_t idx) const
{
assert (idx < args_.size());
return args_[idx];
}
T& argument (size_t idx)
{
assert (idx < args_.size());
return args_[idx];
}
unsigned range (size_t idx) const
{
assert (idx < ranges_.size());
return ranges_[idx];
}
void multiply (TFactor<T>& g)
{
if (args_ == g.arguments()) {
// optimization
Globals::logDomain
? params_ += g.params()
: params_ *= g.params();
return;
}
unsigned range_prod = 1;
bool share_arguments = false;
const vector<T>& g_args = g.arguments();
const Ranges& g_ranges = g.ranges();
const Params& g_params = g.params();
for (size_t i = 0; i < g_args.size(); i++) {
size_t idx = indexOf (g_args[i]);
if (idx == args_.size()) {
range_prod *= g_ranges[i];
args_.push_back (g_args[i]);
ranges_.push_back (g_ranges[i]);
} else {
share_arguments = true;
}
}
if (share_arguments == false) {
// optimization
cartesianProduct (g_params.begin(), g_params.end());
} else {
extend (range_prod);
Params::iterator it = params_.begin();
MapIndexer indexer (args_, ranges_, g_args, g_ranges);
if (Globals::logDomain) {
for (; indexer.valid(); ++it, ++indexer) {
*it += g_params[indexer];
}
} else {
for (; indexer.valid(); ++it, ++indexer) {
*it *= g_params[indexer];
}
}
}
}
void sumOutIndex (size_t idx)
{
assert (idx < args_.size());
assert (args_.size() > 1);
size_t new_size = params_.size() / ranges_[idx];
Params newps (new_size, LogAware::addIdenty());
Params::const_iterator first = params_.begin();
Params::const_iterator last = params_.end();
MapIndexer indexer (ranges_, idx);
if (Globals::logDomain) {
for (; first != last; ++indexer) {
newps[indexer] = Util::logSum (newps[indexer], *first++);
}
} else {
for (; first != last; ++indexer) {
newps[indexer] += *first++;
}
}
params_ = newps;
args_.erase (args_.begin() + idx);
ranges_.erase (ranges_.begin() + idx);
}
void absorveEvidence (const T& arg, unsigned obsIdx)
{
size_t idx = indexOf (arg);
assert (idx != args_.size());
assert (obsIdx < ranges_[idx]);
Params newps;
newps.reserve (params_.size() / ranges_[idx]);
Indexer indexer (ranges_);
for (unsigned i = 0; i < obsIdx; ++i) {
indexer.incrementDimension (idx);
}
while (indexer.valid()) {
newps.push_back (params_[indexer]);
indexer.incrementExceptDimension (idx);
}
params_ = newps;
args_.erase (args_.begin() + idx);
ranges_.erase (ranges_.begin() + idx);
}
void reorderArguments (const vector<T> new_args)
{
assert (new_args.size() == args_.size());
if (new_args == args_) {
return; // already on the desired order
}
Ranges new_ranges;
for (size_t i = 0; i < new_args.size(); i++) {
size_t idx = indexOf (new_args[i]);
assert (idx != args_.size());
new_ranges.push_back (ranges_[idx]);
}
Params newps;
newps.reserve (params_.size());
MapIndexer indexer (new_args, new_ranges, args_, ranges_);
for (; indexer.valid(); ++indexer) {
newps.push_back (params_[indexer]);
}
params_ = newps;
args_ = new_args;
ranges_ = new_ranges;
}
bool contains (const T& arg) const
{
return Util::contains (args_, arg);
}
bool contains (const vector<T>& args) const
{
for (size_t i = 0; i < args.size(); i++) {
if (contains (args[i]) == false) {
return false;
}
}
return true;
}
double& operator[] (size_t idx)
{
assert (idx < params_.size());
return params_[idx];
}
protected:
vector<T> args_;
Ranges ranges_;
Params params_;
unsigned distId_;
private:
void extend (unsigned range_prod)
{
Params backup = params_;
params_.clear();
params_.reserve (backup.size() * range_prod);
Params::const_iterator first = backup.begin();
Params::const_iterator last = backup.end();
for (; first != last; ++first) {
for (unsigned reps = 0; reps < range_prod; ++reps) {
params_.push_back (*first);
}
}
}
void cartesianProduct (
Params::const_iterator first2,
Params::const_iterator last2)
{
Params backup = params_;
params_.clear();
params_.reserve (params_.size() * (last2 - first2));
Params::const_iterator first1 = backup.begin();
Params::const_iterator last1 = backup.end();
Params::const_iterator tmp;
if (Globals::logDomain) {
for (; first1 != last1; ++first1) {
for (tmp = first2; tmp != last2; ++tmp) {
params_.push_back ((*first1) + (*tmp));
}
}
} else {
for (; first1 != last1; ++first1) {
for (tmp = first2; tmp != last2; ++tmp) {
params_.push_back ((*first1) * (*tmp));
}
}
}
}
};
class Factor : public TFactor<VarId>
{
public:
Factor (void) { }
Factor (const Factor&);
Factor (const VarIds&, const Ranges&, const Params&,
unsigned = Util::maxUnsigned());
Factor (const Vars&, const Params&,
unsigned = Util::maxUnsigned());
void sumOut (VarId);
void sumOutAllExcept (VarId);
void sumOutAllExcept (const VarIds&);
void sumOutAllExceptIndex (size_t idx);
void multiply (Factor&);
string getLabel (void) const;
void print (void) const;
private:
void sumOutFirstVariable (void);
void sumOutLastVariable (void);
void sumOutArgs (const vector<bool>& mask);
void clone (const Factor& f);
};
#endif // HORUS_FACTOR_H

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packages/CLPBN/horus2/FactorGraph.cpp
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#include <set>
#include <vector>
#include <algorithm>
#include <iostream>
#include <fstream>
#include <sstream>
#include "FactorGraph.h"
#include "Factor.h"
#include "BayesBall.h"
#include "Util.h"
FactorGraph::FactorGraph (const FactorGraph& fg)
{
const VarNodes& varNodes = fg.varNodes();
for (size_t i = 0; i < varNodes.size(); i++) {
addVarNode (new VarNode (varNodes[i]));
}
const FacNodes& facNodes = fg.facNodes();
for (size_t i = 0; i < facNodes.size(); i++) {
FacNode* facNode = new FacNode (facNodes[i]->factor());
addFacNode (facNode);
const VarNodes& neighs = facNodes[i]->neighbors();
for (size_t j = 0; j < neighs.size(); j++) {
addEdge (varNodes_[neighs[j]->getIndex()], facNode);
}
}
bayesFactors_ = fg.bayesianFactors();
}
void
FactorGraph::readFromUaiFormat (const char* fileName)
{
std::ifstream is (fileName);
if (!is.is_open()) {
cerr << "Error: couldn't open file '" << fileName << "'." ;
exit (EXIT_FAILURE);
}
ignoreLines (is);
string line;
getline (is, line);
if (line != "MARKOV") {
cerr << "Error: the network must be a MARKOV network." << endl;
exit (EXIT_FAILURE);
}
// 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];
}
unsigned nrFactors;
unsigned nrArgs;
unsigned vid;
is >> nrFactors;
vector<VarIds> factorVarIds;
vector<Ranges> 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;
if (vid >= ranges.size()) {
cerr << "Error: invalid variable identifier `" << vid << "'. " ;
cerr << "Identifiers must be between 0 and " << ranges.size() - 1 ;
cerr << "." << endl;
exit (EXIT_FAILURE);
}
factorVarIds.back().push_back (vid);
factorRanges.back().push_back (ranges[vid]);
}
}
// read the parameters
unsigned nrParams;
for (unsigned i = 0; i < nrFactors; i++) {
ignoreLines (is);
is >> nrParams;
if (nrParams != Util::sizeExpected (factorRanges[i])) {
cerr << "Error: invalid number of parameters for factor nº " << i ;
cerr << ", " << Util::sizeExpected (factorRanges[i]);
cerr << " expected, " << nrParams << " given." << endl;
exit (EXIT_FAILURE);
}
Params params (nrParams);
for (unsigned j = 0; j < nrParams; j++) {
is >> params[j];
}
if (Globals::logDomain) {
Util::log (params);
}
addFactor (Factor (factorVarIds[i], factorRanges[i], params));
}
is.close();
}
void
FactorGraph::readFromLibDaiFormat (const char* fileName)
{
std::ifstream is (fileName);
if (!is.is_open()) {
cerr << "Error: couldn't open file '" << fileName << "'." ;
exit (EXIT_FAILURE);
}
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 < nrArgs; j++) {
ignoreLines (is);
is >> vid;
vids.push_back (vid);
}
// 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 && ranges[j] != var->range()) {
cerr << "Error: variable `" << vids[j] << "' appears in two or " ;
cerr << "more factors with a different range." << endl;
}
}
// read parameters
ignoreLines (is);
unsigned nNonzeros;
is >> nNonzeros;
Params params (Util::sizeExpected (ranges), 0);
for (unsigned j = 0; j < nNonzeros; j++) {
ignoreLines (is);
unsigned index;
is >> index;
ignoreLines (is);
double val;
is >> val;
params[index] = val;
}
if (Globals::logDomain) {
Util::log (params);
}
std::reverse (vids.begin(), vids.end());
Factor f (vids, ranges, params);
std::reverse (vids.begin(), vids.end());
f.reorderArguments (vids);
addFactor (f);
}
is.close();
}
FactorGraph::~FactorGraph (void)
{
for (size_t i = 0; i < varNodes_.size(); i++) {
delete varNodes_[i];
}
for (size_t i = 0; i < facNodes_.size(); i++) {
delete facNodes_[i];
}
}
void
FactorGraph::addFactor (const Factor& factor)
{
FacNode* fn = new FacNode (factor);
addFacNode (fn);
const VarIds& vids = fn->factor().arguments();
for (size_t i = 0; i < vids.size(); i++) {
VarMap::const_iterator it = varMap_.find (vids[i]);
if (it != varMap_.end()) {
addEdge (it->second, fn);
} else {
VarNode* vn = new VarNode (vids[i], fn->factor().range (i));
addVarNode (vn);
addEdge (vn, fn);
}
}
}
void
FactorGraph::addVarNode (VarNode* vn)
{
varNodes_.push_back (vn);
vn->setIndex (varNodes_.size() - 1);
varMap_.insert (make_pair (vn->varId(), vn));
}
void
FactorGraph::addFacNode (FacNode* fn)
{
facNodes_.push_back (fn);
fn->setIndex (facNodes_.size() - 1);
}
void
FactorGraph::addEdge (VarNode* vn, FacNode* fn)
{
vn->addNeighbor (fn);
fn->addNeighbor (vn);
}
bool
FactorGraph::isTree (void) const
{
return !containsCycle();
}
BayesBallGraph&
FactorGraph::getStructure (void)
{
assert (bayesFactors_);
if (structure_.empty()) {
for (size_t i = 0; i < varNodes_.size(); i++) {
structure_.addNode (new BBNode (varNodes_[i]));
}
for (size_t i = 0; i < facNodes_.size(); i++) {
const VarIds& vids = facNodes_[i]->factor().arguments();
for (size_t j = 1; j < vids.size(); j++) {
structure_.addEdge (vids[j], vids[0]);
}
}
}
return structure_;
}
void
FactorGraph::print (void) const
{
for (size_t i = 0; i < varNodes_.size(); i++) {
cout << "var id = " << varNodes_[i]->varId() << endl;
cout << "label = " << varNodes_[i]->label() << endl;
cout << "range = " << varNodes_[i]->range() << endl;
cout << "evidence = " << varNodes_[i]->getEvidence() << endl;
cout << "factors = " ;
for (size_t j = 0; j < varNodes_[i]->neighbors().size(); j++) {
cout << varNodes_[i]->neighbors()[j]->getLabel() << " " ;
}
cout << endl << endl;
}
for (size_t i = 0; i < facNodes_.size(); i++) {
facNodes_[i]->factor().print();
}
}
void
FactorGraph::exportToGraphViz (const char* fileName) const
{
ofstream out (fileName);
if (!out.is_open()) {
cerr << "Error: couldn't open file '" << fileName << "'." ;
return;
}
out << "graph \"" << fileName << "\" {" << endl;
for (size_t i = 0; i < varNodes_.size(); i++) {
if (varNodes_[i]->hasEvidence()) {
out << '"' << varNodes_[i]->label() << '"' ;
out << " [style=filled, fillcolor=yellow]" << endl;
}
}
for (size_t i = 0; i < facNodes_.size(); i++) {
out << '"' << facNodes_[i]->getLabel() << '"' ;
out << " [label=\"" << facNodes_[i]->getLabel();
out << "\"" << ", shape=box]" << endl;
}
for (size_t i = 0; i < facNodes_.size(); i++) {
const VarNodes& myVars = facNodes_[i]->neighbors();
for (size_t j = 0; j < myVars.size(); j++) {
out << '"' << facNodes_[i]->getLabel() << '"' ;
out << " -- " ;
out << '"' << myVars[j]->label() << '"' << endl;
}
}
out << "}" << endl;
out.close();
}
void
FactorGraph::exportToUaiFormat (const char* fileName) const
{
ofstream out (fileName);
if (!out.is_open()) {
cerr << "Error: couldn't open file '" << fileName << "'." ;
return;
}
out << "MARKOV" << endl;
out << varNodes_.size() << endl;
VarNodes sortedVns = varNodes_;
std::sort (sortedVns.begin(), sortedVns.end(), sortByVarId());
for (size_t i = 0; i < sortedVns.size(); i++) {
out << ((i != 0) ? " " : "") << sortedVns[i]->range();
}
out << endl << facNodes_.size() << endl;
for (size_t i = 0; i < facNodes_.size(); i++) {
VarIds args = facNodes_[i]->factor().arguments();
out << args.size() << " " << Util::elementsToString (args) << endl;
}
out << endl;
for (size_t i = 0; i < facNodes_.size(); i++) {
Params params = facNodes_[i]->factor().params();
if (Globals::logDomain) {
Util::exp (params);
}
out << params.size() << endl << " " ;
out << Util::elementsToString (params) << endl << endl;
}
out.close();
}
void
FactorGraph::exportToLibDaiFormat (const char* fileName) const
{
ofstream out (fileName);
if (!out.is_open()) {
cerr << "Error: couldn't open file '" << fileName << "'." ;
return;
}
out << facNodes_.size() << endl << endl;
for (size_t i = 0; i < facNodes_.size(); i++) {
Factor f (facNodes_[i]->factor());
out << f.nrArguments() << endl;
out << Util::elementsToString (f.arguments()) << endl;
out << Util::elementsToString (f.ranges()) << endl;
VarIds args = f.arguments();
std::reverse (args.begin(), args.end());
f.reorderArguments (args);
if (Globals::logDomain) {
Util::exp (f.params());
}
out << f.size() << endl;
for (size_t j = 0; j < f.size(); j++) {
out << j << " " << f[j] << endl;
}
out << endl;
}
out.close();
}
void
FactorGraph::ignoreLines (std::ifstream& is) const
{
string ignoreStr;
while (is.peek() == '#' || is.peek() == '\n') {
getline (is, ignoreStr);
}
}
bool
FactorGraph::containsCycle (void) const
{
vector<bool> visitedVars (varNodes_.size(), false);
vector<bool> visitedFactors (facNodes_.size(), false);
for (size_t i = 0; i < varNodes_.size(); i++) {
int v = varNodes_[i]->getIndex();
if (!visitedVars[v]) {
if (containsCycle (varNodes_[i], 0, visitedVars, visitedFactors)) {
return true;
}
}
}
return false;
}
bool
FactorGraph::containsCycle (
const VarNode* v,
const FacNode* p,
vector<bool>& visitedVars,
vector<bool>& visitedFactors) const
{
visitedVars[v->getIndex()] = true;
const FacNodes& adjacencies = v->neighbors();
for (size_t i = 0; i < adjacencies.size(); i++) {
int w = adjacencies[i]->getIndex();
if (!visitedFactors[w]) {
if (containsCycle (adjacencies[i], v, visitedVars, visitedFactors)) {
return true;
}
}
else if (visitedFactors[w] && adjacencies[i] != p) {
return true;
}
}
return false; // no cycle detected in this component
}
bool
FactorGraph::containsCycle (
const FacNode* v,
const VarNode* p,
vector<bool>& visitedVars,
vector<bool>& visitedFactors) const
{
visitedFactors[v->getIndex()] = true;
const VarNodes& adjacencies = v->neighbors();
for (size_t i = 0; i < adjacencies.size(); i++) {
int w = adjacencies[i]->getIndex();
if (!visitedVars[w]) {
if (containsCycle (adjacencies[i], v, visitedVars, visitedFactors)) {
return true;
}
}
else if (visitedVars[w] && adjacencies[i] != p) {
return true;
}
}
return false; // no cycle detected in this component
}

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#ifndef HORUS_FACTORGRAPH_H
#define HORUS_FACTORGRAPH_H
#include <vector>
#include "Factor.h"
#include "BayesBallGraph.h"
#include "Horus.h"
using namespace std;
class FacNode;
class VarNode : public Var
{
public:
VarNode (VarId varId, unsigned nrStates,
int evidence = Constants::NO_EVIDENCE)
: Var (varId, nrStates, evidence) { }
VarNode (const Var* v) : Var (v) { }
void addNeighbor (FacNode* fn) { neighs_.push_back (fn); }
const FacNodes& neighbors (void) const { return neighs_; }
private:
DISALLOW_COPY_AND_ASSIGN (VarNode);
FacNodes neighs_;
};
class FacNode
{
public:
FacNode (const Factor& f) : factor_(f), index_(-1) { }
const Factor& factor (void) const { return factor_; }
Factor& factor (void) { return factor_; }
void addNeighbor (VarNode* vn) { neighs_.push_back (vn); }
const VarNodes& neighbors (void) const { return neighs_; }
size_t getIndex (void) const { return index_; }
void setIndex (size_t index) { index_ = index; }
string getLabel (void) { return factor_.getLabel(); }
private:
DISALLOW_COPY_AND_ASSIGN (FacNode);
VarNodes neighs_;
Factor factor_;
size_t index_;
};
class FactorGraph
{
public:
FactorGraph (void) : bayesFactors_(false) { }
FactorGraph (const FactorGraph&);
~FactorGraph (void);
const VarNodes& varNodes (void) const { return varNodes_; }
const FacNodes& facNodes (void) const { return facNodes_; }
void setFactorsAsBayesian (void) { bayesFactors_ = true; }
bool bayesianFactors (void) const { return bayesFactors_; }
size_t nrVarNodes (void) const { return varNodes_.size(); }
size_t nrFacNodes (void) const { return facNodes_.size(); }
VarNode* getVarNode (VarId vid) const
{
VarMap::const_iterator it = varMap_.find (vid);
return it != varMap_.end() ? it->second : 0;
}
void readFromUaiFormat (const char*);
void readFromLibDaiFormat (const char*);
void addFactor (const Factor& factor);
void addVarNode (VarNode*);
void addFacNode (FacNode*);
void addEdge (VarNode*, FacNode*);
bool isTree (void) const;
BayesBallGraph& getStructure (void);
void print (void) const;
void exportToGraphViz (const char*) const;
void exportToUaiFormat (const char*) const;
void exportToLibDaiFormat (const char*) const;
private:
// DISALLOW_COPY_AND_ASSIGN (FactorGraph);
void ignoreLines (std::ifstream&) const;
bool containsCycle (void) const;
bool containsCycle (const VarNode*, const FacNode*,
vector<bool>&, vector<bool>&) const;
bool containsCycle (const FacNode*, const VarNode*,
vector<bool>&, vector<bool>&) const;
VarNodes varNodes_;
FacNodes facNodes_;
BayesBallGraph structure_;
bool bayesFactors_;
typedef unordered_map<unsigned, VarNode*> VarMap;
VarMap varMap_;
};
struct sortByVarId
{
bool operator()(VarNode* vn1, VarNode* vn2) {
return vn1->varId() < vn2->varId();
}
};
#endif // HORUS_FACTORGRAPH_H

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#include "GroundSolver.h"
#include "Util.h"
#include "BeliefProp.h"
#include "CountingBp.h"
#include "VarElim.h"
void
GroundSolver::printAnswer (const VarIds& vids)
{
Vars unobservedVars;
VarIds unobservedVids;
for (size_t i = 0; i < vids.size(); i++) {
VarNode* vn = fg.getVarNode (vids[i]);
if (vn->hasEvidence() == false) {
unobservedVars.push_back (vn);
unobservedVids.push_back (vids[i]);
}
}
if (unobservedVids.empty() == false) {
Params res = solveQuery (unobservedVids);
vector<string> stateLines = Util::getStateLines (unobservedVars);
for (size_t i = 0; i < res.size(); i++) {
cout << "P(" << stateLines[i] << ") = " ;
cout << std::setprecision (Constants::PRECISION) << res[i];
cout << endl;
}
cout << endl;
}
}
void
GroundSolver::printAllPosterioris (void)
{
VarNodes vars = fg.varNodes();
std::sort (vars.begin(), vars.end(), sortByVarId());
for (size_t i = 0; i < vars.size(); i++) {
printAnswer ({vars[i]->varId()});
}
}
Params
GroundSolver::getJointByConditioning (
GroundSolverType solverType,
FactorGraph fg,
const VarIds& jointVarIds) const
{
VarNodes jointVars;
for (size_t i = 0; i < jointVarIds.size(); i++) {
assert (fg.getVarNode (jointVarIds[i]));
jointVars.push_back (fg.getVarNode (jointVarIds[i]));
}
GroundSolver* solver = 0;
switch (solverType) {
case GroundSolverType::BP: solver = new BeliefProp (fg); break;
case GroundSolverType::CBP: solver = new CountingBp (fg); break;
case GroundSolverType::VE: solver = new VarElim (fg); break;
}
Params prevBeliefs = solver->solveQuery ({jointVarIds[0]});
VarIds observedVids = {jointVars[0]->varId()};
for (size_t i = 1; i < jointVarIds.size(); i++) {
assert (jointVars[i]->hasEvidence() == false);
Params newBeliefs;
Vars observedVars;
Ranges observedRanges;
for (size_t j = 0; j < observedVids.size(); j++) {
observedVars.push_back (fg.getVarNode (observedVids[j]));
observedRanges.push_back (observedVars.back()->range());
}
Indexer indexer (observedRanges, false);
while (indexer.valid()) {
for (size_t j = 0; j < observedVars.size(); j++) {
observedVars[j]->setEvidence (indexer[j]);
}
delete solver;
switch (solverType) {
case GroundSolverType::BP: solver = new BeliefProp (fg); break;
case GroundSolverType::CBP: solver = new CountingBp (fg); break;
case GroundSolverType::VE: solver = new VarElim (fg); break;
}
Params beliefs = solver->solveQuery ({jointVarIds[i]});
for (size_t k = 0; k < beliefs.size(); k++) {
newBeliefs.push_back (beliefs[k]);
}
++ indexer;
}
int count = -1;
for (size_t 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());
}
delete solver;
return prevBeliefs;
}

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#ifndef HORUS_GROUNDSOLVER_H
#define HORUS_GROUNDSOLVER_H
#include <iomanip>
#include "FactorGraph.h"
#include "Var.h"
#include "Horus.h"
using namespace std;
class GroundSolver
{
public:
GroundSolver (const FactorGraph& factorGraph) : fg(factorGraph) { }
virtual ~GroundSolver() { } // ensure that subclass destructor is called
virtual Params solveQuery (VarIds queryVids) = 0;
virtual void printSolverFlags (void) const = 0;
void printAnswer (const VarIds& vids);
void printAllPosterioris (void);
Params getJointByConditioning (GroundSolverType,
FactorGraph, const VarIds& jointVarIds) const;
protected:
const FactorGraph& fg;
};
#endif // HORUS_GROUNDSOLVER_H

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#include <cassert>
#include <algorithm>
#include <numeric>
#include "Histogram.h"
#include "Util.h"
HistogramSet::HistogramSet (unsigned size, unsigned range)
{
size_ = size;
hist_.resize (range, 0);
hist_[0] = size;
}
void
HistogramSet::nextHistogram (void)
{
for (size_t i = hist_.size() - 1; i-- > 0; ) {
if (hist_[i] > 0) {
hist_[i] --;
hist_[i + 1] = maxCount (i + 1);
clearAfter (i + 1);
break;
}
}
assert (std::accumulate (hist_.begin(), hist_.end(), 0)
== (int) size_);
}
unsigned
HistogramSet::operator[] (size_t idx) const
{
assert (idx < hist_.size());
return hist_[idx];
}
unsigned
HistogramSet::nrHistograms (void) const
{
return HistogramSet::nrHistograms (size_, hist_.size());
}
void
HistogramSet::reset (void)
{
std::fill (hist_.begin() + 1, hist_.end(), 0);
hist_[0] = size_;
}
vector<Histogram>
HistogramSet::getHistograms (unsigned N, unsigned R)
{
HistogramSet hs (N, R);
unsigned H = hs.nrHistograms();
vector<Histogram> histograms;
histograms.reserve (H);
for (unsigned i = 0; i < H; i++) {
histograms.push_back (hs.hist_);
hs.nextHistogram();
}
return histograms;
}
unsigned
HistogramSet::nrHistograms (unsigned N, unsigned R)
{
return Util::nrCombinations (N + R - 1, R - 1);
}
size_t
HistogramSet::findIndex (
const Histogram& h,
const vector<Histogram>& hists)
{
vector<Histogram>::const_iterator it = std::lower_bound (
hists.begin(), hists.end(), h, std::greater<Histogram>());
assert (it != hists.end() && *it == h);
return std::distance (hists.begin(), it);
}
vector<double>
HistogramSet::getNumAssigns (unsigned N, unsigned R)
{
HistogramSet hs (N, R);
double N_fac = Util::logFactorial (N);
unsigned H = hs.nrHistograms();
vector<double> numAssigns;
numAssigns.reserve (H);
for (unsigned h = 0; h < H; h++) {
double prod = 0.0;
for (unsigned r = 0; r < R; r++) {
prod += Util::logFactorial (hs[r]);
}
double res = N_fac - prod;
numAssigns.push_back (Globals::logDomain ? res : std::exp (res));
hs.nextHistogram();
}
return numAssigns;
}
ostream& operator<< (ostream &os, const HistogramSet& hs)
{
os << "#" << hs.hist_;
return os;
}
unsigned
HistogramSet::maxCount (size_t idx) const
{
unsigned sum = 0;
for (size_t i = 0; i < idx; i++) {
sum += hist_[i];
}
return size_ - sum;
}
void
HistogramSet::clearAfter (size_t idx)
{
std::fill (hist_.begin() + idx + 1, hist_.end(), 0);
}

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#ifndef HORUS_HISTOGRAM_H
#define HORUS_HISTOGRAM_H
#include <vector>
#include <ostream>
using namespace std;
typedef vector<unsigned> Histogram;
class HistogramSet
{
public:
HistogramSet (unsigned, unsigned);
void nextHistogram (void);
unsigned operator[] (size_t idx) const;
unsigned nrHistograms (void) const;
void reset (void);
static vector<Histogram> getHistograms (unsigned ,unsigned);
static unsigned nrHistograms (unsigned, unsigned);
static size_t findIndex (
const Histogram&, const vector<Histogram>&);
static vector<double> getNumAssigns (unsigned, unsigned);
friend std::ostream& operator<< (ostream &os, const HistogramSet& hs);
private:
unsigned maxCount (size_t) const;
void clearAfter (size_t);
unsigned size_;
Histogram hist_;
};
#endif // HORUS_HISTOGRAM_H

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#ifndef HORUS_HORUS_H
#define HORUS_HORUS_H
#include <limits>
#include <vector>
#define DISALLOW_COPY_AND_ASSIGN(TypeName) \
TypeName(const TypeName&); \
void operator=(const TypeName&)
using namespace std;
class Var;
class Factor;
class VarNode;
class FacNode;
typedef vector<double> Params;
typedef unsigned VarId;
typedef vector<VarId> VarIds;
typedef vector<Var*> Vars;
typedef vector<VarNode*> VarNodes;
typedef vector<FacNode*> FacNodes;
typedef vector<Factor*> Factors;
typedef vector<string> States;
typedef vector<unsigned> Ranges;
typedef unsigned long long ullong;
enum LiftedSolverType
{
LVE, // generalized counting first-order variable elimination (GC-FOVE)
LBP, // lifted first-order belief propagation
LKC // lifted first-order knowledge compilation
};
enum GroundSolverType
{
VE, // variable elimination
BP, // belief propagation
CBP // counting belief propagation
};
namespace Globals {
extern bool logDomain;
// level of debug information
extern unsigned verbosity;
extern LiftedSolverType liftedSolver;
extern GroundSolverType groundSolver;
};
namespace Constants {
// show message calculation for belief propagation
const bool SHOW_BP_CALCS = false;
const int NO_EVIDENCE = -1;
// number of digits to show when printing a parameter
const unsigned PRECISION = 6;
};
namespace BpOptions
{
enum Schedule {
SEQ_FIXED,
SEQ_RANDOM,
PARALLEL,
MAX_RESIDUAL
};
extern Schedule schedule;
extern double accuracy;
extern unsigned maxIter;
}
#endif // HORUS_HORUS_H

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#include <cstdlib>
#include <iostream>
#include <sstream>
#include "FactorGraph.h"
#include "VarElim.h"
#include "BeliefProp.h"
#include "CountingBp.h"
using namespace std;
int readHorusFlags (int, const char* []);
void readFactorGraph (FactorGraph&, const char*);
VarIds readQueryAndEvidence (FactorGraph&, int, const char* [], int);
void runSolver (const FactorGraph&, const VarIds&);
const string USAGE = "usage: ./hcli [HORUS_FLAG=VALUE] \
MODEL_FILE [VARIABLE | OBSERVED_VARIABLE=EVIDENCE] ..." ;
int
main (int argc, const char* argv[])
{
if (argc <= 1) {
cerr << "Error: no probabilistic graphical model was given." << endl;
cerr << USAGE << endl;
exit (EXIT_FAILURE);
}
int idx = readHorusFlags (argc, argv);
FactorGraph fg;
readFactorGraph (fg, argv[idx]);
VarIds queryIds = readQueryAndEvidence (fg, argc, argv, idx + 1);
runSolver (fg, queryIds);
return 0;
}
int
readHorusFlags (int argc, const char* argv[])
{
int i = 1;
for (; i < argc; i++) {
const string& arg = argv[i];
size_t pos = arg.find ('=');
if (pos == std::string::npos) {
return i;
}
string leftArg = arg.substr (0, pos);
string rightArg = arg.substr (pos + 1);
if (leftArg.empty()) {
cerr << "Error: missing left argument." << endl;
cerr << USAGE << endl;
exit (EXIT_FAILURE);
}
if (rightArg.empty()) {
cerr << "Error: missing right argument." << endl;
cerr << USAGE << endl;
exit (EXIT_FAILURE);
}
Util::setHorusFlag (leftArg, rightArg);
}
return i + 1;
}
void
readFactorGraph (FactorGraph& fg, const char* s)
{
string fileName (s);
string extension = fileName.substr (fileName.find_last_of ('.') + 1);
if (extension == "uai") {
fg.readFromUaiFormat (fileName.c_str());
} else if (extension == "fg") {
fg.readFromLibDaiFormat (fileName.c_str());
} else {
cerr << "Error: the probabilistic graphical model must be " ;
cerr << "defined either in a UAI or libDAI file." << endl;
exit (EXIT_FAILURE);
}
}
VarIds
readQueryAndEvidence (
FactorGraph& fg,
int argc,
const char* argv[],
int start)
{
VarIds queryIds;
for (int i = start; i < argc; i++) {
const string& arg = argv[i];
if (arg.find ('=') == std::string::npos) {
if (Util::isInteger (arg) == false) {
cerr << "Error: `" << arg << "' " ;
cerr << "is not a variable id." ;
cerr << endl;
exit (EXIT_FAILURE);
}
VarId vid = Util::stringToUnsigned (arg);
VarNode* queryVar = fg.getVarNode (vid);
if (queryVar == false) {
cerr << "Error: unknow variable with id " ;
cerr << "`" << vid << "'." << endl;
exit (EXIT_FAILURE);
}
queryIds.push_back (vid);
} else {
size_t pos = arg.find ('=');
string leftArg = arg.substr (0, pos);
string rightArg = arg.substr (pos + 1);
if (leftArg.empty()) {
cerr << "Error: missing left argument." << endl;
cerr << USAGE << endl;
exit (EXIT_FAILURE);
}
if (Util::isInteger (leftArg) == false) {
cerr << "Error: `" << leftArg << "' " ;
cerr << "is not a variable id." << endl ;
exit (EXIT_FAILURE);
}
VarId vid = Util::stringToUnsigned (leftArg);
VarNode* observedVar = fg.getVarNode (vid);
if (observedVar == false) {
cerr << "Error: unknow variable with id " ;
cerr << "`" << vid << "'." << endl;
exit (EXIT_FAILURE);
}
if (rightArg.empty()) {
cerr << "Error: missing right argument." << endl;
cerr << USAGE << endl;
exit (EXIT_FAILURE);
}
if (Util::isInteger (rightArg) == false) {
cerr << "Error: `" << rightArg << "' " ;
cerr << "is not a state index." << endl ;
exit (EXIT_FAILURE);
}
unsigned stateIdx = Util::stringToUnsigned (rightArg);
if (observedVar->isValidState (stateIdx) == false) {
cerr << "Error: `" << stateIdx << "' " ;
cerr << "is not a valid state index for variable with id " ;
cerr << "`" << vid << "'." << endl;
exit (EXIT_FAILURE);
}
observedVar->setEvidence (stateIdx);
}
}
return queryIds;
}
void
runSolver (const FactorGraph& fg, const VarIds& queryIds)
{
GroundSolver* solver = 0;
switch (Globals::groundSolver) {
case GroundSolverType::VE:
solver = new VarElim (fg);
break;
case GroundSolverType::BP:
solver = new BeliefProp (fg);
break;
case GroundSolverType::CBP:
solver = new CountingBp (fg);
break;
default:
assert (false);
}
if (Globals::verbosity > 0) {
solver->printSolverFlags();
cout << endl;
}
if (queryIds.empty()) {
solver->printAllPosterioris();
} else {
solver->printAnswer (queryIds);
}
delete solver;
}

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packages/CLPBN/horus2/HorusYap.cpp
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#include <cstdlib>
#include <vector>
#include <iostream>
#include <sstream>
#include <YapInterface.h>
#include "ParfactorList.h"
#include "FactorGraph.h"
#include "LiftedOperations.h"
#include "LiftedVe.h"
#include "VarElim.h"
#include "LiftedBp.h"
#include "CountingBp.h"
#include "BeliefProp.h"
#include "LiftedKc.h"
#include "ElimGraph.h"
#include "BayesBall.h"
using namespace std;
typedef std::pair<ParfactorList*, ObservedFormulas*> LiftedNetwork;
Parfactor* readParfactor (YAP_Term);
void readLiftedEvidence (YAP_Term, ObservedFormulas&);
vector<unsigned> readUnsignedList (YAP_Term list);
Params readParameters (YAP_Term);
YAP_Term fillAnswersPrologList (vector<Params>& results);
int
createLiftedNetwork (void)
{
Parfactors parfactors;
YAP_Term parfactorList = YAP_ARG1;
while (parfactorList != YAP_TermNil()) {
YAP_Term pfTerm = YAP_HeadOfTerm (parfactorList);
parfactors.push_back (readParfactor (pfTerm));
parfactorList = YAP_TailOfTerm (parfactorList);
}
// LiftedUtils::printSymbolDictionary();
if (Globals::verbosity > 2) {
Util::printHeader ("INITIAL PARFACTORS");
for (size_t i = 0; i < parfactors.size(); i++) {
parfactors[i]->print();
cout << endl;
}
}
ParfactorList* pfList = new ParfactorList (parfactors);
if (Globals::verbosity > 2) {
Util::printHeader ("SHATTERED PARFACTORS");
pfList->print();
}
// read evidence
ObservedFormulas* obsFormulas = new ObservedFormulas();
readLiftedEvidence (YAP_ARG2, *(obsFormulas));
LiftedNetwork* net = new LiftedNetwork (pfList, obsFormulas);
YAP_Int p = (YAP_Int) (net);
return YAP_Unify (YAP_MkIntTerm (p), YAP_ARG3);
}
int
createGroundNetwork (void)
{
string factorsType ((char*) YAP_AtomName (YAP_AtomOfTerm (YAP_ARG1)));
FactorGraph* fg = new FactorGraph();
if (factorsType == "bayes") {
fg->setFactorsAsBayesian();
}
YAP_Term factorList = YAP_ARG2;
while (factorList != YAP_TermNil()) {
YAP_Term factor = YAP_HeadOfTerm (factorList);
// read the var ids
VarIds varIds = readUnsignedList (YAP_ArgOfTerm (1, factor));
// read the ranges
Ranges ranges = readUnsignedList (YAP_ArgOfTerm (2, factor));
// read the parameters
Params params = readParameters (YAP_ArgOfTerm (3, factor));
// read dist id
unsigned distId = (unsigned) YAP_IntOfTerm (YAP_ArgOfTerm (4, factor));
fg->addFactor (Factor (varIds, ranges, params, distId));
factorList = YAP_TailOfTerm (factorList);
}
unsigned nrObservedVars = 0;
YAP_Term evidenceList = YAP_ARG3;
while (evidenceList != YAP_TermNil()) {
YAP_Term evTerm = YAP_HeadOfTerm (evidenceList);
unsigned vid = (unsigned) YAP_IntOfTerm ((YAP_ArgOfTerm (1, evTerm)));
unsigned ev = (unsigned) YAP_IntOfTerm ((YAP_ArgOfTerm (2, evTerm)));
assert (fg->getVarNode (vid));
fg->getVarNode (vid)->setEvidence (ev);
evidenceList = YAP_TailOfTerm (evidenceList);
nrObservedVars ++;
}
if (Globals::verbosity > 0) {
cout << "factor graph contains " ;
cout << fg->nrVarNodes() << " variables " ;
cout << "(" << nrObservedVars << " observed) and " ;
cout << fg->nrFacNodes() << " factors " << endl;
}
YAP_Int p = (YAP_Int) (fg);
return YAP_Unify (YAP_MkIntTerm (p), YAP_ARG4);
}
int
runLiftedSolver (void)
{
LiftedNetwork* network = (LiftedNetwork*) YAP_IntOfTerm (YAP_ARG1);
ParfactorList pfListCopy (*network->first);
LiftedOperations::absorveEvidence (pfListCopy, *network->second);
LiftedSolver* solver = 0;
switch (Globals::liftedSolver) {
case LiftedSolverType::LVE: solver = new LiftedVe (pfListCopy); break;
case LiftedSolverType::LBP: solver = new LiftedBp (pfListCopy); break;
case LiftedSolverType::LKC: solver = new LiftedKc (pfListCopy); break;
}
if (Globals::verbosity > 0) {
solver->printSolverFlags();
cout << endl;
}
YAP_Term taskList = YAP_ARG2;
vector<Params> results;
while (taskList != YAP_TermNil()) {
Grounds queryVars;
YAP_Term jointList = YAP_HeadOfTerm (taskList);
while (jointList != YAP_TermNil()) {
YAP_Term ground = YAP_HeadOfTerm (jointList);
if (YAP_IsAtomTerm (ground)) {
string name ((char*) YAP_AtomName (YAP_AtomOfTerm (ground)));
queryVars.push_back (Ground (LiftedUtils::getSymbol (name)));
} else {
assert (YAP_IsApplTerm (ground));
YAP_Functor yapFunctor = YAP_FunctorOfTerm (ground);
string name ((char*) (YAP_AtomName (YAP_NameOfFunctor (yapFunctor))));
unsigned arity = (unsigned) YAP_ArityOfFunctor (yapFunctor);
Symbol functor = LiftedUtils::getSymbol (name);
Symbols args;
for (unsigned i = 1; i <= arity; i++) {
YAP_Term ti = YAP_ArgOfTerm (i, ground);
assert (YAP_IsAtomTerm (ti));
string arg ((char *) YAP_AtomName (YAP_AtomOfTerm (ti)));
args.push_back (LiftedUtils::getSymbol (arg));
}
queryVars.push_back (Ground (functor, args));
}
jointList = YAP_TailOfTerm (jointList);
}
results.push_back (solver->solveQuery (queryVars));
taskList = YAP_TailOfTerm (taskList);
}
delete solver;
return YAP_Unify (fillAnswersPrologList (results), YAP_ARG3);
}
int
runGroundSolver (void)
{
FactorGraph* fg = (FactorGraph*) YAP_IntOfTerm (YAP_ARG1);
vector<VarIds> tasks;
YAP_Term taskList = YAP_ARG2;
while (taskList != YAP_TermNil()) {
tasks.push_back (readUnsignedList (YAP_HeadOfTerm (taskList)));
taskList = YAP_TailOfTerm (taskList);
}
FactorGraph* mfg = fg;
if (fg->bayesianFactors()) {
std::set<VarId> vids;
for (size_t i = 0; i < tasks.size(); i++) {
Util::addToSet (vids, tasks[i]);
}
mfg = BayesBall::getMinimalFactorGraph (
*fg, VarIds (vids.begin(), vids.end()));
}
GroundSolver* solver = 0;
CountingBp::checkForIdenticalFactors = false;
switch (Globals::groundSolver) {
case GroundSolverType::VE: solver = new VarElim (*mfg); break;
case GroundSolverType::BP: solver = new BeliefProp (*mfg); break;
case GroundSolverType::CBP: solver = new CountingBp (*mfg); break;
}
if (Globals::verbosity > 0) {
solver->printSolverFlags();
cout << endl;
}
vector<Params> results;
results.reserve (tasks.size());
for (size_t i = 0; i < tasks.size(); i++) {
results.push_back (solver->solveQuery (tasks[i]));
}
delete solver;
if (fg->bayesianFactors()) {
delete mfg;
}
return YAP_Unify (fillAnswersPrologList (results), YAP_ARG3);
}
int
setParfactorsParams (void)
{
LiftedNetwork* network = (LiftedNetwork*) YAP_IntOfTerm (YAP_ARG1);
ParfactorList* pfList = network->first;
YAP_Term distIdsList = YAP_ARG2;
YAP_Term paramsList = YAP_ARG3;
unordered_map<unsigned, Params> paramsMap;
while (distIdsList != YAP_TermNil()) {
unsigned distId = (unsigned) YAP_IntOfTerm (
YAP_HeadOfTerm (distIdsList));
assert (Util::contains (paramsMap, distId) == false);
paramsMap[distId] = readParameters (YAP_HeadOfTerm (paramsList));
distIdsList = YAP_TailOfTerm (distIdsList);
paramsList = YAP_TailOfTerm (paramsList);
}
ParfactorList::iterator it = pfList->begin();
while (it != pfList->end()) {
assert (Util::contains (paramsMap, (*it)->distId()));
(*it)->setParams (paramsMap[(*it)->distId()]);
++ it;
}
return TRUE;
}
int
setFactorsParams (void)
{
FactorGraph* fg = (FactorGraph*) YAP_IntOfTerm (YAP_ARG1);
YAP_Term distIdsList = YAP_ARG2;
YAP_Term paramsList = YAP_ARG3;
unordered_map<unsigned, Params> paramsMap;
while (distIdsList != YAP_TermNil()) {
unsigned distId = (unsigned) YAP_IntOfTerm (
YAP_HeadOfTerm (distIdsList));
assert (Util::contains (paramsMap, distId) == false);
paramsMap[distId] = readParameters (YAP_HeadOfTerm (paramsList));
distIdsList = YAP_TailOfTerm (distIdsList);
paramsList = YAP_TailOfTerm (paramsList);
}
const FacNodes& facNodes = fg->facNodes();
for (size_t i = 0; i < facNodes.size(); i++) {
unsigned distId = facNodes[i]->factor().distId();
assert (Util::contains (paramsMap, distId));
facNodes[i]->factor().setParams (paramsMap[distId]);
}
return TRUE;
}
int
setVarsInformation (void)
{
Var::clearVarsInfo();
vector<string> labels;
YAP_Term labelsL = YAP_ARG1;
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;
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));
namesL = YAP_TailOfTerm (namesL);
}
Var::addVarInfo (count, labels[count], states);
count ++;
stateNamesL = YAP_TailOfTerm (stateNamesL);
}
return TRUE;
}
int
setHorusFlag (void)
{
string key ((char*) YAP_AtomName (YAP_AtomOfTerm (YAP_ARG1)));
string value;
if (key == "verbosity") {
stringstream ss;
ss << (int) YAP_IntOfTerm (YAP_ARG2);
ss >> value;
} else if (key == "accuracy") {
stringstream ss;
ss << (float) YAP_FloatOfTerm (YAP_ARG2);
ss >> value;
} else if (key == "max_iter") {
stringstream ss;
ss << (int) YAP_IntOfTerm (YAP_ARG2);
ss >> value;
} else {
value = ((char*) YAP_AtomName (YAP_AtomOfTerm (YAP_ARG2)));
}
return Util::setHorusFlag (key, value);
}
int
freeGroundNetwork (void)
{
delete (FactorGraph*) YAP_IntOfTerm (YAP_ARG1);
return TRUE;
}
int
freeLiftedNetwork (void)
{
LiftedNetwork* network = (LiftedNetwork*) YAP_IntOfTerm (YAP_ARG1);
delete network->first;
delete network->second;
delete network;
return TRUE;
}
Parfactor*
readParfactor (YAP_Term pfTerm)
{
// read dist id
unsigned distId = YAP_IntOfTerm (YAP_ArgOfTerm (1, pfTerm));
// read the ranges
Ranges ranges;
YAP_Term rangeList = YAP_ArgOfTerm (3, pfTerm);
while (rangeList != YAP_TermNil()) {
unsigned range = (unsigned) YAP_IntOfTerm (YAP_HeadOfTerm (rangeList));
ranges.push_back (range);
rangeList = YAP_TailOfTerm (rangeList);
}
// read parametric random vars
ProbFormulas formulas;
unsigned count = 0;
unordered_map<YAP_Term, LogVar> lvMap;
YAP_Term pvList = YAP_ArgOfTerm (2, pfTerm);
while (pvList != YAP_TermNil()) {
YAP_Term formulaTerm = YAP_HeadOfTerm (pvList);
if (YAP_IsAtomTerm (formulaTerm)) {
string name ((char*) YAP_AtomName (YAP_AtomOfTerm (formulaTerm)));
Symbol functor = LiftedUtils::getSymbol (name);
formulas.push_back (ProbFormula (functor, ranges[count]));
} else {
LogVars logVars;
YAP_Functor yapFunctor = YAP_FunctorOfTerm (formulaTerm);
string name ((char*) YAP_AtomName (YAP_NameOfFunctor (yapFunctor)));
Symbol functor = LiftedUtils::getSymbol (name);
unsigned arity = (unsigned) YAP_ArityOfFunctor (yapFunctor);
for (unsigned i = 1; i <= arity; i++) {
YAP_Term ti = YAP_ArgOfTerm (i, formulaTerm);
unordered_map<YAP_Term, LogVar>::iterator it = lvMap.find (ti);
if (it != lvMap.end()) {
logVars.push_back (it->second);
} else {
unsigned newLv = lvMap.size();
lvMap[ti] = newLv;
logVars.push_back (newLv);
}
}
formulas.push_back (ProbFormula (functor, logVars, ranges[count]));
}
count ++;
pvList = YAP_TailOfTerm (pvList);
}
// read the parameters
const Params& params = readParameters (YAP_ArgOfTerm (4, pfTerm));
// read the constraint
Tuples tuples;
if (lvMap.size() >= 1) {
YAP_Term tupleList = YAP_ArgOfTerm (5, pfTerm);
while (tupleList != YAP_TermNil()) {
YAP_Term term = YAP_HeadOfTerm (tupleList);
assert (YAP_IsApplTerm (term));
YAP_Functor yapFunctor = YAP_FunctorOfTerm (term);
unsigned arity = (unsigned) YAP_ArityOfFunctor (yapFunctor);
assert (lvMap.size() == arity);
Tuple tuple (arity);
for (unsigned i = 1; i <= arity; i++) {
YAP_Term ti = YAP_ArgOfTerm (i, term);
if (YAP_IsAtomTerm (ti) == false) {
cerr << "Error: the constraint contains free variables." << endl;
exit (EXIT_FAILURE);
}
string name ((char*) YAP_AtomName (YAP_AtomOfTerm (ti)));
tuple[i - 1] = LiftedUtils::getSymbol (name);
}
tuples.push_back (tuple);
tupleList = YAP_TailOfTerm (tupleList);
}
}
return new Parfactor (formulas, params, tuples, distId);
}
void
readLiftedEvidence (
YAP_Term observedList,
ObservedFormulas& obsFormulas)
{
while (observedList != YAP_TermNil()) {
YAP_Term pair = YAP_HeadOfTerm (observedList);
YAP_Term ground = YAP_ArgOfTerm (1, pair);
Symbol functor;
Symbols args;
if (YAP_IsAtomTerm (ground)) {
string name ((char*) YAP_AtomName (YAP_AtomOfTerm (ground)));
functor = LiftedUtils::getSymbol (name);
} else {
assert (YAP_IsApplTerm (ground));
YAP_Functor yapFunctor = YAP_FunctorOfTerm (ground);
string name ((char*) (YAP_AtomName (YAP_NameOfFunctor (yapFunctor))));
functor = LiftedUtils::getSymbol (name);
unsigned arity = (unsigned) YAP_ArityOfFunctor (yapFunctor);
for (unsigned i = 1; i <= arity; i++) {
YAP_Term ti = YAP_ArgOfTerm (i, ground);
assert (YAP_IsAtomTerm (ti));
string arg ((char *) YAP_AtomName (YAP_AtomOfTerm (ti)));
args.push_back (LiftedUtils::getSymbol (arg));
}
}
unsigned evidence = (unsigned) YAP_IntOfTerm (YAP_ArgOfTerm (2, pair));
bool found = false;
for (size_t i = 0; i < obsFormulas.size(); i++) {
if (obsFormulas[i].functor() == functor &&
obsFormulas[i].arity() == args.size() &&
obsFormulas[i].evidence() == evidence) {
obsFormulas[i].addTuple (args);
found = true;
}
}
if (found == false) {
obsFormulas.push_back (ObservedFormula (functor, evidence, args));
}
observedList = YAP_TailOfTerm (observedList);
}
}
vector<unsigned>
readUnsignedList (YAP_Term list)
{
vector<unsigned> vec;
while (list != YAP_TermNil()) {
vec.push_back ((unsigned) YAP_IntOfTerm (YAP_HeadOfTerm (list)));
list = YAP_TailOfTerm (list);
}
return vec;
}
Params
readParameters (YAP_Term paramL)
{
Params params;
assert (YAP_IsPairTerm (paramL));
while (paramL != YAP_TermNil()) {
params.push_back ((double) YAP_FloatOfTerm (YAP_HeadOfTerm (paramL)));
paramL = YAP_TailOfTerm (paramL);
}
if (Globals::logDomain) {
Util::log (params);
}
return params;
}
YAP_Term
fillAnswersPrologList (vector<Params>& results)
{
YAP_Term list = YAP_TermNil();
for (size_t i = results.size(); i-- > 0; ) {
const Params& beliefs = results[i];
YAP_Term queryBeliefsL = YAP_TermNil();
for (size_t j = beliefs.size(); j-- > 0; ) {
YAP_Int sl1 = YAP_InitSlot (list);
YAP_Term belief = YAP_MkFloatTerm (beliefs[j]);
queryBeliefsL = YAP_MkPairTerm (belief, queryBeliefsL);
list = YAP_GetFromSlot (sl1);
YAP_RecoverSlots (1);
}
list = YAP_MkPairTerm (queryBeliefsL, list);
}
return list;
}
extern "C" void
init_predicates (void)
{
YAP_UserCPredicate ("cpp_create_lifted_network",
createLiftedNetwork, 3);
YAP_UserCPredicate ("cpp_create_ground_network",
createGroundNetwork, 4);
YAP_UserCPredicate ("cpp_run_lifted_solver",
runLiftedSolver, 3);
YAP_UserCPredicate ("cpp_run_ground_solver",
runGroundSolver, 3);
YAP_UserCPredicate ("cpp_set_parfactors_params",
setParfactorsParams, 3);
YAP_UserCPredicate ("cpp_set_factors_params",
setFactorsParams, 3);
YAP_UserCPredicate ("cpp_set_vars_information",
setVarsInformation, 2);
YAP_UserCPredicate ("cpp_set_horus_flag",
setHorusFlag, 2);
YAP_UserCPredicate ("cpp_free_lifted_network",
freeLiftedNetwork, 1);
YAP_UserCPredicate ("cpp_free_ground_network",
freeGroundNetwork, 1);
}

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#ifndef HORUS_INDEXER_H
#define HORUS_INDEXER_H
#include <algorithm>
#include <numeric>
#include <sstream>
#include <iomanip>
#include "Util.h"
class Indexer
{
public:
Indexer (const Ranges& ranges, bool calcOffsets = true)
: index_(0), indices_(ranges.size(), 0), ranges_(ranges),
size_(Util::sizeExpected (ranges))
{
if (calcOffsets) {
calculateOffsets();
}
}
void increment (void)
{
for (size_t i = ranges_.size(); i-- > 0; ) {
indices_[i] ++;
if (indices_[i] != ranges_[i]) {
break;
} else {
indices_[i] = 0;
}
}
index_ ++;
}
void incrementDimension (size_t dim)
{
assert (dim < ranges_.size());
assert (ranges_.size() == offsets_.size());
assert (indices_[dim] < ranges_[dim]);
indices_[dim] ++;
index_ += offsets_[dim];
}
void incrementExceptDimension (size_t dim)
{
assert (ranges_.size() == offsets_.size());
for (size_t i = ranges_.size(); i-- > 0; ) {
if (i != dim) {
indices_[i] ++;
index_ += offsets_[i];
if (indices_[i] != ranges_[i]) {
return;
} else {
indices_[i] = 0;
index_ -= offsets_[i] * ranges_[i];
}
}
}
index_ = size_;
}
Indexer& operator++ (void)
{
increment();
return *this;
}
operator size_t (void) const
{
return index_;
}
unsigned operator[] (size_t dim) const
{
assert (valid());
assert (dim < ranges_.size());
return indices_[dim];
}
bool valid (void) const
{
return index_ < size_;
}
void reset (void)
{
std::fill (indices_.begin(), indices_.end(), 0);
index_ = 0;
}
void resetDimension (size_t dim)
{
indices_[dim] = 0;
index_ -= offsets_[dim] * ranges_[dim];
}
size_t size (void) const
{
return size_ ;
}
friend std::ostream& operator<< (std::ostream&, const Indexer&);
private:
void calculateOffsets (void)
{
size_t prod = 1;
offsets_.resize (ranges_.size());
for (size_t i = ranges_.size(); i-- > 0; ) {
offsets_[i] = prod;
prod *= ranges_[i];
}
}
size_t index_;
Ranges indices_;
const Ranges& ranges_;
size_t size_;
vector<size_t> offsets_;
};
inline std::ostream&
operator<< (std::ostream& os, const Indexer& indexer)
{
os << "(" ;
os << std::setw (2) << std::setfill('0') << indexer.index_;
os << ") " ;
os << indexer.indices_;
return os;
}
class MapIndexer
{
public:
MapIndexer (const Ranges& ranges, const vector<bool>& mask)
: index_(0), indices_(ranges.size(), 0), ranges_(ranges),
valid_(true)
{
size_t prod = 1;
offsets_.resize (ranges.size(), 0);
for (size_t i = ranges.size(); i-- > 0; ) {
if (mask[i]) {
offsets_[i] = prod;
prod *= ranges[i];
}
}
assert (ranges.size() == mask.size());
}
MapIndexer (const Ranges& ranges, size_t dim)
: index_(0), indices_(ranges.size(), 0), ranges_(ranges),
valid_(true)
{
size_t prod = 1;
offsets_.resize (ranges.size(), 0);
for (size_t i = ranges.size(); i-- > 0; ) {
if (i != dim) {
offsets_[i] = prod;
prod *= ranges[i];
}
}
}
template <typename T>
MapIndexer (
const vector<T>& allArgs,
const Ranges& allRanges,
const vector<T>& wantedArgs,
const Ranges& wantedRanges)
: index_(0), indices_(allArgs.size(), 0), ranges_(allRanges),
valid_(true)
{
size_t prod = 1;
vector<size_t> offsets (wantedRanges.size());
for (size_t i = wantedRanges.size(); i-- > 0; ) {
offsets[i] = prod;
prod *= wantedRanges[i];
}
offsets_.reserve (allArgs.size());
for (size_t i = 0; i < allArgs.size(); i++) {
size_t idx = Util::indexOf (wantedArgs, allArgs[i]);
offsets_.push_back (idx != wantedArgs.size() ? offsets[idx] : 0);
}
}
MapIndexer& operator++ (void)
{
assert (valid_);
for (size_t i = ranges_.size(); i-- > 0; ) {
indices_[i] ++;
index_ += offsets_[i];
if (indices_[i] != ranges_[i]) {
return *this;
} else {
indices_[i] = 0;
index_ -= offsets_[i] * ranges_[i];
}
}
valid_ = false;
return *this;
}
operator size_t (void) const
{
assert (valid());
return index_;
}
unsigned operator[] (size_t dim) const
{
assert (valid());
assert (dim < ranges_.size());
return indices_[dim];
}
bool valid (void) const
{
return valid_;
}
void reset (void)
{
std::fill (indices_.begin(), indices_.end(), 0);
index_ = 0;
}
friend std::ostream& operator<< (std::ostream&, const MapIndexer&);
private:
size_t index_;
Ranges indices_;
const Ranges& ranges_;
bool valid_;
vector<size_t> offsets_;
};
inline std::ostream&
operator<< (std::ostream &os, const MapIndexer& indexer)
{
os << "(" ;
os << std::setw (2) << std::setfill('0') << indexer.index_;
os << ") " ;
os << indexer.indices_;
return os;
}
#endif // HORUS_INDEXER_H

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#include "LiftedBp.h"
#include "WeightedBp.h"
#include "FactorGraph.h"
#include "LiftedOperations.h"
LiftedBp::LiftedBp (const ParfactorList& parfactorList)
: LiftedSolver (parfactorList)
{
refineParfactors();
createFactorGraph();
solver_ = new WeightedBp (*fg_, getWeights());
}
LiftedBp::~LiftedBp (void)
{
delete solver_;
delete fg_;
}
Params
LiftedBp::solveQuery (const Grounds& query)
{
assert (query.empty() == false);
Params res;
vector<PrvGroup> groups = getQueryGroups (query);
if (query.size() == 1) {
res = solver_->getPosterioriOf (groups[0]);
} else {
ParfactorList::iterator it = pfList_.begin();
size_t idx = pfList_.size();
size_t count = 0;
while (it != pfList_.end()) {
if ((*it)->containsGrounds (query)) {
idx = count;
break;
}
++ it;
++ count;
}
if (idx == pfList_.size()) {
res = getJointByConditioning (pfList_, query);
} else {
VarIds queryVids;
for (unsigned i = 0; i < groups.size(); i++) {
queryVids.push_back (groups[i]);
}
res = solver_->getFactorJoint (fg_->facNodes()[idx], queryVids);
}
}
return res;
}
void
LiftedBp::printSolverFlags (void) const
{
stringstream ss;
ss << "lifted bp [" ;
ss << "schedule=" ;
typedef BpOptions::Schedule Sch;
switch (BpOptions::schedule) {
case Sch::SEQ_FIXED: ss << "seq_fixed"; break;
case Sch::SEQ_RANDOM: ss << "seq_random"; break;
case Sch::PARALLEL: ss << "parallel"; break;
case Sch::MAX_RESIDUAL: ss << "max_residual"; break;
}
ss << ",max_iter=" << BpOptions::maxIter;
ss << ",accuracy=" << BpOptions::accuracy;
ss << ",log_domain=" << Util::toString (Globals::logDomain);
ss << "]" ;
cout << ss.str() << endl;
}
void
LiftedBp::refineParfactors (void)
{
pfList_ = parfactorList;
while (iterate() == false);
if (Globals::verbosity > 2) {
Util::printHeader ("AFTER REFINEMENT");
pfList_.print();
}
}
bool
LiftedBp::iterate (void)
{
ParfactorList::iterator it = pfList_.begin();
while (it != pfList_.end()) {
const ProbFormulas& args = (*it)->arguments();
for (size_t i = 0; i < args.size(); i++) {
LogVarSet lvs = (*it)->logVarSet() - args[i].logVars();
if ((*it)->constr()->isCountNormalized (lvs) == false) {
Parfactors pfs = LiftedOperations::countNormalize (*it, lvs);
it = pfList_.removeAndDelete (it);
pfList_.add (pfs);
return false;
}
}
++ it;
}
return true;
}
vector<PrvGroup>
LiftedBp::getQueryGroups (const Grounds& query)
{
vector<PrvGroup> queryGroups;
for (unsigned i = 0; i < query.size(); i++) {
ParfactorList::const_iterator it = pfList_.begin();
for (; it != pfList_.end(); ++it) {
if ((*it)->containsGround (query[i])) {
queryGroups.push_back ((*it)->findGroup (query[i]));
break;
}
}
}
assert (queryGroups.size() == query.size());
return queryGroups;
}
void
LiftedBp::createFactorGraph (void)
{
fg_ = new FactorGraph();
ParfactorList::const_iterator it = pfList_.begin();
for (; it != pfList_.end(); ++it) {
vector<PrvGroup> groups = (*it)->getAllGroups();
VarIds varIds;
for (size_t i = 0; i < groups.size(); i++) {
varIds.push_back (groups[i]);
}
fg_->addFactor (Factor (varIds, (*it)->ranges(), (*it)->params()));
}
}
vector<vector<unsigned>>
LiftedBp::getWeights (void) const
{
vector<vector<unsigned>> weights;
weights.reserve (pfList_.size());
ParfactorList::const_iterator it = pfList_.begin();
for (; it != pfList_.end(); ++it) {
const ProbFormulas& args = (*it)->arguments();
weights.push_back ({ });
weights.back().reserve (args.size());
for (size_t i = 0; i < args.size(); i++) {
LogVarSet lvs = (*it)->logVarSet() - args[i].logVars();
weights.back().push_back ((*it)->constr()->getConditionalCount (lvs));
}
}
return weights;
}
unsigned
LiftedBp::rangeOfGround (const Ground& gr)
{
ParfactorList::iterator it = pfList_.begin();
while (it != pfList_.end()) {
if ((*it)->containsGround (gr)) {
PrvGroup prvGroup = (*it)->findGroup (gr);
return (*it)->range ((*it)->indexOfGroup (prvGroup));
}
++ it;
}
return std::numeric_limits<unsigned>::max();
}
Params
LiftedBp::getJointByConditioning (
const ParfactorList& pfList,
const Grounds& query)
{
LiftedBp solver (pfList);
Params prevBeliefs = solver.solveQuery ({query[0]});
Grounds obsGrounds = {query[0]};
for (size_t i = 1; i < query.size(); i++) {
Params newBeliefs;
vector<ObservedFormula> obsFs;
Ranges obsRanges;
for (size_t j = 0; j < obsGrounds.size(); j++) {
obsFs.push_back (ObservedFormula (
obsGrounds[j].functor(), 0, obsGrounds[j].args()));
obsRanges.push_back (rangeOfGround (obsGrounds[j]));
}
Indexer indexer (obsRanges, false);
while (indexer.valid()) {
for (size_t j = 0; j < obsFs.size(); j++) {
obsFs[j].setEvidence (indexer[j]);
}
ParfactorList tempPfList (pfList);
LiftedOperations::absorveEvidence (tempPfList, obsFs);
LiftedBp solver (tempPfList);
Params beliefs = solver.solveQuery ({query[i]});
for (size_t k = 0; k < beliefs.size(); k++) {
newBeliefs.push_back (beliefs[k]);
}
++ indexer;
}
int count = -1;
unsigned range = rangeOfGround (query[i]);
for (size_t j = 0; j < newBeliefs.size(); j++) {
if (j % range == 0) {
count ++;
}
newBeliefs[j] *= prevBeliefs[count];
}
prevBeliefs = newBeliefs;
obsGrounds.push_back (query[i]);
}
return prevBeliefs;
}

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packages/CLPBN/horus2/LiftedBp.h
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#ifndef HORUS_LIFTEDBP_H
#define HORUS_LIFTEDBP_H
#include "LiftedSolver.h"
#include "ParfactorList.h"
class FactorGraph;
class WeightedBp;
class LiftedBp : public LiftedSolver
{
public:
LiftedBp (const ParfactorList& pfList);
~LiftedBp (void);
Params solveQuery (const Grounds&);
void printSolverFlags (void) const;
private:
void refineParfactors (void);
bool iterate (void);
vector<PrvGroup> getQueryGroups (const Grounds&);
void createFactorGraph (void);
vector<vector<unsigned>> getWeights (void) const;
unsigned rangeOfGround (const Ground&);
Params getJointByConditioning (const ParfactorList&, const Grounds&);
ParfactorList pfList_;
WeightedBp* solver_;
FactorGraph* fg_;
};
#endif // HORUS_LIFTEDBP_H

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packages/CLPBN/horus2/LiftedKc.cpp
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packages/CLPBN/horus2/LiftedKc.h
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#ifndef HORUS_LIFTEDKC_H
#define HORUS_LIFTEDKC_H
#include "LiftedWCNF.h"
#include "LiftedSolver.h"
#include "ParfactorList.h"
enum CircuitNodeType {
OR_NODE,
AND_NODE,
SET_OR_NODE,
SET_AND_NODE,
INC_EXC_NODE,
LEAF_NODE,
SMOOTH_NODE,
TRUE_NODE,
COMPILATION_FAILED_NODE
};
class CircuitNode
{
public:
CircuitNode (void) { }
virtual ~CircuitNode (void) { }
virtual double weight (void) const = 0;
};
class OrNode : public CircuitNode
{
public:
OrNode (void) : CircuitNode(), leftBranch_(0), rightBranch_(0) { }
~OrNode (void);
CircuitNode** leftBranch (void) { return &leftBranch_; }
CircuitNode** rightBranch (void) { return &rightBranch_; }
double weight (void) const;
private:
CircuitNode* leftBranch_;
CircuitNode* rightBranch_;
};
class AndNode : public CircuitNode
{
public:
AndNode (void) : CircuitNode(), leftBranch_(0), rightBranch_(0) { }
AndNode (CircuitNode* leftBranch, CircuitNode* rightBranch)
: CircuitNode(), leftBranch_(leftBranch), rightBranch_(rightBranch) { }
~AndNode (void);
CircuitNode** leftBranch (void) { return &leftBranch_; }
CircuitNode** rightBranch (void) { return &rightBranch_; }
double weight (void) const;
private:
CircuitNode* leftBranch_;
CircuitNode* rightBranch_;
};
class SetOrNode : public CircuitNode
{
public:
SetOrNode (unsigned nrGroundings)
: CircuitNode(), follow_(0), nrGroundings_(nrGroundings) { }
~SetOrNode (void);
CircuitNode** follow (void) { return &follow_; }
static unsigned nrPositives (void) { return nrPos_; }
static unsigned nrNegatives (void) { return nrNeg_; }
static bool isSet (void) { return nrPos_ >= 0; }
double weight (void) const;
private:
CircuitNode* follow_;
unsigned nrGroundings_;
static int nrPos_;
static int nrNeg_;
};
class SetAndNode : public CircuitNode
{
public:
SetAndNode (unsigned nrGroundings)
: CircuitNode(), follow_(0), nrGroundings_(nrGroundings) { }
~SetAndNode (void);
CircuitNode** follow (void) { return &follow_; }
double weight (void) const;
private:
CircuitNode* follow_;
unsigned nrGroundings_;
};
class IncExcNode : public CircuitNode
{
public:
IncExcNode (void)
: CircuitNode(), plus1Branch_(0), plus2Branch_(0), minusBranch_(0) { }
~IncExcNode (void);
CircuitNode** plus1Branch (void) { return &plus1Branch_; }
CircuitNode** plus2Branch (void) { return &plus2Branch_; }
CircuitNode** minusBranch (void) { return &minusBranch_; }
double weight (void) const;
private:
CircuitNode* plus1Branch_;
CircuitNode* plus2Branch_;
CircuitNode* minusBranch_;
};
class LeafNode : public CircuitNode
{
public:
LeafNode (Clause* clause, const LiftedWCNF& lwcnf)
: CircuitNode(), clause_(clause), lwcnf_(lwcnf) { }
~LeafNode (void);
const Clause* clause (void) const { return clause_; }
Clause* clause (void) { return clause_; }
double weight (void) const;
private:
Clause* clause_;
const LiftedWCNF& lwcnf_;
};
class SmoothNode : public CircuitNode
{
public:
SmoothNode (const Clauses& clauses, const LiftedWCNF& lwcnf)
: CircuitNode(), clauses_(clauses), lwcnf_(lwcnf) { }
~SmoothNode (void);
const Clauses& clauses (void) const { return clauses_; }
Clauses clauses (void) { return clauses_; }
double weight (void) const;
private:
Clauses clauses_;
const LiftedWCNF& lwcnf_;
};
class TrueNode : public CircuitNode
{
public:
TrueNode (void) : CircuitNode() { }
double weight (void) const;
};
class CompilationFailedNode : public CircuitNode
{
public:
CompilationFailedNode (void) : CircuitNode() { }
double weight (void) const;
};
class LiftedCircuit
{
public:
LiftedCircuit (const LiftedWCNF* lwcnf);
~LiftedCircuit (void);
bool isCompilationSucceeded (void) const;
double getWeightedModelCount (void) const;
void exportToGraphViz (const char*);
private:
void compile (CircuitNode** follow, Clauses& clauses);
bool tryUnitPropagation (CircuitNode** follow, Clauses& clauses);
bool tryIndependence (CircuitNode** follow, Clauses& clauses);
bool tryShannonDecomp (CircuitNode** follow, Clauses& clauses);
bool tryInclusionExclusion (CircuitNode** follow, Clauses& clauses);
bool tryIndepPartialGrounding (CircuitNode** follow, Clauses& clauses);
bool tryIndepPartialGroundingAux (Clauses& clauses, ConstraintTree& ct,
LogVars& rootLogVars);
bool tryAtomCounting (CircuitNode** follow, Clauses& clauses);
void shatterCountedLogVars (Clauses& clauses);
bool shatterCountedLogVarsAux (Clauses& clauses);
bool shatterCountedLogVarsAux (Clauses& clauses, size_t idx1, size_t idx2);
bool independentClause (Clause& clause, Clauses& otherClauses) const;
bool independentLiteral (const Literal& lit,
const Literals& otherLits) const;
LitLvTypesSet smoothCircuit (CircuitNode* node);
void createSmoothNode (const LitLvTypesSet& lids,
CircuitNode** prev);
vector<LogVarTypes> getAllPossibleTypes (unsigned nrLogVars) const;
bool containsTypes (const LogVarTypes& typesA,
const LogVarTypes& typesB) const;
CircuitNodeType getCircuitNodeType (const CircuitNode* node) const;
void exportToGraphViz (CircuitNode* node, ofstream&);
void printClauses (CircuitNode* node, ofstream&,
string extraOptions = "");
string escapeNode (const CircuitNode* node) const;
string getExplanationString (CircuitNode* node);
CircuitNode* root_;
const LiftedWCNF* lwcnf_;
bool compilationSucceeded_;
Clauses backupClauses_;
unordered_map<CircuitNode*, Clauses> originClausesMap_;
unordered_map<CircuitNode*, string> explanationMap_;
};
class LiftedKc : public LiftedSolver
{
public:
LiftedKc (const ParfactorList& pfList)
: LiftedSolver(pfList) { }
~LiftedKc (void);
Params solveQuery (const Grounds&);
void printSolverFlags (void) const;
private:
LiftedWCNF* lwcnf_;
LiftedCircuit* circuit_;
ParfactorList pfList_;
};
#endif // HORUS_LIFTEDKC_H

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packages/CLPBN/horus2/LiftedOperations.cpp
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#include "LiftedOperations.h"
void
LiftedOperations::shatterAgainstQuery (
ParfactorList& pfList,
const Grounds& query)
{
for (size_t i = 0; i < query.size(); i++) {
if (query[i].isAtom()) {
continue;
}
bool found = false;
Parfactors newPfs;
ParfactorList::iterator it = pfList.begin();
while (it != pfList.end()) {
if ((*it)->containsGround (query[i])) {
found = true;
std::pair<ConstraintTree*, ConstraintTree*> split;
LogVars queryLvs (
(*it)->constr()->logVars().begin(),
(*it)->constr()->logVars().begin() + query[i].arity());
split = (*it)->constr()->split (query[i].args());
ConstraintTree* commCt = split.first;
ConstraintTree* exclCt = split.second;
newPfs.push_back (new Parfactor (*it, commCt));
if (exclCt->empty() == false) {
newPfs.push_back (new Parfactor (*it, exclCt));
} else {
delete exclCt;
}
it = pfList.removeAndDelete (it);
} else {
++ it;
}
}
if (found == false) {
cerr << "Error: could not find a parfactor with ground " ;
cerr << "`" << query[i] << "'." << endl;
exit (EXIT_FAILURE);
}
pfList.add (newPfs);
}
if (Globals::verbosity > 2) {
Util::printAsteriskLine();
cout << "SHATTERED AGAINST THE QUERY" << endl;
for (size_t i = 0; i < query.size(); i++) {
cout << " -> " << query[i] << endl;
}
Util::printAsteriskLine();
pfList.print();
}
}
void
LiftedOperations::runWeakBayesBall (
ParfactorList& pfList,
const Grounds& query)
{
queue<PrvGroup> todo; // groups to process
set<PrvGroup> done; // processed or in queue
for (size_t i = 0; i < query.size(); i++) {
ParfactorList::iterator it = pfList.begin();
while (it != pfList.end()) {
PrvGroup group = (*it)->findGroup (query[i]);
if (group != numeric_limits<PrvGroup>::max()) {
todo.push (group);
done.insert (group);
break;
}
++ it;
}
}
set<Parfactor*> requiredPfs;
while (todo.empty() == false) {
PrvGroup group = todo.front();
ParfactorList::iterator it = pfList.begin();
while (it != pfList.end()) {
if (Util::contains (requiredPfs, *it) == false &&
(*it)->containsGroup (group)) {
vector<PrvGroup> groups = (*it)->getAllGroups();
for (size_t i = 0; i < groups.size(); i++) {
if (Util::contains (done, groups[i]) == false) {
todo.push (groups[i]);
done.insert (groups[i]);
}
}
requiredPfs.insert (*it);
}
++ it;
}
todo.pop();
}
ParfactorList::iterator it = pfList.begin();
bool foundNotRequired = false;
while (it != pfList.end()) {
if (Util::contains (requiredPfs, *it) == false) {
if (Globals::verbosity > 2) {
if (foundNotRequired == false) {
Util::printHeader ("PARFACTORS TO DISCARD");
foundNotRequired = true;
}
(*it)->print();
}
it = pfList.removeAndDelete (it);
} else {
++ it;
}
}
}
void
LiftedOperations::absorveEvidence (
ParfactorList& pfList,
ObservedFormulas& obsFormulas)
{
for (size_t i = 0; i < obsFormulas.size(); i++) {
Parfactors newPfs;
ParfactorList::iterator it = pfList.begin();
while (it != pfList.end()) {
Parfactor* pf = *it;
it = pfList.remove (it);
Parfactors absorvedPfs = absorve (obsFormulas[i], pf);
if (absorvedPfs.empty() == false) {
if (absorvedPfs.size() == 1 && absorvedPfs[0] == 0) {
// just remove pf;
} else {
Util::addToVector (newPfs, absorvedPfs);
}
delete pf;
} else {
it = pfList.insertShattered (it, pf);
++ it;
}
}
pfList.add (newPfs);
}
if (Globals::verbosity > 2 && obsFormulas.empty() == false) {
Util::printAsteriskLine();
cout << "AFTER EVIDENCE ABSORVED" << endl;
for (size_t i = 0; i < obsFormulas.size(); i++) {
cout << " -> " << obsFormulas[i] << endl;
}
Util::printAsteriskLine();
pfList.print();
}
}
Parfactors
LiftedOperations::countNormalize (
Parfactor* g,
const LogVarSet& set)
{
Parfactors normPfs;
if (set.empty()) {
normPfs.push_back (new Parfactor (*g));
} else {
ConstraintTrees normCts = g->constr()->countNormalize (set);
for (size_t i = 0; i < normCts.size(); i++) {
normPfs.push_back (new Parfactor (g, normCts[i]));
}
}
return normPfs;
}
Parfactor
LiftedOperations::calcGroundMultiplication (Parfactor pf)
{
LogVarSet lvs = pf.constr()->logVarSet();
lvs -= pf.constr()->singletons();
Parfactors newPfs = {new Parfactor (pf)};
for (size_t i = 0; i < lvs.size(); i++) {
Parfactors pfs = newPfs;
newPfs.clear();
for (size_t j = 0; j < pfs.size(); j++) {
bool countedLv = pfs[j]->countedLogVars().contains (lvs[i]);
if (countedLv) {
pfs[j]->fullExpand (lvs[i]);
newPfs.push_back (pfs[j]);
} else {
ConstraintTrees cts = pfs[j]->constr()->ground (lvs[i]);
for (size_t k = 0; k < cts.size(); k++) {
newPfs.push_back (new Parfactor (pfs[j], cts[k]));
}
delete pfs[j];
}
}
}
ParfactorList pfList (newPfs);
Parfactors groundShatteredPfs (pfList.begin(),pfList.end());
for (size_t i = 1; i < groundShatteredPfs.size(); i++) {
groundShatteredPfs[0]->multiply (*groundShatteredPfs[i]);
}
return Parfactor (*groundShatteredPfs[0]);
}
Parfactors
LiftedOperations::absorve (
ObservedFormula& obsFormula,
Parfactor* g)
{
Parfactors absorvedPfs;
const ProbFormulas& formulas = g->arguments();
for (size_t i = 0; i < formulas.size(); i++) {
if (obsFormula.functor() == formulas[i].functor() &&
obsFormula.arity() == formulas[i].arity()) {
if (obsFormula.isAtom()) {
if (formulas.size() > 1) {
g->absorveEvidence (formulas[i], obsFormula.evidence());
} else {
// hack to erase parfactor g
absorvedPfs.push_back (0);
}
break;
}
g->constr()->moveToTop (formulas[i].logVars());
std::pair<ConstraintTree*, ConstraintTree*> res;
res = g->constr()->split (
formulas[i].logVars(),
&(obsFormula.constr()),
obsFormula.constr().logVars());
ConstraintTree* commCt = res.first;
ConstraintTree* exclCt = res.second;
if (commCt->empty() == false) {
if (formulas.size() > 1) {
LogVarSet excl = g->exclusiveLogVars (i);
Parfactor tempPf (g, commCt);
Parfactors countNormPfs = LiftedOperations::countNormalize (
&tempPf, excl);
for (size_t j = 0; j < countNormPfs.size(); j++) {
countNormPfs[j]->absorveEvidence (
formulas[i], obsFormula.evidence());
absorvedPfs.push_back (countNormPfs[j]);
}
} else {
delete commCt;
}
if (exclCt->empty() == false) {
absorvedPfs.push_back (new Parfactor (g, exclCt));
} else {
delete exclCt;
}
if (absorvedPfs.empty()) {
// hack to erase parfactor g
absorvedPfs.push_back (0);
}
break;
} else {
delete commCt;
delete exclCt;
}
}
}
return absorvedPfs;
}

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packages/CLPBN/horus2/LiftedOperations.h
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#ifndef HORUS_LIFTEDOPERATIONS_H
#define HORUS_LIFTEDOPERATIONS_H
#include "ParfactorList.h"
class LiftedOperations
{
public:
static void shatterAgainstQuery (
ParfactorList& pfList, const Grounds& query);
static void runWeakBayesBall (
ParfactorList& pfList, const Grounds&);
static void absorveEvidence (
ParfactorList& pfList, ObservedFormulas& obsFormulas);
static Parfactors countNormalize (Parfactor*, const LogVarSet&);
static Parfactor calcGroundMultiplication (Parfactor pf);
private:
static Parfactors absorve (ObservedFormula&, Parfactor*);
};
#endif // HORUS_LIFTEDOPERATIONS_H

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packages/CLPBN/horus2/LiftedSolver.h
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#ifndef HORUS_LIFTEDSOLVER_H
#define HORUS_LIFTEDSOLVER_H
#include "ParfactorList.h"
#include "Horus.h"
using namespace std;
class LiftedSolver
{
public:
LiftedSolver (const ParfactorList& pfList)
: parfactorList(pfList) { }
virtual ~LiftedSolver() { } // ensure that subclass destructor is called
virtual Params solveQuery (const Grounds& query) = 0;
virtual void printSolverFlags (void) const = 0;
protected:
const ParfactorList& parfactorList;
};
#endif // HORUS_LIFTEDSOLVER_H

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packages/CLPBN/horus2/LiftedUtils.cpp
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#include <cassert>
#include <algorithm>
#include <iostream>
#include <sstream>
#include "LiftedUtils.h"
#include "ConstraintTree.h"
namespace LiftedUtils {
unordered_map<string, unsigned> symbolDict;
Symbol
getSymbol (const string& symbolName)
{
unordered_map<string, unsigned>::iterator it
= symbolDict.find (symbolName);
if (it != symbolDict.end()) {
return it->second;
} else {
symbolDict[symbolName] = symbolDict.size() - 1;
return symbolDict.size() - 1;
}
}
void
printSymbolDictionary (void)
{
unordered_map<string, unsigned>::const_iterator it
= symbolDict.begin();
while (it != symbolDict.end()) {
cout << it->first << " -> " << it->second << endl;
++ it;
}
}
}
ostream& operator<< (ostream &os, const Symbol& s)
{
unordered_map<string, unsigned>::const_iterator it
= LiftedUtils::symbolDict.begin();
while (it != LiftedUtils::symbolDict.end() && it->second != s) {
++ it;
}
assert (it != LiftedUtils::symbolDict.end());
os << it->first;
return os;
}
ostream& operator<< (ostream &os, const LogVar& X)
{
const string labels[] = {
"A", "B", "C", "D", "E", "F",
"G", "H", "I", "J", "K", "M" };
(X >= 12) ? os << "X_" << X.id_ : os << labels[X];
return os;
}
ostream& operator<< (ostream &os, const Tuple& t)
{
os << "(" ;
for (size_t i = 0; i < t.size(); i++) {
os << ((i != 0) ? "," : "") << t[i];
}
os << ")" ;
return os;
}
ostream& operator<< (ostream &os, const Ground& gr)
{
os << gr.functor();
os << "(" ;
for (size_t i = 0; i < gr.args().size(); i++) {
if (i != 0) os << ", " ;
os << gr.args()[i];
}
os << ")" ;
return os;
}
LogVars
Substitution::getDiscardedLogVars (void) const
{
LogVars discardedLvs;
set<LogVar> doneLvs;
unordered_map<LogVar, LogVar>::const_iterator it;
it = subs_.begin();
while (it != subs_.end()) {
if (Util::contains (doneLvs, it->second)) {
discardedLvs.push_back (it->first);
} else {
doneLvs.insert (it->second);
}
++ it;
}
return discardedLvs;
}
ostream& operator<< (ostream &os, const Substitution& theta)
{
unordered_map<LogVar, LogVar>::const_iterator it;
os << "[" ;
it = theta.subs_.begin();
while (it != theta.subs_.end()) {
if (it != theta.subs_.begin()) os << ", " ;
os << it->first << "->" << it->second ;
++ it;
}
os << "]" ;
return os;
}

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#ifndef HORUS_LIFTEDUTILS_H
#define HORUS_LIFTEDUTILS_H
#include <limits>
#include <string>
#include <vector>
#include <unordered_map>
#include "TinySet.h"
#include "Util.h"
using namespace std;
class Symbol
{
public:
Symbol (void) : id_(Util::maxUnsigned()) { }
Symbol (unsigned id) : id_(id) { }
operator unsigned (void) const { return id_; }
bool valid (void) const { return id_ != Util::maxUnsigned(); }
static Symbol invalid (void) { return Symbol(); }
friend ostream& operator<< (ostream &os, const Symbol& s);
private:
unsigned id_;
};
class LogVar
{
public:
LogVar (void) : id_(Util::maxUnsigned()) { }
LogVar (unsigned id) : id_(id) { }
operator unsigned (void) const { return id_; }
LogVar& operator++ (void)
{
assert (valid());
id_ ++;
return *this;
}
bool valid (void) const
{
return id_ != Util::maxUnsigned();
}
friend ostream& operator<< (ostream &os, const LogVar& X);
private:
unsigned id_;
};
namespace std {
template <> struct hash<Symbol> {
size_t operator() (const Symbol& s) const {
return std::hash<unsigned>() (s);
}};
template <> struct hash<LogVar> {
size_t operator() (const LogVar& X) const {
return std::hash<unsigned>() (X);
}};
};
typedef vector<Symbol> Symbols;
typedef vector<Symbol> Tuple;
typedef vector<Tuple> Tuples;
typedef vector<LogVar> LogVars;
typedef TinySet<Symbol> SymbolSet;
typedef TinySet<LogVar> LogVarSet;
typedef TinySet<Tuple> TupleSet;
ostream& operator<< (ostream &os, const Tuple& t);
namespace LiftedUtils {
Symbol getSymbol (const string&);
void printSymbolDictionary (void);
}
class Ground
{
public:
Ground (Symbol f) : functor_(f) { }
Ground (Symbol f, const Symbols& args) : functor_(f), args_(args) { }
Symbol functor (void) const { return functor_; }
Symbols args (void) const { return args_; }
size_t arity (void) const { return args_.size(); }
bool isAtom (void) const { return args_.size() == 0; }
friend ostream& operator<< (ostream &os, const Ground& gr);
private:
Symbol functor_;
Symbols args_;
};
typedef vector<Ground> Grounds;
class Substitution
{
public:
void add (LogVar X_old, LogVar X_new)
{
assert (Util::contains (subs_, X_old) == false);
subs_.insert (make_pair (X_old, X_new));
}
void rename (LogVar X_old, LogVar X_new)
{
assert (Util::contains (subs_, X_old));
subs_.find (X_old)->second = X_new;
}
LogVar newNameFor (LogVar X) const
{
unordered_map<LogVar, LogVar>::const_iterator it;
it = subs_.find (X);
if (it != subs_.end()) {
return subs_.find (X)->second;
}
return X;
}
bool containsReplacementFor (LogVar X) const
{
return Util::contains (subs_, X);
}
size_t nrReplacements (void) const { return subs_.size(); }
LogVars getDiscardedLogVars (void) const;
friend ostream& operator<< (ostream &os, const Substitution& theta);
private:
unordered_map<LogVar, LogVar> subs_;
};
#endif // HORUS_LIFTEDUTILS_H

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#include <algorithm>
#include <set>
#include "LiftedVe.h"
#include "LiftedOperations.h"
#include "Histogram.h"
#include "Util.h"
vector<LiftedOperator*>
LiftedOperator::getValidOps (
ParfactorList& pfList,
const Grounds& query)
{
vector<LiftedOperator*> validOps;
vector<ProductOperator*> multOps;
multOps = ProductOperator::getValidOps (pfList);
validOps.insert (validOps.end(), multOps.begin(), multOps.end());
if (Globals::verbosity > 1 || multOps.empty()) {
vector<SumOutOperator*> sumOutOps;
vector<CountingOperator*> countOps;
vector<GroundOperator*> groundOps;
sumOutOps = SumOutOperator::getValidOps (pfList, query);
countOps = CountingOperator::getValidOps (pfList);
groundOps = GroundOperator::getValidOps (pfList);
validOps.insert (validOps.end(), sumOutOps.begin(), sumOutOps.end());
validOps.insert (validOps.end(), countOps.begin(), countOps.end());
validOps.insert (validOps.end(), groundOps.begin(), groundOps.end());
}
return validOps;
}
void
LiftedOperator::printValidOps (
ParfactorList& pfList,
const Grounds& query)
{
vector<LiftedOperator*> validOps;
validOps = LiftedOperator::getValidOps (pfList, query);
for (size_t i = 0; i < validOps.size(); i++) {
cout << "-> " << validOps[i]->toString();
delete validOps[i];
}
}
vector<ParfactorList::iterator>
LiftedOperator::getParfactorsWithGroup (
ParfactorList& pfList, PrvGroup group)
{
vector<ParfactorList::iterator> iters;
ParfactorList::iterator pflIt = pfList.begin();
while (pflIt != pfList.end()) {
if ((*pflIt)->containsGroup (group)) {
iters.push_back (pflIt);
}
++ pflIt;
}
return iters;
}
double
ProductOperator::getLogCost (void)
{
return std::log (0.0);
}
void
ProductOperator::apply (void)
{
Parfactor* g1 = *g1_;
Parfactor* g2 = *g2_;
g1->multiply (*g2);
pfList_.remove (g1_);
pfList_.removeAndDelete (g2_);
pfList_.addShattered (g1);
}
vector<ProductOperator*>
ProductOperator::getValidOps (ParfactorList& pfList)
{
vector<ProductOperator*> validOps;
ParfactorList::iterator it1 = pfList.begin();
ParfactorList::iterator penultimate = -- pfList.end();
set<Parfactor*> pfs;
while (it1 != penultimate) {
if (Util::contains (pfs, *it1)) {
++ it1;
continue;
}
ParfactorList::iterator it2 = it1;
++ it2;
while (it2 != pfList.end()) {
if (Util::contains (pfs, *it2)) {
++ it2;
continue;
} else {
if (validOp (*it1, *it2)) {
pfs.insert (*it1);
pfs.insert (*it2);
validOps.push_back (new ProductOperator (
it1, it2, pfList));
if (Globals::verbosity < 2) {
return validOps;
}
break;
}
}
++ it2;
}
++ it1;
}
return validOps;
}
string
ProductOperator::toString (void)
{
stringstream ss;
ss << "just multiplicate " ;
ss << (*g1_)->getAllGroups();
ss << " x " ;
ss << (*g2_)->getAllGroups();
ss << " [cost=" << std::exp (getLogCost()) << "]" << endl;
return ss.str();
}
bool
ProductOperator::validOp (Parfactor* g1, Parfactor* g2)
{
TinySet<PrvGroup> g1_gs (g1->getAllGroups());
TinySet<PrvGroup> g2_gs (g2->getAllGroups());
if (g1_gs.contains (g2_gs) || g2_gs.contains (g1_gs)) {
TinySet<PrvGroup> intersect = g1_gs & g2_gs;
for (size_t i = 0; i < intersect.size(); i++) {
if (g1->nrFormulasWithGroup (intersect[i]) != 1 ||
g2->nrFormulasWithGroup (intersect[i]) != 1) {
return false;
}
size_t idx1 = g1->indexOfGroup (intersect[i]);
size_t idx2 = g2->indexOfGroup (intersect[i]);
if (g1->range (idx1) != g2->range (idx2)) {
return false;
}
}
return Parfactor::canMultiply (g1, g2);
}
return false;
}
double
SumOutOperator::getLogCost (void)
{
TinySet<PrvGroup> groupSet;
ParfactorList::const_iterator pfIter = pfList_.begin();
unsigned nrProdFactors = 0;
while (pfIter != pfList_.end()) {
if ((*pfIter)->containsGroup (group_)) {
vector<PrvGroup> groups = (*pfIter)->getAllGroups();
groupSet |= TinySet<PrvGroup> (groups);
++ nrProdFactors;
}
++ pfIter;
}
if (nrProdFactors == 1) {
// best possible case
return std::log (0.0);
}
double cost = 1.0;
for (size_t i = 0; i < groupSet.size(); i++) {
pfIter = pfList_.begin();
while (pfIter != pfList_.end()) {
if ((*pfIter)->containsGroup (groupSet[i])) {
size_t idx = (*pfIter)->indexOfGroup (groupSet[i]);
cost *= (*pfIter)->range (idx);
break;
}
++ pfIter;
}
}
return std::log (cost);
}
void
SumOutOperator::apply (void)
{
vector<ParfactorList::iterator> iters;
iters = getParfactorsWithGroup (pfList_, group_);
Parfactor* product = *(iters[0]);
pfList_.remove (iters[0]);
for (size_t i = 1; i < iters.size(); i++) {
product->multiply (**(iters[i]));
pfList_.removeAndDelete (iters[i]);
}
if (product->nrArguments() == 1) {
delete product;
return;
}
size_t fIdx = product->indexOfGroup (group_);
LogVarSet excl = product->exclusiveLogVars (fIdx);
if (product->constr()->isCountNormalized (excl)) {
product->sumOutIndex (fIdx);
pfList_.addShattered (product);
} else {
Parfactors pfs = LiftedOperations::countNormalize (product, excl);
for (size_t i = 0; i < pfs.size(); i++) {
pfs[i]->sumOutIndex (fIdx);
pfList_.add (pfs[i]);
}
delete product;
}
}
vector<SumOutOperator*>
SumOutOperator::getValidOps (
ParfactorList& pfList,
const Grounds& query)
{
vector<SumOutOperator*> validOps;
set<PrvGroup> allGroups;
ParfactorList::const_iterator it = pfList.begin();
while (it != pfList.end()) {
const ProbFormulas& formulas = (*it)->arguments();
for (size_t i = 0; i < formulas.size(); i++) {
allGroups.insert (formulas[i].group());
}
++ it;
}
set<PrvGroup>::const_iterator groupIt = allGroups.begin();
while (groupIt != allGroups.end()) {
if (validOp (*groupIt, pfList, query)) {
validOps.push_back (new SumOutOperator (*groupIt, pfList));
}
++ groupIt;
}
return validOps;
}
string
SumOutOperator::toString (void)
{
stringstream ss;
vector<ParfactorList::iterator> pfIters;
pfIters = getParfactorsWithGroup (pfList_, group_);
size_t idx = (*pfIters[0])->indexOfGroup (group_);
ProbFormula f = (*pfIters[0])->argument (idx);
TupleSet tupleSet = (*pfIters[0])->constr()->tupleSet (f.logVars());
ss << "sum out " << f.functor() << "/" << f.arity();
ss << "|" << tupleSet << " (group " << group_ << ")";
ss << " [cost=" << std::exp (getLogCost()) << "]" << endl;
return ss.str();
}
bool
SumOutOperator::validOp (
PrvGroup group,
ParfactorList& pfList,
const Grounds& query)
{
vector<ParfactorList::iterator> pfIters;
pfIters = getParfactorsWithGroup (pfList, group);
if (isToEliminate (*pfIters[0], group, query) == false) {
return false;
}
int range = -1;
for (size_t i = 0; i < pfIters.size(); i++) {
if ((*pfIters[i])->nrFormulasWithGroup (group) > 1) {
return false;
}
size_t fIdx = (*pfIters[i])->indexOfGroup (group);
if ((*pfIters[i])->argument (fIdx).contains (
(*pfIters[i])->elimLogVars()) == false) {
return false;
}
if (range == -1) {
range = (*pfIters[i])->range (fIdx);
} else if ((int)(*pfIters[i])->range (fIdx) != range) {
return false;
}
}
return true;
}
bool
SumOutOperator::isToEliminate (
Parfactor* g,
PrvGroup group,
const Grounds& query)
{
size_t fIdx = g->indexOfGroup (group);
const ProbFormula& formula = g->argument (fIdx);
bool toElim = true;
for (size_t i = 0; i < query.size(); i++) {
if (formula.functor() == query[i].functor() &&
formula.arity() == query[i].arity()) {
g->constr()->moveToTop (formula.logVars());
if (g->constr()->containsTuple (query[i].args())) {
toElim = false;
break;
}
}
}
return toElim;
}
double
CountingOperator::getLogCost (void)
{
double cost = 0.0;
size_t fIdx = (*pfIter_)->indexOfLogVar (X_);
unsigned range = (*pfIter_)->range (fIdx);
unsigned size = (*pfIter_)->size() / range;
TinySet<unsigned> counts;
counts = (*pfIter_)->constr()->getConditionalCounts (X_);
for (size_t i = 0; i < counts.size(); i++) {
cost += size * HistogramSet::nrHistograms (counts[i], range);
}
PrvGroup group = (*pfIter_)->argument (fIdx).group();
size_t lvIndex = Util::indexOf (
(*pfIter_)->argument (fIdx).logVars(), X_);
assert (lvIndex != (*pfIter_)->argument (fIdx).logVars().size());
ParfactorList::iterator pfIter = pfList_.begin();
while (pfIter != pfList_.end()) {
if (pfIter != pfIter_) {
size_t fIdx2 = (*pfIter)->indexOfGroup (group);
if (fIdx2 != (*pfIter)->nrArguments()) {
LogVar Y = ((*pfIter)->argument (fIdx2).logVars()[lvIndex]);
if ((*pfIter)->canCountConvert (Y) == false) {
// the real cost should be the cost of grounding Y
cost *= 10.0;
}
}
}
++ pfIter;
}
return std::log (cost);
}
void
CountingOperator::apply (void)
{
if ((*pfIter_)->constr()->isCountNormalized (X_)) {
(*pfIter_)->countConvert (X_);
} else {
Parfactor* pf = *pfIter_;
pfList_.remove (pfIter_);
Parfactors pfs = LiftedOperations::countNormalize (pf, X_);
for (size_t i = 0; i < pfs.size(); i++) {
unsigned condCount = pfs[i]->constr()->getConditionalCount (X_);
bool cartProduct = pfs[i]->constr()->isCartesianProduct (
pfs[i]->countedLogVars() | X_);
if (condCount > 1 && cartProduct) {
pfs[i]->countConvert (X_);
}
pfList_.add (pfs[i]);
}
delete pf;
}
}
vector<CountingOperator*>
CountingOperator::getValidOps (ParfactorList& pfList)
{
vector<CountingOperator*> validOps;
ParfactorList::iterator it = pfList.begin();
while (it != pfList.end()) {
LogVarSet candidates = (*it)->uncountedLogVars();
for (size_t i = 0; i < candidates.size(); i++) {
if (validOp (*it, candidates[i])) {
validOps.push_back (new CountingOperator (
it, candidates[i], pfList));
} else {
}
}
++ it;
}
return validOps;
}
string
CountingOperator::toString (void)
{
stringstream ss;
ss << "count convert " << X_ << " in " ;
ss << (*pfIter_)->getLabel();
ss << " [cost=" << std::exp (getLogCost()) << "]" << endl;
Parfactors pfs = LiftedOperations::countNormalize (*pfIter_, X_);
if ((*pfIter_)->constr()->isCountNormalized (X_) == false) {
for (size_t i = 0; i < pfs.size(); i++) {
ss << " º " << pfs[i]->getLabel() << endl;
}
}
for (size_t i = 0; i < pfs.size(); i++) {
delete pfs[i];
}
return ss.str();
}
bool
CountingOperator::validOp (Parfactor* g, LogVar X)
{
if (g->nrFormulas (X) != 1) {
return false;
}
size_t fIdx = g->indexOfLogVar (X);
if (g->argument (fIdx).isCounting()) {
return false;
}
bool countNormalized = g->constr()->isCountNormalized (X);
if (countNormalized) {
return g->canCountConvert (X);
}
return true;
}
double
GroundOperator::getLogCost (void)
{
vector<pair<PrvGroup, unsigned>> affectedFormulas;
affectedFormulas = getAffectedFormulas();
// cout << "affected formulas: " ;
// for (size_t i = 0; i < affectedFormulas.size(); i++) {
// cout << affectedFormulas[i].first << ":" ;
// cout << affectedFormulas[i].second << " " ;
// }
// cout << "cost =" ;
double totalCost = std::log (0.0);
ParfactorList::iterator pflIt = pfList_.begin();
while (pflIt != pfList_.end()) {
Parfactor* pf = *pflIt;
double reps = 0.0;
double pfSize = std::log (pf->size());
bool willBeAffected = false;
LogVarSet lvsToGround;
for (size_t i = 0; i < affectedFormulas.size(); i++) {
size_t fIdx = pf->indexOfGroup (affectedFormulas[i].first);
if (fIdx != pf->nrArguments()) {
ProbFormula f = pf->argument (fIdx);
LogVar X = f.logVars()[affectedFormulas[i].second];
bool isCountingLv = pf->countedLogVars().contains (X);
if (isCountingLv) {
unsigned nrHists = pf->range (fIdx);
unsigned nrSymbols = pf->constr()->getConditionalCount (X);
unsigned range = pf->argument (fIdx).range();
double power = std::log (range) * nrSymbols;
pfSize = (pfSize - std::log (nrHists)) + power;
} else {
if (lvsToGround.contains (X) == false) {
reps += std::log (pf->constr()->nrSymbols (X));
lvsToGround.insert (X);
}
}
willBeAffected = true;
}
}
if (willBeAffected) {
// cout << " + " << std::exp (reps) << "x" << std::exp (pfSize);
double pfCost = reps + pfSize;
totalCost = Util::logSum (totalCost, pfCost);
}
++ pflIt;
}
// cout << endl;
return totalCost + 3;
}
void
GroundOperator::apply (void)
{
ParfactorList::iterator pfIter;
pfIter = getParfactorsWithGroup (pfList_, group_).front();
Parfactor* pf = *pfIter;
size_t idx = pf->indexOfGroup (group_);
ProbFormula f = pf->argument (idx);
LogVar X = f.logVars()[lvIndex_];
bool countedLv = pf->countedLogVars().contains (X);
pfList_.remove (pfIter);
if (countedLv) {
pf->fullExpand (X);
pfList_.add (pf);
} else {
ConstraintTrees cts = pf->constr()->ground (X);
for (size_t i = 0; i < cts.size(); i++) {
pfList_.add (new Parfactor (pf, cts[i]));
}
delete pf;
}
ParfactorList::iterator pflIt = pfList_.begin();
while (pflIt != pfList_.end()) {
(*pflIt)->simplifyGrounds();
++ pflIt;
}
}
vector<GroundOperator*>
GroundOperator::getValidOps (ParfactorList& pfList)
{
vector<GroundOperator*> validOps;
set<PrvGroup> allGroups;
ParfactorList::const_iterator it = pfList.begin();
while (it != pfList.end()) {
const ProbFormulas& formulas = (*it)->arguments();
for (size_t i = 0; i < formulas.size(); i++) {
if (Util::contains (allGroups, formulas[i].group()) == false) {
const LogVars& lvs = formulas[i].logVars();
for (size_t j = 0; j < lvs.size(); j++) {
if ((*it)->constr()->isSingleton (lvs[j]) == false) {
validOps.push_back (new GroundOperator (
formulas[i].group(), j, pfList));
}
}
allGroups.insert (formulas[i].group());
}
}
++ it;
}
return validOps;
}
string
GroundOperator::toString (void)
{
stringstream ss;
vector<ParfactorList::iterator> pfIters;
pfIters = getParfactorsWithGroup (pfList_, group_);
Parfactor* pf = *(getParfactorsWithGroup (pfList_, group_).front());
size_t idx = pf->indexOfGroup (group_);
ProbFormula f = pf->argument (idx);
LogVar lv = f.logVars()[lvIndex_];
TupleSet tupleSet = pf->constr()->tupleSet ({lv});
string pos = "th";
if (lvIndex_ == 0) {
pos = "st" ;
} else if (lvIndex_ == 1) {
pos = "nd" ;
} else if (lvIndex_ == 2) {
pos = "rd" ;
}
ss << "grounding " << lvIndex_ + 1 << pos << " log var in " ;
ss << f.functor() << "/" << f.arity();
ss << "|" << tupleSet << " (group " << group_ << ")";
ss << " [cost=" << std::exp (getLogCost()) << "]" << endl;
return ss.str();
}
vector<pair<PrvGroup, unsigned>>
GroundOperator::getAffectedFormulas (void)
{
vector<pair<PrvGroup, unsigned>> affectedFormulas;
affectedFormulas.push_back (make_pair (group_, lvIndex_));
queue<pair<PrvGroup, unsigned>> q;
q.push (make_pair (group_, lvIndex_));
while (q.empty() == false) {
pair<PrvGroup, unsigned> front = q.front();
ParfactorList::iterator pflIt = pfList_.begin();
while (pflIt != pfList_.end()) {
size_t idx = (*pflIt)->indexOfGroup (front.first);
if (idx != (*pflIt)->nrArguments()) {
ProbFormula f = (*pflIt)->argument (idx);
LogVar X = f.logVars()[front.second];
const ProbFormulas& fs = (*pflIt)->arguments();
for (size_t i = 0; i < fs.size(); i++) {
if (i != idx && fs[i].contains (X)) {
pair<PrvGroup, unsigned> pair = make_pair (
fs[i].group(), fs[i].indexOf (X));
if (Util::contains (affectedFormulas, pair) == false) {
q.push (pair);
affectedFormulas.push_back (pair);
}
}
}
}
++ pflIt;
}
q.pop();
}
return affectedFormulas;
}
Params
LiftedVe::solveQuery (const Grounds& query)
{
assert (query.empty() == false);
pfList_ = parfactorList;
runSolver (query);
(*pfList_.begin())->normalize();
Params params = (*pfList_.begin())->params();
if (Globals::logDomain) {
Util::exp (params);
}
return params;
}
void
LiftedVe::printSolverFlags (void) const
{
stringstream ss;
ss << "lve [" ;
ss << "log_domain=" << Util::toString (Globals::logDomain);
ss << "]" ;
cout << ss.str() << endl;
}
void
LiftedVe::runSolver (const Grounds& query)
{
largestCost_ = std::log (0);
LiftedOperations::shatterAgainstQuery (pfList_, query);
LiftedOperations::runWeakBayesBall (pfList_, query);
while (true) {
if (Globals::verbosity > 2) {
Util::printDashedLine();
pfList_.print();
if (Globals::verbosity > 3) {
LiftedOperator::printValidOps (pfList_, query);
}
}
LiftedOperator* op = getBestOperation (query);
if (op == 0) {
break;
}
if (Globals::verbosity > 1) {
cout << "best operation: " << op->toString();
if (Globals::verbosity > 2) {
cout << endl;
}
}
op->apply();
delete op;
}
assert (pfList_.size() > 0);
if (pfList_.size() > 1) {
ParfactorList::iterator pfIter = pfList_.begin();
++ pfIter;
while (pfIter != pfList_.end()) {
(*pfList_.begin())->multiply (**pfIter);
++ pfIter;
}
}
if (Globals::verbosity > 0) {
cout << "largest cost = " << std::exp (largestCost_) << endl;
cout << endl;
}
(*pfList_.begin())->simplifyGrounds();
(*pfList_.begin())->reorderAccordingGrounds (query);
}
LiftedOperator*
LiftedVe::getBestOperation (const Grounds& query)
{
double bestCost = 0.0;
LiftedOperator* bestOp = 0;
vector<LiftedOperator*> validOps;
validOps = LiftedOperator::getValidOps (pfList_, query);
for (size_t i = 0; i < validOps.size(); i++) {
double cost = validOps[i]->getLogCost();
if ((bestOp == 0) || (cost < bestCost)) {
bestOp = validOps[i];
bestCost = cost;
}
}
if (bestCost > largestCost_) {
largestCost_ = bestCost;
}
for (size_t i = 0; i < validOps.size(); i++) {
if (validOps[i] != bestOp) {
delete validOps[i];
}
}
return bestOp;
}

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#ifndef HORUS_LIFTEDVE_H
#define HORUS_LIFTEDVE_H
#include "LiftedSolver.h"
#include "ParfactorList.h"
class LiftedOperator
{
public:
virtual ~LiftedOperator (void) { }
virtual double getLogCost (void) = 0;
virtual void apply (void) = 0;
virtual string toString (void) = 0;
static vector<LiftedOperator*> getValidOps (
ParfactorList&, const Grounds&);
static void printValidOps (ParfactorList&, const Grounds&);
static vector<ParfactorList::iterator> getParfactorsWithGroup (
ParfactorList&, PrvGroup group);
};
class ProductOperator : public LiftedOperator
{
public:
ProductOperator (
ParfactorList::iterator g1, ParfactorList::iterator g2,
ParfactorList& pfList) : g1_(g1), g2_(g2), pfList_(pfList) { }
double getLogCost (void);
void apply (void);
static vector<ProductOperator*> getValidOps (ParfactorList&);
string toString (void);
private:
static bool validOp (Parfactor*, Parfactor*);
ParfactorList::iterator g1_;
ParfactorList::iterator g2_;
ParfactorList& pfList_;
};
class SumOutOperator : public LiftedOperator
{
public:
SumOutOperator (PrvGroup group, ParfactorList& pfList)
: group_(group), pfList_(pfList) { }
double getLogCost (void);
void apply (void);
static vector<SumOutOperator*> getValidOps (
ParfactorList&, const Grounds&);
string toString (void);
private:
static bool validOp (PrvGroup, ParfactorList&, const Grounds&);
static bool isToEliminate (Parfactor*, PrvGroup, const Grounds&);
PrvGroup group_;
ParfactorList& pfList_;
};
class CountingOperator : public LiftedOperator
{
public:
CountingOperator (
ParfactorList::iterator pfIter,
LogVar X,
ParfactorList& pfList)
: pfIter_(pfIter), X_(X), pfList_(pfList) { }
double getLogCost (void);
void apply (void);
static vector<CountingOperator*> getValidOps (ParfactorList&);
string toString (void);
private:
static bool validOp (Parfactor*, LogVar);
ParfactorList::iterator pfIter_;
LogVar X_;
ParfactorList& pfList_;
};
class GroundOperator : public LiftedOperator
{
public:
GroundOperator (
PrvGroup group,
unsigned lvIndex,
ParfactorList& pfList)
: group_(group), lvIndex_(lvIndex), pfList_(pfList) { }
double getLogCost (void);
void apply (void);
static vector<GroundOperator*> getValidOps (ParfactorList&);
string toString (void);
private:
vector<pair<PrvGroup, unsigned>> getAffectedFormulas (void);
PrvGroup group_;
unsigned lvIndex_;
ParfactorList& pfList_;
};
class LiftedVe : public LiftedSolver
{
public:
LiftedVe (const ParfactorList& pfList)
: LiftedSolver(pfList) { }
Params solveQuery (const Grounds&);
void printSolverFlags (void) const;
private:
void runSolver (const Grounds&);
LiftedOperator* getBestOperation (const Grounds&);
ParfactorList pfList_;
double largestCost_;
};
#endif // HORUS_LIFTEDVE_H

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#include "LiftedWCNF.h"
#include "ConstraintTree.h"
#include "Indexer.h"
bool
Literal::isGround (ConstraintTree constr, LogVarSet ipgLogVars) const
{
if (logVars_.size() == 0) {
return true;
}
LogVarSet lvs (logVars_);
lvs -= ipgLogVars;
return constr.singletons().contains (lvs);
}
size_t
Literal::indexOfLogVar (LogVar X) const
{
return Util::indexOf (logVars_, X);
}
string
Literal::toString (
LogVarSet ipgLogVars,
LogVarSet posCountedLvs,
LogVarSet negCountedLvs) const
{
stringstream ss;
negated_ ? ss << "¬" : ss << "" ;
ss << "λ" ;
ss << lid_ ;
if (logVars_.empty() == false) {
ss << "(" ;
for (size_t i = 0; i < logVars_.size(); i++) {
if (i != 0) ss << ",";
if (posCountedLvs.contains (logVars_[i])) {
ss << "+" << logVars_[i];
} else if (negCountedLvs.contains (logVars_[i])) {
ss << "-" << logVars_[i];
} else if (ipgLogVars.contains (logVars_[i])) {
LogVar X = logVars_[i];
const string labels[] = {
"a", "b", "c", "d", "e", "f",
"g", "h", "i", "j", "k", "m" };
(X >= 12) ? ss << "x_" << X : ss << labels[X];
} else {
ss << logVars_[i];
}
}
ss << ")" ;
}
return ss.str();
}
std::ostream&
operator<< (ostream &os, const Literal& lit)
{
os << lit.toString();
return os;
}
void
Clause::addLiteralComplemented (const Literal& lit)
{
assert (constr_.logVarSet().contains (lit.logVars()));
literals_.push_back (lit);
literals_.back().complement();
}
bool
Clause::containsLiteral (LiteralId lid) const
{
for (size_t i = 0; i < literals_.size(); i++) {
if (literals_[i].lid() == lid) {
return true;
}
}
return false;
}
bool
Clause::containsPositiveLiteral (
LiteralId lid,
const LogVarTypes& types) const
{
for (size_t i = 0; i < literals_.size(); i++) {
if (literals_[i].lid() == lid
&& literals_[i].isPositive()
&& logVarTypes (i) == types) {
return true;
}
}
return false;
}
bool
Clause::containsNegativeLiteral (
LiteralId lid,
const LogVarTypes& types) const
{
for (size_t i = 0; i < literals_.size(); i++) {
if (literals_[i].lid() == lid
&& literals_[i].isNegative()
&& logVarTypes (i) == types) {
return true;
}
}
return false;
}
void
Clause::removeLiterals (LiteralId lid)
{
size_t i = 0;
while (i != literals_.size()) {
if (literals_[i].lid() == lid) {
removeLiteral (i);
} else {
i ++;
}
}
}
void
Clause::removePositiveLiterals (
LiteralId lid,
const LogVarTypes& types)
{
size_t i = 0;
while (i != literals_.size()) {
if (literals_[i].lid() == lid
&& literals_[i].isPositive()
&& logVarTypes (i) == types) {
removeLiteral (i);
} else {
i ++;
}
}
}
void
Clause::removeNegativeLiterals (
LiteralId lid,
const LogVarTypes& types)
{
size_t i = 0;
while (i != literals_.size()) {
if (literals_[i].lid() == lid
&& literals_[i].isNegative()
&& logVarTypes (i) == types) {
removeLiteral (i);
} else {
i ++;
}
}
}
bool
Clause::isCountedLogVar (LogVar X) const
{
assert (constr_.logVarSet().contains (X));
return posCountedLvs_.contains (X)
|| negCountedLvs_.contains (X);
}
bool
Clause::isPositiveCountedLogVar (LogVar X) const
{
assert (constr_.logVarSet().contains (X));
return posCountedLvs_.contains (X);
}
bool
Clause::isNegativeCountedLogVar (LogVar X) const
{
assert (constr_.logVarSet().contains (X));
return negCountedLvs_.contains (X);
}
bool
Clause::isIpgLogVar (LogVar X) const
{
assert (constr_.logVarSet().contains (X));
return ipgLvs_.contains (X);
}
TinySet<LiteralId>
Clause::lidSet (void) const
{
TinySet<LiteralId> lidSet;
for (size_t i = 0; i < literals_.size(); i++) {
lidSet.insert (literals_[i].lid());
}
return lidSet;
}
LogVarSet
Clause::ipgCandidates (void) const
{
LogVarSet candidates;
LogVarSet allLvs = constr_.logVarSet();
allLvs -= ipgLvs_;
allLvs -= posCountedLvs_;
allLvs -= negCountedLvs_;
for (size_t i = 0; i < allLvs.size(); i++) {
bool valid = true;
for (size_t j = 0; j < literals_.size(); j++) {
if (Util::contains (literals_[j].logVars(), allLvs[i]) == false) {
valid = false;
break;
}
}
if (valid) {
candidates.insert (allLvs[i]);
}
}
return candidates;
}
LogVarTypes
Clause::logVarTypes (size_t litIdx) const
{
LogVarTypes types;
const LogVars& lvs = literals_[litIdx].logVars();
for (size_t i = 0; i < lvs.size(); i++) {
if (posCountedLvs_.contains (lvs[i])) {
types.push_back (LogVarType::POS_LV);
} else if (negCountedLvs_.contains (lvs[i])) {
types.push_back (LogVarType::NEG_LV);
} else {
types.push_back (LogVarType::FULL_LV);
}
}
return types;
}
void
Clause::removeLiteral (size_t litIdx)
{
LogVarSet lvsToRemove = literals_[litIdx].logVarSet()
- getLogVarSetExcluding (litIdx);
ipgLvs_ -= lvsToRemove;
posCountedLvs_ -= lvsToRemove;
negCountedLvs_ -= lvsToRemove;
constr_.remove (lvsToRemove);
literals_.erase (literals_.begin() + litIdx);
}
bool
Clause::independentClauses (Clause& c1, Clause& c2)
{
const Literals& lits1 = c1.literals();
const Literals& lits2 = c2.literals();
for (size_t i = 0; i < lits1.size(); i++) {
for (size_t j = 0; j < lits2.size(); j++) {
if (lits1[i].lid() == lits2[j].lid()
&& c1.logVarTypes (i) == c2.logVarTypes (j)) {
return false;
}
}
}
return true;
}
Clauses
Clause::copyClauses (const Clauses& clauses)
{
Clauses copy;
copy.reserve (clauses.size());
for (size_t i = 0; i < clauses.size(); i++) {
copy.push_back (new Clause (*clauses[i]));
}
return copy;
}
void
Clause::printClauses (const Clauses& clauses)
{
for (size_t i = 0; i < clauses.size(); i++) {
cout << *clauses[i] << endl;
}
}
void
Clause::deleteClauses (Clauses& clauses)
{
for (size_t i = 0; i < clauses.size(); i++) {
delete clauses[i];
}
}
std::ostream&
operator<< (ostream &os, const Clause& clause)
{
for (unsigned i = 0; i < clause.literals_.size(); i++) {
if (i != 0) os << " v " ;
os << clause.literals_[i].toString (clause.ipgLvs_,
clause.posCountedLvs_, clause.negCountedLvs_);
}
if (clause.constr_.empty() == false) {
ConstraintTree copy (clause.constr_);
copy.moveToTop (copy.logVarSet().elements());
os << " | " << copy.tupleSet();
}
return os;
}
LogVarSet
Clause::getLogVarSetExcluding (size_t idx) const
{
LogVarSet lvs;
for (size_t i = 0; i < literals_.size(); i++) {
if (i != idx) {
lvs |= literals_[i].logVars();
}
}
return lvs;
}
std::ostream&
operator<< (std::ostream &os, const LitLvTypes& lit)
{
os << lit.lid_ << "<" ;
for (size_t i = 0; i < lit.lvTypes_.size(); i++) {
switch (lit.lvTypes_[i]) {
case LogVarType::FULL_LV: os << "F" ; break;
case LogVarType::POS_LV: os << "P" ; break;
case LogVarType::NEG_LV: os << "N" ; break;
}
}
os << ">" ;
return os;
}
LiftedWCNF::LiftedWCNF (const ParfactorList& pfList)
: freeLiteralId_(0), pfList_(pfList)
{
addIndicatorClauses (pfList);
addParameterClauses (pfList);
/*
// INCLUSION-EXCLUSION TEST
clauses_.clear();
vector<vector<string>> names = {
{"a1","b1"},{"a2","b2"}
};
Clause* c1 = new Clause (names);
c1->addLiteral (Literal (0, LogVars() = {0}));
c1->addLiteral (Literal (1, LogVars() = {1}));
clauses_.push_back(c1);
*/
/*
// INDEPENDENT PARTIAL GROUND TEST
clauses_.clear();
vector<vector<string>> names = {
{"a1","b1"},{"a2","b2"}
};
Clause* c1 = new Clause (names);
c1->addLiteral (Literal (0, LogVars() = {0,1}));
c1->addLiteral (Literal (1, LogVars() = {0,1}));
clauses_.push_back(c1);
Clause* c2 = new Clause (names);
c2->addLiteral (Literal (2, LogVars() = {0}));
c2->addLiteral (Literal (1, LogVars() = {0,1}));
clauses_.push_back(c2);
*/
/*
// ATOM-COUNTING TEST
clauses_.clear();
vector<vector<string>> names = {
{"p1","p1"},{"p1","p2"},{"p1","p3"},
{"p2","p1"},{"p2","p2"},{"p2","p3"},
{"p3","p1"},{"p3","p2"},{"p3","p3"}
};
Clause* c1 = new Clause (names);
c1->addLiteral (Literal (0, LogVars() = {0}));
c1->addLiteralComplemented (Literal (1, {0,1}));
clauses_.push_back(c1);
Clause* c2 = new Clause (names);
c2->addLiteral (Literal (0, LogVars()={0}));
c2->addLiteralComplemented (Literal (1, {1,0}));
clauses_.push_back(c2);
*/
if (Globals::verbosity > 1) {
cout << "FORMULA INDICATORS:" << endl;
printFormulaIndicators();
cout << endl;
cout << "WEIGHTED INDICATORS:" << endl;
printWeights();
cout << endl;
cout << "CLAUSES:" << endl;
printClauses();
cout << endl;
}
}
LiftedWCNF::~LiftedWCNF (void)
{
Clause::deleteClauses (clauses_);
}
void
LiftedWCNF::addWeight (LiteralId lid, double posW, double negW)
{
weights_[lid] = make_pair (posW, negW);
}
double
LiftedWCNF::posWeight (LiteralId lid) const
{
unordered_map<LiteralId, std::pair<double,double>>::const_iterator it;
it = weights_.find (lid);
return it != weights_.end() ? it->second.first : LogAware::one();
}
double
LiftedWCNF::negWeight (LiteralId lid) const
{
unordered_map<LiteralId, std::pair<double,double>>::const_iterator it;
it = weights_.find (lid);
return it != weights_.end() ? it->second.second : LogAware::one();
}
vector<LiteralId>
LiftedWCNF::prvGroupLiterals (PrvGroup prvGroup)
{
assert (Util::contains (map_, prvGroup));
return map_[prvGroup];
}
Clause*
LiftedWCNF::createClause (LiteralId lid) const
{
for (size_t i = 0; i < clauses_.size(); i++) {
const Literals& literals = clauses_[i]->literals();
for (size_t j = 0; j < literals.size(); j++) {
if (literals[j].lid() == lid) {
ConstraintTree ct = clauses_[i]->constr().projectedCopy (
literals[j].logVars());
Clause* c = new Clause (ct);
c->addLiteral (literals[j]);
return c;
}
}
}
return 0;
}
LiteralId
LiftedWCNF::getLiteralId (PrvGroup prvGroup, unsigned range)
{
assert (Util::contains (map_, prvGroup));
return map_[prvGroup][range];
}
void
LiftedWCNF::addIndicatorClauses (const ParfactorList& pfList)
{
ParfactorList::const_iterator it = pfList.begin();
while (it != pfList.end()) {
const ProbFormulas& formulas = (*it)->arguments();
for (size_t i = 0; i < formulas.size(); i++) {
if (Util::contains (map_, formulas[i].group()) == false) {
ConstraintTree tempConstr = (*it)->constr()->projectedCopy(
formulas[i].logVars());
Clause* clause = new Clause (tempConstr);
vector<LiteralId> lids;
for (size_t j = 0; j < formulas[i].range(); j++) {
clause->addLiteral (Literal (freeLiteralId_, formulas[i].logVars()));
lids.push_back (freeLiteralId_);
freeLiteralId_ ++;
}
clauses_.push_back (clause);
for (size_t j = 0; j < formulas[i].range() - 1; j++) {
for (size_t k = j + 1; k < formulas[i].range(); k++) {
ConstraintTree tempConstr2 = (*it)->constr()->projectedCopy (
formulas[i].logVars());
Clause* clause2 = new Clause (tempConstr2);
clause2->addLiteralComplemented (Literal (clause->literals()[j]));
clause2->addLiteralComplemented (Literal (clause->literals()[k]));
clauses_.push_back (clause2);
}
}
map_[formulas[i].group()] = lids;
}
}
++ it;
}
}
void
LiftedWCNF::addParameterClauses (const ParfactorList& pfList)
{
ParfactorList::const_iterator it = pfList.begin();
while (it != pfList.end()) {
Indexer indexer ((*it)->ranges());
vector<PrvGroup> groups = (*it)->getAllGroups();
while (indexer.valid()) {
LiteralId paramVarLid = freeLiteralId_;
// λu1 ∧ ... ∧ λun ∧ λxi <=> θxi|u1,...,un
//
// ¬λu1 ... ¬λun v θxi|u1,...,un -> clause1
// ¬θxi|u1,...,un v λu1 -> tempClause
// ¬θxi|u1,...,un v λu2 -> tempClause
double posWeight = (**it)[indexer];
addWeight (paramVarLid, posWeight, LogAware::one());
Clause* clause1 = new Clause (*(*it)->constr());
for (unsigned i = 0; i < groups.size(); i++) {
LiteralId lid = getLiteralId (groups[i], indexer[i]);
clause1->addLiteralComplemented (
Literal (lid, (*it)->argument(i).logVars()));
ConstraintTree ct = *(*it)->constr();
Clause* tempClause = new Clause (ct);
tempClause->addLiteralComplemented (Literal (
paramVarLid, (*it)->constr()->logVars()));
tempClause->addLiteral (Literal (lid, (*it)->argument(i).logVars()));
clauses_.push_back (tempClause);
}
clause1->addLiteral (Literal (paramVarLid, (*it)->constr()->logVars()));
clauses_.push_back (clause1);
freeLiteralId_ ++;
++ indexer;
}
++ it;
}
}
void
LiftedWCNF::printFormulaIndicators (void) const
{
if (map_.empty()) {
return;
}
set<PrvGroup> allGroups;
ParfactorList::const_iterator it = pfList_.begin();
while (it != pfList_.end()) {
const ProbFormulas& formulas = (*it)->arguments();
for (size_t i = 0; i < formulas.size(); i++) {
if (Util::contains (allGroups, formulas[i].group()) == false) {
allGroups.insert (formulas[i].group());
cout << formulas[i] << " | " ;
ConstraintTree tempCt = (*it)->constr()->projectedCopy (
formulas[i].logVars());
cout << tempCt.tupleSet();
cout << " indicators => " ;
vector<LiteralId> indicators =
(map_.find (formulas[i].group()))->second;
cout << indicators << endl;
}
}
++ it;
}
}
void
LiftedWCNF::printWeights (void) const
{
unordered_map<LiteralId, std::pair<double,double>>::const_iterator it;
it = weights_.begin();
while (it != weights_.end()) {
cout << "λ" << it->first << " weights: " ;
cout << it->second.first << " " << it->second.second;
cout << endl;
++ it;
}
}
void
LiftedWCNF::printClauses (void) const
{
Clause::printClauses (clauses_);
}

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#ifndef HORUS_LIFTEDWCNF_H
#define HORUS_LIFTEDWCNF_H
#include "ParfactorList.h"
using namespace std;
typedef long LiteralId;
class ConstraintTree;
enum LogVarType
{
FULL_LV,
POS_LV,
NEG_LV
};
typedef vector<LogVarType> LogVarTypes;
class Literal
{
public:
Literal (LiteralId lid, const LogVars& lvs) :
lid_(lid), logVars_(lvs), negated_(false) { }
Literal (const Literal& lit, bool negated) :
lid_(lit.lid_), logVars_(lit.logVars_), negated_(negated) { }
LiteralId lid (void) const { return lid_; }
LogVars logVars (void) const { return logVars_; }
size_t nrLogVars (void) const { return logVars_.size(); }
LogVarSet logVarSet (void) const { return LogVarSet (logVars_); }
void complement (void) { negated_ = !negated_; }
bool isPositive (void) const { return negated_ == false; }
bool isNegative (void) const { return negated_; }
bool isGround (ConstraintTree constr, LogVarSet ipgLogVars) const;
size_t indexOfLogVar (LogVar X) const;
string toString (LogVarSet ipgLogVars = LogVarSet(),
LogVarSet posCountedLvs = LogVarSet(),
LogVarSet negCountedLvs = LogVarSet()) const;
friend std::ostream& operator<< (std::ostream &os, const Literal& lit);
private:
LiteralId lid_;
LogVars logVars_;
bool negated_;
};
typedef vector<Literal> Literals;
class Clause
{
public:
Clause (const ConstraintTree& ct = ConstraintTree({})) : constr_(ct) { }
Clause (vector<vector<string>> names) : constr_(ConstraintTree (names)) { }
void addLiteral (const Literal& l) { literals_.push_back (l); }
const Literals& literals (void) const { return literals_; }
Literals& literals (void) { return literals_; }
size_t nrLiterals (void) const { return literals_.size(); }
const ConstraintTree& constr (void) const { return constr_; }
ConstraintTree constr (void) { return constr_; }
bool isUnit (void) const { return literals_.size() == 1; }
LogVarSet ipgLogVars (void) const { return ipgLvs_; }
void addIpgLogVar (LogVar X) { ipgLvs_.insert (X); }
void addPosCountedLogVar (LogVar X) { posCountedLvs_.insert (X); }
void addNegCountedLogVar (LogVar X) { negCountedLvs_.insert (X); }
LogVarSet posCountedLogVars (void) const { return posCountedLvs_; }
LogVarSet negCountedLogVars (void) const { return negCountedLvs_; }
unsigned nrPosCountedLogVars (void) const { return posCountedLvs_.size(); }
unsigned nrNegCountedLogVars (void) const { return negCountedLvs_.size(); }
void addLiteralComplemented (const Literal& lit);
bool containsLiteral (LiteralId lid) const;
bool containsPositiveLiteral (LiteralId lid, const LogVarTypes&) const;
bool containsNegativeLiteral (LiteralId lid, const LogVarTypes&) const;
void removeLiterals (LiteralId lid);
void removePositiveLiterals (LiteralId lid, const LogVarTypes&);
void removeNegativeLiterals (LiteralId lid, const LogVarTypes&);
bool isCountedLogVar (LogVar X) const;
bool isPositiveCountedLogVar (LogVar X) const;
bool isNegativeCountedLogVar (LogVar X) const;
bool isIpgLogVar (LogVar X) const;
TinySet<LiteralId> lidSet (void) const;
LogVarSet ipgCandidates (void) const;
LogVarTypes logVarTypes (size_t litIdx) const;
void removeLiteral (size_t litIdx);
static bool independentClauses (Clause& c1, Clause& c2);
static vector<Clause*> copyClauses (const vector<Clause*>& clauses);
static void printClauses (const vector<Clause*>& clauses);
static void deleteClauses (vector<Clause*>& clauses);
friend std::ostream& operator<< (ostream &os, const Clause& clause);
private:
LogVarSet getLogVarSetExcluding (size_t idx) const;
Literals literals_;
LogVarSet ipgLvs_;
LogVarSet posCountedLvs_;
LogVarSet negCountedLvs_;
ConstraintTree constr_;
};
typedef vector<Clause*> Clauses;
class LitLvTypes
{
public:
struct CompareLitLvTypes
{
bool operator() (
const LitLvTypes& types1,
const LitLvTypes& types2) const
{
if (types1.lid_ < types2.lid_) {
return true;
}
if (types1.lid_ == types2.lid_) {
return types1.lvTypes_ < types2.lvTypes_;
}
return false;
}
};
LitLvTypes (LiteralId lid, const LogVarTypes& lvTypes) :
lid_(lid), lvTypes_(lvTypes) { }
LiteralId lid (void) const { return lid_; }
const LogVarTypes& logVarTypes (void) const { return lvTypes_; }
void setAllFullLogVars (void) {
std::fill (lvTypes_.begin(), lvTypes_.end(), LogVarType::FULL_LV); }
friend std::ostream& operator<< (std::ostream &os, const LitLvTypes& lit);
private:
LiteralId lid_;
LogVarTypes lvTypes_;
};
typedef TinySet<LitLvTypes,LitLvTypes::CompareLitLvTypes> LitLvTypesSet;
class LiftedWCNF
{
public:
LiftedWCNF (const ParfactorList& pfList);
~LiftedWCNF (void);
const Clauses& clauses (void) const { return clauses_; }
void addWeight (LiteralId lid, double posW, double negW);
double posWeight (LiteralId lid) const;
double negWeight (LiteralId lid) const;
vector<LiteralId> prvGroupLiterals (PrvGroup prvGroup);
Clause* createClause (LiteralId lid) const;
void printFormulaIndicators (void) const;
void printWeights (void) const;
void printClauses (void) const;
private:
LiteralId getLiteralId (PrvGroup prvGroup, unsigned range);
void addIndicatorClauses (const ParfactorList& pfList);
void addParameterClauses (const ParfactorList& pfList);
Clauses clauses_;
LiteralId freeLiteralId_;
const ParfactorList& pfList_;
unordered_map<PrvGroup, vector<LiteralId>> map_;
unordered_map<LiteralId, std::pair<double,double>> weights_;
};
#endif // HORUS_LIFTEDWCNF_H

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packages/CLPBN/horus2/Parfactor.cpp
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@ -1,942 +0,0 @@
#include "Parfactor.h"
#include "Histogram.h"
#include "Indexer.h"
#include "Util.h"
#include "Horus.h"
Parfactor::Parfactor (
const ProbFormulas& formulas,
const Params& params,
const Tuples& tuples,
unsigned distId)
{
args_ = formulas;
params_ = params;
distId_ = distId;
LogVars logVars;
for (size_t i = 0; i < args_.size(); i++) {
ranges_.push_back (args_[i].range());
const LogVars& lvs = args_[i].logVars();
for (size_t j = 0; j < lvs.size(); j++) {
if (Util::contains (logVars, lvs[j]) == false) {
logVars.push_back (lvs[j]);
}
}
}
LogVar newLv = logVars.size();
constr_ = new ConstraintTree (logVars, tuples);
// Change formulas like f(X,X), X in {(p1),(p2),...}
// to be like f(X,Y), (X,Y) in {(p1,p1),(p2,p2),...}.
// This will simplify shattering on the constraint tree.
for (size_t i = 0; i < args_.size(); i++) {
LogVarSet lvSet;
LogVars& lvs = args_[i].logVars();
for (size_t j = 0; j < lvs.size(); j++) {
if (lvSet.contains (lvs[j]) == false) {
lvSet |= lvs[j];
} else {
constr_->cloneLogVar (lvs[j], newLv);
lvs[j] = newLv;
++ newLv;
}
}
}
assert (params_.size() == Util::sizeExpected (ranges_));
}
Parfactor::Parfactor (const Parfactor* g, const Tuple& tuple)
{
args_ = g->arguments();
params_ = g->params();
ranges_ = g->ranges();
distId_ = g->distId();
constr_ = new ConstraintTree (g->logVars(), {tuple});
assert (params_.size() == Util::sizeExpected (ranges_));
}
Parfactor::Parfactor (const Parfactor* g, ConstraintTree* constr)
{
args_ = g->arguments();
params_ = g->params();
ranges_ = g->ranges();
distId_ = g->distId();
constr_ = constr;
assert (params_.size() == Util::sizeExpected (ranges_));
}
Parfactor::Parfactor (const Parfactor& g)
{
args_ = g.arguments();
params_ = g.params();
ranges_ = g.ranges();
distId_ = g.distId();
constr_ = new ConstraintTree (*g.constr());
assert (params_.size() == Util::sizeExpected (ranges_));
}
Parfactor::~Parfactor (void)
{
delete constr_;
}
LogVarSet
Parfactor::countedLogVars (void) const
{
LogVarSet set;
for (size_t i = 0; i < args_.size(); i++) {
if (args_[i].isCounting()) {
set.insert (args_[i].countedLogVar());
}
}
return set;
}
LogVarSet
Parfactor::uncountedLogVars (void) const
{
return constr_->logVarSet() - countedLogVars();
}
LogVarSet
Parfactor::elimLogVars (void) const
{
LogVarSet requiredToElim = constr_->logVarSet();
requiredToElim -= constr_->singletons();
requiredToElim -= countedLogVars();
return requiredToElim;
}
LogVarSet
Parfactor::exclusiveLogVars (size_t fIdx) const
{
assert (fIdx < args_.size());
LogVarSet remaining;
for (size_t i = 0; i < args_.size(); i++) {
if (i != fIdx) {
remaining |= args_[i].logVarSet();
}
}
return args_[fIdx].logVarSet() - remaining;
}
void
Parfactor::sumOutIndex (size_t fIdx)
{
assert (fIdx < args_.size());
assert (args_[fIdx].contains (elimLogVars()));
if (args_[fIdx].isCounting()) {
unsigned N = constr_->getConditionalCount (
args_[fIdx].countedLogVar());
unsigned R = args_[fIdx].range();
vector<double> numAssigns = HistogramSet::getNumAssigns (N, R);
Indexer indexer (ranges_, fIdx);
while (indexer.valid()) {
if (Globals::logDomain) {
params_[indexer] += numAssigns[ indexer[fIdx] ];
} else {
params_[indexer] *= numAssigns[ indexer[fIdx] ];
}
++ indexer;
}
}
LogVarSet excl = exclusiveLogVars (fIdx);
unsigned exp;
if (args_[fIdx].isCounting()) {
// counting log vars were already raised on counting conversion
exp = constr_->getConditionalCount (excl - args_[fIdx].countedLogVar());
} else {
exp = constr_->getConditionalCount (excl);
}
constr_->remove (excl);
TFactor<ProbFormula>::sumOutIndex (fIdx);
LogAware::pow (params_, exp);
}
void
Parfactor::multiply (Parfactor& g)
{
alignAndExponentiate (this, &g);
TFactor<ProbFormula>::multiply (g);
constr_->join (g.constr(), true);
simplifyGrounds();
assert (constr_->isCartesianProduct (countedLogVars()));
}
bool
Parfactor::canCountConvert (LogVar X)
{
if (nrFormulas (X) != 1) {
return false;
}
size_t fIdx = indexOfLogVar (X);
if (args_[fIdx].isCounting()) {
return false;
}
if (constr_->isCountNormalized (X) == false) {
return false;
}
if (constr_->getConditionalCount (X) == 1) {
return false;
}
if (constr_->isCartesianProduct (countedLogVars() | X) == false) {
return false;
}
return true;
}
void
Parfactor::countConvert (LogVar X)
{
size_t fIdx = indexOfLogVar (X);
assert (constr_->isCountNormalized (X));
assert (constr_->getConditionalCount (X) > 1);
assert (canCountConvert (X));
unsigned N = constr_->getConditionalCount (X);
unsigned R = ranges_[fIdx];
unsigned H = HistogramSet::nrHistograms (N, R);
vector<Histogram> histograms = HistogramSet::getHistograms (N, R);
Indexer indexer (ranges_);
vector<Params> sumout (params_.size() / R);
unsigned count = 0;
while (indexer.valid()) {
sumout[count].reserve (R);
for (unsigned r = 0; r < R; r++) {
sumout[count].push_back (params_[indexer]);
indexer.incrementDimension (fIdx);
}
count ++;
indexer.resetDimension (fIdx);
indexer.incrementExceptDimension (fIdx);
}
params_.clear();
params_.reserve (sumout.size() * H);
ranges_[fIdx] = H;
MapIndexer mapIndexer (ranges_, fIdx);
while (mapIndexer.valid()) {
double prod = LogAware::multIdenty();
size_t i = mapIndexer;
unsigned h = mapIndexer[fIdx];
for (unsigned r = 0; r < R; r++) {
if (Globals::logDomain) {
prod += LogAware::pow (sumout[i][r], histograms[h][r]);
} else {
prod *= LogAware::pow (sumout[i][r], histograms[h][r]);
}
}
params_.push_back (prod);
++ mapIndexer;
}
args_[fIdx].setCountedLogVar (X);
simplifyCountingFormulas (fIdx);
}
void
Parfactor::expand (LogVar X, LogVar X_new1, LogVar X_new2)
{
size_t fIdx = indexOfLogVar (X);
assert (fIdx != args_.size());
assert (args_[fIdx].isCounting());
unsigned N1 = constr_->getConditionalCount (X_new1);
unsigned N2 = constr_->getConditionalCount (X_new2);
unsigned N = N1 + N2;
unsigned R = args_[fIdx].range();
unsigned H1 = HistogramSet::nrHistograms (N1, R);
unsigned H2 = HistogramSet::nrHistograms (N2, R);
vector<Histogram> histograms = HistogramSet::getHistograms (N, R);
vector<Histogram> histograms1 = HistogramSet::getHistograms (N1, R);
vector<Histogram> histograms2 = HistogramSet::getHistograms (N2, R);
vector<unsigned> sumIndexes;
sumIndexes.reserve (H1 * H2);
for (unsigned i = 0; i < H1; i++) {
for (unsigned j = 0; j < H2; j++) {
Histogram hist = histograms1[i];
hist += histograms2[j];
sumIndexes.push_back (HistogramSet::findIndex (hist, histograms));
}
}
expandPotential (fIdx, H1 * H2, sumIndexes);
args_.insert (args_.begin() + fIdx + 1, args_[fIdx]);
args_[fIdx].rename (X, X_new1);
args_[fIdx + 1].rename (X, X_new2);
if (H1 == 2) {
args_[fIdx].clearCountedLogVar();
}
if (H2 == 2) {
args_[fIdx + 1].clearCountedLogVar();
}
ranges_.insert (ranges_.begin() + fIdx + 1, H2);
ranges_[fIdx] = H1;
}
void
Parfactor::fullExpand (LogVar X)
{
size_t fIdx = indexOfLogVar (X);
assert (fIdx != args_.size());
assert (args_[fIdx].isCounting());
unsigned N = constr_->getConditionalCount (X);
unsigned R = args_[fIdx].range();
vector<Histogram> originHists = HistogramSet::getHistograms (N, R);
vector<Histogram> expandHists = HistogramSet::getHistograms (1, R);
assert (ranges_[fIdx] == originHists.size());
vector<unsigned> sumIndexes;
sumIndexes.reserve (N * R);
Ranges expandRanges (N, R);
Indexer indexer (expandRanges);
while (indexer.valid()) {
vector<unsigned> hist (R, 0);
for (unsigned n = 0; n < N; n++) {
hist += expandHists[indexer[n]];
}
sumIndexes.push_back (HistogramSet::findIndex (hist, originHists));
++ indexer;
}
expandPotential (fIdx, std::pow (R, N), sumIndexes);
ProbFormula f = args_[fIdx];
args_.erase (args_.begin() + fIdx);
ranges_.erase (ranges_.begin() + fIdx);
LogVars newLvs = constr_->expand (X);
assert (newLvs.size() == N);
for (unsigned i = 0 ; i < N; i++) {
ProbFormula newFormula (f.functor(), f.logVars(), f.range());
newFormula.rename (X, newLvs[i]);
args_.insert (args_.begin() + fIdx + i, newFormula);
ranges_.insert (ranges_.begin() + fIdx + i, R);
}
}
void
Parfactor::reorderAccordingGrounds (const Grounds& grounds)
{
ProbFormulas newFormulas;
for (size_t i = 0; i < grounds.size(); i++) {
for (size_t j = 0; j < args_.size(); j++) {
if (grounds[i].functor() == args_[j].functor() &&
grounds[i].arity() == args_[j].arity()) {
constr_->moveToTop (args_[j].logVars());
if (constr_->containsTuple (grounds[i].args())) {
newFormulas.push_back (args_[j]);
break;
}
}
}
assert (newFormulas.size() == i + 1);
}
reorderArguments (newFormulas);
}
void
Parfactor::absorveEvidence (const ProbFormula& formula, unsigned evidence)
{
size_t fIdx = indexOf (formula);
assert (fIdx != args_.size());
LogVarSet excl = exclusiveLogVars (fIdx);
assert (args_[fIdx].isCounting() == false);
assert (constr_->isCountNormalized (excl));
LogAware::pow (params_, constr_->getConditionalCount (excl));
TFactor<ProbFormula>::absorveEvidence (formula, evidence);
constr_->remove (excl);
}
void
Parfactor::setNewGroups (void)
{
for (size_t i = 0; i < args_.size(); i++) {
args_[i].setGroup (ProbFormula::getNewGroup());
}
}
void
Parfactor::applySubstitution (const Substitution& theta)
{
for (size_t i = 0; i < args_.size(); i++) {
LogVars& lvs = args_[i].logVars();
for (size_t j = 0; j < lvs.size(); j++) {
lvs[j] = theta.newNameFor (lvs[j]);
}
if (args_[i].isCounting()) {
LogVar clv = args_[i].countedLogVar();
args_[i].setCountedLogVar (theta.newNameFor (clv));
}
}
constr_->applySubstitution (theta);
}
size_t
Parfactor::indexOfGround (const Ground& ground) const
{
size_t idx = args_.size();
for (size_t i = 0; i < args_.size(); i++) {
if (args_[i].functor() == ground.functor() &&
args_[i].arity() == ground.arity()) {
constr_->moveToTop (args_[i].logVars());
if (constr_->containsTuple (ground.args())) {
idx = i;
break;
}
}
}
return idx;
}
PrvGroup
Parfactor::findGroup (const Ground& ground) const
{
size_t idx = indexOfGround (ground);
return idx == args_.size()
? numeric_limits<PrvGroup>::max()
: args_[idx].group();
}
bool
Parfactor::containsGround (const Ground& ground) const
{
return findGroup (ground) != numeric_limits<PrvGroup>::max();
}
bool
Parfactor::containsGrounds (const Grounds& grounds) const
{
Tuple tuple;
LogVars tupleLvs;
for (size_t i = 0; i < grounds.size(); i++) {
size_t idx = indexOfGround (grounds[i]);
if (idx == args_.size()) {
return false;
}
LogVars lvs = args_[idx].logVars();
for (size_t j = 0; j < lvs.size(); j++) {
if (Util::contains (tupleLvs, lvs[j]) == false) {
tuple.push_back (grounds[i].args()[j]);
tupleLvs.push_back (lvs[j]);
}
}
}
constr_->moveToTop (tupleLvs);
return constr_->containsTuple (tuple);
}
bool
Parfactor::containsGroup (PrvGroup group) const
{
for (size_t i = 0; i < args_.size(); i++) {
if (args_[i].group() == group) {
return true;
}
}
return false;
}
bool
Parfactor::containsGroups (vector<PrvGroup> groups) const
{
for (size_t i = 0; i < groups.size(); i++) {
if (containsGroup (groups[i]) == false) {
return false;
}
}
return true;
}
unsigned
Parfactor::nrFormulas (LogVar X) const
{
unsigned count = 0;
for (size_t i = 0; i < args_.size(); i++) {
if (args_[i].contains (X)) {
count ++;
}
}
return count;
}
int
Parfactor::indexOfLogVar (LogVar X) const
{
size_t idx = args_.size();
assert (nrFormulas (X) == 1);
for (size_t i = 0; i < args_.size(); i++) {
if (args_[i].contains (X)) {
idx = i;
break;
}
}
return idx;
}
int
Parfactor::indexOfGroup (PrvGroup group) const
{
size_t pos = args_.size();
for (size_t i = 0; i < args_.size(); i++) {
if (args_[i].group() == group) {
pos = i;
break;
}
}
return pos;
}
unsigned
Parfactor::nrFormulasWithGroup (PrvGroup group) const
{
unsigned count = 0;
for (size_t i = 0; i < args_.size(); i++) {
if (args_[i].group() == group) {
count ++;
}
}
return count;
}
vector<PrvGroup>
Parfactor::getAllGroups (void) const
{
vector<PrvGroup> groups (args_.size());
for (size_t i = 0; i < args_.size(); i++) {
groups[i] = args_[i].group();
}
return groups;
}
string
Parfactor::getLabel (void) const
{
stringstream ss;
ss << "phi(" ;
for (size_t i = 0; i < args_.size(); i++) {
if (i != 0) ss << "," ;
ss << args_[i];
}
ss << ")" ;
ConstraintTree copy (*constr_);
copy.moveToTop (copy.logVarSet().elements());
ss << "|" << copy.tupleSet();
return ss.str();
}
void
Parfactor::print (bool printParams) const
{
cout << "Formulas: " ;
for (size_t i = 0; i < args_.size(); i++) {
if (i != 0) cout << ", " ;
cout << args_[i];
}
cout << endl;
if (args_[0].group() != Util::maxUnsigned()) {
vector<string> groups;
for (size_t i = 0; i < args_.size(); i++) {
groups.push_back (string ("g") + Util::toString (args_[i].group()));
}
cout << "Groups: " << groups << endl;
}
cout << "LogVars: " << constr_->logVarSet() << endl;
cout << "Ranges: " << ranges_ << endl;
if (printParams == false) {
cout << "Params: " ;
if (params_.size() <= 32) {
cout.precision(10);
cout << params_ << endl;
} else {
cout << "|" << params_.size() << "|" << endl;
}
}
ConstraintTree copy (*constr_);
copy.moveToTop (copy.logVarSet().elements());
cout << "Tuples: " << copy.tupleSet() << endl;
if (printParams) {
printParameters();
}
}
void
Parfactor::printParameters (void) const
{
vector<string> jointStrings;
Indexer indexer (ranges_);
while (indexer.valid()) {
stringstream ss;
for (size_t i = 0; i < args_.size(); i++) {
if (i != 0) ss << ", " ;
if (args_[i].isCounting()) {
unsigned N = constr_->getConditionalCount (
args_[i].countedLogVar());
HistogramSet hs (N, args_[i].range());
unsigned c = 0;
while (c < indexer[i]) {
hs.nextHistogram();
c ++;
}
ss << hs;
} else {
ss << indexer[i];
}
}
jointStrings.push_back (ss.str());
++ indexer;
}
for (size_t i = 0; i < params_.size(); i++) {
cout << "f(" << jointStrings[i] << ")" ;
cout << " = " << params_[i] << endl;
}
}
void
Parfactor::printProjections (void) const
{
ConstraintTree copy (*constr_);
LogVarSet Xs = copy.logVarSet();
for (size_t i = 0; i < Xs.size(); i++) {
cout << "-> projection of " << Xs[i] << ": " ;
cout << copy.tupleSet ({Xs[i]}) << endl;
}
}
void
Parfactor::expandPotential (
size_t fIdx,
unsigned newRange,
const vector<unsigned>& sumIndexes)
{
ullong newSize = (params_.size() / ranges_[fIdx]) * newRange;
if (newSize > params_.max_size()) {
cerr << "Error: an overflow occurred when performing expansion." ;
cerr << endl;
exit (EXIT_FAILURE);
}
Params backup = params_;
params_.clear();
params_.reserve (newSize);
size_t prod = 1;
vector<size_t> offsets (ranges_.size());
for (size_t i = ranges_.size(); i-- > 0; ) {
offsets[i] = prod;
prod *= ranges_[i];
}
size_t index = 0;
ranges_[fIdx] = newRange;
vector<unsigned> indices (ranges_.size(), 0);
for (size_t k = 0; k < newSize; k++) {
assert (index < backup.size());
params_.push_back (backup[index]);
for (size_t i = ranges_.size(); i-- > 0; ) {
indices[i] ++;
if (i == fIdx) {
if (indices[i] != ranges_[i]) {
int diff = sumIndexes[indices[i]] - sumIndexes[indices[i] - 1];
index += diff * offsets[i];
break;
} else {
// last index contains the old range minus 1
index -= sumIndexes.back() * offsets[i];
indices[i] = 0;
}
} else {
if (indices[i] != ranges_[i]) {
index += offsets[i];
break;
} else {
index -= (ranges_[i] - 1) * offsets[i];
indices[i] = 0;
}
}
}
}
}
void
Parfactor::simplifyCountingFormulas (size_t fIdx)
{
// check if we can simplify the parfactor
for (size_t i = 0; i < args_.size(); i++) {
if (i != fIdx &&
args_[i].isCounting() &&
args_[i].group() == args_[fIdx].group()) {
// if they only differ in the name of the counting log var
if ((args_[i].logVarSet() - args_[i].countedLogVar()) ==
(args_[fIdx].logVarSet()) - args_[fIdx].countedLogVar() &&
ranges_[i] == ranges_[fIdx]) {
simplifyParfactor (fIdx, i);
break;
}
}
}
}
void
Parfactor::simplifyGrounds (void)
{
if (args_.size() == 1) {
return;
}
LogVarSet singletons = constr_->singletons();
for (long i = 0; i < (long)args_.size() - 1; i++) {
for (size_t j = i + 1; j < args_.size(); j++) {
if (args_[i].group() == args_[j].group() &&
singletons.contains (args_[i].logVarSet()) &&
singletons.contains (args_[j].logVarSet())) {
simplifyParfactor (i, j);
i --;
break;
}
}
}
}
bool
Parfactor::canMultiply (Parfactor* g1, Parfactor* g2)
{
std::pair<LogVars, LogVars> res = getAlignLogVars (g1, g2);
LogVarSet Xs_1 (res.first);
LogVarSet Xs_2 (res.second);
LogVarSet Y_1 = g1->logVarSet() - Xs_1;
LogVarSet Y_2 = g2->logVarSet() - Xs_2;
Y_1 -= g1->countedLogVars();
Y_2 -= g2->countedLogVars();
return g1->constr()->isCountNormalized (Y_1) &&
g2->constr()->isCountNormalized (Y_2);
}
void
Parfactor::simplifyParfactor (size_t fIdx1, size_t fIdx2)
{
Params backup = params_;
params_.clear();
Indexer indexer (ranges_);
while (indexer.valid()) {
if (indexer[fIdx1] == indexer[fIdx2]) {
params_.push_back (backup[indexer]);
}
++ indexer;
}
for (size_t i = 0; i < args_[fIdx2].logVars().size(); i++) {
if (nrFormulas (args_[fIdx2].logVars()[i]) == 1) {
constr_->remove ({ args_[fIdx2].logVars()[i] });
}
}
args_.erase (args_.begin() + fIdx2);
ranges_.erase (ranges_.begin() + fIdx2);
}
std::pair<LogVars, LogVars>
Parfactor::getAlignLogVars (Parfactor* g1, Parfactor* g2)
{
g1->simplifyGrounds();
g2->simplifyGrounds();
LogVars Xs_1, Xs_2;
TinySet<size_t> matchedI;
TinySet<size_t> matchedJ;
ProbFormulas& formulas1 = g1->arguments();
ProbFormulas& formulas2 = g2->arguments();
for (size_t i = 0; i < formulas1.size(); i++) {
for (size_t j = 0; j < formulas2.size(); j++) {
if (formulas1[i].group() == formulas2[j].group() &&
g1->range (i) == g2->range (j) &&
matchedI.contains (i) == false &&
matchedJ.contains (j) == false) {
Util::addToVector (Xs_1, formulas1[i].logVars());
Util::addToVector (Xs_2, formulas2[j].logVars());
matchedI.insert (i);
matchedJ.insert (j);
}
}
}
return make_pair (Xs_1, Xs_2);
}
void
Parfactor::alignAndExponentiate (Parfactor* g1, Parfactor* g2)
{
alignLogicalVars (g1, g2);
LogVarSet comm = g1->logVarSet() & g2->logVarSet();
LogVarSet Y_1 = g1->logVarSet() - comm;
LogVarSet Y_2 = g2->logVarSet() - comm;
Y_1 -= g1->countedLogVars();
Y_2 -= g2->countedLogVars();
assert (g1->constr()->isCountNormalized (Y_1));
assert (g2->constr()->isCountNormalized (Y_2));
unsigned condCount1 = g1->constr()->getConditionalCount (Y_1);
unsigned condCount2 = g2->constr()->getConditionalCount (Y_2);
LogAware::pow (g1->params(), 1.0 / condCount2);
LogAware::pow (g2->params(), 1.0 / condCount1);
}
void
Parfactor::alignLogicalVars (Parfactor* g1, Parfactor* g2)
{
std::pair<LogVars, LogVars> res = getAlignLogVars (g1, g2);
const LogVars& alignLvs1 = res.first;
const LogVars& alignLvs2 = res.second;
// cout << "ALIGNING :::::::::::::::::" << endl;
// g1->print();
// cout << "AND" << endl;
// g2->print();
// cout << "-> align lvs1 = " << alignLvs1 << endl;
// cout << "-> align lvs2 = " << alignLvs2 << endl;
LogVar freeLogVar (0);
Substitution theta1, theta2;
for (size_t i = 0; i < alignLvs1.size(); i++) {
bool b1 = theta1.containsReplacementFor (alignLvs1[i]);
bool b2 = theta2.containsReplacementFor (alignLvs2[i]);
if (b1 == false && b2 == false) {
theta1.add (alignLvs1[i], freeLogVar);
theta2.add (alignLvs2[i], freeLogVar);
++ freeLogVar;
} else if (b1 == false && b2) {
theta1.add (alignLvs1[i], theta2.newNameFor (alignLvs2[i]));
} else if (b1 && b2 == false) {
theta2.add (alignLvs2[i], theta1.newNameFor (alignLvs1[i]));
}
}
const LogVarSet& allLvs1 = g1->logVarSet();
for (size_t i = 0; i < allLvs1.size(); i++) {
if (theta1.containsReplacementFor (allLvs1[i]) == false) {
theta1.add (allLvs1[i], freeLogVar);
++ freeLogVar;
}
}
const LogVarSet& allLvs2 = g2->logVarSet();
for (size_t i = 0; i < allLvs2.size(); i++) {
if (theta2.containsReplacementFor (allLvs2[i]) == false) {
theta2.add (allLvs2[i], freeLogVar);
++ freeLogVar;
}
}
// handle this type of situation:
// g1 = p(X), q(X) ; X in {(p1),(p2)}
// g2 = p(X), q(Y) ; (X,Y) in {(p1,p2),(p2,p1)}
LogVars discardedLvs1 = theta1.getDiscardedLogVars();
for (size_t i = 0; i < discardedLvs1.size(); i++) {
if (g1->constr()->isSingleton (discardedLvs1[i]) &&
g1->nrFormulas (discardedLvs1[i]) == 1) {
g1->constr()->remove (discardedLvs1[i]);
} else {
LogVar X_new = ++ g1->constr()->logVarSet().back();
theta1.rename (discardedLvs1[i], X_new);
}
}
LogVars discardedLvs2 = theta2.getDiscardedLogVars();
for (size_t i = 0; i < discardedLvs2.size(); i++) {
if (g2->constr()->isSingleton (discardedLvs2[i]) &&
g2->nrFormulas (discardedLvs2[i]) == 1) {
g2->constr()->remove (discardedLvs2[i]);
} else {
LogVar X_new = ++ g2->constr()->logVarSet().back();
theta2.rename (discardedLvs2[i], X_new);
}
}
// cout << "theta1: " << theta1 << endl;
// cout << "theta2: " << theta2 << endl;
g1->applySubstitution (theta1);
g2->applySubstitution (theta2);
}

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packages/CLPBN/horus2/Parfactor.h
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@ -1,125 +0,0 @@
#ifndef HORUS_PARFACTOR_H
#define HORUS_PARFACTOR_H
#include <list>
#include <unordered_map>
#include "ProbFormula.h"
#include "ConstraintTree.h"
#include "LiftedUtils.h"
#include "Horus.h"
#include "Factor.h"
class Parfactor : public TFactor<ProbFormula>
{
public:
Parfactor (
const ProbFormulas&,
const Params&,
const Tuples&,
unsigned distId);
Parfactor (const Parfactor*, const Tuple&);
Parfactor (const Parfactor*, ConstraintTree*);
Parfactor (const Parfactor&);
~Parfactor (void);
ConstraintTree* constr (void) { return constr_; }
const ConstraintTree* constr (void) const { return constr_; }
const LogVars& logVars (void) const { return constr_->logVars(); }
const LogVarSet& logVarSet (void) const { return constr_->logVarSet(); }
LogVarSet countedLogVars (void) const;
LogVarSet uncountedLogVars (void) const;
LogVarSet elimLogVars (void) const;
LogVarSet exclusiveLogVars (size_t fIdx) const;
void sumOutIndex (size_t fIdx);
void multiply (Parfactor&);
bool canCountConvert (LogVar X);
void countConvert (LogVar);
void expand (LogVar, LogVar, LogVar);
void fullExpand (LogVar);
void reorderAccordingGrounds (const Grounds&);
void absorveEvidence (const ProbFormula&, unsigned);
void setNewGroups (void);
void applySubstitution (const Substitution&);
size_t indexOfGround (const Ground&) const;
PrvGroup findGroup (const Ground&) const;
bool containsGround (const Ground&) const;
bool containsGrounds (const Grounds&) const;
bool containsGroup (PrvGroup) const;
bool containsGroups (vector<PrvGroup>) const;
unsigned nrFormulas (LogVar) const;
int indexOfLogVar (LogVar) const;
int indexOfGroup (PrvGroup) const;
unsigned nrFormulasWithGroup (PrvGroup) const;
vector<PrvGroup> getAllGroups (void) const;
void print (bool = false) const;
void printParameters (void) const;
void printProjections (void) const;
string getLabel (void) const;
void simplifyGrounds (void);
static bool canMultiply (Parfactor*, Parfactor*);
private:
void simplifyCountingFormulas (size_t fIdx);
void simplifyParfactor (size_t fIdx1, size_t fIdx2);
static std::pair<LogVars, LogVars> getAlignLogVars (
Parfactor* g1, Parfactor* g2);
void expandPotential (size_t fIdx, unsigned newRange,
const vector<unsigned>& sumIndexes);
static void alignAndExponentiate (Parfactor*, Parfactor*);
static void alignLogicalVars (Parfactor*, Parfactor*);
ConstraintTree* constr_;
};
typedef vector<Parfactor*> Parfactors;
#endif // HORUS_PARFACTOR_H

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packages/CLPBN/horus2/ParfactorList.cpp
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@ -1,638 +0,0 @@
#include <cassert>
#include "ParfactorList.h"
ParfactorList::ParfactorList (const ParfactorList& pfList)
{
ParfactorList::const_iterator it = pfList.begin();
while (it != pfList.end()) {
addShattered (new Parfactor (**it));
++ it;
}
}
ParfactorList::ParfactorList (const Parfactors& pfs)
{
add (pfs);
}
ParfactorList::~ParfactorList (void)
{
ParfactorList::const_iterator it = pfList_.begin();
while (it != pfList_.end()) {
delete *it;
++ it;
}
}
void
ParfactorList::add (Parfactor* pf)
{
pf->setNewGroups();
addToShatteredList (pf);
}
void
ParfactorList::add (const Parfactors& pfs)
{
for (size_t i = 0; i < pfs.size(); i++) {
pfs[i]->setNewGroups();
addToShatteredList (pfs[i]);
}
}
void
ParfactorList::addShattered (Parfactor* pf)
{
assert (isAllShattered());
pfList_.push_back (pf);
assert (isAllShattered());
}
list<Parfactor*>::iterator
ParfactorList::insertShattered (
list<Parfactor*>::iterator it,
Parfactor* pf)
{
return pfList_.insert (it, pf);
assert (isAllShattered());
}
list<Parfactor*>::iterator
ParfactorList::remove (list<Parfactor*>::iterator it)
{
return pfList_.erase (it);
}
list<Parfactor*>::iterator
ParfactorList::removeAndDelete (list<Parfactor*>::iterator it)
{
delete *it;
return pfList_.erase (it);
}
bool
ParfactorList::isAllShattered (void) const
{
if (pfList_.size() <= 1) {
return true;
}
vector<Parfactor*> pfs (pfList_.begin(), pfList_.end());
for (size_t i = 0; i < pfs.size(); i++) {
assert (isShattered (pfs[i]));
}
for (size_t i = 0; i < pfs.size() - 1; i++) {
for (size_t j = i + 1; j < pfs.size(); j++) {
if (isShattered (pfs[i], pfs[j]) == false) {
return false;
}
}
}
return true;
}
void
ParfactorList::print (void) const
{
Parfactors pfVec (pfList_.begin(), pfList_.end());
std::sort (pfVec.begin(), pfVec.end(), sortByParams());
for (size_t i = 0; i < pfVec.size(); i++) {
pfVec[i]->print();
cout << endl;
}
}
ParfactorList&
ParfactorList::operator= (const ParfactorList& pfList)
{
if (this != &pfList) {
ParfactorList::const_iterator it0 = pfList_.begin();
while (it0 != pfList_.end()) {
delete *it0;
++ it0;
}
pfList_.clear();
ParfactorList::const_iterator it = pfList.begin();
while (it != pfList.end()) {
addShattered (new Parfactor (**it));
++ it;
}
}
return *this;
}
bool
ParfactorList::isShattered (const Parfactor* g) const
{
const ProbFormulas& formulas = g->arguments();
if (formulas.size() < 2) {
return true;
}
ConstraintTree ct (*g->constr());
for (size_t i = 0; i < formulas.size() - 1; i++) {
for (size_t j = i + 1; j < formulas.size(); j++) {
if (formulas[i].group() == formulas[j].group()) {
if (identical (
formulas[i], *(g->constr()),
formulas[j], *(g->constr())) == false) {
g->print();
cout << "-> not identical on positions " ;
cout << i << " and " << j << endl;
return false;
}
} else {
if (disjoint (
formulas[i], *(g->constr()),
formulas[j], *(g->constr())) == false) {
g->print();
cout << "-> not disjoint on positions " ;
cout << i << " and " << j << endl;
return false;
}
}
}
}
return true;
}
bool
ParfactorList::isShattered (
const Parfactor* g1,
const Parfactor* g2) const
{
assert (g1 != g2);
const ProbFormulas& fms1 = g1->arguments();
const ProbFormulas& fms2 = g2->arguments();
for (size_t i = 0; i < fms1.size(); i++) {
for (size_t j = 0; j < fms2.size(); j++) {
if (fms1[i].group() == fms2[j].group()) {
if (identical (
fms1[i], *(g1->constr()),
fms2[j], *(g2->constr())) == false) {
g1->print();
cout << "^" << endl;
g2->print();
cout << "-> not identical on group " << fms1[i].group() << endl;
return false;
}
} else {
if (disjoint (
fms1[i], *(g1->constr()),
fms2[j], *(g2->constr())) == false) {
g1->print();
cout << "^" << endl;
g2->print();
cout << "-> not disjoint on groups " << fms1[i].group();
cout << " and " << fms2[j].group() << endl;
return false;
}
}
}
}
return true;
}
void
ParfactorList::addToShatteredList (Parfactor* g)
{
queue<Parfactor*> residuals;
residuals.push (g);
while (residuals.empty() == false) {
Parfactor* pf = residuals.front();
bool pfSplitted = false;
list<Parfactor*>::iterator pfIter;
pfIter = pfList_.begin();
while (pfIter != pfList_.end()) {
std::pair<Parfactors, Parfactors> shattRes;
shattRes = shatter (*pfIter, pf);
if (shattRes.first.empty() == false) {
pfIter = removeAndDelete (pfIter);
Util::addToQueue (residuals, shattRes.first);
} else {
++ pfIter;
}
if (shattRes.second.empty() == false) {
delete pf;
Util::addToQueue (residuals, shattRes.second);
pfSplitted = true;
break;
}
}
residuals.pop();
if (pfSplitted == false) {
Parfactors res = shatterAgainstMySelf (pf);
if (res.empty()) {
addShattered (pf);
} else {
Util::addToQueue (residuals, res);
}
}
}
assert (isAllShattered());
}
Parfactors
ParfactorList::shatterAgainstMySelf (Parfactor* g)
{
Parfactors pfs;
queue<Parfactor*> residuals;
residuals.push (g);
bool shattered = true;
while (residuals.empty() == false) {
Parfactor* pf = residuals.front();
Parfactors res = shatterAgainstMySelf2 (pf);
if (res.empty()) {
assert (isShattered (pf));
if (shattered) {
return { };
}
pfs.push_back (pf);
} else {
shattered = false;
for (size_t i = 0; i < res.size(); i++) {
assert (res[i]->constr()->empty() == false);
residuals.push (res[i]);
}
delete pf;
}
residuals.pop();
}
return pfs;
}
Parfactors
ParfactorList::shatterAgainstMySelf2 (Parfactor* g)
{
// slip a parfactor with overlapping formulas:
// e.g. {s(X),s(Y)}, with (X,Y) in {(p1,p2),(p1,p3),(p4,p1)}
const ProbFormulas& formulas = g->arguments();
for (size_t i = 0; i < formulas.size() - 1; i++) {
for (size_t j = i + 1; j < formulas.size(); j++) {
if (formulas[i].sameSkeletonAs (formulas[j])) {
Parfactors res = shatterAgainstMySelf (g, i, j);
if (res.empty() == false) {
return res;
}
}
}
}
return Parfactors();
}
Parfactors
ParfactorList::shatterAgainstMySelf (
Parfactor* g,
size_t fIdx1,
size_t fIdx2)
{
/*
Util::printDashedLine();
cout << "-> SHATTERING" << endl;
g->print();
cout << "-> ON: " << g->argument (fIdx1) << "|" ;
cout << g->constr()->tupleSet (g->argument (fIdx1).logVars()) << endl;
cout << "-> ON: " << g->argument (fIdx2) << "|" ;
cout << g->constr()->tupleSet (g->argument (fIdx2).logVars()) << endl;
Util::printDashedLine();
*/
ProbFormula& f1 = g->argument (fIdx1);
ProbFormula& f2 = g->argument (fIdx2);
if (f1.isAtom()) {
cerr << "Error: a ground occurs twice in the same parfactor." << endl;
cerr << endl;
exit (EXIT_FAILURE);
}
assert (g->constr()->empty() == false);
ConstraintTree ctCopy (*g->constr());
if (f1.group() == f2.group()) {
assert (identical (f1, *(g->constr()), f2, ctCopy));
return { };
}
g->constr()->moveToTop (f1.logVars());
ctCopy.moveToTop (f2.logVars());
std::pair<ConstraintTree*,ConstraintTree*> split1 =
g->constr()->split (f1.logVars(), &ctCopy, f2.logVars());
ConstraintTree* commCt1 = split1.first;
ConstraintTree* exclCt1 = split1.second;
if (commCt1->empty()) {
// disjoint
delete commCt1;
delete exclCt1;
return { };
}
PrvGroup newGroup = ProbFormula::getNewGroup();
Parfactors res1 = shatter (g, fIdx1, commCt1, exclCt1, newGroup);
if (res1.empty()) {
res1.push_back (g);
}
Parfactors res;
ctCopy.moveToTop (f1.logVars());
for (size_t i = 0; i < res1.size(); i++) {
res1[i]->constr()->moveToTop (f2.logVars());
std::pair<ConstraintTree*, ConstraintTree*> split2;
split2 = res1[i]->constr()->split (f2.logVars(), &ctCopy, f1.logVars());
ConstraintTree* commCt2 = split2.first;
ConstraintTree* exclCt2 = split2.second;
if (commCt2->empty()) {
if (res1[i] != g) {
res.push_back (res1[i]);
}
delete commCt2;
delete exclCt2;
continue;
}
newGroup = ProbFormula::getNewGroup();
Parfactors res2 = shatter (res1[i], fIdx2, commCt2, exclCt2, newGroup);
if (res2.empty()) {
if (res1[i] != g) {
res.push_back (res1[i]);
}
} else {
Util::addToVector (res, res2);
for (size_t j = 0; j < res2.size(); j++) {
}
if (res1[i] != g) {
delete res1[i];
}
}
}
if (res.empty()) {
g->argument (fIdx2).setGroup (g->argument (fIdx1).group());
updateGroups (f2.group(), f1.group());
}
return res;
}
std::pair<Parfactors, Parfactors>
ParfactorList::shatter (Parfactor* g1, Parfactor* g2)
{
ProbFormulas& formulas1 = g1->arguments();
ProbFormulas& formulas2 = g2->arguments();
assert (g1 != 0 && g2 != 0 && g1 != g2);
for (size_t i = 0; i < formulas1.size(); i++) {
for (size_t j = 0; j < formulas2.size(); j++) {
if (formulas1[i].sameSkeletonAs (formulas2[j])) {
std::pair<Parfactors, Parfactors> res;
res = shatter (i, g1, j, g2);
if (res.first.empty() == false ||
res.second.empty() == false) {
return res;
}
}
}
}
return make_pair (Parfactors(), Parfactors());
}
std::pair<Parfactors, Parfactors>
ParfactorList::shatter (
size_t fIdx1, Parfactor* g1,
size_t fIdx2, Parfactor* g2)
{
ProbFormula& f1 = g1->argument (fIdx1);
ProbFormula& f2 = g2->argument (fIdx2);
/*
Util::printDashedLine();
cout << "-> SHATTERING" << endl;
g1->print();
cout << "-> WITH" << endl;
g2->print();
cout << "-> ON: " << f1 << "|" ;
cout << g1->constr()->tupleSet (f1.logVars()) << endl;
cout << "-> ON: " << f2 << "|" ;
cout << g2->constr()->tupleSet (f2.logVars()) << endl;
Util::printDashedLine();
*/
if (f1.isAtom()) {
f2.setGroup (f1.group());
updateGroups (f2.group(), f1.group());
return { };
}
assert (g1->constr()->empty() == false);
assert (g2->constr()->empty() == false);
if (f1.group() == f2.group()) {
assert (identical (f1, *(g1->constr()), f2, *(g2->constr())));
return { };
}
g1->constr()->moveToTop (f1.logVars());
g2->constr()->moveToTop (f2.logVars());
std::pair<ConstraintTree*,ConstraintTree*> split1 =
g1->constr()->split (f1.logVars(), g2->constr(), f2.logVars());
ConstraintTree* commCt1 = split1.first;
ConstraintTree* exclCt1 = split1.second;
if (commCt1->empty()) {
// disjoint
delete commCt1;
delete exclCt1;
return { };
}
std::pair<ConstraintTree*,ConstraintTree*> split2 =
g2->constr()->split (f2.logVars(), g1->constr(), f1.logVars());
ConstraintTree* commCt2 = split2.first;
ConstraintTree* exclCt2 = split2.second;
assert (commCt1->tupleSet (f1.logVars()) ==
commCt2->tupleSet (f2.logVars()));
// stringstream ss1; ss1 << "" << count << "_A.dot" ;
// stringstream ss2; ss2 << "" << count << "_B.dot" ;
// stringstream ss3; ss3 << "" << count << "_A_comm.dot" ;
// stringstream ss4; ss4 << "" << count << "_A_excl.dot" ;
// stringstream ss5; ss5 << "" << count << "_B_comm.dot" ;
// stringstream ss6; ss6 << "" << count << "_B_excl.dot" ;
// g1->constr()->exportToGraphViz (ss1.str().c_str(), true);
// g2->constr()->exportToGraphViz (ss2.str().c_str(), true);
// commCt1->exportToGraphViz (ss3.str().c_str(), true);
// exclCt1->exportToGraphViz (ss4.str().c_str(), true);
// commCt2->exportToGraphViz (ss5.str().c_str(), true);
// exclCt2->exportToGraphViz (ss6.str().c_str(), true);
if (exclCt1->empty() && exclCt2->empty()) {
// identical
f2.setGroup (f1.group());
updateGroups (f2.group(), f1.group());
delete commCt1;
delete exclCt1;
delete commCt2;
delete exclCt2;
return { };
}
PrvGroup group;
if (exclCt1->empty()) {
group = f1.group();
} else if (exclCt2->empty()) {
group = f2.group();
} else {
group = ProbFormula::getNewGroup();
}
Parfactors res1 = shatter (g1, fIdx1, commCt1, exclCt1, group);
Parfactors res2 = shatter (g2, fIdx2, commCt2, exclCt2, group);
return make_pair (res1, res2);
}
Parfactors
ParfactorList::shatter (
Parfactor* g,
size_t fIdx,
ConstraintTree* commCt,
ConstraintTree* exclCt,
PrvGroup commGroup)
{
ProbFormula& f = g->argument (fIdx);
if (exclCt->empty()) {
delete commCt;
delete exclCt;
f.setGroup (commGroup);
return { };
}
Parfactors result;
if (f.isCounting()) {
LogVar X_new1 = g->constr()->logVarSet().back() + 1;
LogVar X_new2 = g->constr()->logVarSet().back() + 2;
ConstraintTrees cts = g->constr()->jointCountNormalize (
commCt, exclCt, f.countedLogVar(), X_new1, X_new2);
for (size_t i = 0; i < cts.size(); i++) {
Parfactor* newPf = new Parfactor (g, cts[i]);
if (cts[i]->nrLogVars() == g->constr()->nrLogVars() + 1) {
newPf->expand (f.countedLogVar(), X_new1, X_new2);
assert (g->constr()->getConditionalCount (f.countedLogVar()) ==
cts[i]->getConditionalCount (X_new1) +
cts[i]->getConditionalCount (X_new2));
} else {
assert (g->constr()->getConditionalCount (f.countedLogVar()) ==
cts[i]->getConditionalCount (f.countedLogVar()));
}
newPf->setNewGroups();
result.push_back (newPf);
}
delete commCt;
delete exclCt;
} else {
Parfactor* newPf = new Parfactor (g, commCt);
newPf->setNewGroups();
newPf->argument (fIdx).setGroup (commGroup);
result.push_back (newPf);
newPf = new Parfactor (g, exclCt);
newPf->setNewGroups();
result.push_back (newPf);
}
return result;
}
void
ParfactorList::updateGroups (PrvGroup oldGroup, PrvGroup newGroup)
{
for (ParfactorList::iterator it = pfList_.begin();
it != pfList_.end(); ++it) {
ProbFormulas& formulas = (*it)->arguments();
for (size_t i = 0; i < formulas.size(); i++) {
if (formulas[i].group() == oldGroup) {
formulas[i].setGroup (newGroup);
}
}
}
}
bool
ParfactorList::proper (
const ProbFormula& f1, ConstraintTree ct1,
const ProbFormula& f2, ConstraintTree ct2) const
{
return disjoint (f1, ct1, f2, ct2)
|| identical (f1, ct1, f2, ct2);
}
bool
ParfactorList::identical (
const ProbFormula& f1, ConstraintTree ct1,
const ProbFormula& f2, ConstraintTree ct2) const
{
if (f1.sameSkeletonAs (f2) == false) {
return false;
}
if (f1.isAtom()) {
return true;
}
TupleSet ts1 = ct1.tupleSet (f1.logVars());
TupleSet ts2 = ct2.tupleSet (f2.logVars());
return ts1 == ts2;
}
bool
ParfactorList::disjoint (
const ProbFormula& f1, ConstraintTree ct1,
const ProbFormula& f2, ConstraintTree ct2) const
{
if (f1.sameSkeletonAs (f2) == false) {
return true;
}
if (f1.isAtom()) {
return false;
}
TupleSet ts1 = ct1.tupleSet (f1.logVars());
TupleSet ts2 = ct2.tupleSet (f2.logVars());
return (ts1 & ts2).empty();
}

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#ifndef HORUS_PARFACTORLIST_H
#define HORUS_PARFACTORLIST_H
#include <list>
#include <queue>
#include "Parfactor.h"
#include "ProbFormula.h"
using namespace std;
class ParfactorList
{
public:
ParfactorList (void) { }
ParfactorList (const ParfactorList&);
ParfactorList (const Parfactors&);
~ParfactorList (void);
const list<Parfactor*>& parfactors (void) const { return pfList_; }
void clear (void) { pfList_.clear(); }
size_t size (void) const { return pfList_.size(); }
typedef std::list<Parfactor*>::iterator iterator;
iterator begin (void) { return pfList_.begin(); }
iterator end (void) { return pfList_.end(); }
typedef std::list<Parfactor*>::const_iterator const_iterator;
const_iterator begin (void) const { return pfList_.begin(); }
const_iterator end (void) const { return pfList_.end(); }
void add (Parfactor* pf);
void add (const Parfactors& pfs);
void addShattered (Parfactor* pf);
list<Parfactor*>::iterator insertShattered (
list<Parfactor*>::iterator, Parfactor*);
list<Parfactor*>::iterator remove (list<Parfactor*>::iterator);
list<Parfactor*>::iterator removeAndDelete (list<Parfactor*>::iterator);
bool isAllShattered (void) const;
void print (void) const;
ParfactorList& operator= (const ParfactorList& pfList);
private:
bool isShattered (const Parfactor*) const;
bool isShattered (const Parfactor*, const Parfactor*) const;
void addToShatteredList (Parfactor*);
Parfactors shatterAgainstMySelf (Parfactor* g);
Parfactors shatterAgainstMySelf2 (Parfactor* g);
Parfactors shatterAgainstMySelf (
Parfactor* g, size_t fIdx1, size_t fIdx2);
std::pair<Parfactors, Parfactors> shatter (
Parfactor*, Parfactor*);
std::pair<Parfactors, Parfactors> shatter (
size_t, Parfactor*, size_t, Parfactor*);
Parfactors shatter (
Parfactor*,
size_t,
ConstraintTree*,
ConstraintTree*,
PrvGroup);
void updateGroups (PrvGroup group1, PrvGroup group2);
bool proper (
const ProbFormula&, ConstraintTree,
const ProbFormula&, ConstraintTree) const;
bool identical (
const ProbFormula&, ConstraintTree,
const ProbFormula&, ConstraintTree) const;
bool disjoint (
const ProbFormula&, ConstraintTree,
const ProbFormula&, ConstraintTree) const;
struct sortByParams
{
inline bool operator() (const Parfactor* pf1, const Parfactor* pf2)
{
if (pf1->params().size() < pf2->params().size()) {
return true;
} else if (pf1->params().size() == pf2->params().size() &&
pf1->params() < pf2->params()) {
return true;
}
return false;
}
};
list<Parfactor*> pfList_;
};
#endif // HORUS_PARFACTORLIST_H

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#include "ProbFormula.h"
PrvGroup ProbFormula::freeGroup_ = 0;
bool
ProbFormula::sameSkeletonAs (const ProbFormula& f) const
{
return functor_ == f.functor() && logVars_.size() == f.arity();
}
bool
ProbFormula::contains (LogVar lv) const
{
return Util::contains (logVars_, lv);
}
bool
ProbFormula::contains (LogVarSet s) const
{
return LogVarSet (logVars_).contains (s);
}
size_t
ProbFormula::indexOf (LogVar X) const
{
return Util::indexOf (logVars_, X);
}
bool
ProbFormula::isAtom (void) const
{
return logVars_.size() == 0;
}
bool
ProbFormula::isCounting (void) const
{
return countedLogVar_.valid();
}
LogVar
ProbFormula::countedLogVar (void) const
{
assert (isCounting());
return countedLogVar_;
}
void
ProbFormula::setCountedLogVar (LogVar lv)
{
countedLogVar_ = lv;
}
void
ProbFormula::clearCountedLogVar (void)
{
countedLogVar_ = LogVar();
}
void
ProbFormula::rename (LogVar oldName, LogVar newName)
{
for (size_t i = 0; i < logVars_.size(); i++) {
if (logVars_[i] == oldName) {
logVars_[i] = newName;
}
}
if (isCounting() && countedLogVar_ == oldName) {
countedLogVar_ = newName;
}
}
bool operator== (const ProbFormula& f1, const ProbFormula& f2)
{
return f1.group_ == f2.group_ &&
f1.logVars_ == f2.logVars_;
}
std::ostream& operator<< (ostream &os, const ProbFormula& f)
{
os << f.functor_;
if (f.isAtom() == false) {
os << "(" ;
for (size_t i = 0; i < f.logVars_.size(); i++) {
if (i != 0) os << ",";
if (f.isCounting() && f.logVars_[i] == f.countedLogVar_) {
os << "#" ;
}
os << f.logVars_[i];
}
os << ")" ;
}
os << "::" << f.range_;
return os;
}
PrvGroup
ProbFormula::getNewGroup (void)
{
freeGroup_ ++;
assert (freeGroup_ != numeric_limits<PrvGroup>::max());
return freeGroup_;
}
ostream& operator<< (ostream &os, const ObservedFormula& of)
{
os << of.functor_ << "/" << of.arity_;
os << "|" << of.constr_.tupleSet();
os << " [evidence=" << of.evidence_ << "]";
return os;
}

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#ifndef HORUS_PROBFORMULA_H
#define HORUS_PROBFORMULA_H
#include <limits>
#include "ConstraintTree.h"
#include "LiftedUtils.h"
#include "Horus.h"
typedef unsigned long PrvGroup;
class ProbFormula
{
public:
ProbFormula (Symbol f, const LogVars& lvs, unsigned range)
: functor_(f), logVars_(lvs), range_(range),
countedLogVar_(), group_(numeric_limits<PrvGroup>::max()) { }
ProbFormula (Symbol f, unsigned r)
: functor_(f), range_(r), group_(numeric_limits<PrvGroup>::max()) { }
Symbol functor (void) const { return functor_; }
unsigned arity (void) const { return logVars_.size(); }
unsigned range (void) const { return range_; }
LogVars& logVars (void) { return logVars_; }
const LogVars& logVars (void) const { return logVars_; }
LogVarSet logVarSet (void) const { return LogVarSet (logVars_); }
PrvGroup group (void) const { return group_; }
void setGroup (PrvGroup g) { group_ = g; }
bool sameSkeletonAs (const ProbFormula&) const;
bool contains (LogVar) const;
bool contains (LogVarSet) const;
size_t indexOf (LogVar) const;
bool isAtom (void) const;
bool isCounting (void) const;
LogVar countedLogVar (void) const;
void setCountedLogVar (LogVar);
void clearCountedLogVar (void);
void rename (LogVar, LogVar);
static PrvGroup getNewGroup (void);
friend std::ostream& operator<< (ostream &os, const ProbFormula& f);
friend bool operator== (const ProbFormula& f1, const ProbFormula& f2);
private:
Symbol functor_;
LogVars logVars_;
unsigned range_;
LogVar countedLogVar_;
PrvGroup group_;
static PrvGroup freeGroup_;
};
typedef vector<ProbFormula> ProbFormulas;
class ObservedFormula
{
public:
ObservedFormula (Symbol f, unsigned a, unsigned ev)
: functor_(f), arity_(a), evidence_(ev), constr_(a) { }
ObservedFormula (Symbol f, unsigned ev, const Tuple& tuple)
: functor_(f), arity_(tuple.size()), evidence_(ev), constr_(arity_)
{
constr_.addTuple (tuple);
}
Symbol functor (void) const { return functor_; }
unsigned arity (void) const { return arity_; }
unsigned evidence (void) const { return evidence_; }
void setEvidence (unsigned ev) { evidence_ = ev; }
ConstraintTree& constr (void) { return constr_; }
bool isAtom (void) const { return arity_ == 0; }
void addTuple (const Tuple& tuple) { constr_.addTuple (tuple); }
friend ostream& operator<< (ostream &os, const ObservedFormula& of);
private:
Symbol functor_;
unsigned arity_;
unsigned evidence_;
ConstraintTree constr_;
};
typedef vector<ObservedFormula> ObservedFormulas;
#endif // HORUS_PROBFORMULA_H

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#ifndef HORUS_TINYSET_H
#define HORUS_TINYSET_H
#include <vector>
#include <algorithm>
using namespace std;
template <typename T, typename Compare = std::less<T>>
class TinySet
{
public:
typedef typename vector<T>::iterator iterator;
typedef typename vector<T>::const_iterator const_iterator;
TinySet (const TinySet& s)
: vec_(s.vec_), cmp_(s.cmp_) { }
TinySet (const Compare& cmp = Compare())
: vec_(), cmp_(cmp) { }
TinySet (const T& t, const Compare& cmp = Compare())
: vec_(1, t), cmp_(cmp) { }
TinySet (const vector<T>& elements, const Compare& cmp = Compare())
: vec_(elements), cmp_(cmp)
{
std::sort (begin(), end(), cmp_);
iterator it = unique_cmp (begin(), end());
vec_.resize (it - begin());
}
iterator insert (const T& t)
{
iterator it = std::lower_bound (begin(), end(), t, cmp_);
if (it == end() || cmp_(t, *it)) {
vec_.insert (it, t);
}
return it;
}
void insert_sorted (const T& t)
{
vec_.push_back (t);
assert (consistent());
}
void remove (const T& t)
{
iterator it = std::lower_bound (begin(), end(), t, cmp_);
if (it != end()) {
vec_.erase (it);
}
}
const_iterator find (const T& t) const
{
const_iterator it = std::lower_bound (begin(), end(), t, cmp_);
return it == end() || cmp_(t, *it) ? end() : it;
}
iterator find (const T& t)
{
iterator it = std::lower_bound (begin(), end(), t, cmp_);
return it == end() || cmp_(t, *it) ? end() : it;
}
/* set union */
TinySet operator| (const TinySet& s) const
{
TinySet res;
std::set_union (
vec_.begin(), vec_.end(),
s.vec_.begin(), s.vec_.end(),
std::back_inserter (res.vec_),
cmp_);
return res;
}
/* set intersection */
TinySet operator& (const TinySet& s) const
{
TinySet res;
std::set_intersection (
vec_.begin(), vec_.end(),
s.vec_.begin(), s.vec_.end(),
std::back_inserter (res.vec_),
cmp_);
return res;
}
/* set difference */
TinySet operator- (const TinySet& s) const
{
TinySet res;
std::set_difference (
vec_.begin(), vec_.end(),
s.vec_.begin(), s.vec_.end(),
std::back_inserter (res.vec_),
cmp_);
return res;
}
TinySet& operator|= (const TinySet& s)
{
return *this = (*this | s);
}
TinySet& operator&= (const TinySet& s)
{
return *this = (*this & s);
}
TinySet& operator-= (const TinySet& s)
{
return *this = (*this - s);
}
bool contains (const T& t) const
{
return std::binary_search (
vec_.begin(), vec_.end(), t, cmp_);
}
bool contains (const TinySet& s) const
{
return std::includes (
vec_.begin(),
vec_.end(),
s.vec_.begin(),
s.vec_.end(),
cmp_);
}
bool in (const TinySet& s) const
{
return std::includes (
s.vec_.begin(),
s.vec_.end(),
vec_.begin(),
vec_.end(),
cmp_);
}
bool intersects (const TinySet& s) const
{
return (*this & s).size() > 0;
}
const T& operator[] (typename vector<T>::size_type i) const
{
return vec_[i];
}
T& operator[] (typename vector<T>::size_type i)
{
return vec_[i];
}
T front (void) const
{
return vec_.front();
}
T& front (void)
{
return vec_.front();
}
T back (void) const
{
return vec_.back();
}
T& back (void)
{
return vec_.back();
}
const vector<T>& elements (void) const
{
return vec_;
}
bool empty (void) const
{
return size() == 0;
}
typename vector<T>::size_type size (void) const
{
return vec_.size();
}
void clear (void)
{
vec_.clear();
}
void reserve (typename vector<T>::size_type size)
{
vec_.reserve (size);
}
iterator begin (void) { return vec_.begin(); }
iterator end (void) { return vec_.end(); }
const_iterator begin (void) const { return vec_.begin(); }
const_iterator end (void) const { return vec_.end(); }
friend bool operator== (const TinySet& s1, const TinySet& s2)
{
return s1.vec_ == s2.vec_;
}
friend bool operator!= (const TinySet& s1, const TinySet& s2)
{
return ! (s1.vec_ == s2.vec_);
}
friend std::ostream& operator << (std::ostream& out, const TinySet& s)
{
out << "{" ;
typename vector<T>::size_type i;
for (i = 0; i < s.size(); i++) {
out << ((i != 0) ? "," : "") << s.vec_[i];
}
out << "}" ;
return out;
}
private:
iterator unique_cmp (iterator first, iterator last)
{
if (first == last) {
return last;
}
iterator result = first;
while (++first != last) {
if (cmp_(*result, *first)) {
*(++result) = *first;
}
}
return ++result;
}
bool consistent (void) const
{
typename vector<T>::size_type i;
for (i = 0; i < vec_.size() - 1; i++) {
if ( ! cmp_(vec_[i], vec_[i + 1])) {
return false;
}
}
return true;
}
vector<T> vec_;
Compare cmp_;
};
#endif // HORUS_TINYSET_H

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#include <limits>
#include <sstream>
#include <fstream>
#include "Util.h"
#include "Indexer.h"
#include "ElimGraph.h"
namespace Globals {
bool logDomain = false;
unsigned verbosity = 0;
LiftedSolverType liftedSolver = LiftedSolverType::LVE;
GroundSolverType groundSolver = GroundSolverType::VE;
};
namespace BpOptions {
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;
}
namespace Util {
template <> std::string
toString (const bool& b)
{
std::stringstream ss;
ss << std::boolalpha << b;
return ss.str();
}
unsigned
stringToUnsigned (string str)
{
int val;
stringstream ss;
ss << str;
ss >> val;
if (val < 0) {
cerr << "Error: the number readed is negative." << endl;
exit (EXIT_FAILURE);
}
return static_cast<unsigned> (val);
}
double
stringToDouble (string str)
{
double val;
stringstream ss;
ss << str;
ss >> val;
return val;
}
double
factorial (unsigned num)
{
double result = 1.0;
for (unsigned i = 1; i <= num; i++) {
result *= i;
}
return result;
}
double
logFactorial (unsigned num)
{
double result = 0.0;
if (num < 150) {
result = std::log (factorial (num));
} else {
for (unsigned i = 1; i <= num; i++) {
result += std::log (i);
}
}
return result;
}
unsigned
nrCombinations (unsigned n, unsigned k)
{
assert (n >= k);
int diff = n - k;
unsigned result = 0;
if (n < 150) {
unsigned prod = 1;
for (int i = n; i > diff; i--) {
prod *= i;
}
result = prod / factorial (k);
} else {
double prod = 0.0;
for (int i = n; i > diff; i--) {
prod += std::log (i);
}
prod -= logFactorial (k);
result = static_cast<unsigned> (std::exp (prod));
}
return result;
}
size_t
sizeExpected (const Ranges& ranges)
{
return std::accumulate (ranges.begin(),
ranges.end(), 1, multiplies<unsigned>());
}
unsigned
nrDigits (int num)
{
unsigned count = 1;
while (num >= 10) {
num /= 10;
count ++;
}
return count;
}
bool
isInteger (const string& s)
{
stringstream ss1 (s);
stringstream ss2;
int integer;
ss1 >> integer;
ss2 << integer;
return (ss1.str() == ss2.str());
}
string
parametersToString (const Params& v, unsigned precision)
{
stringstream ss;
ss.precision (precision);
ss << "[" ;
for (size_t i = 0; i < v.size(); i++) {
if (i != 0) ss << ", " ;
ss << v[i];
}
ss << "]" ;
return ss.str();
}
vector<string>
getStateLines (const Vars& vars)
{
Ranges ranges;
for (size_t i = 0; i < vars.size(); i++) {
ranges.push_back (vars[i]->range());
}
Indexer indexer (ranges);
vector<string> jointStrings;
while (indexer.valid()) {
stringstream ss;
for (size_t i = 0; i < vars.size(); i++) {
if (i != 0) ss << ", " ;
ss << vars[i]->label() << "=" ;
ss << vars[i]->states()[(indexer[i])];
}
jointStrings.push_back (ss.str());
++ indexer;
}
return jointStrings;
}
bool
setHorusFlag (string key, string value)
{
bool returnVal = true;
if (key == "verbosity") {
stringstream ss;
ss << value;
ss >> Globals::verbosity;
} else if (key == "lifted_solver") {
if ( value == "lve") {
Globals::liftedSolver = LiftedSolverType::LVE;
} else if (value == "lbp") {
Globals::liftedSolver = LiftedSolverType::LBP;
} else if (value == "lkc") {
Globals::liftedSolver = LiftedSolverType::LKC;
} else {
cerr << "warning: invalid value `" << value << "' " ;
cerr << "for `" << key << "'" << endl;
returnVal = false;
}
} else if (key == "ground_solver") {
if ( value == "ve") {
Globals::groundSolver = GroundSolverType::VE;
} else if (value == "bp") {
Globals::groundSolver = GroundSolverType::BP;
} else if (value == "cbp") {
Globals::groundSolver = GroundSolverType::CBP;
} else {
cerr << "warning: invalid value `" << value << "' " ;
cerr << "for `" << key << "'" << endl;
returnVal = false;
}
} else if (key == "elim_heuristic") {
if ( value == "sequential") {
ElimGraph::elimHeuristic = ElimHeuristic::SEQUENTIAL;
} else if (value == "min_neighbors") {
ElimGraph::elimHeuristic = ElimHeuristic::MIN_NEIGHBORS;
} else if (value == "min_weight") {
ElimGraph::elimHeuristic = ElimHeuristic::MIN_WEIGHT;
} else if (value == "min_fill") {
ElimGraph::elimHeuristic = ElimHeuristic::MIN_FILL;
} else if (value == "weighted_min_fill") {
ElimGraph::elimHeuristic = ElimHeuristic::WEIGHTED_MIN_FILL;
} else {
cerr << "warning: invalid value `" << value << "' " ;
cerr << "for `" << key << "'" << endl;
returnVal = false;
}
} else if (key == "schedule") {
if ( value == "seq_fixed") {
BpOptions::schedule = BpOptions::Schedule::SEQ_FIXED;
} else if (value == "seq_random") {
BpOptions::schedule = BpOptions::Schedule::SEQ_RANDOM;
} else if (value == "parallel") {
BpOptions::schedule = BpOptions::Schedule::PARALLEL;
} else if (value == "max_residual") {
BpOptions::schedule = BpOptions::Schedule::MAX_RESIDUAL;
} else {
cerr << "warning: invalid value `" << value << "' " ;
cerr << "for `" << key << "'" << endl;
returnVal = false;
}
} else if (key == "accuracy") {
stringstream ss;
ss << value;
ss >> BpOptions::accuracy;
} else if (key == "max_iter") {
stringstream ss;
ss << value;
ss >> BpOptions::maxIter;
} else if (key == "use_logarithms") {
if ( value == "true") {
Globals::logDomain = true;
} else if (value == "false") {
Globals::logDomain = false;
} else {
cerr << "warning: invalid value `" << value << "' " ;
cerr << "for `" << key << "'" << endl;
returnVal = false;
}
} else {
cerr << "warning: invalid key `" << key << "'" << endl;
returnVal = false;
}
return returnVal;
}
void
printHeader (string header, std::ostream& os)
{
printAsteriskLine (os);
os << header << endl;
printAsteriskLine (os);
}
void
printSubHeader (string header, std::ostream& os)
{
printDashedLine (os);
os << header << endl;
printDashedLine (os);
}
void
printAsteriskLine (std::ostream& os)
{
os << "********************************" ;
os << "********************************" ;
os << endl;
}
void
printDashedLine (std::ostream& os)
{
os << "--------------------------------" ;
os << "--------------------------------" ;
os << endl;
}
}
namespace LogAware {
void
normalize (Params& v)
{
if (Globals::logDomain) {
double sum = std::accumulate (v.begin(), v.end(),
LogAware::addIdenty(), Util::logSum);
assert (sum != -numeric_limits<double>::infinity());
v -= sum;
} else {
double sum = std::accumulate (v.begin(), v.end(), 0.0);
assert (sum != 0.0);
v /= sum;
}
}
double
getL1Distance (const Params& v1, const Params& v2)
{
assert (v1.size() == v2.size());
double dist = 0.0;
if (Globals::logDomain) {
dist = std::inner_product (v1.begin(), v1.end(), v2.begin(), 0.0,
std::plus<double>(), FuncObject::abs_diff_exp<double>());
} else {
dist = std::inner_product (v1.begin(), v1.end(), v2.begin(), 0.0,
std::plus<double>(), FuncObject::abs_diff<double>());
}
return dist;
}
double
getMaxNorm (const Params& v1, const Params& v2)
{
assert (v1.size() == v2.size());
double max = 0.0;
if (Globals::logDomain) {
max = std::inner_product (v1.begin(), v1.end(), v2.begin(), 0.0,
FuncObject::max<double>(), FuncObject::abs_diff_exp<double>());
} else {
max = std::inner_product (v1.begin(), v1.end(), v2.begin(), 0.0,
FuncObject::max<double>(), FuncObject::abs_diff<double>());
}
return max;
}
double
pow (double base, unsigned iexp)
{
return Globals::logDomain
? base * iexp
: std::pow (base, iexp);
}
double
pow (double base, double exp)
{
// `expoent' should not be in log domain
return Globals::logDomain
? base * exp
: std::pow (base, exp);
}
void
pow (Params& v, unsigned iexp)
{
if (iexp == 1) {
return;
}
Globals::logDomain ? v *= iexp : v ^= (int)iexp;
}
void
pow (Params& v, double exp)
{
// `expoent' should not be in log domain
Globals::logDomain ? v *= exp : v ^= exp;
}
}

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#ifndef HORUS_UTIL_H
#define HORUS_UTIL_H
#include <cmath>
#include <cassert>
#include <limits>
#include <algorithm>
#include <vector>
#include <set>
#include <queue>
#include <unordered_map>
#include <sstream>
#include <iostream>
#include "Horus.h"
using namespace std;
namespace {
const double NEG_INF = -numeric_limits<double>::infinity();
};
namespace Util {
template <typename T> void addToVector (vector<T>&, const vector<T>&);
template <typename T> void addToSet (set<T>&, const vector<T>&);
template <typename T> void addToQueue (queue<T>&, const vector<T>&);
template <typename T> bool contains (const vector<T>&, const T&);
template <typename T> bool contains (const set<T>&, const T&);
template <typename K, typename V> bool contains (
const unordered_map<K, V>&, const K&);
template <typename T> size_t indexOf (const vector<T>&, const T&);
template <class Operation>
void apply_n_times (Params& v1, const Params& v2, unsigned repetitions, Operation);
template <typename T> void log (vector<T>&);
template <typename T> void exp (vector<T>&);
template <typename T> string elementsToString (
const vector<T>& v, string sep = " ");
template <typename T> std::string toString (const T&);
template <> std::string toString (const bool&);
double logSum (double, double);
unsigned maxUnsigned (void);
unsigned stringToUnsigned (string);
double stringToDouble (string);
double factorial (unsigned);
double logFactorial (unsigned);
unsigned nrCombinations (unsigned, unsigned);
size_t sizeExpected (const Ranges&);
unsigned nrDigits (int);
bool isInteger (const string&);
string parametersToString (const Params&, unsigned = Constants::PRECISION);
vector<string> getStateLines (const Vars&);
bool setHorusFlag (string key, string value);
void printHeader (string, std::ostream& os = std::cout);
void printSubHeader (string, std::ostream& os = std::cout);
void printAsteriskLine (std::ostream& os = std::cout);
void printDashedLine (std::ostream& os = std::cout);
};
template <typename T> void
Util::addToVector (vector<T>& v, const vector<T>& elements)
{
v.insert (v.end(), elements.begin(), elements.end());
}
template <typename T> void
Util::addToSet (set<T>& s, const vector<T>& elements)
{
s.insert (elements.begin(), elements.end());
}
template <typename T> void
Util::addToQueue (queue<T>& q, const vector<T>& elements)
{
for (size_t i = 0; i < elements.size(); i++) {
q.push (elements[i]);
}
}
template <typename T> bool
Util::contains (const vector<T>& v, const T& e)
{
return std::find (v.begin(), v.end(), e) != v.end();
}
template <typename T> bool
Util::contains (const set<T>& s, const T& e)
{
return s.find (e) != s.end();
}
template <typename K, typename V> bool
Util::contains (const unordered_map<K, V>& m, const K& k)
{
return m.find (k) != m.end();
}
template <typename T> size_t
Util::indexOf (const vector<T>& v, const T& e)
{
return std::distance (v.begin(),
std::find (v.begin(), v.end(), e));
}
template <class Operation> void
Util::apply_n_times (Params& v1, const Params& v2, unsigned repetitions,
Operation unary_op)
{
Params::iterator first = v1.begin();
Params::const_iterator last = v1.end();
Params::const_iterator first2 = v2.begin();
Params::const_iterator last2 = v2.end();
while (first != last) {
for (first2 = v2.begin(); first2 != last2; ++first2) {
std::transform (first, first + repetitions, first,
std::bind1st (unary_op, *first2));
first += repetitions;
}
}
}
template <typename T> void
Util::log (vector<T>& v)
{
std::transform (v.begin(), v.end(), v.begin(), ::log);
}
template <typename T> void
Util::exp (vector<T>& v)
{
std::transform (v.begin(), v.end(), v.begin(), ::exp);
}
template <typename T> string
Util::elementsToString (const vector<T>& v, string sep)
{
stringstream ss;
for (size_t i = 0; i < v.size(); i++) {
ss << ((i != 0) ? sep : "") << v[i];
}
return ss.str();
}
template <typename T> std::string
Util::toString (const T& t)
{
std::stringstream ss;
ss << t;
return ss.str();
}
inline double
Util::logSum (double x, double y)
{
// std::log (std::exp (x) + std::exp (y)) can overflow!
assert (std::isnan (x) == false);
assert (std::isnan (y) == false);
if (x == NEG_INF) {
return y;
}
if (y == NEG_INF) {
return x;
}
// if one value is much smaller than the other,
// keep the larger value
const double tol = 460.517; // log (1e200)
if (x < y - tol) {
return y;
}
if (y < x - tol) {
return x;
}
assert (std::isnan (x - y) == false);
const double exp_diff = std::exp (x - y);
if (std::isfinite (exp_diff) == false) {
// difference is too large
return x > y ? x : y;
}
// otherwise return the sum
return y + std::log (static_cast<double>(1.0) + exp_diff);
}
inline unsigned
Util::maxUnsigned (void)
{
return numeric_limits<unsigned>::max();
}
namespace LogAware {
inline double one() { return Globals::logDomain ? 0.0 : 1.0; }
inline double zero() { return Globals::logDomain ? NEG_INF : 0.0; }
inline double addIdenty() { return Globals::logDomain ? NEG_INF : 0.0; }
inline double multIdenty() { return Globals::logDomain ? 0.0 : 1.0; }
inline double withEvidence() { return Globals::logDomain ? 0.0 : 1.0; }
inline double noEvidence() { return Globals::logDomain ? NEG_INF : 0.0; }
inline double log (double v) { return Globals::logDomain ? ::log (v) : v; }
inline double exp (double v) { return Globals::logDomain ? ::exp (v) : v; }
void normalize (Params&);
double getL1Distance (const Params&, const Params&);
double getMaxNorm (const Params&, const Params&);
double pow (double, unsigned);
double pow (double, double);
void pow (Params&, unsigned);
void pow (Params&, double);
};
template <typename T>
void operator+=(std::vector<T>& v, double val)
{
std::transform (v.begin(), v.end(), v.begin(),
std::bind2nd (plus<double>(), val));
}
template <typename T>
void operator-=(std::vector<T>& v, double val)
{
std::transform (v.begin(), v.end(), v.begin(),
std::bind2nd (minus<double>(), val));
}
template <typename T>
void operator*=(std::vector<T>& v, double val)
{
std::transform (v.begin(), v.end(), v.begin(),
std::bind2nd (multiplies<double>(), val));
}
template <typename T>
void operator/=(std::vector<T>& v, double val)
{
std::transform (v.begin(), v.end(), v.begin(),
std::bind2nd (divides<double>(), val));
}
template <typename T>
void operator+=(std::vector<T>& a, const std::vector<T>& b)
{
assert (a.size() == b.size());
std::transform (a.begin(), a.end(), b.begin(), a.begin(),
plus<double>());
}
template <typename T>
void operator-=(std::vector<T>& a, const std::vector<T>& b)
{
assert (a.size() == b.size());
std::transform (a.begin(), a.end(), b.begin(), a.begin(),
minus<double>());
}
template <typename T>
void operator*=(std::vector<T>& a, const std::vector<T>& b)
{
assert (a.size() == b.size());
std::transform (a.begin(), a.end(), b.begin(), a.begin(),
multiplies<double>());
}
template <typename T>
void operator/=(std::vector<T>& a, const std::vector<T>& b)
{
assert (a.size() == b.size());
std::transform (a.begin(), a.end(), b.begin(), a.begin(),
divides<double>());
}
template <typename T>
void operator^=(std::vector<T>& v, double exp)
{
std::transform (v.begin(), v.end(), v.begin(),
std::bind2nd (ptr_fun<double, double, double> (std::pow), exp));
}
template <typename T>
void operator^=(std::vector<T>& v, int iexp)
{
std::transform (v.begin(), v.end(), v.begin(),
std::bind2nd (ptr_fun<double, int, double> (std::pow), iexp));
}
template <typename T>
std::ostream& operator << (std::ostream& os, const vector<T>& v)
{
os << "[" ;
os << Util::elementsToString (v, ", ");
os << "]" ;
return os;
}
namespace FuncObject {
template<typename T>
struct max : public std::binary_function<T, T, T>
{
T operator() (const T& x, const T& y) const
{
return x < y ? y : x;
}
};
template <typename T>
struct abs_diff : public std::binary_function<T, T, T>
{
T operator() (const T& x, const T& y) const
{
return std::abs (x - y);
}
};
template <typename T>
struct abs_diff_exp : public std::binary_function<T, T, T>
{
T operator() (const T& x, const T& y) const
{
return std::abs (std::exp (x) - std::exp (y));
}
};
}
#endif // HORUS_UTIL_H

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#include <algorithm>
#include <sstream>
#include "Var.h"
using namespace std;
unordered_map<VarId, VarInfo> Var::varsInfo_;
Var::Var (const Var* v)
{
varId_ = v->varId();
range_ = v->range();
evidence_ = v->getEvidence();
index_ = std::numeric_limits<unsigned>::max();
}
Var::Var (VarId varId, unsigned range, int evidence)
{
assert (range != 0);
assert (evidence < (int) range);
varId_ = varId;
range_ = range;
evidence_ = evidence;
index_ = std::numeric_limits<unsigned>::max();
}
bool
Var::isValidState (int stateIndex)
{
return stateIndex >= 0 && stateIndex < (int) range_;
}
bool
Var::isValidState (const string& stateName)
{
States states = Var::getVarInfo (varId_).states;
return Util::contains (states, stateName);
}
void
Var::setEvidence (int ev)
{
assert (ev < (int) range_);
evidence_ = ev;
}
void
Var::setEvidence (const string& ev)
{
States states = Var::getVarInfo (varId_).states;
for (size_t i = 0; i < states.size(); i++) {
if (states[i] == ev) {
evidence_ = i;
return;
}
}
assert (false);
}
string
Var::label (void) const
{
if (Var::varsHaveInfo()) {
return Var::getVarInfo (varId_).label;
}
stringstream ss;
ss << "x" << varId_;
return ss.str();
}
States
Var::states (void) const
{
if (Var::varsHaveInfo()) {
return Var::getVarInfo (varId_).states;
}
States states;
for (unsigned i = 0; i < range_; i++) {
stringstream ss;
ss << i ;
states.push_back (ss.str());
}
return states;
}

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#ifndef HORUS_VAR_H
#define HORUS_VAR_H
#include <cassert>
#include <iostream>
#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 Var
{
public:
Var (const Var*);
Var (VarId, unsigned, int = Constants::NO_EVIDENCE);
virtual ~Var (void) { };
VarId varId (void) const { return varId_; }
unsigned range (void) const { return range_; }
int getEvidence (void) const { return evidence_; }
size_t getIndex (void) const { return index_; }
void setIndex (size_t idx) { index_ = idx; }
bool hasEvidence (void) const
{
return evidence_ != Constants::NO_EVIDENCE;
}
operator size_t (void) const { return index_; }
bool operator== (const Var& var) const
{
assert (!(varId_ == var.varId() && range_ != var.range()));
return varId_ == var.varId();
}
bool operator!= (const Var& 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;
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 getVarInfo (VarId vid)
{
assert (Util::contains (varsInfo_, vid));
return varsInfo_.find (vid)->second;
}
static bool varsHaveInfo (void)
{
return varsInfo_.size() != 0;
}
static void clearVarsInfo (void)
{
varsInfo_.clear();
}
private:
VarId varId_;
unsigned range_;
int evidence_;
size_t index_;
static unordered_map<VarId, VarInfo> varsInfo_;
};
#endif // HORUS_VAR_H

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#include <algorithm>
#include "VarElim.h"
#include "ElimGraph.h"
#include "Factor.h"
#include "Util.h"
VarElim::~VarElim (void)
{
delete factorList_.back();
}
Params
VarElim::solveQuery (VarIds queryVids)
{
if (Globals::verbosity > 1) {
cout << "Solving query on " ;
for (size_t i = 0; i < queryVids.size(); i++) {
if (i != 0) cout << ", " ;
cout << fg.getVarNode (queryVids[i])->label();
}
cout << endl;
}
factorList_.clear();
varFactors_.clear();
elimOrder_.clear();
createFactorList();
absorveEvidence();
findEliminationOrder (queryVids);
processFactorList (queryVids);
Params params = factorList_.back()->params();
if (Globals::logDomain) {
Util::exp (params);
}
return params;
}
void
VarElim::printSolverFlags (void) const
{
stringstream ss;
ss << "variable elimination [" ;
ss << "elim_heuristic=" ;
ElimHeuristic eh = ElimGraph::elimHeuristic;
switch (eh) {
case SEQUENTIAL: ss << "sequential"; break;
case MIN_NEIGHBORS: ss << "min_neighbors"; break;
case MIN_WEIGHT: ss << "min_weight"; break;
case MIN_FILL: ss << "min_fill"; break;
case WEIGHTED_MIN_FILL: ss << "weighted_min_fill"; break;
}
ss << ",log_domain=" << Util::toString (Globals::logDomain);
ss << "]" ;
cout << ss.str() << endl;
}
void
VarElim::createFactorList (void)
{
const FacNodes& facNodes = fg.facNodes();
factorList_.reserve (facNodes.size() * 2);
for (size_t i = 0; i < facNodes.size(); i++) {
factorList_.push_back (new Factor (facNodes[i]->factor()));
const VarNodes& neighs = facNodes[i]->neighbors();
for (size_t j = 0; j < neighs.size(); j++) {
unordered_map<VarId, vector<size_t>>::iterator it
= varFactors_.find (neighs[j]->varId());
if (it == varFactors_.end()) {
it = varFactors_.insert (make_pair (
neighs[j]->varId(), vector<size_t>())).first;
}
it->second.push_back (i);
}
}
}
void
VarElim::absorveEvidence (void)
{
if (Globals::verbosity > 2) {
Util::printDashedLine();
cout << "(initial factor list)" << endl;
printActiveFactors();
}
const VarNodes& varNodes = fg.varNodes();
for (size_t i = 0; i < varNodes.size(); i++) {
if (varNodes[i]->hasEvidence()) {
if (Globals::verbosity > 1) {
cout << "-> aborving evidence on ";
cout << varNodes[i]->label() << " = " ;
cout << varNodes[i]->getEvidence() << endl;
}
const vector<size_t>& idxs =
varFactors_.find (varNodes[i]->varId())->second;
for (size_t j = 0; j < idxs.size(); j++) {
Factor* factor = factorList_[idxs[j]];
if (factor->nrArguments() == 1) {
factorList_[idxs[j]] = 0;
} else {
factorList_[idxs[j]]->absorveEvidence (
varNodes[i]->varId(), varNodes[i]->getEvidence());
}
}
}
}
}
void
VarElim::findEliminationOrder (const VarIds& vids)
{
elimOrder_ = ElimGraph::getEliminationOrder (factorList_, vids);
}
void
VarElim::processFactorList (const VarIds& vids)
{
totalFactorSize_ = 0;
largestFactorSize_ = 0;
for (size_t i = 0; i < elimOrder_.size(); i++) {
if (Globals::verbosity >= 2) {
if (Globals::verbosity >= 3) {
Util::printDashedLine();
printActiveFactors();
}
cout << "-> summing out " ;
cout << fg.getVarNode (elimOrder_[i])->label() << endl;
}
eliminate (elimOrder_[i]);
}
Factor* finalFactor = new Factor();
for (size_t i = 0; i < factorList_.size(); i++) {
if (factorList_[i]) {
finalFactor->multiply (*factorList_[i]);
delete factorList_[i];
factorList_[i] = 0;
}
}
VarIds unobservedVids;
for (size_t i = 0; i < vids.size(); i++) {
if (fg.getVarNode (vids[i])->hasEvidence() == false) {
unobservedVids.push_back (vids[i]);
}
}
finalFactor->reorderArguments (unobservedVids);
finalFactor->normalize();
factorList_.push_back (finalFactor);
if (Globals::verbosity > 0) {
cout << "total factor size: " << totalFactorSize_ << endl;
cout << "largest factor size: " << largestFactorSize_ << endl;
cout << endl;
}
}
void
VarElim::eliminate (VarId elimVar)
{
Factor* result = 0;
vector<size_t>& idxs = varFactors_.find (elimVar)->second;
for (size_t i = 0; i < idxs.size(); i++) {
size_t idx = idxs[i];
if (factorList_[idx]) {
if (result == 0) {
result = new Factor (*factorList_[idx]);
} else {
result->multiply (*factorList_[idx]);
}
delete factorList_[idx];
factorList_[idx] = 0;
}
}
totalFactorSize_ += result->size();
if (result->size() > largestFactorSize_) {
largestFactorSize_ = result->size();
}
if (result != 0 && result->nrArguments() != 1) {
result->sumOut (elimVar);
factorList_.push_back (result);
const VarIds& resultVarIds = result->arguments();
for (size_t i = 0; i < resultVarIds.size(); i++) {
vector<size_t>& idxs =
varFactors_.find (resultVarIds[i])->second;
idxs.push_back (factorList_.size() - 1);
}
}
}
void
VarElim::printActiveFactors (void)
{
for (size_t i = 0; i < factorList_.size(); i++) {
if (factorList_[i] != 0) {
cout << factorList_[i]->getLabel() << " " ;
cout << factorList_[i]->params() << endl;
}
}
}

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#ifndef HORUS_VARELIM_H
#define HORUS_VARELIM_H
#include "unordered_map"
#include "GroundSolver.h"
#include "FactorGraph.h"
#include "Horus.h"
using namespace std;
class VarElim : public GroundSolver
{
public:
VarElim (const FactorGraph& fg) : GroundSolver (fg) { }
~VarElim (void);
Params solveQuery (VarIds);
void printSolverFlags (void) const;
private:
void createFactorList (void);
void absorveEvidence (void);
void findEliminationOrder (const VarIds&);
void processFactorList (const VarIds&);
void eliminate (VarId);
void printActiveFactors (void);
Factors factorList_;
VarIds elimOrder_;
unsigned largestFactorSize_;
unsigned totalFactorSize_;
unordered_map<VarId, vector<size_t>> varFactors_;
};
#endif // HORUS_VARELIM_H

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#include "WeightedBp.h"
WeightedBp::~WeightedBp (void)
{
for (size_t i = 0; i < links_.size(); i++) {
delete links_[i];
}
links_.clear();
}
Params
WeightedBp::getPosterioriOf (VarId vid)
{
if (runned_ == false) {
runSolver();
}
VarNode* var = fg.getVarNode (vid);
assert (var != 0);
Params probs;
if (var->hasEvidence()) {
probs.resize (var->range(), LogAware::noEvidence());
probs[var->getEvidence()] = LogAware::withEvidence();
} else {
probs.resize (var->range(), LogAware::multIdenty());
const BpLinks& links = ninf(var)->getLinks();
if (Globals::logDomain) {
for (size_t i = 0; i < links.size(); i++) {
WeightedLink* l = static_cast<WeightedLink*> (links[i]);
probs += l->powMessage();
}
LogAware::normalize (probs);
Util::exp (probs);
} else {
for (size_t i = 0; i < links.size(); i++) {
WeightedLink* l = static_cast<WeightedLink*> (links[i]);
probs *= l->powMessage();
}
LogAware::normalize (probs);
}
}
return probs;
}
void
WeightedBp::createLinks (void)
{
if (Globals::verbosity > 0) {
cout << "compressed factor graph contains " ;
cout << fg.nrVarNodes() << " variables and " ;
cout << fg.nrFacNodes() << " factors " << endl;
cout << endl;
}
const FacNodes& facNodes = fg.facNodes();
for (size_t i = 0; i < facNodes.size(); i++) {
const VarNodes& neighs = facNodes[i]->neighbors();
for (size_t j = 0; j < neighs.size(); j++) {
if (Globals::verbosity > 1) {
cout << "creating link " ;
cout << facNodes[i]->getLabel();
cout << " -- " ;
cout << neighs[j]->label();
cout << " idx=" << j << ", weight=" << weights_[i][j] << endl;
}
links_.push_back (new WeightedLink (
facNodes[i], neighs[j], j, weights_[i][j]));
}
}
if (Globals::verbosity > 1) {
cout << endl;
}
}
void
WeightedBp::maxResidualSchedule (void)
{
if (nIters_ == 1) {
for (size_t i = 0; i < links_.size(); i++) {
calculateMessage (links_[i]);
SortedOrder::iterator it = sortedOrder_.insert (links_[i]);
linkMap_.insert (make_pair (links_[i], it));
if (Globals::verbosity >= 1) {
cout << "calculating " << links_[i]->toString() << endl;
}
}
return;
}
for (size_t c = 0; c < links_.size(); c++) {
if (Globals::verbosity > 1) {
cout << endl << "current residuals:" << endl;
for (SortedOrder::iterator it = sortedOrder_.begin();
it != sortedOrder_.end(); ++it) {
cout << " " << setw (30) << left << (*it)->toString();
cout << "residual = " << (*it)->residual() << endl;
}
}
SortedOrder::iterator it = sortedOrder_.begin();
BpLink* link = *it;
if (Globals::verbosity >= 1) {
cout << "updating " << (*sortedOrder_.begin())->toString() << endl;
}
if (link->residual() < BpOptions::accuracy) {
return;
}
link->updateMessage();
link->clearResidual();
sortedOrder_.erase (it);
linkMap_.find (link)->second = sortedOrder_.insert (link);
// update the messages that depend on message source --> destin
const FacNodes& factorNeighbors = link->varNode()->neighbors();
for (size_t i = 0; i < factorNeighbors.size(); i++) {
const BpLinks& links = ninf(factorNeighbors[i])->getLinks();
for (size_t j = 0; j < links.size(); j++) {
if (links[j]->varNode() != link->varNode()) {
if (Globals::verbosity > 1) {
cout << " calculating " << links[j]->toString() << endl;
}
calculateMessage (links[j]);
BpLinkMap::iterator iter = linkMap_.find (links[j]);
sortedOrder_.erase (iter->second);
iter->second = sortedOrder_.insert (links[j]);
}
}
}
// in counting bp, the message that a variable X sends to
// to a factor F depends on the message that F sent to the X
const BpLinks& links = ninf(link->facNode())->getLinks();
for (size_t i = 0; i < links.size(); i++) {
if (links[i]->varNode() != link->varNode()) {
if (Globals::verbosity > 1) {
cout << " calculating " << links[i]->toString() << endl;
}
calculateMessage (links[i]);
BpLinkMap::iterator iter = linkMap_.find (links[i]);
sortedOrder_.erase (iter->second);
iter->second = sortedOrder_.insert (links[i]);
}
}
}
}
void
WeightedBp::calcFactorToVarMsg (BpLink* _link)
{
WeightedLink* link = static_cast<WeightedLink*> (_link);
FacNode* src = link->facNode();
const VarNode* dst = link->varNode();
const BpLinks& links = ninf(src)->getLinks();
// calculate the product of messages that were sent
// to factor `src', except from var `dst'
unsigned reps = 1;
unsigned msgSize = Util::sizeExpected (src->factor().ranges());
Params msgProduct (msgSize, LogAware::multIdenty());
if (Globals::logDomain) {
for (size_t i = links.size(); i-- > 0; ) {
const WeightedLink* l = static_cast<const WeightedLink*> (links[i]);
if ( ! (l->varNode() == dst && l->index() == link->index())) {
if (Constants::SHOW_BP_CALCS) {
cout << " message from " << links[i]->varNode()->label();
cout << ": " ;
}
Util::apply_n_times (msgProduct, getVarToFactorMsg (links[i]),
reps, std::plus<double>());
if (Constants::SHOW_BP_CALCS) {
cout << endl;
}
}
reps *= links[i]->varNode()->range();
}
} else {
for (size_t i = links.size(); i-- > 0; ) {
const WeightedLink* l = static_cast<const WeightedLink*> (links[i]);
if ( ! (l->varNode() == dst && l->index() == link->index())) {
if (Constants::SHOW_BP_CALCS) {
cout << " message from " << links[i]->varNode()->label();
cout << ": " ;
}
Util::apply_n_times (msgProduct, getVarToFactorMsg (links[i]),
reps, std::multiplies<double>());
if (Constants::SHOW_BP_CALCS) {
cout << endl;
}
}
reps *= links[i]->varNode()->range();
}
}
Factor result (src->factor().arguments(),
src->factor().ranges(), msgProduct);
assert (msgProduct.size() == src->factor().size());
if (Globals::logDomain) {
result.params() += src->factor().params();
} else {
result.params() *= src->factor().params();
}
if (Constants::SHOW_BP_CALCS) {
cout << " message product: " << msgProduct << endl;
cout << " original factor: " << src->factor().params() << endl;
cout << " factor product: " << result.params() << endl;
}
result.sumOutAllExceptIndex (link->index());
if (Constants::SHOW_BP_CALCS) {
cout << " marginalized: " << result.params() << endl;
}
link->nextMessage() = result.params();
LogAware::normalize (link->nextMessage());
if (Constants::SHOW_BP_CALCS) {
cout << " curr msg: " << link->message() << endl;
cout << " next msg: " << link->nextMessage() << endl;
}
}
Params
WeightedBp::getVarToFactorMsg (const BpLink* _link) const
{
const WeightedLink* link = static_cast<const WeightedLink*> (_link);
const VarNode* src = link->varNode();
const FacNode* dst = link->facNode();
Params msg;
if (src->hasEvidence()) {
msg.resize (src->range(), LogAware::noEvidence());
double value = link->message()[src->getEvidence()];
if (Constants::SHOW_BP_CALCS) {
msg[src->getEvidence()] = value;
cout << msg << "^" << link->weight() << "-1" ;
}
msg[src->getEvidence()] = LogAware::pow (value, link->weight() - 1);
} else {
msg = link->message();
if (Constants::SHOW_BP_CALCS) {
cout << msg << "^" << link->weight() << "-1" ;
}
LogAware::pow (msg, link->weight() - 1);
}
const BpLinks& links = ninf(src)->getLinks();
if (Globals::logDomain) {
for (size_t i = 0; i < links.size(); i++) {
WeightedLink* l = static_cast<WeightedLink*> (links[i]);
if ( ! (l->facNode() == dst && l->index() == link->index())) {
msg += l->powMessage();
}
}
} else {
for (size_t i = 0; i < links.size(); i++) {
WeightedLink* l = static_cast<WeightedLink*> (links[i]);
if ( ! (l->facNode() == dst && l->index() == link->index())) {
msg *= l->powMessage();
if (Constants::SHOW_BP_CALCS) {
cout << " x " << l->nextMessage() << "^" << link->weight();
}
}
}
}
if (Constants::SHOW_BP_CALCS) {
cout << " = " << msg;
}
return msg;
}
void
WeightedBp::printLinkInformation (void) const
{
for (size_t i = 0; i < links_.size(); i++) {
WeightedLink* l = static_cast<WeightedLink*> (links_[i]);
cout << l->toString() << ":" << endl;
cout << " curr msg = " << l->message() << endl;
cout << " next msg = " << l->nextMessage() << endl;
cout << " pow msg = " << l->powMessage() << endl;
cout << " index = " << l->index() << endl;
cout << " weight = " << l->weight() << endl;
cout << " residual = " << l->residual() << endl;
}
}

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packages/CLPBN/horus2/WeightedBp.h
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@ -1,61 +0,0 @@
#ifndef HORUS_WEIGHTEDBP_H
#define HORUS_WEIGHTEDBP_H
#include "BeliefProp.h"
class WeightedLink : public BpLink
{
public:
WeightedLink (FacNode* fn, VarNode* vn, size_t idx, unsigned weight)
: BpLink (fn, vn), index_(idx), weight_(weight),
pwdMsg_(vn->range(), LogAware::one()) { }
size_t index (void) const { return index_; }
unsigned weight (void) const { return weight_; }
const Params& powMessage (void) const { return pwdMsg_; }
void updateMessage (void)
{
pwdMsg_ = *nextMsg_;
swap (currMsg_, nextMsg_);
LogAware::pow (pwdMsg_, weight_);
}
private:
size_t index_;
unsigned weight_;
Params pwdMsg_;
};
class WeightedBp : public BeliefProp
{
public:
WeightedBp (const FactorGraph& fg,
const vector<vector<unsigned>>& weights)
: BeliefProp (fg), weights_(weights) { }
~WeightedBp (void);
Params getPosterioriOf (VarId);
private:
void createLinks (void);
void maxResidualSchedule (void);
void calcFactorToVarMsg (BpLink*);
Params getVarToFactorMsg (const BpLink*) const;
void printLinkInformation (void) const;
vector<vector<unsigned>> weights_;
};
#endif // HORUS_WEIGHTEDBP_H