Factor LC::NewPancake (size_t i, size_t _I, bool & hasNaNs) {
size_t I = nbV(i)[_I];
Factor piet = _pancakes[i];
// recalculate _pancake[i]
VarSet Ivars = factor(I).vars();
Factor A_I;
for( VarSet::const_iterator k = Ivars.begin(); k != Ivars.end(); k++ )
if( var(i) != *k )
A_I *= (_pancakes[findVar(*k)] * factor(I).inverse()).marginal( Ivars / var(i), false );
if( Ivars.size() > 1 )
A_I ^= (1.0 / (Ivars.size() - 1));
Factor A_Ii = (_pancakes[i] * factor(I).inverse() * _phis[i][_I].inverse()).marginal( Ivars / var(i), false );
Factor quot = A_I / A_Ii;
if( props.damping != 0.0 )
quot = (quot^(1.0 - props.damping)) * (_phis[i][_I]^props.damping);
piet *= quot / _phis[i][_I].normalized();
_phis[i][_I] = quot.normalized();
piet.normalize();
if( piet.hasNaNs() ) {
cerr << name() << "::NewPancake(" << i << ", " << _I << "): has NaNs!" << endl;
hasNaNs = true;
}
return piet;
}
Factor LC::belief (const VarSet &ns) const {
if( ns.size() == 0 )
return Factor();
else if( ns.size() == 1 )
return beliefV( findVar( *(ns.begin()) ) );
else {
DAI_THROW(BELIEF_NOT_AVAILABLE);
return Factor();
}
}
Factor ExactInf::belief( const VarSet &ns ) const {
if( ns.size() == 0 )
return Factor();
else if( ns.size() == 1 ) {
return beliefV( findVar( *(ns.begin()) ) );
} else {
size_t I;
for( I = 0; I < nrFactors(); I++ )
if( factor(I).vars() >> ns )
break;
if( I == nrFactors() )
DAI_THROW(BELIEF_NOT_AVAILABLE);
return beliefF(I).marginal(ns);
}
}
/** \param N number of variables
* \param M number of factors
* \param k number of variables that each factor depends on
* \param beta standard-deviation of Gaussian log-factor entries
*/
FactorGraph createHOIFG( size_t N, size_t M, size_t k, Real beta ) {
vector<Var> vars;
vector<Factor> factors;
vars.reserve(N);
for( size_t i = 0; i < N; i++ )
vars.push_back(Var(i,2));
for( size_t I = 0; I < M; I++ ) {
VarSet vars;
while( vars.size() < k ) {
do {
size_t newind = (size_t)(N * rnd_uniform());
Var newvar = Var(newind, 2);
if( !vars.contains( newvar ) ) {
vars |= newvar;
break;
}
} while( 1 );
}
factors.push_back( createFactorExpGauss( vars, beta ) );
}
return FactorGraph( factors.begin(), factors.end(), vars.begin(), vars.end(), factors.size(), vars.size() );
}
void MakeHOIFG( size_t N, size_t M, size_t k, Real sigma, FactorGraph &fg ) {
vector<Var> vars;
vector<Factor> factors;
vars.reserve(N);
for( size_t i = 0; i < N; i++ )
vars.push_back(Var(i,2));
for( size_t I = 0; I < M; I++ ) {
VarSet vars;
while( vars.size() < k ) {
do {
size_t newind = (size_t)(N * rnd_uniform());
Var newvar = Var(newind, 2);
if( !vars.contains( newvar ) ) {
vars |= newvar;
break;
}
} while( 1 );
}
factors.push_back( RandomFactor( vars, sigma ) );
}
fg = FactorGraph( factors.begin(), factors.end(), vars.begin(), vars.end(), factors.size(), vars.size() );
}
void findLoopClusters( const FactorGraph & fg, std::set<VarSet> &allcl, VarSet newcl, const Var & root, size_t length, VarSet vars ) {
for( VarSet::const_iterator in = vars.begin(); in != vars.end(); in++ ) {
VarSet ind = fg.delta( *in );
if( (newcl.size()) >= 2 && ind.contains( root ) ) {
allcl.insert( newcl | *in );
}
else if( length > 1 )
findLoopClusters( fg, allcl, newcl | *in, root, length - 1, ind / newcl );
}
}
/* Convert cell vector of Matlab sets to vector<VarSet> */
vector<VarSet> mx2VarSets(const mxArray *vs, const FactorGraph &fg, long verbose, vector<Permute> &perms) {
vector<VarSet> varsets;
int n1 = mxGetM(vs);
int n2 = mxGetN(vs);
if( n2 != 1 && n1 != 1 )
mexErrMsgTxt("varsets should be a Nx1 or 1xN cell matrix.");
size_t nr_vs = n1;
if( n1 == 1 )
nr_vs = n2;
// interpret vs, linear cell array of varsets
varsets.reserve( nr_vs );
perms.clear();
perms.reserve( nr_vs );
for( size_t cellind = 0; cellind < nr_vs; cellind++ ) {
if( verbose >= 3 )
cerr << "reading varset " << cellind << ": " << endl;
mxArray *cell = mxGetCell(vs, cellind);
if( verbose >= 3 )
cerr << " got cell " << endl;
size_t nr_mem = mxGetN(cell);
if( verbose >= 3 )
cerr << " number members: " << nr_mem << endl;
double *members = mxGetPr(cell);
if( verbose >= 3 )
cerr << " got them! " << endl;
// add variables
VarSet vsvars;
if( verbose >= 3 )
cerr << " vars: ";
vector<long> labels(nr_mem,0);
vector<size_t> dims(nr_mem,0);
for( size_t mi = 0; mi < nr_mem; mi++ ) {
labels[mi] = (long)members[mi];
dims[mi] = fg.var(labels[mi]).states();
if( verbose >= 3 )
cerr << labels[mi] << " ";
vsvars.insert( fg.var(labels[mi]) );
}
if( verbose >= 3 )
cerr << endl;
DAI_ASSERT( nr_mem == vsvars.size() );
varsets.push_back(vsvars);
// calculate permutation matrix
vector<size_t> perm(nr_mem,0);
VarSet::iterator j = vsvars.begin();
for( size_t mi = 0; mi < nr_mem; mi++,j++ ) {
long gezocht = j->label();
vector<long>::iterator piet = find(labels.begin(),labels.end(),gezocht);
perm[mi] = piet - labels.begin();
}
if( verbose >= 3 ) {
cerr << endl << " perm: ";
for( vector<size_t>::iterator r=perm.begin(); r!=perm.end(); r++ )
cerr << *r << " ";
cerr << endl;
}
// create Permute object
vector<size_t> di(nr_mem,0);
size_t prod = 1;
for( size_t k = 0; k < nr_mem; k++ ) {
di[k] = dims[k];
prod *= dims[k];
}
Permute permindex( di, perm );
perms.push_back( permindex );
}
if( verbose >= 3 ) {
for(vector<VarSet>::const_iterator I=varsets.begin(); I!=varsets.end(); I++ )
cerr << *I << endl;
}
return( varsets );
}
void RegionGraph::constructCVM( const FactorGraph &fg, const std::vector<VarSet> &cl, size_t verbose ) {
if( verbose )
cerr << "constructCVM called (" << fg.nrVars() << " vars, " << fg.nrFactors() << " facs, " << cl.size() << " clusters)" << endl;
// Retain only maximal clusters
if( verbose )
cerr << " Constructing ClusterGraph" << endl;
ClusterGraph cg( cl );
if( verbose )
cerr << " Erasing non-maximal clusters" << endl;
cg.eraseNonMaximal();
// Create inner regions - first pass
if( verbose )
cerr << " Creating inner regions (first pass)" << endl;
set<VarSet> betas;
for( size_t alpha = 0; alpha < cg.nrClusters(); alpha++ )
for( size_t alpha2 = alpha; (++alpha2) != cg.nrClusters(); ) {
VarSet intersection = cg.cluster(alpha) & cg.cluster(alpha2);
if( intersection.size() > 0 )
betas.insert( intersection );
}
// Create inner regions - subsequent passes
if( verbose )
cerr << " Creating inner regions (next passes)" << endl;
set<VarSet> new_betas;
do {
new_betas.clear();
for( set<VarSet>::const_iterator gamma = betas.begin(); gamma != betas.end(); gamma++ )
for( set<VarSet>::const_iterator gamma2 = gamma; (++gamma2) != betas.end(); ) {
VarSet intersection = (*gamma) & (*gamma2);
if( (intersection.size() > 0) && (betas.count(intersection) == 0) )
new_betas.insert( intersection );
}
betas.insert(new_betas.begin(), new_betas.end());
} while( new_betas.size() );
// Create inner regions - final phase
if( verbose )
cerr << " Creating inner regions (final phase)" << endl;
vector<Region> irs;
irs.reserve( betas.size() );
for( set<VarSet>::const_iterator beta = betas.begin(); beta != betas.end(); beta++ )
irs.push_back( Region(*beta,0.0) );
// Create edges
if( verbose )
cerr << " Creating edges" << endl;
vector<pair<size_t,size_t> > edges;
for( size_t beta = 0; beta < irs.size(); beta++ )
for( size_t alpha = 0; alpha < cg.nrClusters(); alpha++ )
if( cg.cluster(alpha) >> irs[beta] )
edges.push_back( pair<size_t,size_t>(alpha,beta) );
// Construct region graph
if( verbose )
cerr << " Constructing region graph" << endl;
construct( fg, cg.clusters(), irs, edges );
// Calculate counting numbers
if( verbose )
cerr << " Calculating counting numbers" << endl;
calcCVMCountingNumbers();
if( verbose )
cerr << "Done." << endl;
}
void CobwebGraph::setCountingNumbers( bool debugging ) {
// should handle the case when one region in the msg-region graph is subset of another or even to top regions are the same
_cn.reserve( nrCWs() );
for( size_t R = 0; R < _INRs.size(); R++ ) {
vector<VarSet> topR;
// finding the intersection of messages
SmallSet<VarSet> betas;
for( size_t m1 = 0; m1 < M(R).size(); m1++ ) {
topR.push_back( M(R,m1).msg.vars() );
for( size_t m2 = 0; m2 < M(R).size(); m2++ ) {
if( m1 == m2 )
continue;
VarSet b = M(R,m1).msg.vars() & M(R,m2).msg.vars();
if( b.size() == 0 )
continue;
betas.insert( b );
}
}
if( debugging )
cerr << "topR: " << topR << endl;
// finding the intersections of intersections
bool somechange = true;
while( somechange ) {
SmallSet<VarSet> newbetas;
somechange = false;
bforeach( const VarSet &b1, betas ) {
bforeach( const VarSet &b2, betas ) {
if( b1 == b2 )
continue;
VarSet b3 = b1 & b2;
if( betas.contains(b3) || b3.size() == 0 )
continue;
newbetas |= b3;
somechange = true;
}
}
betas |= newbetas;
}
if( debugging )
cerr << "betas: " << betas << endl;
// set the counting number
_cn.push_back( map<VarSet, pair<int, vector<size_t> > >() );
// adding sub-regions of every message
for( size_t i = 0; i < topR.size(); i++ ) {
M(R,i).subregions.clear();
bforeach( const VarSet& b, betas )
if( b << topR[i] )
M(R,i).subregions.push_back( b );
}
SmallSet<VarSet> subVisited;
SmallSet<VarSet> topRSet( topR.begin(), topR.end(), topR.size() );
// looks to see if all parents of a sub-region got their counting number
while( !betas.empty() ) {
bforeach( const VarSet &beta, betas ) {
bool allparentsset = true;
bforeach( const VarSet &beta2, betas )
if( beta2 >> beta && beta2 != beta ) {
allparentsset = false;
break;
}
if( allparentsset ) {
// the first in the pair is cn and the second the index of top regions containing it
_cn[R][beta] = make_pair( 1, vector<size_t>() );
for( size_t TR = 0; TR < topR.size(); TR++ ) {
if( topR[TR] >> beta ) {
_cn[R][beta].first--;
_cn[R][beta].second.push_back( TR );
}
}
bforeach( const VarSet& possibleparent, subVisited )
if( possibleparent >> beta )
_cn[R][beta].first -= _cn[R][possibleparent].first;
if( debugging )
cerr << "cn[" << R << "][" << beta << "] <- " << _cn[R][beta] << endl;
subVisited.insert( beta );
betas /= beta;
break; // since betas has changed we need to enter the loop again
}
}
}
int main( int argc, char *argv[] ) {
if( argc != 3 ) {
cout << "Usage: " << argv[0] << " <in.fg> <tw>" << endl << endl;
cout << "Reports some characteristics of the .fg network." << endl;
cout << "Also calculates treewidth (which may take some time) unless <tw> == 0." << endl;
return 1;
} else {
// Read factorgraph
FactorGraph fg;
char *infile = argv[1];
int calc_tw = atoi(argv[2]);
fg.ReadFromFile( infile );
cout << "Number of variables: " << fg.nrVars() << endl;
cout << "Number of factors: " << fg.nrFactors() << endl;
cout << "Connected: " << fg.isConnected() << endl;
cout << "Tree: " << fg.isTree() << endl;
cout << "Has short loops: " << hasShortLoops(fg.factors()) << endl;
cout << "Has negatives: " << hasNegatives(fg.factors()) << endl;
cout << "Binary variables? " << fg.isBinary() << endl;
cout << "Pairwise interactions? " << fg.isPairwise() << endl;
if( calc_tw ) {
std::pair<size_t,size_t> tw = treewidth(fg);
cout << "Treewidth: " << tw.first << endl;
cout << "Largest cluster for JTree has " << tw.second << " states " << endl;
}
double stsp = 1.0;
for( size_t i = 0; i < fg.nrVars(); i++ )
stsp *= fg.var(i).states();
cout << "Total state space: " << stsp << endl;
double cavsum_lcbp = 0.0;
double cavsum_lcbp2 = 0.0;
size_t max_Delta_size = 0;
map<size_t,size_t> cavsizes;
for( size_t i = 0; i < fg.nrVars(); i++ ) {
VarSet di = fg.delta(i);
if( cavsizes.count(di.size()) )
cavsizes[di.size()]++;
else
cavsizes[di.size()] = 1;
size_t Ds = fg.Delta(i).nrStates();
if( Ds > max_Delta_size )
max_Delta_size = Ds;
cavsum_lcbp += di.nrStates();
for( VarSet::const_iterator j = di.begin(); j != di.end(); j++ )
cavsum_lcbp2 += j->states();
}
cout << "Maximum pancake has " << max_Delta_size << " states" << endl;
cout << "LCBP with full cavities needs " << cavsum_lcbp << " BP runs" << endl;
cout << "LCBP with only pairinteractions needs " << cavsum_lcbp2 << " BP runs" << endl;
cout << "Cavity sizes: ";
for( map<size_t,size_t>::const_iterator it = cavsizes.begin(); it != cavsizes.end(); it++ )
cout << it->first << "(" << it->second << ") ";
cout << endl;
cout << "Type: " << (fg.isPairwise() ? "pairwise" : "higher order") << " interactions, " << (fg.isBinary() ? "binary" : "nonbinary") << " variables" << endl;
if( fg.isPairwise() ) {
bool girth_reached = false;
size_t loopdepth;
for( loopdepth = 2; loopdepth <= fg.nrVars() && !girth_reached; loopdepth++ ) {
size_t nr_loops = countLoops( fg, loopdepth );
cout << "Loops up to " << loopdepth << " variables: " << nr_loops << endl;
if( nr_loops > 0 )
girth_reached = true;
}
if( girth_reached )
cout << "Girth: " << loopdepth-1 << endl;
else
cout << "Girth: infinity" << endl;
}
return 0;
}
}