TreeEP::TreeEP( const FactorGraph &fg, const PropertySet &opts ) : JTree(fg, opts("updates",string("HUGIN")), false), _maxdiff(0.0), _iters(0), props(), _Q() {
setProperties( opts );
if( opts.hasKey("tree") ) {
construct( fg, opts.getAs<RootedTree>("tree") );
} else {
if( props.type == Properties::TypeType::ORG || props.type == Properties::TypeType::ALT ) {
// ORG: construct weighted graph with as weights a crude estimate of the
// mutual information between the nodes
// ALT: construct weighted graph with as weights an upper bound on the
// effective interaction strength between pairs of nodes
WeightedGraph<Real> wg;
// in order to get a connected weighted graph, we start
// by connecting every variable to the zero'th variable with weight 0
for( size_t i = 1; i < fg.nrVars(); i++ )
wg[UEdge(i,0)] = 0.0;
for( size_t i = 0; i < fg.nrVars(); i++ ) {
SmallSet<size_t> delta_i = fg.bipGraph().delta1( i, false );
const Var& v_i = fg.var(i);
foreach( size_t j, delta_i )
if( i < j ) {
const Var& v_j = fg.var(j);
VarSet v_ij( v_i, v_j );
SmallSet<size_t> nb_ij = fg.bipGraph().nb1Set( i ) | fg.bipGraph().nb1Set( j );
Factor piet;
foreach( size_t I, nb_ij ) {
const VarSet& Ivars = fg.factor(I).vars();
if( props.type == Properties::TypeType::ORG ) {
if( (Ivars == v_i) || (Ivars == v_j) )
piet *= fg.factor(I);
else if( Ivars >> v_ij )
piet *= fg.factor(I).marginal( v_ij );
} else {
if( Ivars >> v_ij )
piet *= fg.factor(I);
}
}
if( props.type == Properties::TypeType::ORG ) {
if( piet.vars() >> v_ij ) {
piet = piet.marginal( v_ij );
Factor pietf = piet.marginal(v_i) * piet.marginal(v_j);
wg[UEdge(i,j)] = dist( piet, pietf, DISTKL );
} else {
// this should never happen...
DAI_ASSERT( 0 == 1 );
wg[UEdge(i,j)] = 0;
}
} else
wg[UEdge(i,j)] = piet.strength(v_i, v_j);
}
SharedParameters::SharedParameters( std::istream &is, const FactorGraph &fg )
: _varsets(), _perms(), _varorders(), _estimation(NULL), _ownEstimation(true)
{
// Read the desired parameter estimation method from the stream
std::string est_method;
PropertySet props;
is >> est_method;
is >> props;
// Construct a corresponding object
_estimation = ParameterEstimation::construct( est_method, props );
// Read in the factors that are to be estimated
size_t num_factors;
is >> num_factors;
for( size_t sp_i = 0; sp_i < num_factors; ++sp_i ) {
std::string line;
while( line.size() == 0 && getline(is, line) )
;
std::vector<std::string> fields;
tokenizeString(line, fields, " \t");
// Lookup the factor in the factorgraph
if( fields.size() < 1 )
DAI_THROWE(INVALID_EMALG_FILE,"Empty line unexpected");
std::istringstream iss;
iss.str( fields[0] );
size_t factor;
iss >> factor;
const VarSet &vs = fg.factor(factor).vars();
if( fields.size() != vs.size() + 1 )
DAI_THROWE(INVALID_EMALG_FILE,"Number of fields does not match factor size");
// Construct the vector of Vars
std::vector<Var> var_order;
var_order.reserve( vs.size() );
for( size_t fi = 1; fi < fields.size(); ++fi ) {
// Lookup a single variable by label
size_t label;
std::istringstream labelparse( fields[fi] );
labelparse >> label;
VarSet::const_iterator vsi = vs.begin();
for( ; vsi != vs.end(); ++vsi )
if( vsi->label() == label )
break;
if( vsi == vs.end() )
DAI_THROWE(INVALID_EMALG_FILE,"Specified variables do not match the factor variables");
var_order.push_back( *vsi );
}
_varorders[factor] = var_order;
}
// Calculate the necessary permutations
setPermsAndVarSetsFromVarOrders();
}
void mexFunction( int nlhs, mxArray *plhs[], int nrhs, const mxArray*prhs[] ) {
char *filename;
// Check for proper number of arguments
if ((nrhs != NR_IN) || (nlhs != NR_OUT)) {
mexErrMsgTxt("Usage: [psi] = dai_readfg(filename);\n\n"
"\n"
"INPUT: filename = filename of a .fg file\n"
"\n"
"OUTPUT: psi = linear cell array containing the factors\n"
" (psi{i} is a structure with a Member field\n"
" and a P field, like a CPTAB).\n");
}
// Get input parameters
size_t buflen;
buflen = mxGetN( FILENAME_IN ) + 1;
filename = (char *)mxCalloc( buflen, sizeof(char) );
mxGetString( FILENAME_IN, filename, buflen );
// Read factorgraph
FactorGraph fg;
try {
fg.ReadFromFile( filename );
} catch( std::exception &e ) {
mexErrMsgTxt( e.what() );
}
// Save factors
vector<Factor> psi;
for( size_t I = 0; I < fg.nrFactors(); I++ )
psi.push_back(fg.factor(I));
// Hand over results to MATLAB
PSI_OUT = Factors2mx(psi);
return;
}