1 /* Copyright (C) 2006-2008 Joris Mooij [j dot mooij at science dot ru dot nl]
2 Radboud University Nijmegen, The Netherlands
4 This file is part of libDAI.
6 libDAI is free software; you can redistribute it and/or modify
7 it under the terms of the GNU General Public License as published by
8 the Free Software Foundation; either version 2 of the License, or
9 (at your option) any later version.
11 libDAI is distributed in the hope that it will be useful,
12 but WITHOUT ANY WARRANTY; without even the implied warranty of
13 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
14 GNU General Public License for more details.
16 You should have received a copy of the GNU General Public License
17 along with libDAI; if not, write to the Free Software
18 Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
30 #include <tr1/unordered_map>
31 #include <dai/factorgraph.h>
41 FactorGraph::FactorGraph( const vector
<Factor
> &P
) : G(), _undoProbs(), _normtype(Prob::NORMPROB
) {
42 // add factors, obtain variables
44 factors
.reserve( P
.size() );
46 for( vector
<Factor
>::const_iterator p2
= P
.begin(); p2
!= P
.end(); p2
++ ) {
47 factors
.push_back( *p2
);
48 copy( p2
->vars().begin(), p2
->vars().end(), inserter( _vars
, _vars
.begin() ) );
49 nrEdges
+= p2
->vars().size();
53 vars
.reserve( _vars
.size() );
54 for( set
<Var
>::const_iterator p1
= _vars
.begin(); p1
!= _vars
.end(); p1
++ )
55 vars
.push_back( *p1
);
57 // create graph structure
58 createGraph( nrEdges
);
62 /// Part of constructors (creates edges, neighbours and adjacency matrix)
63 void FactorGraph::createGraph( size_t nrEdges
) {
64 // create a mapping for indices
65 std::tr1::unordered_map
<size_t, size_t> hashmap
;
67 for( size_t i
= 0; i
< vars
.size(); i
++ )
68 hashmap
[var(i
).label()] = i
;
71 typedef pair
<unsigned,unsigned> Edge
;
73 edges
.reserve( nrEdges
);
74 for( size_t i2
= 0; i2
< nrFactors(); i2
++ ) {
75 const VarSet
& ns
= factor(i2
).vars();
76 for( VarSet::const_iterator q
= ns
.begin(); q
!= ns
.end(); q
++ )
77 edges
.push_back( Edge(hashmap
[q
->label()], i2
) );
80 // create bipartite graph
81 G
.create( nrVars(), nrFactors(), edges
.begin(), edges
.end() );
85 ostream
& operator << (ostream
& os
, const FactorGraph
& fg
) {
86 os
<< fg
.nrFactors() << endl
;
88 for( size_t I
= 0; I
< fg
.nrFactors(); I
++ ) {
90 os
<< fg
.factor(I
).vars().size() << endl
;
91 for( VarSet::const_iterator i
= fg
.factor(I
).vars().begin(); i
!= fg
.factor(I
).vars().end(); i
++ )
92 os
<< i
->label() << " ";
94 for( VarSet::const_iterator i
= fg
.factor(I
).vars().begin(); i
!= fg
.factor(I
).vars().end(); i
++ )
95 os
<< i
->states() << " ";
97 size_t nr_nonzeros
= 0;
98 for( size_t k
= 0; k
< fg
.factor(I
).stateSpace(); k
++ )
99 if( fg
.factor(I
)[k
] != 0.0 )
101 os
<< nr_nonzeros
<< endl
;
102 for( size_t k
= 0; k
< fg
.factor(I
).stateSpace(); k
++ )
103 if( fg
.factor(I
)[k
] != 0.0 ) {
105 sprintf(buf
,"%18.14g", fg
.factor(I
)[k
]);
106 os
<< k
<< " " << buf
<< endl
;
114 istream
& operator >> (istream
& is
, FactorGraph
& fg
) {
118 vector
<Factor
> factors
;
122 while( (is
.peek()) == '#' )
126 throw "ReadFromFile: unable to read number of Factors";
128 cout
<< "Reading " << nr_f
<< " factors..." << endl
;
132 throw "ReadFromFile: empty line expected";
134 for( size_t I
= 0; I
< nr_f
; I
++ ) {
136 cout
<< "Reading factor " << I
<< "..." << endl
;
138 while( (is
.peek()) == '#' )
142 cout
<< " nr_members: " << nr_members
<< endl
;
145 for( size_t mi
= 0; mi
< nr_members
; mi
++ ) {
147 while( (is
.peek()) == '#' )
150 labels
.push_back(mi_label
);
154 copy (labels
.begin(), labels
.end(), ostream_iterator
<int>(cout
, " "));
159 for( size_t mi
= 0; mi
< nr_members
; mi
++ ) {
161 while( (is
.peek()) == '#' )
164 dims
.push_back(mi_dim
);
167 cout
<< " dimensions: ";
168 copy (dims
.begin(), dims
.end(), ostream_iterator
<int>(cout
, " "));
174 for( size_t mi
= 0; mi
< nr_members
; mi
++ )
175 I_vars
.insert( Var(labels
[mi
], dims
[mi
]) );
176 factors
.push_back(Factor(I_vars
,0.0));
178 // calculate permutation sigma (internally, members are sorted)
179 vector
<long> sigma(nr_members
,0);
180 VarSet::iterator j
= I_vars
.begin();
181 for( size_t mi
= 0; mi
< nr_members
; mi
++,j
++ ) {
182 long search_for
= j
->label();
183 vector
<long>::iterator j_loc
= find(labels
.begin(),labels
.end(),search_for
);
184 sigma
[mi
] = j_loc
- labels
.begin();
188 copy( sigma
.begin(), sigma
.end(), ostream_iterator
<int>(cout
," "));
192 // calculate multindices
193 vector
<size_t> sdims(nr_members
,0);
194 for( size_t k
= 0; k
< nr_members
; k
++ ) {
195 sdims
[k
] = dims
[sigma
[k
]];
200 cout
<< " mi.max(): " << mi
.max() << endl
;
202 for( size_t k
=0; k
< nr_members
; k
++ )
203 cout
<< labels
[k
] << " ";
205 for( size_t k
=0; k
< nr_members
; k
++ )
206 cout
<< labels
[sigma
[k
]] << " ";
212 while( (is
.peek()) == '#' )
216 cout
<< " nonzeroes: " << nr_nonzeros
<< endl
;
217 for( size_t k
= 0; k
< nr_nonzeros
; k
++ ) {
220 while( (is
.peek()) == '#' )
223 while( (is
.peek()) == '#' )
227 vector
<size_t> vi
= mi
.vi(li
);
228 vector
<size_t> svi(vi
.size(),0);
229 for( size_t k
= 0; k
< vi
.size(); k
++ )
230 svi
[k
] = vi
[sigma
[k
]];
231 size_t sli
= smi
.li(svi
);
233 cout
<< " " << li
<< ": ";
234 copy( vi
.begin(), vi
.end(), ostream_iterator
<size_t>(cout
," "));
236 copy( svi
.begin(), svi
.end(), ostream_iterator
<size_t>(cout
," "));
237 cout
<< ": " << sli
<< endl
;
239 factors
.back()[sli
] = val
;
244 cout
<< "factors:" << endl
;
245 copy(factors
.begin(), factors
.end(), ostream_iterator
<Factor
>(cout
,"\n"));
248 fg
= FactorGraph(factors
);
257 VarSet
FactorGraph::delta( unsigned i
) const {
258 // calculate Markov Blanket
260 foreach( const Neighbor
&I
, nbV(i
) ) // for all neighboring factors I of i
261 foreach( const Neighbor
&j
, nbF(I
) ) // for all neighboring variables j of I
269 VarSet
FactorGraph::Delta( unsigned i
) const {
270 return( delta(i
) | var(i
) );
274 void FactorGraph::makeCavity( unsigned i
) {
275 // fills all Factors that include var(i) with ones
276 foreach( const Neighbor
&I
, nbV(i
) ) // for all neighboring factors I of i
277 factor(I
).fill( 1.0 );
281 bool FactorGraph::hasNegatives() const {
283 for( size_t I
= 0; I
< nrFactors() && !result
; I
++ )
284 if( factor(I
).hasNegatives() )
290 long FactorGraph::ReadFromFile(const char *filename
) {
292 infile
.open (filename
);
293 if (infile
.is_open()) {
298 cout
<< "ERROR OPENING FILE" << endl
;
304 long FactorGraph::WriteToFile(const char *filename
) const {
306 outfile
.open (filename
);
307 if (outfile
.is_open()) {
317 cout
<< "ERROR OPENING FILE" << endl
;
323 long FactorGraph::WriteToDotFile(const char *filename
) const {
325 outfile
.open (filename
);
326 if (outfile
.is_open()) {
328 outfile
<< "graph G {" << endl
;
329 outfile
<< "graph[size=\"9,9\"];" << endl
;
330 outfile
<< "node[shape=circle,width=0.4,fixedsize=true];" << endl
;
331 for( size_t i
= 0; i
< nrVars(); i
++ )
332 outfile
<< "\tx" << var(i
).label() << ";" << endl
;
333 outfile
<< "node[shape=box,style=filled,color=lightgrey,width=0.3,height=0.3,fixedsize=true];" << endl
;
334 for( size_t I
= 0; I
< nrFactors(); I
++ )
335 outfile
<< "\tp" << I
<< ";" << endl
;
336 for( size_t i
= 0; i
< nrVars(); i
++ )
337 foreach( const Neighbor
&I
, nbV(i
) ) // for all neighboring factors I of i
338 outfile
<< "\tx" << var(i
).label() << " -- p" << I
<< ";" << endl
;
339 outfile
<< "}" << endl
;
347 cout
<< "ERROR OPENING FILE" << endl
;
353 bool hasShortLoops( const vector
<Factor
> &P
) {
355 vector
<Factor
>::const_iterator I
, J
;
356 for( I
= P
.begin(); I
!= P
.end(); I
++ ) {
359 for( ; J
!= P
.end(); J
++ )
360 if( (I
->vars() & J
->vars()).size() >= 2 ) {
371 void RemoveShortLoops(vector
<Factor
> &P
) {
375 vector
<Factor
>::iterator I
, J
;
376 for( I
= P
.begin(); I
!= P
.end(); I
++ ) {
379 for( ; J
!= P
.end(); J
++ )
380 if( (I
->vars() & J
->vars()).size() >= 2 ) {
388 cout
<< "Merging factors " << I
->vars() << " and " << J
->vars() << endl
;
396 vector
<VarSet
> FactorGraph::Cliques() const {
397 vector
<VarSet
> result
;
399 for( size_t I
= 0; I
< nrFactors(); I
++ ) {
401 for( size_t J
= 0; (J
< nrFactors()) && maximal
; J
++ )
402 if( (factor(J
).vars() >> factor(I
).vars()) && !(factor(J
).vars() == factor(I
).vars()) )
406 result
.push_back( factor(I
).vars() );
413 void FactorGraph::clamp( const Var
& n
, size_t i
) {
414 assert( i
<= n
.states() );
416 /* if( do_surgery ) {
417 size_t ni = find( vars().begin(), vars().end(), n) - vars().begin();
419 if( ni != nrVars() ) {
420 for( _nb_cit I = nb1(ni).begin(); I != nb1(ni).end(); I++ ) {
421 if( factor(*I).size() == 1 )
422 // Remove this single-variable factor
423 // I = (_V2.erase(I))--;
424 _E12.erase( _E12.begin() + VV2E(ni, *I) );
426 // Replace it by the slice
427 Index ind_I_min_n( factor(*I), factor(*I) / n );
428 Index ind_n( factor(*I), n );
429 Factor slice_I( factor(*I) / n );
430 for( size_t ind_I = 0; ind_I < factor(*I).stateSpace(); ++ind_I, ++ind_I_min_n, ++ind_n )
432 slice_I[ind_I_min_n] = factor(*I)[ind_I];
433 factor(*I) = slice_I;
435 // Remove the edge between n and I
436 _E12.erase( _E12.begin() + VV2E(ni, *I) );
442 // remove all unconnected factors
443 for( size_t I = 0; I < nrFactors(); I++ )
444 if( nb2(I).size() == 0 )
453 // The cheap solution (at least in terms of coding time) is to multiply every factor
454 // that contains the variable with a delta function
456 Factor
delta_n_i(n
,0.0);
459 // For all factors that contain n
460 for( size_t I
= 0; I
< nrFactors(); I
++ )
461 if( factor(I
).vars() && n
)
462 // Multiply it with a delta function
463 factor(I
) *= delta_n_i
;
469 void FactorGraph::saveProb( size_t I
) {
470 map
<size_t,Prob
>::iterator it
= _undoProbs
.find( I
);
471 if( it
!= _undoProbs
.end() )
472 cout
<< "FactorGraph::saveProb: WARNING: _undoProbs[I] already defined!" << endl
;
473 _undoProbs
[I
] = factor(I
).p();
477 void FactorGraph::undoProb( size_t I
) {
478 map
<size_t,Prob
>::iterator it
= _undoProbs
.find( I
);
479 if( it
!= _undoProbs
.end() ) {
480 factor(I
).p() = (*it
).second
;
481 _undoProbs
.erase(it
);
486 void FactorGraph::saveProbs( const VarSet
&ns
) {
487 if( !_undoProbs
.empty() )
488 cout
<< "FactorGraph::saveProbs: WARNING: _undoProbs not empy!" << endl
;
489 for( size_t I
= 0; I
< nrFactors(); I
++ )
490 if( factor(I
).vars() && ns
)
491 _undoProbs
[I
] = factor(I
).p();
495 void FactorGraph::undoProbs( const VarSet
&ns
) {
496 for( map
<size_t,Prob
>::iterator uI
= _undoProbs
.begin(); uI
!= _undoProbs
.end(); ) {
497 if( factor((*uI
).first
).vars() && ns
) {
498 // cout << "undoing " << factor((*uI).first).vars() << endl;
499 // cout << "from " << factor((*uI).first).p() << " to " << (*uI).second << endl;
500 factor((*uI
).first
).p() = (*uI
).second
;
501 _undoProbs
.erase(uI
++);
508 } // end of namespace dai