Improved documentation of bipgraph.h and added example_bipgraph.cpp

[libdai.git] / src / daialg.cpp

diff --git a/src/daialg.cpp b/src/daialg.cpp
index e199670..79f9daa 100644 (file)
--- a/src/daialg.cpp
+++ b/src/daialg.cpp
@@ -1,6 +1,7 @@
-/*  Copyright (C) 2006-2008  Joris Mooij  [j dot mooij at science dot ru dot nl]
-    Radboud University Nijmegen, The Netherlands
-    
+/*  Copyright (C) 2006-2008  Joris Mooij  [joris dot mooij at tuebingen dot mpg dot de]
+    Radboud University Nijmegen, The Netherlands /
+    Max Planck Institute for Biological Cybernetics, Germany
+
     This file is part of libDAI.
 
     libDAI is free software; you can redistribute it and/or modify
@@ -29,8 +30,7 @@ namespace dai {
 using namespace std;
 
 
-/// Calculate the marginal of obj on ns by clamping 
-/// all variables in ns and calculating logZ for each joined state
+/// Calculates the marginal of obj on ns by clamping all variables in ns and calculating logZ for each joined state.
 Factor calcMarginal( const InfAlg & obj, const VarSet & ns, bool reInit ) {
     Factor Pns (ns);
     
@@ -41,7 +41,7 @@ Factor calcMarginal( const InfAlg & obj, const VarSet & ns, bool reInit ) {
     Real logZ0 = 0.0;
     for( State s(ns); s.valid(); s++ ) {
         // save unclamped factors connected to ns
-        clamped->saveProbs( ns );
+        clamped->backupFactors( ns );
 
         // set clamping Factors to delta functions
         for( VarSet::const_iterator n = ns.begin(); n != ns.end(); n++ )
@@ -50,6 +50,8 @@ Factor calcMarginal( const InfAlg & obj, const VarSet & ns, bool reInit ) {
         // run DAIAlg, calc logZ, store in Pns
         if( reInit )
             clamped->init();
+        else
+            clamped->init(ns);
         clamped->run();
 
         Real Z;
@@ -64,15 +66,16 @@ Factor calcMarginal( const InfAlg & obj, const VarSet & ns, bool reInit ) {
         Pns[s] = Z;
         
         // restore clamped factors
-        clamped->undoProbs( ns );
+        clamped->restoreFactors( ns );
     }
 
     delete clamped;
 
-    return( Pns.normalized(Prob::NORMPROB) );
+    return( Pns.normalized() );
 }
 
 
+/// Calculates beliefs of all pairs in ns (by clamping nodes in ns and calculating logZ and the beliefs for each state).
 vector<Factor> calcPairBeliefs( const InfAlg & obj, const VarSet& ns, bool reInit ) {
     // convert ns to vector<VarSet>
     size_t N = ns.size();
@@ -86,9 +89,9 @@ vector<Factor> calcPairBeliefs( const InfAlg & obj, const VarSet& ns, bool reIni
     for( size_t j = 0; j < N; j++ )
         for( size_t k = 0; k < N; k++ )
             if( j == k )
-                pairbeliefs.push_back(Factor());
+                pairbeliefs.push_back( Factor() );
             else
-                pairbeliefs.push_back(Factor(vns[j] | vns[k]));
+                pairbeliefs.push_back( Factor( VarSet(vns[j], vns[k]) ) );
 
     InfAlg *clamped = obj.clone();
     if( !reInit )
@@ -98,12 +101,11 @@ vector<Factor> calcPairBeliefs( const InfAlg & obj, const VarSet& ns, bool reIni
     for( size_t j = 0; j < N; j++ ) {
         // clamp Var j to its possible values
         for( size_t j_val = 0; j_val < vns[j].states(); j_val++ ) {
-            // save unclamped factors connected to ns
-            clamped->saveProbs( ns );
-            
-            clamped->clamp( vns[j], j_val );
+            clamped->clamp( vns[j], j_val, true );
             if( reInit )
                 clamped->init();
+            else
+                clamped->init(ns);
             clamped->run();
 
             //if( j == 0 )
@@ -127,7 +129,7 @@ vector<Factor> calcPairBeliefs( const InfAlg & obj, const VarSet& ns, bool reIni
                 }
 
             // restore clamped factors
-            clamped->undoProbs( ns );
+            clamped->restoreFactors( ns );
         }
     }
     
@@ -144,6 +146,7 @@ vector<Factor> calcPairBeliefs( const InfAlg & obj, const VarSet& ns, bool reIni
 }
 
 
+/// Calculates beliefs of all pairs in ns (by clamping pairs in ns and calculating logZ for each joined state).
 Factor calcMarginal2ndO( const InfAlg & obj, const VarSet& ns, bool reInit ) {
     // returns a a probability distribution whose 1st order interactions
     // are unspecified, whose 2nd order interactions approximate those of 
@@ -155,10 +158,11 @@ Factor calcMarginal2ndO( const InfAlg & obj, const VarSet& ns, bool reInit ) {
     for( size_t ij = 0; ij < pairbeliefs.size(); ij++ )
         Pns *= pairbeliefs[ij];
     
-    return( Pns.normalized(Prob::NORMPROB) );
+    return( Pns.normalized() );
 }
 
 
+/// Calculates 2nd order interactions of the marginal of obj on ns.
 vector<Factor> calcPairBeliefsNew( const InfAlg & obj, const VarSet& ns, bool reInit ) {
     vector<Factor> result;
     result.reserve( ns.size() * (ns.size() - 1) / 2 );
@@ -172,18 +176,20 @@ vector<Factor> calcPairBeliefsNew( const InfAlg & obj, const VarSet& ns, bool re
     for( long j = 0; j < (long)ns.size() - 1; j++, nj++ ) {
         size_t k = 0;
         for( VarSet::const_iterator nk = nj; (++nk) != ns.end(); k++ ) {
-            Factor pairbelief( *nj | *nk );
+            Factor pairbelief( VarSet(*nj, *nk) );
 
             // clamp Vars j and k to their possible values
             for( size_t j_val = 0; j_val < nj->states(); j_val++ ) 
                 for( size_t k_val = 0; k_val < nk->states(); k_val++ ) {
                     // save unclamped factors connected to ns
-                    clamped->saveProbs( ns );
+                    clamped->backupFactors( ns );
             
                     clamped->clamp( *nj, j_val );
                     clamped->clamp( *nk, k_val );
                     if( reInit )
                         clamped->init();
+                    else
+                        clamped->init(ns);
                     clamped->run();
 
                     double Z_xj = 1.0;
@@ -199,7 +205,7 @@ vector<Factor> calcPairBeliefsNew( const InfAlg & obj, const VarSet& ns, bool re
                     pairbelief[j_val + (k_val * nj->states())] = Z_xj;
 
                     // restore clamped factors
-                    clamped->undoProbs( ns );
+                    clamped->restoreFactors( ns );
                 }
         
             result.push_back( pairbelief );