Merge branch 'master' of https://github.com/tacgomes/yap6.3

packages/CLPBN/Makefile.in

@@ -28,9 +28,9 @@ INSTALL=@INSTALL@
 INSTALL_DATA=@INSTALL_DATA@
 INSTALL_PROGRAM=@INSTALL_PROGRAM@
 srcdir=@srcdir@
+PDFLATEX=pdflatex
 
-CLPBN_TOP= $(srcdir)/clpbn.yap \
+PFL_MANUAL = $(srcdir)/pfl
-	$(srcdir)/pfl.yap
 
 CLPBN_SRCDIR = $(srcdir)/clpbn
 
@@ -38,6 +38,10 @@ CLPBN_LEARNING_SRCDIR = $(srcdir)/learning
 
 CLPBN_EXDIR = $(srcdir)/examples
 
+CLPBN_TOP= \
+	$(srcdir)/clpbn.yap \
+	$(srcdir)/pfl.yap
+
 CLPBN_PROGRAMS= \
 	$(CLPBN_SRCDIR)/aggregates.yap \
 	$(CLPBN_SRCDIR)/bdd.yap \
@@ -74,15 +78,24 @@ CLPBN_LEARNING_PROGRAMS= \
 	$(CLPBN_LEARNING_SRCDIR)/learn_utils.yap \
 	$(CLPBN_LEARNING_SRCDIR)/mle.yap
 
+CLPBN_EXAMPLES= \
+	$(CLPBN_EXDIR)/burglary-alarm.fg \
+	$(CLPBN_EXDIR)/burglary-alarm.pfl \
+	$(CLPBN_EXDIR)/burglary-alarm.uai \
+	$(CLPBN_EXDIR)/cg.yap \
+	$(CLPBN_EXDIR)/city.pfl \
+	$(CLPBN_EXDIR)/comp_workshops.pfl \
+	$(CLPBN_EXDIR)/social_network1.pfl \
+	$(CLPBN_EXDIR)/social_network2.pfl \
+	$(CLPBN_EXDIR)/sprinkler.pfl \
+	$(CLPBN_EXDIR)/workshop_attrs.pfl
+
 CLPBN_SCHOOL_EXAMPLES= \
 	$(CLPBN_EXDIR)/School/README \
 	$(CLPBN_EXDIR)/School/evidence_128.yap \
-	$(CLPBN_EXDIR)/School/schema.yap \
 	$(CLPBN_EXDIR)/School/parschema.pfl \
 	$(CLPBN_EXDIR)/School/school_128.yap \
 	$(CLPBN_EXDIR)/School/school_32.yap \
-	$(CLPBN_EXDIR)/School/sch32.yap \
-	$(CLPBN_EXDIR)/School/school32_data.yap \
 	$(CLPBN_EXDIR)/School/school_64.yap \
 	$(CLPBN_EXDIR)/School/tables.yap
 
@@ -102,20 +115,8 @@ CLPBN_LEARNING_EXAMPLES= \
 	$(CLPBN_EXDIR)/learning/sprinkler_params.yap \
 	$(CLPBN_EXDIR)/learning/train.yap
 
-CLPBN_EXAMPLES= \
-	$(CLPBN_EXDIR)/burglary-alarm.fg \
-	$(CLPBN_EXDIR)/burglary-alarm.pfl \
-	$(CLPBN_EXDIR)/burglary-alarm.uai \
-	$(CLPBN_EXDIR)/cg.yap \
-	$(CLPBN_EXDIR)/city.pfl \
-	$(CLPBN_EXDIR)/comp_workshops.pfl \
-	$(CLPBN_EXDIR)/social_domain1.pfl \
-	$(CLPBN_EXDIR)/social_domain2.pfl \
-	$(CLPBN_EXDIR)/sprinkler.pfl \
-	$(CLPBN_EXDIR)/workshop_attrs.pfl
 
-
+install: $(CLBN_TOP) $(CLBN_PROGRAMS) $(CLPBN_LEARNING_PROGRAMS) $(CLPBN_SCHOOL_EXAMPLES) $(CLPBN_HMMER_EXAMPLES) $(CLPBN_LEARNING_EXAMPLES)
-install: $(CLBN_TOP) $(CLBN_PROGRAMS) $(CLPBN_PROGRAMS)
 	mkdir -p $(DESTDIR)$(SHAREDIR)/clpbn
 	mkdir -p $(DESTDIR)$(SHAREDIR)/clpbn/learning
 	mkdir -p $(DESTDIR)$(EXDIR)
@@ -130,3 +131,13 @@ install: $(CLBN_TOP) $(CLBN_PROGRAMS) $(CLPBN_PROGRAMS)
 	for h in $(CLPBN_HMMER_EXAMPLES); do $(INSTALL_DATA) $$h $(DESTDIR)$(EXDIR)/HMMer; done
 	for h in $(CLPBN_LEARNING_EXAMPLES); do $(INSTALL_DATA) $$h $(DESTDIR)$(EXDIR)/learning; done
 
+
+docs: $(MANUAL)
+	$(PDFLATEX) $(PFL_MANUAL)
+	$(PDFLATEX) $(PFL_MANUAL)
+	rm -f pfl.aux pfl.bbl pfl.blg pfl.log pfl.out
+
+
+install_docs: docs
+	$(INSTALL_DATA) pfl.pdf $(DESTDIR)$(EXDIR)
+

packages/CLPBN/README.txt

@@ -1,111 +0,0 @@
-Prolog Factor Language (PFL)
-
-Prolog Factor Language (PFL) is a extension of the Prolog language that
-allows a natural representation of this first-order probabilistic models
-(either directed or undirected). PFL is also capable of solving probabilistic 
-queries on this models through the implementation of several inference
-techniques: variable elimination, belief propagation, lifted variable
-elimination and lifted belief propagation.
-
-Language
--------------------------------------------------------------------------------
-A graphical model in PFL is represented using parfactors. A PFL parfactor
-has the following four components:
-
-Type ; Formulas ; Phi ; Constraint .
-
-- Type refers the type of the network over which the parfactor is defined.
-It can be bayes for directed networks, or markov for undirected ones.
-- Formulas is a sequence of Prolog terms that define sets of random variables
-under the constraint.
-- Phi is either a list of parameters or a call to a Prolog goal that will
-unify its last argument with a list of parameters.
-- Constraint is a list (possible empty) of Prolog goals that will impose
-bindings on the logical variables that appear in the formulas.
-
-The "examples" directory contains some popular graphical models described
-using PFL.
-
-Querying
--------------------------------------------------------------------------------
-Now we show how to use PFL to solve probabilistic queries. We will
-use the burlgary alarm network as an example. First, we load the model:
-
-$ yap -l examples/burglary-alarm.yap
-
-Now let's suppose that we want to estimate the probability of a earthquake
-ocurred given that mary called. We can do it with the following query:
-
-?- earthquake(X), mary_calls(t).
-
-Suppose now that we want the joint distribution for john_calls and
-mary_calls. We can obtain this with the following query:
-
-?- john_calls(X), mary_calls(Y).
-
-
-Inference Options
--------------------------------------------------------------------------------
-PFL supports both ground and lifted inference. The inference algorithm
-can be chosen using the set_solver/1 predicate. The following algorithms
-are supported:
-- lve:  generalized counting first-order variable elimination (GC-FOVE)
-- hve:  (ground) variable elimination
-- lbp:  lifted first-order belief propagation
-- cbp:  counting belief propagation
-- bp:   (ground) belief propagation
-- lkc:  lifted first-order knowledge compilation
-
-For example, if we want to use ground variable elimination to solve some
-query, we need to call first the following goal:
-
-?- set_solver(hve).
-
-It is possible to tweak several parameters of PFL through the
-set_horus_flag/2 predicate. The first argument is a key that
-identifies the parameter that we desire to tweak, while the second
-is some possible value for this key.
-
-The verbosity key controls the level of log information that will be
-printed by the corresponding solver. Its possible values are positive
-integers. The bigger the number, more log information will be printed.
-For example, to view some basic log information we need to call the 
-following goal:
-
-?- set_horus_flag(verbosity, 1).
-
-The use_logarithms key controls whether the calculations performed
-during inference should be done in the log domain or not. Its values
-can be true or false. By default is false.
-
-There are also keys specific to the inference algorithm. For example,
-elim_heuristic key controls the elimination heuristic that will be
-used by ground variable elimination. The following heuristics are
-supported:
-- sequential
-- min_neighbors
-- min_weight
-- min_fill
-- weighted_min_fill
-
-An explanation of this heuristics can be found in Probabilistic Graphical
-Models by Daphne Koller.
-
-The schedule, accuracy and max_iter keys are specific for inference
-algorithms based on message passing, namely lbp, cbp and bp.
-The key schedule can be used to specify the order in which the messages
-are sent in belief propagation. The possible values are:
-- seq_fixed: at each iteration, all messages are sent in the same order
-- seq_random: at each iteration, the messages are sent with a random order
-- parallel: at each iteration, the messages are all calculated using the
-values of the previous iteration.
-- max_residual: the next message to be sent is the one with maximum residual,
-(Residual Belief Propagation:Informed Scheduling for Asynchronous Message
-Passing)
-
-The max_iter key sets the maximum number of iterations. One iteration
-consists in sending all possible messages. The accuracy key indicate
-when we should stop sending messages. If the largest difference between
-a message sent in the current iteration and one message sent in the previous
-iteration is less that accuracy value given, we terminate belief propagation.
-

packages/CLPBN/benchmarks/benchs.sh

@@ -1,5 +1,4 @@
 
-
 function prepare_new_run
 {
   YAP=~/bin/$SHORTNAME-$SOLVER
@@ -17,32 +16,33 @@ function prepare_new_run
 
 function run_solver
 {
-  constraint=$1
+  echo $LOG_FILE
+  CONSTRAINT=$1
   solver_flag=true
   if [ -n "$2" ]; then
     if [ $SOLVER = hve ]; then
-      solver_flag=clpbn_horus:set_horus_flag\(elim_heuristic,$2\)
+      SOLVER_FLAG=set_horus_flag\(hve_elim_heuristic,$2\)
     elif [ $SOLVER = bp ]; then
-      solver_flag=clpbn_horus:set_horus_flag\(schedule,$2\)
+      SOLVER_FLAG=set_horus_flag\(bp_msg_schedule,$2\)
     elif [ $SOLVER = cbp ]; then
-      solver_flag=clpbn_horus:set_horus_flag\(schedule,$2\)
+      SOLVER_FLAG=set_horus_flag\(bp_msg_schedule,$2\)
     elif [ $SOLVER = lbp ]; then
-      solver_flag=clpbn_horus:set_horus_flag\(schedule,$2\)
+      SOLVER_FLAG=set_horus_flag\(bp_msg_schedule,$2\)
     else
       echo "unknow flag $2"
     fi
   fi
   /usr/bin/time -o $LOG_FILE -a -f "%U\t%S\t%e\t%M" \
-      $YAP << EOF >> $LOG_FILE &>> ignore.$LOG_FILE
+      $YAP << EOF >> ignore.$LOG_FILE 2>> ignore.$LOG_FILE
 nogc.
 [$NETWORK].
-[$constraint].
+[$CONSTRAINT].
-clpbn_horus:set_solver($SOLVER).
+set_solver($SOLVER).
-clpbn_horus:set_horus_flag(use_logarithms, true).
+set_horus_flag(verbosity, 1).
-clpbn_horus:set_horus_flag(verbosity, 1).
+set_horus_flag(use_logarithms, true).
-$solver_flag.
+$SOLVER_FLAG.
 $QUERY.
-open("$LOG_FILE", 'append', S), format(S, '$constraint ~15+ ', []), close(S).
+open("$LOG_FILE", 'append', S), format(S, "$CONSTRAINT ~15+ ", []), close(S).
 EOF
 }
 
@@ -52,12 +52,16 @@ function clear_log_files
 {
   rm -f *~
   rm -f ../*~
-  rm -f school/*.log school/*~
-  rm -f ../school/*.log ../school/*~
-  rm -f city/*.log city/*~
-  rm -f ../city/*.log ../city/*~
   rm -f workshop_attrs/*.log workshop_attrs/*~
   rm -f ../workshop_attrs/*.log ../workshop_attrs/*~
+  rm -f comp_workshops/*.log comp_workshops/*~
+  rm -f ../comp_workshops/*.log ../comp_workshops/*~
+  rm -f city/*.log city/*~
+  rm -f ../city/*.log ../city/*~
+  rm -f social_network2/*.log social_network2/*~
+  rm -f ../social_network2/*.log ../social_network2/*~
+  rm -f social_network2_evidence/*.log social_network2_evidence/*~
+  rm -f ../social_network2_evidence/*.log ../social_network2_evidence/*~
   echo all done!
 }
 

packages/CLPBN/benchmarks/city/bp_tests.sh

@@ -33,5 +33,5 @@ function run_all_graphs
 }
 
 prepare_new_run
-run_all_graphs "bp(shedule=seq_fixed)                 " seq_fixed
+run_all_graphs "bp(bp_msg_shedule=seq_fixed)          " seq_fixed
 

packages/CLPBN/benchmarks/city/cbp_tests.sh

@@ -32,5 +32,5 @@ function run_all_graphs
 }
 
 prepare_new_run
-run_all_graphs "cbp(shedule=seq_fixed)                " seq_fixed
+run_all_graphs "cbp(bp_msg_shedule=seq_fixed)         " seq_fixed
 

packages/CLPBN/benchmarks/city/city.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-NETWORK="'../../examples/city'"
+NETWORK="'../../examples/city.pfl'"
 SHORTNAME="city"
 QUERY="is_joe_guilty(X)"
 

packages/CLPBN/benchmarks/city/gen_city.sh

@@ -19,7 +19,7 @@ main :-
 generate_people(S, N, Counting) :-
     Counting > N, !.
 generate_people(S, N, Counting) :-
-    format(S, 'people(p~w, nyc).~n', [Counting]),
+    format(S, 'person(p~w, nyc).~n', [Counting]),
     Counting1 is Counting + 1,
     generate_people(S, N, Counting1).
 

packages/CLPBN/benchmarks/city/hve_tests.sh

@@ -33,5 +33,5 @@ function run_all_graphs
 }
 
 prepare_new_run
-run_all_graphs "hve(elim_heuristic=min_neighbors)     " min_neighbors
+run_all_graphs "hve(hve_elim_heuristic=min_neighbors) " min_neighbors
 

packages/CLPBN/benchmarks/city/lbp_tests.sh

@@ -32,5 +32,5 @@ function run_all_graphs
 }
 
 prepare_new_run
-run_all_graphs "lbp(shedule=seq_fixed)                " seq_fixed
+run_all_graphs "lbp(bp_msg_shedule=seq_fixed)         " seq_fixed
 

packages/CLPBN/benchmarks/comp_workshops/bp_tests.sh

@@ -27,5 +27,5 @@ function run_all_graphs
 }
 
 prepare_new_run
-run_all_graphs "bp(shedule=seq_fixed)                 " seq_fixed
+run_all_graphs "bp(bp_msg_shedule=seq_fixed)          " seq_fixed
 

packages/CLPBN/benchmarks/comp_workshops/cbp_tests.sh

@@ -26,5 +26,5 @@ function run_all_graphs
 }
 
 prepare_new_run
-run_all_graphs "cbp(shedule=seq_fixed)                " seq_fixed
+run_all_graphs "cbp(bp_msg_shedule=seq_fixed)         " seq_fixed
 

packages/CLPBN/benchmarks/comp_workshops/cw.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-NETWORK="'../../examples/comp_workshops'"
+NETWORK="'../../examples/comp_workshops.pfl'"
 SHORTNAME="cw"
 QUERY="series(X)"
 

packages/CLPBN/benchmarks/comp_workshops/gen_workshops.sh

@@ -29,7 +29,7 @@ gen(S, NP, NW, Count) :-
 gen_workshops(_, _, NW, Count) :-
     Count > NW, !.
 gen_workshops(S, P, NW, Count) :-
-    format(S, 'c(p~w,w~w).~n', [P,Count]),
+    format(S, 'reg(p~w,w~w).~n', [P,Count]),
     Count1 is Count + 1,
     gen_workshops(S, P, NW, Count1).
 

packages/CLPBN/benchmarks/comp_workshops/hve_tests.sh

@@ -26,5 +26,5 @@ function run_all_graphs
 }
 
 prepare_new_run
-run_all_graphs "hve(elim_heuristic=min_neighbors)     " min_neighbors
+run_all_graphs "hve(hve_elim_heuristic=min_neighbors) " min_neighbors
 

packages/CLPBN/benchmarks/comp_workshops/lbp_tests.sh

@@ -26,5 +26,5 @@ function run_all_graphs
 }
 
 prepare_new_run
-run_all_graphs "lbp(shedule=seq_fixed)                " seq_fixed
+run_all_graphs "lbp(bp_msg_shedule=seq_fixed)         " seq_fixed
 

packages/CLPBN/benchmarks/run_all.sh

@@ -24,7 +24,7 @@ source lbp_tests.sh
 source cbp_tests.sh
 cd ..
 
-cd smokers
+cd social_network2
 source hve_tests.sh
 source bp_tests.sh
 source lve_tests.sh

packages/CLPBN/benchmarks/school/run_school_tests.sh

@@ -1,95 +1,64 @@
 #!/bin/bash
 
-#cp ~/bin/yap ~/bin/school_all
+source ../benchs.sh
-#YAP=~/bin/school_all
-YAP=~/bin/yap
 
-#OUT_FILE_NAME=results`date "+ %H:%M:%S %d-%m-%Y"`.log
+SHORTNAME="school"
-OUT_FILE_NAME=results.log
+SOLVER="school"
-rm -f $OUT_FILE_NAME
-rm -f ignore.$OUT_FILE_NAME
 
-# yap -g "['../../../../examples/School/sch32'], [missing5], use_module(library(clpbn/learning/em)), graph(L), clpbn:set_clpbn_flag(em_solver,bp), clpbn_horus:set_horus_flag(inf_alg, bp), statistics(runtime, _), em(L,0.01,10,_,Lik), statistics(runtime, [T,_])."
 
-function run_solver
+function learn_params
 {
-if [ $2 = bp ]
+  NETWORK="'./../../examples/School/school_32'"
-then
+  CONSTRAINT=$2
-  if [ $4 = ve ]
+  SOLVER=$1
-  then
+  echo $NETWORK
-    extra_flag1=clpbn_horus:set_horus_flag\(inf_alg,$4\)
+  /usr/bin/time -o $LOG_FILE -a -f "%U\t%S\t%e\t%M" \
-    extra_flag2=clpbn_horus:set_horus_flag\(elim_heuristic,$5\)
+      $YAP << EOF >> ignore.$LOG_FILE 2>> ignore.$LOG_FILE
-  else
+use_module(library(pfl)).
-    extra_flag1=clpbn_horus:set_horus_flag\(inf_alg,$4\)
+use_module(library(clpbn/learning/em)).
-    extra_flag2=clpbn_horus:set_horus_flag\(schedule,$5\)
+[$NETWORK].
-  fi
+[$CONSTRAINT].
-else
+set_em_solver($SOLVER).
-  extra_flag1=true
-  extra_flag2=true
-fi
-/usr/bin/time -o "$OUT_FILE_NAME" -a -f "real:%E\tuser:%U\tsys:%S" $YAP << EOF &>> "ignore.$OUT_FILE_NAME"
-:- [pos:train].
-:- ['../../../../examples/School/sch32'].
-:- use_module(library(clpbn/learning/em)).
-:- use_module(library(clpbn/bp)).
-[$1].
 graph(L),
-  clpbn:set_clpbn_flag(em_solver,$2),
+%	em(L, 0.01, 10, _, Lik),
-  $extra_flag1, $extra_flag2,
+	open("$LOG_FILE", 'append', S),
-  em(L,0.01,10,_,Lik),
+        format(S, "$CONSTRAINT: ~15+ Lik = ~3f\t", [Lik]),
-  open("$OUT_FILE_NAME", 'append',S),
-  format(S, '$3: ~11+ Lik = ~3f, ',[Lik]),
 	close(S).
 EOF
 }
 
 
-function run_all_graphs
+prepare_new_run
-{
-  echo "************************************************************************" >> "$OUT_FILE_NAME"
-  echo "results for solver $2" >> "$OUT_FILE_NAME"
-  echo "************************************************************************" >> "$OUT_FILE_NAME"
-  run_solver  missing5   $1  missing5   $3  $4  $5
-  run_solver  missing10  $1  missing10  $3  $4  $5
-  #run_solver  missing20  $1  missing20  $3  $4  $5
-  #run_solver  missing30  $1  missing30  $3  $4  $5
-  #run_solver  missing40  $1  missing40  $3  $4  $5
-  #run_solver  missing50  $1  missing50  $3  $4  $5
-}
 
+write_header hve
+learn_params  hve  missing5
+learn_params  hve  missing10
+learn_params  hve  missing20
+#learn_params  hve  missing30
+#learn_params  hve  missing40
+#learn_params  hve  missing50
 
-#run_all_graphs  bp     "hve(min_neighbors) "  ve   min_neighbors
+write_header ve
-#run_all_graphs  bp     "bp(seq_fixed)      "  bp   seq_fixed
+learn_params  ve  missing5
-#run_all_graphs  bp     "cbp(seq_fixed)     "  cbp  seq_fixed
+learn_params  ve  missing10
-exit
+learn_params  ve  missing20
+#learn_params  ve  missing30
+#learn_params  ve  missing40
+#learn_params  hve  missing50
 
+write_header bp
+learn_params  bp  missing5
+learn_params  bp  missing10
+learn_params  bp  missing20
+#learn_params  bp  missing30
+#learn_params  bp  missing40
+#learn_params  bp missing50
 
-run_all_graphs  bp    "hve(min_neighbors) "  ve   min_neighbors
+write_header cbp
-run_all_graphs  bp    "hve(min_weight)    "  ve   min_weight
+learn_params  cbp  missing5
-run_all_graphs  bp    "hve(min_fill)      "  ve   min_fill
+learn_params  cbp  missing10
-run_all_graphs  bp    "hve(w_min_fill)    "  ve   weighted_min_fill
+learn_params  cbp  missing20
-run_all_graphs  bp    "bp(seq_fixed)      "  bp   seq_fixed
+#learn_params  cbp  missing30
-run_all_graphs  bp    "bp(max_residual)   "  bp   max_residual
+#learn_params  cbp  missing40
-run_all_graphs  bp    "cbp(seq_fixed)     "  cbp  seq_fixed
+#learn_params  cbp missing50
-run_all_graphs  bp    "cbp(max_residual)  "  cbp  max_residual
-run_all_graphs  gibbs "gibbs              "
-echo "************************************************************************" >> "$OUT_FILE_NAME"
-echo "results for solver ve" >> "$OUT_FILE_NAME"
-echo "************************************************************************" >> "$OUT_FILE_NAME"
-run_solver  missing5   ve  missing5   $3  $4  $5
-run_solver  missing10  ve  missing10  $3  $4  $5
-run_solver  missing20  ve  missing20  $3  $4  $5
-run_solver  missing30  ve  missing30  $3  $4  $5
-run_solver  missing40  ve  missing40  $3  $4  $5
-#run_solver  missing50  ve  missing50  $3  $4  $5 #+24h!
-echo "************************************************************************" >> "$OUT_FILE_NAME"
-echo "results for solver jt" >> "$OUT_FILE_NAME"
-echo "************************************************************************" >> "$OUT_FILE_NAME"
-run_solver  missing5   jt  missing5   $3  $4  $5
-run_solver  missing10  jt  missing10  $3  $4  $5
-run_solver  missing20  jt  missing20  $3  $4  $5
-#run_solver  missing30  jt  missing30  $3  $4  $5 #+24h!
-#run_solver  missing40  jt  missing40  $3  $4  $5 #+24h!
-#run_solver  missing50  jt  missing50  $3  $4  $5 #+24h!
-exit
 

packages/CLPBN/benchmarks/smokers_evidence/sm.sh

@@ -1,8 +0,0 @@
-#!/bin/bash
-
-NETWORK="'../../examples/social_domain2'"
-SHORTNAME="sm"
-QUERY="query(X)"
-
-POP=500
-

packages/CLPBN/benchmarks/social_network2/bp_tests.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-source sm.sh
+source sn2.sh
 source ../benchs.sh
 
 SOLVER="bp"
@@ -26,5 +26,5 @@ function run_all_graphs
 }
 
 prepare_new_run
-run_all_graphs "bp(shedule=seq_fixed)                 " seq_fixed
+run_all_graphs "bp(bp_msg_shedule=seq_fixed)          " seq_fixed
 

packages/CLPBN/benchmarks/social_network2/cbp_tests.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-source sm.sh
+source sn2.sh
 source ../benchs.sh
 
 SOLVER="cbp"
@@ -26,5 +26,5 @@ function run_all_graphs
 }
 
 prepare_new_run
-run_all_graphs "cbp(shedule=seq_fixed)                " seq_fixed
+run_all_graphs "cbp(bp_msg_shedule=seq_fixed)         " seq_fixed
 

packages/CLPBN/benchmarks/social_network2/gen_people.sh

@@ -17,7 +17,7 @@ main :-
 generate_people(S, N, Counting) :-
     Counting > N, !.
 generate_people(S, N, Counting) :-
-    format(S, 'people(p~w).~n', [Counting]),
+    format(S, 'person(p~w).~n', [Counting]),
     Counting1 is Counting + 1,
     generate_people(S, N, Counting1).
 

packages/CLPBN/benchmarks/social_network2/hve_tests.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-source sm.sh
+source sn2.sh
 source ../benchs.sh
 
 SOLVER="hve"
@@ -26,8 +26,8 @@ function run_all_graphs
 }
 
 prepare_new_run
-run_all_graphs "hve(elim_heuristic=min_neighbors)     " min_neighbors
+run_all_graphs "hve(hve_elim_heuristic=min_neighbors) " min_neighbors
-#run_all_graphs "hve(elim_heuristic=min_weight)        " min_weight
+#run_all_graphs "hve(hve_elim_heuristic=min_weight)    " min_weight
-#run_all_graphs "hve(elim_heuristic=min_fill)          " min_fill
+#run_all_graphs "hve(hve_elim_heuristic=min_fill)      " min_fill
-#run_all_graphs "hve(elim_heuristic=weighted_min_fill) " weighted_min_fill
+#run_all_graphs "hve(hve_elim_heuristic=weighted_min_fill) " weighted_min_fill
 

packages/CLPBN/benchmarks/social_network2/lbp_tests.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-source sm.sh
+source sn2.sh
 source ../benchs.sh
 
 SOLVER="lbp"
@@ -26,5 +26,5 @@ function run_all_graphs
 }
 
 prepare_new_run
-run_all_graphs "lbp(shedule=seq_fixed)                " seq_fixed
+run_all_graphs "lbp(bp_msg_shedule=seq_fixed)         " seq_fixed
 

packages/CLPBN/benchmarks/social_network2/lve_tests.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-source sm.sh
+source sn2.sh
 source ../benchs.sh
 
 SOLVER="lve"

packages/CLPBN/benchmarks/social_network2/sn2.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 
-NETWORK="'../../examples/social_domain2'"
+NETWORK="'../../examples/social_network2.pfl'"
-SHORTNAME="sm"
+SHORTNAME="sn2"
 #QUERY="smokes(p1,t), smokes(p2,t), friends(p1,p2,X)"
 QUERY="friends(p1,p2,X)"
 

packages/CLPBN/benchmarks/social_network2_evidence/bp_tests.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-source sm.sh
+source sn2ev.sh
 source ../benchs.sh
 
 SOLVER="bp"
@@ -30,5 +30,5 @@ function run_all_graphs
 }
 
 prepare_new_run
-run_all_graphs "bp(shedule=seq_fixed)                 " seq_fixed
+run_all_graphs "bp(bp_msg_shedule=seq_fixed)          " seq_fixed
 

packages/CLPBN/benchmarks/social_network2_evidence/cbp_tests.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-source sm.sh
+source sn2ev.sh
 source ../benchs.sh
 
 SOLVER="cbp"
@@ -30,5 +30,5 @@ function run_all_graphs
 }
 
 prepare_new_run
-run_all_graphs "cbp(shedule=seq_fixed)                " seq_fixed
+run_all_graphs "cbp(bp_msg_shedule=seq_fixed)         " seq_fixed
 

packages/CLPBN/benchmarks/social_network2_evidence/gen_people.sh

@@ -26,7 +26,7 @@ main :-
 generate_people(S, N, Counting) :-
     Counting > N, !.
 generate_people(S, N, Counting) :-
-    format(S, 'people(p~w).~n', [Counting]),
+    format(S, 'person(p~w).~n', [Counting]),
     Counting1 is Counting + 1,
     generate_people(S, N, Counting1).
 

packages/CLPBN/benchmarks/social_network2_evidence/hve_tests.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-source sm.sh
+source sn2ev.sh
 source ../benchs.sh
 
 SOLVER="hve"
@@ -30,8 +30,8 @@ function run_all_graphs
 }
 
 prepare_new_run
-run_all_graphs "hve(elim_heuristic=min_neighbors)     " min_neighbors
+run_all_graphs "hve(hve_elim_heuristic=min_neighbors) " min_neighbors
-#run_all_graphs "hve(elim_heuristic=min_weight)        " min_weight
+#run_all_graphs "hve(hve_elim_heuristic=min_weight)    " min_weight
-#run_all_graphs "hve(elim_heuristic=min_fill)          " min_fill
+#run_all_graphs "hve(hve_elim_heuristic=min_fill)      " min_fill
-#run_all_graphs "hve(elim_heuristic=weighted_min_fill) " weighted_min_fill
+#run_all_graphs "hve(hve_elim_heuristic=weighted_min_fill) " weighted_min_fill
 

packages/CLPBN/benchmarks/social_network2_evidence/lve_tests.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-source sm.sh
+source sn2ev.sh
 source ../benchs.sh
 
 SOLVER="lve"

packages/CLPBN/benchmarks/social_network2_evidence/sn2ev.sh

@@ -0,0 +1,8 @@
+#!/bin/bash
+
+NETWORK="'../../examples/social_network2.pfl'"
+SHORTNAME="sn2ev"
+QUERY="query(X)"
+
+POP=500
+

packages/CLPBN/benchmarks/workshop_attrs/bp_tests.sh

@@ -33,5 +33,5 @@ function run_all_graphs
 }
 
 prepare_new_run
-run_all_graphs "bp(shedule=seq_fixed)                 " seq_fixed
+run_all_graphs "bp(bp_msg_shedule=seq_fixed)          " seq_fixed
 

packages/CLPBN/benchmarks/workshop_attrs/cbp_tests.sh

@@ -32,5 +32,5 @@ function run_all_graphs
 }
 
 prepare_new_run
-run_all_graphs "cbp(shedule=seq_fixed)                " seq_fixed
+run_all_graphs "cbp(bp_msg_shedule=seq_fixed)         " seq_fixed
 

packages/CLPBN/benchmarks/workshop_attrs/gen_attrs.sh

@@ -23,7 +23,7 @@ main :-
 generate_people(S, N, Counting) :-
     Counting > N, !.
 generate_people(S, N, Counting) :-
-    format(S, 'people(p~w).~n', [Counting]),
+    format(S, 'person(p~w).~n', [Counting]),
     Counting1 is Counting + 1,
     generate_people(S, N, Counting1).
 
@@ -31,9 +31,9 @@ generate_people(S, N, Counting) :-
 generate_attrs(S, N, Counting) :-
     Counting > N, !.
 generate_attrs(S, N, Counting) :-
-    %format(S, 'people(p~w).~n', [Counting]),
+    %format(S, 'person(p~w).~n', [Counting]),
     format(S, 'markov attends(P)::[t,f], attr~w::[t,f]', [Counting]),
-    format(S, '; [0.7, 0.3, 0.3, 0.3] ; [people(P)].~n',[]),
+    format(S, '; [0.7, 0.3, 0.3, 0.3] ; [person(P)].~n',[]),
     Counting1 is Counting + 1,
     generate_attrs(S, N, Counting1).
 

packages/CLPBN/benchmarks/workshop_attrs/hve_tests.sh

@@ -32,5 +32,5 @@ function run_all_graphs
 }
 
 prepare_new_run
-run_all_graphs "hve(elim_heuristic=min_neighbors)     " min_neighbors
+run_all_graphs "hve(hve_elim_heuristic=min_neighbors) " min_neighbors
 

packages/CLPBN/benchmarks/workshop_attrs/lbp_tests.sh

@@ -32,5 +32,5 @@ function run_all_graphs
 }
 
 prepare_new_run
-run_all_graphs "lbp(shedule=seq_fixed)                " seq_fixed
+run_all_graphs "lbp(bp_msg_shedule=seq_fixed)         " seq_fixed
 

packages/CLPBN/benchmarks/workshop_attrs/wa.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-NETWORK="'../../examples/workshop_attrs'"
+NETWORK="'../../examples/workshop_attrs.pfl'"
 SHORTNAME="wa"
 QUERY="series(X)"
 

packages/CLPBN/clpbn.yap

@@ -1,40 +1,36 @@
 
-:- module(clpbn, [{}/1,
+:- module(clpbn,
+		[{}/1,
 		 clpbn_flag/2,
 		 set_clpbn_flag/2,
+		 set_solver/1,
+		 set_em_solver/1,
 		 clpbn_flag/3,
 		 clpbn_key/2,
+		 clpbn_init_graph/1,
 		 clpbn_init_solver/4,
 		 clpbn_run_solver/3,
-		  pfl_init_solver/6,
+		 pfl_init_solver/5,
-		  pfl_run_solver/4,
+		 pfl_run_solver/3,
-		  clpbn_finalize_solver/1,
+		 pfl_end_solver/1,
-		  clpbn_init_solver/5,
-		  clpbn_run_solver/4,
-		  clpbn_init_graph/1,
 		 probability/2,
 		 conditional_probability/3,
 		 use_parfactors/1,
-		  op( 500, xfy, with)]).
+		 op(500, xfy, with)
+		]).
 
 :- use_module(library(atts)).
+
 :- use_module(library(bhash)).
+
 :- use_module(library(lists)).
+
 :- use_module(library(terms)).
+
 :- use_module(library(maplist)).
 
-%
-% avoid the overhead of using goal_expansion/2.
-%
-:- multifile
-	user:term_expansion/2.
-
-:- dynamic
-	user:term_expansion/2.
-
 :- attribute key/1, dist/2, evidence/1.
 
-
 :- use_module('clpbn/ve',
 		[ve/3,
 		 check_if_ve_done/1,
@@ -45,22 +41,6 @@
 		 call_ve_ground_solver/6
 		]).
 
-:- use_module('clpbn/horus_ground',
-	      [call_horus_ground_solver/6,
-	       check_if_horus_ground_solver_done/1,
-	       init_horus_ground_solver/5,
-	       run_horus_ground_solver/4,
-	       finalize_horus_ground_solver/1
-	      ]).
-
-:- use_module('clpbn/horus_lifted',
-	      [call_horus_lifted_solver/3,
-	       check_if_horus_lifted_solver_done/1,
-	       init_horus_lifted_solver/4,
-	       run_horus_lifted_solver/3,
-	       finalize_horus_lifted_solver/1
-	      ]).
-
 :- use_module('clpbn/jt',
 		[jt/3,
 		 init_jt_solver/4,
@@ -76,11 +56,6 @@
 		 call_bdd_ground_solver/6
 		]).
 
-%% :- use_module('clpbn/bnt',
-%% 	      [do_bnt/3,
-%% 	       check_if_bnt_done/1
-%% 	      ]).
-
 :- use_module('clpbn/gibbs',
 		[gibbs/3,
 		 check_if_gibbs_done/1,
@@ -89,19 +64,34 @@
 		]).
 
 :- use_module('clpbn/pgrammar',
-	      [init_pcg_solver/4,
+		[pcg_init_graph/0,
-	       run_pcg_solver/3,
+		 init_pcg_solver/4,
-	       pcg_init_graph/0
+		 run_pcg_solver/3
 		]).
 
-:- use_module('clpbn/graphs',
+:- use_module('clpbn/horus_ground',
-	      [
+		[call_horus_ground_solver/6,
-	       clpbn2graph/1
+		 check_if_horus_ground_solver_done/1,
+		 init_horus_ground_solver/5,
+		 run_horus_ground_solver/3,
+		 end_horus_ground_solver/1
 		]).
 
+:- use_module('clpbn/horus_lifted',
+		[call_horus_lifted_solver/3,
+		 check_if_horus_lifted_solver_done/1,
+		 init_horus_lifted_solver/4,
+		 run_horus_lifted_solver/3,
+		 end_horus_lifted_solver/1
+		]).
+
+%% :- use_module('clpbn/bnt',
+%%		[do_bnt/3,
+%%		 check_if_bnt_done/1
+%%		]).
+
 :- use_module('clpbn/dists',
-	      [
+		[dist/4,
-	       dist/4,
 		 get_dist/4,
 		 get_evidence_position/3,
 		 get_evidence_from_position/3,
@@ -109,39 +99,65 @@
 		]).
 
 :- use_module('clpbn/evidence',
-	      [
+		[store_evidence/1,
-	       store_evidence/1,
 		 add_stored_evidence/2,
 		 incorporate_evidence/2,
 		 check_stored_evidence/2,
 		 put_evidence/2
 		]).
 
+:- use_module('clpbn/ground_factors',
+		[generate_network/5]).
+
 :- use_module('clpbn/utils',
-	      [
+		[sort_vars_by_key/3]).
-	       sort_vars_by_key/3
+
-	      ]).
+:- use_module('clpbn/graphs',
+		[clpbn2graph/1]).
 
 :- use_module('clpbn/graphviz',
 		[clpbn2gviz/4]).
 
-:- use_module(clpbn/ground_factors,
+%
-	[generate_network/5]).
+% avoid the overhead of using goal_expansion/2.
+%
+:- multifile user:term_expansion/2.
 
+:- dynamic user:term_expansion/2.
 
-:- dynamic solver/1,output/1,use/1,suppress_attribute_display/1, parameter_softening/1, em_solver/1, use_parfactors/1.
+:- dynamic
-
+	solver/1,
-solver(ve).
+	em_solver/1,
-em_solver(bp).
+	suppress_attribute_display/1,
+	parameter_softening/1,
+	use_parfactors/1,
+	output/1,
+	use/1.
 
 :- meta_predicate probability(:,-), conditional_probability(:,:,-).
 
-%output(xbif(user_error)).
+
-%output(gviz(user_error)).
+solver(hve).
-output(no).
+em_solver(hve).
 suppress_attribute_display(false).
 parameter_softening(m_estimate(10)).
 use_parfactors(off).
+output(no).
+%output(xbif(user_error)).
+%output(gviz(user_error)).
+
+ground_solver(ve).
+ground_solver(hve).
+ground_solver(jt).
+ground_solver(bdd).
+ground_solver(bp).
+ground_solver(cbp).
+ground_solver(gibbs).
+
+lifted_solver(lve).
+lifted_solver(lkc).
+lifted_solver(lbp).
+
 
 clpbn_flag(Flag, Option) :-
 	clpbn_flag(Flag, Option, Option).
@@ -149,34 +165,48 @@ clpbn_flag(Flag,Option) :-
 set_clpbn_flag(Flag,Option) :-
 	clpbn_flag(Flag, _, Option).
 
-clpbn_flag(output,Before,After) :-
-	retract(output(Before)),
-	assert(output(After)).
 clpbn_flag(solver,Before,After) :-
 	retract(solver(Before)),
 	assert(solver(After)).
+
 clpbn_flag(em_solver,Before,After) :-
 	retract(em_solver(Before)),
 	assert(em_solver(After)).
+
 clpbn_flag(bnt_solver,Before,After) :-
 	retract(bnt:bnt_solver(Before)),
 	assert(bnt:bnt_solver(After)).
+
 clpbn_flag(bnt_path,Before,After) :-
 	retract(bnt:bnt_path(Before)),
 	assert(bnt:bnt_path(After)).
+
 clpbn_flag(bnt_model,Before,After) :-
 	retract(bnt:bnt_model(Before)),
 	assert(bnt:bnt_model(After)).
+
 clpbn_flag(suppress_attribute_display,Before,After) :-
 	retract(suppress_attribute_display(Before)),
 	assert(suppress_attribute_display(After)).
+
 clpbn_flag(parameter_softening,Before,After) :-
 	retract(parameter_softening(Before)),
 	assert(parameter_softening(After)).
+
 clpbn_flag(use_factors,Before,After) :-
 	retract(use_parfactors(Before)),
 	assert(use_parfactors(After)).
 
+clpbn_flag(output,Before,After) :-
+	retract(output(Before)),
+	assert(output(After)).
+
+set_solver(Solver) :-
+	set_clpbn_flag(solver,Solver).
+
+set_em_solver(Solver) :-
+	set_clpbn_flag(em_solver,Solver).
+
 {_} :-
 	solver(none), !.
 { Var = Key with Dist } :-
@@ -203,8 +233,10 @@ init_clpbn_vars(El) :-
 	create_mutable(El, Mutable),
 	b_setval(clpbn_qvars, Mutable).
 
-check_constraint(Constraint, _, _, Constraint) :- var(Constraint), !.
+check_constraint(Constraint, _, _, Constraint) :-
-check_constraint((A->D), _, _, (A->D)) :- var(A), !.
+	var(Constraint), !.
+check_constraint((A->D), _, _, (A->D)) :-
+	var(A), !.
 check_constraint((([A|B].L)->D), Vars, NVars, (([A|B].NL)->D)) :- !,
 	check_cpt_input_vars(L, Vars, NVars, NL).
 check_constraint(Dist, _, _, Dist).
@@ -240,11 +272,13 @@ clpbn_marginalise(V, Dist) :-
 %
 project_attributes(GVars0, _AVars0) :-
 	use_parfactors(on),
-	clpbn_flag(solver, Solver), Solver \= fove, !,
+	clpbn_flag(solver, Solver),
+	ground_solver(Solver),
 	generate_network(GVars0, GKeys, Keys, Factors, Evidence),
 	b_setval(clpbn_query_variables, f(GVars0,Evidence)),
 	simplify_query(GVars0, GVars),
-	( GKeys = [] 
+	(
+	  GKeys = []
 	->
 	  GVars0 = [V|_],
 	  clpbn_display:put_atts(V, [posterior([],[],[],[])])
@@ -322,35 +356,27 @@ get_rid_of_ev_vars([V|LVs0],[V|LVs]) :-
 	get_rid_of_ev_vars(LVs0,LVs).
 
 
-% do nothing if we don't have query variables to compute.
+% Call a solver with keys, not actual variables
-write_out(_, [], _, _) :- !.
-write_out(graphs, _, AVars, _) :-
-	clpbn2graph(AVars).
-write_out(ve, GVars, AVars, DiffVars) :-
-	ve(GVars, AVars, DiffVars).
-write_out(jt, GVars, AVars, DiffVars) :-
-	jt(GVars, AVars, DiffVars).
-write_out(bdd, GVars, AVars, DiffVars) :-
-	bdd(GVars, AVars, DiffVars).
-write_out(bp, _GVars, _AVars, _DiffVars) :- 
-    writeln('interface not supported any longer').
-	%bp(GVars, AVars, DiffVars).
-write_out(gibbs, GVars, AVars, DiffVars) :-
-	gibbs(GVars, AVars, DiffVars).
-write_out(bnt, GVars, AVars, DiffVars) :-
-	do_bnt(GVars, AVars, DiffVars).
-write_out(fove, GVars, AVars, DiffVars) :-
-	call_horus_lifted_solver(GVars, AVars, DiffVars).
-
-% call a solver with keys, not actual variables
-call_ground_solver(bp, GVars, GoalKeys, Keys, Factors, Evidence) :- !,
-	call_horus_ground_solver(GVars, GoalKeys, Keys, Factors, Evidence, _Answ).
-call_ground_solver(bdd, GVars, GoalKeys, Keys, Factors, Evidence) :- !,
-	call_bdd_ground_solver(GVars, GoalKeys, Keys, Factors, Evidence, _Answ).
 call_ground_solver(ve, GVars, GoalKeys, Keys, Factors, Evidence) :- !,
 	call_ve_ground_solver(GVars, GoalKeys, Keys, Factors, Evidence, _Answ).
+
+call_ground_solver(hve, GVars, GoalKeys, Keys, Factors, Evidence) :- !,
+	clpbn_horus:set_horus_flag(ground_solver, ve),
+	call_horus_ground_solver(GVars, GoalKeys, Keys, Factors, Evidence, _Answ).
+
+call_ground_solver(bdd, GVars, GoalKeys, Keys, Factors, Evidence) :- !,
+	call_bdd_ground_solver(GVars, GoalKeys, Keys, Factors, Evidence, _Answ).
+
+call_ground_solver(bp, GVars, GoalKeys, Keys, Factors, Evidence) :- !,
+	clpbn_horus:set_horus_flag(ground_solver, bp),
+	call_horus_ground_solver(GVars, GoalKeys, Keys, Factors, Evidence, _Answ).
+
+call_ground_solver(cbp, GVars, GoalKeys, Keys, Factors, Evidence) :- !,
+	clpbn_horus:set_horus_flag(ground_solver, cbp),
+	call_horus_ground_solver(GVars, GoalKeys, Keys, Factors, Evidence, _Answ).
+
 call_ground_solver(Solver, GVars, _GoalKeys, Keys, Factors, Evidence) :-
-	% traditional solver
+	% fall back to traditional solver
 	b_hash_new(Hash0),
 	foldl(gvar_in_hash, GVars, Hash0, HashI),
 	foldl(key_to_var, Keys, AllVars, HashI, Hash1),
@@ -362,6 +388,44 @@ call_ground_solver(Solver, GVars, _GoalKeys, Keys, Factors, Evidence) :-
 	write_out(Solver, [GVars], AllVars, _),
 	assert(use_parfactors(on)).
 
+
+% do nothing if we don't have query variables to compute.
+write_out(_, [], _, _) :- !.
+
+write_out(graphs, _, AVars, _) :- !,
+	clpbn2graph(AVars).
+
+write_out(ve, GVars, AVars, DiffVars) :- !,
+	ve(GVars, AVars, DiffVars).
+
+write_out(jt, GVars, AVars, DiffVars) :- !,
+	jt(GVars, AVars, DiffVars).
+
+write_out(bdd, GVars, AVars, DiffVars) :- !,
+	bdd(GVars, AVars, DiffVars).
+
+write_out(gibbs, GVars, AVars, DiffVars) :- !,
+	gibbs(GVars, AVars, DiffVars).
+
+write_out(lve, GVars, AVars, DiffVars) :- !,
+	clpbn_horus:set_horus_flag(lifted_solver, lve),
+	call_horus_lifted_solver(GVars, AVars, DiffVars).
+
+write_out(lkc, GVars, AVars, DiffVars) :- !,
+	clpbn_horus:set_horus_flag(lifted_solver, lkc),
+	call_horus_lifted_solver(GVars, AVars, DiffVars).
+
+write_out(lbp, GVars, AVars, DiffVars) :- !,
+	clpbn_horus:set_horus_flag(lifted_solver, lbp),
+	call_horus_lifted_solver(GVars, AVars, DiffVars).
+
+write_out(bnt, GVars, AVars, DiffVars) :- !,
+	do_bnt(GVars, AVars, DiffVars).
+
+write_out(Solver, _, _, _) :-
+	format("Error: solver '~w' is unknown.", [Solver]),
+	fail.
+
 %
 % convert a PFL network (without constraints)
 % into CLP(BN) for evaluation
@@ -466,14 +530,11 @@ bind_clpbn(T, Var, Key, Dist, Parents, []) :- var(T),
 	;
 	  fail
 	).
-bind_clpbn(_, Var, _, _, _, _, []) :-
-	use(bnt),
-	check_if_bnt_done(Var), !.
 bind_clpbn(_, Var, _, _, _, _, []) :-
 	use(ve),
 	check_if_ve_done(Var), !.
 bind_clpbn(_, Var, _, _, _, _, []) :-
-	use(bp),
+	use(hve),
 	check_if_horus_ground_solver_done(Var), !.
 bind_clpbn(_, Var, _, _, _, _, []) :-
 	use(jt),
@@ -481,6 +542,15 @@ bind_clpbn(_, Var, _, _, _, _, []) :-
 bind_clpbn(_, Var, _, _, _, _, []) :-
 	use(bdd),
 	check_if_bdd_done(Var), !.
+bind_clpbn(_, Var, _, _, _, _, []) :-
+	use(bp),
+	check_if_horus_ground_solver_done(Var), !.
+bind_clpbn(_, Var, _, _, _, _, []) :-
+	use(cbp),
+	check_if_horus_ground_solver_done(Var), !.
+bind_clpbn(_, Var, _, _, _, _, []) :-
+	use(bnt),
+	check_if_bnt_done(Var), !.
 bind_clpbn(T, Var, Key0, _, _, _, []) :-
 	get_atts(Var, [key(Key)]), !,
 	(
@@ -532,6 +602,15 @@ user:term_expansion((A :- {}), ( :- true )) :-	 !, % evidence
 clpbn_key(Var,Key) :-
 	get_atts(Var, [key(Key)]).
 
+
+%
+% only useful for probabilistic context free grammars
+%
+clpbn_init_graph(pcg) :- !,
+	pcg_init_graph.
+clpbn_init_graph(_).
+
+
 %
 % This is a routine to start a solver, called by the learning procedures (ie, em).
 % LVs is a list of lists of variables one is interested in eventually marginalising out
@@ -544,90 +623,112 @@ clpbn_init_solver(LVs, Vs0, VarsWithUnboundKeys, State) :-
 	solver(Solver),
 	clpbn_init_solver(Solver, LVs, Vs0, VarsWithUnboundKeys, State).
 
-clpbn_init_solver(gibbs, LVs, Vs0, VarsWithUnboundKeys, State) :-
-	init_gibbs_solver(LVs, Vs0, VarsWithUnboundKeys, State).
 clpbn_init_solver(ve, LVs, Vs0, VarsWithUnboundKeys, State) :-
 	init_ve_solver(LVs, Vs0, VarsWithUnboundKeys, State).
-clpbn_init_solver(bp, LVs, Vs0, VarsWithUnboundKeys, State) :-
+
-	init_horus_ground_solver(LVs, Vs0, VarsWithUnboundKeys, State).
 clpbn_init_solver(jt, LVs, Vs0, VarsWithUnboundKeys, State) :-
 	init_jt_solver(LVs, Vs0, VarsWithUnboundKeys, State).
+
 clpbn_init_solver(bdd, LVs, Vs0, VarsWithUnboundKeys, State) :-
 	init_bdd_solver(LVs, Vs0, VarsWithUnboundKeys, State).
+
+clpbn_init_solver(gibbs, LVs, Vs0, VarsWithUnboundKeys, State) :-
+	init_gibbs_solver(LVs, Vs0, VarsWithUnboundKeys, State).
+
 clpbn_init_solver(pcg, LVs, Vs0, VarsWithUnboundKeys, State) :-
 	init_pcg_solver(LVs, Vs0, VarsWithUnboundKeys, State).
 
-%
-% This is a routine to start a solver, called by the learning procedures (ie, em).
-% LVs is a list of lists of variables one is interested in eventually marginalising out
-% Vs0 gives the original graph
-% AllDiffs gives variables that are not fully constrainted, ie, we don't fully know
-% the key. In this case, we assume different instances will be bound to different
-% values at the end of the day.
-%
-pfl_init_solver(QueryKeys, AllKeys, Factors, Evidence, VE, bdd) :-
-	init_bdd_ground_solver(QueryKeys, AllKeys, Factors, Evidence, VE).
-pfl_init_solver(QueryKeys, AllKeys, Factors, Evidence, VE, ve) :-
-	init_ve_ground_solver(QueryKeys, AllKeys, Factors, Evidence, VE).
-pfl_init_solver(QueryKeys, AllKeys, Factors, Evidence, VE, bp) :-
-	init_horus_ground_solver(QueryKeys, AllKeys, Factors, Evidence, VE).
-pfl_init_solver(QueryKeys, AllKeys, Factors, Evidence, VE, hve) :-
-	init_horus_ground_solver(QueryKeys, AllKeys, Factors, Evidence, VE).
-
-
 %
 % LVs is the list of lists of variables to marginalise
 % Vs is the full graph
 % Ps are the probabilities on LVs.
 %
-%
 clpbn_run_solver(LVs, LPs, State) :-
 	solver(Solver),
 	clpbn_run_solver(Solver, LVs, LPs, State).
 
-clpbn_run_solver(gibbs, LVs, LPs, State) :-
-	run_gibbs_solver(LVs, LPs, State).
-
 clpbn_run_solver(ve, LVs, LPs, State) :-
 	run_ve_solver(LVs, LPs, State).
 
-clpbn_run_solver(bp, LVs, LPs, State) :-
-	run_horus_ground_solver(LVs, LPs, State).
-
 clpbn_run_solver(jt, LVs, LPs, State) :-
 	run_jt_solver(LVs, LPs, State).
 
 clpbn_run_solver(bdd, LVs, LPs, State) :-
 	run_bdd_solver(LVs, LPs, State).
 
+clpbn_run_solver(gibbs, LVs, LPs, State) :-
+	run_gibbs_solver(LVs, LPs, State).
+
 clpbn_run_solver(pcg, LVs, LPs, State) :-
 	run_pcg_solver(LVs, LPs, State).
 
-pfl_run_solver(LVs, LPs, State, ve) :-
+%
+% This is a routine to start a solver, called by the learning procedures (ie, em).
+%
+pfl_init_solver(QueryKeys, AllKeys, Factors, Evidence, State) :-
+	em_solver(Solver),
+	(lifted_solver(Solver) ->
+	  format("Error: you cannot use a lifted solver for learning.", [Solver]), fail
+	;
+	  true
+	),
+	(ground_solver(Solver) ->
+	  true
+	;
+	  format("Error: solver '~w' is unknown.", [Solver]), fail
+	),
+	pfl_init_solver(QueryKeys, AllKeys, Factors, Evidence, State, Solver).
+
+pfl_init_solver(QueryKeys, AllKeys, Factors, Evidence, State, ve) :- !,
+	init_ve_ground_solver(QueryKeys, AllKeys, Factors, Evidence, State).
+
+pfl_init_solver(QueryKeys, AllKeys, Factors, Evidence, State, hve) :- !,
+	clpbn_horus:set_horus_flag(ground_solver, ve),
+	init_horus_ground_solver(QueryKeys, AllKeys, Factors, Evidence, State).
+
+pfl_init_solver(QueryKeys, AllKeys, Factors, Evidence, State, bdd) :- !,
+	init_bdd_ground_solver(QueryKeys, AllKeys, Factors, Evidence, State).
+
+pfl_init_solver(QueryKeys, AllKeys, Factors, Evidence, State, bp) :- !,
+	clpbn_horus:set_horus_flag(ground_solver, bp),
+	init_horus_ground_solver(QueryKeys, AllKeys, Factors, Evidence, State).
+
+pfl_init_solver(QueryKeys, AllKeys, Factors, Evidence, State, cbp) :- !,
+	clpbn_horus:set_horus_flag(ground_solver, cbp),
+	init_horus_ground_solver(QueryKeys, AllKeys, Factors, Evidence, State).
+
+pfl_init_solver(_, _, _, _, _, Solver) :-
+	format("Error: solver '~w' can't be used for learning.", [Solver]),
+	fail.
+
+
+pfl_run_solver(LVs, LPs, State) :-
+	em_solver(Solver),
+	pfl_run_solver(LVs, LPs, State, Solver).
+
+pfl_run_solver(LVs, LPs, State, ve) :- !,
 	run_ve_ground_solver(LVs, LPs, State).
-pfl_run_solver(LVs, LPs, State, bdd) :-
+
+pfl_run_solver(LVs, LPs, State, hve) :- !,
+	run_horus_ground_solver(LVs, LPs, State).
+
+pfl_run_solver(LVs, LPs, State, bdd) :- !,
 	run_bdd_ground_solver(LVs, LPs, State).
-pfl_run_solver(LVs, LPs, State, bp) :-
+
-	run_horus_ground_solver(LVs, LPs, State, bp).
+pfl_run_solver(LVs, LPs, State, bp) :- !,
-pfl_run_solver(LVs, LPs, State, hve) :-
+	run_horus_ground_solver(LVs, LPs, State).
-    run_horus_ground_solver(LVs, LPs, State, hve).
+
+pfl_run_solver(LVs, LPs, State, cbp) :- !,
+	run_horus_ground_solver(LVs, LPs, State).
+
+pfl_end_solver(State) :-
+	(em_solver(hve) ; em_solver(bp) ; em_solver(cbp)),
+	end_horus_ground_solver(State).
+pfl_end_solver(_State).
 
 
 add_keys(Key1+V1,_Key2,Key1+V1).
 
-%
-% only useful for probabilistic context free grammars
-%
-clpbn_init_graph(pcg) :- !,
-	pcg_init_graph.
-clpbn_init_graph(_).
-
-clpbn_finalize_solver(State) :-
-	solver(bp), !,
-	functor(State, _, Last),
-	arg(Last, State, Info),
-	finalize_horus_ground_solver(Info).
-clpbn_finalize_solver(_State).
 
 probability(Goal, Prob) :-
 	findall(Prob, do_probability(Goal, [], Prob), [Prob]).

packages/CLPBN/clpbn/aggregates.yap

@@ -1,8 +1,8 @@
 %
 % generate explicit CPTs
 %
-:- module(clpbn_aggregates, [
+:- module(clpbn_aggregates,
-        check_for_agg_vars/2,
+		[check_for_agg_vars/2,
 		 cpt_average/6,
 		 cpt_average/7,
 		 cpt_max/6,
@@ -10,7 +10,8 @@
 		 avg_factors/5
 		]).
 
-:- use_module(library(clpbn), [{}/1]).
+:- use_module(library(clpbn),
+		[{}/1]).
 
 :- use_module(library(lists),
 		[last/2,
@@ -24,19 +25,21 @@
 :- use_module(library(matrix),
 		[matrix_new/3,
 		 matrix_to_list/2,
-	matrix_set/3]).
+		 matrix_set/3
+		]).
 
 :- use_module(library(clpbn/dists),
-	      [
+		[add_dist/6,
-	       add_dist/6,
+		 get_dist_domain_size/2
-	       get_dist_domain_size/2]).
+		]).
 
 :- use_module(library(clpbn/matrix_cpt_utils),
 		[normalise_CPT_on_lines/3]).
 
 :- use_module(library(pfl),
 		[skolem/2,
-	 add_ground_factor/5]).
+		 add_ground_factor/5
+		]).
 
 :- use_module(library(bhash)).
 
@@ -270,7 +273,9 @@ include_qevidence(_, MAT, MAT, NewParents, NewParents, _, Vs, Vs).
 check_consistency(L1, Ev, MAT0, MAT1, L1, MAT, NewParents0, NewParents, Vs, IVs, NewVs) :-
 	sumlist(L1, Tot),
 	nth0(Ev, L1, Val),
-	(Val == Tot ->
+	(
+	  Val == Tot
+	->
 	  MAT1 = MAT,
 	  NewParents = [],
 	  Vs = NewVs

packages/CLPBN/clpbn/bdd.yap

@@ -1064,4 +1064,3 @@ build_cnf(CNF, IVs, Indics, AllParms, AllParmValues, Val) :-
 	set_to_ones(Extra),
 	ddnnf_is(F, Val).
 
-

packages/CLPBN/clpbn/bnt.yap

@@ -1,20 +1,23 @@
-:- module(bnt, [do_bnt/3,
+:- module(bnt,
+		[do_bnt/3,
 		 create_bnt_graph/2,
-		check_if_bnt_done/1]).
+		 check_if_bnt_done/1
+		]).
 
-:- use_module(library('clpbn/display'), [
+:- use_module(library('clpbn/display'),
-	clpbn_bind_vals/3]).
+		[clpbn_bind_vals/3]).
 
-:- use_module(library('clpbn/dists'), [
+:- use_module(library('clpbn/dists'),
-				       get_dist_domain_size/2,
+		[get_dist_domain_size/2,
 		 get_dist_domain/2,
 		 get_dist_params/2
 		]).
 
-:- use_module(library('clpbn/discrete_utils'), [
+:- use_module(library('clpbn/discrete_utils'),
-	reorder_CPT/5]).
+		[reorder_CPT/5]).
 
-:- use_module(library(matlab), [start_matlab/1,
+:- use_module(library(matlab),
+		[start_matlab/1,
 		 close_matlab/0,
 		 matlab_on/0,
 		 matlab_eval_string/1,
@@ -27,7 +30,8 @@
 		 matlab_call/2
 		]).
 
-:- use_module(library(dgraphs), [dgraph_new/1,
+:- use_module(library(dgraphs),
+		[dgraph_new/1,
 		 dgraph_add_vertices/3,
 		 dgraph_add_edges/3,
 		 dgraph_top_sort/2,
@@ -35,11 +39,13 @@
 		 dgraph_edges/2
 		]).
 
-:- use_module(library(lists), [append/3,
+:- use_module(library(lists),
-	member/2,nth/3]).
+		[append/3,
+		 member/2,nth/3
+		]).
 
-:- use_module(library(ordsets), [
+:- use_module(library(ordsets),
-	ord_insert/3]).
+		[ord_insert/3]).
 
 :- yap_flag(write_strings,on).
 
@@ -422,4 +428,3 @@ mk_evidence_query([V|L], [H|T], [ar(1,Pos,El)|LN]) :-
 	nth(El,D,H),
 	mk_evidence_query(L, T, LN).
 
-

packages/CLPBN/clpbn/connected.yap

@@ -3,8 +3,8 @@
 		[influences/3,
 		 factor_influences/4,
 		 init_influences/3,
-	 influences/4]
+		 influences/4
-	 ).
+		]).
 
 :- use_module(library(maplist)).
 
@@ -14,13 +14,15 @@
 		 dgraph_add_vertex/3,
 		 dgraph_neighbors/3,
 		 dgraph_edge/3,
-	dgraph_transpose/2]).
+		 dgraph_transpose/2
+		]).
 
 :- use_module(library(rbtrees),
 		[rb_new/1,
 		 rb_lookup/3,
 		 rb_insert/4,
-	rb_visit/2]).
+		 rb_visit/2
+		]).
 
 factor_influences(Vs, QVars, Ev, LV) :-
 	init_factor_influences(Vs, G, RG),
@@ -90,7 +92,8 @@ process_new_variable(V, Evs, G, RG, Vs0, Vs2) :-
 throw_below(Evs, G, RG, Child, Vs0, Vs1) :-
 	rb_lookup(Child, [_|B], Vs0), !,
 	(
-	    B == b ->
+	  B == b
+	->
 	  Vs0 = Vs1  % been there before
 	;
 	  B = b, % mark it
@@ -120,7 +123,8 @@ handle_ball_from_above(V, Evs, G, RG, Vs0, Vs1) :-
 throw_above(Evs, G, RG, Parent, Vs0, Vs1) :-
 	rb_lookup(Parent, [T|_], Vs0), !,
 	(
-	    T == t ->
+	  T == t
+	->
 	  Vs1 = Vs0  % been there before
 	;
 	  T = t, % mark it

packages/CLPBN/clpbn/discrete_utils.yap

@@ -1,10 +1,14 @@
 
-:- module(discrete_utils, [project_from_CPT/3,
+:- module(discrete_utils,
+		[project_from_CPT/3,
 		 reorder_CPT/5,
-			   get_dist_size/2]).
+		 get_dist_size/2
+		]).
 
-:- use_module(library(clpbn/dists), [get_dist_domain_size/2,
+:- use_module(library(clpbn/dists),
-		      get_dist_domain/2]).
+		[get_dist_domain_size/2,
+		 get_dist_domain/2
+		]).
 %
 % remove columns from a table
 %
@@ -143,4 +147,3 @@ get_sizes([V|Deps], [Sz|Sizes]) :-
 	get_dist_domain_size(Id,Sz),
 	get_sizes(Deps, Sizes).
 
-

packages/CLPBN/clpbn/display.yap

@@ -1,17 +1,20 @@
-:- module(clpbn_display, [
+
-	clpbn_bind_vals/3]).
+:- module(clpbn_display,
+		[clpbn_bind_vals/3]).
 
 :- use_module(library(lists),
-	      [
+		[member/2]).
-	       member/2
-	      ]).
 
-:- use_module(library(clpbn/dists), [get_dist_domain/2]).
+:- use_module(library(clpbn/dists),
+		[get_dist_domain/2]).
 
-:- use_module(library(clpbn), [use_parfactors/1]).
+:- use_module(library(clpbn),
+		[use_parfactors/1]).
 
 :- use_module(library(maplist)).
 
+:- use_module(library(atts)).
+
 :- attribute posterior/4.
 
 

packages/CLPBN/clpbn/dists.yap

@@ -3,8 +3,7 @@
 %
 
 :- module(clpbn_dist,
-	  [
+		[dist/1,
-	   dist/1,
 		 dist/4,
 		 dists/1,
 		 dist_new_table/2,
@@ -30,7 +29,10 @@
 		 additive_dists/6
 		]).
 
-:- use_module(library(lists),[nth0/3,append/3]).
+:- use_module(library(lists),
+		[nth0/3,
+		 append/3
+		]).
 
 :- use_module(library(clpbn),
 		[use_parfactors/1]).
@@ -39,11 +41,13 @@
 		[matrix_new/4,
 		 matrix_new/3,
 		 matrix_to_list/2,
-	       matrix_to_logs/1]).
+		 matrix_to_logs/1
+		]).
 
 :- use_module(library(clpbn/matrix_cpt_utils),
 		[random_CPT/2,
-	       uniform_CPT/2]).
+		 uniform_CPT/2
+		]).
 
 /*
 :- mode dist(+, -).
@@ -365,3 +369,4 @@ reset_all_dists.
 additive_dists(ip(Domain,Tabs1), ip(Domain,Tabs2), Parents1, Parents2, ip(Domain,Tabs), Parents) :-
 	append(Tabs1, Tabs2, Tabs),
 	append(Parents1, Parents2, Parents).
+

packages/CLPBN/clpbn/evidence.yap

@@ -4,26 +4,24 @@
 %
 
 :- module(clpbn_evidence,
-	  [
+		[store_evidence/1,
-	   store_evidence/1,
 		 incorporate_evidence/2,
 		 check_stored_evidence/2,
 		 add_stored_evidence/2,
 		 put_evidence/2
 		]).
 
-:- use_module(library(clpbn), [
+:- use_module(library(clpbn),
-	{}/1,
+		[{}/1,
 		 clpbn_flag/3,
 		 set_clpbn_flag/2
 		]).
 
-:- use_module(library('clpbn/dists'), [
+:- use_module(library('clpbn/dists'),
-	get_dist/4
+		[get_dist/4]).
-    ]).
 
-:- use_module(library(rbtrees), [
+:- use_module(library(rbtrees),
-	rb_new/1,
+		[rb_new/1,
 		 rb_lookup/3,
 		 rb_insert/4
 		]).
@@ -86,7 +84,6 @@ add_links([K0|TVs],K) :-
 	assert(edge(K,K0)),
 	add_links(TVs,K).
 
-
 incorporate_evidence(Vs,AllVs) :-
 	rb_new(Cache0),
 	create_open_list(Vs, OL, FL, Cache0, CacheI),

packages/CLPBN/clpbn/gibbs.yap

@@ -11,48 +11,51 @@
 		[gibbs/3,
 		 check_if_gibbs_done/1,
 		 init_gibbs_solver/4,
-	   run_gibbs_solver/3]).
+		 run_gibbs_solver/3
+		]).
 
 :- use_module(library(rbtrees),
 		[rb_new/1,
 		 rb_insert/4,
-	       rb_lookup/3]).
+		 rb_lookup/3
+		]).
 
 :- use_module(library(lists),
 		[member/2,
 		 append/3,
 		 delete/3,
 		 max_list/2,
-	       sum_list/2]).
+		 sum_list/2
+		]).
 
 :- use_module(library(ordsets),
 		[ord_subtract/3]).
 
-:- use_module(library('clpbn/matrix_cpt_utils'), [
+:- use_module(library('clpbn/matrix_cpt_utils'),
-	project_from_CPT/3,
+		[project_from_CPT/3,
 		 reorder_CPT/5,
 		 multiply_possibly_deterministic_factors/3,
 		 column_from_possibly_deterministic_CPT/3,
 		 normalise_possibly_deterministic_CPT/2,
-	list_from_CPT/2]).
+		 list_from_CPT/2
+		]).
 
-:- use_module(library('clpbn/utils'), [
+:- use_module(library('clpbn/utils'),
-	check_for_hidden_vars/3]).
+		[check_for_hidden_vars/3]).
 
-:- use_module(library('clpbn/dists'), [
+:- use_module(library('clpbn/dists'),
-	get_possibly_deterministic_dist_matrix/5,
+		[get_possibly_deterministic_dist_matrix/5,
-	get_dist_domain_size/2]).
+		 get_dist_domain_size/2
+		]).
 
-:- use_module(library('clpbn/topsort'), [
+:- use_module(library('clpbn/topsort'),
-	topsort/2]).
+		[topsort/2]).
 
-:- use_module(library('clpbn/display'), [
+:- use_module(library('clpbn/display'),
-	clpbn_bind_vals/3]).
+		[clpbn_bind_vals/3]).
 
 :- use_module(library('clpbn/connected'),
-	      [
+		[influences/3]).
-	       influences/3
-	      ]).
 
 :- dynamic gibbs_params/3.
 
@@ -542,5 +545,3 @@ divide_list([C|Add], Sum, [P|Dist]) :-
 	P is C/Sum,
 	divide_list(Add, Sum, Dist).
 
-
-

packages/CLPBN/clpbn/graphs.yap

@@ -3,13 +3,14 @@
 % Just output a graph with all the variables.
 %
 
-:- module(clpbn2graph, [clpbn2graph/1]).
+:- module(clpbn2graph,
+		[clpbn2graph/1]).
 
-:- use_module(library('clpbn/utils'), [
+:- use_module(library('clpbn/utils'),
-	check_for_hidden_vars/3]).
+		[check_for_hidden_vars/3]).
 
-:- use_module(library('clpbn/dists'), [
+:- use_module(library('clpbn/dists'),
-	get_dist/4]).
+		[get_dist/4]).
 
 :- attribute node/0.
 
@@ -37,7 +38,3 @@ translate_vars([V|Vs],[K|Ks]) :-
 	clpbn:get_atts(V, [key(K)]),
 	translate_vars(Vs,Ks).
 
-
-
-
-

packages/CLPBN/clpbn/graphviz.yap

@@ -1,4 +1,6 @@
-:- module(clpbn_gviz, [clpbn2gviz/4]).
+
+:- module(clpbn_gviz,
+		[clpbn2gviz/4]).
 
 clpbn2gviz(Stream, Name, Network, Output) :-
 	format(Stream, 'digraph ~w {

packages/CLPBN/clpbn/ground_factors.yap

@@ -1,40 +1,34 @@
 
-%parfactor(
+:- module(pfl_ground_factors,
-%	[ability(P),grade(C,S), satisfaction(C,S,P)],
+		[generate_network/5,
-%        \phi = [....], 
-%       [P,C,S],
-%	[P \in [p1,p2,p4], C \in [c1,c3], S \in [s2,s3]]).
-%	[S \= s2])
-
-
-:- module(pfl_ground_factors, [
-          generate_network/5,
 		 f/3
 		]).
 
-:- use_module(library(bhash), [
+:- use_module(library(bhash),
-          b_hash_new/1,
+		[b_hash_new/1,
 		 b_hash_lookup/3,
 		 b_hash_insert/4,
-	  b_hash_to_list/2]).
+		 b_hash_to_list/2
+		]).
 
-:- use_module(library(lists), [
+:- use_module(library(lists),
-          delete/3,
+		[member/2]).
-	  nth0/3,
-	  member/2]).
 
 :- use_module(library(maplist)).
 
-:- use_module(library(pfl), [
+:- use_module(library(atts)).
-          factor/6,
+
+:- use_module(library(pfl),
+		[factor/6,
 		 defined_in_factor/2,
-	  skolem/2]).
+		 skolem/2
+		]).
 
-:- use_module(library(clpbn/aggregates), [
+:- use_module(library(clpbn/aggregates),
-          avg_factors/5]).
+		[avg_factors/5]).
 
-:- use_module(library(clpbn/dists), [
+:- use_module(library(clpbn/dists),
-          dist/4]).
+		[dist/4]).
 
 :- dynamic currently_defined/1, queue/1, f/4.
 
@@ -140,7 +134,8 @@ do_propagate(_K) :-
 
 add_factor(factor(Type, Id, Ks, _, _Phi, Constraints), NKs) :-
 %	writeln(+Ks),
-	( Ks = [K,Els], var(Els)
+	(
+	  Ks = [K,Els], var(Els)
 	->
 	  % aggregate factor
 	  once(run(Constraints)),

packages/CLPBN/clpbn/hmm.yap

@@ -1,8 +1,9 @@
 
-
+:- module(hmm,
-:- module(hmm, [init_hmm/0,
+		[init_hmm/0,
 		 hmm_state/1,
-		  emission/1]).
+		 emission/1
+		]).
 
 :- ensure_loaded(library(clpbn)).
 
@@ -49,18 +50,15 @@ hmm_state(N/A,Mod) :-
 	  (First > 2 ->
 	    Last = Key, !
 	  ;
-		  nb_getval(trie, Trie), trie_check_entry(Trie, Key, _)
+	    nb_getval(trie, Trie), trie_check_entry(Trie, Key, _) ->
-		->
 	      % leave work for solver!
-		  %
 	      Last = Key, !
 	    ;
 	      % first time we saw this entry
 	      nb_getval(trie, Trie), trie_put_entry(Trie, Key, _),
 	      fail
 	  )
-	      )
+	)).
-	      ).
 
 build_args(4,[A,B,C,D],[A,B,C],A,D).
 build_args(3,  [A,B,C],  [A,B],A,C).
@@ -79,5 +77,3 @@ cvt_vals([A|B],[A|B]).
 find_probs(Logs,Nth,Log) :-
 	arg(Nth,Logs,Log).
 
-
-

packages/CLPBN/clpbn/horus.yap

@@ -5,12 +5,11 @@
 ********************************************************/
 
 :- module(clpbn_horus,
-          [set_solver/1,
+		[set_horus_flag/2,
-           set_horus_flag/1,
 		 cpp_create_lifted_network/3,
 		 cpp_create_ground_network/4,
-           cpp_set_parfactors_params/2,
+		 cpp_set_parfactors_params/3,
-           cpp_set_factors_params/2,
+		 cpp_set_factors_params/3,
 		 cpp_run_lifted_solver/3,
 		 cpp_run_ground_solver/3,
 		 cpp_set_vars_information/2,
@@ -19,8 +18,9 @@
 		 cpp_free_ground_network/1
 		]).
 
-:- use_module(library(clpbn),
+
-	[set_clpbn_flag/2]).
+:- catch(load_foreign_files([horus], [], init_predicates), _, patch_things_up)
+	-> true ; warning.
 
 
 patch_things_up :-
@@ -28,38 +28,29 @@ patch_things_up :-
 
 
 warning :-
-  format(user_error,"Horus library not installed: cannot use bp, fove~n.",[]).
+	format(user_error,"Horus library not installed: cannot use hve, bp, cbp, lve, lkc and lbp~n.",[]).
-
-
-:- catch(load_foreign_files([horus], [], init_predicates), _, patch_things_up)
-    -> true ; warning.
-
-
-set_solver(ve)    :- !, set_clpbn_flag(solver,ve).
-set_solver(bdd)   :- !, set_clpbn_flag(solver,bdd).
-set_solver(jt)    :- !, set_clpbn_flag(solver,jt).
-set_solver(gibbs) :- !, set_clpbn_flag(solver,gibbs).
-set_solver(lve)   :- !, set_clpbn_flag(solver,fove), set_horus_flag(lifted_solver, lve).
-set_solver(lbp)   :- !, set_clpbn_flag(solver,fove), set_horus_flag(lifted_solver, lbp).
-set_solver(lkc)   :- !, set_clpbn_flag(solver,fove), set_horus_flag(lifted_solver, lkc).
-set_solver(hve)   :- !, set_clpbn_flag(solver,bp),   set_horus_flag(ground_solver, ve).
-set_solver(bp)    :- !, set_clpbn_flag(solver,bp),   set_horus_flag(ground_solver, bp).
-set_solver(cbp)   :- !, set_clpbn_flag(solver,bp),   set_horus_flag(ground_solver, cbp).
-set_solver(S)     :- throw(error('unknown solver ', S)).
 
 
 set_horus_flag(K,V) :- cpp_set_horus_flag(K,V).
 
 
-:- cpp_set_horus_flag(schedule, seq_fixed).
+:- cpp_set_horus_flag(verbosity, 0).
-%:- cpp_set_horus_flag(schedule, seq_random).
-%:- cpp_set_horus_flag(schedule, parallel).
-%:- cpp_set_horus_flag(schedule, max_residual).
 
-:- cpp_set_horus_flag(accuracy, 0.0001).
+%:- cpp_set_horus_flag(use_logarithms, false).
+:- cpp_set_horus_flag(use_logarithms, true).
 
-:- cpp_set_horus_flag(max_iter, 1000).
+%:- cpp_set_horus_flag(hve_elim_heuristic, sequential).
+%:- cpp_set_horus_flag(hve_elim_heuristic, min_neighbors).
+%:- cpp_set_horus_flag(hve_elim_heuristic, min_weight).
+%:- cpp_set_horus_flag(hve_elim_heuristic, min_fill).
+:- cpp_set_horus_flag(hve_elim_heuristic, weighted_min_fill).
 
-:- cpp_set_horus_flag(use_logarithms, false).
+:- cpp_set_horus_flag(bp_msg_schedule, seq_fixed).
-% :- cpp_set_horus_flag(use_logarithms, true).
+%:- cpp_set_horus_flag(bp_msg_schedule, seq_random).
+%:- cpp_set_horus_flag(bp_msg_schedule, parallel).
+%:- cpp_set_horus_flag(bp_msg_schedule, max_residual).
+
+:- cpp_set_horus_flag(bp_accuracy, 0.0001).
+
+:- cpp_set_horus_flag(bp_max_iter, 1000).
 

packages/CLPBN/clpbn/horus_ground.yap

@@ -11,92 +11,79 @@
 		[call_horus_ground_solver/6,
 		 check_if_horus_ground_solver_done/1,
 		 init_horus_ground_solver/5,
-           run_horus_ground_solver/4,
+		 run_horus_ground_solver/3,
-           finalize_horus_ground_solver/1
+		 end_horus_ground_solver/1
 		]).
 
 :- use_module(horus,
 		[cpp_create_ground_network/4,
-           cpp_set_factors_params/2,
+		 cpp_set_factors_params/3,
 		 cpp_run_ground_solver/3,
-           cpp_set_vars_information/2,
 		 cpp_free_ground_network/1,
-	   set_solver/1
+		 cpp_set_vars_information/2
 		]).
 
-:- use_module(library('clpbn/dists'),
+:- use_module(library('clpbn/numbers'),
-          [dist/4,
+		[lists_of_keys_to_ids/6,
-           get_dist_domain/2,
+		 keys_to_numbers/7
-           get_dist_domain_size/2,
-           get_dist_params/2
 		]).
 
 :- use_module(library('clpbn/display'),
 		[clpbn_bind_vals/3]).
 
-:- use_module(library(clpbn/numbers)).
+:- use_module(library(pfl),
+		[get_pfl_parameters/2,
+		 skolem/2
+		]).
 
 :- use_module(library(charsio),
 		[term_to_atom/2]).
 
-:- use_module(library(pfl),
-          [skolem/2]).
-
 :- use_module(library(maplist)).
 
-:- use_module(library(lists)).
 
-:- use_module(library(atts)).
+call_horus_ground_solver(QueryVars, QueryKeys, AllKeys, Factors, Evidence,
-
+		Output) :-
-:- use_module(library(bhash)).
-
-
-call_horus_ground_solver(QueryVars, QueryKeys, AllKeys, Factors, Evidence, Output) :-
 	init_horus_ground_solver(QueryKeys, AllKeys, Factors, Evidence, State),
-  run_solver(State, [QueryKeys], Solutions),
+	run_horus_ground_solver([QueryKeys], Solutions, State),
 	clpbn_bind_vals([QueryVars], Solutions, Output),
-  finalize_horus_ground_solver(State).
+	end_horus_ground_solver(State).
 
 
-init_horus_ground_solver(QueryKeys, AllKeys, Factors, Evidence, state(Network,Hash4,Id4)) :-
+init_horus_ground_solver(QueryKeys, AllKeys, Factors, Evidence,
-  get_factors_type(Factors, Type),
+		state(Network,Hash,Id,DistIds)) :-
-  keys_to_numbers(AllKeys, Factors, Evidence, Hash4, Id4, FactorIds, EvidenceIds),
+	factors_type(Factors, Type),
-  cpp_create_ground_network(Type, FactorIds, EvidenceIds, Network),
+	keys_to_numbers(AllKeys, Factors, Evidence, Hash, Id, FacIds, EvIds),
-  %writeln(network:(Type, FactorIds, EvidenceIds, Network)), writeln(''),
+	%writeln(network:(type=Type, factors=FacIds, evidence=EvIds)), nl,
-  maplist(get_var_information, AllKeys, StatesNames),
+	cpp_create_ground_network(Type, FacIds, EvIds, Network),
-  maplist(term_to_atom, AllKeys, KeysAtoms),
+	%maplist(term_to_atom, AllKeys, VarNames),
-  cpp_set_vars_information(KeysAtoms, StatesNames).
+	%maplist(get_domain, AllKeys, Domains),
+	%cpp_set_vars_information(VarNames, Domains),
+    maplist(get_dist_id, FacIds, DistIds0),
+    sort(DistIds0, DistIds).
 
 
-run_horus_ground_solver(_QueryVars, Solutions, horus(GKeys, Keys, Factors, Evidence), Solver) :- 
+run_horus_ground_solver(QueryKeys, Solutions,
-  set_solver(Solver),
+		state(Network,Hash,Id, DistIds)) :-
-  call_horus_ground_solver_for_probabilities(GKeys, Keys, Factors, Evidence, Solutions).
-
-
-% TODO this is not beeing called!
-finalize_horus_ground_solver(state(Network,_Hash,_Id)) :-
-  cpp_free_ground_network(Network).
-
-
-run_solver(state(Network,Hash,Id), QueryKeys, Solutions) :-
-  %get_dists_parameters(DistIds, DistsParams),
-  %cpp_set_factors_params(Network, DistsParams),
 	lists_of_keys_to_ids(QueryKeys, QueryIds, Hash, _, Id, _),
+	%maplist(get_pfl_parameters, DistIds, DistParams),
+	%cpp_set_factors_params(Network, DistIds, DistParams),
 	cpp_run_ground_solver(Network, QueryIds, Solutions).
 
 
-get_factors_type([f(bayes, _, _)|_], bayes) :- ! .
+end_horus_ground_solver(state(Network,_Hash,_Id, _DistIds)) :-
-get_factors_type([f(markov, _, _)|_], markov) :- ! .
+	cpp_free_ground_network(Network).
 
 
-get_var_information(_:Key, Domain) :- !,
+factors_type([f(bayes, _, _)|_], bayes) :- ! .
+factors_type([f(markov, _, _)|_], markov) :- ! .
+
+
+get_dist_id(f(_, _, _, DistId), DistId).
+
+
+get_domain(_:Key, Domain) :- !,
 	skolem(Key, Domain).
-get_var_information(Key, Domain) :-
+get_domain(Key, Domain) :-
 	skolem(Key, Domain).
 
-
-%get_dists_parameters([],[]).
-%get_dists_parameters([Id|Ids], [dist(Id, Params)|DistsInfo]) :-
-%  get_dist_params(Id, Params),
-%  get_dists_parameters(Ids, DistsInfo).
-

packages/CLPBN/clpbn/horus_lifted.yap

@@ -12,12 +12,12 @@
 		 check_if_horus_lifted_solver_done/1,
 		 init_horus_lifted_solver/4,
 		 run_horus_lifted_solver/3,
-           finalize_horus_lifted_solver/1
+		 end_horus_lifted_solver/1
 		]).
 
 :- use_module(horus,
 		[cpp_create_lifted_network/3,
-           cpp_set_parfactors_params/2,
+		 cpp_set_parfactors_params/3,
 		 cpp_run_lifted_solver/3,
 		 cpp_free_lifted_network/1
 		]).
@@ -25,83 +25,65 @@
 :- use_module(library('clpbn/display'),
 		[clpbn_bind_vals/3]).
 
-:- use_module(library('clpbn/dists'),
-          [get_dist_params/2]).
-
 :- use_module(library(pfl),
 		[factor/6,
 		 skolem/2,
 		 get_pfl_parameters/2
 		]).
 
+:- use_module(library(maplist)).
+
 
 call_horus_lifted_solver(QueryVars, AllVars, Output) :-
 	init_horus_lifted_solver(_, AllVars, _, State),
 	run_horus_lifted_solver(QueryVars, Solutions, State),
 	clpbn_bind_vals(QueryVars, Solutions, Output),
-  finalize_horus_lifted_solver(State).
+	end_horus_lifted_solver(State).
 
 
-init_horus_lifted_solver(_, AllVars, _, state(ParfactorList, DistIds)) :-
+init_horus_lifted_solver(_, AllVars, _, state(Network, DistIds)) :-
 	get_parfactors(Parfactors),
-  get_dist_ids(Parfactors, DistIds0),
+	get_observed_keys(AllVars, ObservedKeys),
-  sort(DistIds0, DistIds),
+	%writeln(network:(parfactors=Parfactors, evidence=ObservedKeys)), nl,
-  get_observed_vars(AllVars, ObservedVars),
+	cpp_create_lifted_network(Parfactors, ObservedKeys, Network),
-  %writeln(parfactors:Parfactors:'\n'),
+	maplist(get_dist_id, Parfactors, DistIds0),
-  %writeln(evidence:ObservedVars:'\n'),
+	sort(DistIds0, DistIds).
-  cpp_create_lifted_network(Parfactors, ObservedVars, ParfactorList).
 
 
-run_horus_lifted_solver(QueryVars, Solutions, state(ParfactorList, DistIds)) :-
+run_horus_lifted_solver(QueryVars, Solutions, state(Network, DistIds)) :-
-  get_query_keys(QueryVars, QueryKeys),
+	maplist(get_query_keys, QueryVars, QueryKeys),
-  get_dists_parameters(DistIds, DistsParams),
+	%maplist(get_pfl_parameters, DistIds,DistsParams),
-  %writeln(dists:DistsParams), writeln(''),
+	%cpp_set_parfactors_params(Network, DistIds, DistsParams),
-  cpp_set_parfactors_params(ParfactorList, DistsParams),
+	cpp_run_lifted_solver(Network, QueryKeys, Solutions).
-  cpp_run_lifted_solver(ParfactorList, QueryKeys, Solutions).
 
 
-finalize_horus_lifted_solver(state(ParfactorList, _)) :-
+end_horus_lifted_solver(state(Network, _)) :-
-  cpp_free_lifted_network(ParfactorList).
+	cpp_free_lifted_network(Network).
-
 
+%
+% Enumerate all parfactors and enumerate their domain as tuples.
+%
 :- table get_parfactors/1.
 
-%
-% enumerate all parfactors and enumerate their domain as tuples.
-%
-% output is list of pf(
-%   Id: an unique number
-%   Ks: a list of keys, also known as the pf formula [a(X),b(Y),c(X,Y)]
-%   Vs: the list of free variables [X,Y]
-%   Phi: the table following usual CLP(BN) convention
-%   Tuples: ground bindings for variables in Vs, of the form [fv(x,y)]
-%
 get_parfactors(Factors) :-
 	findall(F, is_factor(F), Factors).
 
 
 is_factor(pf(Id, Ks, Rs, Phi, Tuples)) :-
 	factor(_Type, Id, Ks, Vs, Table, Constraints),
-  get_ranges(Ks,Rs),
+	maplist(get_range, Ks, Rs),
 	Table \= avg,
 	gen_table(Table, Phi),
 	all_tuples(Constraints, Vs, Tuples).
 
 
-get_ranges([],[]).
+get_range(K, Range) :-
-get_ranges(K.Ks, Range.Rs) :- !,
 	skolem(K, Domain),
-  length(Domain,Range),
+	length(Domain, Range).
-  get_ranges(Ks, Rs).
 
 
 gen_table(Table, Phi) :-
-  ( is_list(Table)
+	( is_list(Table) -> Phi = Table ; call(user:Table, Phi) ).
-      -> 
-    Phi = Table
-      ;
-    call(user:Table, Phi)
-  ).
 
 
 all_tuples(Constraints, Tuple, Tuples) :-
@@ -114,35 +96,20 @@ run(Goal.Constraints) :-
 	run(Constraints).
 
 
-get_dist_ids([], []).
+get_dist_id(pf(DistId, _, _, _, _), DistId).
-get_dist_ids(pf(Id, _, _, _, _).Parfactors, Id.DistIds) :-
-  get_dist_ids(Parfactors, DistIds).
 
 
-get_observed_vars([], []).
+get_observed_keys([], []).
-get_observed_vars(V.AllAttVars, [K:E|ObservedVars]) :-
+get_observed_keys(V.AllAttVars, [K:E|ObservedKeys]) :-
 	clpbn:get_atts(V,[key(K)]),
 	( clpbn:get_atts(V,[evidence(E)]) ; pfl:evidence(K,E) ), !,
-  get_observed_vars(AllAttVars, ObservedVars).
+	get_observed_keys(AllAttVars, ObservedKeys).
-get_observed_vars(V.AllAttVars, ObservedVars) :-
+get_observed_keys(_V.AllAttVars, ObservedKeys) :-
-  clpbn:get_atts(V,[key(_K)]), !,
+	get_observed_keys(AllAttVars, ObservedKeys).
-  get_observed_vars(AllAttVars, ObservedVars).
 
 
 get_query_keys([], []).
-get_query_keys(E1.L1, E2.L2) :-
+get_query_keys(V.AttVars, K.Ks) :-
-  get_query_keys_2(E1,E2),
+	clpbn:get_atts(V,[key(K)]), !,
-  get_query_keys(L1, L2).
+	get_query_keys(AttVars, Ks).
-
-
-get_query_keys_2([], []).
-get_query_keys_2(V.AttVars, [RV|RVs]) :-
-  clpbn:get_atts(V,[key(RV)]), !,
-  get_query_keys_2(AttVars, RVs).
-
-
-get_dists_parameters([], []).
-get_dists_parameters([Id|Ids], [dist(Id, Params)|DistsInfo]) :-
-  get_pfl_parameters(Id, Params),
-  get_dists_parameters(Ids, DistsInfo).
 

packages/CLPBN/clpbn/jt.yap

@@ -1,8 +1,9 @@
 
-:- module(jt, [jt/3,
+:- module(jt,
+		[jt/3,
 		 init_jt_solver/4,
-	       run_jt_solver/3]).
+		 run_jt_solver/3
-
+		]).
 
 :- use_module(library(dgraphs),
 		[dgraph_new/1,
@@ -41,14 +42,16 @@
 :- use_module(library(rbtrees),
 		[rb_new/1,
 		 rb_insert/4,
-	       rb_lookup/3]).
+		 rb_lookup/3
+		]).
 
 :- use_module(library(ordsets),
 		[ord_subset/2,
 		 ord_insert/3,
 		 ord_intersection/3,
 		 ord_del_element/3,
-	       ord_memberchk/2]).
+		 ord_memberchk/2
+		]).
 
 :- use_module(library(lists),
 		[reverse/2]).
@@ -61,7 +64,8 @@
 :- use_module(library('clpbn/dists'),
 		[get_dist_domain_size/2,
 		 get_dist_domain/2,
-	       get_dist_matrix/5]).
+		 get_dist_matrix/5
+		]).
 
 :- use_module(library('clpbn/matrix_cpt_utils'),
 		[project_from_CPT/3,
@@ -74,14 +78,14 @@
 		 get_CPT_sizes/2,
 		 reset_CPT_that_disagrees/5,
 		 sum_out_from_CPT/4,
-	       list_from_CPT/2]).
+		 list_from_CPT/2
+		]).
 
-:- use_module(library('clpbn/display'), [
+:- use_module(library('clpbn/display'),
-	clpbn_bind_vals/3]).
+		[clpbn_bind_vals/3]).
 
 :- use_module(library('clpbn/connected'),
-	      [
+		[init_influences/3,
-	       init_influences/3,
 		 influences/4
 		]).
 
@@ -290,8 +294,7 @@ add_clique_edges([], _, _, Edges, Edges).
 add_clique_edges([Clique1|Cliques], Clique, Sz, Edges0, EdgesF) :-
 	ord_intersection(Clique1, Clique, Int),
 	Int \== Clique,
-	(
+	(Int = [] ->
-	 Int = [] ->
 	  add_clique_edges(Cliques, Clique, Sz, Edges0, EdgesF)
 	;
 	  % we connect

packages/CLPBN/clpbn/matrix_cpt_utils.yap

@@ -1,3 +1,4 @@
+
 :- module(clpbn_matrix_utils,
 		[init_CPT/3,
 		 project_from_CPT/3,
@@ -21,7 +22,8 @@
 		 random_CPT/2,
 		 uniform_CPT/2,
 		 uniform_CPT_as_list/2,
-	   normalise_CPT_on_lines/3]).
+		 normalise_CPT_on_lines/3
+		]).
 
 :- use_module(library(matrix),
 		[matrix_new/4,
@@ -45,7 +47,8 @@
 		 matrix_agg_lines/3,
 		 matrix_agg_cols/3,
 		 matrix_op_to_lines/4,
-	       matrix_column/3]).
+		 matrix_column/3
+		]).
 
 init_CPT(List, Sizes, TAB) :-
 	matrix_new(floats, Sizes, List, TAB),

packages/CLPBN/clpbn/numbers.yap

@@ -1,13 +1,13 @@
 
 :- module(clpbn_numbers,
-	[
+		[keys_to_numbers/7,
-         keys_to_numbers/7, 
 		 keys_to_numbers/9,
 		 lists_of_keys_to_ids/6
 		]).
 
 :- use_module(library(bhash)).
 :- use_module(library(maplist)).
+
 :- use_module(library(pfl),
 		[skolem/2,
 		 get_pfl_cpt/5
@@ -60,4 +60,3 @@ evidence_to_id(Key=Ev, I0=Ev, Hash0, Hash, I0, I) :-
 	b_hash_insert(Hash0, Key, I0, Hash),
 	I is I0+1.
 
-

packages/CLPBN/clpbn/pgrammar.yap

@@ -2,21 +2,20 @@
 
 :- style_check(all).
 
-:- module(clpbn_pgrammar,[grammar_to_atts/1,
+:- module(clpbn_pgrammar,
+		[grammar_to_atts/1,
 		 grammar_prob/2,
 		 grammar_mle/2,
 		 init_pcg_solver/4,
 		 run_pcg_solver/3,
-			  pcg_init_graph/0]).
+		 pcg_init_graph/0
+		]).
 
 :- load_files([library(clpbn)],
-	      [ if(not_loaded),
+		[if(not_loaded), silent(true)]).
-		silent(true)
-	      ]).
 
 :- use_module([library(lists)],
-	      [ sum_list/2
+		[sum_list/2]).
-	      ]).
 
 :- use_module([library(matrix)],
 		[matrix_new/3,

packages/CLPBN/clpbn/table.yap

@@ -29,7 +29,8 @@
 :- use_module(library(bhash),
 		[b_hash_new/4,
 		 b_hash_lookup/3,
-	 b_hash_insert/4]).
+		 b_hash_insert/4
+		]).
 
 :- meta_predicate clpbn_table(:),
 	clpbn_tabled_clause(:.?),
@@ -43,14 +44,13 @@
 	clpbn_tabled_number_of_clauses(:,-),
 	clpbn_is_tabled(:).
 
-:- use_module(library(terms), [
+:- use_module(library(terms),
-			       instantiated_term_hash/4,
+		[instantiated_term_hash/4,
 		 variant/2
 		]).
 
-:- use_module(evidence, [
+:- use_module(evidence,
-			       put_evidence/2
+		[put_evidence/2]).
-			       ]).
 
 :- dynamic clpbn_table/3.
 
@@ -108,8 +108,7 @@ clpbn_table(F/N,M) :-
 	L0 = [_|Args0],
 	IGoal =.. [NF|Args0],
 	asserta(clpbn_table(S, M, IGoal)),
-	assert(
+	assert((M:S :-
-	       (M:S :-
 	  !,
 %	  write(S: ' ' ),
 	  b_getval(clpbn_tables, Tab),
@@ -130,8 +129,7 @@ clpbn_table(F/N,M) :-
 	    ;
 	      throw(error(tabled_clpbn_predicate_should_never_fail,S))
 	  )
-	       )
+	)).
-	      ).
 
 take_tail([V], V, [], V1, [V1]) :- !.
 take_tail([A|L0], V, [A|L1], V1, [A|L2]) :-
@@ -154,8 +152,7 @@ clpbn_tableallargs(F/N,M) :-
 	atom_concat(F, '___tabled', NF),
 	NKey =.. [NF|Args],
 	asserta(clpbn_table(Key, M, NKey)),
-	assert(
+	assert((M:Key :-
-	       (M:Key :-
 	  !,
 	  b_getval(clpbn_tables, Tab),
 	  (b_hash_lookup(Key, Out, Tab) ->
@@ -165,8 +162,7 @@ clpbn_tableallargs(F/N,M) :-
 	    b_setval(clpbn_tables, NewTab),
 	    once(M:NKey)
 	  )
-	       )
+	)).
-	      ).
 
 clpbn_table_nondet(M:X) :- !,
 	clpbn_table_nondet(X,M).
@@ -185,8 +181,8 @@ clpbn_table_nondet(F/N,M) :-
 	atom_concat(F, '___tabled', NF),
 	NKey =.. [NF|Args],
 	asserta(clpbn_table(Key, M, NKey)),
-	assert(
+	assert((M:Key :-
-	       (M:Key :- % writeln(in:Key),
+	  % writeln(in:Key),
 	  b_getval(clpbn_tables, Tab),
 	  (b_hash_lookup(Key, Out, Tab) ->
 	    fail
@@ -195,8 +191,7 @@ clpbn_table_nondet(F/N,M) :-
 	    b_setval(clpbn_tables, NewTab),
 	    M:NKey
 	  )
-	       )
+	)).
-	      ).
 
 user:term_expansion((P :- Gs), NC) :-
 	clpbn_table(P, M, NP),
@@ -364,4 +359,3 @@ clpbn_is_tabled(M:Clause, _) :- !,
 clpbn_is_tabled(Head, M) :-
 	clpbn_table(Head, M, _).
 
-

packages/CLPBN/clpbn/topsort.yap

@@ -1,11 +1,13 @@
 
-:- module(topsort, [topsort/2]).
+:- module(topsort,
+		[topsort/2]).
 
 :- use_module(library(dgraphs),
 		[dgraph_new/1,
 		 dgraph_add_edges/3,
 		 dgraph_add_vertices/3,
-	       dgraph_top_sort/2]).
+		 dgraph_top_sort/2
+		]).
 
 /* simple implementation of a topological sorting algorithm */
 /* graph is as Node-[Parents] */
@@ -31,4 +33,3 @@ add_edges([], _V) --> [].
 add_edges([P|Parents], V) --> [P-V],
 	add_edges(Parents, V).
 
-

packages/CLPBN/clpbn/utils.yap

@@ -1,9 +1,11 @@
-:- module(clpbn_utils, [
+
-	clpbn_not_var_member/2,
+:- module(clpbn_utils,
+		[clpbn_not_var_member/2,
 		 clpbn_var_member/2,
 		 check_for_hidden_vars/3,
 		 sort_vars_by_key/3,
-	sort_vars_by_key_and_parents/3]).
+		 sort_vars_by_key_and_parents/3
+		]).
 
 %
 % It may happen that variables from a previous query may still be around.
@@ -52,12 +54,10 @@ get_keys([_|AVars], KeysVars) :-  % may be non-CLPBN vars.
 merge_same_key([], [], _, []).
 merge_same_key([K1-V1,K2-V2|Vs], SortedAVars, Ks, UnifiableVars) :-
 	K1 == K2, !,
-	(clpbn:get_atts(V1, [evidence(E)])
+	(clpbn:get_atts(V1, [evidence(E)]) ->
-        ->
 	  clpbn:put_atts(V2, [evidence(E)])
 	;
-	    clpbn:get_atts(V2, [evidence(E)])
+	  clpbn:get_atts(V2, [evidence(E)]) ->
-	->
 	    clpbn:put_atts(V1, [evidence(E)])
 	  ;
 	    true
@@ -113,4 +113,3 @@ transform_parents([P|Parents0],[P|NParents],KeyVarsF,KeyVars0) :-
 transform_parents([P|Parents0],[V|NParents],[P-V|KeyVarsF],KeyVars0) :-
 	transform_parents(Parents0,NParents,KeyVarsF,KeyVars0).
 
-

packages/CLPBN/clpbn/ve.yap

@@ -14,41 +14,45 @@
 
 *********************************/
 
-:- module(clpbn_ve, [ve/3,
+:- module(clpbn_ve,
+		[ve/3,
 		 check_if_ve_done/1,
 		 init_ve_solver/4,
 		 run_ve_solver/3,
 		 init_ve_ground_solver/5,
 		 run_ve_ground_solver/3,
-		     call_ve_ground_solver/6]).
+		 call_ve_ground_solver/6
+		]).
 
-:- attribute size/1, all_diffs/1.
+:- use_module(library(atts)).
 
 :- use_module(library(ordsets),
 		[ord_union/3,
-	 ord_member/2]).
+		 ord_member/2
+		]).
 
-:- use_module(library('clpbn/xbif'), [clpbn2xbif/3]).
+:- use_module(library('clpbn/xbif'),
+		[clpbn2xbif/3]).
 
-:- use_module(library('clpbn/graphviz'), [clpbn2gviz/4]).
+:- use_module(library('clpbn/graphviz'),
+		[clpbn2gviz/4]).
 
 :- use_module(library('clpbn/dists'),
-	      [
+		[dist/4,
-	       dist/4,
 		 get_dist_domain_size/2,
 		 get_dist_params/2,
 		 get_dist_domain_size/2,
-	       get_dist_matrix/5]).
+		 get_dist_matrix/5
+		]).
 
-:- use_module(library('clpbn/utils'), [
+:- use_module(library('clpbn/utils'),
-	clpbn_not_var_member/2]).
+		[clpbn_not_var_member/2]).
 
-:- use_module(library('clpbn/display'), [
+:- use_module(library('clpbn/display'),
-	clpbn_bind_vals/3]).
+		[clpbn_bind_vals/3]).
 
 :- use_module(library('clpbn/connected'),
-	      [
+		[init_influences/3,
-	       init_influences/3,
 		 influences/4,
 		 factor_influences/4
 		]).
@@ -58,8 +62,7 @@
 :- use_module(library(clpbn/numbers)).
 
 :- use_module(library(lists),
-	      [
+		[member/2,
-	       member/2,
 		 append/3,
 		 delete/3
 		]).
@@ -73,6 +76,8 @@
 :- use_module(library('clpbn/aggregates'),
 		[check_for_agg_vars/2]).
 
+:- attribute size/1, all_diffs/1.
+
 %
 % uses a bipartite graph where bigraph(Vs, NFs, Fs)
 % Vs=map variables to lists of factors
@@ -472,4 +477,3 @@ multiply([F0|Fs], Vs, T) :-
 multiply_factor(f(_,Vs1,T1), f(_,Vs0,T0), f(_,Vs,T)) :-
 	multiply_CPTs(T1, Vs1, T0, Vs0, T, Vs).
 
-

packages/CLPBN/clpbn/viterbi.yap

@@ -1,11 +1,13 @@
 
 %:- style_check(all).
 
-:- module(viterbi, [viterbi/4]).
+:- module(viterbi,
+		[viterbi/4]).
 
 :- use_module(library(lists),
 		[nth/3,
-	       member/2]).
+		 member/2
+		]).
 
 :- use_module(library(assoc)).
 
@@ -17,8 +19,8 @@
 
 :- ensure_loaded(library('clpbn/hmm')).
 
-:- use_module(library('clpbn/dists'), [
+:- use_module(library('clpbn/dists'),
-	get_dist_params/2]).
+		[get_dist_params/2]).
 
 :- meta_predicate viterbi(:,:,+,-).
 
@@ -231,5 +233,3 @@ trace(L1,Next,Dump,Map,Trace0,Trace) :-
 	matrix_get(Dump,[NL,P],New),
 	trace(NL,New,Dump,Map,[Key|Trace0],Trace).
 
-
-	

packages/CLPBN/clpbn/vmap.yap

@@ -1,7 +1,6 @@
 
 :- module(clpbn_vmap,
-	[
+		[init_vmap/1, % init_vmap(-Vmap)
-         init_vmap/1, % init_vmap(-Vmap)
 		 add_to_vmap/4, % add_to_vmap(+V,-I,+VMap0,VMapF)
 		 get_from_vmap/3, % add_to_vmap(+V,-I,+VMap0)
 		 vars_to_numbers/4, % vars_to_numbers(+Vs,-Is,+VMap0,VMapF)
@@ -39,6 +38,3 @@ lvars_to_numbers(LVs, LIs, VMap0, VMap) :-
 vmap_to_list(vmap(_,Map), L) :-
 	rb_visit(Map, L).
 
-
-
-

packages/CLPBN/clpbn/xbif.yap

@@ -2,10 +2,11 @@
 % XMLBIF support for CLP(BN)
 %
 
-:- module(xbif, [clpbn2xbif/3]).
+:- module(xbif,
+		[clpbn2xbif/3]).
 
-:- use_module(library('clpbn/dists'), [
+:- use_module(library('clpbn/dists'),
-	get_dist_domain/2]).
+		[get_dist_domain/2]).
 
 clpbn2xbif(Stream, Name, Network) :-
 	format(Stream, '<?xml version="1.0" encoding="US-ASCII"?>

packages/CLPBN/examples/HMMer/fasta.yap

@@ -5,7 +5,10 @@
 % support for a single sequence.
 %
 
-:- module(fasta, [fa2atoms/2,fa2atoms/3]).
+:- module(fasta,
+		[fa2atoms/2,
+		 fa2atoms/3
+		]).
 
 fa2atoms(F, L) :-
 	fa2atoms(F, L, []).
@@ -44,4 +47,3 @@ skip_header(_,S) :-
 	skip_header(C,S).
 
 
-	

packages/CLPBN/examples/HMMer/scan.yap

@@ -327,4 +327,3 @@ max_index([_|L],I0,Max0,MaxIndex0,Max,MaxIndex) :-
 	I is I0+1,
 	max_index(L,I,Max0,MaxIndex0,Max,MaxIndex).
 
-

packages/CLPBN/examples/HMMer/score.yap

@@ -9,8 +9,7 @@
 		[fa2atoms/3]).
 
 :- use_module(library(lists),
-	      [
+		[nth/3,
-	       nth/3,
 		 append/3
 		]).
 

packages/CLPBN/examples/School/README

@@ -1,18 +1,14 @@
 
 This is a version of the school database, based on the PRM School example.
 
-There are four main files:
+There are the following main files:
 
-school_128.yap: a school with 128 professors, 256 courses and 4096 students.
+school_32.yap:   school with 32 professors, 64 courses and 256 students
-school_64.yap: medium size school
+school_64.yap:   school with 64 professors, 128 courses and 1024 students
-school_32.yap: small school (CLP(BN))
+school_128.yap:  school with 128 professors, 256 courses and 4096 students
-
-sch32.yap: small school (PFL)
 
 parschema.pfl:   the PFL schema
 
-schema.yap: the CLP(BN) schema
-
 tables:          CPTs
 
 =============================================================================

packages/CLPBN/examples/School/sch32.yap

@@ -1,25 +0,0 @@
-/*
-total_professors(32).
-
-total_courses(64).
-
-total_students(256).
-
-*/
-
-:- use_module(library(pfl)).
-
-:- source.
-
-:- style_check(all).
-
-:- yap_flag(unknown,error).
-
-:- yap_flag(write_strings,on).
-
-:- ensure_loaded('parschema.pfl').
-
-:- ensure_loaded(school32_data).
-
-:- set_solver(hve).
-

packages/CLPBN/examples/School/schema.yap

@@ -1,68 +0,0 @@
-/* Base file for school database. Supposed to be called from school_*.yap */
-
-professor_key(Key) :-
-	professor(Key).
-
-professor_ability(Key,Abi) :-
-	abi_table(Key, AbiDist),
-	{ Abi = ability(Key) with p([h,m,l], AbiDist)   }.
-
-professor_popularity(Key, Pop) :-
-	professor_ability(Key, Abi),
-	pop_table(Key,PopTable),
-	{ Pop = popularity(Key) with
-		p([h,m,l], PopTable,[Abi]) }.
-
-registration_key(Key) :-
-	registration(Key, _, _).
-
-registration_course(Key, CKey) :-
-	registration(Key, CKey, _).
-
-registration_student(Key, SKey) :-
-	registration(Key, _, SKey).
-
-registration_grade(Key, Grade) :-
-	registration(Key, CKey, SKey),
-	course_difficulty(CKey, Dif),
-	student_intelligence(SKey, Int),
-	grade_table(Int, Dif, Table),
-	{ Grade = grade(Key) with Table }.
-
-% registration_satisfaction(r0, h) :- {}.
-registration_satisfaction(Key, Sat) :-
-	registration_course(Key, CKey),
-	course_professor(CKey, PKey),
-	professor_ability(PKey, Abi),
-	registration_grade(Key, Grade),
-	satisfaction_table(Abi, Grade, Table),
-	{ Sat = satisfaction(Key) with Table }.
-
-course_key(Key) :-
-	course(Key,_).
-	
-course_professor(Key, PKey) :-
-	course(Key, PKey).
-	
-course_rating(CKey, Rat) :-
-	setof(Sat, RKey^(registration_course(RKey,CKey), registration_satisfaction(RKey,Sat)), Sats),
-	{ Rat =  rating(CKey) with avg([h,m,l],Sats) }.
-
-course_difficulty(Key, Dif) :-
-	dif_table(Key, Dist),
-	{ Dif = difficulty(Key) with p([h,m,l], Dist) }.
-
-student_key(Key) :-
-	student(Key).
-
-student_intelligence(Key, Int) :-
-	int_table(Key, IDist, Domain),
-	{ Int = intelligence(Key) with p(Domain, IDist) }.
-
-student_ranking(Key, Rank) :-
-	setof(Grade, CKey^(registration_student(CKey,Key),
-			 registration_grade(CKey, Grade)), Grades),
-	{ Rank = ranking(Key) with avg([a,b,c,d],Grades) }.
-
-:- ensure_loaded(tables).
-

packages/CLPBN/examples/School/school_128.yap

@@ -4,9 +4,10 @@ total_professors(128).
 total_courses(256).
 
 total_students(4096).
-
 */
 
+:- use_module(library(pfl)).
+
 :- source.
 
 :- style_check(all).
@@ -15,9 +16,7 @@ total_students(4096).
 
 :- yap_flag(write_strings,on).
 
-:- use_module(library(clpbn)).
+:- ensure_loaded('parschema.pfl').
-
-:- [-schema].
 
 professor(p0).
 professor(p1).

packages/CLPBN/examples/School/school_64.yap

@@ -4,9 +4,10 @@ total_professors(64).
 total_courses(128).
 
 total_students(1024).
-
 */
 
+:- use_module(library(pfl)).
+
 :- source.
 
 :- style_check(all).
@@ -15,9 +16,7 @@ total_students(1024).
 
 :- yap_flag(write_strings,on).
 
-:- use_module(library(clpbn)).
+:- ensure_loaded('parschema.pfl').
-
-:- [-schema].
 
 professor(p0).
 professor(p1).

packages/CLPBN/examples/School/tables.yap

@@ -1,33 +1,26 @@
+/* CTPs for school database. */
 
 abi_table(
 /* h */ [ 0.50,
 /* m */   0.40,
 /* l */   0.10 ]).
 
-abi_table(_, T) :- abi_table(T).
-
 pop_table(
 /*        h     m    l */
 /* h */ [ 0.9,  0.2, 0.01,
 /* m */   0.09, 0.6, 0.09,
 /* l */   0.01, 0.2, 0.9  ]).
 
-pop_table(_, T) :- pop_table(T). 
-
 diff_table(
 /* h */ [ 0.25,
 /* m */   0.50,
 /* l */   0.25 ]).
 
-dif_table(_, T) :- diff_table(T). 
-
 int_table(
 /* h */ [ 0.5,
 /* m */   0.4,
 /* l */   0.1 ]).
 
-int_table(_,T ,[h,m,l]) :- int_table(T).
-
 grade_table(
 /*        h h   h m   h l   m h  m m   m l   l h   l m   l l */
 /* a */ [ 0.2,  0.7,  0.85, 0.1, 0.2,  0.5,  0.01, 0.05, 0.1,
@@ -35,27 +28,9 @@ grade_table(
 /* c */   0.15, 0.04, 0.02, 0.4, 0.15, 0.12, 0.5,  0.6,  0.4,
 /* d */   0.05, 0.01, 0.01, 0.2, 0.05, 0.03, 0.45, 0.2,  0.1 ]).
 
-grade_table(I, D, 
-	p([a,b,c,d], T, [I,D])) :- grade_table(T).
-    
 sat_table(
 /*        h a   h b   h c   h d  m a   m b  m c  m d   l a   l b  l c   l d */
 /* h */ [ 0.98, 0.9,  0.8 , 0.6, 0.9,  0.4, 0.2, 0.01, 0.5,  0.2, 0.01, 0.01,
 /* m */   0.01, 0.09, 0.15, 0.3, 0.05, 0.4, 0.3, 0.04, 0.35, 0.3, 0.09, 0.01,
 /* l */   0.01, 0.01, 0.05, 0.1, 0.05, 0.2, 0.5, 0.95, 0.15, 0.5, 0.9,  0.98 ]).
 
-satisfaction_table(A, G, p([h,m,l], T, [A,G])) :- sat_table(T).
-
-
-% The idea is quite simple:
-%  hs = h -> r = ( 0.9, 0.1, 0)
-%  hs = m -> r = ( 0.2, 0.6, 0.2)
-%  hs = l -> r = ( 0, 0.1, 0.9)
-%
-% add all and divide on the number of elements on the table!
-%
-rating_prob_table(
-  [ 0.9,  0.05, 0.01,
-    0.09, 0.9,  0.09,
-    0.01, 0.05, 0.9  ]).
-

packages/CLPBN/examples/burglary-alarm.uai

@@ -1,28 +1,26 @@
-MARKOV
+BAYES
+
 5
 2 2 2 2 2
 5
 1 0
 1 1
-3 2 0 1
+3 0 1 2
-2 3 2
+2 2 3
-2 4 2
+2 2 4
 
 2
- .001 .999
+ 0.001 0.999
 
 2
- .002 .998 
+ 0.002 0.998
 
 8
- .95 .94 .29 .001
+ 0.95 0.05 0.94 0.06 0.29 0.71 0.001 0.999
- .05 .06 .71 .999
 
 4
- .9 .05
+ 0.9 0.1 0.05 0.95
- .1 .95
 
 4
- .7 .01 
+ 0.7 0.3 0.01 0.99
- .3 .99
 

packages/CLPBN/examples/cg.yap

@@ -1,35 +0,0 @@
-
-%
-% adapted from Hendrik Blockeel's ILP04 paper.
-%
-
-:- use_module(library(clpbn)).
-
-cg(X,1,C):-
-    father(Y,X),
-    cg(Y,1,C1),cg(Y,2,C2),
-    parent_cpt(cg(X,1), C1, C2, C).
-
-cg(X,2,C):-
-    mother(Y,X),
-    cg(Y,1,C1),cg(Y,2,C2),
-    parent_cpt(cg(X,2), C1, C2, C).
-
-
-
-cg(f,X,C) :-
-    prior_cpt(cg(f,X),C).
-
-cg(m,X,C) :-
-    prior_cpt(cg(m,X),C).
-
-
-prior_cpt(CKEY, C) :-
-    { C = CKEY with p([p,w], [0.5,0.5])}.
-
-parent_cpt(CKEY, C1, C2, C) :-
-    { C = CKEY with p([p,w], [   1,0.5,0.5,0.0,
-                               0.0,0.5,0.5,  1],[C1,C2])}.
-
-father(f,s).
-mother(m,s).

packages/CLPBN/examples/city.pfl

@@ -1,3 +1,8 @@
+/*
+ Model from the paper "First-order
+ probabilistic inference"
+*/
+
 :- use_module(library(pfl)).
 
 :- set_solver(hve).
@@ -11,14 +16,14 @@
 %:- set_solver(lkc).
 %:- set_solver(lbp).
 
-:- multifile people/2.
+:- multifile person/2.
 :- multifile ev/1.
 
-people(joe,nyc).
+person(joe,nyc).
-people(p2, nyc).
+person(p2, nyc).
-people(p3, nyc).
+person(p3, nyc).
-people(p4, nyc).
+person(p4, nyc).
-people(p5, nyc).
+person(p5, nyc).
 
 ev(descn(p2, fits)).
 ev(descn(p3, fits)).
@@ -26,81 +31,76 @@ ev(descn(p4, fits)).
 ev(descn(p5, fits)).
 
 bayes city_conservativeness(C)::[high,low] ;
-    cons_table(C) ;
+	cons_table ;
-    [people(_,C)].
+	[person(_,C)].
 
 bayes gender(P)::[male,female] ;
-    gender_table(P) ;
+	gender_table ;
-    [people(P,_)].
+	[person(P,_)].
 
 bayes hair_color(P)::[dark,bright], city_conservativeness(C) ;
-    hair_color_table(P) ;
+	hair_color_table ;
-    [people(P,C)].
+	[person(P,C)].
 
 bayes car_color(P)::[dark,bright], hair_color(P) ;
-    car_color_table(P) ;
+	car_color_table ;
-    [people(P,_)].
+	[person(P,_)].
 
 bayes height(P)::[tall,short], gender(P) ;
-    height_table(P) ;
+	height_table ;
-    [people(P,_)].
+	[person(P,_)].
 
 bayes shoe_size(P)::[big,small], height(P) ;
-    shoe_size_table(P) ;
+	shoe_size_table ;
-    [people(P,_)].
+	[person(P,_)].
 
 bayes guilty(P)::[y,n] ;
-    guilty_table(P) ;
+	guilty_table ;
-    [people(P,_)].
+	[person(P,_)].
 
 bayes descn(P)::[fits,dont_fit], car_color(P),
 		hair_color(P), height(P), guilty(P) ;
-    descn_table(P) ;
+	descn_table ;
-    [people(P,_)].
+	[person(P,_)].
 
 bayes witness(C), descn(Joe), descn(P2) ;
 	witness_table ;
-    [people(_,C), Joe=joe, P2=p2].
+	[person(_,C), Joe=joe, P2=p2].
 
 
-cons_table(amsterdam,
+cons_table(
-% special case for amsterdam: amsterdam is
-% less conservative than other cities (is it?)
-/* y        */ [ 0.2,
-/* n        */   0.8 ]) :- !. % FIXME
-cons_table(_,
 /* y        */ [ 0.8,
 /* n        */   0.2 ]).
 
-gender_table(_,
+gender_table(
 /* male     */ [ 0.55,
 /* female   */   0.45 ]).
 
-hair_color_table(_,
+hair_color_table(
 /*               high  low  */
 /* dark     */ [ 0.05, 0.1,
 /* bright   */   0.95, 0.9 ]).
 
-car_color_table(_,
+car_color_table(
 /*               dark bright */
 /* dark     */ [ 0.9, 0.2,
 /* bright   */   0.1, 0.8 ]).
 
-height_table(_,
+height_table(
 /*               male female */
 /* tall     */ [ 0.6, 0.4,
 /* short    */   0.4, 0.6 ]).
 
-shoe_size_table(_,
+shoe_size_table(
 /*               tall short */
 /* big      */ [ 0.9, 0.1,
 /* small    */   0.1, 0.9 ]).
 
-guilty_table(_,
+guilty_table(
 /* yes      */ [ 0.23,
 /* no       */   0.77 ]).
 
-descn_table(_,
+descn_table(
 /*               car_color(P), hair_color(P), height(P), guilty(P) */
 /* fits     */ [ 0.99, 0.5,  0.23, 0.88, 0.41, 0.3,  0.76, 0.87,
 /* fits     */   0.44, 0.43, 0.29, 0.72, 0.23, 0.91, 0.95, 0.92,

packages/CLPBN/examples/comp_workshops.pfl

@@ -1,3 +1,8 @@
+/*
+ Model from the paper "Lifted Probabilistic
+ Inference with Counting Formulas"
+*/
+
 :- use_module(library(pfl)).
 
 :- set_solver(hve).
@@ -10,31 +15,31 @@
 %:- set_solver(lkc).
 %:- set_solver(lbp).
 
-:- multifile c/2.
+:- multifile reg/2.
 
-c(p1,w1).
+reg(p1,w1).
-c(p1,w2).
+reg(p1,w2).
-c(p1,w3).
+reg(p1,w3).
-c(p2,w1).
+reg(p2,w1).
-c(p2,w2).
+reg(p2,w2).
-c(p2,w3).
+reg(p2,w3).
-c(p3,w1).
+reg(p3,w1).
-c(p3,w2).
+reg(p3,w2).
-c(p3,w3).
+reg(p3,w3).
-c(p4,w1).
+reg(p4,w1).
-c(p4,w2).
+reg(p4,w2).
-c(p4,w3).
+reg(p4,w3).
-c(p5,w1).
+reg(p5,w1).
-c(p5,w2).
+reg(p5,w2).
-c(p5,w3).
+reg(p5,w3).
 
 markov attends(P), hot(W) ;
 	[0.2, 0.8, 0.8, 0.8] ;
-    [c(P,W)].
+	[reg(P,W)].
 
 markov attends(P), series ;
 	[0.501, 0.499, 0.499, 0.499] ;
-    [c(P,_)].
+	[reg(P,_)].
 
-?- series(X).
+% ?- series(X).
 

packages/CLPBN/examples/learning/debug_school.yap

@@ -2,16 +2,17 @@
 
 /* We do not consider aggregates yet.      */
 
-:- [pos:train].
-
-:- ['../../examples/School/sch32'].
-
 :- use_module(library(clpbn/learning/em)).
 
-%:- clpbn:set_clpbn_flag(em_solver,gibbs).
+:- [pos:train].
-%:- clpbn:set_clpbn_flag(em_solver,jt).
+
- :- clpbn:set_clpbn_flag(em_solver,ve).
+:- ['../../examples/School/parschema.pfl'].
-%:- clpbn:set_clpbn_flag(em_solver,bp).
+
+:- set_em_solver(ve).
+%:- set_em_solver(hve).
+%:- set_em_solver(bdd).
+%:- set_em_solver(bp).
+%:- set_em_solver(cbp).
 
 debug_school :-
 	graph(L),

packages/CLPBN/examples/learning/prof_params.pfl

@@ -4,12 +4,11 @@
 
 :- use_module(library(clpbn/learning/em)).
 
-%:- clpbn:set_clpbn_flag(em_solver,gibbs).
+:- set_em_solver(ve).
-%:- clpbn:set_clpbn_flag(em_solver,jt).
+%:- set_em_solver(hve).
-%:- clpbn:set_clpbn_flag(em_solver,hve).
+%:- set_em_solver(bdd).
-:- clpbn:set_clpbn_flag(em_solver,ve).
+%:- set_em_solver(bp).
-%:- clpbn:set_clpbn_flag(em_solver,bp).
+%:- set_em_solver(cbp).
-%:- clpbn:set_clpbn_flag(em_solver,bdd).
 
 professor(p0).
 professor(p1).

packages/CLPBN/examples/learning/school_params.yap

@@ -2,16 +2,17 @@
 
 /* We do not consider aggregates yet.      */
 
-:- [pos:train].
-
-:- ['../../examples/School/sch32'].
-
 :- use_module(library(clpbn/learning/em)).
 
-%:- clpbn:set_clpbn_flag(em_solver,gibbs).
+:- [pos:train].
-%:- clpbn:set_clpbn_flag(em_solver,jt).
+
- :- clpbn:set_clpbn_flag(em_solver,ve).
+:- ['../../examples/School/school_32'].
-%:- clpbn:set_clpbn_flag(em_solver,bp).
+
+:- set_em_solver(ve).
+%:- set_em_solver(hve).
+%:- set_em_solver(bdd).
+%:- set_em_solver(bp).
+%:- set_em_solver(cbp).
 
 timed_main :-
 	statistics(runtime, _),

packages/CLPBN/examples/learning/sprinkler_params.yap

@@ -4,12 +4,11 @@
 
 :- use_module(library(clpbn/learning/em)).
 
-%:- set_pfl_flag(em_solver,gibbs).
+:- set_em_solver(ve).
-%:- set_pfl_flag(em_solver,jt).
+%:- set_em_solver(hve).
-%:- set_pfl_flag(em_solver,hve).
+%:- set_em_solver(bdd).
-%:- set_pfl_flag(em_solver,bp).
+%:- set_em_solver(bp).
-%:- set_pfl_flag(em_solver,ve).
+%:- set_em_solver(cbp).
-:- set_pfl_flag(em_solver,bdd).
 
 :- dynamic id/1.
 

packages/CLPBN/examples/social_domain1.pfl

@@ -1,38 +0,0 @@
-:- use_module(library(pfl)).
-
-:- set_solver(hve).
-%:- set_solver(ve).
-%:- set_solver(jt).
-%:- set_solver(bdd).
-%:- set_solver(bp).
-%:- set_solver(cbp).
-%:- set_solver(gibbs).
-%:- set_solver(lve).
-%:- set_solver(lkc).
-%:- set_solver(lbp).
-
-:- multifile people/1.
-
-people @ 5.
-
-people(X,Y) :-
-    people(X),
-    people(Y),
-    X \== Y.
-
-markov smokes(X) ; [1.0, 4.0552]; [people(X)].
-
-markov cancer(X) ; [1.0, 9.9742]; [people(X)].
-
-markov friends(X,Y) ; [1.0, 99.48432] ; [people(X,Y)].
-
-markov smokes(X), cancer(X) ;
-    [4.48169, 4.48169, 1.0, 4.48169] ;
-    [people(X)].
-
-markov friends(X,Y), smokes(X), smokes(Y) ;
-    [3.004166, 3.004166, 3.004166, 3.004166, 3.004166, 1.0, 1.0, 3.004166] ;
-    [people(X,Y)].
-
-% ?- friends(p1,p2,X).
-

packages/CLPBN/examples/social_domain2.pfl

@@ -1,38 +0,0 @@
-:- use_module(library(pfl)).
-
-:- set_solver(hve).
-%:- set_solver(ve).
-%:- set_solver(jt).
-%:- set_solver(bdd).
-%:- set_solver(bp).
-%:- set_solver(cbp).
-%:- set_solver(gibbs).
-%:- set_solver(lve).
-%:- set_solver(lkc).
-%:- set_solver(lbp).
-
-:- multifile people/1.
-
-people @ 5.
-
-people(X,Y) :-
-    people(X),
-    people(Y).
-%    X \== Y.
-
-markov smokes(X) ; [1.0, 4.0552]; [people(X)].
-
-markov asthma(X) ; [1.0, 9.9742] ; [people(X)].
-
-markov friends(X,Y) ; [1.0, 99.48432] ; [people(X,Y)].
-
-markov asthma(X), smokes(X) ;
-    [4.48169, 4.48169, 1.0, 4.48169] ;
-    [people(X)].
-
-markov asthma(X), friends(X,Y), smokes(Y) ;
-    [3.004166, 3.004166, 3.004166, 3.004166, 3.004166, 1.0, 1.0, 3.004166] ;
-    [people(X,Y)].
-
-% ?- smokes(p1,t), smokes(p2,t), friends(p1,p2,X).
-

packages/CLPBN/examples/social_network1.pfl

@@ -0,0 +1,44 @@
+/*
+ Model from the paper "Lifted First-Order
+ Belief Propagation"
+*/
+
+:- use_module(library(pfl)).
+
+:- set_solver(hve).
+%:- set_solver(ve).
+%:- set_solver(jt).
+%:- set_solver(bdd).
+%:- set_solver(bp).
+%:- set_solver(cbp).
+%:- set_solver(gibbs).
+%:- set_solver(lve).
+%:- set_solver(lkc).
+%:- set_solver(lbp).
+
+:- multifile person/1.
+
+person @ 5.
+
+person(X,Y) :-
+	person(X),
+	person(Y)
+%	,X \== Y
+	.
+
+markov smokes(X) ; [1.0, 4.0552]; [person(X)].
+
+markov cancer(X) ; [1.0, 9.9742]; [person(X)].
+
+markov friends(X,Y) ; [1.0, 99.48432] ; [person(X,Y)].
+
+markov smokes(X), cancer(X) ;
+	[4.48169, 4.48169, 1.0, 4.48169] ;
+	[person(X)].
+
+markov friends(X,Y), smokes(X), smokes(Y) ;
+	[3.004166, 3.004166, 3.004166, 3.004166, 3.004166, 1.0, 1.0, 3.004166] ;
+	[person(X,Y)].
+
+% ?- friends(p1,p2,X).
+

packages/CLPBN/examples/social_network2.pfl

@@ -0,0 +1,44 @@
+/*
+ Model from the paper "Lifted Inference Seen
+ from the Other Side: The Tractable Features"
+*/
+
+:- use_module(library(pfl)).
+
+:- set_solver(hve).
+%:- set_solver(ve).
+%:- set_solver(jt).
+%:- set_solver(bdd).
+%:- set_solver(bp).
+%:- set_solver(cbp).
+%:- set_solver(gibbs).
+%:- set_solver(lve).
+%:- set_solver(lkc).
+%:- set_solver(lbp).
+
+:- multifile person/1.
+
+person @ 5.
+
+person(X,Y) :-
+	person(X),
+	person(Y)
+%	,X \== Y
+	.
+
+markov smokes(X) ; [1.0, 4.0552]; [person(X)].
+
+markov asthma(X) ; [1.0, 9.9742] ; [person(X)].
+
+markov friends(X,Y) ; [1.0, 99.48432] ; [person(X,Y)].
+
+markov asthma(X), smokes(X) ;
+	[4.48169, 4.48169, 1.0, 4.48169] ;
+	[person(X)].
+
+markov asthma(X), friends(X,Y), smokes(Y) ;
+	[3.004166, 3.004166, 3.004166, 3.004166, 3.004166, 1.0, 1.0, 3.004166] ;
+	[person(X,Y)].
+
+% ?- smokes(p1,t), smokes(p2,t), friends(p1,p2,X).
+

packages/CLPBN/examples/sprinkler.pfl

@@ -24,16 +24,16 @@ cloudy_table(
       0.5 ]).
 
 sprinkler_table(
-    [ 0.5, 0.9,
+    [ 0.1, 0.5,
-		  0.5, 0.1 ]).
+      0.9, 0.5 ]).
 
 rain_table(
     [ 0.8, 0.2,
       0.2, 0.8 ]).
 
 wet_grass_table(
-    [ 1.0, 0.1, 0.1, 0.01,
+    [ 0.99, 0.9, 0.9, 0.0,
-      0.0, 0.9, 0.9, 0.99 ]).
+      0.01, 0.1, 0.1, 1.0 ]).
 
 % ?- wet_grass(X).
 

packages/CLPBN/examples/workshop_attrs.pfl

@@ -1,3 +1,8 @@
+/*
+ Model from the paper "Lifted Probabilistic
+ Inference with Counting Formulas"
+*/
+
 :- use_module(library(pfl)).
 
 :- set_solver(hve).
@@ -11,23 +16,23 @@
 %:- set_solver(lkc).
 %:- set_solver(lbp).
 
-:- multifile people/1.
+:- multifile person/1.
 
-people @ 5.
+person @ 5.
 
-markov attends(P), attr1 ; [0.7, 0.3, 0.3, 0.3] ; [people(P)].
+markov attends(P), attr1 ; [0.7, 0.3, 0.3, 0.3] ; [person(P)].
 
-markov attends(P), attr2 ; [0.7, 0.3, 0.3, 0.3] ; [people(P)].
+markov attends(P), attr2 ; [0.7, 0.3, 0.3, 0.3] ; [person(P)].
 
-markov attends(P), attr3 ; [0.7, 0.3, 0.3, 0.3] ; [people(P)].
+markov attends(P), attr3 ; [0.7, 0.3, 0.3, 0.3] ; [person(P)].
 
-markov attends(P), attr4 ; [0.7, 0.3, 0.3, 0.3] ; [people(P)].
+markov attends(P), attr4 ; [0.7, 0.3, 0.3, 0.3] ; [person(P)].
 
-markov attends(P), attr5 ; [0.7, 0.3, 0.3, 0.3] ; [people(P)].
+markov attends(P), attr5 ; [0.7, 0.3, 0.3, 0.3] ; [person(P)].
 
-markov attends(P), attr6 ; [0.7, 0.3, 0.3, 0.3] ; [people(P)].
+markov attends(P), attr6 ; [0.7, 0.3, 0.3, 0.3] ; [person(P)].
 
-markov attends(P), series ; [0.501, 0.499, 0.499, 0.499] ; [people(P)].
+markov attends(P), series ; [0.501, 0.499, 0.499, 0.499] ; [person(P)].
 
 % ?- series(X).
 

packages/CLPBN/horus/BayesBall.cpp

@@ -1,12 +1,6 @@
-#include <cstdlib>
 #include <cassert>
 
-#include <iostream>
-#include <fstream>
-#include <sstream>
-
 #include "BayesBall.h"
-#include "Util.h"
 
 
 FactorGraph*

packages/CLPBN/horus/BayesBall.h

@@ -4,7 +4,6 @@
 #include <vector>
 #include <queue>
 #include <list>
-#include <map>
 
 #include "FactorGraph.h"
 #include "BayesBallGraph.h"
@@ -15,8 +14,8 @@ using namespace std;
 
 struct ScheduleInfo
 {
-  ScheduleInfo (BBNode* n, bool vfp, bool vfc) : 
+  ScheduleInfo (BBNode* n, bool vfp, bool vfc)
-      node(n), visitedFromParent(vfp), visitedFromChild(vfc) { }
+      : node(n), visitedFromParent(vfp), visitedFromChild(vfc) { }
 
   BBNode*  node;
   bool     visitedFromParent;

packages/CLPBN/horus/BayesBallGraph.cpp

@@ -2,8 +2,8 @@
 #include <cassert>
 
 #include <iostream>
-#include <fstream>
 #include <sstream>
+#include <fstream>
 
 #include "BayesBallGraph.h"
 #include "Util.h"
@@ -79,9 +79,8 @@ BayesBallGraph::exportToGraphViz (const char* fileName)
 {
   ofstream out (fileName);
   if (!out.is_open()) {
-    cerr << "error: cannot open file to write at " ;
+    cerr << "Error: couldn't open file '" << fileName << "'." ;
-    cerr << "BayesBallGraph::exportToDotFile()" << endl;
+    return;
-    abort();
   }
   out << "digraph {" << endl;
   out << "ranksep=1" << endl;

packages/CLPBN/horus/BayesBallGraph.h

@@ -2,9 +2,7 @@
 #define HORUS_BAYESBALLGRAPH_H
 
 #include <vector>
-#include <queue>
+#include <unordered_map>
-#include <list>
-#include <map>
 
 #include "Var.h"
 #include "Horus.h"

packages/CLPBN/horus/BeliefProp.cpp

@@ -1,17 +1,19 @@
 #include <cassert>
-#include <limits>
 
 #include <algorithm>
 
 #include <iostream>
 
 #include "BeliefProp.h"
-#include "FactorGraph.h"
-#include "Factor.h"
 #include "Indexer.h"
 #include "Horus.h"
 
 
+double      BeliefProp::accuracy_ = 0.0001;
+unsigned    BeliefProp::maxIter_  = 1000;
+MsgSchedule BeliefProp::schedule_ = MsgSchedule::SEQ_FIXED;
+
+
 BeliefProp::BeliefProp (const FactorGraph& fg) : GroundSolver (fg)
 {
   runned_ = false;
@@ -50,16 +52,15 @@ BeliefProp::printSolverFlags (void) const
 {
   stringstream ss;
   ss << "belief propagation [" ;
-  ss << "schedule=" ;
+  ss << "bp_msg_schedule=" ;
-  typedef BpOptions::Schedule Sch;
+  switch (schedule_) {
-  switch (BpOptions::schedule) {
+    case MsgSchedule::SEQ_FIXED:    ss << "seq_fixed";    break;
-    case Sch::SEQ_FIXED:    ss << "seq_fixed";    break;
+    case MsgSchedule::SEQ_RANDOM:   ss << "seq_random";   break;
-    case Sch::SEQ_RANDOM:   ss << "seq_random";   break;
+    case MsgSchedule::PARALLEL:     ss << "parallel";     break;
-    case Sch::PARALLEL:     ss << "parallel";     break;
+    case MsgSchedule::MAX_RESIDUAL: ss << "max_residual"; break;
-    case Sch::MAX_RESIDUAL: ss << "max_residual"; break;
   }
-  ss << ",max_iter="   << Util::toString (BpOptions::maxIter);
+  ss << ",bp_max_iter="   << Util::toString (maxIter_);
-  ss << ",accuracy="   << Util::toString (BpOptions::accuracy);
+  ss << ",bp_accuracy="   << Util::toString (accuracy_);
   ss << ",log_domain=" << Util::toString (Globals::logDomain);
   ss << "]" ;
   cout << ss.str() << endl;
@@ -156,21 +157,21 @@ BeliefProp::runSolver (void)
 {
   initializeSolver();
   nIters_ = 0;
-  while (!converged() && nIters_ < BpOptions::maxIter) {
+  while (!converged() && nIters_ < maxIter_) {
     nIters_ ++;
     if (Globals::verbosity > 1) {
       Util::printHeader (string ("Iteration ") + Util::toString (nIters_));
     }
-    switch (BpOptions::schedule) {
+    switch (schedule_) {
-     case BpOptions::Schedule::SEQ_RANDOM:
+     case MsgSchedule::SEQ_RANDOM:
        std::random_shuffle (links_.begin(), links_.end());
        // no break
-      case BpOptions::Schedule::SEQ_FIXED:
+      case MsgSchedule::SEQ_FIXED:
         for (size_t i = 0; i < links_.size(); i++) {
           calculateAndUpdateMessage (links_[i]);
         }
         break;
-      case BpOptions::Schedule::PARALLEL:
+      case MsgSchedule::PARALLEL:
         for (size_t i = 0; i < links_.size(); i++) {
           calculateMessage (links_[i]);
         }
@@ -178,13 +179,13 @@ BeliefProp::runSolver (void)
           updateMessage(links_[i]);
         }
         break;
-      case BpOptions::Schedule::MAX_RESIDUAL:
+      case MsgSchedule::MAX_RESIDUAL:
         maxResidualSchedule();
         break;
     }
   }
   if (Globals::verbosity > 0) {
-    if (nIters_ < BpOptions::maxIter) {
+    if (nIters_ < maxIter_) {
       cout << "Belief propagation converged in " ;
       cout << nIters_ << " iterations" << endl;
     } else {
@@ -236,7 +237,7 @@ BeliefProp::maxResidualSchedule (void)
 
     SortedOrder::iterator it = sortedOrder_.begin();
     BpLink* link = *it;
-    if (link->residual() < BpOptions::accuracy) {
+    if (link->residual() < accuracy_) {
       return;
     }
     updateMessage (link);
@@ -410,7 +411,7 @@ BeliefProp::initializeSolver (void)
 bool
 BeliefProp::converged (void)
 {
-  if (links_.size() == 0) {
+  if (links_.empty()) {
     return true;
   }
   if (nIters_ == 0) {
@@ -426,9 +427,9 @@ BeliefProp::converged (void)
     return false;
   }
   bool converged = true;
-  if (BpOptions::schedule == BpOptions::Schedule::MAX_RESIDUAL) {
+  if (schedule_ == MsgSchedule::MAX_RESIDUAL) {
     double maxResidual = (*(sortedOrder_.begin()))->residual();
-    if (maxResidual > BpOptions::accuracy) {
+    if (maxResidual > accuracy_) {
       converged = false;
     } else {
       converged = true;
@@ -439,7 +440,7 @@ BeliefProp::converged (void)
       if (Globals::verbosity > 1) {
         cout << links_[i]->toString() + " residual = " << residual << endl;
       }
-      if (residual > BpOptions::accuracy) {
+      if (residual > accuracy_) {
         converged = false;
         if (Globals::verbosity < 2) {
           break;

packages/CLPBN/horus/BeliefProp.h

@@ -3,16 +3,24 @@
 
 #include <set>
 #include <vector>
+
 #include <sstream>
 
 #include "GroundSolver.h"
-#include "Factor.h"
 #include "FactorGraph.h"
-#include "Util.h"
+
 
 using namespace std;
 
 
+enum MsgSchedule {
+  SEQ_FIXED,
+  SEQ_RANDOM,
+  PARALLEL,
+  MAX_RESIDUAL
+};
+
+
 class BpLink
 {
   public:
@@ -68,6 +76,9 @@ class BpLink
     Params*   currMsg_;
     Params*   nextMsg_;
     double    residual_;
+
+  private:
+    DISALLOW_COPY_AND_ASSIGN (BpLink);
 };
 
 typedef vector<BpLink*> BpLinks;
@@ -76,10 +87,12 @@ typedef vector<BpLink*> BpLinks;
 class SPNodeInfo
 {
   public:
+    SPNodeInfo (void) { }
     void addBpLink (BpLink* link) { links_.push_back (link); }
     const BpLinks& getLinks (void) { return links_; }
   private:
     BpLinks links_;
+    DISALLOW_COPY_AND_ASSIGN (SPNodeInfo);
 };
 
 
@@ -98,22 +111,20 @@ class BeliefProp : public GroundSolver
 
     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&);
 
+    static double accuracy (void) { return accuracy_; }
+
+    static void setAccuracy (double acc) { accuracy_ = acc; }
+
+    static unsigned maxIterations (void) { return maxIter_; }
+
+    static void setMaxIterations (unsigned mi) { maxIter_ = mi; }
+
+    static MsgSchedule msgSchedule (void) { return schedule_; }
+
+    static void setMsgSchedule (MsgSchedule sch) { schedule_ = sch; }
+
   protected:
     SPNodeInfo* ninf (const VarNode* var) const
     {
@@ -164,6 +175,18 @@ class BeliefProp : public GroundSolver
       }
     };
 
+    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;
+
     BpLinks              links_;
     unsigned             nIters_;
     vector<SPNodeInfo*>  varsI_;
@@ -176,12 +199,18 @@ class BeliefProp : public GroundSolver
     typedef unordered_map<BpLink*, SortedOrder::iterator> BpLinkMap;
     BpLinkMap linkMap_;
 
+    static double       accuracy_;
+    static unsigned     maxIter_;
+    static MsgSchedule  schedule_;
+
   private:
     void initializeSolver (void);
 
     bool converged (void);
 
     virtual void printLinkInformation (void) const;
+
+    DISALLOW_COPY_AND_ASSIGN (BeliefProp);
 };
 
 #endif // HORUS_BELIEFPROP_H

packages/CLPBN/horus/ConstraintTree.cpp

@@ -120,7 +120,7 @@ CTNode::copySubtree (const CTNode* root1)
          chIt != n1->childs().end(); ++ chIt) {
       CTNode* chCopy = new CTNode (**chIt);
       n2->childs().insert_sorted (chCopy);
-      if ((*chIt)->nrChilds() != 0) {
+      if ((*chIt)->nrChilds() > 0) {
         stack.push_back (StackPair (*chIt, chCopy));
       }
     }
@@ -521,13 +521,12 @@ ConstraintTree::exportToGraphViz (
 {
   ofstream out (fileName);
   if (!out.is_open()) {
-    cerr << "error: cannot open file to write at " ;
+    cerr << "Error: couldn't open file '" << fileName << "'." ;
-    cerr << "ConstraintTree::exportToDotFile()" << endl;
+    return;
-    abort();
   }
   out << "digraph {" << endl;
   ConstraintTree copy (*this);
-  // copy.moveToTop (copy.logVarSet_.elements());
+  copy.moveToTop (copy.logVarSet_.elements());
   CTNodes nodes = getNodesBelow (copy.root_);
   out << "\"" << copy.root_ << "\"" << " [label=\"R\"]" << endl;
   for (CTNodes::const_iterator it = ++ nodes.begin();
@@ -814,10 +813,10 @@ ConstraintTree::jointCountNormalize (
     cts[i]->join (exclCt);
   }
 
-  if (excl1 != 0) {
+  if (excl1) {
     cts.push_back (excl1);
   }
-  if (excl2 != 0) {
+  if (excl2) {
     cts.push_back (excl2);
   }
 
@@ -883,7 +882,7 @@ ConstraintTree::ground (LogVar X)
 
 
 void
-ConstraintTree::copyLogVar (LogVar X_1, LogVar X_2)
+ConstraintTree::cloneLogVar (LogVar X_1, LogVar X_2)
 {
   moveToBottom ({X_1});
   CTNodes leafs = getNodesAtLevel (logVars_.size());
@@ -1073,7 +1072,7 @@ ConstraintTree::getTuples (
     CTNodes& continuationNodes) const
 {
   if (n->isRoot() == false) {
-    if (currTuples.size() == 0) {
+    if (currTuples.empty()) {
         currTuples.push_back ({ n->symbol()});
     } else {
       for (size_t i = 0; i < currTuples.size(); i++) {

packages/CLPBN/horus/ConstraintTree.h

@@ -23,7 +23,6 @@ typedef vector<ConstraintTree*> ConstraintTrees;
 class CTNode
 {
   public:
-
     struct CompareSymbol
     {
       bool operator() (const CTNode* n1, const CTNode* n2) const
@@ -33,11 +32,9 @@ class CTNode
     };
 
   private:
-
     typedef TinySet<CTNode*, CompareSymbol> CTChilds_;
 
   public:
-
     CTNode (const CTNode& n, const CTChilds_& chs = CTChilds_()) 
         : symbol_(n.symbol()), childs_(chs), level_(n.level()) { }
 
@@ -52,8 +49,6 @@ class CTNode
 
     void setSymbol (const Symbol s) { symbol_ = s; }
 
-  public:
-
     CTChilds_& childs (void) { return childs_; }
 
     const CTChilds_& childs (void) const { return childs_; }
@@ -92,6 +87,8 @@ class CTNode
     Symbol     symbol_;
     CTChilds_  childs_;
     unsigned   level_;
+
+    DISALLOW_ASSIGN (CTNode);
 };
 
 ostream& operator<< (ostream &out, const CTNode&);
@@ -200,7 +197,7 @@ class ConstraintTree
 
     ConstraintTrees ground (LogVar);
 
-    void copyLogVar (LogVar,LogVar);
+    void cloneLogVar (LogVar, LogVar);
 
     ConstraintTree& operator= (const ConstraintTree& ct);
 

packages/CLPBN/horus/CountingBp.cpp

@@ -2,7 +2,7 @@
 #include "WeightedBp.h"
 
 
-bool CountingBp::checkForIdenticalFactors = true;
+bool CountingBp::fif_ = true;
 
 
 CountingBp::CountingBp (const FactorGraph& fg)
@@ -36,19 +36,17 @@ CountingBp::printSolverFlags (void) const
 {
   stringstream ss;
   ss << "counting bp [" ;
-  ss << "schedule=" ;
+  ss << "bp_msg_schedule=" ;
-  typedef BpOptions::Schedule Sch;
+  switch (WeightedBp::msgSchedule()) {
-  switch (BpOptions::schedule) {
+    case MsgSchedule::SEQ_FIXED:    ss << "seq_fixed";    break;
-    case Sch::SEQ_FIXED:    ss << "seq_fixed";    break;
+    case MsgSchedule::SEQ_RANDOM:   ss << "seq_random";   break;
-    case Sch::SEQ_RANDOM:   ss << "seq_random";   break;
+    case MsgSchedule::PARALLEL:     ss << "parallel";     break;
-    case Sch::PARALLEL:     ss << "parallel";     break;
+    case MsgSchedule::MAX_RESIDUAL: ss << "max_residual"; break;
-    case Sch::MAX_RESIDUAL: ss << "max_residual"; break;
   }
-  ss << ",max_iter=" << BpOptions::maxIter;
+  ss << ",bp_max_iter=" << WeightedBp::maxIterations();
-  ss << ",accuracy=" << BpOptions::accuracy;
+  ss << ",bp_accuracy=" << WeightedBp::accuracy();
   ss << ",log_domain=" << Util::toString (Globals::logDomain);
-  ss << ",chkif=" << 
+  ss << ",fif=" << Util::toString (CountingBp::fif_);
-      Util::toString (CountingBp::checkForIdenticalFactors);
   ss << "]" ;
   cout << ss.str() << endl;
 }
@@ -82,7 +80,7 @@ CountingBp::solveQuery (VarIds queryVids)
         reprArgs.push_back (getRepresentative (queryVids[i]));
       }
       FacNode* reprFac = getRepresentative (facNodes[idx]);
-      assert (reprFac != 0);
+      assert (reprFac);
       res = solver_->getFactorJoint (reprFac, reprArgs);
     }
   }
@@ -95,8 +93,7 @@ void
 CountingBp::findIdenticalFactors()
 {
   const FacNodes& facNodes = fg.facNodes();
-  if (checkForIdenticalFactors == false ||
+  if (fif_ == false || facNodes.size() == 1) {
-      facNodes.size() == 1) {
     return;
   }
   for (size_t i = 0; i < facNodes.size(); i++) {