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),
+	close(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
-#run_all_graphs  bp     "hve(min_neighbors) "  ve   min_neighbors
+learn_params  hve  missing5
-#run_all_graphs  bp     "bp(seq_fixed)      "  bp   seq_fixed
+learn_params  hve  missing10
-#run_all_graphs  bp     "cbp(seq_fixed)     "  cbp  seq_fixed
+learn_params  hve  missing20
-exit
+#learn_params  hve  missing30
+#learn_params  hve  missing40
+#learn_params  hve  missing50
 
+write_header ve
+learn_params  ve  missing5
+learn_params  ve  missing10
+learn_params  ve  missing20
+#learn_params  ve  missing30
+#learn_params  ve  missing40
+#learn_params  hve  missing50
 
-run_all_graphs  bp    "hve(min_neighbors) "  ve   min_neighbors
+write_header bp
-run_all_graphs  bp    "hve(min_weight)    "  ve   min_weight
+learn_params  bp  missing5
-run_all_graphs  bp    "hve(min_fill)      "  ve   min_fill
+learn_params  bp  missing10
-run_all_graphs  bp    "hve(w_min_fill)    "  ve   weighted_min_fill
+learn_params  bp  missing20
-run_all_graphs  bp    "bp(seq_fixed)      "  bp   seq_fixed
+#learn_params  bp  missing30
-run_all_graphs  bp    "bp(max_residual)   "  bp   max_residual
+#learn_params  bp  missing40
-run_all_graphs  bp    "cbp(seq_fixed)     "  cbp  seq_fixed
+#learn_params  bp missing50
-run_all_graphs  bp    "cbp(max_residual)  "  cbp  max_residual
+
-run_all_graphs  gibbs "gibbs              "
+write_header cbp
-echo "************************************************************************" >> "$OUT_FILE_NAME"
+learn_params  cbp  missing5
-echo "results for solver ve" >> "$OUT_FILE_NAME"
+learn_params  cbp  missing10
-echo "************************************************************************" >> "$OUT_FILE_NAME"
+learn_params  cbp  missing20
-run_solver  missing5   ve  missing5   $3  $4  $5
+#learn_params  cbp  missing30
-run_solver  missing10  ve  missing10  $3  $4  $5
+#learn_params  cbp  missing40
-run_solver  missing20  ve  missing20  $3  $4  $5
+#learn_params  cbp missing50
-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

@@ -1,210 +1,242 @@
 
-:- module(clpbn, [{}/1,
+:- module(clpbn,
-		  clpbn_flag/2,
+		[{}/1,
-		  set_clpbn_flag/2,
+		 clpbn_flag/2,
-		  clpbn_flag/3,
+		 set_clpbn_flag/2,
-		  clpbn_key/2,
+		 set_solver/1,
-		  clpbn_init_solver/4,
+		 set_em_solver/1,
-		  clpbn_run_solver/3,
+		 clpbn_flag/3,
-		  pfl_init_solver/6,
+		 clpbn_key/2,
-		  pfl_run_solver/4,
+		 clpbn_init_graph/1,
-		  clpbn_finalize_solver/1,
+		 clpbn_init_solver/4,
-		  clpbn_init_solver/5,
+		 clpbn_run_solver/3,
-		  clpbn_run_solver/4,
+		 pfl_init_solver/5,
-		  clpbn_init_graph/1,
+		 pfl_run_solver/3,
-		  probability/2,
+		 pfl_end_solver/1,
-		  conditional_probability/3,
+		 probability/2,
-		  use_parfactors/1,
+		 conditional_probability/3,
-		  op( 500, xfy, with)]).
+		 use_parfactors/1,
+		 op(500, xfy, with)
+		]).
 
 :- use_module(library(atts)).
+
 :- use_module(library(bhash)).
+
 :- use_module(library(lists)).
+
 :- use_module(library(terms)).
+
 :- use_module(library(maplist)).
 
+:- attribute key/1, dist/2, evidence/1.
+
+:- use_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
+		]).
+
+:- use_module('clpbn/jt',
+		[jt/3,
+		 init_jt_solver/4,
+		 run_jt_solver/3
+		]).
+
+:- use_module('clpbn/bdd',
+		[bdd/3,
+		 init_bdd_solver/4,
+		 run_bdd_solver/3,
+		 init_bdd_ground_solver/5,
+		 run_bdd_ground_solver/3,
+		 call_bdd_ground_solver/6
+		]).
+
+:- use_module('clpbn/gibbs',
+		[gibbs/3,
+		 check_if_gibbs_done/1,
+		 init_gibbs_solver/4,
+		 run_gibbs_solver/3
+		]).
+
+:- use_module('clpbn/pgrammar',
+		[pcg_init_graph/0,
+		 init_pcg_solver/4,
+		 run_pcg_solver/3
+		]).
+
+:- 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/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,
+		 get_dist/4,
+		 get_evidence_position/3,
+		 get_evidence_from_position/3,
+		 additive_dists/6
+		]).
+
+:- use_module('clpbn/evidence',
+		[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]).
+
+:- use_module('clpbn/graphs',
+		[clpbn2graph/1]).
+
+:- use_module('clpbn/graphviz',
+		[clpbn2gviz/4]).
+
 %
 % avoid the overhead of using goal_expansion/2.
 %
-:- multifile
+:- multifile user:term_expansion/2.
-	user:term_expansion/2.
+
+:- dynamic user:term_expansion/2.
 
 :- dynamic
-	user:term_expansion/2.
+	solver/1,
-
+	em_solver/1,
-:- attribute key/1, dist/2, evidence/1.
+	suppress_attribute_display/1,
-
+	parameter_softening/1,
-
+	use_parfactors/1,
-:- use_module('clpbn/ve',
+	output/1,
-	      [ve/3,
+	use/1.
-	       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
-	      ]).
-
-:- 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,
-	       run_jt_solver/3
-	      ]).
-
-:- use_module('clpbn/bdd',
-	      [bdd/3,
-	       init_bdd_solver/4,
-	       run_bdd_solver/3,
-	       init_bdd_ground_solver/5,
-	       run_bdd_ground_solver/3,
-	       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,
-	       init_gibbs_solver/4,
-	       run_gibbs_solver/3
-	      ]).
-
-:- use_module('clpbn/pgrammar',
-	      [init_pcg_solver/4,
-	       run_pcg_solver/3,
-	       pcg_init_graph/0
-	      ]).
-
-:- use_module('clpbn/graphs',
-	      [
-	       clpbn2graph/1
-	      ]).
-
-:- use_module('clpbn/dists',
-	      [
-	       dist/4,
-	       get_dist/4,
-	       get_evidence_position/3,
-	       get_evidence_from_position/3,
-	       additive_dists/6
-	      ]).
-
-:- use_module('clpbn/evidence',
-	      [
-	       store_evidence/1,
-	       add_stored_evidence/2,
-	       incorporate_evidence/2,
-	       check_stored_evidence/2,
-	       put_evidence/2
-	      ]).
-
-:- use_module('clpbn/utils',
-	      [
-	       sort_vars_by_key/3
-	      ]).
-
-:- use_module('clpbn/graphviz',
-	[clpbn2gviz/4]).
-
-:- use_module(clpbn/ground_factors,
-	[generate_network/5]).
-
-
-:- dynamic solver/1,output/1,use/1,suppress_attribute_display/1, parameter_softening/1, em_solver/1, use_parfactors/1.
-
-solver(ve).
-em_solver(bp).
 
 :- 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)).
 
-clpbn_flag(Flag,Option) :-
+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).
 
 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} :-
+{ Var = Key with Dist } :-
 	put_atts(El,[key(Key),dist(DistInfo,Parents)]),
 	dist(Dist, DistInfo, Key, Parents),
 	add_evidence(Var,Key,DistInfo,El)
 %	,writeln({Var = Key with Dist})
-.
+	.
 
 %
 % make sure a query variable is reachable by the garbage collector.
 %
 % we use a mutable variable to avoid unnecessary trailing.
 %
-store_var(El) :- 
+store_var(El) :-
-	nb_current(clpbn_qvars, Mutable), 
+	nb_current(clpbn_qvars, Mutable),
 	nonvar(Mutable), !,
 	get_mutable(Tail, Mutable),
 	update_mutable(El.Tail, Mutable).
-store_var(El) :- 
+store_var(El) :-
-       init_clpbn_vars(El).
+	init_clpbn_vars(El).
-	
+
 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).
@@ -240,17 +272,19 @@ 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([],[],[],[])])
 	;
 	  call_ground_solver(Solver, GVars, GKeys, Keys, Factors, Evidence)
-        ).
+	).
 project_attributes(GVars, AVars) :-
 	suppress_attribute_display(false),
 	AVars = [_|_],
@@ -264,11 +298,11 @@ project_attributes(GVars, AVars) :-
 	(output(xbif(XBifStream)) -> clpbn2xbif(XBifStream,ve,AllVars) ; true),
 	(output(gviz(XBifStream)) -> clpbn2gviz(XBifStream,sort,AllVars,GVars) ; true),
 	(
-	    Solver = graphs
+	  Solver = graphs
 	->
-	    write_out(Solver, [[]], AllVars, DiffVars)
+	  write_out(Solver, [[]], AllVars, DiffVars)
 	;
-	    write_out(Solver, [CLPBNGVars], AllVars, DiffVars)
+	  write_out(Solver, [CLPBNGVars], AllVars, DiffVars)
 	).
 project_attributes(_, _).
 
@@ -322,37 +356,29 @@ 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(gvar_in_hash, GVars, Hash0, HashI),
 	foldl(key_to_var, Keys, AllVars, HashI, Hash1),
 	foldl(evidence_to_v, Evidence, _EVars, Hash1, Hash),
 	%writeln(Keys:AllVars),
@@ -362,13 +388,51 @@ 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
 %
 gvar_in_hash(V, Hash0, Hash) :-
 	get_atts(V, [key(K)]),
-	b_hash_insert(Hash0, K, V, Hash). 
+	b_hash_insert(Hash0, K, V, Hash).
 
 key_to_var(K, V, Hash0, Hash0) :-
 	b_hash_lookup(K, V, Hash0), !.
@@ -429,15 +493,15 @@ find_var([_|DVars], V, Key, [_|DKeys]) :-
 
 process_vars([], []).
 process_vars([V|Vs], [K|Ks]) :-
-        process_var(V, K),
+	process_var(V, K),
 	process_vars(Vs, Ks).
 
-process_var(V, K) :- get_atts(V, [key(K)]), !. 
+process_var(V, K) :- get_atts(V, [key(K)]), !.
 % oops: this variable has no attributes.
 process_var(V, _) :- throw(error(instantiation_error,clpbn(attribute_goal(V)))).
 
 %
-% unify a CLPBN variable with something. 
+% unify a CLPBN variable with something.
 %
 verify_attributes(Var, T, Goal) :-
 	get_atts(Var, [key(Key),dist(Dist,Parents)]), !,
@@ -452,28 +516,25 @@ bind_clpbn(T, Var, _, _, _, do_not_bind_variable([put_evidence(T,Var)])) :-
 bind_clpbn(T, Var, Key, Dist, Parents, []) :- var(T),
 	get_atts(T, [key(Key1),dist(Dist1,Parents1)]),
 	(
-	 bind_clpbns(Key, Dist, Parents, Key1, Dist1, Parents1)
+	  bind_clpbns(Key, Dist, Parents, Key1, Dist1, Parents1)
 	->
-	 (
+	  (
-	  get_atts(T, [evidence(Ev1)]) ->
+	    get_atts(T, [evidence(Ev1)]) ->
-	    bind_evidence_from_extra_var(Ev1,Var)
+	      bind_evidence_from_extra_var(Ev1,Var)
-	 ;
+	    ;
-	  get_atts(Var, [evidence(Ev)]) ->
+	      get_atts(Var, [evidence(Ev)]) ->
-	    bind_evidence_from_extra_var(Ev,T)
+	        bind_evidence_from_extra_var(Ev,T)
-	 ;
+	      ;
-	  true
+	        true
-	 )
+	  )
 	;
-	 fail
+	  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),
@@ -481,12 +542,21 @@ 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)]), !,
 	(
 	  Key = Key0 -> true
 	;
-	 % let us not loose whatever we had.
+	  % let us not loose whatever we had.
 	  put_evidence(T,Var)
 	).
 
@@ -495,8 +565,8 @@ fresh_attvar(Var, NVar) :-
 	put_atts(NVar, LAtts).
 
 % I will now allow two CLPBN variables to be bound together.
-%bind_clpbns(Key, Dist, Parents, Key, Dist, Parents).
+% bind_clpbns(Key, Dist, Parents, Key, Dist, Parents).
-bind_clpbns(Key, Dist, Parents, Key1, Dist1, Parents1) :- 
+bind_clpbns(Key, Dist, Parents, Key1, Dist1, Parents1) :-
 	Key == Key1, !,
 	get_dist(Dist,_Type,_Domain,_Table),
 	get_dist(Dist1,_Type1,_Domain1,_Table1),
@@ -525,13 +595,22 @@ bind_evidence_from_extra_var(Ev1,Var) :-
 bind_evidence_from_extra_var(Ev1,Var) :-
 	put_atts(Var, [evidence(Ev1)]).
 
-user:term_expansion((A :- {}), ( :- true )) :-	 !, % evidence
+user:term_expansion((A :- {}), ( :- true )) :- !, % evidence
 	prolog_load_context(module, M),
 	store_evidence(M:A).
 
 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
@@ -544,94 +623,116 @@ 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]).
-	
+
 conditional_probability(Goal, ListOfGoals, Prob) :-
 	\+ ground(Goal),
 	throw(error(ground(Goal),conditional_probability(Goal, ListOfGoals, Prob))).
@@ -665,26 +766,26 @@ evidence_to_var(Goal, C, VItem, V) :-
 	Goal =.. [L|Args],
 	variabilise_last(Args, C, NArgs, V),
 	VItem =.. [L|NArgs].
-	
+
 variabilise_last([Arg], Arg, [V], V).
 variabilise_last([Arg1,Arg2|Args], Arg, Arg1.NArgs, V) :-
 	variabilise_last(Arg2.Args, Arg, NArgs, V).
 
 match_probability(VPs, Goal, C, V, Prob) :-
-    match_probabilities(VPs, Goal, C, V, Prob).
+	match_probabilities(VPs, Goal, C, V, Prob).
 
 match_probabilities([p(V0=C)=Prob|_], _, C, V, Prob) :-
-    V0 == V,
+	V0 == V,
-    !.
+	!.
 match_probabilities([_|Probs], G, C, V, Prob) :-
-    match_probabilities(Probs, G, C, V, Prob).
+	match_probabilities(Probs, G, C, V, Prob).
 
 goal_to_key(_:Goal, Skolem) :-
-    goal_to_key(Goal, Skolem).
+	goal_to_key(Goal, Skolem).
 goal_to_key(Goal, Skolem) :-
-    functor(Goal, Na, Ar),
+	functor(Goal, Na, Ar),
-    Ar1 is Ar-1,
+	Ar1 is Ar-1,
-    functor(Skolem, Na, Ar1).
+	functor(Skolem, Na, Ar1).
 
 :- use_parfactors(on) -> true ; assert(use_parfactors(off)).
 

packages/CLPBN/clpbn/aggregates.yap

@@ -1,42 +1,45 @@
-				%
+%
 % generate explicit CPTs
 %
-:- module(clpbn_aggregates, [
+:- module(clpbn_aggregates,
-        check_for_agg_vars/2,
+		[check_for_agg_vars/2,
-	cpt_average/6,
+		 cpt_average/6,
-	cpt_average/7,
+		 cpt_average/7,
-	cpt_max/6,
+		 cpt_max/6,
-	cpt_min/6,
+		 cpt_min/6,
-        avg_factors/5
+		 avg_factors/5
-	]).
+		]).
 
-:- use_module(library(clpbn), [{}/1]).
+:- use_module(library(clpbn),
+		[{}/1]).
 
 :- use_module(library(lists),
-	[last/2,
+		[last/2,
-	sumlist/2,
+		 sumlist/2,
-	sum_list/3,
+		 sum_list/3,
-	max_list/2,
+		 max_list/2,
-	min_list/2,
+		 min_list/2,
-	nth0/3
+		 nth0/3
-    ]).
+		]).
 
 :- use_module(library(matrix),
-	[matrix_new/3,
+		[matrix_new/3,
-	matrix_to_list/2,
+		 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]).
+		[normalise_CPT_on_lines/3]).
 
 :- use_module(library(pfl),
-	[skolem/2,
+		[skolem/2,
-	 add_ground_factor/5]).
+		 add_ground_factor/5
+		]).
 
 :- use_module(library(bhash)).
 
@@ -60,9 +63,9 @@ simplify_dist(_, _, _, _, Vs0, Vs0).
 
 %
 avg_factors(Key, Parents, _Smoothing, NewParents, Id) :-
-    % we keep ev as a list
+	% we keep ev as a list
-    skolem(Key, Domain),
+	skolem(Key, Domain),
-    avg_table(Parents, Parents, Domain, Key, 0, 1.0, NewParents, [], _ExtraSkolems, Id).
+	avg_table(Parents, Parents, Domain, Key, 0, 1.0, NewParents, [], _ExtraSkolems, Id).
 
 % there are 4 cases:
 % no evidence on top node
@@ -70,17 +73,17 @@ avg_factors(Key, Parents, _Smoothing, NewParents, Id) :-
 % evidence on top node *entailed* by values of parents (so there is no real connection)
 % evidence incompatible with parents
 query_evidence(Key, EvHash, MAT0, MAT, NewParents0, NewParents, Vs, IVs, NewVs) :-
-    b_hash_lookup(Key, Ev, EvHash), !,
+	b_hash_lookup(Key, Ev, EvHash), !,
-    normalise_CPT_on_lines(MAT0, MAT1, L1),
+	normalise_CPT_on_lines(MAT0, MAT1, L1),
-    check_consistency(L1, Ev, MAT0, MAT1, L1, MAT, NewParents0, NewParents, Vs, IVs, NewVs).
+	check_consistency(L1, Ev, MAT0, MAT1, L1, MAT, NewParents0, NewParents, Vs, IVs, NewVs).
 query_evidence(_, _, MAT, MAT, NewParents, NewParents, _, Vs, Vs).
 
 hash_ev(K=V, Es0, Es) :-
-    b_hash_insert(Es0, K, V, Es).
+	b_hash_insert(Es0, K, V, Es).
 
 find_ev(Ev, Key, RemKeys, RemKeys, Ev0, EvF) :-
-    b_hash_lookup(Key, V, Ev), !,
+	b_hash_lookup(Key, V, Ev), !,
-    EvF is Ev0+V.
+	EvF is Ev0+V.
 find_ev(_Evs, Key, RemKeys, [Key|RemKeys], Ev, Ev).
 
 
@@ -93,11 +96,11 @@ find_ev(_Evs, Key, RemKeys, [Key|RemKeys], Ev, Ev).
 % +final CPT
 % - New Parents
 % + - list of new keys
-% 
+%
 avg_table(Vars, OVars, Domain, Key, TotEvidence, Softness, Vars, Vs, Vs, Id) :-
 	length(Domain, SDomain),
 	int_power(Vars, SDomain, 1, TabSize),
-	TabSize =< 256, 
+	TabSize =< 256,
 	/* case gmp is not there !! */
 	TabSize > 0, !,
 	average_cpt(Vars, OVars, Domain, TotEvidence,  Softness, CPT),
@@ -115,7 +118,7 @@ avg_table(Vars, OVars, Domain, Key, TotEvidence, Softness, [V1,V2], Vs, [V1,V2|N
 	average_cpt([V1,V2], OVars, Domain, TotEvidence, Softness, CPT),
 	matrix_to_list(CPT, Mat),
 	add_ground_factor(bayes, Domain, [Key,V1,V2], Mat, Id).
-	
+
 intermediate_table(1,_,[V],V, _, _, I, I, Vs, Vs) :- !.
 intermediate_table(2, Op, [V1,V2], V, Key, Softness, I0, If, Vs, Vs) :- !,
 	If is I0+1,
@@ -167,7 +170,7 @@ cpt_min([_|Vars], Key, Els0, CPT, Vs, NewVs) :-
 build_avg_table(Vars, OVars, Domain, _, TotEvidence, Softness, CPT, Vars, Vs, Vs) :-
 	length(Domain, SDomain),
 	int_power(Vars, SDomain, 1, TabSize),
-	TabSize =< 256, 
+	TabSize =< 256,
 	/* case gmp is not there !! */
 	TabSize > 0, !,
 	average_cpt(Vars, OVars, Domain, TotEvidence,  Softness, CPT).
@@ -181,11 +184,11 @@ build_avg_table(Vars, OVars, Domain, Key, TotEvidence, Softness, CPT, [V1,V2], V
 	build_intermediate_table(LL1, sum(Min,Max), L1, V1, Key,  1.0, 0, I1, Vs, Vs1),
 	build_intermediate_table(LL2, sum(Min,Max), L2, V2, Key, 1.0, I1, _, Vs1, NewVs),
 	average_cpt([V1,V2], OVars, Domain, TotEvidence, Softness, CPT).
-	
+
 build_max_table(Vars, Domain, Softness, p(Domain, CPT, Vars), Vs, Vs) :-
 	length(Domain, SDomain),
 	int_power(Vars, SDomain, 1, TabSize),
-	TabSize =< 16, 
+	TabSize =< 16,
 	/* case gmp is not there !! */
 	TabSize > 0, !,
 	max_cpt(Vars, Domain, Softness, CPT).
@@ -197,11 +200,11 @@ build_max_table(Vars, Domain, Softness, p(Domain, CPT, [V1,V2]), Vs, [V1,V2|NewV
 	build_intermediate_table(LL1, max(Domain,CPT), L1, V1, Key, 1.0,  0, I1, Vs, Vs1),
 	build_intermediate_table(LL2, max(Domain,CPT), L2, V2, Key, 1.0, I1, _, Vs1, NewVs),
 	max_cpt([V1,V2], Domain, Softness, CPT).
-	
+
 build_min_table(Vars, Domain, Softness, p(Domain, CPT, Vars), Vs, Vs) :-
 	length(Domain, SDomain),
 	int_power(Vars, SDomain, 1, TabSize),
-	TabSize =< 16, 
+	TabSize =< 16,
 	/* case gmp is not there !! */
 	TabSize > 0, !,
 	min_cpt(Vars, Domain, Softness, CPT).
@@ -213,7 +216,7 @@ build_min_table(Vars, Domain, Softness, p(Domain, CPT, [V1,V2]), Vs, [V1,V2|NewV
 	build_intermediate_table(LL1, min(Domain,CPT), L1, V1, Key, 1.0,  0, I1, Vs, Vs1),
 	build_intermediate_table(LL2, min(Domain,CPT), L2, V2, Key, 1.0, I1, _, Vs1, NewVs),
 	min_cpt([V1,V2], Domain, Softness, CPT).
-	
+
 int_power([], _, TabSize, TabSize).
 int_power([_|L], X, I0, TabSize) :-
 	I is I0*X,
@@ -270,19 +273,21 @@ 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 ->
+	(
-	    MAT1 = MAT,
+	  Val == Tot
-	    NewParents = [],
+	->
-	    Vs = NewVs
+	  MAT1 = MAT,
+	  NewParents = [],
+	  Vs = NewVs
 	;
-	 Val == 0.0 ->
+	  Val == 0.0 ->
 	    throw(error(domain_error(incompatible_evidence),evidence(Ev)))
-	;
+	  ;
 	    MAT0 = MAT,
 	    NewParents = NewParents0,
 	    IVs = NewVs
 	).
-	
+
 
 %
 % generate actual table, instead of trusting the solver
@@ -299,7 +304,7 @@ get_ds_lengths([],[]).
 get_ds_lengths([V|Vs],[Sz|Lengs]) :-
 	get_vdist_size(V, Sz),
 	get_ds_lengths(Vs,Lengs).
-	
+
 fill_in_average(Lengs, N, Base, MCPT) :-
 	generate(Lengs, Case),
 	average(Case, N, Base, Val),
@@ -369,10 +374,10 @@ fill_in_min(_,_).
 
 
 get_vdist_size(V, Sz) :-
-        var(V), !,
+	var(V), !,
 	clpbn:get_atts(V, [dist(Dist,_)]),
 	get_dist_domain_size(Dist, Sz).
 get_vdist_size(V, Sz) :-
-	skolem(V, Dom), 
+	skolem(V, Dom),
 	length(Dom, Sz).
 

packages/CLPBN/clpbn/bdd.yap

@@ -9,41 +9,41 @@ V = v(Va, Vb, Vc)
 
 The generic formula is
 
-V <- X, Y 
+V <- X, Y
 
 Va <- P*X1*Y1 + Q*X2*Y2 + ...
 
 
- 
+
 **************************************************/
 
 :- module(clpbn_bdd,
-          [bdd/3,
+		[bdd/3,
-           set_solver_parameter/2,
+		 set_solver_parameter/2,
-           init_bdd_solver/4,
+		 init_bdd_solver/4,
-           init_bdd_ground_solver/5,
+		 init_bdd_ground_solver/5,
-           run_bdd_solver/3,
+		 run_bdd_solver/3,
-           run_bdd_ground_solver/3,
+		 run_bdd_ground_solver/3,
-           finalize_bdd_solver/1,
+		 finalize_bdd_solver/1,
-	   check_if_bdd_done/1,
+		 check_if_bdd_done/1,
-	   call_bdd_ground_solver/6
+		 call_bdd_ground_solver/6
-          ]).
+		]).
 
 
 :- use_module(library('clpbn/dists'),
-          [dist/4,
+		[dist/4,
-           get_dist_domain/2,
+		 get_dist_domain/2,
-           get_dist_domain_size/2,
+		 get_dist_domain_size/2,
-           get_dist_all_sizes/2,
+		 get_dist_all_sizes/2,
-           get_dist_params/2
+		 get_dist_params/2
-          ]).
+		]).
 
 
 :- use_module(library('clpbn/display'),
-         [clpbn_bind_vals/3]).
+		[clpbn_bind_vals/3]).
 
 :- use_module(library('clpbn/aggregates'),
-	      [check_for_agg_vars/2]).
+		[check_for_agg_vars/2]).
 
 
 :- use_module(library(atts)).
@@ -80,8 +80,8 @@ bdds(bdd).
 
 %
 % QVars: all query variables?
-% 
+%
-% 
+%
 init_bdd_ground_solver(QueryKeys, AllKeys, Factors, Evidence, bdd(QueryKeys, AllKeys, Factors, Evidence)).
 
 %
@@ -93,37 +93,37 @@ run_bdd_ground_solver(_QueryVars, Solutions, bdd(GKeys, Keys, Factors, Evidence)
 check_if_bdd_done(_Var).
 
 call_bdd_ground_solver(QueryVars, QueryKeys, AllKeys, Factors, Evidence, Output) :-
-    call_bdd_ground_solver_for_probabilities([QueryKeys], AllKeys, Factors, Evidence, Solutions),
+	call_bdd_ground_solver_for_probabilities([QueryKeys], AllKeys, Factors, Evidence, Solutions),
-    clpbn_bind_vals([QueryVars], Solutions, Output).
+	clpbn_bind_vals([QueryVars], Solutions, Output).
 
 call_bdd_ground_solver_for_probabilities(QueryKeys, AllKeys, Factors, Evidence, Solutions) :-
-    keys_to_numbers(AllKeys, Factors, Evidence, Hash4, Id4, FactorIds, EvidenceIds),
+	keys_to_numbers(AllKeys, Factors, Evidence, Hash4, Id4, FactorIds, EvidenceIds),
-    init_bdd(FactorIds, EvidenceIds, Hash4, Id4, BDD),
+	init_bdd(FactorIds, EvidenceIds, Hash4, Id4, BDD),
-    run_solver(QueryKeys, Solutions, BDD).
+	run_solver(QueryKeys, Solutions, BDD).
 
 init_bdd(FactorIds, EvidenceIds, Hash, Id, bdd(Term, Leaves, Tops, Hash, Id)) :-
-    sort_keys(FactorIds, AllVars, Leaves),
+	sort_keys(FactorIds, AllVars, Leaves),
-    rb_new(OrderVs0),
+	rb_new(OrderVs0),
-    foldl2(order_key, AllVars, 0, _, OrderVs0, OrderVs),
+	foldl2(order_key, AllVars, 0, _, OrderVs0, OrderVs),
-    rb_new(Vars0),
+	rb_new(Vars0),
-    rb_new(Pars0),
+	rb_new(Pars0),
-    rb_new(Ev0),
+	rb_new(Ev0),
-    foldl(evtotree,EvidenceIds,Ev0,Ev),
+	foldl(evtotree,EvidenceIds,Ev0,Ev),
-    rb_new(Fs0),
+	rb_new(Fs0),
-    foldl(ftotree,FactorIds,Fs0,Fs),
+	foldl(ftotree,FactorIds,Fs0,Fs),
-    init_tops(Leaves,Tops),
+	init_tops(Leaves,Tops),
-    get_keys_info(AllVars, Ev, Fs, OrderVs, Vars0, _Vars, Pars0, _Pars, Leaves, Tops, Term, []).
+	get_keys_info(AllVars, Ev, Fs, OrderVs, Vars0, _Vars, Pars0, _Pars, Leaves, Tops, Term, []).
 
 order_key( Id, I0, I, OrderVs0, OrderVs) :-
-    I is I0+1,
+	I is I0+1,
-    rb_insert(OrderVs0, Id, I0, OrderVs).
+	rb_insert(OrderVs0, Id, I0, OrderVs).
 
 evtotree(K=V,Ev0,Ev) :-
-    rb_insert(Ev0, K, V, Ev).
+	rb_insert(Ev0, K, V, Ev).
 
 ftotree(F, Fs0, Fs) :-
-    F = f([K|_Parents],_,_,_),
+	F = f([K|_Parents],_,_,_),
-    rb_insert(Fs0, K, F, Fs).
+	rb_insert(Fs0, K, F, Fs).
 
 bdd([[]],_,_) :- !.
 bdd([QueryVars], AllVars, AllDiffs) :-
@@ -155,59 +155,59 @@ init_tops([_|Leaves],[_|Tops]) :-
 	init_tops(Leaves,Tops).
 
 sort_keys(AllFs, AllVars, Leaves) :-
-    dgraph_new(Graph0),
+	dgraph_new(Graph0),
-    foldl(add_node, AllFs, Graph0, Graph),
+	foldl(add_node, AllFs, Graph0, Graph),
-    dgraph_leaves(Graph, Leaves),
+	dgraph_leaves(Graph, Leaves),
-    dgraph_top_sort(Graph, AllVars).
+	dgraph_top_sort(Graph, AllVars).
 
 add_node(f([K|Parents],_,_,_), Graph0, Graph) :-
-    dgraph_add_vertex(Graph0, K, Graph1), 
+	dgraph_add_vertex(Graph0, K, Graph1),
-    foldl(add_edge(K), Parents, Graph1, Graph).
+	foldl(add_edge(K), Parents, Graph1, Graph).
-    
+
 add_edge(K, K0, Graph0, Graph) :-
-    dgraph_add_edge(Graph0, K0, K, Graph).
+	dgraph_add_edge(Graph0, K0, K, Graph).
 
 sort_vars(AllVars0, AllVars, Leaves) :-
-    dgraph_new(Graph0),
+	dgraph_new(Graph0),
-    build_graph(AllVars0, Graph0, Graph),
+	build_graph(AllVars0, Graph0, Graph),
-    dgraph_leaves(Graph, Leaves),
+	dgraph_leaves(Graph, Leaves),
-    dgraph_top_sort(Graph, AllVars).
+	dgraph_top_sort(Graph, AllVars).
 
 build_graph([], Graph, Graph).
 build_graph([V|AllVars0], Graph0, Graph) :-
-    clpbn:get_atts(V, [dist(_DistId, Parents)]), !,
+	clpbn:get_atts(V, [dist(_DistId, Parents)]), !,
-    dgraph_add_vertex(Graph0, V, Graph1), 
+	dgraph_add_vertex(Graph0, V, Graph1),
-    add_parents(Parents, V, Graph1, GraphI),
+	add_parents(Parents, V, Graph1, GraphI),
-    build_graph(AllVars0, GraphI, Graph).
+	build_graph(AllVars0, GraphI, Graph).
 build_graph(_V.AllVars0, Graph0, Graph) :-
-    build_graph(AllVars0, Graph0, Graph).
+	build_graph(AllVars0, Graph0, Graph).
 
 add_parents([], _V, Graph, Graph).
 add_parents([V0|Parents], V, Graph0, GraphF) :-
-    dgraph_add_edge(Graph0, V0, V, GraphI), 
+	dgraph_add_edge(Graph0, V0, V, GraphI),
-    add_parents(Parents, V, GraphI, GraphF).
+	add_parents(Parents, V, GraphI, GraphF).
 
 get_keys_info([], _, _, _, Vs, Vs, Ps, Ps, _, _) --> [].
 get_keys_info([V|MoreVs], Evs, Fs, OrderVs, Vs, VsF, Ps, PsF, Lvs, Outs) -->
-    { rb_lookup(V, F, Fs) }, !,
+	{ rb_lookup(V, F, Fs) }, !,
-    { F = f([V|Parents], _, _, DistId) },
+	{ F = f([V|Parents], _, _, DistId) },
 %{writeln(v:DistId:Parents)},
-    [DIST],
+	[DIST],
-    {  get_key_info(V, F, Fs, Evs, OrderVs, DistId, Parents, Vs, Vs2, Ps, Ps1, Lvs, Outs, DIST) },
+	{ get_key_info(V, F, Fs, Evs, OrderVs, DistId, Parents, Vs, Vs2, Ps, Ps1, Lvs, Outs, DIST) },
-    get_keys_info(MoreVs, Evs, Fs, OrderVs, Vs2, VsF, Ps1, PsF, Lvs, Outs).
+	get_keys_info(MoreVs, Evs, Fs, OrderVs, Vs2, VsF, Ps1, PsF, Lvs, Outs).
 
 get_key_info(V, F, Fs, Evs, OrderVs, DistId, Parents0, Vs, Vs2, Ps, Ps1, Lvs, Outs, DIST) :-
-    reorder_keys(Parents0, OrderVs, Parents, Map),
+	reorder_keys(Parents0, OrderVs, Parents, Map),
-    check_key_p(DistId, F, Map, Parms, _ParmVars, Ps, Ps1),
+	check_key_p(DistId, F, Map, Parms, _ParmVars, Ps, Ps1),
-    unbound_parms(Parms, ParmVars),
+	unbound_parms(Parms, ParmVars),
-    F = f(_,[Size|_],_,_),
+	F = f(_,[Size|_],_,_),
-    check_key(V, Size, DIST, Vs, Vs1),
+	check_key(V, Size, DIST, Vs, Vs1),
-    DIST = info(V, Tree, Ev, Values, Formula, ParmVars, Parms),
+	DIST = info(V, Tree, Ev, Values, Formula, ParmVars, Parms),
-    % get a list of form [[P00,P01], [P10,P11], [P20,P21]]
+	% get a list of form [[P00,P01], [P10,P11], [P20,P21]]
-    foldl(get_key_parent(Fs), Parents, PVars, Vs1, Vs2),
+	foldl(get_key_parent(Fs), Parents, PVars, Vs1, Vs2),
-    cross_product(Values, Ev, PVars, ParmVars, Formula0),
+	cross_product(Values, Ev, PVars, ParmVars, Formula0),
 %	(numbervars(Formula0,0,_),writeln(formula0:Ev:Formula0), fail ; true),
-    get_key_evidence(V, Evs, DistId, Tree, Ev, Formula0, Formula, Lvs, Outs).
+	get_key_evidence(V, Evs, DistId, Tree, Ev, Formula0, Formula, Lvs, Outs).
 %	(numbervars(Formula,0,_),writeln(formula:Formula), fail ; true).
 
 get_vars_info([], Vs, Vs, Ps, Ps, _, _) --> [].
@@ -215,7 +215,7 @@ get_vars_info([V|MoreVs], Vs, VsF, Ps, PsF, Lvs, Outs) -->
 	{ clpbn:get_atts(V, [dist(DistId, Parents)]) }, !,
 %{writeln(v:DistId:Parents)},
 	[DIST],
-	{  get_var_info(V, DistId, Parents, Vs, Vs2, Ps, Ps1, Lvs, Outs, DIST) },
+	{ get_var_info(V, DistId, Parents, Vs, Vs2, Ps, Ps1, Lvs, Outs, DIST) },
 	get_vars_info(MoreVs, Vs2, VsF, Ps1, PsF, Lvs, Outs).
 get_vars_info([_|MoreVs], Vs0, VsF, Ps0, PsF, VarsInfo, Lvs, Outs) :-
 	get_vars_info(MoreVs, Vs0, VsF, Ps0, PsF, VarsInfo, Lvs, Outs).
@@ -298,17 +298,17 @@ generate_3tree(OUT, [[P0,P1,P2]], I00, I10, I20, IR0, N0, N1, N2, R, Exp, _ExpF)
 	IR is IR0-1,
 	( satisf(I00+1, I10, I20, IR, N0, N1, N2, R, Exp) ->
 	  L0 = [P0|L1]
-	  ;
+	;
 	  L0 = L1
 	),
 	( satisf(I00, I10+1, I20, IR, N0, N1, N2, R, Exp) ->
 	  L1 = [P1|L2]
-	  ;
+	;
 	  L1 = L2
 	),
 	( satisf(I00, I10, I20+1, IR, N0, N1, N2, R, Exp) ->
 	  L2 = [P2]
-	  ;
+	;
 	  L2 = []
 	),
 	to_disj(L0, OUT).
@@ -316,23 +316,23 @@ generate_3tree(OUT, [[P0,P1,P2]|Ps], I00, I10, I20, IR0, N0, N1, N2, R, Exp, Exp
 	IR is IR0-1,
 	( satisf(I00+1, I10, I20, IR, N0, N1, N2, R, Exp) ->
 	  I0 is I00+1, generate_3tree(O0, Ps, I0, I10, I20, IR, N0, N1, N2, R, Exp, ExpF)
-	  ->
+	->
 	  L0 = [P0*O0|L1]
-	  ;
+	;
 	  L0 = L1
 	),
 	( satisf(I00, I10+1, I20, IR0, N0, N1, N2, R, Exp) ->
 	  I1 is I10+1, generate_3tree(O1, Ps, I00, I1, I20, IR, N0, N1, N2, R, Exp, ExpF)
-	  ->
+	->
 	  L1 = [P1*O1|L2]
-	  ;
+	;
 	  L1 = L2
 	),
 	( satisf(I00, I10, I20+1, IR0, N0, N1, N2, R, Exp) ->
 	  I2 is I20+1, generate_3tree(O2, Ps, I00, I10, I2, IR, N0, N1, N2, R, Exp, ExpF)
-	  ->	  
+	->
 	  L2 = [P2*O2]
-	  ;
+	;
 	  L2 = []
 	),
 	to_disj(L0, OUT).
@@ -378,18 +378,18 @@ avg_tree([Vals|PVars], P, Max, Im, IM, Size, O, H0, HF) :-
 	MaxI is Max-(Size-1),
 	avg_exp(Vals, PVars, 0, P, MaxI, Size, Im, IM, HI, HF, Exp),
 	simplify_exp(Exp, Simp).
-	
+
 avg_exp([], _, _, _P, _Max, _Size, _Im, _IM, H, H, 0).
 avg_exp([Val|Vals], PVars, I0, P0, Max, Size, Im, IM, HI, HF, O) :-
 	(Vals = [] -> O=O1 ; O = Val*O1+not(Val)*O2 ),
 	Im1 is max(0, Im-I0),
 	IM1 is IM-I0,
-	( IM1 < 0 -> O1 = 0, H2 = HI;      /* we have exceed maximum */
+	( IM1 < 0 -> O1 = 0, H2 = HI ;  /* we have exceed maximum */
-	  Im1 > Max -> O1 = 0, H2 = HI;  /* we cannot make to minimum */
+	  Im1 > Max -> O1 = 0, H2 = HI ;  /* we cannot make to minimum */
-	  Im1 = 0, IM1 > Max -> O1 = 1, H2 = HI;  /* we cannot exceed maximum */
+	  Im1 = 0, IM1 > Max -> O1 = 1, H2 = HI ;  /* we cannot exceed maximum */
 	  P is P0+1,
 	  avg_tree(PVars, P, Max, Im1, IM1, Size, O1, HI, H2)
-        ),
+	),
 	I is I0+1,
 	avg_exp(Vals, PVars, I, P0, Max, Size, Im, IM, H2, HF, O2).
 
@@ -434,14 +434,14 @@ bup_avg(V, Size, Domain, Parents0, Vs, Vs2, Lvs, Outs, DIST) :-
 bin_sums(Vs, Sums, F) :-
 	 vs_to_sums(Vs, Sums0),
 	 bin_sums(Sums0, Sums, F, []).
-	
+
 vs_to_sums([], []).
 vs_to_sums([V|Vs], [Sum|Sums0]) :-
-	  Sum =.. [sum|V],
+	Sum =.. [sum|V],
-	  vs_to_sums(Vs, Sums0).
+	vs_to_sums(Vs, Sums0).
 
 bin_sums([Sum], Sum) --> !.
-bin_sums(LSums, Sum) --> 
+bin_sums(LSums, Sum) -->
 	{ halve(LSums, Sums1, Sums2) },
 	bin_sums(Sums1, Sum1),
 	bin_sums(Sums2, Sum2),
@@ -458,14 +458,14 @@ head(Take, [H|L], [H|Sums1], Sum2) :-
 	head(Take1, L, Sums1, Sum2).
 
 sum(Sum1, Sum2, Sum) -->
-	  { functor(Sum1, _, M1),
+	{ functor(Sum1, _, M1),
-	    functor(Sum2, _, M2),
+	  functor(Sum2, _, M2),
-	    Max is M1+M2-2,
+	  Max is M1+M2-2,
-	    Max1 is Max+1,
+	  Max1 is Max+1,
-	    Max0 is M2-1,
+	  Max0 is M2-1,
-	    functor(Sum, sum, Max1),
+	  functor(Sum, sum, Max1),
-	    Sum1 =.. [_|PVals] },
+	  Sum1 =.. [_|PVals] },
-	  expand_sums(PVals, 0, Max0, Max1, M2, Sum2, Sum).
+	expand_sums(PVals, 0, Max0, Max1, M2, Sum2, Sum).
 
 %
 % bottom up step by step
@@ -509,12 +509,12 @@ expand_sums(Parents, I0, Max0, Max, Size, Sums, Prot, NewSums, [O=SUM*1|F], F0)
 	arg(I, NewSums, O),
 	sum_all(Parents, 0, I0, Max0, Sums, List),
 	to_disj(List, SUM),
-        expand_sums(Parents, I, Max0, Max, Size, Sums, Prot, NewSums, F, F0).
+	expand_sums(Parents, I, Max0, Max, Size, Sums, Prot, NewSums, F, F0).
 expand_sums(Parents, I0, Max0, Max, Size, Sums, Prot, NewSums, F, F0) :-
 	I is I0+1,
 	arg(I, Sums, O),
 	arg(I, NewSums, O),
-        expand_sums(Parents, I, Max0, Max, Size, Sums, Prot, NewSums, F, F0).
+	expand_sums(Parents, I, Max0, Max, Size, Sums, Prot, NewSums, F, F0).
 
 %
 %inner loop: find all parents that contribute to A_ji,
@@ -536,14 +536,14 @@ sum_all([_V|Vs], Pos, I, Max0, Sums, List) :-
 
 gen_arg(J, Sums, Max, S0) :-
 	gen_arg(0, Max, J, Sums, S0).
-	
+
 gen_arg(Max, Max, J, Sums, S0) :- !,
-	     I is Max+1,
+	I is Max+1,
-	     arg(I, Sums, A),
+	arg(I, Sums, A),
 	( Max = J -> S0 = A ; S0 = not(A)).
 gen_arg(I0, Max, J, Sums, S) :-
-	     I is I0+1,
+	I is I0+1,
-	     arg(I, Sums, A),
+	arg(I, Sums, A),
 	( I0 = J -> S = A*S0 ; S = not(A)*S0),
 	gen_arg(I, Max, J, Sums, S0).
 
@@ -647,19 +647,19 @@ copy(N, [], [], Ms, Parms0, Parms, ParmVars) :-!,
 	copy(N, Ms, NewMs, NewMs, Parms0, Parms, ParmVars).
 copy(N, D.Ds, ND.NDs, New, El.Parms0, NEl.Parms, V.ParmVars) :-
 	N1 is N-1,
-	(El == 0.0 -> 
+	(El == 0.0 ->
 	    NEl = 0,
 	    V = NEl,
 	    ND = D
-	;El == 1.0 -> 
+	;El == 1.0 ->
 	    NEl = 1,
 	    V = NEl,
 	    ND = 0.0
-	;El == 0 -> 
+	;El == 0 ->
 	    NEl = 0,
 	    V = NEl,
 	    ND = D
-	;El =:= 1 -> 
+	;El =:= 1 ->
 	    NEl = 1,
 	    V = NEl,
 	    ND = 0.0,
@@ -692,9 +692,9 @@ get_parents(V.Parents, Values.PVars, Vs0, Vs) :-
 	get_parents(Parents, PVars, Vs1, Vs).
 
 get_key_parent(Fs, V, Values, Vs0, Vs) :-
-    INFO = info(V, _Parent, _Ev, Values, _, _, _),
+	INFO = info(V, _Parent, _Ev, Values, _, _, _),
-    rb_lookup(V, f(_, [Size|_], _, _), Fs),
+	rb_lookup(V, f(_, [Size|_], _, _), Fs),
-    check_key(V, Size, INFO, Vs0, Vs).
+	check_key(V, Size, INFO, Vs0, Vs).
 
 check_key(V, _, INFO, Vs, Vs) :-
 	rb_lookup(V, INFO, Vs), !.
@@ -809,20 +809,20 @@ skim_for_theta([[P|Other]|More], not(P)*Ps, [Other|Left], New ) :-
 	skim_for_theta(More, Ps, Left, New ).
 
 get_key_evidence(V, Evs, _, Tree, Ev, F0, F, Leaves, Finals) :-
-    rb_lookup(V, Pos, Evs), !,
+	rb_lookup(V, Pos, Evs), !,
-    zero_pos(0, Pos, Ev),
+	zero_pos(0, Pos, Ev),
-    insert_output(Leaves, V, Finals, Tree, Outs, SendOut),
+	insert_output(Leaves, V, Finals, Tree, Outs, SendOut),
-    get_outs(F0, F, SendOut, Outs).
+	get_outs(F0, F, SendOut, Outs).
 % hidden deterministic node, can be removed.
 %% get_key_evidence(V, _, DistId, _Tree, Ev, F0, [], _Leaves, _Finals) :-
-%%         deterministic(V, DistId),
+%% 	deterministic(V, DistId),
 %% 	!,
 %% 	one_list(Ev),
-%% 	eval_outs(F0).	
+%% 	eval_outs(F0).
 %% no evidence !!!
 get_key_evidence(V, _, _, Tree, _Values, F0, F1, Leaves, Finals) :-
-    insert_output(Leaves, V, Finals, Tree, Outs, SendOut),
+	insert_output(Leaves, V, Finals, Tree, Outs, SendOut),
-    get_outs(F0, F1, SendOut, Outs).
+	get_outs(F0, F1, SendOut, Outs).
 
 get_evidence(V, Tree, Ev, F0, F, Leaves, Finals) :-
 	clpbn:get_atts(V, [evidence(Pos)]), !,
@@ -836,17 +836,17 @@ get_evidence(V, _Tree, Ev, F0, [], _Leaves, _Finals) :-
 	( Name = 'AVG' ; Name = 'MAX' ; Name = 'MIN' ),
 	!,
 	one_list(Ev),
-	eval_outs(F0).	
+	eval_outs(F0).
 %% no evidence !!!
 get_evidence(V, Tree, _Values, F0, F1, Leaves, Finals) :-
 	insert_output(Leaves, V, Finals, Tree, Outs, SendOut),
 	get_outs(F0, F1, SendOut, Outs).
 
 zero_pos(_, _Pos, []).
-zero_pos(Pos, Pos, [1|Values]) :- !, 
+zero_pos(Pos, Pos, [1|Values]) :- !,
 	I is Pos+1,
 	zero_pos(I, Pos, Values).
-zero_pos(I0, Pos, [0|Values]) :- 
+zero_pos(I0, Pos, [0|Values]) :-
 	I is I0+1,
 	zero_pos(I, Pos, Values).
 
@@ -855,7 +855,7 @@ one_list(1.Ev) :-
 	one_list(Ev).
 
 %
-% insert a node with the disj of all alternatives, this is only done if node ends up to be in the output 
+% insert a node with the disj of all alternatives, this is only done if node ends up to be in the output
 %
 insert_output([], _V, [], _Out, _Outs, []).
 insert_output(V._Leaves, V0, [Top|_], Top, Outs, [Top = Outs]) :- V == V0, !.
@@ -863,7 +863,7 @@ insert_output(_.Leaves, V, _.Finals, Top, Outs, SendOut) :-
 	insert_output(Leaves, V, Finals, Top, Outs, SendOut).
 
 
-get_outs([V=F], [V=NF|End], End,  V) :- !,
+get_outs([V=F], [V=NF|End], End, V) :- !,
 %	writeln(f0:F),
 	simplify_exp(F,NF).
 get_outs([(V=F)|Outs], [(V=NF)|NOuts], End, (F0 + V)) :-
@@ -878,11 +878,11 @@ eval_outs([(V=F)|Outs]) :-
 	eval_outs(Outs).
 
 run_solver(Qs, LLPs, bdd(Term, Leaves, Nodes, Hash, Id)) :-
-    lists_of_keys_to_ids(Qs, QIds, Hash, _, Id, _),
+	lists_of_keys_to_ids(Qs, QIds, Hash, _, Id, _),
-    findall(LPs,
+	findall(LPs,
-	    (member(Q, QIds),
+	  (member(Q, QIds),
-	     run_bdd_solver([Q],LPs,bdd(Term,Leaves,Nodes))),
+	    run_bdd_solver([Q],LPs,bdd(Term,Leaves,Nodes))),
-	    LLPs).
+	  LLPs).
 
 run_bdd_solver([Vs], LPs, bdd(Term, _Leaves, Nodes)) :-
 	build_out_node(Nodes, Node),
@@ -988,7 +988,7 @@ all_cnfs([info(_V, Tree, Ev, Values, Formula, ParmVars, Parms)|Term], BindsF, IV
 
 v_in(V, [V0|_]) :- V == V0, !.
 v_in(V, [_|Vs]) :-
-    v_in(V, Vs).
+	v_in(V, Vs).
 
 all_indicators(Values) -->
 	{ values_to_disj(Values, Disj) },
@@ -1017,7 +1017,7 @@ parameters([(V0=Disj*_I0)|Formula], Tree) -->
 	parameters(Formula, Tree).
 
 % transform V0<- A*B+C*(D+not(E))
-%        [V0+not(A)+not(B),V0+not(C)+not(D),V0+not(C)+E]
+%    [V0+not(A)+not(B),V0+not(C)+not(D),V0+not(C)+E]
 conj(Disj, V0) -->
 	{ conj2(Disj, [[V0]], LVs) },
 	to_disjs(LVs).
@@ -1057,11 +1057,10 @@ generate_exclusions([V0|SeenVs], V) -->
 
 build_cnf(CNF, IVs, Indics, AllParms, AllParmValues, Val) :-
 %(numbervars(CNF,1,_), writeln(cnf_to_ddnnf(CNF, Vars, IVs, [], F)), fail ; true ),
-	cnf_to_ddnnf(CNF, AllParms, F), 
+	cnf_to_ddnnf(CNF, AllParms, F),
 	AllParms = AllParmValues,
 	IVs = Indics,
 	term_variables(CNF, Extra),
 	set_to_ones(Extra),
 	ddnnf_is(F, Val).
 
-

packages/CLPBN/clpbn/bnt.yap

@@ -1,45 +1,51 @@
-:- module(bnt, [do_bnt/3,
+:- module(bnt,
-		create_bnt_graph/2,
+		[do_bnt/3,
-		check_if_bnt_done/1]).
+		 create_bnt_graph/2,
+		 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_domain/2,
-				       get_dist_params/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),
-				close_matlab/0,
+		[start_matlab/1,
-				matlab_on/0,
+		 close_matlab/0,
-				matlab_eval_string/1,
+		 matlab_on/0,
-				matlab_eval_string/2,
+		 matlab_eval_string/1,
-				matlab_matrix/4,
+		 matlab_eval_string/2,
-				matlab_vector/2,
+		 matlab_matrix/4,
-				matlab_sequence/3,
+		 matlab_vector/2,
-				matlab_initialized_cells/4,
+		 matlab_sequence/3,
-				matlab_get_variable/2,
+		 matlab_initialized_cells/4,
-				matlab_call/2
+		 matlab_get_variable/2,
-			      ]).
+		 matlab_call/2
+		]).
 
-:- use_module(library(dgraphs), [dgraph_new/1,
+:- use_module(library(dgraphs),
-				dgraph_add_vertices/3,
+		[dgraph_new/1,
-				dgraph_add_edges/3,
+		 dgraph_add_vertices/3,
-				dgraph_top_sort/2,
+		 dgraph_add_edges/3,
-				dgraph_vertices/2,
+		 dgraph_top_sort/2,
-				dgraph_edges/2
+		 dgraph_vertices/2,
-			      ]).
+		 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).
 
@@ -95,7 +101,7 @@ do_bnt(QueryVars, AllVars, AllDiffs)  :-
 	add_evidence(SortedVertices, Size, NumberedVertices),
 	marginalize(QueryVars, SortedVertices, NumberedVertices, Ps),
 	clpbn_bind_vals(QueryVars, Ps, AllDiffs).
-	
+
 create_bnt_graph(AllVars, Representatives) :-
 	create_bnt_graph(AllVars, Representatives, _, _, _).
 
@@ -148,7 +154,7 @@ extract_kvars([V|AllVars],[N-i(V,Parents)|KVars]) :-
 	extract_kvars(AllVars,KVars).
 
 split_tied_vars([],[],[]).
-split_tied_vars([N-i(V,Par)|More],[N-g(Vs,Ns,Es)|TVars],[N|LNs]) :-	
+split_tied_vars([N-i(V,Par)|More],[N-g(Vs,Ns,Es)|TVars],[N|LNs]) :-
 	get_pars(Par,N,V,NPs,[],Es0,Es),
 	get_tied(More,N,Vs,[V],Ns,NPs,Es,Es0,SVars),
 	split_tied_vars(SVars,TVars,LNs).
@@ -200,7 +206,7 @@ extract_graph(AllVars, Graph) :-
 	dgraph_add_vertices(Graph0, AllVars, Graph1),
 	get_edges(AllVars,Edges),
 	dgraph_add_edges(Graph1, Edges, Graph).
-	
+
 get_edges([],[]).
 get_edges([V|AllVars],Edges) :-
 	clpbn:get_atts(V, [dist(_,Parents)]),
@@ -218,13 +224,13 @@ number_graph([V|SortedGraph], [I|Is], I0, IF) :-
 %	clpbn:get_atts(V,[key(K)]),
 %	write(I:K),nl,
 	number_graph(SortedGraph, Is, I, IF).
-	
+
 init_bnet(propositional, SortedGraph, NumberedGraph, Size, []) :-
 	build_dag(SortedGraph, Size),
 	init_discrete_nodes(SortedGraph, Size),
 	bnet <-- mk_bnet(dag, node_sizes, \discrete, discrete_nodes),
 	dump_cpts(SortedGraph, NumberedGraph).
-	
+
 init_bnet(tied, SortedGraph, NumberedGraph, Size, Representatives) :-
 	build_dag(SortedGraph, Size),
 	init_discrete_nodes(SortedGraph, Size),
@@ -314,7 +320,7 @@ get_sizes_and_ids([V|Parents],[Id-V|Ids]) :-
 extract_vars([], L, L).
 extract_vars([_-V|NIds], NParents, Vs) :-
 	extract_vars(NIds, [V|NParents], Vs).
-	
+
 mkcpt(BayesNet, I, Tab) :-
 	(BayesNet.'CPD'({I})) <-- tabular_CPD(BayesNet,I,Tab).
 
@@ -330,7 +336,7 @@ create_class_vector([], [], [],[]).
 create_class_vector([V|Graph], [I|Is],  [Id|Classes], [Id-v(V,I,Parents)|Sets]) :-
 	clpbn:get_atts(V, [dist(Id,Parents)]),
 	create_class_vector(Graph, Is,Classes,Sets).
-	
+
 representatives([],[]).
 representatives([Class-Rep|Reps1],[Class-Rep|Reps]) :-
 	nonrepresentatives(Reps1, Class, Reps2),
@@ -376,7 +382,7 @@ add_evidence(Graph, Size, Is) :-
 	mk_evidence(Graph, Is, LN),
 	matlab_initialized_cells( 1, Size, LN, evidence),
 	[engine_ev, loglik] <-- enter_evidence(engine, evidence).
-	
+
 mk_evidence([], [], []).
 mk_evidence([V|L], [I|Is], [ar(1,I,EvVal1)|LN]) :-
 	clpbn:get_atts(V, [evidence(EvVal)]), !,
@@ -384,7 +390,7 @@ mk_evidence([V|L], [I|Is], [ar(1,I,EvVal1)|LN]) :-
 	mk_evidence(L, Is, LN).
 mk_evidence([_|L], [_|Is], LN) :-
 	mk_evidence(L, Is, LN).
-	
+
 evidence_val(Ev,Val,[Ev|_],Val) :- !.
 evidence_val(Ev,I0,[_|Domain],Val) :-
 	I1 is I0+1,
@@ -403,7 +409,7 @@ marginalize([Vs], SortedVars, NumberedVars,Ps) :-
 	length(SortedVars,L),
 	cycle_values(Den, Ev, Vs, L, Vals, Ps).
 
-cycle_values(_D, _Ev, _Vs, _Size, [], []).	
+cycle_values(_D, _Ev, _Vs, _Size, [], []).
 
 cycle_values(Den,Ev,Vs,Size,[H|T],[HP|TP]):-
 	mk_evidence_query(Vs, H, EvQuery),
@@ -421,5 +427,4 @@ mk_evidence_query([V|L], [H|T], [ar(1,Pos,El)|LN]) :-
 	get_dist_domain(Id,D),
 	nth(El,D,H),
 	mk_evidence_query(L, T, LN).
-	
 

packages/CLPBN/clpbn/connected.yap

@@ -1,26 +1,28 @@
 
 :- module(clpbn_connected,
-	[influences/3,
+		[influences/3,
-	 factor_influences/4,
+		 factor_influences/4,
-	 init_influences/3,
+		 init_influences/3,
-	 influences/4]
+		 influences/4
-	 ).
+		]).
 
 :- use_module(library(maplist)).
 
 :- use_module(library(dgraphs),
-	[dgraph_new/1,
+		[dgraph_new/1,
-	dgraph_add_edges/3,
+		 dgraph_add_edges/3,
-	dgraph_add_vertex/3,
+		 dgraph_add_vertex/3,
-	dgraph_neighbors/3,
+		 dgraph_neighbors/3,
-	dgraph_edge/3,
+		 dgraph_edge/3,
-	dgraph_transpose/2]).
+		 dgraph_transpose/2
+		]).
 
 :- use_module(library(rbtrees),
-	[rb_new/1,
+		[rb_new/1,
-	rb_lookup/3,
+		 rb_lookup/3,
-	rb_insert/4,
+		 rb_insert/4,
-	rb_visit/2]).
+		 rb_visit/2
+		]).
 
 factor_influences(Vs, QVars, Ev, LV) :-
 	init_factor_influences(Vs, G, RG),
@@ -59,13 +61,13 @@ build_edges([P|Parents], V, [P-V|Edges]) :-
 
 % search for the set of variables that influence V
 influences(Vs, G, RG, Vars) :-
-    influences(Vs, [], G, RG, Vars).
+	influences(Vs, [], G, RG, Vars).
 
 % search for the set of variables that influence V
 influences(Vs, Evs, G, RG, Vars) :-
-    rb_new(Visited0),
+	rb_new(Visited0),
-    foldl(influence(Evs, G, RG), Vs, Visited0, Visited),
+	foldl(influence(Evs, G, RG), Vs, Visited0, Visited),
-    all_top(Visited, Evs, Vars).
+	all_top(Visited, Evs, Vars).
 
 influence(_, _G, _RG, V, Vs, Vs) :-
 	rb_lookup(V, [T|B], Vs), T == t, B == b, !.
@@ -89,76 +91,78 @@ process_new_variable(V, Evs, G, RG, Vs0, Vs2) :-
 % visited
 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
-          handle_ball_from_above(Child, Evs, G, RG, Vs0, Vs1)
+	  handle_ball_from_above(Child, Evs, G, RG, Vs0, Vs1)
-        ).
+	).
 throw_below(Evs, G, RG, Child, Vs0, Vs2) :-
 	rb_insert(Vs0, Child, [_|b], Vs1),
 	handle_ball_from_above(Child, Evs, G, RG, Vs1, Vs2).
 
 % share this with parents, if we have evidence
 handle_ball_from_above(V, Evs, G, RG, Vs0, Vs1) :-
-    var(V),
+	var(V),
-    clpbn:get_atts(V,[evidence(_)]), !,
+	clpbn:get_atts(V,[evidence(_)]), !,
-    dgraph_neighbors(V, RG, Parents),
+	dgraph_neighbors(V, RG, Parents),
-    foldl(throw_above(Evs, G, RG), Parents, Vs0, Vs1).
+	foldl(throw_above(Evs, G, RG), Parents, Vs0, Vs1).
 handle_ball_from_above(V, Evs, G, RG, Vs0, Vs1) :-
-    nonvar(V),
+	nonvar(V),
-    rb_lookup(V,_,Evs), !,
+	rb_lookup(V,_,Evs), !,
-    dgraph_neighbors(V, RG, Parents),
+	dgraph_neighbors(V, RG, Parents),
-    foldl(throw_above(Evs, G, RG), Parents, Vs0, Vs1).
+	foldl(throw_above(Evs, G, RG), Parents, Vs0, Vs1).
 % propagate to kids, if we do not
 handle_ball_from_above(V, Evs, G, RG, Vs0, Vs1) :-
-    dgraph_neighbors(V, G, Children),
+	dgraph_neighbors(V, G, Children),
-    foldl(throw_below(Evs, G, RG), Children, Vs0, Vs1).
+	foldl(throw_below(Evs, G, RG), Children, Vs0, Vs1).
-	
+
 % visited
 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
-          handle_ball_from_below(Parent, Evs, G, RG, Vs0, Vs1)
+	  handle_ball_from_below(Parent, Evs, G, RG, Vs0, Vs1)
-        ).
+	).
 throw_above(Evs, G, RG, Parent, Vs0, Vs2) :-
 	rb_insert(Vs0, Parent, [t|_], Vs1),
 	handle_ball_from_below(Parent, Evs, G, RG, Vs1, Vs2).
 
 % share this with parents, if we have evidence
 handle_ball_from_below(V, _Evs, _, _, Vs, Vs) :-
-    var(V),
+	var(V),
-    clpbn:get_atts(V,[evidence(_)]), !.
+	clpbn:get_atts(V,[evidence(_)]), !.
 handle_ball_from_below(V, Evs, _, _, Vs, Vs) :-
-    nonvar(V),
+	nonvar(V),
-    rb_lookup(V, _, Evs), !.
+	rb_lookup(V, _, Evs), !.
 % propagate to kids, if we do not
 handle_ball_from_below(V, Evs, G, RG, Vs0, Vs1) :-
-    dgraph_neighbors(V, RG, Parents),
+	dgraph_neighbors(V, RG, Parents),
-    propagate_ball_from_below(Parents, Evs, V, G, RG, Vs0, Vs1).
+	propagate_ball_from_below(Parents, Evs, V, G, RG, Vs0, Vs1).
 
 propagate_ball_from_below([], Evs, V, G, RG, Vs0, Vs1) :- !,
-    dgraph_neighbors(V, G, Children),
+	dgraph_neighbors(V, G, Children),
-    foldl(throw_below(Evs, G, RG), Children, Vs0, Vs1).
+	foldl(throw_below(Evs, G, RG), Children, Vs0, Vs1).
 propagate_ball_from_below(Parents, Evs, _V, G, RG, Vs0, Vs1) :-
-    foldl(throw_above(Evs, G, RG), Parents, Vs0, Vs1).
+	foldl(throw_above(Evs, G, RG), Parents, Vs0, Vs1).
 
 all_top(T, Evs, Vs) :-
-    rb_visit(T, Pairs),
+	rb_visit(T, Pairs),
-    foldl( get_top(Evs), Pairs, [], Vs).
+	foldl( get_top(Evs), Pairs, [], Vs).
 
 get_top(_EVs, V-[T|_], Vs, [V|Vs]) :-
-    T == t, !.
+	T == t, !.
 get_top(_EVs, V-_, Vs, [V|Vs]) :-
-    var(V),
+	var(V),
-    clpbn:get_atts(V,[evidence(_)]), !.
+	clpbn:get_atts(V,[evidence(_)]), !.
 get_top(EVs, V-_, Vs, [V|Vs]) :-
-    nonvar(V),
+	nonvar(V),
-    rb_lookup(V, _, EVs), !.
+	rb_lookup(V, _, EVs), !.
 get_top(_, _, Vs, Vs).
 

packages/CLPBN/clpbn/discrete_utils.yap

@@ -1,10 +1,14 @@
 
-:- module(discrete_utils, [project_from_CPT/3,
+:- module(discrete_utils,
-			   reorder_CPT/5,
+		[project_from_CPT/3,
-			   get_dist_size/2]).
+		 reorder_CPT/5,
+		 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
 %
@@ -20,11 +24,11 @@ propagate_evidence(V, Evs) :-
 	clpbn:get_atts(V, [evidence(Ev),dist(Id,_)]), !,
 	get_dist_domain(Id, Out),
 	generate_szs_with_evidence(Out,Ev,0,Evs,Found),
-	(var(Found) -> 
+	(var(Found) ->
-	    clpbn:get_atts(V, [key(K)]),
+	  clpbn:get_atts(V, [key(K)]),
-	    throw(clpbn(evidence_does_not_match,K,Ev,[Out]))
+	  throw(clpbn(evidence_does_not_match,K,Ev,[Out]))
 	;
-	     true
+	  true
 	).
 propagate_evidence(_, _).
 
@@ -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.
 
 
@@ -75,7 +78,7 @@ clpbn_bind_vals([Vs|MoreVs],[Ps|MorePs],AllDiffs) :-
 
 clpbn_bind_vals2([],_,_) :- !.
 % simple case, we want a distribution on a single variable.
-clpbn_bind_vals2([V],Ps,AllDiffs) :- 
+clpbn_bind_vals2([V],Ps,AllDiffs) :-
 	use_parfactors(on), !,
 	clpbn:get_atts(V, [key(K)]),
 	pfl:skolem(K,Vals),

packages/CLPBN/clpbn/dists.yap

@@ -3,47 +3,51 @@
 %
 
 :- module(clpbn_dist,
-	  [
+		[dist/1,
-	   dist/1,
+		 dist/4,
-	   dist/4,
+		 dists/1,
-	   dists/1,
+		 dist_new_table/2,
-	   dist_new_table/2,
+		 get_dist/4,
-	   get_dist/4,
+		 get_dist_matrix/5,
-	   get_dist_matrix/5,
+		 get_possibly_deterministic_dist_matrix/5,
-	   get_possibly_deterministic_dist_matrix/5,
+		 get_dist_domain/2,
-	   get_dist_domain/2,
+		 get_dist_domain_size/2,
-	   get_dist_domain_size/2,
+		 get_dist_params/2,
-	   get_dist_params/2,
+		 get_dist_key/2,
-	   get_dist_key/2,
+		 get_dist_all_sizes/2,
-	   get_dist_all_sizes/2,
+		 get_evidence_position/3,
-	   get_evidence_position/3,
+		 get_evidence_from_position/3,
-	   get_evidence_from_position/3,
+		 dist_to_term/2,
-	   dist_to_term/2,
+		 empty_dist/2,
-	   empty_dist/2,
+		 all_dist_ids/1,
-	   all_dist_ids/1,
+		 randomise_all_dists/0,
-	   randomise_all_dists/0,
+		 randomise_dist/1,
-	   randomise_dist/1,
+		 uniformise_all_dists/0,
-	   uniformise_all_dists/0,
+		 uniformise_dist/1,
-	   uniformise_dist/1,
+		 reset_all_dists/0,
-	   reset_all_dists/0,
+		 add_dist/6,
-	   add_dist/6,
+		 additive_dists/6
-	   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]).
+		[use_parfactors/1]).
 
 :- use_module(library(matrix),
-	      [matrix_new/4,
+		[matrix_new/4,
-	       matrix_new/3,
+		 matrix_new/3,
-	       matrix_to_list/2,
+		 matrix_to_list/2,
-	       matrix_to_logs/1]).
+		 matrix_to_logs/1
+		]).
 
 :- use_module(library(clpbn/matrix_cpt_utils),
-	      [random_CPT/2,
+		[random_CPT/2,
-	       uniform_CPT/2]).
+		 uniform_CPT/2
+		]).
 
 /*
 :- mode dist(+, -).
@@ -86,7 +90,7 @@ where Id is the id,
     dna for [a,c,g,t]
     rna for [a,c,g,u]
     reals
-	
+
 
 ********************************************/
 
@@ -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

@@ -4,36 +4,34 @@
 %
 
 :- module(clpbn_evidence,
-	  [
+		[store_evidence/1,
-	   store_evidence/1,
+		 incorporate_evidence/2,
-	   incorporate_evidence/2,
+		 check_stored_evidence/2,
-	   check_stored_evidence/2,
+		 add_stored_evidence/2,
-	   add_stored_evidence/2,
+		 put_evidence/2
-	   put_evidence/2
+		]).
-	  ]).
 
-:- use_module(library(clpbn), [
+:- use_module(library(clpbn),
-	{}/1,
+		[{}/1,
-	clpbn_flag/3,
+		 clpbn_flag/3,
-	set_clpbn_flag/2
+		 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_lookup/3,
-	rb_insert/4
+		 rb_insert/4
-    ]).
+		]).
 
 :- meta_predicate store_evidence(:).
 
 :- dynamic node/3, edge/2, evidence/2.
 
 %
-% new evidence storage algorithm. The idea is that instead of 
+% new evidence storage algorithm. The idea is that instead of
 % redoing all the evidence every time we query the network, we shall
 % keep a precompiled version around.
 %
@@ -53,9 +51,9 @@ compute_evidence(_,PreviousSolver) :-
 	set_clpbn_flag(solver, PreviousSolver).
 
 get_clpbn_vars(G, Vars) :-
-%	attributes:all_attvars(Vars0),	
+%	attributes:all_attvars(Vars0),
 	once(G),
-	attributes:all_attvars(Vars).	
+	attributes:all_attvars(Vars).
 
 evidence_error(Ball,PreviousSolver) :-
 	set_clpbn_flag(solver,PreviousSolver),
@@ -63,7 +61,7 @@ evidence_error(Ball,PreviousSolver) :-
 
 store_graph([]).
 store_graph([V|Vars]) :-
-	clpbn:get_atts(V,[key(K),dist(Id,Vs)]),        
+	clpbn:get_atts(V,[key(K),dist(Id,Vs)]),
 	\+ node(K, Id, _), !,
 	translate_vars(Vs,TVs),
 	assert(node(K,Id,TVs)),
@@ -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

@@ -8,51 +8,54 @@
 %
 
 :- module(clpbn_gibbs,
-	  [gibbs/3,
+		[gibbs/3,
-	   check_if_gibbs_done/1,
+		 check_if_gibbs_done/1,
-	   init_gibbs_solver/4,
+		 init_gibbs_solver/4,
-	   run_gibbs_solver/3]).
+		 run_gibbs_solver/3
+		]).
 
 :- use_module(library(rbtrees),
-	      [rb_new/1,
+		[rb_new/1,
-	       rb_insert/4,
+		 rb_insert/4,
-	       rb_lookup/3]).
+		 rb_lookup/3
+		]).
 
 :- use_module(library(lists),
-	      [member/2,
+		[member/2,
-	       append/3,
+		 append/3,
-	       delete/3,
+		 delete/3,
-	       max_list/2,
+		 max_list/2,
-	       sum_list/2]).
+		 sum_list/2
+		]).
 
 :- use_module(library(ordsets),
-	      [ord_subtract/3]).
+		[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,
+		 reorder_CPT/5,
-	multiply_possibly_deterministic_factors/3,
+		 multiply_possibly_deterministic_factors/3,
-	column_from_possibly_deterministic_CPT/3,
+		 column_from_possibly_deterministic_CPT/3,
-	normalise_possibly_deterministic_CPT/2,
+		 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.
 
@@ -134,7 +137,7 @@ graph_representation([V|Vs], Graph, I0, Keys, [I-IParents|TGraph]) :-
 	graph_representation(Vs, Graph, I, Keys, TGraph).
 
 write_pars([]).
-write_pars([V|Parents]) :- 
+write_pars([V|Parents]) :-
 	clpbn:get_atts(V, [key(K),dist(I,_)]),write(K:I),nl,
 	write_pars(Parents).
 
@@ -146,7 +149,7 @@ get_sizes([V|Parents], [Sz|Szs]) :-
 
 parent_indices([], _, []).
 parent_indices([V|Parents], Keys, [I|IParents]) :-
-	rb_lookup(V, I, Keys),	
+	rb_lookup(V, I, Keys),
 	parent_indices(Parents, Keys, IParents).
 
 
@@ -171,7 +174,7 @@ propagate2parents([V|NewParents], Table, Variables, Graph, Keys) :-
 	propagate2parents(NewParents,Table, Variables, Graph, Keys).
 
 add2graph(V, Vals, Table, IParents, Graph, Keys) :-
-	rb_lookup(V, Index, Keys),	
+	rb_lookup(V, Index, Keys),
 	(var(Vals) -> true ; length(Vals,Sz)),
 	arg(Index, Graph, var(V,Index,_,Vals,Sz,VarSlot,_,_,_)),
 	member(tabular(Table,Index,IParents), VarSlot), !.
@@ -236,7 +239,7 @@ mult_list([Sz|Sizes],Mult0,Mult) :-
 	MultI is Sz*Mult0,
 	mult_list(Sizes,MultI,Mult).
 
-% compile node as set of facts, faster execution 
+% compile node as set of facts, faster execution
 compile_var(TotSize,I,_Vals,Sz,CPTs,Parents,_Sizes,Graph) :-
 	TotSize < 1024*64, TotSize > 0, !,
 	multiply_all(I,Parents,CPTs,Sz,Graph).
@@ -246,11 +249,11 @@ compile_var(_,_,_,_,_,_,_,_).
 multiply_all(I,Parents,CPTs,Sz,Graph) :-
 	markov_blanket_instance(Parents,Graph,Values),
 	(
-	    multiply_all(CPTs,Graph,Probs)
+	  multiply_all(CPTs,Graph,Probs)
 	->
-	    store_mblanket(I,Values,Probs)
+	  store_mblanket(I,Values,Probs)
 	;
-	    throw(error(domain_error(bayesian_domain),gibbs_cpt(I,Parents,Values,Sz)))
+	  throw(error(domain_error(bayesian_domain),gibbs_cpt(I,Parents,Values,Sz)))
 	),
 	fail.
 multiply_all(I,_,_,_,_) :-
@@ -280,7 +283,7 @@ fetch_parents([], _, []).
 fetch_parents([P|Parents], Graph, [Val|Vals]) :-
 	arg(P,Graph,var(_,_,Val,_,_,_,_,_,_)),
 	fetch_parents(Parents, Graph, Vals).
-	
+
 multiply_more([],_,Probs0,LProbs) :-
 	normalise_possibly_deterministic_CPT(Probs0, Probs),
 	list_from_CPT(Probs, LProbs0),
@@ -296,7 +299,7 @@ accumulate_up_list([P|LProbs], P0, [P1|L]) :-
 	P1 is P0+P,
 	accumulate_up_list(LProbs, P1, L).
 
-	
+
 store_mblanket(I,Values,Probs) :-
 	recordz(mblanket,m(I,Values,Probs),_).
 
@@ -364,8 +367,8 @@ generate_est_mults([], [], _, [], 1).
 generate_est_mults([V|Vs], [I|Is], Graph, [M0|Mults], M) :-
 	arg(V,Graph,var(_,I,_,_,Sz,_,_,_,_)),
 	generate_est_mults(Vs, Is, Graph, Mults, M0),
-	M is M0*Sz.	
+	M is M0*Sz.
-	
+
 gen_e0(0,[]) :- !.
 gen_e0(Sz,[0|E0L]) :-
 	Sz1 is Sz-1,
@@ -455,7 +458,7 @@ get_estimate_pos([I|Is], Sample, [M|Mult], V0, V) :-
 	get_estimate_pos(Is, Sample, Mult, VI, V).
 
 update_estimate_for_var(V0,[X|T],[X1|NT]) :-
-	( V0 == 0 ->
+	(V0 == 0 ->
 	  X1 is X+1,
 	  NT = T
 	;
@@ -496,7 +499,7 @@ do_probs([E|Es],Sum,[P|Ps]) :-
 
 show_sorted([], _) :- nl.
 show_sorted([I|VarOrder], Graph) :-
-	arg(I,Graph,var(V,I,_,_,_,_,_,_,_)),		
+	arg(I,Graph,var(V,I,_,_,_,_,_,_,_)),
 	clpbn:get_atts(V,[key(K)]),
 	format('~w ',[K]),
 	show_sorted(VarOrder, Graph).
@@ -528,7 +531,7 @@ add_up_mes(Counts,[me(_,_,Cs)|Chains], Add) :-
 	sum_lists(Counts, Cs, NCounts),
 	add_up_mes(NCounts, Chains, Add).
 
-sum_lists([],[],[]).	
+sum_lists([],[],[]).
 sum_lists([Count|Counts], [C|Cs], [NC|NCounts]) :-
 	NC is Count+C,
 	sum_lists(Counts, Cs, NCounts).
@@ -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 {
@@ -48,7 +50,7 @@ output_parents1(Stream,[V|L]) :-
 	put_code(Stream, 0' ), %'
 	output_parents1(Stream,L).
 
-output_v(V,Stream) :- 
+output_v(V,Stream) :-
 	clpbn:get_atts(V,[key(Key)]),
 	output_key(Stream,Key).
 

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 = [....], 
+		 f/3
-%       [P,C,S],
+		]).
-%	[P \in [p1,p2,p4], C \in [c1,c3], S \in [s2,s3]]).
-%	[S \= s2])
 
+:- use_module(library(bhash),
+		[b_hash_new/1,
+		 b_hash_lookup/3,
+		 b_hash_insert/4,
+		 b_hash_to_list/2
+		]).
 
-:- module(pfl_ground_factors, [
+:- use_module(library(lists),
-          generate_network/5,
+		[member/2]).
-	  f/3
-	]).
-
-:- use_module(library(bhash), [
-          b_hash_new/1,
-          b_hash_lookup/3,
-	  b_hash_insert/4,
-	  b_hash_to_list/2]).
-
-:- use_module(library(lists), [
-          delete/3,
-	  nth0/3,
-	  member/2]).
 
 :- use_module(library(maplist)).
 
-:- use_module(library(pfl), [
+:- use_module(library(atts)).
-          factor/6,
-          defined_in_factor/2,
-	  skolem/2]).
 
-:- use_module(library(clpbn/aggregates), [
+:- use_module(library(pfl),
-          avg_factors/5]).
+		[factor/6,
+		 defined_in_factor/2,
+		 skolem/2
+		]).
 
-:- use_module(library(clpbn/dists), [
+:- use_module(library(clpbn/aggregates),
-          dist/4]).
+		[avg_factors/5]).
+
+:- use_module(library(clpbn/dists),
+		[dist/4]).
 
 :- dynamic currently_defined/1, queue/1, f/4.
 
@@ -48,7 +42,7 @@ generate_network(QueryVars, QueryKeys, Keys, Factors, EList) :-
 	b_hash_new(Evidence0),
 	foldl(include_evidence,AVars, Evidence0, Evidence1),
 	static_evidence(Evidence1, Evidence),
-	b_hash_to_list(Evidence, EList0), 
+	b_hash_to_list(Evidence, EList0),
 	maplist(pair_to_evidence,EList0, EList),
 	maplist(queue_evidence, EList),
 	foldl(run_through_query(Evidence), QueryVars, [], QueryKeys),
@@ -59,20 +53,20 @@ generate_network(QueryVars, QueryKeys, Keys, Factors, EList) :-
 % clean global stateq
 %
 init_global_search :-
-	  retractall(queue(_)),
+	retractall(queue(_)),
-	  retractall(currently_defined(_)),
+	retractall(currently_defined(_)),
-	  retractall(f(_,_,_)).
+	retractall(f(_,_,_)).
 
 pair_to_evidence(K-E, K=E).
 
 include_evidence(V, Evidence0, Evidence) :-
 	clpbn:get_atts(V,[key(K),evidence(E)]), !,
 	(
-	    b_hash_lookup(K, E1, Evidence0)
+	  b_hash_lookup(K, E1, Evidence0)
 	->
-	    (E \= E1 -> throw(clpbn:incompatible_evidence(K,E,E1)) ; Evidence = Evidence0)
+	  (E \= E1 -> throw(clpbn:incompatible_evidence(K,E,E1)) ; Evidence = Evidence0)
 	;
-	    b_hash_insert(Evidence0, K, E, Evidence)
+	  b_hash_insert(Evidence0, K, E, Evidence)
 	).
 include_evidence(_, Evidence, Evidence).
 
@@ -82,16 +76,16 @@ static_evidence(Evidence0, Evidence) :-
 
 include_static_evidence(K=E, Evidence0, Evidence) :-
 	(
-	    b_hash_lookup(K, E1, Evidence0)
+	  b_hash_lookup(K, E1, Evidence0)
 	->
-	    (E \= E1 -> throw(incompatible_evidence(K,E,E1)) ; Evidence = Evidence0)
+	  (E \= E1 -> throw(incompatible_evidence(K,E,E1)) ; Evidence = Evidence0)
 	;
-	    b_hash_insert(Evidence0, K, E, Evidence)
+	  b_hash_insert(Evidence0, K, E, Evidence)
 	).
 
 
 queue_evidence(K=_) :-
-        queue_in(K).
+	queue_in(K).
 
 run_through_query(Evidence, V, QueryKeys, QueryKeys) :-
 	clpbn:get_atts(V,[key(K)]),
@@ -122,11 +116,11 @@ propagate.
 do_propagate(K) :-
 	%writeln(-K),
 	\+ currently_defined(K),
-	( ground(K) -> 	assert(currently_defined(K)) ; true),
+	( ground(K) -> assert(currently_defined(K)) ; true),
 	(
 	  defined_in_factor(K, ParFactor),
 	  add_factor(ParFactor, Ks)
-	 *->
+	*->
 	  true
 	;
 	  throw(error(no_defining_factor(K)))
@@ -136,28 +130,29 @@ do_propagate(K) :-
 	queue_in(K1),
 	fail.
 do_propagate(_K) :-
-        propagate.
+	propagate.
 
 add_factor(factor(Type, Id, Ks, _, _Phi, Constraints), NKs) :-
-%    writeln(+Ks),
+%	writeln(+Ks),
-	( Ks = [K,Els], var(Els)
+	(
-	 ->
+	  Ks = [K,Els], var(Els)
-	% aggregate factor
+	->
+	  % aggregate factor
 	  once(run(Constraints)),
 	  avg_factors(K, Els, 0.0, NewKeys, NewId),
 	  NKs = [K|NewKeys]
-        ; 
+	;
 	  run(Constraints),
 	  NKs = Ks,
 	  Id = NewId
 	),
 	(
-          f(Type, NewId, NKs)
+	  f(Type, NewId, NKs)
-        ->
+	->
 	  true
-        ;
+	;
 	  assert(f(Type, NewId, NKs))
-         ).
+	).
 
 run([Goal|Goals]) :-
 	call(user:Goal),

packages/CLPBN/clpbn/hmm.yap

@@ -1,19 +1,20 @@
 
-
+:- module(hmm,
-:- module(hmm, [init_hmm/0,
+		[init_hmm/0,
-		  hmm_state/1,
+		 hmm_state/1,
-		  emission/1]).
+		 emission/1
+		]).
 
 :- ensure_loaded(library(clpbn)).
 
 :- use_module(library(lists),
-	      [nth/3]).
+		[nth/3]).
 
 :- use_module(library(nbhash),
-	      [nb_hash_new/2,
+		[nb_hash_new/2,
-	       nb_hash_lookup/3,
+		 nb_hash_lookup/3,
-	       nb_hash_insert/3
+		 nb_hash_insert/3
-	      ]).
+		]).
 
 :- ensure_loaded(library(tries)).
 
@@ -46,22 +47,19 @@ hmm_state(N/A,Mod) :-
 	Key =.. [T|KArgs],
 	Head =.. [N|LArgs],
 	asserta_static( (Mod:Head :-
-	        ( First > 2 -> 
+	  (First > 2 ->
-		  Last = Key, !
+	    Last = Key, !
-		;
+	  ;
-		  nb_getval(trie, Trie), trie_check_entry(Trie, Key, _)
+	    nb_getval(trie, Trie), trie_check_entry(Trie, Key, _) ->
-		->
+	      % leave work for solver!
-		  % leave work for solver!
+	      Last = Key, !
-		  %
+	    ;
-		  Last = Key, !
+	      % first time we saw this entry
-		;
+	      nb_getval(trie, Trie), trie_put_entry(Trie, Key, _),
-		  % first time we saw this entry
+	      fail
-		  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).
 build_args(2,    [A,B],    [A],A,B).
@@ -79,5 +77,3 @@ cvt_vals([A|B],[A|B]).
 find_probs(Logs,Nth,Log) :-
 	arg(Nth,Logs,Log).
 
-
-

packages/CLPBN/clpbn/horus.yap

@@ -1,65 +1,56 @@
 /*******************************************************
 
  Horus Interface
- 
+
 ********************************************************/
 
 :- module(clpbn_horus,
-          [set_solver/1,
+		[set_horus_flag/2,
-           set_horus_flag/1,
+		 cpp_create_lifted_network/3,
-           cpp_create_lifted_network/3,
+		 cpp_create_ground_network/4,
-           cpp_create_ground_network/4,
+		 cpp_set_parfactors_params/3,
-           cpp_set_parfactors_params/2,
+		 cpp_set_factors_params/3,
-           cpp_set_factors_params/2,
+		 cpp_run_lifted_solver/3,
-           cpp_run_lifted_solver/3,
+		 cpp_run_ground_solver/3,
-           cpp_run_ground_solver/3,
+		 cpp_set_vars_information/2,
-           cpp_set_vars_information/2,
+		 cpp_set_horus_flag/2,
-           cpp_set_horus_flag/2,
+		 cpp_free_lifted_network/1,
-           cpp_free_lifted_network/1,
+		 cpp_free_ground_network/1
-           cpp_free_ground_network/1
+		]).
-          ]).
-
-:- use_module(library(clpbn),
-	[set_clpbn_flag/2]).
-
-
-patch_things_up :-
-  assert_static(clpbn_horus:cpp_set_horus_flag(_,_)).
-
-
-warning :-
-  format(user_error,"Horus library not installed: cannot use bp, fove~n.",[]).
 
 
 :- catch(load_foreign_files([horus], [], init_predicates), _, patch_things_up)
-    -> true ; warning.
+	-> true ; warning.
 
 
-set_solver(ve)    :- !, set_clpbn_flag(solver,ve).
+patch_things_up :-
-set_solver(bdd)   :- !, set_clpbn_flag(solver,bdd).
+	assert_static(clpbn_horus:cpp_set_horus_flag(_,_)).
-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).
+warning :-
-set_solver(lbp)   :- !, set_clpbn_flag(solver,fove), set_horus_flag(lifted_solver, lbp).
+	format(user_error,"Horus library not installed: cannot use hve, bp, cbp, lve, lkc and lbp~n.",[]).
-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

@@ -1,102 +1,89 @@
 /*******************************************************
 
  Interface to Horus Ground Solvers. Used by:
-   - Variable Elimination
+	- Variable Elimination
-   - Belief Propagation
+	- Belief Propagation
-   - Counting Belief Propagation
+	- Counting Belief Propagation
- 
+
 ********************************************************/
 
 :- module(clpbn_horus_ground,
-          [call_horus_ground_solver/6,
+		[call_horus_ground_solver/6,
-           check_if_horus_ground_solver_done/1,
+		 check_if_horus_ground_solver_done/1,
-           init_horus_ground_solver/5,
+		 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_create_ground_network/4,
-           cpp_set_factors_params/2,
+		 cpp_set_factors_params/3,
-           cpp_run_ground_solver/3,
+		 cpp_run_ground_solver/3,
-           cpp_set_vars_information/2,
+		 cpp_free_ground_network/1,
-           cpp_free_ground_network/1,
+		 cpp_set_vars_information/2
-	   set_solver/1
+		]).
-          ]).
 
-:- 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]).
+		[clpbn_bind_vals/3]).
-
-:- use_module(library(clpbn/numbers)).
-
-:- use_module(library(charsio),
-          [term_to_atom/2]).
 
 :- use_module(library(pfl),
-          [skolem/2]).
+		[get_pfl_parameters/2,
+		 skolem/2
+		]).
+
+:- use_module(library(charsio),
+		[term_to_atom/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)).
+	init_horus_ground_solver(QueryKeys, AllKeys, Factors, Evidence, State),
+	run_horus_ground_solver([QueryKeys], Solutions, State),
+	clpbn_bind_vals([QueryVars], Solutions, Output),
+	end_horus_ground_solver(State).
 
 
-call_horus_ground_solver(QueryVars, QueryKeys, AllKeys, Factors, Evidence, Output) :-
+init_horus_ground_solver(QueryKeys, AllKeys, Factors, Evidence,
-  init_horus_ground_solver(QueryKeys, AllKeys, Factors, Evidence, State),
+		state(Network,Hash,Id,DistIds)) :-
-  run_solver(State, [QueryKeys], Solutions),
+	factors_type(Factors, Type),
-  clpbn_bind_vals([QueryVars], Solutions, Output),
+	keys_to_numbers(AllKeys, Factors, Evidence, Hash, Id, FacIds, EvIds),
-  finalize_horus_ground_solver(State).
+	%writeln(network:(type=Type, factors=FacIds, evidence=EvIds)), nl,
+	cpp_create_ground_network(Type, FacIds, EvIds, Network),
+	%maplist(term_to_atom, AllKeys, VarNames),
+	%maplist(get_domain, AllKeys, Domains),
+	%cpp_set_vars_information(VarNames, Domains),
+    maplist(get_dist_id, FacIds, DistIds0),
+    sort(DistIds0, DistIds).
 
 
-init_horus_ground_solver(QueryKeys, AllKeys, Factors, Evidence, state(Network,Hash4,Id4)) :-
+run_horus_ground_solver(QueryKeys, Solutions,
-  get_factors_type(Factors, Type),
+		state(Network,Hash,Id, DistIds)) :-
-  keys_to_numbers(AllKeys, Factors, Evidence, Hash4, Id4, FactorIds, EvidenceIds),
+	lists_of_keys_to_ids(QueryKeys, QueryIds, Hash, _, Id, _),
-  cpp_create_ground_network(Type, FactorIds, EvidenceIds, Network),
+	%maplist(get_pfl_parameters, DistIds, DistParams),
-  %writeln(network:(Type, FactorIds, EvidenceIds, Network)), writeln(''),
+	%cpp_set_factors_params(Network, DistIds, DistParams),
-  maplist(get_var_information, AllKeys, StatesNames),
+	cpp_run_ground_solver(Network, QueryIds, Solutions).
-  maplist(term_to_atom, AllKeys, KeysAtoms),
-  cpp_set_vars_information(KeysAtoms, StatesNames).
 
 
-run_horus_ground_solver(_QueryVars, Solutions, horus(GKeys, Keys, Factors, Evidence), Solver) :- 
+end_horus_ground_solver(state(Network,_Hash,_Id, _DistIds)) :-
-  set_solver(Solver),
+	cpp_free_ground_network(Network).
-  call_horus_ground_solver_for_probabilities(GKeys, Keys, Factors, Evidence, Solutions).
 
 
-% TODO this is not beeing called!
+factors_type([f(bayes, _, _)|_], bayes) :- ! .
-finalize_horus_ground_solver(state(Network,_Hash,_Id)) :-
+factors_type([f(markov, _, _)|_], markov) :- ! .
-  cpp_free_ground_network(Network).
 
 
-run_solver(state(Network,Hash,Id), QueryKeys, Solutions) :-
+get_dist_id(f(_, _, _, DistId), DistId).
-  %get_dists_parameters(DistIds, DistsParams),
-  %cpp_set_factors_params(Network, DistsParams),
-  lists_of_keys_to_ids(QueryKeys, QueryIds, Hash, _, Id, _),
-  cpp_run_ground_solver(Network, QueryIds, Solutions).
 
 
-get_factors_type([f(bayes, _, _)|_], bayes) :- ! .
+get_domain(_:Key, Domain) :- !,
-get_factors_type([f(markov, _, _)|_], markov) :- ! .
+	skolem(Key, Domain).
-
+get_domain(Key, Domain) :-
-
+	skolem(Key, Domain).
-get_var_information(_:Key, Domain) :- !,
-    skolem(Key, Domain).
-get_var_information(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

@@ -1,148 +1,115 @@
 /*******************************************************
 
  Interface to Horus Lifted Solvers. Used by:
-   - Generalized Counting First-Order Variable Elimination (GC-FOVE)
+	- Generalized Counting First-Order Variable Elimination (GC-FOVE)
-   - Lifted First-Order Belief Propagation
+	- Lifted First-Order Belief Propagation
-   - Lifted First-Order Knowledge Compilation
+	- Lifted First-Order Knowledge Compilation
 
 ********************************************************/
 
 :- module(clpbn_horus_lifted,
-          [call_horus_lifted_solver/3,
+		[call_horus_lifted_solver/3,
-           check_if_horus_lifted_solver_done/1,
+		 check_if_horus_lifted_solver_done/1,
-           init_horus_lifted_solver/4,
+		 init_horus_lifted_solver/4,
-           run_horus_lifted_solver/3,
+		 run_horus_lifted_solver/3,
-           finalize_horus_lifted_solver/1
+		 end_horus_lifted_solver/1
-          ]).
+		]).
 
 :- use_module(horus,
-          [cpp_create_lifted_network/3,
+		[cpp_create_lifted_network/3,
-           cpp_set_parfactors_params/2,
+		 cpp_set_parfactors_params/3,
-           cpp_run_lifted_solver/3,
+		 cpp_run_lifted_solver/3,
-           cpp_free_lifted_network/1
+		 cpp_free_lifted_network/1
-          ]).
+		]).
 
 :- use_module(library('clpbn/display'),
-          [clpbn_bind_vals/3]).
+		[clpbn_bind_vals/3]).
-
-:- use_module(library('clpbn/dists'),
-          [get_dist_params/2]).
 
 :- use_module(library(pfl),
-          [factor/6,
+		[factor/6,
-           skolem/2,
+		 skolem/2,
-           get_pfl_parameters/2
+		 get_pfl_parameters/2
-          ]).
+		]).
+
+:- use_module(library(maplist)).
 
 
 call_horus_lifted_solver(QueryVars, AllVars, Output) :-
-  init_horus_lifted_solver(_, AllVars, _, State),
+	init_horus_lifted_solver(_, AllVars, _, State),
-  run_horus_lifted_solver(QueryVars, Solutions, State),
+	run_horus_lifted_solver(QueryVars, Solutions, State),
-  clpbn_bind_vals(QueryVars, Solutions, Output),
+	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_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).
+	findall(F, is_factor(F), Factors).
 
 
 is_factor(pf(Id, Ks, Rs, Phi, Tuples)) :-
-  factor(_Type, Id, Ks, Vs, Table, Constraints),
+	factor(_Type, Id, Ks, Vs, Table, Constraints),
-  get_ranges(Ks,Rs),
+	maplist(get_range, Ks, Rs),
-  Table \= avg,
+	Table \= avg,
-  gen_table(Table, Phi),
+	gen_table(Table, Phi),
-  all_tuples(Constraints, Vs, Tuples).
+	all_tuples(Constraints, Vs, Tuples).
 
 
-get_ranges([],[]).
+get_range(K, Range) :-
-get_ranges(K.Ks, Range.Rs) :- !,
+	skolem(K, Domain),
-  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) :-
-  setof(Tuple, Constraints^run(Constraints), Tuples).
+	setof(Tuple, Constraints^run(Constraints), Tuples).
 
 
 run([]).
 run(Goal.Constraints) :-
-  user:Goal,
+	user:Goal,
-  run(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,[key(K)]),
-  ( clpbn:get_atts(V,[evidence(E)]) ; pfl:evidence(K,E) ), !,
+	( 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

@@ -1,89 +1,93 @@
 
-:- module(jt, [jt/3,
+:- module(jt,
-	       init_jt_solver/4,
+		[jt/3,
-	       run_jt_solver/3]).
+		 init_jt_solver/4,
-
+		 run_jt_solver/3
+		]).
 
 :- use_module(library(dgraphs),
-	      [dgraph_new/1,
+		[dgraph_new/1,
-	       dgraph_add_edges/3,
+		 dgraph_add_edges/3,
-	       dgraph_add_vertex/3,
+		 dgraph_add_vertex/3,
-	       dgraph_add_vertices/3,
+		 dgraph_add_vertices/3,
-	       dgraph_edges/2,
+		 dgraph_edges/2,
-	       dgraph_vertices/2,
+		 dgraph_vertices/2,
-	       dgraph_transpose/2,
+		 dgraph_transpose/2,
-	       dgraph_to_ugraph/2,
+		 dgraph_to_ugraph/2,
-	       ugraph_to_dgraph/2,
+		 ugraph_to_dgraph/2,
-	       dgraph_neighbors/3
+		 dgraph_neighbors/3
-	      ]).
+		]).
 
 :- use_module(library(undgraphs),
-	      [undgraph_new/1,
+		[undgraph_new/1,
-	       undgraph_add_edge/4,
+		 undgraph_add_edge/4,
-	       undgraph_add_edges/3,
+		 undgraph_add_edges/3,
-	       undgraph_del_vertex/3,
+		 undgraph_del_vertex/3,
-	       undgraph_del_vertices/3,
+		 undgraph_del_vertices/3,
-	       undgraph_vertices/2,
+		 undgraph_vertices/2,
-	       undgraph_edges/2,
+		 undgraph_edges/2,
-	       undgraph_neighbors/3,
+		 undgraph_neighbors/3,
-	       undgraph_edge/3,
+		 undgraph_edge/3,
-	       dgraph_to_undgraph/2
+		 dgraph_to_undgraph/2
-	      ]).
+		]).
 
 :- use_module(library(wundgraphs),
-	      [wundgraph_new/1,
+		[wundgraph_new/1,
-	       wundgraph_max_tree/3,
+		 wundgraph_max_tree/3,
-	       wundgraph_add_edges/3,
+		 wundgraph_add_edges/3,
-	       wundgraph_add_vertices/3,
+		 wundgraph_add_vertices/3,
-	       wundgraph_to_undgraph/2
+		 wundgraph_to_undgraph/2
-	      ]).
+		]).
 
 :- use_module(library(rbtrees),
-	      [rb_new/1,
+		[rb_new/1,
-	       rb_insert/4,
+		 rb_insert/4,
-	       rb_lookup/3]).
+		 rb_lookup/3
+		]).
 
 :- use_module(library(ordsets),
-	      [ord_subset/2,
+		[ord_subset/2,
-	       ord_insert/3,
+		 ord_insert/3,
-	       ord_intersection/3,
+		 ord_intersection/3,
-	       ord_del_element/3,
+		 ord_del_element/3,
-	       ord_memberchk/2]).
+		 ord_memberchk/2
+		]).
 
 :- use_module(library(lists),
-	      [reverse/2]).
+		[reverse/2]).
 
 :- use_module(library(maplist)).
 
 :- use_module(library('clpbn/aggregates'),
-	      [check_for_agg_vars/2]).
+		[check_for_agg_vars/2]).
 
 :- use_module(library('clpbn/dists'),
-	      [get_dist_domain_size/2,
+		[get_dist_domain_size/2,
-	       get_dist_domain/2,
+		 get_dist_domain/2,
-	       get_dist_matrix/5]).
+		 get_dist_matrix/5
+		]).
 
 :- use_module(library('clpbn/matrix_cpt_utils'),
-	      [project_from_CPT/3,
+		[project_from_CPT/3,
-	       reorder_CPT/5,
+		 reorder_CPT/5,
-	       unit_CPT/2,
+		 unit_CPT/2,
-	       multiply_CPTs/4,
+		 multiply_CPTs/4,
-	       divide_CPTs/3,
+		 divide_CPTs/3,
-	       normalise_CPT/2,
+		 normalise_CPT/2,
-	       expand_CPT/4,
+		 expand_CPT/4,
-	       get_CPT_sizes/2,
+		 get_CPT_sizes/2,
-	       reset_CPT_that_disagrees/5,
+		 reset_CPT_that_disagrees/5,
-	       sum_out_from_CPT/4,
+		 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
-	       influences/4
+		]).
-	      ]).
 
 
 jt([[]],_,_) :- !.
@@ -94,7 +98,7 @@ jt(LLVs,Vs0,AllDiffs) :-
 
 
 init_jt_solver(LLVs, Vs0, _, State) :-
-	check_for_agg_vars(Vs0, Vs1), 
+	check_for_agg_vars(Vs0, Vs1),
 	init_influences(Vs1, G, RG),
 	maplist(init_jt_solver_for_question(G, RG), LLVs, State).
 
@@ -131,7 +135,7 @@ run_vars([V|LVs], Edges, [V|Vs], [CPTVars-dist([V|Parents],Id)|CPTs], Ev) :-
 add_evidence_from_vars(V, [e(V,P)|Evs], Evs) :-
 	clpbn:get_atts(V, [evidence(P)]), !.
 add_evidence_from_vars(_, Evs, Evs).
-	
+
 find_nth0([Id|_], Id, P, P) :- !.
 find_nth0([_|D], Id, P0, P) :-
 	P1 is P0+1,
@@ -159,7 +163,7 @@ initial_graph(_,Parents, CPTs) :-
 	% from the very beginning.
 	dgraph_transpose(V1, V2),
 	dgraph_to_ugraph(V2, Parents).
-	
+
 
 problem_graph([], []).
 problem_graph([V|BNet], GraphF) :-
@@ -171,7 +175,7 @@ add_parents([], _, Graph, Graph).
 add_parents([P|Parents], V, Graph0, [P-V|GraphF]) :-
 	add_parents(Parents, V, Graph0, GraphF).
 
-	      
+
 % From David Page's lectures
 test_graph(0,
 	   [1-3,2-3,2-4,5-4,5-7,10-7,10-9,11-9,3-6,4-6,7-8,9-8,6-12,8-12],
@@ -228,19 +232,19 @@ choose([V|Vertices], Graph, Score0, _, _, Best, _, Cliques0, Cliques, EdgesF) :-
 	ord_insert(Neighbors, V, PossibleClique),
 	new_edges(Neighbors, Graph, NewEdges),
 	(
-           % simplicial edge
+	  % simplicial edge
-	   NewEdges == []
+	  NewEdges == []
 	->
-	   !,
+	  !,
-	   Best = V,
+	  Best = V,
-	   NewEdges = EdgesF,
+	  NewEdges = EdgesF,
-	   length(PossibleClique,L),
+	  length(PossibleClique,L),
-	   Cliques = [L-PossibleClique|Cliques0]
+	  Cliques = [L-PossibleClique|Cliques0]
 	;
-%	   cliquelength(PossibleClique,1,CL),
+%	  cliquelength(PossibleClique,1,CL),
-	 length(PossibleClique,CL),
+	  length(PossibleClique,CL),
-	   CL < Score0, !,
+	  CL < Score0, !,
-	   choose(Vertices,Graph,CL,NewEdges, V, Best, CL-PossibleClique, Cliques0,Cliques,EdgesF)
+	  choose(Vertices,Graph,CL,NewEdges, V, Best, CL-PossibleClique, Cliques0,Cliques,EdgesF)
 	).
 choose([_|Vertices], Graph, Score0, Edges0, BestSoFar, Best, Clique, Cliques0, Cliques, EdgesF) :-
 	choose(Vertices,Graph,Score0,Edges0, BestSoFar, Best, Clique, Cliques0,Cliques,EdgesF).
@@ -285,18 +289,17 @@ get_links([Sz-Clique|Cliques], SoFar, Vertices, Edges0, Edges) :-
 	get_links(Cliques, [Clique|SoFar], Vertices, EdgesI, Edges).
 get_links([_|Cliques], SoFar, Vertices, Edges0, Edges) :-
 	get_links(Cliques, SoFar, Vertices, Edges0, Edges).
-	
+
 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)
-	 add_clique_edges(Cliques, Clique, Sz, Edges0, EdgesF)
 	;
-	 % we connect
+	  % we connect
-	 length(Int, LSz),
+	  length(Int, LSz),
-	 add_clique_edges(Cliques, Clique, Sz, [Clique-(Clique1-LSz)|Edges0], EdgesF)
+	  add_clique_edges(Cliques, Clique, Sz, [Clique-(Clique1-LSz)|Edges0], EdgesF)
 	).
 
 root(WTree, JTree) :-
@@ -358,25 +361,25 @@ get_cpts([], _, [], []).
 get_cpts([CPT|CPts], [], [], [CPT|CPts]) :- !.
 get_cpts([[I|MCPT]-Info|CPTs], [J|Clique], MyCPTs, MoreCPTs) :-
 	compare(C,I,J),
-	( C == < ->
+	(C == < ->
 	  % our CPT cannot be a part of the clique.
 	  MoreCPTs = [[I|MCPT]-Info|LeftoverCPTs],
 	  get_cpts(CPTs, [J|Clique], MyCPTs, LeftoverCPTs)
 	;
-	   C == = ->
+	  C == = ->
-	  % our CPT cannot be a part of the clique.
+	    % our CPT cannot be a part of the clique.
-	  get_cpt(MCPT, Clique, I, Info, MyCPTs, MyCPTs0, MoreCPTs, MoreCPTs0),
+	    get_cpt(MCPT, Clique, I, Info, MyCPTs, MyCPTs0, MoreCPTs, MoreCPTs0),
-	  get_cpts(CPTs, [J|Clique], MyCPTs0, MoreCPTs0)
+	    get_cpts(CPTs, [J|Clique], MyCPTs0, MoreCPTs0)
-	;
+	  ;
-	  % the first element in our CPT may not be in a clique
+	    % the first element in our CPT may not be in a clique
-	  get_cpts([[I|MCPT]-Info|CPTs], Clique, MyCPTs, MoreCPTs)
+	    get_cpts([[I|MCPT]-Info|CPTs], Clique, MyCPTs, MoreCPTs)
 	).
 
 get_cpt(MCPT, Clique, I, Info, [[I|MCPT]-Info|MyCPTs], MyCPTs, MoreCPTs, MoreCPTs) :-
 	ord_subset(MCPT, Clique), !.
 get_cpt(MCPT, _, I, Info, MyCPTs, MyCPTs, [[I|MCPT]-Info|MoreCPTs], MoreCPTs).
 
-	
+
 translate_edges([], [], []).
 translate_edges([E1-E2|Edges], [(E1-A)-(E2-B)|NEdges], [E1-A,E2-B|Vs]) :-
 	translate_edges(Edges, NEdges, Vs).
@@ -385,13 +388,13 @@ match_vs(_,[]).
 match_vs([K-A|Cls],[K1-B|KVs]) :-
 	compare(C, K, K1),
 	(C == = ->
-	 A = B,
+	  A = B,
-	 match_vs([K-A|Cls], KVs)
+	  match_vs([K-A|Cls], KVs)
 	;
-	 C = < ->
+	  C = < ->
-	 match_vs(Cls,[K1-B|KVs])
+	  match_vs(Cls,[K1-B|KVs])
 	;
-	 match_vs([K-A|Cls],KVs)
+	  match_vs([K-A|Cls],KVs)
 	).
 
 fill_with_cpts(tree(Clique-Dists,Leafs), tree(Clique-NewDists,NewLeafs)) :-

packages/CLPBN/clpbn/matrix_cpt_utils.yap

@@ -1,51 +1,54 @@
+
 :- module(clpbn_matrix_utils,
-	  [init_CPT/3,
+		[init_CPT/3,
-	   project_from_CPT/3,
+		 project_from_CPT/3,
-	   sum_out_from_CPT/5,
+		 sum_out_from_CPT/5,
-	   project_from_CPT/6,
+		 project_from_CPT/6,
-	   reorder_CPT/5,
+		 reorder_CPT/5,
-	   get_CPT_sizes/2,
+		 get_CPT_sizes/2,
-	   normalise_CPT/2,
+		 normalise_CPT/2,
-	   multiply_CPTs/4,
+		 multiply_CPTs/4,
-	   multiply_CPTs/6,
+		 multiply_CPTs/6,
-	   divide_CPTs/3,
+		 divide_CPTs/3,
-	   expand_CPT/4,
+		 expand_CPT/4,
-	   reset_CPT_that_disagrees/5,
+		 reset_CPT_that_disagrees/5,
-	   unit_CPT/2,
+		 unit_CPT/2,
-	   sum_out_from_CPT/4,
+		 sum_out_from_CPT/4,
-	   list_from_CPT/2,
+		 list_from_CPT/2,
-	   multiply_factors/3,
+		 multiply_factors/3,
-	   normalise_possibly_deterministic_CPT/2,
+		 normalise_possibly_deterministic_CPT/2,
-	   column_from_possibly_deterministic_CPT/3,
+		 column_from_possibly_deterministic_CPT/3,
-	   multiply_possibly_deterministic_factors/3,
+		 multiply_possibly_deterministic_factors/3,
-	   random_CPT/2,
+		 random_CPT/2,
-	   uniform_CPT/2,
+		 uniform_CPT/2,
-	   uniform_CPT_as_list/2,
+		 uniform_CPT_as_list/2,
-	   normalise_CPT_on_lines/3]).
+		 normalise_CPT_on_lines/3
+		]).
 
 :- use_module(library(matrix),
-	      [matrix_new/4,
+		[matrix_new/4,
-	       matrix_new_set/4,
+		 matrix_new_set/4,
-	       matrix_select/4,
+		 matrix_select/4,
-	       matrix_dims/2,
+		 matrix_dims/2,
-	       matrix_size/2,
+		 matrix_size/2,
-	       matrix_shuffle/3,
+		 matrix_shuffle/3,
-	       matrix_expand/3,
+		 matrix_expand/3,
-	       matrix_op/4,
+		 matrix_op/4,
-	       matrix_dims/2,
+		 matrix_dims/2,
-	       matrix_sum/2,
+		 matrix_sum/2,
-	       matrix_sum_logs_out/3,
+		 matrix_sum_logs_out/3,
-	       matrix_sum_out/3,
+		 matrix_sum_out/3,
-	       matrix_sum_logs_out_several/3,
+		 matrix_sum_logs_out_several/3,
-	       matrix_op_to_all/4,
+		 matrix_op_to_all/4,
-	       matrix_to_exps2/1,
+		 matrix_to_exps2/1,
-	       matrix_to_logs/1,
+		 matrix_to_logs/1,
-	       matrix_set_all_that_disagree/5,
+		 matrix_set_all_that_disagree/5,
-	       matrix_to_list/2,
+		 matrix_to_list/2,
-	       matrix_agg_lines/3,
+		 matrix_agg_lines/3,
-	       matrix_agg_cols/3,
+		 matrix_agg_cols/3,
-	       matrix_op_to_lines/4,
+		 matrix_op_to_lines/4,
-	       matrix_column/3]).
+		 matrix_column/3
+		]).
 
 init_CPT(List, Sizes, TAB) :-
 	matrix_new(floats, Sizes, List, TAB),
@@ -84,7 +87,7 @@ evidence(V, Pos) :-
 	clpbn:get_atts(V, [evidence(Pos)]).
 
 vnth([V1|Deps], N, V, N, Deps) :-
-	V == V1, !.	
+	V == V1, !.
 vnth([V1|Deps], N0, V, N, [V1|NDeps]) :-
 	N1 is N0+1,
 	vnth(Deps, N1, V, N, NDeps).
@@ -93,21 +96,21 @@ reorder_CPT(Vs0,T0,Vs,TF,Sizes) :-
 	var(Vs), !,
 	order_vec(Vs0,Vs,Map),
 	(
-	 Vs == Vs0
+	  Vs == Vs0
 	->
-	 TF = T0
+	  TF = T0
 	;
-	 matrix_shuffle(T0,Map,TF)
+	  matrix_shuffle(T0,Map,TF)
 	),
 	matrix_dims(TF, Sizes).
 reorder_CPT(Vs0,T0,Vs,TF,Sizes) :-
 	mapping(Vs0,Vs,Map),
 	(
-	 Vs == Vs0
+	  Vs == Vs0
 	->
-	 TF = T0
+	  TF = T0
 	;
-	 matrix_shuffle(T0,Map,TF)
+	  matrix_shuffle(T0,Map,TF)
 	),
 	matrix_dims(TF, Sizes).
 
@@ -124,7 +127,7 @@ add_indices([V|Vs0],I0,[V-I0|Is]) :-
 get_els([], [], []).
 get_els([V-I|NIs], [V|Vs], [I|Map]) :-
 	get_els(NIs, Vs, Map).
-	
+
 mapping(Vs0,Vs,Map) :-
 	add_indices(Vs0,0,I1s),
 	add_indices( Vs,I2s),
@@ -167,26 +170,26 @@ expand_tabs([], [], [V2|Deps2], [S2|Sz2], [S2|Map1], [0|Map2], [V2|NDeps]) :-
 expand_tabs([V1|Deps1], [S1|Sz1], [V2|Deps2], [S2|Sz2], Map1, Map2, NDeps) :-
 	compare(C,V1,V2),
 	(C == = ->
-	 NDeps = [V1|MDeps],
+	  NDeps = [V1|MDeps],
-	 Map1 = [0|M1],
+	  Map1 = [0|M1],
-	 Map2 = [0|M2],
+	  Map2 = [0|M2],
-	 NDeps = [V1|MDeps],
+	  NDeps = [V1|MDeps],
-	 expand_tabs(Deps1, Sz1, Deps2, Sz2, M1, M2, MDeps)
+	  expand_tabs(Deps1, Sz1, Deps2, Sz2, M1, M2, MDeps)
 	;
-	 C == < ->
+	  C == < ->
-	 NDeps = [V1|MDeps],
+	    NDeps = [V1|MDeps],
-	 Map1 = [0|M1],
+	    Map1 = [0|M1],
-	 Map2 = [S1|M2],
+	    Map2 = [S1|M2],
-	 NDeps = [V1|MDeps],
+	    NDeps = [V1|MDeps],
-	 expand_tabs(Deps1, Sz1, [V2|Deps2], [S2|Sz2], M1, M2, MDeps)
+	    expand_tabs(Deps1, Sz1, [V2|Deps2], [S2|Sz2], M1, M2, MDeps)
-	;
+	  ;
-	 NDeps = [V2|MDeps],
+	    NDeps = [V2|MDeps],
-	 Map1 = [S2|M1],
+	    Map1 = [S2|M1],
-	 Map2 = [0|M2],
+	    Map2 = [0|M2],
-	 NDeps = [V2|MDeps],
+	    NDeps = [V2|MDeps],
-	 expand_tabs([V1|Deps1], [S1|Sz1], Deps2, Sz2, M1, M2, MDeps)
+	    expand_tabs([V1|Deps1], [S1|Sz1], Deps2, Sz2, M1, M2, MDeps)
 	).
-	
+
 normalise_CPT(MAT,NMAT) :-
 	matrix_to_exps2(MAT),
 	matrix_sum(MAT, Sum),
@@ -204,9 +207,9 @@ generate_map([V|DimsNew], [V0|Dims0], [0|Map]) :- V == V0, !,
 	generate_map(DimsNew, Dims0, Map).
 generate_map([V|DimsNew], Dims0, [Sz|Map]) :-
 	clpbn:get_atts(V, [dist(Id,_)]),
-	clpbn_dist:get_dist_domain_size(Id, Sz),	
+	clpbn_dist:get_dist_domain_size(Id, Sz),
 	generate_map(DimsNew, Dims0, Map).
-	
+
 unit_CPT(V,CPT) :-
 	clpbn:get_atts(V, [dist(Id,_)]),
 	clpbn_dist:get_dist_domain_size(Id, Sz),
@@ -284,7 +287,7 @@ uniform_CPT(Dims, M) :-
 	normalise_possibly_deterministic_CPT(M1, M).
 
 normalise_CPT_on_lines(MAT0, MAT2, L1) :-
-	matrix_agg_cols(MAT0, +, MAT1), 
+	matrix_agg_cols(MAT0, +, MAT1),
 	matrix_sum(MAT1, SUM),
 	matrix_op_to_all(MAT1, /, SUM, MAT2),
 	matrix:matrix_to_list(MAT2,L1).

packages/CLPBN/clpbn/numbers.yap

@@ -1,17 +1,17 @@
 
 :- module(clpbn_numbers,
-	[
+		[keys_to_numbers/7,
-         keys_to_numbers/7, 
+		 keys_to_numbers/9,
-         keys_to_numbers/9, 
+		 lists_of_keys_to_ids/6
-	 lists_of_keys_to_ids/6
+		]).
-     ]).
 
 :- use_module(library(bhash)).
 :- use_module(library(maplist)).
+
 :- use_module(library(pfl),
-          [skolem/2,
+		[skolem/2,
-           get_pfl_cpt/5
+		 get_pfl_cpt/5
-          ]).
+		]).
 
 %
 % convert key representation into numeric representation
@@ -30,16 +30,16 @@ keys_to_numbers(AllKeys, Factors, Evidence, Hash0, Hash4, Id0, Id4, FactorIds, E
 	foldl2(key_to_id, SKeys, _, Hash3, Hash4, Id3, Id4).
 
 lists_of_keys_to_ids(QueryKeys, QueryIds, Hash0, Hash, Id0, Id) :-
-        foldl2(list_of_keys_to_ids, QueryKeys, QueryIds, Hash0, Hash, Id0, Id).
+	foldl2(list_of_keys_to_ids, QueryKeys, QueryIds, Hash0, Hash, Id0, Id).
 
 list_of_keys_to_ids(List, IdList, Hash0, Hash, I0, I) :-
 	foldl2(key_to_id, List, IdList, Hash0, Hash, I0, I).
 
 key_to_id(Key, Id, Hash0, Hash0, I0, I0) :-
-    b_hash_lookup(Key, Id, Hash0), !.
+	b_hash_lookup(Key, Id, Hash0), !.
 key_to_id(Key, I0, Hash0, Hash, I0, I) :-
-    b_hash_insert(Hash0, Key, I0, Hash),
+	b_hash_insert(Hash0, Key, I0, Hash),
-    I is I0+1.
+	I is I0+1.
 
 factor_to_id(Ev, f(_, DistId, Keys), f(Ids, Ranges, CPT, DistId), Hash0, Hash, I0, I) :-
 	get_pfl_cpt(DistId, Keys, Ev, NKeys, CPT),
@@ -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

@@ -2,30 +2,29 @@
 
 :- style_check(all).
 
-:- module(clpbn_pgrammar,[grammar_to_atts/1,
+:- module(clpbn_pgrammar,
-			  grammar_prob/2,
+		[grammar_to_atts/1,
-			  grammar_mle/2,
+		 grammar_prob/2,
-			  init_pcg_solver/4,
+		 grammar_mle/2,
-			  run_pcg_solver/3,
+		 init_pcg_solver/4,
-			  pcg_init_graph/0]).
+		 run_pcg_solver/3,
+		 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,
+		[matrix_new/3,
-		matrix_add/3,
+		 matrix_add/3,
-		matrix_get/3,
+		 matrix_get/3,
-		matrix_op/4,
+		 matrix_op/4,
-		matrix_op_to_all/4,
+		 matrix_op_to_all/4,
-		matrix_set_all/2
+		 matrix_set_all/2
-	      ]).
+		]).
 
 :- op(600, xfy,'::').
 
@@ -71,9 +70,9 @@ grammar_mle(S,_,P) :-
 	nb_getval(best,p(P,S)), P > 0.0.
 
 user:term_expansion((P::H --> B), Goal) :-
-        functor(H,A0,_),
+	functor(H,A0,_),
-        % a-->b to a(p(K,P,C,[Cs])) --> b(Cs)
+	% a-->b to a(p(K,P,C,[Cs])) --> b(Cs)
-        convert_to_internal(H, B, IH, IB, Id),
+	convert_to_internal(H, B, IH, IB, Id),
 	expand_term((IH --> IB),(NH :- NB)),
 	prolog_load_context(module, Mod),
 	functor(NH,N,A),
@@ -99,8 +98,8 @@ add_to_predicate(M:EH1,M:EH,M:H0,NH,NB,Key,Choice,P,Id,(EH1:-NB)) :-
 	% now ensure_tabled works.
 	ensure_tabled(M,H0,EH),
 	assert_static(M:(EH :-
-			clpbn_pgrammar:p_rule(M,EH,Key,Choice),
+		clpbn_pgrammar:p_rule(M,EH,Key,Choice),
-			 M:EH1)),
+		M:EH1)),
 	Choice = 1,
 	new_id(Key,P,Choice,Id),
 	assert_static(M:ptab(EH,Choice,P)),
@@ -140,18 +139,18 @@ convert_body_to_internal({A}, {A}) --> !.
 convert_body_to_internal(B, IB) -->
 	[V],
 	{
-	 B =.. [Na|Args],
+	  B =.. [Na|Args],
-	 build_internal(Na,NaInternal),
+	  build_internal(Na,NaInternal),
-	 IB =.. [NaInternal,V|Args]
+	  IB =.. [NaInternal,V|Args]
 	}.
 
 new_id(Key,P,Choice,Id) :-
 	(
-	 predicate_property(id(_,_,_,_),number_of_clauses(Id))
+	  predicate_property(id(_,_,_,_),number_of_clauses(Id))
 	->
-	 true
+	  true
 	;
-	 Id = 0
+	  Id = 0
 	),
 	assert(id(Id,Key,P,Choice)).
 
@@ -177,7 +176,7 @@ get_internal(S, InternalS, Arg) :-
 
 extract_probability(p(Id,Goals), P) :-
 	id(Id,_,P0,_),
-	LogP0 is log(P0),	
+	LogP0 is log(P0),
 	extract_logprobability(Goals, LogP0, LogP),
 	P is exp(LogP).
 
@@ -211,11 +210,11 @@ path_choices(InternalS, Proof) :-
 
 new_id(Id) :-
 	(nb_getval(grammar_id,Id) ->
-	 I1 is Id+1,
+	  I1 is Id+1,
-	 nb_setval(grammar_id,I1)
+	  nb_setval(grammar_id,I1)
 	;
-	 nb_setval(grammar_id,1),
+	  nb_setval(grammar_id,1),
-	 Id = 0
+	  Id = 0
 	).
 
 find_dom(K, Vs, Ps) :-

packages/CLPBN/clpbn/table.yap

@@ -8,49 +8,49 @@
 */
 
 :- module(clpbn_table,
-	[clpbn_table/1,
+		[clpbn_table/1,
-	 clpbn_tableallargs/1,
+		 clpbn_tableallargs/1,
-	 clpbn_table_nondet/1,
+		 clpbn_table_nondet/1,
-	 clpbn_tabled_clause/2,
+		 clpbn_tabled_clause/2,
-	 clpbn_tabled_clause_ref/3,
+		 clpbn_tabled_clause_ref/3,
-	 clpbn_tabled_retract/2,
+		 clpbn_tabled_retract/2,
-	 clpbn_tabled_abolish/1,
+		 clpbn_tabled_abolish/1,
-	 clpbn_tabled_asserta/1,
+		 clpbn_tabled_asserta/1,
-	 clpbn_tabled_assertz/1,
+		 clpbn_tabled_assertz/1,
-	 clpbn_tabled_asserta/2,
+		 clpbn_tabled_asserta/2,
-	 clpbn_tabled_assertz/2,
+		 clpbn_tabled_assertz/2,
-	 clpbn_tabled_dynamic/1,
+		 clpbn_tabled_dynamic/1,
-	 clpbn_tabled_number_of_clauses/2,
+		 clpbn_tabled_number_of_clauses/2,
-	 clpbn_reset_tables/0,
+		 clpbn_reset_tables/0,
-	 clpbn_reset_tables/1,
+		 clpbn_reset_tables/1,
-	 clpbn_is_tabled/1
+		 clpbn_is_tabled/1
-	]).
+		]).
 
 :- use_module(library(bhash),
-	[b_hash_new/4,
+		[b_hash_new/4,
-	 b_hash_lookup/3,
+		 b_hash_lookup/3,
-	 b_hash_insert/4]).
+		 b_hash_insert/4
+		]).
 
 :- meta_predicate clpbn_table(:),
 	clpbn_tabled_clause(:.?),
 	clpbn_tabled_clause_ref(:.?,?),
 	clpbn_tabled_retract(:),
 	clpbn_tabled_abolish(:),
-	clpbn_tabled_asserta(:), 
+	clpbn_tabled_asserta(:),
-	clpbn_tabled_assertz(:), 
+	clpbn_tabled_assertz(:),
-	clpbn_tabled_asserta(:,-), 
+	clpbn_tabled_asserta(:,-),
-	clpbn_tabled_assertz(:,-), 
+	clpbn_tabled_assertz(:,-),
-	clpbn_tabled_number_of_clauses(:,-), 
+	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
+		 variant/2
-			       ]).
+		]).
 
-:- use_module(evidence, [
+:- use_module(evidence,
-			       put_evidence/2
+		[put_evidence/2]).
-			       ]).
 
 :- dynamic clpbn_table/3.
 
@@ -108,30 +108,28 @@ clpbn_table(F/N,M) :-
 	L0 = [_|Args0],
 	IGoal =.. [NF|Args0],
 	asserta(clpbn_table(S, M, IGoal)),
-	assert(
+	assert((M:S :-
-	       (M:S :-
+	  !,
-	        !,
+%	  write(S: ' ' ),
-%		write(S: ' ' ),
+	  b_getval(clpbn_tables, Tab),
-	        b_getval(clpbn_tables, Tab),
+	  % V2 is unbound.
-		% V2 is unbound.
+	  (b_hash_lookup(Key, V2, Tab) ->
-		( b_hash_lookup(Key, V2, Tab) ->
+%	    (attvar(V2) -> writeln(ok:A0:V2) ; writeln(error(V2:should_be_attvar(S)))),
-%		 (attvar(V2) -> writeln(ok:A0:V2) ; writeln(error(V2:should_be_attvar(S)))),
+	    (var(A0) -> A0 = V2 ; put_evidence(A0, V2))
-		 ( var(A0) -> A0 = V2 ; put_evidence(A0, V2) )
+	  ;
-		;
+%	    writeln(new),
-%		writeln(new),
+	    b_hash_insert(Tab, Key, V2, NewTab),
-		  b_hash_insert(Tab, Key, V2, NewTab),
+	    b_setval(clpbn_tables,NewTab),
-		  b_setval(clpbn_tables,NewTab),
+	    once(M:Goal), !,
-		  once(M:Goal), !,
+	    % enter evidence after binding.
-		  % enter evidence after binding.
+	    (var(A0) -> A0 = V2 ; put_evidence(A0, V2))
-		  ( var(A0) -> A0 = V2 ; put_evidence(A0, V2) )
+	  ;
-		;
+	    clpbn:clpbn_flag(solver,none) ->
-		  clpbn:clpbn_flag(solver,none) ->
+	      true
-		  true
+	    ;
-	        ;
+	      throw(error(tabled_clpbn_predicate_should_never_fail,S))
-		  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]) :-
@@ -154,19 +152,17 @@ 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_getval(clpbn_tables, Tab),
+	  (b_hash_lookup(Key, Out, Tab) ->
-		( b_hash_lookup(Key, Out, Tab) ->
+	    true
-		  true
+	  ;
-		;
+	    b_hash_insert(Tab, Key, Out, NewTab),
-		  b_hash_insert(Tab, Key, Out, NewTab),
+	    b_setval(clpbn_tables, NewTab),
-	          b_setval(clpbn_tables, NewTab),
+	    once(M:NKey)
-		  once(M:NKey)
+	  )
-		)
+	)).
-	       )
-	      ).
 
 clpbn_table_nondet(M:X) :- !,
 	clpbn_table_nondet(X,M).
@@ -185,18 +181,17 @@ 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_getval(clpbn_tables, Tab),
-		( b_hash_lookup(Key, Out, Tab) ->
+	  (b_hash_lookup(Key, Out, Tab) ->
-		  fail
+	    fail
-		;
+	  ;
-		  b_hash_insert(Tab, Key, Out, NewTab),
+	    b_hash_insert(Tab, Key, Out, NewTab),
-	          b_setval(clpbn_tables, NewTab),
+	    b_setval(clpbn_tables, NewTab),
-		  M:NKey
+	    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_new/1,
-	       dgraph_add_edges/3,
+		 dgraph_add_edges/3,
-	       dgraph_add_vertices/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_var_member/2,
+		[clpbn_not_var_member/2,
-	check_for_hidden_vars/3,
+		 clpbn_var_member/2,
-	sort_vars_by_key/3,
+		 check_for_hidden_vars/3,
-	sort_vars_by_key_and_parents/3]).
+		 sort_vars_by_key/3,
+		 sort_vars_by_key_and_parents/3
+		]).
 
 %
 % It may happen that variables from a previous query may still be around.
@@ -52,21 +54,19 @@ 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:put_atts(V2, [evidence(E)])
 	;
-	    clpbn:get_atts(V2, [evidence(E)])
+	  clpbn:get_atts(V2, [evidence(E)]) ->
-	->
 	    clpbn:put_atts(V1, [evidence(E)])
-	;
+	  ;
-	     true
+	    true
 	),
 %	V1 = V2,
 	attributes:fast_unify_attributed(V1,V2),
 	merge_same_key([K1-V1|Vs], SortedAVars, Ks, UnifiableVars).
 merge_same_key([K1-V1,K2-V2|Vs], [V1|SortedAVars], Ks, [K1|UnifiableVars]) :-
-	(in_keys(K1, Ks) ; \+ \+ K1 == K2), !, 
+	(in_keys(K1, Ks) ; \+ \+ K1 == K2), !,
 	add_to_keys(K1, Ks, NKs),
 	merge_same_key([K2-V2|Vs], SortedAVars, NKs, UnifiableVars).
 merge_same_key([K-V|Vs], [V|SortedAVars], Ks, UnifiableVars) :-
@@ -74,9 +74,9 @@ merge_same_key([K-V|Vs], [V|SortedAVars], Ks, UnifiableVars) :-
 	merge_same_key(Vs, SortedAVars, NKs, UnifiableVars).
 
 in_keys(K1,[K|_]) :- \+ \+ K1 = K, !.
-in_keys(K1,[_|Ks]) :- 
+in_keys(K1,[_|Ks]) :-
 	in_keys(K1,Ks).
-	
+
 add_to_keys(K1, Ks, Ks) :- ground(K1), !.
 add_to_keys(K1, Ks, [K1|Ks]).
 
@@ -102,7 +102,7 @@ add_parents(Parents,V,Id,KeyVarsF,KeyVars0) :-
 
 all_vars([]).
 all_vars([P|Parents]) :-
-	var(P), 
+	var(P),
 	all_vars(Parents).
 
 
@@ -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

@@ -11,58 +11,61 @@
       all tables they connect to;
       multiply their size
       order by size
-  
+
 *********************************/
 
-:- module(clpbn_ve, [ve/3,
+:- module(clpbn_ve,
-		     check_if_ve_done/1,
+		[ve/3,
-		     init_ve_solver/4,
+		 check_if_ve_done/1,
-		     run_ve_solver/3,
+		 init_ve_solver/4,
-		     init_ve_ground_solver/5,
+		 run_ve_solver/3,
-		     run_ve_ground_solver/3,
+		 init_ve_ground_solver/5,
-		     call_ve_ground_solver/6]).
+		 run_ve_ground_solver/3,
+		 call_ve_ground_solver/6
+		]).
 
-:- attribute size/1, all_diffs/1.
+:- use_module(library(atts)).
 
 :- use_module(library(ordsets),
-	[ord_union/3, 
+		[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_domain_size/2,
+		 get_dist_params/2,
-	       get_dist_params/2,
+		 get_dist_domain_size/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,
-	       influences/4,
+		 factor_influences/4
-	       factor_influences/4
+		]).
-	      ]).
 
 :- use_module(library(clpbn/matrix_cpt_utils)).
 
 :- use_module(library(clpbn/numbers)).
 
 :- use_module(library(lists),
-	      [
+		[member/2,
-	       member/2,
+		 append/3,
-	       append/3,
+		 delete/3
-	       delete/3
+		]).
-	      ]).
 
 :- use_module(library(maplist)).
 
@@ -71,7 +74,9 @@
 :- use_module(library(clpbn/vmap)).
 
 :- use_module(library('clpbn/aggregates'),
-	      [check_for_agg_vars/2]).
+		[check_for_agg_vars/2]).
+
+:- attribute size/1, all_diffs/1.
 
 %
 % uses a bipartite graph where bigraph(Vs, NFs, Fs)
@@ -88,23 +93,23 @@ check_if_ve_done(Var) :-
 % new PFL like interface...
 %
 call_ve_ground_solver(QueryVars, QueryKeys, AllKeys, Factors, Evidence, Output) :-
-    call_ve_ground_solver_for_probabilities([QueryKeys], AllKeys, Factors, Evidence, Solutions),
+	call_ve_ground_solver_for_probabilities([QueryKeys], AllKeys, Factors, Evidence, Solutions),
-    clpbn_bind_vals([QueryVars], Solutions, Output).
+	clpbn_bind_vals([QueryVars], Solutions, Output).
 
 call_ve_ground_solver_for_probabilities(QueryKeys, AllKeys, Factors, Evidence, Solutions) :-
-    init_ve_ground_solver(QueryKeys, AllKeys, Factors, Evidence, VE),
+	init_ve_ground_solver(QueryKeys, AllKeys, Factors, Evidence, VE),
-    run_ve_ground_solver(QueryKeys, Solutions, VE).
+	run_ve_ground_solver(QueryKeys, Solutions, VE).
 
 simulate_ve_ground_solver(_QueryVars, QueryKeys, AllKeys, Factors, Evidence, Output) :-
-    simulate_ve_ground_solver_for_probabilities([QueryKeys], AllKeys, Factors, Evidence, Output).
+	simulate_ve_ground_solver_for_probabilities([QueryKeys], AllKeys, Factors, Evidence, Output).
 
 simulate_ve_ground_solver_for_probabilities(QueryKeys, AllKeys, Factors, Evidence, Solutions) :-
-    init_ve_ground_solver(QueryKeys, AllKeys, Factors, Evidence, VE),
+	init_ve_ground_solver(QueryKeys, AllKeys, Factors, Evidence, VE),
-    simulate_solver(QueryKeys, Solutions, VE).
+	simulate_solver(QueryKeys, Solutions, VE).
 
 init_ve_ground_solver(_QueryKeys, AllKeys, Factors, Evidence, VE) :-
-    keys_to_numbers(AllKeys, Factors, Evidence, Hash4, Id4, FactorIds, EvidenceIds),
+	keys_to_numbers(AllKeys, Factors, Evidence, Hash4, Id4, FactorIds, EvidenceIds),
-    init_ve(FactorIds, EvidenceIds, Hash4, Id4, VE).
+	init_ve(FactorIds, EvidenceIds, Hash4, Id4, VE).
 
 
 %
@@ -112,11 +117,11 @@ init_ve_ground_solver(_QueryKeys, AllKeys, Factors, Evidence, VE) :-
 %
 ve([[]],_,_) :- !.
 ve(LLVs,Vs0,AllDiffs) :-
-    init_ve_solver(LLVs, Vs0, AllDiffs, State),
+	init_ve_solver(LLVs, Vs0, AllDiffs, State),
-				% variable elimination proper
+	% variable elimination proper
-    run_ve_solver(LLVs, LLPs, State),
+	run_ve_solver(LLVs, LLPs, State),
-				% bind Probs back to variables so that they can be output.
+	% bind Probs back to variables so that they can be output.
-    clpbn_bind_vals(LLVs,LLPs,AllDiffs).
+	clpbn_bind_vals(LLVs,LLPs,AllDiffs).
 
 
 init_ve(FactorIds, EvidenceIds, Hash, Id, ve(FactorIds, Hash, Id, Ev)) :-
@@ -129,7 +134,7 @@ evtotree(K=V,Ev0,Ev) :-
 factor_to_graph( f(Nodes, Sizes, _Pars0, Id), Factors0, Factors, Edges0, Edges, I0, I) :-
 	I is I0+1,
 	pfl:get_pfl_parameters(Id, Pars0),
-	init_CPT(Pars0, Sizes, CPT0), 
+	init_CPT(Pars0, Sizes, CPT0),
 	reorder_CPT(Nodes, CPT0, FIPs, CPT, _),
 	F = f(I0, FIPs, CPT),
 	rb_insert(Factors0, I0, F, Factors),
@@ -172,7 +177,7 @@ vars_to_bigraph(VMap, bigraph(VInfo, IF, Fs), Evs) :-
 
 id_to_factor(VMap, V-I, IF0, IF, Fs0, Fs, Evs0, Evs) :-
 	% process evidence for variable
-	clpbn:get_atts(V, [evidence(E), dist(_,Ps)]), 
+	clpbn:get_atts(V, [evidence(E), dist(_,Ps)]),
 	checklist(noparent_of_interest(VMap), Ps), !,
 	% I don't need to get a factor here
 	Evs = [I=E|Evs0],
@@ -181,17 +186,17 @@ id_to_factor(VMap, V-I, IF0, IF, Fs0, Fs, Evs0, Evs) :-
 id_to_factor(VMap, V-I, IF0, IF, Fs0, Fs, Evs0, Evs) :-
 	%  process distribution/factors
 	(
-	    clpbn:get_atts(V, [evidence(E)])
+	  clpbn:get_atts(V, [evidence(E)])
-	 ->
+	->
-	    Evs = [I=E|Evs0]
+	  Evs = [I=E|Evs0]
 	;
-	    Evs = Evs0
+	  Evs = Evs0
-	),	    
+	),
 	clpbn:get_atts(V, [dist(D, Ps)]),
 	get_dist_params(D, Pars0),
 	get_dist_domain_size(D, DS),
 	maplist(parent_to_id(VMap), Ps, Sizes, IPs),
-	init_CPT(Pars0, [DS|Sizes], CPT0), 
+	init_CPT(Pars0, [DS|Sizes], CPT0),
 	reorder_CPT([I|IPs], CPT0, FIPs, CPT, _),
 	rb_insert(Fs0, IF0, f(IF0, FIPs, CPT), Fs),
 	IF is IF0+1.
@@ -239,29 +244,29 @@ collect_factors(SFVs, _Fs, _V, [], SFVs).
 % solve each query independently
 % use a findall to recover space without needing for GC
 run_ve_ground_solver(LQVs, LLPs, ve(FactorIds, Hash, Id, Ev)) :-
-    rb_new(Fs0),
+	rb_new(Fs0),
-    foldl3(factor_to_graph, FactorIds, Fs0, Fs, [], FVs, 0, IF),
+	foldl3(factor_to_graph, FactorIds, Fs0, Fs, [], FVs, 0, IF),
-    sort(FVs, SFVs),
+	sort(FVs, SFVs),
-    rb_new(VInfo0),
+	rb_new(VInfo0),
-    add_vs(SFVs, Fs, VInfo0, VInfo),
+	add_vs(SFVs, Fs, VInfo0, VInfo),
-    BG = bigraph(VInfo, IF, Fs),
+	BG = bigraph(VInfo, IF, Fs),
-    lists_of_keys_to_ids(LQVs, LQIds, Hash, _, Id, _),
+	lists_of_keys_to_ids(LQVs, LQIds, Hash, _, Id, _),
-    findall(LPs, solve(LQIds, FactorIds, BG, Ev, LPs), LLPs).
+	findall(LPs, solve(LQIds, FactorIds, BG, Ev, LPs), LLPs).
 
 solve([QVs|_], FIds, Bigraph, Evs, LPs) :-
-    factor_influences(FIds, QVs, Evs, LVs),
+	factor_influences(FIds, QVs, Evs, LVs),
-    do_solve(QVs, LVs, Bigraph, Evs, LPs).
+	do_solve(QVs, LVs, Bigraph, Evs, LPs).
 solve([_|LQVs], FIds, Bigraph, Ev, LPs) :-
-    solve(LQVs, FIds, Bigraph, Ev, LPs).
+	solve(LQVs, FIds, Bigraph, Ev, LPs).
 
 do_solve(IQVs, IVs, bigraph(OldVs, IF, _Fs), Ev, Ps) :-
-    % get only what is relevant to query,
+	% get only what is relevant to query,
-    project_to_query_related(IVs, OldVs, SVs, Fs1), 
+	project_to_query_related(IVs, OldVs, SVs, Fs1),
-    % and also prune using evidence
+	% and also prune using evidence
-    rb_visit(Ev, EvL),
+	rb_visit(Ev, EvL),
-    foldl2(clean_v_ev, EvL, Fs1, Fs2, SVs, EVs), 
+	foldl2(clean_v_ev, EvL, Fs1, Fs2, SVs, EVs),
-    % eliminate
+	% eliminate
-    eliminate(IQVs, digraph(EVs, IF, Fs2), Dist),
+	eliminate(IQVs, digraph(EVs, IF, Fs2), Dist),
 % writeln(m:Dist),matrix:matrix_to_list(Dist,LD),writeln(LD),
 %exps(LD,LDE),writeln(LDE),
 	% move from potentials back to probabilities
@@ -269,18 +274,18 @@ do_solve(IQVs, IVs, bigraph(OldVs, IF, _Fs), Ev, Ps) :-
 	list_from_CPT(MPs, Ps).
 
 simulate_solver(LQVs, Choices, ve(FIds, Hash, Id, BG, Evs)) :-
-    lists_of_keys_to_ids(LQVs, [QVs], Hash, _, Id, _),
+	lists_of_keys_to_ids(LQVs, [QVs], Hash, _, Id, _),
-    factor_influences(FIds, QVs, Evs, LVs),
+	factor_influences(FIds, QVs, Evs, LVs),
-    do_simulate(QVs, LVs, BG, Evs, Choices).
+	do_simulate(QVs, LVs, BG, Evs, Choices).
 
 do_simulate(IQVs, IVs, bigraph(OldVs, IF, _Fs), Ev, Choices) :-
-    % get only what is relevant to query,
+	% get only what is relevant to query,
-    project_to_query_related(IVs, OldVs, SVs, Fs1), 
+	project_to_query_related(IVs, OldVs, SVs, Fs1),
-    % and also prune using evidence
+	% and also prune using evidence
-    rb_visit(Ev, EvL),
+	rb_visit(Ev, EvL),
-    foldl2(clean_v_ev, EvL, Fs1, Fs2, SVs, EVs), 
+	foldl2(clean_v_ev, EvL, Fs1, Fs2, SVs, EVs),
-    % eliminate
+	% eliminate
-    simulate_eiminate(IQVs, digraph(EVs, IF, Fs2), Choices).
+	simulate_eiminate(IQVs, digraph(EVs, IF, Fs2), Choices).
 
 % solve each query independently
 % use a findall to recover space without needing for GC
@@ -295,9 +300,9 @@ run_ve_solver(_, LLPs, state(LQVs, LVs, _VMap,  Bigraph, Ev)) :-
 %
 solve_ve([IQVs|_], [IVs|_], bigraph(OldVs, IF, _Fs), Ev, Ps) :-
 	% get only what is relevant to query,
-	project_to_query_related(IVs, OldVs, SVs, Fs1), 
+	project_to_query_related(IVs, OldVs, SVs, Fs1),
 	% and also prune using evidence
-	foldl2(clean_v_ev, Ev, Fs1, Fs2, SVs, EVs), 
+	foldl2(clean_v_ev, Ev, Fs1, Fs2, SVs, EVs),
 	% eliminate
 	eliminate(IQVs, digraph(EVs, IF, Fs2), Dist),
 % writeln(m:Dist),matrix:matrix_to_list(Dist,LD),writeln(LD),
@@ -314,7 +319,7 @@ solve_ve([_|MoreLVs], [_|MoreLVis], Digraph, Ev, Ps) :-
 project_to_query_related(IVs0, OldVs, NVs, NFs) :-
 	sort(IVs0, IVs),
 	rb_new(Vs0),
-	foldl(cp_to_vs, IVs, Vs0, AuxVs), 
+	foldl(cp_to_vs, IVs, Vs0, AuxVs),
 	rb_new(NFs0),
 	foldl(simplify_graph_node(OldVs, AuxVs), IVs, VFs, NFs0, NFs),
 	list_to_rbtree(VFs, NVs).
@@ -338,31 +343,31 @@ simplify_graph_node(OldVs, NVs, V, V-RemFs, NFs0, NFs) :-
 %
 % Two cases: first time factor comes up: all its vars must be in subgraph
 % second case: second time it comes up, it must be already in graph
-% 
+%
-% args: +Factor F, +current V (int), +rbtree with all Vs, 
+% args: +Factor F, +current V (int), +rbtree with all Vs,
 %       -Factors in new Graph, +factors in current graph, -rbtree of factors
 %
 %
 check_factor(V, NVs, F, NFs0, NFs, RemFs, NewRemFs) :-
 	F = f(IF, [V|More], _), !,
-	( 
+	(
 	  checklist(check_v(NVs), More)
 	->
 	  rb_insert(NFs0, IF, F, NFs),
 	  NewRemFs = [F|RemFs]
-        ;
+	;
 	  NFs0 = NFs,
 	  NewRemFs = RemFs
-        ).
+	).
 check_factor(_V, _NVs, F, NFs, NFs, RemFs, NewRemFs) :-
 	F = f(Id, _, _),
-	( 
+	(
 	  rb_lookup(Id, F, NFs)
 	->
 	  NewRemFs = [F|RemFs]
-        ;
+	;
 	  NewRemFs = RemFs
-        ).
+	).
 
 check_v(NVs, V) :-
 	rb_lookup(V, _, NVs).
@@ -425,15 +430,15 @@ best_var(QVs, I, _Node, Info, Info) :-
 	!.
 % pick the variable with less factors
 best_var(_Qs, I, Node, i(ValSoFar,_,_), i(NewVal,I,Node)) :-
-        foldl(szfac,Node,1,NewVal),
+	foldl(szfac,Node,1,NewVal),
 	%length(Node, NewVal),
 	NewVal < ValSoFar,
 	!.
 best_var(_, _I, _Node, Info, Info).
 
 szfac(f(_,Vs,_), I0, I) :-
-    length(Vs,L),
+	length(Vs,L),
-    I is I0*L.
+	I is I0*L.
 
 % delete one factor, need to also touch all variables
 del_fac(f(I,FVs,_), Fs0, Fs, Vs0, Vs) :-
@@ -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,
+		[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(:,:,+,-).
 
@@ -75,21 +77,21 @@ fetch_edges([V|Parents], Key0, EdgesF, Edges0, [Slice-AKey|PKeys]) :-
 	clpbn:get_atts(V,[key(Key)]),
 	abstract_key(Key, AKey, Slice),
 	(
-	 Slice < 3
+	  Slice < 3
 	->
-	 EdgesF = [Key0-AKey|EdgesI]
+	  EdgesF = [Key0-AKey|EdgesI]
 	;
-	 EdgesF = EdgesI
+	  EdgesF = EdgesI
 	),
 	fetch_edges(Parents, Key0, EdgesI, Edges0, PKeys).
 fetch_edges([Key|Parents], Key0, EdgesF, Edges0, [Slice-AKey|PKeys]) :-
 	abstract_key(Key, AKey, Slice),
 	(
-	 Slice < 3
+	  Slice < 3
 	->
-	 EdgesF = [Key0-AKey|EdgesI]
+	  EdgesF = [Key0-AKey|EdgesI]
 	;
-	 EdgesF = EdgesI
+	  EdgesF = EdgesI
 	),
 	fetch_edges(Parents, Key0, EdgesI, Edges0, PKeys).
 fetch_edges([], _, Edges, Edges, []).
@@ -122,20 +124,20 @@ compile_keys([], _, []).
 % add a random symbol to the end.
 compile_emission([],_) --> !, [].
 compile_emission(EmissionTerm,IKey) --> [emit(IKey,EmissionTerm)].
-	
+
 compile_propagation([],[],_,_) --> [].
 compile_propagation([0-PKey|Ps], [Prob|Probs], IKey, KeyMap) -->
-	 [prop_same(IKey,Parent,Prob)],
+	[prop_same(IKey,Parent,Prob)],
-	 { get_assoc(PKey,KeyMap,nodeinfo(Parent,_,_,_)) },
+	{ get_assoc(PKey,KeyMap,nodeinfo(Parent,_,_,_)) },
-	 compile_propagation(Ps, Probs, IKey, KeyMap).
+	compile_propagation(Ps, Probs, IKey, KeyMap).
 compile_propagation([2-PKey|Ps], [Prob|Probs], IKey, KeyMap) -->
-	 [prop_same(IKey,Parent,Prob)],
+	[prop_same(IKey,Parent,Prob)],
-	 { get_assoc(PKey,KeyMap,nodeinfo(Parent,_,_,_)) },
+	{ get_assoc(PKey,KeyMap,nodeinfo(Parent,_,_,_)) },
-	 compile_propagation(Ps, Probs, IKey, KeyMap).
+	compile_propagation(Ps, Probs, IKey, KeyMap).
 compile_propagation([3-PKey|Ps], [Prob|Probs], IKey, KeyMap) -->
-	 [prop_next(IKey,Parent,Prob)],
+	[prop_next(IKey,Parent,Prob)],
-	 { get_assoc(PKey,KeyMap,nodeinfo(Parent,_,_,_)) },
+	{ get_assoc(PKey,KeyMap,nodeinfo(Parent,_,_,_)) },
-	 compile_propagation(Ps, Probs, IKey, KeyMap).
+	compile_propagation(Ps, Probs, IKey, KeyMap).
 
 get_id(_:S, Map, SI) :- !,
 	get_id(S, Map, SI).
@@ -148,9 +150,9 @@ get_id(S, Map, SI) :-
 compile_trace(Trace, Emissions) :-
 	user:hmm_domain(Domain),
 	(atom(Domain) ->
-	 hmm:cvt_vals(Domain, Vals)
+	  hmm:cvt_vals(Domain, Vals)
 	;
-	 Vals = Domain
+	  Vals = Domain
 	),
 	compile_trace(Trace, Vals, Emissions).
 
@@ -192,22 +194,22 @@ run_inst(prop_same(I,P,Prob), _, SP, Current, _, Trace) :-
 	NP is PI+Prob,
 	matrix_get(Current, [P], P0),
 	(NP > P0 ->
-	 matrix_set(Current, [P], NP),
+	  matrix_set(Current, [P], NP),
-	 matrix_set(Trace, [SP,P], I)
+	  matrix_set(Trace, [SP,P], I)
 	;
-	 true
+	  true
 	).
 run_inst(prop_next(I,P,Prob), _, SP, Current, Next, Trace) :-
 	matrix_get(Current, [I], PI),
 	NP is PI+Prob,
 	matrix_get(Next, [P], P0),
 	(NP > P0 ->
-	 matrix_set(Next, [P], NP),
+	  matrix_set(Next, [P], NP),
-	 SP1 is SP+1,
+	  SP1 is SP+1,
-	 IN is -I,
+	  IN is -I,
-	 matrix_set(Trace, [SP1,P], IN)
+	  matrix_set(Trace, [SP1,P], IN)
 	;
-	 true
+	  true
 	).
 
 backtrace(Dump, EI, Map, L, Trace) :-
@@ -219,11 +221,11 @@ backtrace(Dump, EI, Map, L, Trace) :-
 trace(0,0,_,_,Trace,Trace) :- !.
 trace(L1,Next,Dump,Map,Trace0,Trace) :-
 	(Next < 0 ->
-	 NL is L1-1,
+	  NL is L1-1,
-	 P is -Next
+	  P is -Next
 	;
-	 NL = L1,
+	  NL = L1,
-	 P = Next
+	  P = Next
 	),
 	once(member(P-AKey,Map)),
 	AKey=..[N|Args],
@@ -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

@@ -1,23 +1,22 @@
 
 :- 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)
-         add_to_vmap/4, % add_to_vmap(+V,-I,+VMap0,VMapF)
+		 get_from_vmap/3, % add_to_vmap(+V,-I,+VMap0)
-         get_from_vmap/3, % add_to_vmap(+V,-I,+VMap0)
+		 vars_to_numbers/4, % vars_to_numbers(+Vs,-Is,+VMap0,VMapF)
-	 vars_to_numbers/4, % vars_to_numbers(+Vs,-Is,+VMap0,VMapF)
+		 lvars_to_numbers/4, % lvars_to_numbers(+LVs,-LIs,+VMap0,VMapF)
-	 lvars_to_numbers/4, % lvars_to_numbers(+LVs,-LIs,+VMap0,VMapF)
+		 vmap_to_list/2
-	vmap_to_list/2
+		]).
-     ]).
 
 :- use_module(library(rbtrees)).
 :- use_module(library(maplist)).
 
 %
-% vmap: map V->I 
+% vmap: map V->I
 % contiguous Vs to contiguous integers
 %
 init_vmap(vmap(0,Empty)) :-
-    rb_new(Empty).
+	rb_new(Empty).
 
 get_from_vmap(V, I, VMap0) :-
 	VMap0 = vmap(_I,Map0),
@@ -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, []).
@@ -25,8 +28,8 @@ read_chars(10,S) --> !,
 read_chars(C,S) -->
 	[AC],
 	{
-	 cvt_c(C,AC),
+	  cvt_c(C,AC),
-	 get0(S,MC)
+	  get0(S,MC)
 	},
 	read_chars(MC, S).
 
@@ -44,4 +47,3 @@ skip_header(_,S) :-
 	skip_header(C,S).
 
 
-	

packages/CLPBN/examples/HMMer/globin.yap

@@ -32,9 +32,9 @@ g_f_cpt(-8455,1.0,0.00284964910984409).
 
 %Null state emission CPT.
 nule_cpt(
-     e(595,-1558,85,338,-294,453,-1158,197,249,902,-1085,-142,-21,-313,45,531,201,384,-1998,-644),
+    e(595,-1558,85,338,-294,453,-1158,197,249,902,-1085,-142,-21,-313,45,531,201,384,-1998,-644),
-     0.05,
+    0.05,
-     e(0.0755236292781413,0.0169810785568618,0.0530343870684108,0.0632001549226403,0.0407818746669505,0.0684441906545919,0.0224066674892351,0.0573156092864189,0.0594191552528466,0.093432734688318,0.023569613397956,0.0453130969133667,0.0492774668469685,0.0402483068810561,0.051584158965068,0.0722465198961763,0.0574747424017338,0.0652477473844479,0.0125173406963917,0.0319968103461077)).
+    e(0.0755236292781413,0.0169810785568618,0.0530343870684108,0.0632001549226403,0.0407818746669505,0.0684441906545919,0.0224066674892351,0.0573156092864189,0.0594191552528466,0.093432734688318,0.023569613397956,0.0453130969133667,0.0492774668469685,0.0402483068810561,0.051584158965068,0.0722465198961763,0.0574747424017338,0.0652477473844479,0.0125173406963917,0.0319968103461077)).
 
 %Reaching first D.
 b_d_cpt(-110,-3765,-110).

packages/CLPBN/examples/HMMer/scan.yap

@@ -14,7 +14,7 @@ stop(S,W,Info) :-
 	gen_program(W, Info).
 stop(_,_,_) :-
 	format(user_error,"Bad HMM~n", []).
-   
+
 parse_model(S,Info) :-
 	get_line(S, Line, Info),
 %	format('~s~n',[Line]),
@@ -45,7 +45,7 @@ match_field(hmmer(_,_,_,Alph,_,_,_,_),_) --> "ALPH", !, % aminos or bases
 match_field(_,_) --> "RF", !, scanner_skip.
 match_field(_,_) --> "CS", !, scanner_skip.
 match_field(hmmer(_,_,_,_,_,_,_,MAP),_) --> "MAP", !,
-        scanner_skip_blanks,
+	scanner_skip_blanks,
 	to_lower(Codes),
 	{ map_code(Codes,MAP) }.
 match_field(_,_) --> "COM", !, scanner_skip.
@@ -76,11 +76,11 @@ match_field(_,_) --> "EVD", !,
 match_field(Info,S) --> "HMM", !, 
 	scanner_skip,
 	{
-	 get_line(S,_,Info),
+	  get_line(S,_,Info),
-	 Info = hmmer(_,_,NOfStates,Alph,_,_,model(BD,NBD,Transitions),MAP),
+	  Info = hmmer(_,_,NOfStates,Alph,_,_,model(BD,NBD,Transitions),MAP),
-	 nof_symbols(Alph,N),
+	  nof_symbols(Alph,N),
-	 scan_model(S,NOfStates,N,BD,NBD,Transitions,MAP,Info),
+	  scan_model(S,NOfStates,N,BD,NBD,Transitions,MAP,Info),
-	 throw(done(Info))
+	  throw(done(Info))
 	}.
 
 scan_model(S,NOfStates,N,BD,NBD,Transitions,MAP,Info) :-
@@ -95,7 +95,7 @@ scan_states(NOfStates, N, Stream, MAP, [t(E,I,S)|Transitions], Info) :-
 	scan_states(NOfStates1, N, Stream, NMAP, Transitions, Info).
 
 scan_state(Stream, E,I,MAP,s(MM,MI,MD,IM,II,DM,DD,BM,ME), N, NMAP, Info) :-
-        get_line(Stream, ELine, Info),
+	get_line(Stream, ELine, Info),
 	get_line(Stream, ILine, Info),
 	get_line(Stream, SLine, Info),
 %	format('~s~n~s~n~s~n',[ELine,ILine,SLine]),
@@ -265,7 +265,7 @@ gen_model(W, model(BD,NBD,States),PsCPT) :-
 	format(W, '~n%Reaching first D.~n',[]),
 	format(W, 'b_d_cpt(~w,~w,~w).~n',[BD,NBD,BDCPT]),
 	gen_states(W, States,1,PsCPT).
-	
+
 gen_states(_, [],_,_).
 gen_states(W, [State|States],StateNo,PsCPT) :-
 	gen_state(W, State,StateNo,PsCPT),
@@ -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

@@ -6,13 +6,12 @@
 :- ensure_loaded(library('clpbn/viterbi')).
 
 :- use_module(fasta,
-	      [fa2atoms/3]).
+		[fa2atoms/3]).
 
 :- use_module(library(lists),
-	      [
+		[nth/3,
-	       nth/3,
+		 append/3
-	       append/3
+		]).
-	      ]).
 
 :- [plan7].
 

packages/CLPBN/examples/School/README

@@ -1,19 +1,15 @@
 
 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
 
-parschema.pfl: the PFL schema
+tables:          CPTs
-
-schema.yap: the CLP(BN) schema
-
-tables: CPTs
 
 =============================================================================
 

packages/CLPBN/examples/School/parlearn.yap

@@ -41,4 +41,4 @@ write_cpts([CPT|CPTs]) :-
 	matrix_to_list(CPT,L),
 	format('CPT=~w~n',[L]),
 	write_cpts(CPTs).
-	
+

packages/CLPBN/examples/School/parschema.pfl

@@ -55,7 +55,7 @@ professor_popularity(P,A) :- pop(P,A).
 course_difficulty(P,A) :- diff(P,A).
 
 student_intelligence(P,A) :- int(P,A).
-	
+
 course_rating(C,X) :- rat(C,X).
 
 registration_grade(R,A) :-

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).
@@ -18428,5 +18427,5 @@ registration(r13919,c221,s4095).
 registration(r13920,c39,s4095).
 
 
- :- [evidence_128].
+:- [evidence_128].
 

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)).
@@ -26,85 +31,80 @@ 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) ;
+		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 ;
+	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,
-/* dont_fit */   0.01, 0.5,  0.77, 0.12, 0.59, 0.7,  0.24, 0.13, 
+/* dont_fit */   0.01, 0.5,  0.77, 0.12, 0.59, 0.7,  0.24, 0.13,
 /* dont_fit */   0.56, 0.57, 0.71, 0.28, 0.77, 0.09, 0.05, 0.08 ]).
 
 witness_table(
@@ -114,20 +114,20 @@ witness_table(
 
 
 runall(G, Wrapper) :-
-    findall(G, Wrapper, L),
+	findall(G, Wrapper, L),
-    execute_all(L).
+	execute_all(L).
 
 
 execute_all([]).
 execute_all(G.L) :-
-    call(G),
+	call(G),
-    execute_all(L).
+	execute_all(L).
 
 
 is_joe_guilty(Guilty) :-
-    witness(nyc, t),
+	witness(nyc, t),
-    runall(X, ev(X)),
+	runall(X, ev(X)),
-    guilty(joe, Guilty).
+	guilty(joe, Guilty).
 
 
 % ?- is_joe_guilty(Guilty).

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] ;
+	[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] ;
+	[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;
@@ -30,7 +29,7 @@ typedef queue<ScheduleInfo, list<ScheduleInfo>> Scheduling;
 class BayesBall
 {
   public:
-    BayesBall (FactorGraph& fg) 
+    BayesBall (FactorGraph& fg)
         : fg_(fg) , dag_(fg.getStructure())
     {
       dag_.clear();
@@ -63,7 +62,7 @@ inline void
 BayesBall::scheduleParents (const BBNode* n, Scheduling& sch) const
 {
   const vector<BBNode*>& ps = n->parents();
-  for (vector<BBNode*>::const_iterator it = ps.begin(); 
+  for (vector<BBNode*>::const_iterator it = ps.begin();
       it != ps.end(); ++it) {
     sch.push (ScheduleInfo (*it, false, true));
   }

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"
@@ -14,7 +12,7 @@ using namespace std;
 class BBNode : public Var
 {
   public:
-    BBNode (Var* v) : Var (v) , visited_(false),
+    BBNode (Var* v) : Var (v), visited_(false),
         markedOnTop_(false), markedOnBottom_(false) { }
 
     const vector<BBNode*>& childs (void) const { return childs_;  }
@@ -30,15 +28,15 @@ class BBNode : public Var
     void addChild (BBNode* c) { childs_.push_back (c); }
 
     bool isVisited (void) const { return visited_; }
- 
+
     void setAsVisited (void) { visited_ = true; }
 
     bool isMarkedOnTop (void) const { return markedOnTop_; }
- 
+
     void markOnTop (void) { markedOnTop_ = true; }
 
     bool isMarkedOnBottom (void) const { return markedOnBottom_; }
- 
+
     void markOnBottom (void) { markedOnBottom_ = true; }
 
     void clear (void) { visited_ = markedOnTop_ = markedOnBottom_ = false; }
@@ -63,7 +61,7 @@ class BayesBallGraph
     void addEdge (VarId vid1, VarId vid2);
 
     const BBNode* getNode (VarId vid) const;
- 
+
     BBNode* getNode (VarId vid);
 
     bool empty (void) const { return nodes_.empty(); }

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;
@@ -146,7 +147,7 @@ BeliefProp::getFactorJoint (
   if (Globals::logDomain) {
     Util::exp (jointDist);
   }
-  return jointDist; 
+  return jointDist;
 }
 
 
@@ -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]);
         }
@@ -178,14 +179,14 @@ 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 << "Belief propagation converged in " ;
       cout << nIters_ << " iterations" << endl;
     } else {
       cout << "The maximum number of iterations was hit, terminating..." ;
@@ -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;
@@ -459,7 +460,7 @@ void
 BeliefProp::printLinkInformation (void) const
 {
   for (size_t i = 0; i < links_.size(); i++) {
-    BpLink* l = links_[i]; 
+    BpLink* l = links_[i];
     cout << l->toString() << ":" << endl;
     cout << "    curr msg = " ;
     cout << l->message() << endl;

packages/CLPBN/horus/BeliefProp.h

@@ -3,21 +3,29 @@
 
 #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:
     BpLink (FacNode* fn, VarNode* vn)
-    { 
+    {
       fac_ = fn;
       var_ = vn;
       v1_.resize (vn->range(), LogAware::log (1.0 / vn->range()));
@@ -43,10 +51,10 @@ class BpLink
 
     void updateResidual (void)
     {
-      residual_ = LogAware::getMaxNorm (v1_,v2_);
+      residual_ = LogAware::getMaxNorm (v1_, v2_);
     }
 
-    virtual void updateMessage (void) 
+    virtual void updateMessage (void)
     {
       swap (currMsg_, nextMsg_);
     }
@@ -59,7 +67,7 @@ class BpLink
       ss << var_->label();
       return ss.str();
     }
- 
+
   protected:
     FacNode*  fac_;
     VarNode*  var_;
@@ -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);
 };
 
 
@@ -97,23 +110,21 @@ class BeliefProp : public GroundSolver
     virtual Params getPosterioriOf (VarId);
 
     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