add more support for FOVE.

packages/CLPBN/Makefile.in

@@ -16,6 +16,11 @@ YAPLIBDIR=@libdir@/Yap
 #
 SHAREDIR=$(ROOTDIR)/share/Yap
 #
+# where YAP should store documentation
+#
+DOCDIR=$(ROOTDIR)/share/doc/Yap
+EXDIR=$(DOCDIR)/examples/CLPBN
+#
 #
 # You shouldn't need to change what follows.
 #
@@ -35,6 +40,7 @@ CLPBN_EXDIR = $(srcdir)/examples
 
 CLPBN_PROGRAMS= \
 	$(CLPBN_SRCDIR)/aggregates.yap \
+	$(CLPBN_SRCDIR)/bdd.yap \
 	$(CLPBN_SRCDIR)/bnt.yap \
 	$(CLPBN_SRCDIR)/bp.yap \
 	$(CLPBN_SRCDIR)/connected.yap \
@@ -48,6 +54,7 @@ CLPBN_PROGRAMS= \
 	$(CLPBN_SRCDIR)/graphviz.yap \
 	$(CLPBN_SRCDIR)/ground_factors.yap \
 	$(CLPBN_SRCDIR)/hmm.yap \
+	$(CLPBN_SRCDIR)/horus.yap \
 	$(CLPBN_SRCDIR)/jt.yap \
 	$(CLPBN_SRCDIR)/matrix_cpt_utils.yap \
 	$(CLPBN_SRCDIR)/pgrammar.yap \
@@ -72,6 +79,8 @@ CLPBN_SCHOOL_EXAMPLES= \
 	$(CLPBN_EXDIR)/School/parschema.yap \
 	$(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
 
@@ -92,12 +101,13 @@ CLPBN_EXAMPLES= \
 install: $(CLBN_TOP) $(CLBN_PROGRAMS) $(CLPBN_PROGRAMS)
 	mkdir -p $(DESTDIR)$(SHAREDIR)/clpbn
 	mkdir -p $(DESTDIR)$(SHAREDIR)/clpbn/learning
-	mkdir -p $(DESTDIR)$(SHAREDIR)/clpbn/examples/School
+	mkdir -p $(DESTDIR)$(EXDIR)
-	mkdir -p $(DESTDIR)$(SHAREDIR)/clpbn/examples/HMMer
+	mkdir -p $(DESTDIR)$(EXDIR)/School
+	mkdir -p $(DESTDIR)$(EXDIR)/HMMer
 	for h in $(CLPBN_TOP); do $(INSTALL_DATA) $$h $(DESTDIR)$(SHAREDIR); done
 	for h in $(CLPBN_PROGRAMS); do $(INSTALL_DATA) $$h $(DESTDIR)$(SHAREDIR)/clpbn; done
 	for h in $(CLPBN_LEARNING_PROGRAMS); do $(INSTALL_DATA) $$h $(DESTDIR)$(SHAREDIR)/clpbn/learning; done
-	for h in $(CLPBN_EXAMPLES); do $(INSTALL_DATA) $$h $(DESTDIR)$(SHAREDIR)/clpbn/examples; done
+	for h in $(CLPBN_EXAMPLES); do $(INSTALL_DATA) $$h $(DESTDIR)$(EXDIR); done
-	for h in $(CLPBN_SCHOOL_EXAMPLES); do $(INSTALL_DATA) $$h $(DESTDIR)$(SHAREDIR)/clpbn/examples/School; done
+	for h in $(CLPBN_SCHOOL_EXAMPLES); do $(INSTALL_DATA) $$h $(DESTDIR)$(EXDIR)/School; done
-	for h in $(CLPBN_HMMER_EXAMPLES); do $(INSTALL_DATA) $$h $(DESTDIR)$(SHAREDIR)/clpbn/examples/HMMer; done
+	for h in $(CLPBN_HMMER_EXAMPLES); do $(INSTALL_DATA) $$h $(DESTDIR)$(EXDIR)/HMMer; done
 

packages/CLPBN/clpbn.yap

@@ -5,6 +5,7 @@
 		  set_clpbn_flag/2,
 		  clpbn_flag/3,
 		  clpbn_key/2,
+		  clpbn_language/1,
 		  clpbn_init_solver/4,
 		  clpbn_run_solver/3,
 		  clpbn_finalize_solver/1,
@@ -61,6 +62,12 @@
 	       run_jt_solver/3
 	      ]).
 
+:- use_module('clpbn/bdd',
+	      [bdd/3,
+	       init_bdd_solver/4,
+	       run_bdd_solver/3
+	      ]).
+
 :- use_module('clpbn/bnt',
 	      [do_bnt/3,
 	       check_if_bnt_done/1
@@ -140,6 +147,9 @@ clpbn_flag(output,Before,After) :-
 clpbn_flag(solver,Before,After) :-
 	retract(solver(Before)),
 	assert(solver(After)).
+clpbn_flag(language,Before,After) :-
+	retract(clpbn_language(Before)),
+	assert(clpbn_language(After)).
 clpbn_flag(em_solver,Before,After) :-
 	retract(em_solver(Before)),
 	assert(em_solver(After)).
@@ -244,7 +254,8 @@ project_attributes(GVars, AVars0) :-
 project_attributes(_, _).
 
 generate_vars(GVars, _, NewAVars) :-
-	use_parfactors(on), !,
+	use_parfactors(on),
+	clpbn_flag(solver, Solver), Solver \= fove, !,
 	generate_bn(GVars, NewAVars).
 generate_vars(_GVars, AVars, AVars).
 
@@ -289,6 +300,8 @@ 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) :-
 	bp(GVars, AVars, DiffVars).
 write_out(gibbs, GVars, AVars, DiffVars) :-
@@ -382,6 +395,9 @@ bind_clpbn(_, Var, _, _, _, _, []) :-
 bind_clpbn(_, Var, _, _, _, _, []) :-
 	use(jt),
 	check_if_ve_done(Var), !.
+bind_clpbn(_, Var, _, _, _, _, []) :-
+	use(bdd),
+	check_if_bdd_done(Var), !.
 bind_clpbn(T, Var, Key0, _, _, _, []) :-
 	get_atts(Var, [key(Key)]), !,
 	(
@@ -452,6 +468,8 @@ clpbn_init_solver(bp, LVs, Vs0, VarsWithUnboundKeys, State) :-
 	init_bp_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(pcg, LVs, Vs0, VarsWithUnboundKeys, State) :-
 	init_pcg_solver(LVs, Vs0, VarsWithUnboundKeys, State).
 
@@ -478,6 +496,9 @@ clpbn_run_solver(bp, 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(pcg, LVs, LPs, State) :-
 	run_pcg_solver(LVs, LPs, State).
 
@@ -538,4 +559,18 @@ match_probability([p(V0=C)=Prob|_], C, V, Prob) :-
 match_probability([_|Probs], C, V, Prob) :-
 	match_probability(Probs, C, V, Prob).
 
+:- dynamic clpbn_language/1.
+
+pfl_not_clpbn :-
+	clpbn_language(clpbn), !,
+	throw(error(pfl('should be called before clpbn'))).
+pfl_not_clpbn :-
+	assert(clpbn_language(pfl)).
+
+clpbn_not_pfl :-
+	clpbn_language(pfl), !.
+clpbn_not_pfl :-
+	assert(clpbn_language(clpbn)).
+
+:- clpbn_not_pfl.
 

packages/CLPBN/clpbn/bdd.yap

@@ -0,0 +1,352 @@
+
+/************************************************
+
+  BDDs in CLP(BN)
+
+A variable is represented by the N possible cases it can take
+
+V = v(Va, Vb, Vc)
+
+The generic formula is
+
+V <- X, Y 
+
+Va <- P*X1*Y1 + Q*X2*Y2 + ...
+
+
+ 
+**************************************************/
+
+:- module(clpbn_bdd,
+          [bdd/3,
+           set_solver_parameter/2,
+           init_bdd_solver/4,
+           run_bdd_solver/3,
+           finalize_bdd_solver/1,
+	   check_if_bdd_done/1
+          ]).
+
+
+:- use_module(library('clpbn/dists'),
+          [dist/4,
+           get_dist_domain/2,
+           get_dist_domain_size/2,
+           get_dist_params/2
+          ]).
+
+
+:- use_module(library('clpbn/display'),
+         [clpbn_bind_vals/3]).
+
+:- use_module(library('clpbn/aggregates'),
+	      [check_for_agg_vars/2]).
+
+:- use_module(library(atts)).
+
+:- use_module(library(lists)).
+
+:- use_module(library(dgraphs)).
+
+:- use_module(library(bdd)).
+
+:- use_module(library(rbtrees)).
+
+:- attribute id/1.
+
+:- dynamic network_counting/1.
+
+
+check_if_bdd_done(_Var).
+
+bdd([[]],_,_) :- !.
+bdd([QueryVars], AllVars, AllDiffs) :-
+	init_bdd_solver(_, AllVars, _, BayesNet),
+	run_bdd_solver([QueryVars], LPs, BayesNet),
+	finalize_bdd_solver(BayesNet),
+	clpbn_bind_vals([QueryVars], [LPs], AllDiffs).
+
+init_bdd_solver(_, AllVars0, _, bdd(Term, Leaves)) :-
+	check_for_agg_vars(AllVars0, AllVars1),
+	sort_vars(AllVars1, AllVars, Leaves),
+	rb_new(Vars0),
+	rb_new(Pars0),
+	get_vars_info(AllVars, Vars0, _Vars, Pars0, _Pars, Term, []).
+
+sort_vars(AllVars0, AllVars, Leaves) :-
+	dgraph_new(Graph0),
+	build_graph(AllVars0, Graph0, Graph),
+	dgraph_leaves(Graph, Leaves),
+	dgraph_top_sort(Graph, RAllVars),
+	reverse(RAllVars, AllVars).
+
+build_graph([], Graph, Graph).
+build_graph(V.AllVars0, Graph0, Graph) :-
+	clpbn:get_atts(V, [dist(_DistId, Parents)]), !,
+	dgraph_add_vertex(Graph0, V, Graph1), 
+	add_parents(Parents, V, Graph1, GraphI),
+	build_graph(AllVars0, GraphI, Graph).
+build_graph(_V.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), 
+	add_parents(Parents, V, GraphI, GraphF).
+
+
+get_vars_info([], Vs, Vs, Ps, Ps) --> [].
+get_vars_info([V|MoreVs], Vs, VsF, Ps, PsF) -->
+	{ clpbn:get_atts(V, [dist(DistId, Parents)]) }, !,
+	[DIST],
+	{ check_p(DistId, Parms, _ParmVars, Ps, Ps1),
+	  unbound_parms(Parms, ParmVars),
+	  check_v(V, DistId, DIST, Vs, Vs1),
+	  DIST = info(V, Tree, Ev, Values, Formula, ParmVars, Parms),
+	  get_parents(Parents, PVars, Vs1, Vs2),
+	  cross_product(Values, Ev, PVars, ParmVars, Formula0),
+	  get_evidence(V, Tree, Ev, Formula0, Formula)
+%	  (numbervars(Formula,0,_),writeln(formula:Formula), fail ; true)
+        },
+	get_vars_info(MoreVs, Vs2, VsF, Ps1, PsF).
+get_vars_info([_|MoreVs], Vs0, VsF, Ps0, PsF, VarsInfo) :-
+	get_vars_info(MoreVs, Vs0, VsF, Ps0, PsF, VarsInfo).
+
+%
+% look for parameters in the rb-tree, or add a new.
+% distid is the key
+%
+check_p(DistId, Parms, ParmVars, Ps, Ps) :-
+	rb_lookup(DistId, theta(Parms, ParmVars), Ps), !.
+check_p(DistId, Parms, ParmVars, Ps, PsF) :-
+	get_dist_params(DistId, Parms0),
+	length(Parms0, L0),
+	get_dist_domain_size(DistId, Size),
+	L1 is L0 div Size,
+	L is L0-L1,
+	initial_maxes(L1, Multipliers),
+	copy(L, Multipliers, NextMults, NextMults, Parms0, Parms, ParmVars),
+	rb_insert(Ps, DistId, theta(DistId, Parms, ParmVars), PsF).
+
+%
+% we are using switches by two
+%
+initial_maxes(0, []) :- !.
+initial_maxes(Size, [1.0|Multipliers]) :- !,
+	Size1 is Size-1,
+	initial_maxes(Size1, Multipliers).
+
+copy(0, [], [], _, _Parms0, [], []) :- !.
+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, _.ParmVars) :-
+	N1 is N-1,
+	NEl is El/D,
+	ND is D-El,
+	copy(N1, Ds, NDs, New, Parms0, Parms, ParmVars).
+
+unbound_parms([], []).
+unbound_parms(_.Parms, _.ParmVars) :-
+	  unbound_parms(Parms, ParmVars).
+
+check_v(V, _, INFO, Vs, Vs) :-
+	rb_lookup(V, INFO, Vs), !.
+check_v(V, DistId, INFO, Vs0, Vs) :-
+	get_dist_domain_size(DistId, Size),
+	length(Values, Size),
+	length(Ev, Size),
+	INFO = info(V, _Tree, Ev, Values, _Formula, _, _),
+	rb_insert(Vs0, V, INFO, Vs).
+
+get_parents([], [], Vs, Vs).
+get_parents(V.Parents, Values.PVars, Vs0, Vs) :-
+	clpbn:get_atts(V, [dist(DistId, _)]),
+	check_v(V, DistId, INFO, Vs0, Vs1),
+	INFO = info(V, _Parent, _Ev, Values, _, _, _),
+	get_parents(Parents, PVars, Vs1, Vs).
+
+%
+% construct the formula, this is the key...
+%
+cross_product(Values, Ev, PVars, ParmVars, Formulas) :-
+	arrangements(PVars, Arranges),
+	apply_parents_first(Values, Ev, ParmCombos, ParmCombos, Arranges, Formulas, ParmVars).
+
+%
+% if we have the parent variables with two values, we get
+% [[XP,YP],[XP,YN],[XN,YP],[XN,YN]]
+%
+arrangements([], [[]]).
+arrangements([L1|Ls],O) :-
+	arrangements(Ls, LN),
+	expand(L1, LN, O, []).
+
+expand([], _LN) --> [].
+expand([H|L1], LN) -->
+	concatenate_all(H, LN),
+	expand(L1, LN).
+
+concatenate_all(_H, []) --> [].
+concatenate_all(H, L.LN) -->
+	[[H|L]],
+	concatenate_all(H, LN).
+
+%
+% core of algorithm
+%
+% Values -> Output Vars for BDD
+% Es -> Evidence variables
+% Previous -> top of difference list with parameters used so far
+% P0 -> end of difference list with parameters used so far
+% Pvars -> Parents
+% Eqs -> Output Equations
+% Pars -> Output Theta Parameters
+%
+apply_parents_first([Value], [E], Previous, [], PVars, [Value=Disj*E], Parameters) :- !,
+	apply_last_parent(PVars, Previous, Disj),
+	flatten(Previous, Parameters).
+apply_parents_first([Value|Values], [E|Ev], Previous, P0, PVars, (Value=Disj*E).Formulas, Parameters) :-
+	P0 = [TheseParents|End],
+	apply_first_parent(PVars, Disj, TheseParents),
+	apply_parents_second(Values, Ev, Previous, End, PVars, Formulas, Parameters).
+
+apply_parents_second([Value], [E], Previous, [], PVars, [Value=Disj*E], Parameters) :- !,
+	apply_last_parent(PVars, Previous, Disj),
+	flatten(Previous, Parameters).
+apply_parents_second([Value|Values], [E|Ev], Previous, P0, PVars, (Value=Disj*E).Formulas, Parameters) :-
+	apply_middle_parent(PVars, Previous, Disj, TheseParents),
+	% this must be done after applying middle parents because of the var
+	% test.
+	P0 = [TheseParents|End],
+	apply_parents_second(Values, Ev, Previous, End, PVars, Formulas, Parameters).
+
+apply_first_parent([Parents], Conj, [Theta]) :- !,
+	parents_to_conj(Parents,Theta,Conj).
+apply_first_parent(Parents.PVars, Disj+Conj, Theta.TheseParents) :-
+	parents_to_conj(Parents,Theta,Conj),
+	apply_first_parent(PVars, Disj, TheseParents).
+
+apply_last_parent([Parents], Other, Conj) :- !,
+	parents_to_conj(Parents,(Theta),Conj),
+	skim_for_theta(Other, Theta, _, _).
+apply_last_parent(Parents.PVars, Other, Conj+Disj) :-
+	parents_to_conj(Parents,(Theta),Conj),
+	skim_for_theta(Other, Theta, Remaining, _),
+	apply_last_parent(PVars, Remaining, Disj).
+
+apply_middle_parent([Parents], Other, Conj, [ThetaPar]) :- !,
+	parents_to_conj(Parents,(Theta),Conj),
+	skim_for_theta(Other, Theta, _, ThetaPar).
+apply_middle_parent(Parents.PVars, Other, Conj+Disj, ThetaPar.TheseParents) :-
+	parents_to_conj(Parents,(Theta),Conj),
+	skim_for_theta(Other, Theta, Remaining, ThetaPar),
+	apply_middle_parent(PVars, Remaining, Disj, TheseParents).
+
+parents_to_conj([],Theta,Theta).
+parents_to_conj(P.Parents,Theta,Conj*P) :-
+	parents_to_conj(Parents,Theta,Conj).
+
+%
+% first case we haven't reached the end of the list so we need
+% to create a new parameter variable
+%
+skim_for_theta([[P|Other]|V], New*not(P), [Other|_], New) :- var(V), !.
+%
+% last theta, it is just negation of the other ones
+%
+skim_for_theta([[P|Other]], not(P), [Other], _) :- !.
+%
+% recursive case, build-up
+%
+skim_for_theta([[P|Other]|More], Ps*not(P), [Other|Left], New ) :-
+	skim_for_theta(More, Ps, Left, New ).
+
+get_evidence(V, Tree, Values, F0, F) :-
+	clpbn:get_atts(V, [evidence(Pos)]), !,
+	zero_pos(0, Pos, Tree, Values, F0, F).
+%% no evidence !!!
+get_evidence(_V, Tree, _Values, F0, (Tree=Outs).F0) :-
+	get_outs(F0, Outs).
+
+zero_pos(_, _Pos, _Tree, [], [], []) :- !.
+zero_pos(Pos, Pos, Tree, 1.Values, [Tree=Vs|F], [Tree=Vs]) :- 
+	I is Pos+1,
+	zero_pos(I, Pos, Tree, Values, F, []).
+zero_pos(I0, Pos, Tree, 0.Values, _.F, NF) :- 
+	I is I0+1,
+	zero_pos(I, Pos, Tree, Values, F, NF).
+
+get_outs([V=_F], V) :- !.
+get_outs((V=_F).Outs, (V + F0)) :-
+	get_outs(Outs, F0).
+
+run_bdd_solver([[V]], LPs, bdd(Term, Leaves)) :-
+	build_out_node(Term, Leaves, Node),
+	findall(Prob, get_prob(Term, Node, V, Prob),TermProbs),
+	sumlist(TermProbs, Sum),
+	normalise(TermProbs, Sum, LPs).
+
+build_out_node(Term, [Leaf], Top) :- !,
+	find_exp(Leaf, Term, Top).
+build_out_node(Term, [Leaf|Leaves], Tops*Top) :-
+	find_exp(Leaf, Term, Top),
+	build_out_node(Term, Leaves, Tops).
+
+find_exp(Leaf, info(V, Top, _Ev, _Values, _Formula, _ParmVars, _Parms)._, Top) :-
+	V == Leaf, !.
+find_exp(Leaf, _.Term, Top) :-
+	find_exp(Leaf, Term, Top).
+
+get_prob(Term, Top, V, SP) :-
+	bind_all(Term, V, AllParms, AllParmValues),
+	term_variables(AllParms, NVs),
+	build_bdd(Top, NVs, AllParms, AllParmValues, Bdd),
+	bdd_to_probability_sum_product(Bdd, SP),
+	bdd_close(Bdd).
+
+build_bdd(X, NVs, VTheta, Theta, Bdd) :-
+	bdd_new(X, NVs, Bdd),
+	bdd_tree(Bdd, bdd(_F,Tree,_Vs)), length(Tree, Len),
+	VTheta = Theta,
+	writeln(length=Len).
+        
+bind_all([], _V, [], []).
+bind_all(info(V, _Tree, Ev, _Values, Formula, ParmVars, Parms).Term, V0, ParmVars.AllParms, Parms.AllTheta) :-
+	V0 == V, !,
+	set_to_one_zeros(Ev),
+	bind_formula(Formula),
+	bind_all(Term, V0, AllParms, AllTheta).
+bind_all(info(_V, _Tree, Ev, _Values, Formula, ParmVars, Parms).Term, V0, ParmVars.AllParms, Parms.AllTheta) :-
+	set_to_ones(Ev),!,
+	bind_formula(Formula),
+	bind_all(Term, V0, AllParms, AllTheta).
+% evidence: no need to add any stuff.
+bind_all(info(_V, _Tree, _Ev, _Values, Formula, ParmVars, Parms).Term, V0, ParmVars.AllParms, Parms.AllTheta) :-
+	bind_formula(Formula),
+	bind_all(Term, V0, AllParms, AllTheta).
+
+
+bind_formula([]).
+bind_formula((A=A).Formula) :-
+	bind_formula(Formula).
+
+
+set_to_one_zeros([1|Values]) :-
+	set_to_zeros(Values).
+set_to_one_zeros([0|Values]) :-
+	set_to_one_zeros(Values).
+
+set_to_zeros([]).
+set_to_zeros(0.Values) :-
+	set_to_zeros(Values).
+
+set_to_ones([]).
+set_to_ones(1.Values) :-
+	set_to_ones(Values).
+
+normalise([], _Sum, []).
+normalise(P.TermProbs, Sum, NP.LPs) :-
+	NP is P/Sum,
+	normalise(TermProbs, Sum, LPs).
+
+finalize_bdd_solver(_).
+

packages/CLPBN/clpbn/bp.yap

@@ -35,7 +35,7 @@
 :- use_module(library(lists)).
 :- use_module(library(charsio)).
 
-:- load_foreign_files(['horus'], [], init_predicates).
+:- use_module(horus).
 
 :- attribute id/1.
 

packages/CLPBN/clpbn/discrete_utils.yap

@@ -3,7 +3,7 @@
 			   reorder_CPT/5,
 			   get_dist_size/2]).
 
-:- use_module(dists, [get_dist_domain_size/2,
+:- use_module(library(clpbn/dists), [get_dist_domain_size/2,
 		      get_dist_domain/2]).
 %
 % remove columns from a table

packages/CLPBN/clpbn/display.yap

@@ -6,7 +6,7 @@
 	       member/2
 	      ]).
 
-:- use_module(dists, [get_dist_domain/2]).
+:- use_module(library(clpbn/dists), [get_dist_domain/2]).
 
 :- attribute posterior/4.
 
@@ -60,9 +60,13 @@ get_all_combs(Vs, Vals) :-
 
 get_all_doms([], []).
 get_all_doms([V|Vs], [D|Ds]) :-
-	clpbn:get_atts(V, [dist(Id,_)]),
+	clpbn:get_atts(V, [dist(Id,_)]), !,
 	get_dist_domain(Id,D),
 	get_all_doms(Vs, Ds).
+get_all_doms([V|Vs], [D|Ds]) :-
+	clpbn:get_atts(V, [key(K)]),
+	pfl:skolem(K,D),
+	get_all_doms(Vs, Ds).
 
 ms([], []).
 ms([H|L], [El|Els]) :-

packages/CLPBN/clpbn/dists.yap

@@ -1,4 +1,4 @@
-%
+s%
 % routines to manipulate distributions
 %
 
@@ -224,6 +224,10 @@ get_dsizes([P|Parents], [Sz|Sizes], Sizes0) :-
 get_dist_params(Id, Parms) :-
 	recorded(clpbn_dist_db, db(Id, _, Parms, _, _, _, _), _).
 
+get_dist_domain_size(DistId, DSize) :-
+	clpbn:clpbn_language(pfl), !,
+	pfl:get_pfl_parameters(DistId, Dist),
+	length(Dist, DSize).
 get_dist_domain_size(avg(D,_), DSize) :- !,
 	length(D, DSize).
 get_dist_domain_size(ip(D,_,_), DSize) :- !,
@@ -234,6 +238,9 @@ get_dist_domain_size(Id, DSize) :-
 get_dist_domain(Id, Domain) :-
 	recorded(clpbn_dist_db, db(Id, _, _, _, Domain, _, _), _).
 
+get_dist_key(Id, Key) :-
+	clpbn:clpbn_language(pfl), !,
+	pfl:get_first_pvariable(Id, Key).
 get_dist_key(Id, Key) :-
 	recorded(clpbn_dist_db, db(Id, Key, _, _, _, _, _), _).
 
@@ -264,12 +271,20 @@ get_evidence_from_position(El, Id, Pos) :-
 
 dist_to_term(_Id,_Term).
 
+empty_dist(Dist, TAB) :-
+	clpbn:clpbn_language(pfl), !,
+	pfl:get_pfl_factor_sizes(Dist, DSizes),
+	matrix_new(floats, DSizes, TAB).
 empty_dist(Dist, TAB) :-
 	recorded(clpbn_dist_psizes,db(Dist, DSizes),_), !,
 	matrix_new(floats, DSizes, TAB).
 empty_dist(Dist, TAB) :-
 	throw(error(domain_error(no_distribution,Dist),empty_dist(Dist,TAB))).
 
+dist_new_table(DistId, NewMat) :-
+	clpbn:clpbn_language(pfl), !,
+	matrix_to_list(NewMat, List),
+	pfl:set_pfl_parameters(DistId, List).
 dist_new_table(Id, NewMat) :-
 	matrix_to_list(NewMat, List),
 	recorded(clpbn_dist_db, db(Id, Key, _, A, B, C, D), R),
@@ -297,7 +312,13 @@ randomise_all_dists :-
 randomise_all_dists.
 
 randomise_dist(Dist) :-
-	recorded(clpbn_dist_psizes, db(Dist,DSizes), _),
+	(
+	    clpbn:clpbn_language(pfl)
+	->
+	    pfl:get_pfl_factor_sizes(Dist, DSizes)
+	;
+	    recorded(clpbn_dist_psizes, db(Dist,DSizes), _)
+	),
 	random_CPT(DSizes, NewCPT),
 	dist_new_table(Dist, NewCPT).
 
@@ -307,7 +328,13 @@ uniformise_all_dists :-
 uniformise_all_dists.
 
 uniformise_dist(Dist) :-
-	recorded(clpbn_dist_psizes, db(Dist,DSizes), _),
+	(
+	    clpbn:clpbn_language(pfl)
+	->
+	    pfl:get_pfl_factor_sizes(Dist, DSizes)
+	;
+	    recorded(clpbn_dist_psizes, db(Dist,DSizes), _)
+	),
 	uniform_CPT(DSizes, NewCPT),
 	dist_new_table(Dist, NewCPT).
 

packages/CLPBN/clpbn/ground_factors.yap

@@ -62,7 +62,7 @@ run_through_factors(V.Vars, H0, HF) -->
 % aggregates are special.
 construct_clpbn_node(K, V, HI) -->
 	% and get the corresponding factor
-	{ factor(Id, [K|Ks], _, avg, Constraints) }, !,
+	{ factor(_Id, [K|Ks], _, avg, Constraints) }, !,
 	{
           skolem(K, Domain),
 	  dist(avg(Domain, Parents), DistId, K, Parents),

packages/CLPBN/clpbn/horus.yap

@@ -0,0 +1,16 @@
+
+:- module(clpbn_horus,
+	[
+    create_lifted_network/3,
+    create_ground_network/2,
+    set_parfactor_graph_params/2,
+    set_bayes_net_params/2,
+    run_lifted_solver/3,
+    run_other_solvers/3,
+    set_extra_vars_info/2,
+    set_horus_flag/2,
+    free_bayesian_network/1,
+    free_parfactor_graph/1
+    ]).
+
+:- load_foreign_files(['horus'], [], init_predicates).

packages/CLPBN/clpbn/matrix_cpt_utils.yap

@@ -20,10 +20,14 @@
 	   uniform_CPT_as_list/2,
 	   normalise_CPT_on_lines/3]).
 
-:- use_module(dists,
+:- writeln(h0).
+
+:- use_module(library(dists),
 	      [get_dist_domain_size/2,
 	       get_dist_domain/2]).
 
+:- writeln(h1).
+
 :- use_module(library(matrix),
 	      [matrix_new/4,
 	       matrix_new_set/4,

packages/CLPBN/examples/School/README

@@ -5,9 +5,14 @@ There are four main files:
 
 school_128.yap: a school with 128 professors, 256 courses and 4096 students.
 school_64.yap: medium size school
-school_32.yap: small school
+school_32.yap: small school (pfl)
+
+sch32.yap: small school (clp(bn))
+
+parschema.yap: the CLP(BN) schema
+
+schema.yap: the PFL schema
 
-schema.yap: the schema
 tables: CPTs
 
 

packages/CLPBN/learning/example/school_params.yap

@@ -4,7 +4,7 @@
 
 :- [pos:train].
 
-:- ['../../examples/School/school_32'].
+:- ['../../examples/School/sch32'].
 
 :- use_module(library(clpbn/learning/em)).
 

packages/CLPBN/pfl.yap

@@ -3,26 +3,42 @@
 %
 %
 
-:- module(clpbn_parfactors, [
+:- module(pfl, [
           factor/5,
 	  skolem/2,
+	  get_pfl_parameters/2, % given id return par factor parameter
+	  new_pfl_parameters/2, % given id  set new parameters
+	  get_first_pvariable/2, % given id get firt pvar (useful in bayesian)
+	  get_factor_pvariable/2, % given id get any pvar
 	  op(550,yfx,::),
 	  op(1150,fx,bayes),
+	  op(1150,fx,markov),
 	  op(1150,fx,parfactor)]).
 
 :- use_module(library(lists),
 	[nth0/3,
-	 append/3]).
+	 append/3,
+	 member/2]).
 
 :- dynamic factor/5, skolem_in/2, skolem/2, preprocess/3, evidence/2, id/1.
 
 :- reexport(library(clpbn),
-	[clpbn_flag/3,
+	[clpbn_flag/2,
-	 set_clpbn_flag/2]).
+	 clpbn_flag/2 as pfl_flag,
+	 set_clpbn_flag/2,
+	 set_clpbn_flag/2 as set_pfl_flag]).
 
-:- set_clpbn_flag(use_factors,on).
+:- set_pfl_flag(use_factors,on).
 
-user:term_expansion( bayes((Formula ; Phi ; Constraints)), clpbn_parfactors:factor(Id,FList,FV,Phi,Constraints)) :-
+:- pfl_not_clpbn.
+
+user:term_expansion( bayes((Formula ; Phi ; Constraints)), pfl:factor(Id,FList,FV,Phi,Constraints)) :-
+	!,
+	term_variables(Formula, FreeVars),
+	FV =.. [fv|FreeVars],
+	new_id(Id),
+	process_args(Formula, Id, 0, _, FList, []).
+user:term_expansion( markov((Formula ; Phi ; Constraints)), pfl:factor(Id,FList,FV,Phi,Constraints)) :-
 	!,
 	term_variables(Formula, FreeVars),
 	FV =.. [fv|FreeVars],
@@ -32,7 +48,7 @@ user:term_expansion( Goal, [] ) :-
 	preprocess(Goal, Sk,Var), !,
 	(ground(Goal) -> true ; throw(error('non ground evidence',Goal))),
 %	prolog_load_context(module, M),
-	assert(evidence(Sk,Var)).
+	assert(pfl:evidence(Sk,Var)).
 
 id(0).
 
@@ -78,7 +94,10 @@ interface_predicate(Sk) :-
 	ESk =.. ESKAs,
 	assert(preprocess(ESk, Sk, Var)),
 	assert_static((user:ESk :-
-	     var(Var) -> insert_atts(Var,Sk) ; add_evidence(Sk,Var) )
+	     evidence(Sk,Ev) -> Ev = Var;
+	     var(Var) -> insert_atts(Var,Sk) ;
+	     add_evidence(Sk,Var)
+	  )
 	).
 
 insert_atts(Var,Sk) :-
@@ -90,3 +109,36 @@ add_evidence(Sk,Var) :-
 	clpbn:put_atts(_V,[key(Sk),evidence(E)]).
 
 
+get_pfl_parameters(Id,Out) :-
+	factor(Id,_FList,_FV,Phi,_Constraints),
+	writeln(factor(Id,_FList,_FV,_Phi,_Constraints)),
+	( is_list(Phi) -> Out = Phi ; call(user:Phi, Out) ).
+
+
+new_pfl_parameters(Id, NewPhi) :-
+	retract(factor(Id,FList,FV,_Phi,Constraints)),
+	assert(factor(Id,FList,FV,NewPhi,Constraints)),
+	fail.
+new_pfl_parameters(_Id, _NewPhi).
+
+get_pfl_factor_sizes(Id, DSizes) :-
+	factor(Id, FList, _FV, _Phi, _Constraints),
+	get_sizes(FList, DSizes).
+
+get_sizes([], []).
+get_sizes(Key.FList, Sz.DSizes) :-
+	skolem(Key, Domain),
+	length(Domain, Sz),
+	get_sizes(FList, DSizes).
+	
+% only makes sense for bayesian networks
+get_first_pvariable(Id,Var) :-
+	factor(Id,Var._FList,_FV,_Phi,_Constraints).
+
+% only makes sense for bayesian networks
+get_factor_pvariable(Id,Var) :-
+	factor(Id,FList,_FV,_Phi,_Constraints),
+	member(Var, FList).
+
+
+