CLP(BN) related fixes

git-svn-id: https://yap.svn.sf.net/svnroot/yap/trunk@1914 b08c6af1-5177-4d33-ba66-4b1c6b8b522a

CLPBN/Makefile.in

@@ -33,6 +33,7 @@ CLPBN_PROGRAMS= \
 	$(CLPBN_SRCDIR)/aggregates.yap \
 	$(CLPBN_SRCDIR)/bnt.yap \
 	$(CLPBN_SRCDIR)/discrete_utils.yap \
+	$(CLPBN_SRCDIR)/display.yap \
 	$(CLPBN_SRCDIR)/evidence.yap \
 	$(CLPBN_SRCDIR)/gibbs.yap \
 	$(CLPBN_SRCDIR)/graphs.yap \
@@ -53,6 +54,7 @@ CLPBN_EXAMPLES= \
 	$(CLPBN_EXDIR)/School/school_32.yap \
 	$(CLPBN_EXDIR)/School/school_64.yap \
 	$(CLPBN_EXDIR)/School/tables.yap \
+	$(CLPBN_EXDIR)/sprinkler.yap
 
 
 install: $(CLBN_TOP) $(CLBN_PROGRAMS) $(CLPBN_PROGRAMS)

CLPBN/clpbn.yap

@@ -25,14 +25,14 @@
 :- attribute key/1, dist/3, evidence/1, starter/0.
 
 
-:- use_module('clpbn/bnt', [dump_as_bnt/2,
-		    check_if_bnt_done/1
-		    ]).
-
 :- use_module('clpbn/vel', [vel/3,
 		    check_if_vel_done/1
 		    ]).
 
+:- use_module('clpbn/bnt', [do_bnt/3,
+		    check_if_bnt_done/1
+		    ]).
+
 :- use_module('clpbn/gibbs', [gibbs/3,
 		    check_if_gibbs_done/1
 		    ]).
@@ -70,6 +70,12 @@ clpbn_flag(output,Before,After) :-
 clpbn_flag(solver,Before,After) :-
 	retract(solver(Before)),
 	assert(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)).
 
 {Var = Key with Dist} :-
 	put_atts(El,[key(Key),dist(Domain,Table,Parents)]),
@@ -143,8 +149,8 @@ write_out(vel, GVars, AVars, DiffVars) :-
 	vel(GVars, AVars, DiffVars).
 write_out(gibbs, GVars, AVars, DiffVars) :-
 	gibbs(GVars, AVars, DiffVars).
-write_out(bnt, GVars, AVars, _) :-
+write_out(bnt, GVars, AVars, DiffVars) :-
-	dump_as_bnt(GVars, AVars).
+	do_bnt(GVars, AVars, DiffVars).
 write_out(graphs, _, AVars, _) :-
 	clpbn2graph(AVars).
 

CLPBN/clpbn/bnt.yap

@@ -1,494 +1,225 @@
 
-:- module(bnt, [dump_as_bnt/2,
+:- module(bnt, [do_bnt/3,
 		check_if_bnt_done/1]).
 
-:- use_module(library(matlab), [start_matlab/2,
+:- use_module(library('clpbn/display'), [
-				close_matlab/1,
+	clpbn_bind_vals/3]).
-				eval_string/2
+
+:- use_module(library(matlab), [start_matlab/1,
+				close_matlab/0,
+				matlab_on/0,
+				matlab_eval_string/1,
+				matlab_eval_string/2,
+				matlab_matrix/4,
+				matlab_sequence/3,
+				matlab_initialized_cells/4,
+				matlab_get_variable/2,
+				matlab_call/2
 			      ]).
 
-:- attribute topord/1, map/1.
+:- use_module(library(dgraphs), [dgraph_new/1,
+				dgraph_add_vertices/3,
+				dgraph_add_edges/3,
+				dgraph_top_sort/2,
+				dgraph_vertices/2,
+				dgraph_edges/2
+			      ]).
+
+:- yap_flag(write_strings,on).
+
+% syntactic sugar for matlab_call.
+:- op(800,yfx,<--).
+
+G <-- Y :-
+	matlab_call(Y,G).
+
+:- attribute bnt_id/1.
+
+:- dynamic bnt/1.
+
+:- dynamic bnt_solver/1, bnt_path/1.
+
+% belprop
+bnt_solver(jtree).
+% likelihood_weighting
+
+bnt_path('/u/vitor/Yap/CLPBN/FullBNT-1.0.3/BNT').
+
+
+
+/*****************************************
+
+BNT uses:
+  bnet
+  dag
+  discrete_nodes: which nodes are discrete (all by now),
+  node_sizes
+  engine
+  evidence
+  marg
+
+*****************************************/
+
 
 check_if_bnt_done(Var) :-
 	get_atts(Var, [map(_)]).
 
-dump_as_bnt(GVars, [_|_]) :-
+do_bnt([], _, _) :- !.
-	start_matlab(´-nojvm -nosplash',MatEnv),
+do_bnt(QueryVars, AllVars, AllDiffs)  :-
-	get_value(clpbn_key, Key),
+	init_matlab,
-	eval_string(MatEnv, 'cd /u/vitor/sw/BNT'),
+	extract_graph(AllVars, Graph),
-	eval_string(MatEnv, 'add_BNT_to_path'),
+	dgraph_top_sort(Graph, SortedVertices),
-	extract_graph(GVars, Graph),
+	number_graph(SortedVertices, NumberedVertices, 0, Size),
-	dgraph_top_sort(Graph, SortedGraph),
+	init_bnet(SortedVertices, NumberedVertices, Size),
-	number_graph(SortedGraph),
+	set_inference,
-	zeros(MatEnv, GLength, GLength, dag),
+	add_evidence(SortedVertices, Size, NumberedVertices),
-	build_dag(SortedGraph),
+	marginalize(QueryVars, Ps),
-	dump_cpts(SortedGraph).
+	clpbn_bind_vals(QueryVars, Ps, AllDiffs).
 
+% make sure MATLAB works.
+init_matlab :-
+	bnt(on), !.
+init_matlab :-
+	start_matlab,
+	bnt_path(Path),
+	atom_concat('cd ', Path, Command),
+	matlab_eval_string(Command),
+	matlab_eval_string('add_BNT_to_path',_),
+	assert(bnt(on)).
 
+start_matlab :-
+	matlab_on, !.
+start_matlab :-
+	start_matlab('matlab -nojvm -nosplash').
 
+extract_graph(AllVars, Graph) :-
+	dgraph_new(Graph0),
+	dgraph_add_vertices(AllVars, Graph0, Graph1),
+	get_edges(AllVars,Edges),
+	dgraph_add_edges(Edges, Graph1, Graph).
 	
-%	send_command(CommandStream, Answer, 'cd /home/vitor/Yap/CLPBN/BNT;~n', []),
+get_edges([],[]).
-	send_command(CommandStream, Answer, 'add_BNT_to_path;~n', []),
+get_edges([V|AllVars],Edges) :-
-	send_command(CommandStream, Answer, '~w = ~w;~n', ['$VAR'(Key), Key]),
+	clpbn:get_atts(V, [dist(_,_,Parents)]),
-	send_command(CommandStream, Answer, 'dag = zeros(~w,~w);~n', ['$VAR'(Key), '$VAR'(Key)]),
+	add_parent_child(Parents,V,Edges,Edges0),
-	Key1 is Key-1,
+	get_edges(AllVars,Edges0).
-        dump_variable_indices(Key1, Vs, Heap, CommandStream, Answer),
-	write_deps(Heap, CommandStream, Answer),
-        find_observables(GVars, Observables),
-	mknet(Vs, Key, Observables, CommandStream, Answer),
-	dump_cpds(Vs, CommandStream, Answer),
-	inf_engine(Vs, Key, CommandStream, Answer),
-	output_answer(Observables, CommandStream, Answer),
-	close(CommandStream),
-	close(Answer).
 
+add_parent_child([],_,Edges,Edges).
+add_parent_child([P|Parents],V,[P-V|Edges],Edges0) :-
+	add_parent_child(Parents,V,Edges,Edges0).
 
-dump_variable_indices(I, LF, HF, CommandStream, Answer) :-
+number_graph([], [], I, I).
-	all_vars_with_deps(I, LDeps, LNoDeps),
+number_graph([V|SortedGraph], [I|Is], I0, IF) :-
-	sort(LNoDeps, S0),
-	empty_heap(H0),
-	topsort(LDeps, S0, LNoDeps, LF, H0, HF),
-	reverse(LF, Vs),
-	dump_vlist(Vs, 0, CommandStream, Answer).
-
-all_vars_with_deps(0, LDeps, LNoDeps) :- !,
-	var_with_deps(0, LDeps, [], LNoDeps, []).
-all_vars_with_deps(I, LDeps, LNoDeps) :-
-	var_with_deps(I, LDeps, LDeps0, LNoDeps, LNoDeps0),
-	I1 is I-1,
-	all_vars_with_deps(I1, LDeps0, LNoDeps0).
-
-var_with_deps(Indx, Deps, Deps0, NoDeps, NoDeps0) :-
-	array_element(clpbn, Indx, V),
-	clpbn:get_atts(V, [dist(_,_,VDeps)]), !,
-	(VDeps = [] ->
-	    NoDeps = [V|NoDeps0], Deps = Deps0 ;
-	    sort(VDeps,SVDeps),
-	    Deps = [[V|SVDeps]|Deps0], NoDeps = NoDeps0 ).
-	
-%
-% this is a silly quadratic algorithm for topological sorting.
-% it will have to do for now.
-%
-% to speedup things a bit I keep a sorted and unsorted version
-% of the variables sorted so far.
-%
-topsort([], _, S, S, H, H) :- !.
-topsort(LDeps, Sorted0, S0, SF, H, HF) :- !,
-	delete_all(LDeps, Sorted0, S0, LI, SI, Sorted, H, HI),
-	topsort(LI, Sorted, SI, SF, HI, HF).
-
-delete_all([], SS, S, [], S, SS, H, H).
-delete_all([[V|VDeps]|LDeps], SS, S, LF, SF, SSF, H0, HF) :-
-	ord_subtract(VDeps, SS, VDepsI),
-	ord_subtract(VDeps, VDepsI, Parents),
-	add_parents_to_heap(Parents, V, H0, HI),
-	( VDepsI = [] ->
-	    LF = LI, ord_add_element(SS,V,SSI), SI = [V|S];
-	    LF = [[V|VDepsI]|LI], SI = S, SSI = SS),
-	delete_all(LDeps, SSI, SI, LI, SF, SSF, HI, HF).
-
-add_parents_to_heap([], _, H, H).
-add_parents_to_heap([P|Parents], V, H0, HF) :-
-	add_to_heap(H0, P, V, HI), % if I put a HF here I get the debugger to loop
-	add_parents_to_heap(Parents, V, HI, HF).
-
-dump_vlist([], _, _, _).
-dump_vlist([V|Vs], I, CommandStream, Answer) :-
-	I1 is I+1,
-	clpbn:get_atts(V,[key(_)]),
-	send_command(CommandStream, Answer, '~w = ~w;~n', ['$VAR'(I), I1]),
-	put_atts(V, [topord(I)]),
-	I1 is I+1,
-	dump_vlist(Vs, I1, CommandStream, Answer).
-
-write_deps(H, CommandStream, Answer) :-
-	heap_to_list(H,L),
-	write_list_deps(L, CommandStream, Answer).
-
-write_list_deps([], _, _).
-write_list_deps([V-A|L], CommandStream, Answer) :-
-	fetch_same_key(L, V, SK, LN),
-	write_dep_relation([A|SK], V, CommandStream, Answer),
-	write_list_deps(LN, CommandStream, Answer).
-
-fetch_same_key([], _, [], []) :- !.
-fetch_same_key([V1-A|L], V, [A|SK], LN) :- V1 == V, !,
-	fetch_same_key(L, V, SK, LN).
-fetch_same_key(L, _, [], L).
-
-write_dep_relation([], _, _) :- !.
-write_dep_relation([V], D, CommandStream, Answer) :- !,
-	get_atts(V, [topord(IV)]),
-	get_atts(D, [topord(ID)]),
-	send_command(CommandStream, Answer, "dag(~w,~w) = 1;~n", ['$VAR'(ID),'$VAR'(IV)]).
-write_dep_relation(Vs, D, CommandStream, Answer) :-
-	get_atts(D, [topord(ID)]),
-	my_format(CommandStream, "dag(~w,[",['$VAR'(ID)]),
-	write_anc_list(Vs, start, CommandStream),
-	send_command(CommandStream, Answer, "]) = 1;~n", []).
-	
-write_anc_list([], _, _).
-write_anc_list([V|Vs], start, CommandStream) :- !,
-	get_atts(V, [topord(I)]),
-	my_format(CommandStream, "~w",['$VAR'(I)]),
-	write_anc_list(Vs, cont, CommandStream).
-write_anc_list([V|Vs], cont, CommandStream) :-
-	get_atts(V, [topord(I)]),
-	my_format(CommandStream, " ~w",['$VAR'(I)]),
-	write_anc_list(Vs, cont, CommandStream).
-
-mknet(Vs, Key, Observables, CommandStream, Answer) :-
-	mknet_all_discrete(Vs, Key, Observables, CommandStream, Answer).
-
-
-mknet_all_discrete(Vs, Key, Observables, CommandStream, Answer) :-
-	send_command(CommandStream, Answer, "discrete_nodes = 1:~w;~n",['$VAR'(Key)]),
-	my_format(CommandStream, "ns = [", []),
-	reverse(Vs, RVs),
-	send_var_sizes(RVs, CommandStream),
-	send_command(CommandStream, Answer, "];~n", []),
-	my_format(CommandStream, "onodes = [", []),
-	dump_observables(Observables, start, CommandStream),
-	send_command(CommandStream, Answer, "];~n", []),
-	send_command(CommandStream, Answer, "bnet = mk_bnet(dag, ns, 'discrete', discrete_nodes, 'observed', onodes);~n", []).
-
-send_var_sizes([V], CommandStream) :- !,
-	clpbn:get_atts(V, [dist(_,Tab,_)]),
-	length(Tab, Sz),
-	my_format(CommandStream, "~w", [Sz]).
-send_var_sizes([V|Vs], CommandStream) :-
-	clpbn:get_atts(V, [dist(_,Tab,_)]),
-	length(Tab, Sz),
-	my_format(CommandStream, "~w ", [Sz]),
-	send_var_sizes(Vs, CommandStream).
-
-
-dump_observables([], _, _) :- !.
-dump_observables([Observable|Observables], start, CommandStream) :- !,
-	get_atts(Observable, [topord(I)]),	
-	my_format(CommandStream, "~w",['$VAR'(I)]),
-	dump_observables(Observables, mid, CommandStream).
-dump_observables([Observable|Observables], mid, CommandStream) :-
-	get_atts(Observable, [topord(I)]),	
-	my_format(CommandStream, " ~w",['$VAR'(I)]),
-	dump_observables(Observables, mid, CommandStream).
-	
-dump_cpds([], _, _).
-dump_cpds([V|Vs], CommandStream, Answer) :-
-	clpbn:get_atts(V, [dist(Domain,_,_)]),
-	dump_cpds(Vs, CommandStream, Answer),
-	dump_dist(Domain, V, CommandStream, Answer).
-
-%
-% this is a discrete distribution
-%
-dump_dist(Vs, average, Ss, V, CommandStream, Answer) :- !,
-	vals_map(Vs, 1, Map),
-	get_atts(V, [topord(I)]),
-	my_format(CommandStream, "bnet.CPD{~w} = deterministic_CPD(bnet, ~w, inline('round(mean([",['$VAR'(I),'$VAR'(I)]),
-	put_atts(V, [map(Map)]),
-	length(Ss, Len),
-	dump_indices(0,Len,CommandStream),
-	send_command(CommandStream, Answer, "]))'));~n",[]).
-dump_dist(Vs, sum, Ss, V, CommandStream, Answer) :- !,
-	vals_map(Vs, 1, Map),
-	get_atts(V, [topord(I)]),
-	my_format(CommandStream, "bnet.CPD{~w} = deterministic_CPD(bnet, ~w, inline('sum([",['$VAR'(I),'$VAR'(I)]),
-	put_atts(V, [map(Map)]),
-	length(Ss, Len),
-	dump_indices(0,Len,CommandStream),
-	send_command(CommandStream, Answer, "])'));~n",[]).
-dump_dist(Vs, normalised_average(N), Ss, V, CommandStream, Answer) :- !,
-	vals_map(Vs, 1, Map),
-	get_atts(V, [topord(I)]),
-	my_format(CommandStream, "bnet.CPD{~w} = deterministic_CPD(bnet, ~w, inline('round((sum([",['$VAR'(I),'$VAR'(I)]),
-	put_atts(V, [map(Map)]),
-	length(Ss, Len),
-	dump_indices(0,Len,CommandStream),
-	N2 is N//2,
-	send_command(CommandStream, Answer, "])+~d)/~d)'));~n",[N2,N]).
-dump_dist(Vs,Ds,Ss0, V, CommandStream, Answer) :- !,
-	vals_map(Vs, 1, Map),
-	get_atts(V, [topord(I)]),
-	my_format(CommandStream, "bnet.CPD{~w} = tabular_CPD(bnet, ~w, [ ",['$VAR'(I),'$VAR'(I)]),
-	put_atts(V, [map(Map)]),
-	reverse([V|Ss0], Ss),
-	get_numbers_for_vars(Ss, Ns),
-	calculate_new_numbers(Ds,Ns,0,KDs0),
-	keysort(KDs0,KDs),
-	dump_elements(KDs, CommandStream),
-	send_command(CommandStream, Answer, "]);~n",[]).
-
-vals_map([], _, []).
-vals_map([V|Vs], I, [[V|I]|Map]) :-
-	I1 is I+1,
-	vals_map(Vs, I1, Map).
-
-get_numbers_for_vars(Ss, Ns) :-
-	numb_vars(Ss, 0, 1, VPs0),
-	keysort(VPs0, VPs),
-	compute_new_factors(VPs, 1, Int0),
-	keysort(Int0, Int),
-	select_factors(Int, [], Ns).
-	
-
-numb_vars([], _, _, []).
-numb_vars([V|Vs], I, A0, [T-p(I,A0,L)|VPs]) :-
-	get_atts(V, [map(Map),topord(T)]),
-	length(Map,L),
-	I1 is I+1,
-	Ai is A0*L,
-	numb_vars(Vs, I1, Ai, VPs).
-
-compute_new_factors([], _, []).
-compute_new_factors([_-p(I,Siz,L)|VPs], Div, [I-f(Siz,Div)|Os]) :-
-	NDiv is Div*L,
-	compute_new_factors(VPs, NDiv, Os).
-
-select_factors([], L, L).
-select_factors([_-Fac|Int], Ns0, Nsf) :-
-	select_factors(Int, [Fac|Ns0], Nsf).
-
-calculate_new_numbers([],_, _,[]).
-calculate_new_numbers([P|Ps], Ls, I0, [Pos-P|KDs]) :-
-	compute_new_position(Ls, I0, 0, Pos),
 	I is I0+1,
-	calculate_new_numbers(Ps, Ls, I, KDs).
+	put_atts(V, [bnt_id(I)]),
+	number_graph(SortedGraph, Is, I, IF).
 	
-compute_new_position([], _, P, P).
+init_bnet(SortedGraph, NumberedGraph, Size) :-
-compute_new_position([f(Siz,Div)|Ls], I0, P0, Pf) :-
+	build_dag(SortedGraph, Size),
-	A is I0 // Siz,
+	matlab_sequence(1,Size,discrete_nodes),
-	I1 is I0 mod Siz,
+	mksizes(SortedGraph, Size),
-	B is A*Div,
+	bnet <-- mk_bnet(dag, node_sizes, \discrete, discrete_nodes),
-	Pi is P0+B,
+	dump_cpts(SortedGraph, NumberedGraph).
-	compute_new_position(Ls, I1, Pi, Pf).
 
-dump_indices(Len,Len,_) :- !.
+build_dag(SortedVertices, Size) :-
-dump_indices(I0,Len,CommandStream) :-
+	get_numbered_edges(SortedVertices, Edges),
-	I is I0+1,
+	mkdag(Size, Edges).
-	my_format(CommandStream, "x(~d) ",[I]),	
-	dump_indices(I,Len,CommandStream).
 
-dump_elements([], _).
+get_numbered_edges([], []).
-dump_elements([_-P|KDs], CommandStream) :-
+get_numbered_edges([V|SortedVertices], Edges) :-
-	my_format(CommandStream, "~w~n",[P]),
+	clpbn:get_atts(V, [dist(_,_,Ps)]),
-	dump_elements(KDs, CommandStream).
+	v2number(V,N),
+	add_numbered_edges(Ps, N, Edges, Edges0),
+	get_numbered_edges(SortedVertices, Edges0).
 
-dump_problist([], _).
+add_numbered_edges([], _, Edges, Edges).
-dump_problist([P|KDs], CommandStream) :-
+add_numbered_edges([P|Ps], N, [PN-N|Edges], Edges0) :-
-	my_format(CommandStream, "~w~n",[P]),
+	v2number(P,PN),
-	dump_problist(KDs, CommandStream).
+	add_numbered_edges(Ps, N, Edges, Edges0).
 
-dump_dlist((D1;D2), Start, CommandStream) :- !,
+v2number(V,N) :-
-	dump_dlist(D1, Start, CommandStream),
+	get_atts(V,[bnt_id(N)]).
-	dump_dlist(D2, mid, CommandStream).
-dump_dlist((_ = V), Pos, CommandStream) :- !,
-	dump_dlist(V, Pos, CommandStream).
-dump_dlist((_ -> V), Pos, CommandStream) :- !,
-	dump_dlist(V, Pos, CommandStream).
-dump_dlist(V, start, CommandStream) :- !,
-	my_format(CommandStream, "~w~n",[V]).
-dump_dlist(V, mid, CommandStream) :-
-	my_format(CommandStream, "~w~n",[V]).
 
-find_map((D1;D2), I0, N, LF, L0) :- !,
+mkdag(N,Els) :-
-	find_map(D1, I0, I, LF, LI),
+	Tot is N*N,
-	find_map(D2, I,  N, LI, L0).
+	functor(Dag,dag,Tot),
-find_map((M->_), I, I1, [[M|I]|L0], L0) :-
+	add_els(Els,N,Dag),
-	I1 is I+1.
+	Dag=..[_|L],
+	addzeros(L),
+	matlab_matrix(N,N,L,dag).
 
-inf_engine(Vs, Key, CommandStream, Answer) :-
+add_els([],_,_).
-	send_command(CommandStream, Answer, "engine = jtree_inf_engine(bnet)~n", []),
+add_els([X-Y|Els],N,Dag) :-
-%	send_command(CommandStream, Answer, "engine = var_elim_inf_engine(bnet)~n", []),
+	Pos is (X-1)*N+Y,
-	send_command(CommandStream, Answer, "evidence = cell(1,~w)~n", ['$VAR'(Key)]),
+	arg(Pos,Dag,1),
-	dump_evidence(Vs, CommandStream, Answer),
+	add_els(Els,N,Dag).
-	send_command(CommandStream, Answer, "[engine, loglik] = enter_evidence(engine, evidence)~n",[]).
 
-dump_evidence([], _, _).
+addzeros([]).
-dump_evidence([V|Vs], CommandStream, Answer) :-
+addzeros([0|L]) :- !,
-	clpbn:get_atts(V, [evidence(Ev)]), !,
+	addzeros(L).
-	get_atts(V, [topord(I),map(M)]), !,
+addzeros([1|L]) :-
-	follow_map(M,Ev,NEv),
+	addzeros(L).
-	send_command(CommandStream, Answer, "evidence{~w} = ~w~n", ['$VAR'(I),NEv]),
-	dump_evidence(Vs, CommandStream, Answer).
-dump_evidence([_|Vs], CommandStream, Answer) :-
-	dump_evidence(Vs, CommandStream, Answer).
 
-follow_map([[K|V]|_], K, V) :- !.
+mksizes(SortedVertices, Size) :-
-follow_map([_|Map], K, V) :- !,
+	get_szs(SortedVertices,Sizes),
-	follow_map(Map, K, V).
+	matlab_matrix(1,Size,Sizes,node_sizes).
 
-find_observables([], []).
+get_szs([],[]).
-find_observables([Var|GVars], [Var|Observables]) :-
+get_szs([V|SortedVertices],[LD|Sizes]) :-
-	clpbn:get_atts(Var, [dist(_,_,_)]), !,
+	clpbn:get_atts(V, [dist(Dom,_,_)]),
-	find_observables(GVars, Observables).
+	length(Dom,LD),
-find_observables([_|GVars], Observables) :-
+	get_szs(SortedVertices,Sizes).
-	find_observables(GVars, Observables).
 
-output_answer(Observables, CommandStream, Answer) :-
+dump_cpts([], []).
-	split_by_cliques(Observables, Cliques),
+dump_cpts([V|SortedGraph], [I|Is]) :-
-	output_cliques(Cliques, CommandStream, Answer).
+	clpbn:get_atts(V, [dist(_,CPT,_)]),
+	mkcpt(bnet,I,CPT),
+	dump_cpts(SortedGraph, Is).
 
-split_by_cliques([], []).
+mkcpt(BayesNet, V, Tab) :-
-split_by_cliques([V|Vs], Cliques) :-
+	(BayesNet.'CPD'({V})) <-- tabular_CPD(BayesNet,V,Tab).
-	split_by_cliques(Vs, Cliques0),
-	add_to_cliques(Cliques0, V, Cliques).
 
-add_to_cliques([], V, [[V]]).
+set_inference :-
-add_to_cliques([Cl|L], V, [[V|Cl]|L]) :-
+	bnt_solver(Solver),
-	in_clique(Cl,V), !.
+	init_solver(Solver).
-add_to_cliques([Cl|L], V, [Cl|LN]) :-
-	add_to_cliques(L, V, LN).
 
-in_clique([], _).
+init_solver(jtree) :-
-in_clique([V1|L], V) :-
+	engine <-- jtree_inf_engine(bnet).
-	child(V, V1), !,
+init_solver(belprop) :-
-	in_clique(L, V).
+	engine <-- belprop_inf_engine(bnet).
-in_clique([V1|L], V) :-
+init_solver(likelihood_weighting) :-
-	child(V1, V),
+	engine <-- likelihood_weighting_inf_engine(bnet).
-	in_clique(L,V).
+init_solver(enumerative) :-
+	engine <-- enumerative_inf_engine(bnet).
+init_solver(gibbs) :-
+	engine <-- gibbs_inf_engine(bnet).
+init_solver(global_joint) :-
+	engine <-- global_joint_inf_engine(bnet).
+init_solver(pearl) :-
+	engine <-- pearl_inf_engine(bnet).
+init_solver(var_elim) :-
+	engine <-- var_elim_inf_engine(bnet).
 
-child(V,V1) :-
+add_evidence(Graph, Size, Is) :-
-	clpbn:get_atts(V, [dist(_,_,LVs)]),
+	mk_evidence(Graph, Is, LN),
-	varmember(LVs, V1).
+	matlab_initialized_cells( 1, Size, LN, evidence),
+	[engine, loglik] <-- enter_evidence(engine, evidence).
 
-varmember([H|_], V1) :- H == V1, !.
+mk_evidence([], [], []).
-varmember([_|L], V1) :-
+mk_evidence([V|L], [I|Is], [ar(1,I,Val)|LN]) :-
-	varmember(L, V1).
+	clpbn:get_atts(V, [evidence(Ev),dist(Domain,_,_)]), !,
+	evidence_val(Ev,1,Domain,Val),
+	mk_evidence(L, Is, LN).
+mk_evidence([_|L], [_|Is], LN) :-
+	mk_evidence(L, Is, LN).
 	
-output_cliques([], _, _).
+evidence_val(Ev,Val,[Ev|_],Val) :- !.
-output_cliques([Observables|Cliques], CommandStream, Answer) :-
+evidence_val(Ev,I0,[_|Domain],Val) :-
-	marginal(Observables, CommandStream, Answer),
+	I1 is I0+1,
-	read_answer(Answer, -1, MargDis),
+	evidence_val(Ev,I1,Domain,Val).
-	parse_observables(Observables, MargDis),
-	output_cliques(Cliques, CommandStream, Answer).
 
-marginal(Margs, CommandStream, Answer) :-
+marginalize([V], Ps) :- !,
-	my_format(CommandStream, "marg = marginal_nodes(engine, ", []),
+	v2number(V,Pos),
-	write_margs(Margs, CommandStream),
+	marg <-- marginal_nodes(engine, Pos),
-	send_command(CommandStream, Answer, ")~n", []),
+	matlab_get_variable( marg.'T', Ps).
-	my_format(CommandStream, "p = marg.T~n", []).
-
-
-write_margs([], _) :- !.
-write_margs([V], CommandStream) :- !,
-	get_atts(V, [topord(IV)]),
-	my_format(CommandStream, "~w", ['$VAR'(IV)]).
-write_margs(Vs, CommandStream) :-
-	my_format(CommandStream, "[", []),
-	write_anc_list(Vs, start, CommandStream),
-	my_format(CommandStream, "]", []).
-
-
-	
-read_answer(Answer, C0, [C1|L]) :-
-	get0(Answer, C1),
-	put(user_error, C1),
-	( (( C0 = 10 ; C0 = 85) ,C1 = 62) ->
-	    L = []
-	;
-	    read_answer(Answer, C1, L)
-	).
-
-wait_for_matlab_prompt(Answer) :-
-	fetch_prompt(Answer, -1). 
-
-fetch_prompt(Answer, C0) :-
-	get0(Answer, C1),
-	put(user_error, C1),
-	( ((C0 = 62 ; C0 = 85) ,C1 = 62) ->
-	    true
-	;
-	    fetch_prompt(Answer, C1)
-	).
-
-send_command(OStream, IStream, String, Args) :-
-	my_format(OStream, String, Args),
-	wait_for_matlab_prompt(IStream).
-
-parse_observables([Obs], MargDis) :- !,
-	get_atts(Obs, [map(Map)]),
-	skip_to_eq(MargDis, L1),
-	fetch_map(Map, L1, Out),
-	clpbn:get_atts(Obs, [key(Key)]),
-	Obs = {Key:Out}.
-parse_observables(LObs, MargDis) :-
-	joint_map(LObs, Map),
-	skip_to_eq(MargDis, L1),
-	fetch_maps(Map, L1, Out),
-	bind_lobs(LObs, Key, Key, Out).
-
-fetch_map([[Name|_]], L, (Name -> P)) :- !,
-	get_next_float(L, P, _).
-fetch_map([[Name|_]|Names], L0, (Name->P ; Rest)) :-
-	get_next_float(L0, P, Lf),
-	fetch_map(Names, Lf, Rest).
-
-get_next_float(L0, P, Lf) :-
-	skip_spaces(L0, Li),
-	fetch_float(Li,Ls, Lf),
-	number_codes(P, Ls).
-
-skip_to_eq([61|L], L) :- !.
-skip_to_eq([_|L], LF) :-
-	skip_to_eq(L, LF).
-
-skip_spaces([10|L], LF) :- !, skip_spaces(L, LF).
-skip_spaces([32|L], LF) :- !, skip_spaces(L, LF).
-skip_spaces(L, L).
-
-fetch_float([10|L], [], L) :- !.
-fetch_float([32|L], [], L) :- !.
-fetch_float([C|Li], [C|Ls], Lf) :-
-	fetch_float(Li, Ls, Lf).
-
-joint_map(Vars,FMap) :-
-	fetch_maps(Vars,Maps),
-	join_maps(Maps, FMap).
-
-fetch_maps([], []).
-fetch_maps([V|Vs], [M|Ms]) :-
-	get_atts(V, [map(M)]),
-	fetch_maps(Vs, Ms).
-
-join_maps([], [[]]).
-join_maps([Map|Maps], Rf) :-
-	join_maps(Maps, R1),
-	add(Map, R1, Rf).
-
-add([], _, []).
-add([[Name|_]|R], R1, RsF) :-
-	add_head(R1, Name, RsF, Rs0),
-	add(R, R1, Rs0).
-
-add_head([], _, Rs, Rs).
-add_head([H|L], A, [[A|H]|Rs], Rs0) :-
-	add_head(L, A, Rs, Rs0).
-
-
-fetch_maps([Name1], L, (Name2 -> P)) :- !,
-	generate_name(Name1, Name2),
-	get_next_float(L, P, _).
-fetch_maps([Name1|Names], L0, (Name2->P ; Rest)) :-
-	generate_name(Name1, Name2),
-	get_next_float(L0, P, Lf),
-	fetch_maps(Names, Lf, Rest).
-
-generate_name([Name], Name) :- !.
-generate_name([Name|Names], (Name,New)) :-
-	generate_name(Names, New).
-
-bind_lobs([Obs], Key, FullKey, Out) :- !,
-	clpbn:get_atts(Obs, [key(Key)]),
-	Obs = {FullKey:Out}.
-bind_lobs([Obs|Lobs], (Key,Rest), FullKey, Out) :-
-	clpbn:get_atts(Obs, [key(Key)]),
-	Obs = {FullKey:Out},
-	bind_lobs(Lobs, Rest, FullKey, Out).
-
-
-my_format(Stream, String, Args) :-
-	format(user_error, String, Args),
-	format(Stream, String, Args).
 

CLPBN/clpbn/examples/cg.yap

@@ -1,3 +1,4 @@
+
 %
 % adapted from Hendrik Blockeel's ILP04 paper.
 %

CLPBN/clpbn/vel.yap

@@ -17,7 +17,7 @@
 :- module(vel, [vel/3,
 		check_if_vel_done/1]).
 
-:- attribute size/1, posterior/4, all_diffs/1.
+:- attribute size/1, all_diffs/1.
 
 :- use_module(library(ordsets), [ord_union/3]).
 
@@ -29,6 +29,9 @@
 	clpbn_not_var_member/2,
 	check_for_hidden_vars/3]).
 
+:- use_module(library('clpbn/display'), [
+	clpbn_bind_vals/3]).
+
 :- use_module(library('clpbn/discrete_utils'), [
 	project_from_CPT/3,
 	reorder_CPT/5,
@@ -36,8 +39,7 @@
 
 :- use_module(library(lists),
 	      [
-	       append/3,
+	       append/3
-	       member/2
 	      ]).
 
 check_if_vel_done(Var) :-
@@ -59,7 +61,7 @@ do_vel(LVs,Vs0,AllDiffs) :-
 	process(LVi, LVs, tab(Dist,_,_)),
 	Dist =.. [_|Ps0],
 	normalise(Ps0,Ps),
-	bind_vals(LVs,Ps,AllDiffs).
+	clpbn_bind_vals(LVs,Ps,AllDiffs).
 
 %
 % some variables might already have evidence in the data-base.
@@ -67,7 +69,7 @@ do_vel(LVs,Vs0,AllDiffs) :-
 get_rid_of_ev_vars([],[]).
 get_rid_of_ev_vars([V|LVs0],LVs) :-
 	clpbn:get_atts(V, [evidence(Ev)]), !,
-	put_atts(V, [posterior([],Ev,[],[])]), !,
+	clpbn_display:put_atts(V, [posterior([],Ev,[],[])]), !,
 	get_rid_of_ev_vars(LVs0,LVs).
 get_rid_of_ev_vars([V|LVs0],[V|LVs]) :-
 	get_rid_of_ev_vars(LVs0,LVs).
@@ -252,32 +254,6 @@ update_tables([tab(Tab0,Vs,Sz)|Tabs],[tab(Tab0,Vs,Sz)|NTabs],Table,V) :-
 update_tables([_|Tabs],NTabs,Table,V) :-
 	update_tables(Tabs,NTabs,Table,V).
 
-bind_vals([],_,_) :- !.
-% simple case, we want a distribution on a single variable.
-%bind_vals([V],Ps) :- !,
-%	clpbn:get_atts(V, [dist(Vals,_,_)]),
-%	put_atts(V, posterior([V], Vals, Ps)).
-% complex case, we want a joint distribution, do it on a leader.
-% should split on cliques ?
-bind_vals(Vs,Ps,AllDiffs) :-
-	get_all_combs(Vs, Vals),
-	Vs = [V|_],
-	put_atts(V, posterior(Vs, Vals, Ps, AllDiffs)).
-
-get_all_combs(Vs, Vals) :-
-	get_all_doms(Vs,Ds),
-	findall(L,ms(Ds,L),Vals).
-
-get_all_doms([], []).
-get_all_doms([V|Vs], [D|Ds]) :-
-	clpbn:get_atts(V, [dist(D,_,_)]),
-	get_all_doms(Vs, Ds).
-
-ms([], []).
-ms([H|L], [El|Els]) :-
-	member(El,H),
-	ms(L, Els).
-
 normalise(Ps0,Ps) :-
 	add_all(Ps0,0.0,Sum),
 	divide_by_sum(Ps0,Sum,Ps).
@@ -293,31 +269,6 @@ divide_by_sum([P|Ps0],Sum,[PN|Ps]) :-
 	divide_by_sum(Ps0,Sum,Ps).
 
 
-%
-% what is actually output
-%
-attribute_goal(V, G) :-
-	get_atts(V, [posterior(Vs,Vals,Ps,AllDiffs)]),
-	massage_out(Vs, Vals, Ps, G, AllDiffs, V).
-
-massage_out([], Ev, _, V=Ev, _, V) :- !.
-massage_out(Vs, [D], [P], p(CEqs)=P, AllDiffs, _) :- !,
-	gen_eqs(Vs,D,Eqs),
-	add_alldiffs(AllDiffs,Eqs,CEqs).
-massage_out(Vs, [D|Ds], [P|Ps], (p(CEqs)=P,G) , AllDiffs, V) :-
-	gen_eqs(Vs,D,Eqs),
-	add_alldiffs(AllDiffs,Eqs,CEqs),
-	massage_out(Vs, Ds, Ps, G, AllDiffs, V).
-
-gen_eqs([V], [D], (V=D)) :- !.
-gen_eqs([V], D, (V=D)) :- !.
-gen_eqs([V|Vs], [D|Ds], ((V=D),Eqs)) :-
-	gen_eqs(Vs,Ds,Eqs).
-
-add_alldiffs([],Eqs,Eqs).
-add_alldiffs(AllDiffs,Eqs,(Eqs/alldiff(AllDiffs))).
-
-
 vel_get_dist_size(V,Sz) :-
 	get_atts(V, [size(Sz)]), !.
 vel_get_dist_size(V,Sz) :-

changes-5.1.html

@@ -16,6 +16,8 @@
 
 <h2>Yap-5.1.3:</h2>
 <ul>
+<li> FIXED: CLP(BN) with BNT.</li>
+<li> FIXED: allow dgraphs with graphs of vars.</li>
 <li> FIXED: add matrix library documentation.</li>
 <li> NEW: start atom_gc by default.</li>
 <li> FIXED: array add was not working for dyamic arrays (obs from Rui

library/dgraphs.yap

@@ -85,7 +85,8 @@ all_vertices_in_edges([V1-V2|Edges],[V1,V2|Vertices]) :-
 	all_vertices_in_edges(Edges,Vertices).	 
 
 edges2graphl([], [], []).
-edges2graphl([V|Vertices], [V-V1|SortedEdges], [V-[V1|Children]|GraphL]) :- !,
+edges2graphl([V|Vertices], [VV-V1|SortedEdges], [V-[V1|Children]|GraphL]) :-
+	V == VV, !,
 	get_extra_children(SortedEdges,V,Children,RemEdges),
 	edges2graphl(Vertices, RemEdges, GraphL).
 edges2graphl([V|Vertices], SortedEdges, [V-[]|GraphL]) :-
@@ -101,7 +102,7 @@ dgraph_add_edges([V|Vs],Es) --> !,
 	dgraph_update_vertex(V,[]),
 	dgraph_add_edges(Vs,Es).
 
-get_extra_children([V-C|Es],V,[C|Children],REs) :- !,
+get_extra_children([V-C|Es],VV,[C|Children],REs) :- V == VV, !,
 	get_extra_children(Es,V,Children,REs).
 get_extra_children(Es,_,[],Es).
 
@@ -318,14 +319,14 @@ dup([_|AllVs], [_|Q]) :-
 	dup(AllVs, Q).
 
 start_queue([], [], RQ, RQ).
-start_queue([V|AllVs], [V-e(S,B,S,E)|InvertedEdges], Q, RQ) :- !,
+start_queue([V|AllVs], [VV-e(S,B,S,E)|InvertedEdges], Q, RQ) :- V == VV, !,
-	link_edges(InvertedEdges, V, B, S, E, RemainingEdges),
+	link_edges(InvertedEdges, VV, B, S, E, RemainingEdges),
 	start_queue(AllVs, RemainingEdges, Q, RQ).
 start_queue([V|AllVs], InvertedEdges, [V|Q], RQ) :-
 	start_queue(AllVs, InvertedEdges, Q, RQ).
 
-link_edges([V-e(A,B,S,E)|InvertedEdges], V, A, S, E, RemEdges) :- !,
+link_edges([V-e(A,B,S,E)|InvertedEdges], VV, A, S, E, RemEdges) :- V == VV, !,
-	link_edges(InvertedEdges, V, B, S, E, RemEdges).
+	link_edges(InvertedEdges, VV, B, S, E, RemEdges).
 link_edges(RemEdges, _, A, _, A, RemEdges).
 
 continue_queue([], _, []).

library/matlab.yap

@@ -19,7 +19,8 @@
 	   matlab_item/4,
 	   matlab_item1/3,
 	   matlab_item1/4,
-	   matlab_sequence/3]).
+	   matlab_sequence/3,
+	   matlab_call/2]).
 
 :- ensure_loaded(library(lists)).
 
@@ -74,12 +75,14 @@ build_outputs([Out|Outs],[Out,' '|L],L0) :-
 	build_outputs(Outs,L,L0).
 
 build_args([],L,L).	
-build_args([Arg],Lf,L0) :-
+build_args([Arg],Lf,L0) :- !,
 	build_arg(Arg,Lf,[')'|L0]).
 build_args([Arg|Args],L,L0) :-
 	build_arg(Arg,L,[', '|L1]),
 	build_args(Args,L1,L0).
 
+build_arg(V,_,_) :- var(V), !,
+	throw(error(instantiation_error)).
 build_arg(Arg,[Arg|L],L) :- atomic(Arg), !.
 build_arg(\S0,['\'',S0,'\''|L],L) :-
 	atom(S0), !.
@@ -96,7 +99,8 @@ build_arg(F,[N,'{'|L],L0) :- %N({A}) = N{A}
 	F=..[N,{A}], !,
 	build_arg(A,L,['}'|L0]).
 build_arg(F,[N,'('|L],L0) :-
-	build_args(A,L,L0).
+	F=..[N|As],
+	build_args(As,L,L0).
 
 build_arglist([A],L,L0) :- !,
 	build_arg(A,L,[' ]'|L0]).