encapsulate access to distribution, so that they are not stored in the

constraint itself.


git-svn-id: https://yap.svn.sf.net/svnroot/yap/trunk@1916 b08c6af1-5177-4d33-ba66-4b1c6b8b522a

CLPBN/Makefile.in

@@ -34,6 +34,7 @@ CLPBN_PROGRAMS= \
 	$(CLPBN_SRCDIR)/bnt.yap \
 	$(CLPBN_SRCDIR)/discrete_utils.yap \
 	$(CLPBN_SRCDIR)/display.yap \
+	$(CLPBN_SRCDIR)/dists.yap \
 	$(CLPBN_SRCDIR)/evidence.yap \
 	$(CLPBN_SRCDIR)/gibbs.yap \
 	$(CLPBN_SRCDIR)/graphs.yap \

CLPBN/clpbn.yap

@@ -22,7 +22,7 @@
 :- dynamic
 	user:term_expansion/2.
 
-:- attribute key/1, dist/3, evidence/1, starter/0.
+:- attribute key/1, dist/2, evidence/1, starter/0.
 
 
 :- use_module('clpbn/vel', [vel/3,
@@ -41,6 +41,11 @@
 		    clpbn2graph/1
 		    ]).
 
+:- use_module('clpbn/dists', [
+		    dist/3,
+		    get_dist/4
+		    ]).
+
 :- use_module('clpbn/evidence', [
 	store_evidence/1,
 	incorporate_evidence/2
@@ -78,26 +83,10 @@ clpbn_flag(bnt_path,Before,After) :-
 	assert(bnt:bnt_path(After)).
 
 {Var = Key with Dist} :-
-	put_atts(El,[key(Key),dist(Domain,Table,Parents)]),
+	put_atts(El,[key(Key),dist(DistInfo,Parents)]),
-	extract_dist(Dist, Table, Parents, Domain),
+	dist(Dist, DistInfo, Parents),
 	add_evidence(Var,El).
 
-extract_dist(V, Tab, Inps, Domain) :- var(V), !,
-	V = p(Domain, Tab, Inps).
-extract_dist(p(Domain, trans(L), Parents), Tab, Inps, Domain) :- !,
-	compress_hmm_table(L, Parents, Tab, Inps).
-extract_dist(p(Domain, Tab, Inps), Tab, Inps, Domain).
-extract_dist(p(Domain, Tab), Tab, [], Domain).
-
-compress_hmm_table(L, Parents, trans(Tab), Inps) :-
-	get_rid_of_nuls(L,Parents,Tab,Inps).
-
-get_rid_of_nuls([], [], [], []).
-get_rid_of_nuls([*|L],[_|Parents],NL,NParents) :- !,
-	get_rid_of_nuls(L,Parents,NL,NParents).
-get_rid_of_nuls([Prob|L],[P|Parents],[Prob|NL],[P|NParents]) :-
-	get_rid_of_nuls(L,Parents,NL,NParents).
-
 check_constraint(Constraint, _, _, Constraint) :- var(Constraint), !.
 check_constraint((A->D), _, _, (A->D)) :- var(A), !.
 check_constraint((([A|B].L)->D), Vars, NVars, (([A|B].NL)->D)) :- !,
@@ -155,8 +144,9 @@ write_out(graphs, _, AVars, _) :-
 	clpbn2graph(AVars).
 
 get_bnode(Var, Goal) :-
-	get_atts(Var, [key(Key),dist(A,B,C)]),
+	get_atts(Var, [key(Key),dist(Dist,Parents)]),
-	(C = [] -> X = tab(A,B) ; X = tab(A,B,C)),
+	get_dist(Dist,_,Domain,CPT),
+	(Parents = [] -> X = tab(Domain,CPT) ; X = tab(Domain,CPT,Parents)),
 	dist_goal(X, Key, Goal0),
 	include_evidence(Var, Goal0, Key, Goali),
 	include_starter(Var, Goali, Key, Goal).
@@ -204,16 +194,16 @@ process_var(V, _) :- throw(error(instantiation_error,clpbn(attribute_goal(V)))).
 % unify a CLPBN variable with something. 
 %
 verify_attributes(Var, T, Goals) :-
-	get_atts(Var, [key(Key),dist(Domain,Table,Parents)]), !,
+	get_atts(Var, [key(Key),dist(Dist,Parents)]), !,
 	/* oops, someone trying to bind a clpbn constrained variable */
 	Goals = [],
-	bind_clpbn(T, Var, Key, Domain, Table, Parents).
+	bind_clpbn(T, Var, Key, Dist, Parents).
 verify_attributes(_, _, []).
 
 
-bind_clpbn(T, Var, Key, Domain, Table, Parents) :- var(T),
+bind_clpbn(T, Var, Key, Dist, Parents) :- var(T),
-	get_atts(T, [key(Key1),dist(Doman1,Table1,Parents1)]), !,
+	get_atts(T, [key(Key1),dist(Dist1,Parents1)]), !,
-	bind_clpbns(Key, Domain, Table, Parents, Key1, Doman1, Table1, Parents1),
+	bind_clpbns(Key, Dist, Parents, Key1, Dist1, Parents1),
 	(
 	  get_atts(T, [evidence(Ev1)]) ->
 	    bind_evidence_from_extra_var(Ev1,Var)
@@ -241,10 +231,12 @@ fresh_attvar(Var, NVar) :-
 	put_atts(NVar, LAtts).
 
 % I will now allow two CLPBN variables to be bound together.
-%bind_clpbns(Key, Domain, Table, Parents, Key, Domain, Table, Parents).
+%bind_clpbns(Key, Dist, Parents, Key, Dist, Parents).
-bind_clpbns(Key, Domain, Table, Parents, Key1, Domain1, Table1, Parents1) :- 
+bind_clpbns(Key, Dist, Parents, Key1, Dist1, Parents1) :- 
 	Key == Key1, !,
-	( Domain == Domain1, Table == Table1, Parents == Parents1 -> true ; throw(error(domain_error(bayesian_domain),bind_clpbns(var(Key, Domain, Table, Parents),var(Key1, Domain1, Table1, Parents1))))).
+	get_dist(Dist,Type,Domain,Table),
+	get_dist(Dist1,Type1,Domain1,Table1),
+	( Dist == Dist1, Parents == Parents1 -> true ; throw(error(domain_error(bayesian_domain),bind_clpbns(var(Key, Type, Domain, Table, Parents),var(Key1, Type1, Domain1, Table1, Parents1))))).
 bind_clpbns(Key, _, _, _, Key1, _, _, _) :-
 	Key\=Key1, !, fail.
 bind_clpbns(_, _, _, _, _, _, _, _) :-

CLPBN/clpbn/aggregates.yap

@@ -10,6 +10,8 @@
 
 :- use_module(library(lists), [last/2]).
 
+:- use_module(dists, [get_dist_domain_size/2]).
+
 cpt_average(Vars, Key, Els0, CPT) :-
 	check_domain(Els0, Els),
 	length(Els, SDomain),
@@ -162,7 +164,7 @@ generate_indices([_|Ls],[I|Inds],I,Av) :-
 combine_all([], [[]]).
 combine_all([V|LV], Cs) :-
 	combine_all(LV, Cs0),
-	get_dist_size(V,Sz),
+	get_vdist_size(V,Sz),
 	generate_indices(0, Sz, Vals),
 	add_vals(Vals, Cs0, Cs).
 
@@ -291,7 +293,7 @@ sm([V|_], V, _) :- !.
 sm([_|Vs], C, El) :-
 	sm(Vs, C, El).
 
-get_dist_size(V, Sz) :-
+get_vdist_size(V, Sz) :-
-	clpbn:get_atts(V, [dist(Vals,_,_)]),
+	clpbn:get_atts(V, [dist(Dist,_)]),
-	length(Vals, Sz).
+	get_dist_domain_size(Dist, Sz),
 

CLPBN/clpbn/bnt.yap

@@ -5,6 +5,11 @@
 :- use_module(library('clpbn/display'), [
 	clpbn_bind_vals/3]).
 
+:- use_module(library('clpbn/dists'), [
+	get_dist_domain_size/2,
+	get_dist_domain/2,
+	get_dist_params/2]).
+
 :- use_module(library(matlab), [start_matlab/1,
 				close_matlab/0,
 				matlab_on/0,
@@ -100,7 +105,7 @@ extract_graph(AllVars, Graph) :-
 	
 get_edges([],[]).
 get_edges([V|AllVars],Edges) :-
-	clpbn:get_atts(V, [dist(_,_,Parents)]),
+	clpbn:get_atts(V, [dist(_,Parents)]),
 	add_parent_child(Parents,V,Edges,Edges0),
 	get_edges(AllVars,Edges0).
 
@@ -127,7 +132,7 @@ build_dag(SortedVertices, Size) :-
 
 get_numbered_edges([], []).
 get_numbered_edges([V|SortedVertices], Edges) :-
-	clpbn:get_atts(V, [dist(_,_,Ps)]),
+	clpbn:get_atts(V, [dist(_,Ps)]),
 	v2number(V,N),
 	add_numbered_edges(Ps, N, Edges, Edges0),
 	get_numbered_edges(SortedVertices, Edges0).
@@ -166,13 +171,14 @@ mksizes(SortedVertices, Size) :-
 
 get_szs([],[]).
 get_szs([V|SortedVertices],[LD|Sizes]) :-
-	clpbn:get_atts(V, [dist(Dom,_,_)]),
+	clpbn:get_atts(V, [dist(Id,_)]),
-	length(Dom,LD),
+	get_dist_domain_size(Id,LD),
 	get_szs(SortedVertices,Sizes).
 
 dump_cpts([], []).
 dump_cpts([V|SortedGraph], [I|Is]) :-
-	clpbn:get_atts(V, [dist(_,CPT,_)]),
+	clpbn:get_atts(V, [dist(Id,_)]),
+	get_dist_params(Id,CPT),
 	mkcpt(bnet,I,CPT),
 	dump_cpts(SortedGraph, Is).
 
@@ -207,7 +213,8 @@ add_evidence(Graph, Size, Is) :-
 
 mk_evidence([], [], []).
 mk_evidence([V|L], [I|Is], [ar(1,I,Val)|LN]) :-
-	clpbn:get_atts(V, [evidence(Ev),dist(Domain,_,_)]), !,
+	clpbn:get_atts(V, [evidence(Ev),dist(Id,_)]), !,
+	get_dist_domain(Id, Domain),
 	evidence_val(Ev,1,Domain,Val),
 	mk_evidence(L, Is, LN).
 mk_evidence([_|L], [_|Is], LN) :-

CLPBN/clpbn/discrete_utils.yap

@@ -3,6 +3,8 @@
 			   reorder_CPT/5,
 			   get_dist_size/2]).
 
+:- use_module(dists, [get_dist_domain_size/2,
+		      get_dist_domain/2]).
 %
 % remove columns from a table
 %
@@ -15,7 +17,8 @@ project_from_CPT(V,tab(Table,Deps,Szs),tab(NewTable,NDeps,NSzs)) :-
 	NewTable =.. [t|NTabl].
 
 propagate_evidence(V, Evs) :-
-	clpbn:get_atts(V, [evidence(Ev),dist(Out,_,_)]), !,
+	clpbn:get_atts(V, [evidence(Ev),dist(Id,_)]), !,
+	get_dist_domain(Id, Out),
 	generate_szs_with_evidence(Out,Ev,Evs,Found),
 	(var(Found) -> 
 	    clpbn:get_atts(V, [key(K)]),
@@ -135,10 +138,8 @@ convert_factor([F0|F0s], [F|Fs], I, OUT) :-
 
 get_sizes([], []).
 get_sizes([V|Deps], [Sz|Sizes]) :-
-	get_dist_size(V,Sz),
+	clpbn:get_atts(V, [dist(Id,_)]),
+	get_dist_domain_size(Id,Sz),
 	get_sizes(Deps, Sizes).
 
-get_dist_size(V,Sz) :-
-	clpbn:get_atts(V, [dist(Vals,_,_)]),
-	length(Vals,Sz).
 

CLPBN/clpbn/display.yap

@@ -6,6 +6,8 @@
 	       member/2
 	      ]).
 
+:- use_module(dists, [get_dist_domain/2]).
+
 :- attribute posterior/4.
 
 
@@ -52,7 +54,8 @@ get_all_combs(Vs, Vals) :-
 
 get_all_doms([], []).
 get_all_doms([V|Vs], [D|Ds]) :-
-	clpbn:get_atts(V, [dist(D,_,_)]),
+	clpbn:get_atts(V, [dist(Id,_)]),
+	get_dist_domain(Id,D),
 	get_all_doms(Vs, Ds).
 
 ms([], []).

CLPBN/clpbn/dists.yap

@@ -0,0 +1,159 @@
+%
+% distribution
+%
+
+:- module(clpbn_dist,[
+	dist/1,
+	dist/3,
+	get_dist/4,
+	get_dist_domain/2,
+	get_dist_params/2,
+	get_dist_domain_size/2,
+	get_dist_tparams/2,
+	dist_to_term/2
+	]).
+
+:- use_module(library(lists),[is_list/1]).
+
+
+/*
+:- mode dist(+, -).
+
+:- mode get_dist(+, -, -, -).
+
+:- mode get_dist_params(+, -).
+
+:- mode get_dist_domain_size(+, -).
+
+:- mode get_dist_domain(+, -).
+
+:- mode get_dist_nparams(+, -).
+
+:- mode dist(?).
+
+:- mode dist_to_term(+,-).
+*/
+
+/*******************************************
+
+store stuff in a DB of the form:
+	db(Id, CPT, Type, Domain, CPTSize, DSize)
+
+where Id is the id,
+	cptsize is the table size or -1,
+	DSize is the domain size,
+	Type is
+	     tab for tabular
+	     trans  for HMMs
+	     continuous
+	Domain is
+	   a list of values
+	   bool for [t,f]
+	   aminoacids for [a,c,d,e,f,g,h,i,k,l,m,n,p,q,r,s,t,v,w,y]
+	   dna for [a,c,g,t]
+	   rna for [a,c,g,u]
+	   reals
+	
+
+********************************************/
+
+ :- dynamic id/1, db/6.
+
+id(1).
+
+new_id(Id) :-
+	retract(id(Id)),
+	Id1 is Id+1,
+	assert(id(Id1)).
+
+
+dist(V, Id, Parents) :-
+	var(V), !,
+	freeze(V, dist(V, Id, Parents)).
+dist(p(Type, CPT, Parents), Id, FParents) :-
+	when(
+	 (ground(Type), ground(CPT))
+	,
+	 distribution(Type, CPT, Id, Parents, FParents)
+	).
+dist(p(Type, CPT), Id, FParents) :-
+	  when(
+	   (ground(Type), ground(CPT))
+	,
+	    distribution(Type, CPT, Id, [], FParents)
+	).
+
+distribution(bool, trans(CPT), Id, Parents, FParents) :-
+	is_list(CPT), !,
+	compress_hmm_table(CPT, Parents, Tab, FParents),
+	add_dist([t,f], trans, Tab, Id).
+distribution(bool, CPT, Id, Parents, Parents) :-
+	is_list(CPT), !,
+	add_dist([t,f], tab, CPT, Id).
+distribution(aminoacids, trans(CPT), Id, Parents, FParents) :-
+	is_list(CPT), !,
+	compress_hmm_table(CPT, Parents, Tab, FParents),
+	add_dist([a,c,d,e,f,g,h,i,k,l,m,n,p,q,r,s,t,v,w,y], trans, Tab, Id).
+distribution(aminoacids, CPT, Id, Parents, Parents) :-
+	is_list(CPT), !,
+	add_dist([a,c,d,e,f,g,h,i,k,l,m,n,p,q,r,s,t,v,w,y], tab, CPT, Id).
+distribution(dna, trans(CPT), Id, Parents, FParents) :-
+	is_list(CPT), !,
+	compress_hmm_table(CPT, Parents, Tab, FParents),
+	add_dist([a,c,g,t], trans, Tab, Id).
+distribution(dna, CPT, Id, Parents, Parents) :-
+	is_list(CPT), !,
+	add_dist([a,c,g,t], tab, CPT, Id).
+distribution(rna, trans(CPT), Id, Parents, FParents) :-
+	is_list(CPT), !,
+	compress_hmm_table(CPT, Parents, Tab, FParents),
+	add_dist([a,c,g,u], trans, Tab, Id).
+distribution(rna, CPT, Id, Parents, Parents) :-
+	is_list(CPT), !,
+	add_dist([a,c,g,u], tab, CPT, Id).
+distribution(Domain, trans(CPT), Id, Parents, FParents) :-
+	is_list(Domain),
+	is_list(CPT), !,
+	compress_hmm_table(CPT, Parents, Tab, FParents),
+	add_dist(Domain, trans, Tab, Id).
+distribution(Domain, CPT, Id, Parents, Parents) :-
+	is_list(Domain),
+	is_list(CPT), !,
+	add_dist(Domain, tab, CPT, Id).
+
+add_dist(Domain, Type, CPT, Id) :-
+	db(Id, CPT, Type, Domain, _, _), !.
+add_dist(Domain, Type, CPT, Id) :-
+	length(CPT, CPTSize),
+	length(Domain, DSize),
+	new_id(Id),
+	assert(db(Id, CPT, Type, Domain, CPTSize, DSize)).
+
+%
+% Often, * is used to code empty in HMMs.
+%
+compress_hmm_table([], [], [], []).
+compress_hmm_table([*|L],[_|Parents],NL,NParents) :- !,
+	compress_hmm_table(L,Parents,NL,NParents).
+compress_hmm_table([Prob|L],[P|Parents],[Prob|NL],[P|NParents]) :-
+	compress_hmm_table(L,Parents,NL,NParents).
+
+dist(Id) :-
+	db(Id, _, _, _, _, _).
+
+get_dist(Id, Type, Domain, Tab) :-
+	db(Id, Tab, Type, Domain, _, _).
+
+get_dist_params(Id, Parms) :-
+	db(Id, Parms, _, _, _, _).
+
+get_dist_domain_size(Id, DSize) :-
+	db(Id, _, _, _, _, DSize).
+
+get_dist_domain(Id, Domain) :-
+	db(Id, _, _, Domain, _, _).
+
+get_dist_nparams(Id, NParms) :-
+	db(Id, _, _, _, NParms, _).
+
+dist_to_term(_Id,_Term).

CLPBN/clpbn/evidence.yap

@@ -3,8 +3,6 @@
 %
 %
 
-
-
 :- module(clpbn_evidence, [
 	store_evidence/1,
         incorporate_evidence/2

CLPBN/clpbn/gibbs.yap

@@ -31,6 +31,10 @@
 :- use_module(library('clpbn/utils'), [
 	check_for_hidden_vars/3]).
 
+:- use_module(library('clpbn/dists'), [
+	get_dist/4,
+	get_dist_domain_size/2]).
+
 :- use_module(library('clpbn/topsort'), [
 	topsort/2]).
 
@@ -76,7 +80,8 @@ gen_keys([V|Vs], I0, If, Keys0, Keys) :-
 graph_representation([],_,_,_,[]).
 graph_representation([V|Vs], Graph, I0, Keys, TGraph) :-
 	clpbn:get_atts(V,[evidence(_)]), !,
-	clpbn:get_atts(V, [dist(Vals,Table,Parents)]),
+	clpbn:get_atts(V, [dist(Id,Parents)]),
+	get_dist(Id, _, Vals, Table),
 	get_sizes(Parents, Szs),
 	length(Vals,Sz),
 	project_evidence_out([V|Parents],[V|Parents],Table,[Sz|Szs],Variables,NewTable),
@@ -85,7 +90,8 @@ graph_representation([V|Vs], Graph, I0, Keys, TGraph) :-
 	graph_representation(Vs, Graph, I0, Keys, TGraph).
 graph_representation([V|Vs], Graph, I0, Keys, [I-IParents|TGraph]) :-
 	I is I0+1,
-	clpbn:get_atts(V, [dist(Vals,Table,Parents)]),
+	clpbn:get_atts(V, [dist(Id,Parents)]),
+	get_dist(Id, _, Vals, Table),
 	get_sizes(Parents, Szs),
 	length(Vals,Sz),
 	project_evidence_out([V|Parents],[V|Parents],Table,[Sz|Szs],Variables,NewTable),
@@ -106,8 +112,8 @@ write_pars([V|Parents]) :-
 
 get_sizes([], []).
 get_sizes([V|Parents], [Sz|Szs]) :-
-	clpbn:get_atts(V, [dist(Vals,_,_)]),
+	clpbn:get_atts(V, [dist(Id,_)]),
-	length(Vals,Sz),
+	get_dist_domain_size(Id, Sz),
 	get_sizes(Parents, Szs).
 
 parent_indices([], _, []).

CLPBN/clpbn/graphs.yap

@@ -8,6 +8,9 @@
 :- use_module(library('clpbn/utils'), [
 	check_for_hidden_vars/3]).
 
+:- use_module(library('clpbn/dists'), [
+	get_dist/4]).
+
 :- attribute node/0.
 
 clpbn2graph(Vs) :-
@@ -24,7 +27,8 @@ clpbn2graph2([V|Vs]) :-
 %
 attribute_goal(V, node(K,Dom,CPT,TVs,Ev)) :-
 	get_atts(V, [node]),
-	clpbn:get_atts(V, [key(K),dist(Dom,CPT,Vs)]),
+	clpbn:get_atts(V, [key(K),dist(Id,Vs)]),
+	get_dist(Id,_,Dom,CPT),
 	translate_vars(Vs,TVs),
 	( clpbn:get_atts(V, [evidence(Ev)]) -> true ; true).
 

CLPBN/clpbn/graphviz.yap

@@ -18,7 +18,7 @@ output_var(Stream, V) :-
 	format(Stream, ' [ shape=box, style=filled, fillcolor=red, fontsize=18.0  ]~n',[]),
 	fail.
 output_var(Stream, V) :-
-	clpbn:get_atts(V,[key(Key),dist(_,_,Parents)]),
+	clpbn:get_atts(V,[key(Key),dist(_,Parents)]),
 	Parents = [_|_], !,
 	format(Stream, '	',[]),
 	output_parents(Stream, Parents),

CLPBN/clpbn/hmm.yap

@@ -69,7 +69,8 @@ emission(Vals,CPT,Ev,V) :-
 
 cvt_vals(aminoacids,[a,  c,  d,  e,  f,  g,  h,  i,  k,  l,  m,  n,  p,  q,  r,  s,  t,  v,  w,  y]).
 cvt_vals(bool,[t,f]).
-cvt_vals(bases,[a,c,g,t]).
+cvt_vals(dna,[a,c,g,t]).
+cvt_vals(rna,[a,c,g,u]).
 cvt_vals([A|B],[A|B]).
 
 % first, try standard representation

CLPBN/clpbn/utils.yap

@@ -17,7 +17,7 @@ check_for_hidden_vars([V|Vs], AllVs0, [V|NVs]) :-
 
 check_for_extra_variables(V,AllVs0, AllVs, Vs, IVs) :-
 	var(V),
-	clpbn:get_atts(V, [dist(_,_,[V1|LV])]), !,
+	clpbn:get_atts(V, [dist(_,[V1|LV])]), !,
 	add_old_variables([V1|LV], AllVs0, AllVs, Vs, IVs).
 check_for_extra_variables(_,AllVs, AllVs, Vs, Vs).
 
@@ -75,17 +75,17 @@ sort_vars_by_key_and_parents(AVars, SortedAVars, UnifiableVars) :-
 
 get_keys_and_parents([], []).
 get_keys_and_parents([V|AVars], [K-V|KeysVarsF]) :-
-	clpbn:get_atts(V, [key(K),dist(D,T,Parents)]), !,
+	clpbn:get_atts(V, [key(K),dist(Id,Parents)]), !,
-	add_parents(Parents,V,D,T,KeysVarsF,KeysVars0),
+	add_parents(Parents,V,Id,KeysVarsF,KeysVars0),
 	get_keys_and_parents(AVars, KeysVars0).
 get_keys_and_parents([_|AVars], KeysVars) :-  % may be non-CLPBN vars.
 	get_keys_and_parents(AVars, KeysVars).
 
-add_parents(Parents,_,_,_,KeyVars,KeyVars) :-
+add_parents(Parents,_,_,KeyVars,KeyVars) :-
 	all_vars(Parents), !.
-add_parents(Parents,V,D,T,KeyVarsF,KeyVars0) :-
+add_parents(Parents,V,Id,KeyVarsF,KeyVars0) :-
 	transform_parents(Parents,NParents,KeyVarsF,KeyVars0),
-	clpbn:put_atts(V, [dist(D,T,NParents)]).
+	clpbn:put_atts(V, [dist(Id,NParents)]).
 
 
 all_vars([]).

CLPBN/clpbn/vel.yap

@@ -25,6 +25,10 @@
 
 :- use_module(library('clpbn/graphviz'), [clpbn2gviz/4]).
 
+:- use_module(library('clpbn/dists'), [
+	get_dist_domain_size/2,
+	get_dist/4]).
+
 :- use_module(library('clpbn/utils'), [
 	clpbn_not_var_member/2,
 	check_for_hidden_vars/3]).
@@ -34,8 +38,7 @@
 
 :- use_module(library('clpbn/discrete_utils'), [
 	project_from_CPT/3,
-	reorder_CPT/5,
+	reorder_CPT/5]).
-	get_dist_size/2]).
 
 :- use_module(library(lists),
 	      [
@@ -89,7 +92,8 @@ find_all_clpbn_vars([V|Vs], [Var|LV], ProcessedVars, [table(I,Table,Parents,Size
 	find_all_clpbn_vars(Vs, LV, ProcessedVars0, Tables).
 
 var_with_deps(V, Table, Deps, Sizes, Ev, Vals) :-
-	clpbn:get_atts(V, [dist(Vals,OTable,Parents)]),
+	clpbn:get_atts(V, [dist(Id,Parents)]),
+	get_dist(Id,_,Vals,OTable),
 	( clpbn:get_atts(V, [evidence(Ev)]) -> true ; true),
 	reorder_CPT([V|Parents],OTable,Deps0,Table0,Sizes0),
 	simplify_evidence(Deps0, Table0, Deps0, Sizes0, Table, Deps, Sizes).
@@ -272,6 +276,7 @@ divide_by_sum([P|Ps0],Sum,[PN|Ps]) :-
 vel_get_dist_size(V,Sz) :-
 	get_atts(V, [size(Sz)]), !.
 vel_get_dist_size(V,Sz) :-
-	get_dist_size(V,Sz), !,
+	clpbn:get_atts(V,dist(Id,_)), !,
+	get_dist_domain_size(Id,Sz),
 	put_atts(V, [size(Sz)]).
 

CLPBN/clpbn/viterbi.yap

@@ -8,8 +8,12 @@
 
 :- use_module(library(clpbn), []).
 
+:- use_module(library('clpbn/dists'), [
+	get_dist_params/2]).
+
 :- attribute prob/1, emission/1, backp/1, ancestors/1.
 
+
 viterbi(Start,End,Trace,Ticks,Slices) :-
 	attributes:all_attvars(Vars0),
 	group_vars_by_key_and_parents(Vars0,Ticks,Slices),
@@ -47,16 +51,16 @@ get_keys([_|AVars], Trees) :-  % may be non-CLPBN vars.
 
 get_parents([], _).
 get_parents([V|AVars], Trees) :-
-	clpbn:get_atts(V, [dist(D,T,Parents)]), !,
+	clpbn:get_atts(V, [dist(Id,Parents)]), !,
 %clpbn:get_atts(V, [key(K)]), format('~w (~w): ~w~n',[V,K,Parents]),
-	add_parents(Parents,V,D,T,Trees),
+	add_parents(Parents,V,Id,Trees),
 	get_parents(AVars, Trees).
 get_parents([_|AVars], Trees) :-  % may be non-CLPBN vars.
 	get_parents(AVars, Trees).
 
-add_parents(Parents,V,D,T,Trees) :-
+add_parents(Parents,V,Id,Trees) :-
 	transform_parents(Parents,NParents,Copy,Trees),
-	( var(Copy) -> true ; clpbn:put_atts(V, [dist(D,T,NParents)]) ).
+	( var(Copy) -> true ; clpbn:put_atts(V, [dist(Id,NParents)]) ).
 
 transform_parents([],[],_,_).
 transform_parents([P|Parents0],[P|NParents],Copy,Trees) :-
@@ -102,7 +106,8 @@ viterbi_alg([V|Vs], Rs) :-
 % format('<< ~w~n',[V]),
 	% get the current status
 	get_atts(V,[prob(P0)]), !,
-	clpbn:get_atts(V,[dist(_,trans(Probs),States)]),
+	clpbn:get_atts(V,[dist(Id,States)]),
+	get_dist_params(Id,Probs),
 	% adjust to consider emission probabilities
 	adjust_for_emission(V, P0, Pf),
 	propagate(Probs,States,Pf,V,Rs,NRs),

CLPBN/clpbn/xbif.yap

@@ -4,6 +4,9 @@
 
 :- module(xbif, [clpbn2xbif/3]).
 
+:- use_module(library('clpbn/dists'), [
+	get_dist_domain/2]).
+
 clpbn2xbif(Stream, Name, Network) :-
 	format(Stream, '<?xml version="1.0" encoding="US-ASCII"?>
 
@@ -48,7 +51,8 @@ output_vars(Stream, [V|Vs]) :-
 	output_vars(Stream, Vs).
 
 output_var(Stream, V) :-
-	clpbn:get_atts(V,[key(Key),dist(Domain,_,_)]),
+	clpbn:get_atts(V,[key(Key),dist(Id,_)]),
+	get_dist_domain(Id, Domain),
 	format(Stream, '<VARIABLE TYPE="nature">
 	<NAME>',[]),
 	output_key(Stream,Key),