7acacd1618
git-svn-id: https://yap.svn.sf.net/svnroot/yap/trunk@1212 b08c6af1-5177-4d33-ba66-4b1c6b8b522a
500 lines
15 KiB
Prolog
500 lines
15 KiB
Prolog
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:- module(bnt, [dump_as_bnt/2,
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check_if_bnt_done/1]).
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:- use_module(library(terms), [term_variables/2
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]).
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:- use_module(library(ordsets), [ord_subtract/3,
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ord_add_element/3
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]).
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:- use_module(library(lists), [reverse/2
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]).
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:- use_module(library(atts)).
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:- use_module(library(heaps), [empty_heap/1,
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add_to_heap/4,
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heap_to_list/2
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]).
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:- use_module(library(system), [exec/3
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]).
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:- attribute topord/1, map/1.
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check_if_bnt_done(Var) :-
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get_atts(Var, [map(_)]).
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dump_as_bnt(GVars, [_|_]) :-
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exec('matlab -nojvm -nosplash',[pipe(CommandStream),pipe(Answer),pipe(Answer)],_),
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wait_for_matlab_prompt(Answer),
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get_value(clpbn_key, Key),
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send_command(CommandStream, Answer, 'cd /u/vitor/sw/BNT;~n', []),
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% send_command(CommandStream, Answer, 'cd /home/vitor/Yap/CLPBN/BNT;~n', []),
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send_command(CommandStream, Answer, 'add_BNT_to_path;~n', []),
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send_command(CommandStream, Answer, '~w = ~w;~n', ['$VAR'(Key), Key]),
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send_command(CommandStream, Answer, 'dag = zeros(~w,~w);~n', ['$VAR'(Key), '$VAR'(Key)]),
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Key1 is Key-1,
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dump_variable_indices(Key1, Vs, Heap, CommandStream, Answer),
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write_deps(Heap, CommandStream, Answer),
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find_observables(GVars, Observables),
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mknet(Vs, Key, Observables, CommandStream, Answer),
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dump_cpds(Vs, CommandStream, Answer),
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inf_engine(Vs, Key, CommandStream, Answer),
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output_answer(Observables, CommandStream, Answer),
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close(CommandStream),
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close(Answer).
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dump_variable_indices(I, LF, HF, CommandStream, Answer) :-
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all_vars_with_deps(I, LDeps, LNoDeps),
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sort(LNoDeps, S0),
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empty_heap(H0),
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topsort(LDeps, S0, LNoDeps, LF, H0, HF),
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reverse(LF, Vs),
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dump_vlist(Vs, 0, CommandStream, Answer).
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all_vars_with_deps(0, LDeps, LNoDeps) :- !,
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var_with_deps(0, LDeps, [], LNoDeps, []).
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all_vars_with_deps(I, LDeps, LNoDeps) :-
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var_with_deps(I, LDeps, LDeps0, LNoDeps, LNoDeps0),
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I1 is I-1,
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all_vars_with_deps(I1, LDeps0, LNoDeps0).
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var_with_deps(Indx, Deps, Deps0, NoDeps, NoDeps0) :-
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array_element(clpbn, Indx, V),
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clpbn:get_atts(V, [dist(_,_,VDeps)]), !,
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(VDeps = [] ->
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NoDeps = [V|NoDeps0], Deps = Deps0 ;
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sort(VDeps,SVDeps),
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Deps = [[V|SVDeps]|Deps0], NoDeps = NoDeps0 ).
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%
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% this is a silly quadratic algorithm for topological sorting.
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% it will have to do for now.
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%
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% to speedup things a bit I keep a sorted and unsorted version
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% of the variables sorted so far.
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%
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topsort([], _, S, S, H, H) :- !.
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topsort(LDeps, Sorted0, S0, SF, H, HF) :- !,
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delete_all(LDeps, Sorted0, S0, LI, SI, Sorted, H, HI),
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topsort(LI, Sorted, SI, SF, HI, HF).
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delete_all([], SS, S, [], S, SS, H, H).
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delete_all([[V|VDeps]|LDeps], SS, S, LF, SF, SSF, H0, HF) :-
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ord_subtract(VDeps, SS, VDepsI),
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ord_subtract(VDeps, VDepsI, Parents),
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add_parents_to_heap(Parents, V, H0, HI),
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( VDepsI = [] ->
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LF = LI, ord_add_element(SS,V,SSI), SI = [V|S];
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LF = [[V|VDepsI]|LI], SI = S, SSI = SS),
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delete_all(LDeps, SSI, SI, LI, SF, SSF, HI, HF).
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add_parents_to_heap([], _, H, H).
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add_parents_to_heap([P|Parents], V, H0, HF) :-
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add_to_heap(H0, P, V, HI), % if I put a HF here I get the debugger to loop
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add_parents_to_heap(Parents, V, HI, HF).
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dump_vlist([], _, _, _).
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dump_vlist([V|Vs], I, CommandStream, Answer) :-
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I1 is I+1,
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clpbn:get_atts(V,[key(_)]),
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send_command(CommandStream, Answer, '~w = ~w;~n', ['$VAR'(I), I1]),
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put_atts(V, [topord(I)]),
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I1 is I+1,
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dump_vlist(Vs, I1, CommandStream, Answer).
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write_deps(H, CommandStream, Answer) :-
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heap_to_list(H,L),
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write_list_deps(L, CommandStream, Answer).
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write_list_deps([], _, _).
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write_list_deps([V-A|L], CommandStream, Answer) :-
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fetch_same_key(L, V, SK, LN),
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write_dep_relation([A|SK], V, CommandStream, Answer),
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write_list_deps(LN, CommandStream, Answer).
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fetch_same_key([], _, [], []) :- !.
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fetch_same_key([V1-A|L], V, [A|SK], LN) :- V1 == V, !,
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fetch_same_key(L, V, SK, LN).
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fetch_same_key(L, _, [], L).
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write_dep_relation([], _, _) :- !.
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write_dep_relation([V], D, CommandStream, Answer) :- !,
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get_atts(V, [topord(IV)]),
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get_atts(D, [topord(ID)]),
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send_command(CommandStream, Answer, "dag(~w,~w) = 1;~n", ['$VAR'(ID),'$VAR'(IV)]).
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write_dep_relation(Vs, D, CommandStream, Answer) :-
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get_atts(D, [topord(ID)]),
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my_format(CommandStream, "dag(~w,[",['$VAR'(ID)]),
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write_anc_list(Vs, start, CommandStream),
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send_command(CommandStream, Answer, "]) = 1;~n", []).
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write_anc_list([], _, _).
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write_anc_list([V|Vs], start, CommandStream) :- !,
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get_atts(V, [topord(I)]),
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my_format(CommandStream, "~w",['$VAR'(I)]),
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write_anc_list(Vs, cont, CommandStream).
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write_anc_list([V|Vs], cont, CommandStream) :-
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get_atts(V, [topord(I)]),
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my_format(CommandStream, " ~w",['$VAR'(I)]),
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write_anc_list(Vs, cont, CommandStream).
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mknet(Vs, Key, Observables, CommandStream, Answer) :-
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mknet_all_discrete(Vs, Key, Observables, CommandStream, Answer).
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mknet_all_discrete(Vs, Key, Observables, CommandStream, Answer) :-
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send_command(CommandStream, Answer, "discrete_nodes = 1:~w;~n",['$VAR'(Key)]),
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my_format(CommandStream, "ns = [", []),
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reverse(Vs, RVs),
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send_var_sizes(RVs, CommandStream),
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send_command(CommandStream, Answer, "];~n", []),
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my_format(CommandStream, "onodes = [", []),
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dump_observables(Observables, start, CommandStream),
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send_command(CommandStream, Answer, "];~n", []),
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send_command(CommandStream, Answer, "bnet = mk_bnet(dag, ns, 'discrete', discrete_nodes, 'observed', onodes);~n", []).
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send_var_sizes([V], CommandStream) :- !,
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clpbn:get_atts(V, [dist(_,Tab,_)]),
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length(Tab, Sz),
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my_format(CommandStream, "~w", [Sz]).
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send_var_sizes([V|Vs], CommandStream) :-
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clpbn:get_atts(V, [dist(_,Tab,_)]),
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length(Tab, Sz),
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my_format(CommandStream, "~w ", [Sz]),
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send_var_sizes(Vs, CommandStream).
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dump_observables([], _, _) :- !.
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dump_observables([Observable|Observables], start, CommandStream) :- !,
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get_atts(Observable, [topord(I)]),
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my_format(CommandStream, "~w",['$VAR'(I)]),
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dump_observables(Observables, mid, CommandStream).
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dump_observables([Observable|Observables], mid, CommandStream) :-
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get_atts(Observable, [topord(I)]),
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my_format(CommandStream, " ~w",['$VAR'(I)]),
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dump_observables(Observables, mid, CommandStream).
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dump_cpds([], _, _).
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dump_cpds([V|Vs], CommandStream, Answer) :-
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clpbn:get_atts(V, [dist(Domain,_,_)]),
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dump_cpds(Vs, CommandStream, Answer),
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dump_dist(Domain, V, CommandStream, Answer).
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%
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% this is a discrete distribution
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%
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dump_dist(Vs, average, Ss, V, CommandStream, Answer) :- !,
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vals_map(Vs, 1, Map),
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get_atts(V, [topord(I)]),
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my_format(CommandStream, "bnet.CPD{~w} = deterministic_CPD(bnet, ~w, inline('round(mean([",['$VAR'(I),'$VAR'(I)]),
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put_atts(V, [map(Map)]),
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length(Ss, Len),
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dump_indices(0,Len,CommandStream),
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send_command(CommandStream, Answer, "]))'));~n",[]).
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dump_dist(Vs, sum, Ss, V, CommandStream, Answer) :- !,
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vals_map(Vs, 1, Map),
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get_atts(V, [topord(I)]),
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my_format(CommandStream, "bnet.CPD{~w} = deterministic_CPD(bnet, ~w, inline('sum([",['$VAR'(I),'$VAR'(I)]),
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put_atts(V, [map(Map)]),
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length(Ss, Len),
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dump_indices(0,Len,CommandStream),
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send_command(CommandStream, Answer, "])'));~n",[]).
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dump_dist(Vs, normalised_average(N), Ss, V, CommandStream, Answer) :- !,
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vals_map(Vs, 1, Map),
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get_atts(V, [topord(I)]),
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my_format(CommandStream, "bnet.CPD{~w} = deterministic_CPD(bnet, ~w, inline('round((sum([",['$VAR'(I),'$VAR'(I)]),
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put_atts(V, [map(Map)]),
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length(Ss, Len),
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dump_indices(0,Len,CommandStream),
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N2 is N//2,
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send_command(CommandStream, Answer, "])+~d)/~d)'));~n",[N2,N]).
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dump_dist(Vs,Ds,Ss0, V, CommandStream, Answer) :- !,
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vals_map(Vs, 1, Map),
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get_atts(V, [topord(I)]),
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my_format(CommandStream, "bnet.CPD{~w} = tabular_CPD(bnet, ~w, [ ",['$VAR'(I),'$VAR'(I)]),
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put_atts(V, [map(Map)]),
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reverse([V|Ss0], Ss),
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get_numbers_for_vars(Ss, Ns),
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calculate_new_numbers(Ds,Ns,0,KDs0),
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keysort(KDs0,KDs),
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dump_elements(KDs, CommandStream),
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send_command(CommandStream, Answer, "]);~n",[]).
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vals_map([], _, []).
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vals_map([V|Vs], I, [[V|I]|Map]) :-
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I1 is I+1,
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vals_map(Vs, I1, Map).
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get_numbers_for_vars(Ss, Ns) :-
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numb_vars(Ss, 0, 1, VPs0),
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keysort(VPs0, VPs),
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compute_new_factors(VPs, 1, Int0),
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keysort(Int0, Int),
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select_factors(Int, [], Ns).
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numb_vars([], _, _, []).
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numb_vars([V|Vs], I, A0, [T-p(I,A0,L)|VPs]) :-
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get_atts(V, [map(Map),topord(T)]),
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length(Map,L),
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I1 is I+1,
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Ai is A0*L,
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numb_vars(Vs, I1, Ai, VPs).
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compute_new_factors([], _, []).
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compute_new_factors([_-p(I,Siz,L)|VPs], Div, [I-f(Siz,Div)|Os]) :-
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NDiv is Div*L,
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compute_new_factors(VPs, NDiv, Os).
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select_factors([], L, L).
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select_factors([_-Fac|Int], Ns0, Nsf) :-
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select_factors(Int, [Fac|Ns0], Nsf).
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calculate_new_numbers([],_, _,[]).
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calculate_new_numbers([P|Ps], Ls, I0, [Pos-P|KDs]) :-
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compute_new_position(Ls, I0, 0, Pos),
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I is I0+1,
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calculate_new_numbers(Ps, Ls, I, KDs).
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compute_new_position([], _, P, P).
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compute_new_position([f(Siz,Div)|Ls], I0, P0, Pf) :-
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A is I0 // Siz,
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I1 is I0 mod Siz,
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B is A*Div,
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Pi is P0+B,
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compute_new_position(Ls, I1, Pi, Pf).
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dump_indices(Len,Len,_) :- !.
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dump_indices(I0,Len,CommandStream) :-
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I is I0+1,
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my_format(CommandStream, "x(~d) ",[I]),
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dump_indices(I,Len,CommandStream).
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dump_elements([], _).
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dump_elements([_-P|KDs], CommandStream) :-
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my_format(CommandStream, "~w~n",[P]),
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dump_elements(KDs, CommandStream).
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dump_problist([], _).
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dump_problist([P|KDs], CommandStream) :-
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my_format(CommandStream, "~w~n",[P]),
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dump_problist(KDs, CommandStream).
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dump_dlist((D1;D2), Start, CommandStream) :- !,
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dump_dlist(D1, Start, CommandStream),
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dump_dlist(D2, mid, CommandStream).
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dump_dlist((_ = V), Pos, CommandStream) :- !,
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dump_dlist(V, Pos, CommandStream).
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dump_dlist((_ -> V), Pos, CommandStream) :- !,
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dump_dlist(V, Pos, CommandStream).
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dump_dlist(V, start, CommandStream) :- !,
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my_format(CommandStream, "~w~n",[V]).
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dump_dlist(V, mid, CommandStream) :-
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my_format(CommandStream, "~w~n",[V]).
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find_map((D1;D2), I0, N, LF, L0) :- !,
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find_map(D1, I0, I, LF, LI),
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find_map(D2, I, N, LI, L0).
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find_map((M->_), I, I1, [[M|I]|L0], L0) :-
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I1 is I+1.
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inf_engine(Vs, Key, CommandStream, Answer) :-
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send_command(CommandStream, Answer, "engine = jtree_inf_engine(bnet)~n", []),
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% send_command(CommandStream, Answer, "engine = var_elim_inf_engine(bnet)~n", []),
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send_command(CommandStream, Answer, "evidence = cell(1,~w)~n", ['$VAR'(Key)]),
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dump_evidence(Vs, CommandStream, Answer),
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send_command(CommandStream, Answer, "[engine, loglik] = enter_evidence(engine, evidence)~n",[]).
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dump_evidence([], _, _).
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dump_evidence([V|Vs], CommandStream, Answer) :-
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clpbn:get_atts(V, [evidence(Ev)]), !,
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get_atts(V, [topord(I),map(M)]), !,
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follow_map(M,Ev,NEv),
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send_command(CommandStream, Answer, "evidence{~w} = ~w~n", ['$VAR'(I),NEv]),
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dump_evidence(Vs, CommandStream, Answer).
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dump_evidence([_|Vs], CommandStream, Answer) :-
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dump_evidence(Vs, CommandStream, Answer).
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follow_map([[K|V]|_], K, V) :- !.
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follow_map([_|Map], K, V) :- !,
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follow_map(Map, K, V).
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find_observables([], []).
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find_observables([Var|GVars], [Var|Observables]) :-
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clpbn:get_atts(Var, [dist(_,_,_)]), !,
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find_observables(GVars, Observables).
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find_observables([_|GVars], Observables) :-
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find_observables(GVars, Observables).
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output_answer(Observables, CommandStream, Answer) :-
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split_by_cliques(Observables, Cliques),
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output_cliques(Cliques, CommandStream, Answer).
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split_by_cliques([], []).
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split_by_cliques([V|Vs], Cliques) :-
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split_by_cliques(Vs, Cliques0),
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add_to_cliques(Cliques0, V, Cliques).
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add_to_cliques([], V, [[V]]).
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add_to_cliques([Cl|L], V, [[V|Cl]|L]) :-
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in_clique(Cl,V), !.
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add_to_cliques([Cl|L], V, [Cl|LN]) :-
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add_to_cliques(L, V, LN).
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in_clique([], _).
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in_clique([V1|L], V) :-
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child(V, V1), !,
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in_clique(L, V).
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in_clique([V1|L], V) :-
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child(V1, V),
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in_clique(L,V).
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child(V,V1) :-
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clpbn:get_atts(V, [dist(_,_,LVs)]),
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varmember(LVs, V1).
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varmember([H|_], V1) :- H == V1, !.
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varmember([_|L], V1) :-
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varmember(L, V1).
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output_cliques([], _, _).
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output_cliques([Observables|Cliques], CommandStream, Answer) :-
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marginal(Observables, CommandStream, Answer),
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read_answer(Answer, -1, MargDis),
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parse_observables(Observables, MargDis),
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output_cliques(Cliques, CommandStream, Answer).
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marginal(Margs, CommandStream, Answer) :-
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my_format(CommandStream, "marg = marginal_nodes(engine, ", []),
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write_margs(Margs, CommandStream),
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send_command(CommandStream, Answer, ")~n", []),
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my_format(CommandStream, "p = marg.T~n", []).
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write_margs([], _) :- !.
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write_margs([V], CommandStream) :- !,
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get_atts(V, [topord(IV)]),
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my_format(CommandStream, "~w", ['$VAR'(IV)]).
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write_margs(Vs, CommandStream) :-
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my_format(CommandStream, "[", []),
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write_anc_list(Vs, start, CommandStream),
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my_format(CommandStream, "]", []).
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read_answer(Answer, C0, [C1|L]) :-
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get0(Answer, C1),
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put(user_error, C1),
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( (( C0 = 10 ; C0 = 85) ,C1 = 62) ->
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L = []
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;
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read_answer(Answer, C1, L)
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).
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wait_for_matlab_prompt(Answer) :-
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fetch_prompt(Answer, -1).
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fetch_prompt(Answer, C0) :-
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get0(Answer, C1),
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put(user_error, C1),
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( ((C0 = 62 ; C0 = 85) ,C1 = 62) ->
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true
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;
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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).
|
|
|