diogo
/
yap-6.3
Archived
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Use the same convetion for module import and export

This commit is contained in:
Tiago Gomes 2012-12-17 14:50:12 +00:00
parent 2738c0fb56
commit 409a230826
27 changed files with 632 additions and 614 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

151
packages/CLPBN/clpbn.yap
View File

@ -1,21 +1,21 @@
:- module(clpbn,
[{}/1,
clpbn_flag/2,
set_clpbn_flag/2,
clpbn_flag/3,
clpbn_key/2,
clpbn_init_graph/1,
clpbn_init_solver/4,
clpbn_run_solver/3,
clpbn_finalize_solver/1,
pfl_init_solver/5,
pfl_run_solver/3,
probability/2,
conditional_probability/3,
use_parfactors/1,
op(500, xfy, with)
]).
[{}/1,
clpbn_flag/2,
set_clpbn_flag/2,
clpbn_flag/3,
clpbn_key/2,
clpbn_init_graph/1,
clpbn_init_solver/4,
clpbn_run_solver/3,
clpbn_finalize_solver/1,
pfl_init_solver/5,
pfl_run_solver/3,
probability/2,
conditional_probability/3,
use_parfactors/1,
op(500, xfy, with)
]).
:- use_module(library(atts)).
@ -30,92 +30,91 @@
:- attribute key/1, dist/2, evidence/1.
:- use_module('clpbn/ve',
[ve/3,
check_if_ve_done/1,
init_ve_solver/4,
run_ve_solver/3,
init_ve_ground_solver/5,
run_ve_ground_solver/3,
call_ve_ground_solver/6
]).
[ve/3,
check_if_ve_done/1,
init_ve_solver/4,
run_ve_solver/3,
init_ve_ground_solver/5,
run_ve_ground_solver/3,
call_ve_ground_solver/6
]).
:- use_module('clpbn/jt',
[jt/3,
init_jt_solver/4,
run_jt_solver/3
]).
[jt/3,
init_jt_solver/4,
run_jt_solver/3
]).
:- use_module('clpbn/bdd',
[bdd/3,
init_bdd_solver/4,
run_bdd_solver/3,
init_bdd_ground_solver/5,
run_bdd_ground_solver/3,
call_bdd_ground_solver/6
]).
[bdd/3,
init_bdd_solver/4,
run_bdd_solver/3,
init_bdd_ground_solver/5,
run_bdd_ground_solver/3,
call_bdd_ground_solver/6
]).
:- use_module('clpbn/gibbs',
[gibbs/3,
check_if_gibbs_done/1,
init_gibbs_solver/4,
run_gibbs_solver/3
]).
[gibbs/3,
check_if_gibbs_done/1,
init_gibbs_solver/4,
run_gibbs_solver/3
]).
%% :- use_module('clpbn/bnt',
%% [do_bnt/3,
%% check_if_bnt_done/1
%% ]).
%% [do_bnt/3,
%% check_if_bnt_done/1
%% ]).
:- use_module('clpbn/pgrammar',
[init_pcg_solver/4,
run_pcg_solver/3,
pcg_init_graph/0
]).
[init_pcg_solver/4,
run_pcg_solver/3,
pcg_init_graph/0
]).
:- use_module('clpbn/horus_ground',
[call_horus_ground_solver/6,
check_if_horus_ground_solver_done/1,
init_horus_ground_solver/5,
run_horus_ground_solver/3,
finalize_horus_ground_solver/1
]).
[call_horus_ground_solver/6,
check_if_horus_ground_solver_done/1,
init_horus_ground_solver/5,
run_horus_ground_solver/3,
finalize_horus_ground_solver/1
]).
:- use_module('clpbn/horus_lifted',
[call_horus_lifted_solver/3,
check_if_horus_lifted_solver_done/1,
init_horus_lifted_solver/4,
run_horus_lifted_solver/3,
finalize_horus_lifted_solver/1
]).
[call_horus_lifted_solver/3,
check_if_horus_lifted_solver_done/1,
init_horus_lifted_solver/4,
run_horus_lifted_solver/3,
finalize_horus_lifted_solver/1
]).
:- use_module('clpbn/dists',
[dist/4,
get_dist/4,
get_evidence_position/3,
get_evidence_from_position/3,
additive_dists/6
]).
[dist/4,
get_dist/4,
get_evidence_position/3,
get_evidence_from_position/3,
additive_dists/6
]).
:- use_module('clpbn/evidence',
[store_evidence/1,
add_stored_evidence/2,
incorporate_evidence/2,
check_stored_evidence/2,
put_evidence/2
]).
[store_evidence/1,
add_stored_evidence/2,
incorporate_evidence/2,
check_stored_evidence/2,
put_evidence/2
]).
:- use_module('clpbn/ground_factors',
[generate_network/5]).
[generate_network/5]).
:- use_module('clpbn/utils',
[sort_vars_by_key/3]).
[sort_vars_by_key/3]).
:- use_module('clpbn/graphs',
[clpbn2graph/1]).
[clpbn2graph/1]).
:- use_module('clpbn/graphviz',
[clpbn2gviz/4]).
[clpbn2gviz/4]).
%
% avoid the overhead of using goal_expansion/2.

55
packages/CLPBN/clpbn/aggregates.yap
View File

@ -1,42 +1,45 @@
%
% generate explicit CPTs
%
:- module(clpbn_aggregates, [
check_for_agg_vars/2,
cpt_average/6,
cpt_average/7,
cpt_max/6,
cpt_min/6,
avg_factors/5
]).
:- module(clpbn_aggregates,
[check_for_agg_vars/2,
cpt_average/6,
cpt_average/7,
cpt_max/6,
cpt_min/6,
avg_factors/5
]).
:- use_module(library(clpbn), [{}/1]).
:- use_module(library(clpbn),
[{}/1]).
:- use_module(library(lists),
[last/2,
sumlist/2,
sum_list/3,
max_list/2,
min_list/2,
nth0/3
]).
[last/2,
sumlist/2,
sum_list/3,
max_list/2,
min_list/2,
nth0/3
]).
:- use_module(library(matrix),
[matrix_new/3,
matrix_to_list/2,
matrix_set/3]).
[matrix_new/3,
matrix_to_list/2,
matrix_set/3
]).
:- use_module(library(clpbn/dists),
[
add_dist/6,
get_dist_domain_size/2]).
[add_dist/6,
get_dist_domain_size/2
]).
:- use_module(library(clpbn/matrix_cpt_utils),
[normalise_CPT_on_lines/3]).
[normalise_CPT_on_lines/3]).
:- use_module(library(pfl),
[skolem/2,
add_ground_factor/5]).
[skolem/2,
add_ground_factor/5
]).
:- use_module(library(bhash)).
@ -369,7 +372,7 @@ fill_in_min(_,_).
get_vdist_size(V, Sz) :-
var(V), !,
var(V), !,
clpbn:get_atts(V, [dist(Dist,_)]),
get_dist_domain_size(Dist, Sz).
get_vdist_size(V, Sz) :-

37
packages/CLPBN/clpbn/bdd.yap
View File

@ -18,32 +18,32 @@ Va <- P*X1*Y1 + Q*X2*Y2 + ...
**************************************************/
:- module(clpbn_bdd,
[bdd/3,
set_solver_parameter/2,
init_bdd_solver/4,
init_bdd_ground_solver/5,
run_bdd_solver/3,
run_bdd_ground_solver/3,
finalize_bdd_solver/1,
check_if_bdd_done/1,
call_bdd_ground_solver/6
]).
[bdd/3,
set_solver_parameter/2,
init_bdd_solver/4,
init_bdd_ground_solver/5,
run_bdd_solver/3,
run_bdd_ground_solver/3,
finalize_bdd_solver/1,
check_if_bdd_done/1,
call_bdd_ground_solver/6
]).
:- use_module(library('clpbn/dists'),
[dist/4,
get_dist_domain/2,
get_dist_domain_size/2,
get_dist_all_sizes/2,
get_dist_params/2
]).
[dist/4,
get_dist_domain/2,
get_dist_domain_size/2,
get_dist_all_sizes/2,
get_dist_params/2
]).
:- use_module(library('clpbn/display'),
[clpbn_bind_vals/3]).
[clpbn_bind_vals/3]).
:- use_module(library('clpbn/aggregates'),
[check_for_agg_vars/2]).
[check_for_agg_vars/2]).
:- use_module(library(atts)).
@ -1064,4 +1064,3 @@ build_cnf(CNF, IVs, Indics, AllParms, AllParmValues, Val) :-
set_to_ones(Extra),
ddnnf_is(F, Val).

78
packages/CLPBN/clpbn/bnt.yap
View File

@ -1,45 +1,51 @@
:- module(bnt, [do_bnt/3,
create_bnt_graph/2,
check_if_bnt_done/1]).
:- module(bnt,
[do_bnt/3,
create_bnt_graph/2,
check_if_bnt_done/1
]).
:- use_module(library('clpbn/display'), [
clpbn_bind_vals/3]).
:- 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('clpbn/dists'),
[get_dist_domain_size/2,
get_dist_domain/2,
get_dist_params/2
]).
:- use_module(library('clpbn/discrete_utils'), [
reorder_CPT/5]).
:- use_module(library('clpbn/discrete_utils'),
[reorder_CPT/5]).
:- 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_vector/2,
matlab_sequence/3,
matlab_initialized_cells/4,
matlab_get_variable/2,
matlab_call/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_vector/2,
matlab_sequence/3,
matlab_initialized_cells/4,
matlab_get_variable/2,
matlab_call/2
]).
:- 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
]).
:- 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
]).
:- use_module(library(lists), [append/3,
member/2,nth/3]).
:- use_module(library(lists),
[append/3,
member/2,nth/3
]).
:- use_module(library(ordsets), [
ord_insert/3]).
:- use_module(library(ordsets),
[ord_insert/3]).
:- yap_flag(write_strings,on).
@ -421,5 +427,5 @@ mk_evidence_query([V|L], [H|T], [ar(1,Pos,El)|LN]) :-
get_dist_domain(Id,D),
nth(El,D,H),
mk_evidence_query(L, T, LN).

32
packages/CLPBN/clpbn/connected.yap
View File

@ -1,26 +1,28 @@
:- module(clpbn_connected,
[influences/3,
factor_influences/4,
init_influences/3,
influences/4]
).
[influences/3,
factor_influences/4,
init_influences/3,
influences/4
]).
:- use_module(library(maplist)).
:- use_module(library(dgraphs),
[dgraph_new/1,
dgraph_add_edges/3,
dgraph_add_vertex/3,
dgraph_neighbors/3,
dgraph_edge/3,
dgraph_transpose/2]).
[dgraph_new/1,
dgraph_add_edges/3,
dgraph_add_vertex/3,
dgraph_neighbors/3,
dgraph_edge/3,
dgraph_transpose/2
]).
:- use_module(library(rbtrees),
[rb_new/1,
rb_lookup/3,
rb_insert/4,
rb_visit/2]).
[rb_new/1,
rb_lookup/3,
rb_insert/4,
rb_visit/2
]).
factor_influences(Vs, QVars, Ev, LV) :-
init_factor_influences(Vs, G, RG),

15
packages/CLPBN/clpbn/discrete_utils.yap
View File

@ -1,10 +1,14 @@
:- module(discrete_utils, [project_from_CPT/3,
reorder_CPT/5,
get_dist_size/2]).
:- module(discrete_utils,
[project_from_CPT/3,
reorder_CPT/5,
get_dist_size/2
]).
:- use_module(library(clpbn/dists), [get_dist_domain_size/2,
get_dist_domain/2]).
:- use_module(library(clpbn/dists),
[get_dist_domain_size/2,
get_dist_domain/2
]).
%
% remove columns from a table
%
@ -143,4 +147,3 @@ get_sizes([V|Deps], [Sz|Sizes]) :-
get_dist_domain_size(Id,Sz),
get_sizes(Deps, Sizes).

14
packages/CLPBN/clpbn/display.yap
View File

@ -1,14 +1,14 @@
:- module(clpbn_display, [
clpbn_bind_vals/3]).
:- module(clpbn_display,
[clpbn_bind_vals/3]).
:- use_module(library(lists),
[
member/2
]).
[member/2]).
:- use_module(library(clpbn/dists), [get_dist_domain/2]).
:- use_module(library(clpbn/dists),
[get_dist_domain/2]).
:- use_module(library(clpbn), [use_parfactors/1]).
:- use_module(library(clpbn),
[use_parfactors/1]).
:- use_module(library(maplist)).

85
packages/CLPBN/clpbn/dists.yap
View File

@ -3,47 +3,51 @@
%
:- module(clpbn_dist,
[
dist/1,
dist/4,
dists/1,
dist_new_table/2,
get_dist/4,
get_dist_matrix/5,
get_possibly_deterministic_dist_matrix/5,
get_dist_domain/2,
get_dist_domain_size/2,
get_dist_params/2,
get_dist_key/2,
get_dist_all_sizes/2,
get_evidence_position/3,
get_evidence_from_position/3,
dist_to_term/2,
empty_dist/2,
all_dist_ids/1,
randomise_all_dists/0,
randomise_dist/1,
uniformise_all_dists/0,
uniformise_dist/1,
reset_all_dists/0,
add_dist/6,
additive_dists/6
]).
[dist/1,
dist/4,
dists/1,
dist_new_table/2,
get_dist/4,
get_dist_matrix/5,
get_possibly_deterministic_dist_matrix/5,
get_dist_domain/2,
get_dist_domain_size/2,
get_dist_params/2,
get_dist_key/2,
get_dist_all_sizes/2,
get_evidence_position/3,
get_evidence_from_position/3,
dist_to_term/2,
empty_dist/2,
all_dist_ids/1,
randomise_all_dists/0,
randomise_dist/1,
uniformise_all_dists/0,
uniformise_dist/1,
reset_all_dists/0,
add_dist/6,
additive_dists/6
]).
:- use_module(library(lists),[nth0/3,append/3]).
:- use_module(library(lists),
[nth0/3,
append/3
]).
:- use_module(library(clpbn),
[use_parfactors/1]).
[use_parfactors/1]).
:- use_module(library(matrix),
[matrix_new/4,
matrix_new/3,
matrix_to_list/2,
matrix_to_logs/1]).
[matrix_new/4,
matrix_new/3,
matrix_to_list/2,
matrix_to_logs/1
]).
:- use_module(library(clpbn/matrix_cpt_utils),
[random_CPT/2,
uniform_CPT/2]).
[random_CPT/2,
uniform_CPT/2
]).
/*
:- mode dist(+, -).
@ -322,11 +326,11 @@ randomise_all_dists.
randomise_dist(Dist) :-
(
use_parfactors(on)
use_parfactors(on)
->
pfl:get_pfl_factor_sizes(Dist, DSizes)
pfl:get_pfl_factor_sizes(Dist, DSizes)
;
recorded(clpbn_dist_psizes, db(Dist,DSizes), _)
recorded(clpbn_dist_psizes, db(Dist,DSizes), _)
),
random_CPT(DSizes, NewCPT),
dist_new_table(Dist, NewCPT).
@ -338,11 +342,11 @@ uniformise_all_dists.
uniformise_dist(Dist) :-
(
use_parfactors(on)
use_parfactors(on)
->
pfl:get_pfl_factor_sizes(Dist, DSizes)
pfl:get_pfl_factor_sizes(Dist, DSizes)
;
recorded(clpbn_dist_psizes, db(Dist,DSizes), _)
recorded(clpbn_dist_psizes, db(Dist,DSizes), _)
),
uniform_CPT(DSizes, NewCPT),
dist_new_table(Dist, NewCPT).
@ -365,3 +369,4 @@ reset_all_dists.
additive_dists(ip(Domain,Tabs1), ip(Domain,Tabs2), Parents1, Parents2, ip(Domain,Tabs), Parents) :-
append(Tabs1, Tabs2, Tabs),
append(Parents1, Parents2, Parents).

38
packages/CLPBN/clpbn/evidence.yap
View File

@ -4,29 +4,27 @@
%
:- module(clpbn_evidence,
[
store_evidence/1,
incorporate_evidence/2,
check_stored_evidence/2,
add_stored_evidence/2,
put_evidence/2
]).
[store_evidence/1,
incorporate_evidence/2,
check_stored_evidence/2,
add_stored_evidence/2,
put_evidence/2
]).
:- use_module(library(clpbn), [
{}/1,
clpbn_flag/3,
set_clpbn_flag/2
]).
:- use_module(library(clpbn),
[{}/1,
clpbn_flag/3,
set_clpbn_flag/2
]).
:- use_module(library('clpbn/dists'), [
get_dist/4
]).
:- use_module(library('clpbn/dists'),
[get_dist/4]).
:- use_module(library(rbtrees), [
rb_new/1,
rb_lookup/3,
rb_insert/4
]).
:- use_module(library(rbtrees),
[rb_new/1,
rb_lookup/3,
rb_insert/4
]).
:- meta_predicate store_evidence(:).

69
packages/CLPBN/clpbn/gibbs.yap
View File

@ -8,51 +8,54 @@
%
:- module(clpbn_gibbs,
[gibbs/3,
check_if_gibbs_done/1,
init_gibbs_solver/4,
run_gibbs_solver/3]).
[gibbs/3,
check_if_gibbs_done/1,
init_gibbs_solver/4,
run_gibbs_solver/3
]).
:- use_module(library(rbtrees),
[rb_new/1,
rb_insert/4,
rb_lookup/3]).
[rb_new/1,
rb_insert/4,
rb_lookup/3
]).
:- use_module(library(lists),
[member/2,
append/3,
delete/3,
max_list/2,
sum_list/2]).
[member/2,
append/3,
delete/3,
max_list/2,
sum_list/2
]).
:- use_module(library(ordsets),
[ord_subtract/3]).
[ord_subtract/3]).
:- use_module(library('clpbn/matrix_cpt_utils'), [
project_from_CPT/3,
reorder_CPT/5,
multiply_possibly_deterministic_factors/3,
column_from_possibly_deterministic_CPT/3,
normalise_possibly_deterministic_CPT/2,
list_from_CPT/2]).
:- use_module(library('clpbn/matrix_cpt_utils'),
[project_from_CPT/3,
reorder_CPT/5,
multiply_possibly_deterministic_factors/3,
column_from_possibly_deterministic_CPT/3,
normalise_possibly_deterministic_CPT/2,
list_from_CPT/2
]).
:- use_module(library('clpbn/utils'), [
check_for_hidden_vars/3]).
:- use_module(library('clpbn/utils'),
[check_for_hidden_vars/3]).
:- use_module(library('clpbn/dists'), [
get_possibly_deterministic_dist_matrix/5,
get_dist_domain_size/2]).
:- use_module(library('clpbn/dists'),
[get_possibly_deterministic_dist_matrix/5,
get_dist_domain_size/2
]).
:- use_module(library('clpbn/topsort'), [
topsort/2]).
:- use_module(library('clpbn/topsort'),
[topsort/2]).
:- use_module(library('clpbn/display'), [
clpbn_bind_vals/3]).
:- use_module(library('clpbn/display'),
[clpbn_bind_vals/3]).
:- use_module(library('clpbn/connected'),
[
influences/3
]).
[influences/3]).
:- dynamic gibbs_params/3.
@ -542,5 +545,3 @@ divide_list([C|Add], Sum, [P|Dist]) :-
P is C/Sum,
divide_list(Add, Sum, Dist).

15
packages/CLPBN/clpbn/graphs.yap
View File

@ -3,13 +3,14 @@
% Just output a graph with all the variables.
%
:- module(clpbn2graph, [clpbn2graph/1]).
:- module(clpbn2graph,
[clpbn2graph/1]).
:- use_module(library('clpbn/utils'), [
check_for_hidden_vars/3]).
:- use_module(library('clpbn/utils'),
[check_for_hidden_vars/3]).
:- use_module(library('clpbn/dists'), [
get_dist/4]).
:- use_module(library('clpbn/dists'),
[get_dist/4]).
:- attribute node/0.
@ -37,7 +38,3 @@ translate_vars([V|Vs],[K|Ks]) :-
clpbn:get_atts(V, [key(K)]),
translate_vars(Vs,Ks).

4
packages/CLPBN/clpbn/graphviz.yap
View File

@ -1,4 +1,6 @@
:- module(clpbn_gviz, [clpbn2gviz/4]).
:- module(clpbn_gviz,
[clpbn2gviz/4]).
clpbn2gviz(Stream, Name, Network, Output) :-
format(Stream, 'digraph ~w {

30
packages/CLPBN/clpbn/ground_factors.yap
View File

@ -1,34 +1,34 @@
:- module(pfl_ground_factors,
[generate_network/5,
f/3
]).
[generate_network/5,
f/3
]).
:- use_module(library(bhash),
[b_hash_new/1,
b_hash_lookup/3,
b_hash_insert/4,
b_hash_to_list/2
]).
[b_hash_new/1,
b_hash_lookup/3,
b_hash_insert/4,
b_hash_to_list/2
]).
:- use_module(library(lists),
[member/2]).
[member/2]).
:- use_module(library(maplist)).
:- use_module(library(atts)).
:- use_module(library(pfl),
[factor/6,
defined_in_factor/2,
skolem/2
]).
[factor/6,
defined_in_factor/2,
skolem/2
]).
:- use_module(library(clpbn/aggregates),
[avg_factors/5]).
[avg_factors/5]).
:- use_module(library(clpbn/dists),
[dist/4]).
[dist/4]).
:- dynamic currently_defined/1, queue/1, f/4.

21
packages/CLPBN/clpbn/hmm.yap
View File

@ -1,19 +1,20 @@
:- module(hmm, [init_hmm/0,
hmm_state/1,
emission/1]).
:- module(hmm,
[init_hmm/0,
hmm_state/1,
emission/1
]).
:- ensure_loaded(library(clpbn)).
:- use_module(library(lists),
[nth/3]).
[nth/3]).
:- use_module(library(nbhash),
[nb_hash_new/2,
nb_hash_lookup/3,
nb_hash_insert/3
]).
[nb_hash_new/2,
nb_hash_lookup/3,
nb_hash_insert/3
]).
:- ensure_loaded(library(tries)).
@ -79,5 +80,3 @@ cvt_vals([A|B],[A|B]).
find_probs(Logs,Nth,Log) :-
arg(Nth,Logs,Log).

130
packages/CLPBN/clpbn/jt.yap
View File

@ -1,89 +1,93 @@
:- module(jt, [jt/3,
init_jt_solver/4,
run_jt_solver/3]).
:- module(jt,
[jt/3,
init_jt_solver/4,
run_jt_solver/3
]).
:- use_module(library(dgraphs),
[dgraph_new/1,
dgraph_add_edges/3,
dgraph_add_vertex/3,
dgraph_add_vertices/3,
dgraph_edges/2,
dgraph_vertices/2,
dgraph_transpose/2,
dgraph_to_ugraph/2,
ugraph_to_dgraph/2,
dgraph_neighbors/3
]).
[dgraph_new/1,
dgraph_add_edges/3,
dgraph_add_vertex/3,
dgraph_add_vertices/3,
dgraph_edges/2,
dgraph_vertices/2,
dgraph_transpose/2,
dgraph_to_ugraph/2,
ugraph_to_dgraph/2,
dgraph_neighbors/3
]).
:- use_module(library(undgraphs),
[undgraph_new/1,
undgraph_add_edge/4,
undgraph_add_edges/3,
undgraph_del_vertex/3,
undgraph_del_vertices/3,
undgraph_vertices/2,
undgraph_edges/2,
undgraph_neighbors/3,
undgraph_edge/3,
dgraph_to_undgraph/2
]).
[undgraph_new/1,
undgraph_add_edge/4,
undgraph_add_edges/3,
undgraph_del_vertex/3,
undgraph_del_vertices/3,
undgraph_vertices/2,
undgraph_edges/2,
undgraph_neighbors/3,
undgraph_edge/3,
dgraph_to_undgraph/2
]).
:- use_module(library(wundgraphs),
[wundgraph_new/1,
wundgraph_max_tree/3,
wundgraph_add_edges/3,
wundgraph_add_vertices/3,
wundgraph_to_undgraph/2
]).
[wundgraph_new/1,
wundgraph_max_tree/3,
wundgraph_add_edges/3,
wundgraph_add_vertices/3,
wundgraph_to_undgraph/2
]).
:- use_module(library(rbtrees),
[rb_new/1,
rb_insert/4,
rb_lookup/3]).
[rb_new/1,
rb_insert/4,
rb_lookup/3
]).
:- use_module(library(ordsets),
[ord_subset/2,
ord_insert/3,
ord_intersection/3,
ord_del_element/3,
ord_memberchk/2]).
[ord_subset/2,
ord_insert/3,
ord_intersection/3,
ord_del_element/3,
ord_memberchk/2
]).
:- use_module(library(lists),
[reverse/2]).
[reverse/2]).
:- use_module(library(maplist)).
:- use_module(library('clpbn/aggregates'),
[check_for_agg_vars/2]).
[check_for_agg_vars/2]).
:- use_module(library('clpbn/dists'),
[get_dist_domain_size/2,
get_dist_domain/2,
get_dist_matrix/5]).
[get_dist_domain_size/2,
get_dist_domain/2,
get_dist_matrix/5
]).
:- use_module(library('clpbn/matrix_cpt_utils'),
[project_from_CPT/3,
reorder_CPT/5,
unit_CPT/2,
multiply_CPTs/4,
divide_CPTs/3,
normalise_CPT/2,
expand_CPT/4,
get_CPT_sizes/2,
reset_CPT_that_disagrees/5,
sum_out_from_CPT/4,
list_from_CPT/2]).
[project_from_CPT/3,
reorder_CPT/5,
unit_CPT/2,
multiply_CPTs/4,
divide_CPTs/3,
normalise_CPT/2,
expand_CPT/4,
get_CPT_sizes/2,
reset_CPT_that_disagrees/5,
sum_out_from_CPT/4,
list_from_CPT/2
]).
:- use_module(library('clpbn/display'), [
clpbn_bind_vals/3]).
:- use_module(library('clpbn/display'),
[clpbn_bind_vals/3]).
:- use_module(library('clpbn/connected'),
[
init_influences/3,
influences/4
]).
[init_influences/3,
influences/4
]).
jt([[]],_,_) :- !.
@ -171,7 +175,7 @@ add_parents([], _, Graph, Graph).
add_parents([P|Parents], V, Graph0, [P-V|GraphF]) :-
add_parents(Parents, V, Graph0, GraphF).
% From David Page's lectures
test_graph(0,
[1-3,2-3,2-4,5-4,5-7,10-7,10-9,11-9,3-6,4-6,7-8,9-8,6-12,8-12],

92
packages/CLPBN/clpbn/matrix_cpt_utils.yap
View File

@ -1,51 +1,53 @@
:- module(clpbn_matrix_utils,
[init_CPT/3,
project_from_CPT/3,
sum_out_from_CPT/5,
project_from_CPT/6,
reorder_CPT/5,
get_CPT_sizes/2,
normalise_CPT/2,
multiply_CPTs/4,
multiply_CPTs/6,
divide_CPTs/3,
expand_CPT/4,
reset_CPT_that_disagrees/5,
unit_CPT/2,
sum_out_from_CPT/4,
list_from_CPT/2,
multiply_factors/3,
normalise_possibly_deterministic_CPT/2,
column_from_possibly_deterministic_CPT/3,
multiply_possibly_deterministic_factors/3,
random_CPT/2,
uniform_CPT/2,
uniform_CPT_as_list/2,
normalise_CPT_on_lines/3]).
[init_CPT/3,
project_from_CPT/3,
sum_out_from_CPT/5,
project_from_CPT/6,
reorder_CPT/5,
get_CPT_sizes/2,
normalise_CPT/2,
multiply_CPTs/4,
multiply_CPTs/6,
divide_CPTs/3,
expand_CPT/4,
reset_CPT_that_disagrees/5,
unit_CPT/2,
sum_out_from_CPT/4,
list_from_CPT/2,
multiply_factors/3,
normalise_possibly_deterministic_CPT/2,
column_from_possibly_deterministic_CPT/3,
multiply_possibly_deterministic_factors/3,
random_CPT/2,
uniform_CPT/2,
uniform_CPT_as_list/2,
normalise_CPT_on_lines/3
]).
:- use_module(library(matrix),
[matrix_new/4,
matrix_new_set/4,
matrix_select/4,
matrix_dims/2,
matrix_size/2,
matrix_shuffle/3,
matrix_expand/3,
matrix_op/4,
matrix_dims/2,
matrix_sum/2,
matrix_sum_logs_out/3,
matrix_sum_out/3,
matrix_sum_logs_out_several/3,
matrix_op_to_all/4,
matrix_to_exps2/1,
matrix_to_logs/1,
matrix_set_all_that_disagree/5,
matrix_to_list/2,
matrix_agg_lines/3,
matrix_agg_cols/3,
matrix_op_to_lines/4,
matrix_column/3]).
[matrix_new/4,
matrix_new_set/4,
matrix_select/4,
matrix_dims/2,
matrix_size/2,
matrix_shuffle/3,
matrix_expand/3,
matrix_op/4,
matrix_dims/2,
matrix_sum/2,
matrix_sum_logs_out/3,
matrix_sum_out/3,
matrix_sum_logs_out_several/3,
matrix_op_to_all/4,
matrix_to_exps2/1,
matrix_to_logs/1,
matrix_set_all_that_disagree/5,
matrix_to_list/2,
matrix_agg_lines/3,
matrix_agg_cols/3,
matrix_op_to_lines/4,
matrix_column/3
]).
init_CPT(List, Sizes, TAB) :-
matrix_new(floats, Sizes, List, TAB),

17
packages/CLPBN/clpbn/numbers.yap
View File

@ -1,17 +1,17 @@
:- module(clpbn_numbers,
[
keys_to_numbers/7,
keys_to_numbers/9,
lists_of_keys_to_ids/6
]).
[keys_to_numbers/7,
keys_to_numbers/9,
lists_of_keys_to_ids/6
]).
:- use_module(library(bhash)).
:- use_module(library(maplist)).
:- use_module(library(pfl),
[skolem/2,
get_pfl_cpt/5
]).
[skolem/2,
get_pfl_cpt/5
]).
%
% convert key representation into numeric representation
@ -60,4 +60,3 @@ evidence_to_id(Key=Ev, I0=Ev, Hash0, Hash, I0, I) :-
b_hash_insert(Hash0, Key, I0, Hash),
I is I0+1.

35
packages/CLPBN/clpbn/pgrammar.yap
View File

@ -2,30 +2,29 @@
:- style_check(all).
:- module(clpbn_pgrammar,[grammar_to_atts/1,
grammar_prob/2,
grammar_mle/2,
init_pcg_solver/4,
run_pcg_solver/3,
pcg_init_graph/0]).
:- module(clpbn_pgrammar,
[grammar_to_atts/1,
grammar_prob/2,
grammar_mle/2,
init_pcg_solver/4,
run_pcg_solver/3,
pcg_init_graph/0
]).
:- load_files([library(clpbn)],
[ if(not_loaded),
silent(true)
]).
[if(not_loaded), silent(true)]).
:- use_module([library(lists)],
[ sum_list/2
]).
[sum_list/2]).
:- use_module([library(matrix)],
[ matrix_new/3,
matrix_add/3,
matrix_get/3,
matrix_op/4,
matrix_op_to_all/4,
matrix_set_all/2
]).
[matrix_new/3,
matrix_add/3,
matrix_get/3,
matrix_op/4,
matrix_op_to_all/4,
matrix_set_all/2
]).
:- op(600, xfy,'::').

55
packages/CLPBN/clpbn/table.yap
View File

@ -8,28 +8,29 @@
*/
:- module(clpbn_table,
[clpbn_table/1,
clpbn_tableallargs/1,
clpbn_table_nondet/1,
clpbn_tabled_clause/2,
clpbn_tabled_clause_ref/3,
clpbn_tabled_retract/2,
clpbn_tabled_abolish/1,
clpbn_tabled_asserta/1,
clpbn_tabled_assertz/1,
clpbn_tabled_asserta/2,
clpbn_tabled_assertz/2,
clpbn_tabled_dynamic/1,
clpbn_tabled_number_of_clauses/2,
clpbn_reset_tables/0,
clpbn_reset_tables/1,
clpbn_is_tabled/1
]).
[clpbn_table/1,
clpbn_tableallargs/1,
clpbn_table_nondet/1,
clpbn_tabled_clause/2,
clpbn_tabled_clause_ref/3,
clpbn_tabled_retract/2,
clpbn_tabled_abolish/1,
clpbn_tabled_asserta/1,
clpbn_tabled_assertz/1,
clpbn_tabled_asserta/2,
clpbn_tabled_assertz/2,
clpbn_tabled_dynamic/1,
clpbn_tabled_number_of_clauses/2,
clpbn_reset_tables/0,
clpbn_reset_tables/1,
clpbn_is_tabled/1
]).
:- use_module(library(bhash),
[b_hash_new/4,
b_hash_lookup/3,
b_hash_insert/4]).
[b_hash_new/4,
b_hash_lookup/3,
b_hash_insert/4
]).
:- meta_predicate clpbn_table(:),
clpbn_tabled_clause(:.?),
@ -43,14 +44,13 @@
clpbn_tabled_number_of_clauses(:,-),
clpbn_is_tabled(:).
:- use_module(library(terms), [
instantiated_term_hash/4,
variant/2
]).
:- use_module(library(terms),
[instantiated_term_hash/4,
variant/2
]).
:- use_module(evidence, [
put_evidence/2
]).
:- use_module(evidence,
[put_evidence/2]).
:- dynamic clpbn_table/3.
@ -364,4 +364,3 @@ clpbn_is_tabled(M:Clause, _) :- !,
clpbn_is_tabled(Head, M) :-
clpbn_table(Head, M, _).

13
packages/CLPBN/clpbn/topsort.yap
View File

@ -1,11 +1,13 @@
:- module(topsort, [topsort/2]).
:- module(topsort,
[topsort/2]).
:- use_module(library(dgraphs),
[dgraph_new/1,
dgraph_add_edges/3,
dgraph_add_vertices/3,
dgraph_top_sort/2]).
[dgraph_new/1,
dgraph_add_edges/3,
dgraph_add_vertices/3,
dgraph_top_sort/2
]).
/* simple implementation of a topological sorting algorithm */
/* graph is as Node-[Parents] */
@ -31,4 +33,3 @@ add_edges([], _V) --> [].
add_edges([P|Parents], V) --> [P-V],
add_edges(Parents, V).

15
packages/CLPBN/clpbn/utils.yap
View File

@ -1,9 +1,11 @@
:- module(clpbn_utils, [
clpbn_not_var_member/2,
clpbn_var_member/2,
check_for_hidden_vars/3,
sort_vars_by_key/3,
sort_vars_by_key_and_parents/3]).
:- module(clpbn_utils,
[clpbn_not_var_member/2,
clpbn_var_member/2,
check_for_hidden_vars/3,
sort_vars_by_key/3,
sort_vars_by_key_and_parents/3
]).
%
% It may happen that variables from a previous query may still be around.
@ -113,4 +115,3 @@ transform_parents([P|Parents0],[P|NParents],KeyVarsF,KeyVars0) :-
transform_parents([P|Parents0],[V|NParents],[P-V|KeyVarsF],KeyVars0) :-
transform_parents(Parents0,NParents,KeyVarsF,KeyVars0).

68
packages/CLPBN/clpbn/ve.yap
View File

@ -14,55 +14,58 @@
*********************************/
:- module(clpbn_ve, [ve/3,
check_if_ve_done/1,
init_ve_solver/4,
run_ve_solver/3,
init_ve_ground_solver/5,
run_ve_ground_solver/3,
call_ve_ground_solver/6]).
:- module(clpbn_ve,
[ve/3,
check_if_ve_done/1,
init_ve_solver/4,
run_ve_solver/3,
init_ve_ground_solver/5,
run_ve_ground_solver/3,
call_ve_ground_solver/6
]).
:- use_module(library(atts)).
:- use_module(library(ordsets),
[ord_union/3,
ord_member/2]).
[ord_union/3,
ord_member/2
]).
:- use_module(library('clpbn/xbif'), [clpbn2xbif/3]).
:- use_module(library('clpbn/xbif'),
[clpbn2xbif/3]).
:- use_module(library('clpbn/graphviz'), [clpbn2gviz/4]).
:- use_module(library('clpbn/graphviz'),
[clpbn2gviz/4]).
:- use_module(library('clpbn/dists'),
[
dist/4,
get_dist_domain_size/2,
get_dist_params/2,
get_dist_domain_size/2,
get_dist_matrix/5]).
[dist/4,
get_dist_domain_size/2,
get_dist_params/2,
get_dist_domain_size/2,
get_dist_matrix/5
]).
:- use_module(library('clpbn/utils'), [
clpbn_not_var_member/2]).
:- use_module(library('clpbn/utils'),
[clpbn_not_var_member/2]).
:- use_module(library('clpbn/display'), [
clpbn_bind_vals/3]).
:- use_module(library('clpbn/display'),
[clpbn_bind_vals/3]).
:- use_module(library('clpbn/connected'),
[
init_influences/3,
influences/4,
factor_influences/4
]).
[init_influences/3,
influences/4,
factor_influences/4
]).
:- use_module(library(clpbn/matrix_cpt_utils)).
:- use_module(library(clpbn/numbers)).
:- use_module(library(lists),
[
member/2,
append/3,
delete/3
]).
[member/2,
append/3,
delete/3
]).
:- use_module(library(maplist)).
@ -71,7 +74,7 @@
:- use_module(library(clpbn/vmap)).
:- use_module(library('clpbn/aggregates'),
[check_for_agg_vars/2]).
[check_for_agg_vars/2]).
:- attribute size/1, all_diffs/1.
@ -474,4 +477,3 @@ multiply([F0|Fs], Vs, T) :-
multiply_factor(f(_,Vs1,T1), f(_,Vs0,T0), f(_,Vs,T)) :-
multiply_CPTs(T1, Vs1, T0, Vs0, T, Vs).

14
packages/CLPBN/clpbn/viterbi.yap
View File

@ -1,11 +1,13 @@
%:- style_check(all).
:- module(viterbi, [viterbi/4]).
:- module(viterbi,
[viterbi/4]).
:- use_module(library(lists),
[nth/3,
member/2]).
[nth/3,
member/2
]).
:- use_module(library(assoc)).
@ -17,8 +19,8 @@
:- ensure_loaded(library('clpbn/hmm')).
:- use_module(library('clpbn/dists'), [
get_dist_params/2]).
:- use_module(library('clpbn/dists'),
[get_dist_params/2]).
:- meta_predicate viterbi(:,:,+,-).
@ -231,5 +233,3 @@ trace(L1,Next,Dump,Map,Trace0,Trace) :-
matrix_get(Dump,[NL,P],New),
trace(NL,New,Dump,Map,[Key|Trace0],Trace).

18
packages/CLPBN/clpbn/vmap.yap
View File

@ -1,13 +1,12 @@
:- module(clpbn_vmap,
[
init_vmap/1, % init_vmap(-Vmap)
add_to_vmap/4, % add_to_vmap(+V,-I,+VMap0,VMapF)
get_from_vmap/3, % add_to_vmap(+V,-I,+VMap0)
vars_to_numbers/4, % vars_to_numbers(+Vs,-Is,+VMap0,VMapF)
lvars_to_numbers/4, % lvars_to_numbers(+LVs,-LIs,+VMap0,VMapF)
vmap_to_list/2
]).
[init_vmap/1, % init_vmap(-Vmap)
add_to_vmap/4, % add_to_vmap(+V,-I,+VMap0,VMapF)
get_from_vmap/3, % add_to_vmap(+V,-I,+VMap0)
vars_to_numbers/4, % vars_to_numbers(+Vs,-Is,+VMap0,VMapF)
lvars_to_numbers/4, % lvars_to_numbers(+LVs,-LIs,+VMap0,VMapF)
vmap_to_list/2
]).
:- use_module(library(rbtrees)).
:- use_module(library(maplist)).
@ -39,6 +38,3 @@ lvars_to_numbers(LVs, LIs, VMap0, VMap) :-
vmap_to_list(vmap(_,Map), L) :-
rb_visit(Map, L).

7
packages/CLPBN/clpbn/xbif.yap
View File

@ -2,10 +2,11 @@
% XMLBIF support for CLP(BN)
%
:- module(xbif, [clpbn2xbif/3]).
:- module(xbif,
[clpbn2xbif/3]).
:- use_module(library('clpbn/dists'), [
get_dist_domain/2]).
:- use_module(library('clpbn/dists'),
[get_dist_domain/2]).
clpbn2xbif(Stream, Name, Network) :-
format(Stream, '<?xml version="1.0" encoding="US-ASCII"?>

86
packages/CLPBN/learning/em.yap
View File

@ -5,67 +5,67 @@
:- module(clpbn_em, [em/5]).
:- reexport(library(clpbn),
[clpbn_flag/2,
clpbn_flag/3
]).
[clpbn_flag/2,
clpbn_flag/3
]).
:- use_module(library(clpbn),
[clpbn_init_graph/1,
clpbn_init_solver/4,
clpbn_run_solver/3,
clpbn_finalize_solver/1,
pfl_init_solver/5,
pfl_run_solver/3,
conditional_probability/3,
clpbn_flag/2
]).
[clpbn_init_graph/1,
clpbn_init_solver/4,
clpbn_run_solver/3,
clpbn_finalize_solver/1,
pfl_init_solver/5,
pfl_run_solver/3,
conditional_probability/3,
clpbn_flag/2
]).
:- use_module(library('clpbn/dists'),
[get_dist_domain_size/2,
empty_dist/2,
dist_new_table/2,
get_dist_key/2,
randomise_all_dists/0,
uniformise_all_dists/0
]).
[get_dist_domain_size/2,
empty_dist/2,
dist_new_table/2,
get_dist_key/2,
randomise_all_dists/0,
uniformise_all_dists/0
]).
:- use_module(library('clpbn/ground_factors'),
[generate_network/5,
f/3
]).
[generate_network/5,
f/3
]).
:- use_module(library('clpbn/utils'),
[check_for_hidden_vars/3,
sort_vars_by_key/3
]).
[check_for_hidden_vars/3,
sort_vars_by_key/3
]).
:- use_module(library('clpbn/learning/learn_utils'),
[run_all/1,
clpbn_vars/2,
normalise_counts/2,
compute_likelihood/3,
soften_sample/2
]).
[run_all/1,
clpbn_vars/2,
normalise_counts/2,
compute_likelihood/3,
soften_sample/2
]).
:- use_module(library(bhash),
[b_hash_new/1,
b_hash_lookup/3,
b_hash_insert/4
]).
[b_hash_new/1,
b_hash_lookup/3,
b_hash_insert/4
]).
:- use_module(library(matrix),
[matrix_add/3,
matrix_to_list/2
]).
[matrix_add/3,
matrix_to_list/2
]).
:- use_module(library(lists),
[member/2]).
[member/2]).
:- use_module(library(rbtrees),
[rb_new/1,
rb_insert/4,
rb_lookup/3
]).
[rb_new/1,
rb_insert/4,
rb_lookup/3
]).
:- use_module(library(maplist)).

52
packages/CLPBN/pfl.yap
View File

@ -4,34 +4,34 @@
%
:- module(pfl,
[op(550,yfx,@),
op(550,yfx,::),
op(1150,fx,bayes),
op(1150,fx,markov),
factor/6,
skolem/2,
defined_in_factor/2,
get_pfl_cpt/5, % given id and keys, return new keys and cpt
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
add_ground_factor/5 %add a new bayesian variable (for now)
]).
[op(550,yfx,@),
op(550,yfx,::),
op(1150,fx,bayes),
op(1150,fx,markov),
factor/6,
skolem/2,
defined_in_factor/2,
get_pfl_cpt/5, % given id and keys, return new keys and cpt
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
add_ground_factor/5 %add a new bayesian variable (for now)
]).
:- reexport(library(clpbn),
[clpbn_flag/2 as pfl_flag,
set_clpbn_flag/2 as set_pfl_flag,
conditional_probability/3,
pfl_init_solver/5,
pfl_run_solver/3
]).
[clpbn_flag/2 as pfl_flag,
set_clpbn_flag/2 as set_pfl_flag,
conditional_probability/3,
pfl_init_solver/5,
pfl_run_solver/3
]).
:- reexport(library(clpbn/horus),
[set_solver/1]).
[set_solver/1]).
:- reexport(library(clpbn/aggregates),
[avg_factors/5]).
[avg_factors/5]).
:- ( % if clp(bn) has done loading, we're top-level
predicate_property(set_pfl_flag(_,_), imported_from(clpbn))
@ -47,10 +47,10 @@
:- use_module(library(atts)).
:- use_module(library(lists),
[nth0/3,
append/3,
member/2
]).
[nth0/3,
append/3,
member/2
]).
:- dynamic factor/6, skolem_in/2, skolem/2, preprocess/3, evidence/2, id/1.