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

Merge branch 'master' of https://github.com/tacgomes/yap6.3

Browse Source 
Conflicts:
	packages/CLPBN/clpbn/horus.yap
This commit is contained in:
Vitor Santos Costa 2012-06-04 16:29:56 +01:00
commit 3669cb894f
139 changed files with 9203 additions and 7699 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

28
C/index.c
View File

@ -3298,6 +3298,28 @@ code_to_indexcl(yamop *ipc, int is_lu)
return ret;
}
static void
increase_expand_depth(yamop *ipc, struct intermediates *cint)
{
yamop *ncode;
cint->term_depth++;
if (/* ipc->opc == Yap_opcode(_switch_on_sub_arg_type) && */
(ncode = ipc->u.sllll.l4)->opc == Yap_opcode(_expand_clauses)) {
if (ncode->u.sssllp.s2 != cint->last_depth_size) {
cint->last_index_new_depth = cint->term_depth;
cint->last_depth_size = ncode->u.sssllp.s2;
}
}
}
static void
zero_expand_depth(PredEntry *ap, struct intermediates *cint)
{
cint->term_depth = cint->last_index_new_depth;
cint->last_depth_size = ap->cs.p_code.NOfClauses;
}
static yamop **
expand_index(struct intermediates *cint) {
CACHE_REGS
@ -3499,6 +3521,7 @@ expand_index(struct intermediates *cint) {
break;
/* instructions type e */
case _switch_on_type:
zero_expand_depth(ap, cint);
t = Deref(ARG1);
argno = 1;
i = 0;
@ -3520,6 +3543,7 @@ expand_index(struct intermediates *cint) {
parentcl = index_jmp(parentcl, parentcl, ipc, is_lu, e_code);
break;
case _switch_list_nl:
zero_expand_depth(ap, cint);
t = Deref(ARG1);
argno = 1;
i = 0;
@ -3548,6 +3572,7 @@ expand_index(struct intermediates *cint) {
parentcl = index_jmp(parentcl, parentcl, ipc, is_lu, e_code);
break;
case _switch_on_arg_type:
zero_expand_depth(ap, cint);
argno = arg_from_x(ipc->u.xllll.x);
i = 0;
t = Deref(XREGS[argno]);
@ -3578,12 +3603,14 @@ expand_index(struct intermediates *cint) {
ipc = ipc->u.sllll.l4;
i++;
} else if (IsPairTerm(t)) {
increase_expand_depth(ipc, cint);
s_reg = RepPair(t);
sp = push_stack(sp, -i-1, AbsPair(NULL), TermNil, cint);
labp = &(ipc->u.sllll.l1);
ipc = ipc->u.sllll.l1;
i = 0;
} else if (IsApplTerm(t)) {
increase_expand_depth(ipc, cint);
sp = push_stack(sp, -i-1, AbsAppl((CELL *)FunctorOfTerm(t)), TermNil, cint);
ipc = ipc->u.sllll.l3;
i = 0;
@ -3591,6 +3618,7 @@ expand_index(struct intermediates *cint) {
/* We don't push stack here, instead we go over to next argument
sp = push_stack(sp, -i-1, t, cint);
*/
increase_expand_depth(ipc, cint);
sp = push_stack(sp, -i-1, t, TermNil, cint);
ipc = ipc->u.sllll.l2;
i++;

8
Makefile.in
View File

@ -706,7 +706,7 @@ all: startup.yss
@ENABLE_SEMWEB@ @INSTALL_DLLS@ (cd packages/semweb; $(MAKE))
@ENABLE_SGML@ @INSTALL_DLLS@ (cd packages/sgml; $(MAKE))
@ENABLE_REAL@ (cd packages/real; $(MAKE))
@ENABLE_CLPBN_BP@ (cd packages/CLPBN/clpbn/bp ; $(MAKE))
@ENABLE_CLPBN_BP@ (cd packages/CLPBN/horus; $(MAKE))
@ENABLE_MINISAT@ (cd packages/swi-minisat2/C; $(MAKE))
@ENABLE_ZLIB@ @INSTALL_DLLS@ (cd packages/zlib; $(MAKE))
@ENABLE_CPLINT@ (cd packages/cplint/approx/simplecuddLPADs; $(MAKE))
@ -775,7 +775,7 @@ install_unix: startup.yss libYap.a
@ENABLE_SEMWEB@ @INSTALL_DLLS@ (cd packages/semweb; $(MAKE) install)
@ENABLE_SGML@ @INSTALL_DLLS@ (cd packages/sgml; $(MAKE) install)
@ENABLE_ZLIB@ @INSTALL_DLLS@ (cd packages/zlib; $(MAKE) @ZLIB_INSTALL@)
@ENABLE_CLPBN_BP@ @INSTALL_DLLS@ (cd packages/CLPBN/clpbn/bp ; $(MAKE) install)
@ENABLE_CLPBN_BP@ @INSTALL_DLLS@ (cd packages/CLPBN/horus; $(MAKE) install)
@ENABLE_MINISAT@ (cd packages/swi-minisat2/C; $(MAKE) install)
@INSTALL_MATLAB@ (cd library/matlab; $(MAKE) install)
@ENABLE_REAL@ (cd packages/real; $(MAKE) install)
@ -839,7 +839,7 @@ install_win32: startup.yss @ENABLE_WINCONSOLE@ pl-yap@EXEC_SUFFIX@
@ENABLE_SGML@ (cd packages/sgml; $(MAKE) install)
@ENABLE_ZLIB@ (cd packages/zlib; $(MAKE) @ZLIB_INSTALL@)
(cd packages/CLPBN ; $(MAKE) install)
@ENABLE_CLPBN_BP@ (cd packages/CLPBN/clpbn/bp ; $(MAKE) install)
@ENABLE_CLPBN_BP@ (cd packages/CLPBN/horus; $(MAKE) install)
@ENABLE_JPL@ (cd packages/jpl ; $(MAKE) install)
@ENABLE_MINISAT@ (cd packages/swi-minisat2/C; $(MAKE) install)
@ENABLE_CPLINT@ (cd packages/cplint; $(MAKE) install)
@ -904,7 +904,7 @@ clean: clean_docs
@ENABLE_SGML@ @INSTALL_DLLS@ (cd packages/sgml; $(MAKE) clean)
@ENABLE_REAL@ (cd packages/real; $(MAKE) clean)
@ENABLE_MINISAT@ (cd packages/swi-minisat2; $(MAKE) clean)
@ENABLE_CLPBN_BP@ (cd packages/CLPBN/clpbn/bp; $(MAKE) clean)
@ENABLE_CLPBN_BP@ (cd packages/CLPBN/horus; $(MAKE) clean)
@ENABLE_ZLIB@ @INSTALL_DLLS@ (cd packages/zlib; $(MAKE) clean)
@ENABLE_PRISM@ (cd packages/prism/src/c; $(MAKE) clean)
@ENABLE_PRISM@ (cd packages/prism/src/prolog; $(MAKE) clean)

8
configure vendored
View File

@ -10519,8 +10519,7 @@ mkdir -p packages/clib/maildrop/rfc822
mkdir -p packages/clib/maildrop/rfc2045
mkdir -p packages/CLPBN
mkdir -p packages/CLPBN/clpbn
mkdir -p packages/CLPBN/clpbn/bp
mkdir -p packages/CLPBN/clpbn/bp/xmlParser
mkdir -p packages/CLPBN/horus
mkdir -p packages/clpqr
mkdir -p packages/cplint
mkdir -p packages/cplint/approx
@ -10673,6 +10672,7 @@ ac_config_files="$ac_config_files packages/zlib/Makefile"
fi
if test "$ENABLE_CUDD" = ""; then
ac_config_files="$ac_config_files packages/bdd/Makefile"
@ -10695,7 +10695,7 @@ ac_config_files="$ac_config_files packages/real/Makefile"
fi
if test "$ENABLE_CLPBN_BP" = ""; then
ac_config_files="$ac_config_files packages/CLPBN/clpbn/bp/Makefile"
ac_config_files="$ac_config_files packages/CLPBN/horus/Makefile"
fi
@ -11464,7 +11464,7 @@ do
"packages/swi-minisat2/Makefile") CONFIG_FILES="$CONFIG_FILES packages/swi-minisat2/Makefile" ;;
"packages/swi-minisat2/C/Makefile") CONFIG_FILES="$CONFIG_FILES packages/swi-minisat2/C/Makefile" ;;
"packages/real/Makefile") CONFIG_FILES="$CONFIG_FILES packages/real/Makefile" ;;
"packages/CLPBN/clpbn/bp/Makefile") CONFIG_FILES="$CONFIG_FILES packages/CLPBN/clpbn/bp/Makefile" ;;
"packages/CLPBN/horus/Makefile") CONFIG_FILES="$CONFIG_FILES packages/CLPBN/horus/Makefile" ;;
"library/gecode/Makefile") CONFIG_FILES="$CONFIG_FILES library/gecode/Makefile" ;;
"packages/prism/src/c/Makefile") CONFIG_FILES="$CONFIG_FILES packages/prism/src/c/Makefile" ;;
"packages/prism/src/prolog/Makefile") CONFIG_FILES="$CONFIG_FILES packages/prism/src/prolog/Makefile" ;;

6
configure.in
View File

@ -2300,8 +2300,7 @@ mkdir -p packages/clib/maildrop/rfc822
mkdir -p packages/clib/maildrop/rfc2045
mkdir -p packages/CLPBN
mkdir -p packages/CLPBN/clpbn
mkdir -p packages/CLPBN/clpbn/bp
mkdir -p packages/CLPBN/clpbn/bp/xmlParser
mkdir -p packages/CLPBN/horus
mkdir -p packages/clpqr
mkdir -p packages/cplint
mkdir -p packages/cplint/approx
@ -2415,6 +2414,7 @@ if test "$ENABLE_ZLIB" = ""; then
AC_CONFIG_FILES([packages/zlib/Makefile])
fi
if test "$ENABLE_CUDD" = ""; then
AC_CONFIG_FILES([packages/bdd/Makefile])
AC_CONFIG_FILES([packages/ProbLog/simplecudd/Makefile])
@ -2431,7 +2431,7 @@ AC_CONFIG_FILES([packages/real/Makefile])
fi
if test "$ENABLE_CLPBN_BP" = ""; then
AC_CONFIG_FILES([packages/CLPBN/clpbn/bp/Makefile])
AC_CONFIG_FILES([packages/CLPBN/horus/Makefile])
fi
if test "$ENABLE_GECODE" = ""; then

14
packages/CLPBN/Makefile.in
View File

@ -42,19 +42,19 @@ CLPBN_PROGRAMS= \
$(CLPBN_SRCDIR)/aggregates.yap \
$(CLPBN_SRCDIR)/bdd.yap \
$(CLPBN_SRCDIR)/bnt.yap \
$(CLPBN_SRCDIR)/bp.yap \
$(CLPBN_SRCDIR)/connected.yap \
$(CLPBN_SRCDIR)/discrete_utils.yap \
$(CLPBN_SRCDIR)/display.yap \
$(CLPBN_SRCDIR)/dists.yap \
$(CLPBN_SRCDIR)/evidence.yap \
$(CLPBN_SRCDIR)/fove.yap \
$(CLPBN_SRCDIR)/gibbs.yap \
$(CLPBN_SRCDIR)/graphs.yap \
$(CLPBN_SRCDIR)/graphviz.yap \
$(CLPBN_SRCDIR)/ground_factors.yap \
$(CLPBN_SRCDIR)/hmm.yap \
$(CLPBN_SRCDIR)/horus.yap \
$(CLPBN_SRCDIR)/horus_ground.yap \
$(CLPBN_SRCDIR)/horus_lifted.yap \
$(CLPBN_SRCDIR)/jt.yap \
$(CLPBN_SRCDIR)/matrix_cpt_utils.yap \
$(CLPBN_SRCDIR)/pgrammar.yap \
@ -94,8 +94,16 @@ CLPBN_HMMER_EXAMPLES= \
$(CLPBN_EXDIR)/HMMer/score.yap
CLPBN_EXAMPLES= \
$(CLPBN_EXDIR)/burglary-alarm.fg \
$(CLPBN_EXDIR)/burglary-alarm.yap \
$(CLPBN_EXDIR)/burglary-alarm.uai \
$(CLPBN_EXDIR)/cg.yap \
$(CLPBN_EXDIR)/sprinkler.yap
$(CLPBN_EXDIR)/city.yap \
$(CLPBN_EXDIR)/comp_workshops.yap \
$(CLPBN_EXDIR)/social_domain1.yap \
$(CLPBN_EXDIR)/social_domain2.yap \
$(CLPBN_EXDIR)/sprinkler.yap \
$(CLPBN_EXDIR)/workshop_attrs.yap
install: $(CLBN_TOP) $(CLBN_PROGRAMS) $(CLPBN_PROGRAMS)

78
packages/CLPBN/benchmarks/benchs.sh Executable file
View File

@ -0,0 +1,78 @@
function prepare_new_run
{
YAP=~/bin/$SHORTNAME-$SOLVER
LOG_FILE=$SOLVER.log
#LOG_FILE=results`date "+ %H:%M:%S %d-%m-%Y"`.
rm -f $LOG_FILE
rm -f ignore.$LOG_FILE
cp ~/bin/yap $YAP
}
function run_solver
{
constraint=$1
solver_flag=true
if [ -n "$2" ]; then
if [ $SOLVER = hve ]; then
solver_flag=clpbn_horus:set_horus_flag\(elim_heuristic,$2\)
elif [ $SOLVER = bp ]; then
solver_flag=clpbn_horus:set_horus_flag\(schedule,$2\)
elif [ $SOLVER = cbp ]; then
solver_flag=clpbn_horus:set_horus_flag\(schedule,$2\)
else
echo "unknow flag $2"
fi
fi
/usr/bin/time -o $LOG_FILE -a -f "%U\t%S\t%e\t%M" \
$YAP << EOF >> $LOG_FILE &>> ignore.$LOG_FILE
nogc.
[$NETWORK].
[$constraint].
clpbn_horus:set_solver($SOLVER).
clpbn_horus:set_horus_flag(use_logarithms, true).
clpbn_horus:set_horus_flag(verbosity, 1).
$solver_flag.
$QUERY.
open("$LOG_FILE", 'append', S), format(S, '$constraint ~15+ ', []), close(S).
EOF
}
function clear_log_files
{
rm -f *~
rm -f ../*~
rm -f school/*.log school/*~
rm -f ../school/*.log ../school/*~
rm -f city/*.log city/*~
rm -f ../city/*.log ../city/*~
rm -f workshop_attrs/*.log workshop_attrs/*~
rm -f ../workshop_attrs/*.log ../workshop_attrs/*~
echo all done!
}
function write_header
{
echo -n "****************************************" >> $LOG_FILE
echo "****************************************" >> $LOG_FILE
echo "results for solver $1 user(s) sys(s) real(s), mem(kB)" >> $LOG_FILE
echo -n "****************************************" >> $LOG_FILE
echo "****************************************" >> $LOG_FILE
}
if [ $1 ] && [ $1 == "clean" ]; then
clear_log_files
fi

37
packages/CLPBN/benchmarks/city/bp_tests.sh Executable file
View File

@ -0,0 +1,37 @@
#!/bin/bash
source city.sh
source ../benchs.sh
SOLVER="bp"
function run_all_graphs
{
write_header $1
run_solver city1000 $2
run_solver city5000 $2
run_solver city10000 $2
run_solver city15000 $2
run_solver city20000 $2
run_solver city25000 $2
run_solver city30000 $2
run_solver city35000 $2
run_solver city40000 $2
run_solver city45000 $2
run_solver city50000 $2
run_solver city55000 $2
run_solver city60000 $2
run_solver city65000 $2
return
run_solver city70000 $2
run_solver city75000 $2
run_solver city80000 $2
run_solver city85000 $2
run_solver city90000 $2
run_solver city95000 $2
run_solver city100000 $2
}
prepare_new_run
run_all_graphs "bp(shedule=seq_fixed) " seq_fixed

36
packages/CLPBN/benchmarks/city/cbp_tests.sh Executable file
View File

@ -0,0 +1,36 @@
#!/bin/bash
source city.sh
source ../benchs.sh
SOLVER="cbp"
function run_all_graphs
{
write_header $1
run_solver city1000 $2
run_solver city5000 $2
run_solver city10000 $2
run_solver city15000 $2
run_solver city20000 $2
run_solver city25000 $2
run_solver city30000 $2
run_solver city35000 $2
run_solver city40000 $2
run_solver city45000 $2
run_solver city50000 $2
run_solver city55000 $2
run_solver city60000 $2
run_solver city65000 $2
run_solver city70000 $2
run_solver city75000 $2
run_solver city80000 $2
run_solver city85000 $2
run_solver city90000 $2
run_solver city95000 $2
run_solver city100000 $2
}
prepare_new_run
run_all_graphs "cbp(shedule=seq_fixed) " seq_fixed

6
packages/CLPBN/benchmarks/city/city.sh Executable file
View File

@ -0,0 +1,6 @@
#!/bin/bash
NETWORK="'../../examples/city'"
SHORTNAME="city"
QUERY="is_joe_guilty(X)"

36
packages/CLPBN/benchmarks/city/fove_tests.sh Executable file
View File

@ -0,0 +1,36 @@
#!/bin/bash
source city.sh
source ../benchs.sh
SOLVER="fove"
function run_all_graphs
{
write_header $1
run_solver city1000 $2
run_solver city5000 $2
run_solver city10000 $2
run_solver city15000 $2
run_solver city20000 $2
run_solver city25000 $2
run_solver city30000 $2
run_solver city35000 $2
run_solver city40000 $2
run_solver city45000 $2
run_solver city50000 $2
run_solver city55000 $2
run_solver city60000 $2
run_solver city65000 $2
run_solver city70000 $2
run_solver city75000 $2
run_solver city80000 $2
run_solver city85000 $2
run_solver city90000 $2
run_solver city95000 $2
run_solver city100000 $2
}
prepare_new_run
run_all_graphs "fove "

20
packages/CLPBN/clpbn/bp/benchmarks/city/city_generator.sh → packages/CLPBN/benchmarks/city/gen_city.sh
View File

@ -1,21 +1,17 @@
#!/home/tiago/bin/yap -L --
#! /home/tgomes/bin/yap -L --
:- initialization(main).
main :-
unix(argv([H])),
generate_town(H).
generate_town(N) :-
atomic_concat(['city_', N, '.yap'], FileName),
unix(argv([N])),
atomic_concat(['city', N, '.yap'], FileName),
open(FileName, 'write', S),
atom_number(N, N2),
generate_people(S, N2, 4),
generate_people(S, N2, 1),
write(S, '\n'),
generate_query(S, N2, 4),
generate_evidence(S, N2, 1),
write(S, '\n'),
close(S).
@ -28,10 +24,10 @@ generate_people(S, N, Counting) :-
generate_people(S, N, Counting1).
generate_query(S, N, Counting) :-
generate_evidence(S, N, Counting) :-
Counting > N, !.
generate_query(S, N, Counting) :- !,
generate_evidence(S, N, Counting) :- !,
format(S, 'ev(descn(p~w, t)).~n', [Counting]),
Counting1 is Counting + 1,
generate_query(S, N, Counting1).
generate_evidence(S, N, Counting1).

37
packages/CLPBN/benchmarks/city/hve_tests.sh Executable file
View File

@ -0,0 +1,37 @@
#!/bin/bash
source city.sh
source ../benchs.sh
SOLVER="hve"
function run_all_graphs
{
write_header $1
run_solver city1000 $2
run_solver city5000 $2
run_solver city10000 $2
run_solver city15000 $2
run_solver city20000 $2
run_solver city25000 $2
run_solver city30000 $2
run_solver city35000 $2
run_solver city40000 $2
run_solver city45000 $2
run_solver city50000 $2
run_solver city55000 $2
run_solver city60000 $2
run_solver city65000 $2
run_solver city70000 $2
run_solver city75000 $2
run_solver city80000 $2
run_solver city85000 $2
run_solver city90000 $2
run_solver city95000 $2
run_solver city100000 $2
}
prepare_new_run
run_all_graphs "hve(elim_heuristic=min_neighbors) " min_neighbors

31
packages/CLPBN/benchmarks/comp_workshops/bp_tests.sh Executable file
View File

@ -0,0 +1,31 @@
#!/bin/bash
source cw.sh
source ../benchs.sh
SOLVER="bp"
function run_all_graphs
{
write_header $1
run_solver p1000w$N_WORKSHOPS $2
run_solver p5000w$N_WORKSHOPS $2
run_solver p10000w$N_WORKSHOPS $2
run_solver p15000w$N_WORKSHOPS $2
run_solver p20000w$N_WORKSHOPS $2
run_solver p25000w$N_WORKSHOPS $2
return
run_solver p30000w$N_WORKSHOPS $2
run_solver p35000w$N_WORKSHOPS $2
run_solver p40000w$N_WORKSHOPS $2
run_solver p45000w$N_WORKSHOPS $2
run_solver p50000w$N_WORKSHOPS $2
run_solver p55000w$N_WORKSHOPS $2
run_solver p60000w$N_WORKSHOPS $2
run_solver p65000w$N_WORKSHOPS $2
run_solver p70000w$N_WORKSHOPS $2
}
prepare_new_run
run_all_graphs "bp(shedule=seq_fixed) " seq_fixed

30
packages/CLPBN/benchmarks/comp_workshops/cbp_tests.sh Executable file
View File

@ -0,0 +1,30 @@
#!/bin/bash
source cw.sh
source ../benchs.sh
SOLVER="cbp"
function run_all_graphs
{
write_header $1
run_solver p1000w$N_WORKSHOPS $2
run_solver p5000w$N_WORKSHOPS $2
run_solver p10000w$N_WORKSHOPS $2
run_solver p15000w$N_WORKSHOPS $2
run_solver p20000w$N_WORKSHOPS $2
run_solver p25000w$N_WORKSHOPS $2
run_solver p30000w$N_WORKSHOPS $2
run_solver p35000w$N_WORKSHOPS $2
run_solver p40000w$N_WORKSHOPS $2
run_solver p45000w$N_WORKSHOPS $2
run_solver p50000w$N_WORKSHOPS $2
run_solver p55000w$N_WORKSHOPS $2
run_solver p60000w$N_WORKSHOPS $2
run_solver p65000w$N_WORKSHOPS $2
run_solver p70000w$N_WORKSHOPS $2
}
prepare_new_run
run_all_graphs "cbp(shedule=seq_fixed) " seq_fixed

8
packages/CLPBN/benchmarks/comp_workshops/cw.sh Executable file
View File

@ -0,0 +1,8 @@
#!/bin/bash
NETWORK="'../../examples/comp_workshops'"
SHORTNAME="cw"
QUERY="series(X)"
N_WORKSHOPS=10

31
packages/CLPBN/benchmarks/comp_workshops/fove_tests.sh Executable file
View File

@ -0,0 +1,31 @@
#!/bin/bash
source cw.sh
source ../benchs.sh
SOLVER="fove"
function run_all_graphs
{
write_header $1
run_solver p1000w$N_WORKSHOPS $2
run_solver p5000w$N_WORKSHOPS $2
run_solver p10000w$N_WORKSHOPS $2
run_solver p15000w$N_WORKSHOPS $2
run_solver p20000w$N_WORKSHOPS $2
run_solver p25000w$N_WORKSHOPS $2
run_solver p30000w$N_WORKSHOPS $2
run_solver p35000w$N_WORKSHOPS $2
run_solver p40000w$N_WORKSHOPS $2
run_solver p45000w$N_WORKSHOPS $2
run_solver p50000w$N_WORKSHOPS $2
run_solver p55000w$N_WORKSHOPS $2
run_solver p60000w$N_WORKSHOPS $2
run_solver p65000w$N_WORKSHOPS $2
run_solver p70000w$N_WORKSHOPS $2
}
prepare_new_run
run_all_graphs "fove "

35
packages/CLPBN/benchmarks/comp_workshops/gen_workshops.sh Executable file
View File

@ -0,0 +1,35 @@
#!/home/tgomes/bin/yap -L --
:- use_module(library(lists)).
:- initialization(main).
main :-
unix(argv(Args)),
nth(1, Args, NP), % number of invitees
nth(2, Args, NW), % number of workshops
atomic_concat(['p', NP , 'w', NW, '.yap'], FileName),
open(FileName, 'write', S),
atom_number(NP, NP2),
atom_number(NW, NW2),
gen(S, NP2, NW2, 1),
write(S, '\n'),
close(S).
gen(_, NP, _, Count) :-
Count > NP, !.
gen(S, NP, NW, Count) :-
gen_workshops(S, Count, NW, 1),
Count1 is Count + 1,
gen(S, NP, NW, Count1).
gen_workshops(_, _, NW, Count) :-
Count > NW, !.
gen_workshops(S, P, NW, Count) :-
format(S, 'c(p~w,w~w).~n', [P,Count]),
Count1 is Count + 1,
gen_workshops(S, P, NW, Count1).

30
packages/CLPBN/benchmarks/comp_workshops/hve_tests.sh Executable file
View File

@ -0,0 +1,30 @@
#!/bin/bash
source cw.sh
source ../benchs.sh
SOLVER="hve"
function run_all_graphs
{
write_header $1
run_solver p1000w$N_WORKSHOPS $2
run_solver p5000w$N_WORKSHOPS $2
run_solver p10000w$N_WORKSHOPS $2
run_solver p15000w$N_WORKSHOPS $2
run_solver p20000w$N_WORKSHOPS $2
run_solver p25000w$N_WORKSHOPS $2
run_solver p30000w$N_WORKSHOPS $2
run_solver p35000w$N_WORKSHOPS $2
run_solver p40000w$N_WORKSHOPS $2
run_solver p45000w$N_WORKSHOPS $2
run_solver p50000w$N_WORKSHOPS $2
run_solver p55000w$N_WORKSHOPS $2
run_solver p60000w$N_WORKSHOPS $2
run_solver p65000w$N_WORKSHOPS $2
run_solver p70000w$N_WORKSHOPS $2
}
prepare_new_run
run_all_graphs "hve(elim_heuristic=min_neighbors) " min_neighbors

0
packages/CLPBN/clpbn/bp/benchmarks/school/missing10.yap → packages/CLPBN/benchmarks/school/missing10.yap
View File

0
packages/CLPBN/clpbn/bp/benchmarks/school/missing20.yap → packages/CLPBN/benchmarks/school/missing20.yap
View File

0
packages/CLPBN/clpbn/bp/benchmarks/school/missing30.yap → packages/CLPBN/benchmarks/school/missing30.yap
View File

0
packages/CLPBN/clpbn/bp/benchmarks/school/missing40.yap → packages/CLPBN/benchmarks/school/missing40.yap
View File

0
packages/CLPBN/clpbn/bp/benchmarks/school/missing5.yap → packages/CLPBN/benchmarks/school/missing5.yap
View File

0
packages/CLPBN/clpbn/bp/benchmarks/school/missing50.yap → packages/CLPBN/benchmarks/school/missing50.yap
View File

0
packages/CLPBN/clpbn/bp/benchmarks/school/run_school_tests.sh → packages/CLPBN/benchmarks/school/run_school_tests.sh
View File

30
packages/CLPBN/benchmarks/smokers/bp_tests.sh Executable file
View File

@ -0,0 +1,30 @@
#!/bin/bash
source sm.sh
source ../benchs.sh
SOLVER="bp"
function run_all_graphs
{
write_header $1
run_solver pop100 $2
run_solver pop200 $2
run_solver pop300 $2
run_solver pop400 $2
run_solver pop500 $2
run_solver pop600 $2
run_solver pop700 $2
run_solver pop800 $2
run_solver pop900 $2
run_solver pop1000 $2
run_solver pop1100 $2
run_solver pop1200 $2
run_solver pop1300 $2
run_solver pop1400 $2
run_solver pop1500 $2
}
prepare_new_run
run_all_graphs "bp(shedule=seq_fixed) " seq_fixed

30
packages/CLPBN/benchmarks/smokers/cbp_tests.sh Executable file
View File

@ -0,0 +1,30 @@
#!/bin/bash
source sm.sh
source ../benchs.sh
SOLVER="cbp"
function run_all_graphs
{
write_header $1
run_solver pop100 $2
run_solver pop200 $2
run_solver pop300 $2
run_solver pop400 $2
run_solver pop500 $2
run_solver pop600 $2
run_solver pop700 $2
run_solver pop800 $2
run_solver pop900 $2
run_solver pop1000 $2
run_solver pop1100 $2
run_solver pop1200 $2
run_solver pop1300 $2
run_solver pop1400 $2
run_solver pop1500 $2
}
prepare_new_run
run_all_graphs "cbp(shedule=seq_fixed) " seq_fixed

31
packages/CLPBN/benchmarks/smokers/fove_tests.sh Executable file
View File

@ -0,0 +1,31 @@
#!/bin/bash
source sm.sh
source ../benchs.sh
SOLVER="fove"
function run_all_graphs
{
write_header $1
run_solver pop100 $2
run_solver pop200 $2
run_solver pop300 $2
run_solver pop400 $2
run_solver pop500 $2
run_solver pop600 $2
run_solver pop700 $2
run_solver pop800 $2
run_solver pop900 $2
run_solver pop1000 $2
run_solver pop1100 $2
run_solver pop1200 $2
run_solver pop1300 $2
run_solver pop1400 $2
run_solver pop1500 $2
}
prepare_new_run
run_all_graphs "fove "

10
packages/CLPBN/clpbn/bp/benchmarks/workshop_attrs/people_generator.sh → packages/CLPBN/benchmarks/smokers/gen_people.sh
View File

@ -1,16 +1,12 @@
#!/home/tiago/bin/yap -L --
#!/home/tgomes/bin/yap -L --
:- initialization(main).
main :-
unix(argv([H])),
generate_town(H).
generate_town(N) :-
atomic_concat(['pop_', N, '.yap'], FileName),
unix(argv([N])),
atomic_concat(['pop', N, '.yap'], FileName),
open(FileName, 'write', S),
atom_number(N, N2),
generate_people(S, N2, 4),

33
packages/CLPBN/benchmarks/smokers/hve_tests.sh Executable file
View File

@ -0,0 +1,33 @@
#!/bin/bash
source sm.sh
source ../benchs.sh
SOLVER="hve"
function run_all_graphs
{
write_header $1
run_solver pop100 $2
#run_solver pop200 $2
#run_solver pop300 $2
#run_solver pop400 $2
#run_solver pop500 $2
#run_solver pop600 $2
#run_solver pop700 $2
#run_solver pop800 $2
#run_solver pop900 $2
#run_solver pop1000 $2
#run_solver pop1100 $2
#run_solver pop1200 $2
#run_solver pop1300 $2
#run_solver pop1400 $2
#run_solver pop1500 $2
}
prepare_new_run
run_all_graphs "hve(elim_heuristic=min_neighbors) " min_neighbors
#run_all_graphs "hve(elim_heuristic=min_weight) " min_weight
#run_all_graphs "hve(elim_heuristic=min_fill) " min_fill
#run_all_graphs "hve(elim_heuristic=weighted_min_fill) " weighted_min_fill

6
packages/CLPBN/benchmarks/smokers/sm.sh Executable file
View File

@ -0,0 +1,6 @@
#!/bin/bash
NETWORK="'../../examples/social_domain2'"
SHORTNAME="sm"
QUERY="smokes(p1,t), smokes(p2,t), friends(p1,p2,X)"

37
packages/CLPBN/benchmarks/workshop_attrs/bp_tests.sh Executable file
View File

@ -0,0 +1,37 @@
#!/bin/bash
source wa.sh
source ../benchs.sh
SOLVER="bp"
function run_all_graphs
{
write_header $1
run_solver p1000attrs$N_ATTRS $2
run_solver p5000attrs$N_ATTRS $2
run_solver p10000attrs$N_ATTRS $2
run_solver p15000attrs$N_ATTRS $2
run_solver p20000attrs$N_ATTRS $2
run_solver p25000attrs$N_ATTRS $2
run_solver p30000attrs$N_ATTRS $2
run_solver p35000attrs$N_ATTRS $2
return
run_solver p40000attrs$N_ATTRS $2
run_solver p45000attrs$N_ATTRS $2
run_solver p50000attrs$N_ATTRS $2
run_solver p55000attrs$N_ATTRS $2
run_solver p60000attrs$N_ATTRS $2
run_solver p65000attrs$N_ATTRS $2
run_solver p70000attrs$N_ATTRS $2
run_solver p75000attrs$N_ATTRS $2
run_solver p80000attrs$N_ATTRS $2
run_solver p85000attrs$N_ATTRS $2
run_solver p90000attrs$N_ATTRS $2
run_solver p95000attrs$N_ATTRS $2
run_solver p100000attrs$N_ATTRS $2
}
prepare_new_run
run_all_graphs "bp(shedule=seq_fixed) " seq_fixed

36
packages/CLPBN/benchmarks/workshop_attrs/cbp_tests.sh Executable file
View File

@ -0,0 +1,36 @@
#!/bin/bash
source wa.sh
source ../benchs.sh
SOLVER="cbp"
function run_all_graphs
{
write_header $1
run_solver p1000attrs$N_ATTRS $2
run_solver p5000attrs$N_ATTRS $2
run_solver p10000attrs$N_ATTRS $2
run_solver p15000attrs$N_ATTRS $2
run_solver p20000attrs$N_ATTRS $2
run_solver p25000attrs$N_ATTRS $2
run_solver p30000attrs$N_ATTRS $2
run_solver p35000attrs$N_ATTRS $2
run_solver p40000attrs$N_ATTRS $2
run_solver p45000attrs$N_ATTRS $2
run_solver p50000attrs$N_ATTRS $2
run_solver p55000attrs$N_ATTRS $2
run_solver p60000attrs$N_ATTRS $2
run_solver p65000attrs$N_ATTRS $2
run_solver p70000attrs$N_ATTRS $2
run_solver p75000attrs$N_ATTRS $2
run_solver p80000attrs$N_ATTRS $2
run_solver p85000attrs$N_ATTRS $2
run_solver p90000attrs$N_ATTRS $2
run_solver p95000attrs$N_ATTRS $2
run_solver p100000attrs$N_ATTRS $2
}
prepare_new_run
run_all_graphs "cbp(shedule=seq_fixed) " seq_fixed

37
packages/CLPBN/benchmarks/workshop_attrs/fove_tests.sh Executable file
View File

@ -0,0 +1,37 @@
#!/bin/bash
source wa.sh
source ../benchs.sh
SOLVER="fove"
function run_all_graphs
{
write_header $1
run_solver p1000attrs$N_ATTRS $2
run_solver p5000attrs$N_ATTRS $2
run_solver p10000attrs$N_ATTRS $2
run_solver p15000attrs$N_ATTRS $2
run_solver p20000attrs$N_ATTRS $2
run_solver p25000attrs$N_ATTRS $2
run_solver p30000attrs$N_ATTRS $2
run_solver p35000attrs$N_ATTRS $2
run_solver p40000attrs$N_ATTRS $2
run_solver p45000attrs$N_ATTRS $2
run_solver p50000attrs$N_ATTRS $2
run_solver p55000attrs$N_ATTRS $2
run_solver p60000attrs$N_ATTRS $2
run_solver p65000attrs$N_ATTRS $2
run_solver p70000attrs$N_ATTRS $2
run_solver p75000attrs$N_ATTRS $2
run_solver p80000attrs$N_ATTRS $2
run_solver p85000attrs$N_ATTRS $2
run_solver p90000attrs$N_ATTRS $2
run_solver p95000attrs$N_ATTRS $2
run_solver p100000attrs$N_ATTRS $2
}
prepare_new_run
run_all_graphs "fove "

39
packages/CLPBN/benchmarks/workshop_attrs/gen_attrs.sh Executable file
View File

@ -0,0 +1,39 @@
#!/home/tgomes/bin/yap -L --
:- use_module(library(lists)).
:- initialization(main).
main :-
unix(argv(Args)),
nth(1, Args, NP), % number of invitees
nth(2, Args, NA), % number of attributes
atomic_concat(['p', NP , 'attrs', NA, '.yap'], FileName),
open(FileName, 'write', S),
atom_number(NP, NP2),
atom_number(NA, NA2),
generate_people(S, NP2, 1),
write(S, '\n'),
generate_attrs(S, NA2, 7),
write(S, '\n'),
close(S).
generate_people(S, N, Counting) :-
Counting > N, !.
generate_people(S, N, Counting) :-
format(S, 'people(p~w).~n', [Counting]),
Counting1 is Counting + 1,
generate_people(S, N, Counting1).
generate_attrs(S, N, Counting) :-
Counting > N, !.
generate_attrs(S, N, Counting) :-
%format(S, 'people(p~w).~n', [Counting]),
format(S, 'markov attends(P)::[t,f], attr~w::[t,f]', [Counting]),
format(S, '; [0.7, 0.3, 0.3, 0.3] ; [people(P)].~n',[]),
Counting1 is Counting + 1,
generate_attrs(S, N, Counting1).

36
packages/CLPBN/benchmarks/workshop_attrs/hve_tests.sh Executable file
View File

@ -0,0 +1,36 @@
#!/bin/bash
source wa.sh
source ../benchs.sh
SOLVER="hve"
function run_all_graphs
{
write_header $1
run_solver p1000attrs$N_ATTRS $2
run_solver p5000attrs$N_ATTRS $2
run_solver p10000attrs$N_ATTRS $2
run_solver p15000attrs$N_ATTRS $2
run_solver p20000attrs$N_ATTRS $2
run_solver p25000attrs$N_ATTRS $2
run_solver p30000attrs$N_ATTRS $2
run_solver p35000attrs$N_ATTRS $2
run_solver p40000attrs$N_ATTRS $2
run_solver p45000attrs$N_ATTRS $2
run_solver p50000attrs$N_ATTRS $2
run_solver p55000attrs$N_ATTRS $2
run_solver p60000attrs$N_ATTRS $2
run_solver p65000attrs$N_ATTRS $2
run_solver p70000attrs$N_ATTRS $2
run_solver p75000attrs$N_ATTRS $2
run_solver p80000attrs$N_ATTRS $2
run_solver p85000attrs$N_ATTRS $2
run_solver p90000attrs$N_ATTRS $2
run_solver p95000attrs$N_ATTRS $2
run_solver p100000attrs$N_ATTRS $2
}
prepare_new_run
run_all_graphs "hve(elim_heuristic=min_neighbors) " min_neighbors

9
packages/CLPBN/benchmarks/workshop_attrs/wa.sh Executable file
View File

@ -0,0 +1,9 @@
#!/bin/bash
NETWORK="'../../examples/workshop_attrs'"
SHORTNAME="wa"
QUERY="series(X)"
N_ATTRS=6

44
packages/CLPBN/clpbn.yap
View File

@ -1,5 +1,4 @@
:- module(clpbn, [{}/1,
clpbn_flag/2,
set_clpbn_flag/2,
@ -39,24 +38,22 @@
run_ve_solver/3
]).
:- use_module('clpbn/bp',
[bp/3,
check_if_bp_done/1,
init_bp_solver/4,
run_bp_solver/3,
call_bp_ground/6,
finalize_bp_solver/1
:- use_module('clpbn/horus_ground',
[call_horus_ground_solver/6,
check_if_horus_ground_solver_done/1,
init_horus_ground_solver/4,
run_horus_ground_solver/3,
finalize_horus_ground_solver/1
]).
:- use_module('clpbn/fove',
[fove/3,
check_if_fove_done/1,
init_fove_solver/4,
run_fove_solver/3,
finalize_fove_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
]).
:- use_module('clpbn/jt',
[jt/3,
init_jt_solver/4,
@ -306,18 +303,19 @@ write_out(jt, GVars, AVars, DiffVars) :-
jt(GVars, AVars, DiffVars).
write_out(bdd, GVars, AVars, DiffVars) :-
bdd(GVars, AVars, DiffVars).
write_out(bp, GVars, AVars, DiffVars) :-
bp(GVars, AVars, DiffVars).
write_out(bp, _GVars, _AVars, _DiffVars) :-
writeln('interface not supported anymore').
%bp(GVars, AVars, DiffVars).
write_out(gibbs, GVars, AVars, DiffVars) :-
gibbs(GVars, AVars, DiffVars).
write_out(bnt, GVars, AVars, DiffVars) :-
do_bnt(GVars, AVars, DiffVars).
write_out(fove, GVars, AVars, DiffVars) :-
fove(GVars, AVars, DiffVars).
call_horus_lifted_solver(GVars, AVars, DiffVars).
% call a solver with keys, not actual variables
call_ground_solver(bp, GVars, GoalKeys, Keys, Factors, Evidence, Answ) :-
call_bp_ground(GVars, GoalKeys, Keys, Factors, Evidence, Answ).
call_horus_ground_solver(GVars, GoalKeys, Keys, Factors, Evidence, Answ).
get_bnode(Var, Goal) :-
@ -400,7 +398,7 @@ bind_clpbn(_, Var, _, _, _, _, []) :-
check_if_ve_done(Var), !.
bind_clpbn(_, Var, _, _, _, _, []) :-
use(bp),
check_if_bp_done(Var), !.
check_if_horus_ground_solver_done(Var), !.
bind_clpbn(_, Var, _, _, _, _, []) :-
use(jt),
check_if_ve_done(Var), !.
@ -475,7 +473,7 @@ clpbn_init_solver(gibbs, LVs, Vs0, VarsWithUnboundKeys, State) :-
clpbn_init_solver(ve, LVs, Vs0, VarsWithUnboundKeys, State) :-
init_ve_solver(LVs, Vs0, VarsWithUnboundKeys, State).
clpbn_init_solver(bp, LVs, Vs0, VarsWithUnboundKeys, State) :-
init_bp_solver(LVs, Vs0, VarsWithUnboundKeys, State).
init_horus_ground_solver(LVs, Vs0, VarsWithUnboundKeys, State).
clpbn_init_solver(jt, LVs, Vs0, VarsWithUnboundKeys, State) :-
init_jt_solver(LVs, Vs0, VarsWithUnboundKeys, State).
clpbn_init_solver(bdd, LVs, Vs0, VarsWithUnboundKeys, State) :-
@ -501,7 +499,7 @@ clpbn_run_solver(ve, LVs, LPs, State) :-
run_ve_solver(LVs, LPs, State).
clpbn_run_solver(bp, LVs, LPs, State) :-
run_bp_solver(LVs, LPs, State).
run_horus_ground_solver(LVs, LPs, State).
clpbn_run_solver(jt, LVs, LPs, State) :-
run_jt_solver(LVs, LPs, State).
@ -522,7 +520,7 @@ clpbn_finalize_solver(State) :-
solver(bp), !,
functor(State, _, Last),
arg(Last, State, Info),
finalize_bp_solver(Info).
finalize_horus_ground_solver(Info).
clpbn_finalize_solver(_State).
probability(Goal, Prob) :-

493
packages/CLPBN/clpbn/bp/BpSolver.cpp
View File

@ -1,493 +0,0 @@
#include <cassert>
#include <limits>
#include <algorithm>
#include <iostream>
#include "BpSolver.h"
#include "FactorGraph.h"
#include "Factor.h"
#include "Indexer.h"
#include "Horus.h"
BpSolver::BpSolver (const FactorGraph& fg) : Solver (fg)
{
fg_ = &fg;
runned_ = false;
}
BpSolver::~BpSolver (void)
{
for (unsigned i = 0; i < varsI_.size(); i++) {
delete varsI_[i];
}
for (unsigned i = 0; i < facsI_.size(); i++) {
delete facsI_[i];
}
for (unsigned i = 0; i < links_.size(); i++) {
delete links_[i];
}
}
Params
BpSolver::solveQuery (VarIds queryVids)
{
assert (queryVids.empty() == false);
if (queryVids.size() == 1) {
return getPosterioriOf (queryVids[0]);
} else {
return getJointDistributionOf (queryVids);
}
}
Params
BpSolver::getPosterioriOf (VarId vid)
{
if (runned_ == false) {
runSolver();
}
assert (fg_->getVarNode (vid));
VarNode* var = fg_->getVarNode (vid);
Params probs;
if (var->hasEvidence()) {
probs.resize (var->range(), LogAware::noEvidence());
probs[var->getEvidence()] = LogAware::withEvidence();
} else {
probs.resize (var->range(), LogAware::multIdenty());
const SpLinkSet& links = ninf(var)->getLinks();
if (Globals::logDomain) {
for (unsigned i = 0; i < links.size(); i++) {
Util::add (probs, links[i]->getMessage());
}
LogAware::normalize (probs);
Util::fromLog (probs);
} else {
for (unsigned i = 0; i < links.size(); i++) {
Util::multiply (probs, links[i]->getMessage());
}
LogAware::normalize (probs);
}
}
return probs;
}
Params
BpSolver::getJointDistributionOf (const VarIds& jointVarIds)
{
if (runned_ == false) {
runSolver();
}
int idx = -1;
VarNode* vn = fg_->getVarNode (jointVarIds[0]);
const FacNodes& facNodes = vn->neighbors();
for (unsigned i = 0; i < facNodes.size(); i++) {
if (facNodes[i]->factor().contains (jointVarIds)) {
idx = i;
break;
}
}
if (idx == -1) {
return getJointByConditioning (jointVarIds);
} else {
Factor res (facNodes[idx]->factor());
const SpLinkSet& links = ninf(facNodes[idx])->getLinks();
for (unsigned i = 0; i < links.size(); i++) {
Factor msg ({links[i]->getVariable()->varId()},
{links[i]->getVariable()->range()},
getVar2FactorMsg (links[i]));
res.multiply (msg);
}
res.sumOutAllExcept (jointVarIds);
res.reorderArguments (jointVarIds);
res.normalize();
Params jointDist = res.params();
if (Globals::logDomain) {
Util::fromLog (jointDist);
}
return jointDist;
}
}
void
BpSolver::runSolver (void)
{
clock_t start;
if (Constants::COLLECT_STATS) {
start = clock();
}
initializeSolver();
nIters_ = 0;
while (!converged() && nIters_ < BpOptions::maxIter) {
nIters_ ++;
if (Constants::DEBUG >= 2) {
Util::printHeader (string ("Iteration ") + Util::toString (nIters_));
// cout << endl;
}
switch (BpOptions::schedule) {
case BpOptions::Schedule::SEQ_RANDOM:
random_shuffle (links_.begin(), links_.end());
// no break
case BpOptions::Schedule::SEQ_FIXED:
for (unsigned i = 0; i < links_.size(); i++) {
calculateAndUpdateMessage (links_[i]);
}
break;
case BpOptions::Schedule::PARALLEL:
for (unsigned i = 0; i < links_.size(); i++) {
calculateMessage (links_[i]);
}
for (unsigned i = 0; i < links_.size(); i++) {
updateMessage(links_[i]);
}
break;
case BpOptions::Schedule::MAX_RESIDUAL:
maxResidualSchedule();
break;
}
if (Constants::DEBUG >= 2) {
cout << endl;
}
}
if (Constants::DEBUG >= 2) {
cout << endl;
if (nIters_ < BpOptions::maxIter) {
cout << "Sum-Product converged in " ;
cout << nIters_ << " iterations" << endl;
} else {
cout << "The maximum number of iterations was hit, terminating..." ;
cout << endl;
}
}
unsigned size = fg_->varNodes().size();
if (Constants::COLLECT_STATS) {
unsigned nIters = 0;
bool loopy = fg_->isTree() == false;
if (loopy) nIters = nIters_;
double time = (double (clock() - start)) / CLOCKS_PER_SEC;
Statistics::updateStatistics (size, loopy, nIters, time);
}
runned_ = true;
}
void
BpSolver::createLinks (void)
{
const FacNodes& facNodes = fg_->facNodes();
for (unsigned i = 0; i < facNodes.size(); i++) {
const VarNodes& neighbors = facNodes[i]->neighbors();
for (unsigned j = 0; j < neighbors.size(); j++) {
links_.push_back (new SpLink (facNodes[i], neighbors[j]));
}
}
}
void
BpSolver::maxResidualSchedule (void)
{
if (nIters_ == 1) {
for (unsigned i = 0; i < links_.size(); i++) {
calculateMessage (links_[i]);
SortedOrder::iterator it = sortedOrder_.insert (links_[i]);
linkMap_.insert (make_pair (links_[i], it));
}
return;
}
for (unsigned c = 0; c < links_.size(); c++) {
if (Constants::DEBUG >= 2) {
cout << "current residuals:" << endl;
for (SortedOrder::iterator it = sortedOrder_.begin();
it != sortedOrder_.end(); it ++) {
cout << " " << setw (30) << left << (*it)->toString();
cout << "residual = " << (*it)->getResidual() << endl;
}
}
SortedOrder::iterator it = sortedOrder_.begin();
SpLink* link = *it;
if (link->getResidual() < BpOptions::accuracy) {
return;
}
updateMessage (link);
link->clearResidual();
sortedOrder_.erase (it);
linkMap_.find (link)->second = sortedOrder_.insert (link);
// update the messages that depend on message source --> destin
const FacNodes& factorNeighbors = link->getVariable()->neighbors();
for (unsigned i = 0; i < factorNeighbors.size(); i++) {
if (factorNeighbors[i] != link->getFactor()) {
const SpLinkSet& links = ninf(factorNeighbors[i])->getLinks();
for (unsigned j = 0; j < links.size(); j++) {
if (links[j]->getVariable() != link->getVariable()) {
calculateMessage (links[j]);
SpLinkMap::iterator iter = linkMap_.find (links[j]);
sortedOrder_.erase (iter->second);
iter->second = sortedOrder_.insert (links[j]);
}
}
}
}
if (Constants::DEBUG >= 2) {
Util::printDashedLine();
}
}
}
void
BpSolver::calculateFactor2VariableMsg (SpLink* link)
{
FacNode* src = link->getFactor();
const VarNode* dst = link->getVariable();
const SpLinkSet& links = ninf(src)->getLinks();
// calculate the product of messages that were sent
// to factor `src', except from var `dst'
unsigned msgSize = 1;
for (unsigned i = 0; i < links.size(); i++) {
msgSize *= links[i]->getVariable()->range();
}
unsigned repetitions = 1;
Params msgProduct (msgSize, LogAware::multIdenty());
if (Globals::logDomain) {
for (int i = links.size() - 1; i >= 0; i--) {
if (links[i]->getVariable() != dst) {
Util::add (msgProduct, getVar2FactorMsg (links[i]), repetitions);
repetitions *= links[i]->getVariable()->range();
} else {
unsigned ds = links[i]->getVariable()->range();
Util::add (msgProduct, Params (ds, 1.0), repetitions);
repetitions *= ds;
}
}
} else {
for (int i = links.size() - 1; i >= 0; i--) {
if (links[i]->getVariable() != dst) {
if (Constants::DEBUG >= 5) {
cout << " message from " << links[i]->getVariable()->label();
cout << ": " << endl;
}
Util::multiply (msgProduct, getVar2FactorMsg (links[i]), repetitions);
repetitions *= links[i]->getVariable()->range();
} else {
unsigned ds = links[i]->getVariable()->range();
Util::multiply (msgProduct, Params (ds, 1.0), repetitions);
repetitions *= ds;
}
}
}
Factor result (src->factor().arguments(),
src->factor().ranges(), msgProduct);
result.multiply (src->factor());
if (Constants::DEBUG >= 5) {
cout << " message product: " << msgProduct << endl;
cout << " original factor: " << src->factor().params() << endl;
cout << " factor product: " << result.params() << endl;
}
result.sumOutAllExcept (dst->varId());
if (Constants::DEBUG >= 5) {
cout << " marginalized: " ;
cout << result.params() << endl;
}
const Params& resultParams = result.params();
Params& message = link->getNextMessage();
for (unsigned i = 0; i < resultParams.size(); i++) {
message[i] = resultParams[i];
}
LogAware::normalize (message);
if (Constants::DEBUG >= 5) {
cout << " curr msg: " << link->getMessage() << endl;
cout << " next msg: " << message << endl;
}
}
Params
BpSolver::getVar2FactorMsg (const SpLink* link) const
{
const VarNode* src = link->getVariable();
const FacNode* dst = link->getFactor();
Params msg;
if (src->hasEvidence()) {
msg.resize (src->range(), LogAware::noEvidence());
msg[src->getEvidence()] = LogAware::withEvidence();
if (Constants::DEBUG >= 5) {
cout << msg;
}
} else {
msg.resize (src->range(), LogAware::one());
}
if (Constants::DEBUG >= 5) {
cout << msg;
}
const SpLinkSet& links = ninf (src)->getLinks();
if (Globals::logDomain) {
for (unsigned i = 0; i < links.size(); i++) {
if (links[i]->getFactor() != dst) {
Util::add (msg, links[i]->getMessage());
}
}
} else {
for (unsigned i = 0; i < links.size(); i++) {
if (links[i]->getFactor() != dst) {
Util::multiply (msg, links[i]->getMessage());
if (Constants::DEBUG >= 5) {
cout << " x " << links[i]->getMessage();
}
}
}
}
if (Constants::DEBUG >= 5) {
cout << " = " << msg;
}
return msg;
}
Params
BpSolver::getJointByConditioning (const VarIds& jointVarIds) const
{
VarNodes jointVars;
for (unsigned i = 0; i < jointVarIds.size(); i++) {
assert (fg_->getVarNode (jointVarIds[i]));
jointVars.push_back (fg_->getVarNode (jointVarIds[i]));
}
FactorGraph* fg = new FactorGraph (*fg_);
BpSolver solver (*fg);
solver.runSolver();
Params prevBeliefs = solver.getPosterioriOf (jointVarIds[0]);
VarIds observedVids = {jointVars[0]->varId()};
for (unsigned i = 1; i < jointVarIds.size(); i++) {
assert (jointVars[i]->hasEvidence() == false);
Params newBeliefs;
Vars observedVars;
for (unsigned j = 0; j < observedVids.size(); j++) {
observedVars.push_back (fg->getVarNode (observedVids[j]));
}
StatesIndexer idx (observedVars, false);
while (idx.valid()) {
for (unsigned j = 0; j < observedVars.size(); j++) {
observedVars[j]->setEvidence (idx[j]);
}
++ idx;
BpSolver solver (*fg);
solver.runSolver();
Params beliefs = solver.getPosterioriOf (jointVarIds[i]);
for (unsigned k = 0; k < beliefs.size(); k++) {
newBeliefs.push_back (beliefs[k]);
}
}
int count = -1;
for (unsigned j = 0; j < newBeliefs.size(); j++) {
if (j % jointVars[i]->range() == 0) {
count ++;
}
newBeliefs[j] *= prevBeliefs[count];
}
prevBeliefs = newBeliefs;
observedVids.push_back (jointVars[i]->varId());
}
return prevBeliefs;
}
void
BpSolver::initializeSolver (void)
{
const VarNodes& varNodes = fg_->varNodes();
varsI_.reserve (varNodes.size());
for (unsigned i = 0; i < varNodes.size(); i++) {
varsI_.push_back (new SPNodeInfo());
}
const FacNodes& facNodes = fg_->facNodes();
facsI_.reserve (facNodes.size());
for (unsigned i = 0; i < facNodes.size(); i++) {
facsI_.push_back (new SPNodeInfo());
}
createLinks();
for (unsigned i = 0; i < links_.size(); i++) {
FacNode* src = links_[i]->getFactor();
VarNode* dst = links_[i]->getVariable();
ninf (dst)->addSpLink (links_[i]);
ninf (src)->addSpLink (links_[i]);
}
}
bool
BpSolver::converged (void)
{
if (links_.size() == 0) {
return true;
}
if (nIters_ <= 1) {
return false;
}
bool converged = true;
if (BpOptions::schedule == BpOptions::Schedule::MAX_RESIDUAL) {
double maxResidual = (*(sortedOrder_.begin()))->getResidual();
if (maxResidual > BpOptions::accuracy) {
converged = false;
} else {
converged = true;
}
} else {
for (unsigned i = 0; i < links_.size(); i++) {
double residual = links_[i]->getResidual();
if (Constants::DEBUG >= 2) {
cout << links_[i]->toString() + " residual = " << residual << endl;
}
if (residual > BpOptions::accuracy) {
converged = false;
if (Constants::DEBUG == 0) break;
}
}
if (Constants::DEBUG >= 2) {
cout << endl;
}
}
return converged;
}
void
BpSolver::printLinkInformation (void) const
{
for (unsigned i = 0; i < links_.size(); i++) {
SpLink* l = links_[i];
cout << l->toString() << ":" << endl;
cout << " curr msg = " ;
cout << l->getMessage() << endl;
cout << " next msg = " ;
cout << l->getNextMessage() << endl;
cout << " residual = " << l->getResidual() << endl;
}
}

339
packages/CLPBN/clpbn/bp/CFactorGraph.cpp
View File

@ -1,339 +0,0 @@
#include "CFactorGraph.h"
#include "Factor.h"
bool CFactorGraph::checkForIdenticalFactors = true;
CFactorGraph::CFactorGraph (const FactorGraph& fg)
{
groundFg_ = &fg;
freeColor_ = 0;
const VarNodes& varNodes = fg.varNodes();
varSignatures_.reserve (varNodes.size());
for (unsigned i = 0; i < varNodes.size(); i++) {
unsigned c = (varNodes[i]->neighbors().size() * 2) + 1;
varSignatures_.push_back (Signature (c));
}
const FacNodes& facNodes = fg.facNodes();
facSignatures_.reserve (facNodes.size());
for (unsigned i = 0; i < facNodes.size(); i++) {
unsigned c = facNodes[i]->neighbors().size() + 1;
facSignatures_.push_back (Signature (c));
}
varColors_.resize (varNodes.size());
facColors_.resize (facNodes.size());
setInitialColors();
createGroups();
}
CFactorGraph::~CFactorGraph (void)
{
for (unsigned i = 0; i < varClusters_.size(); i++) {
delete varClusters_[i];
}
for (unsigned i = 0; i < facClusters_.size(); i++) {
delete facClusters_[i];
}
}
void
CFactorGraph::setInitialColors (void)
{
// create the initial variable colors
VarColorMap colorMap;
const VarNodes& varNodes = groundFg_->varNodes();
for (unsigned i = 0; i < varNodes.size(); i++) {
unsigned dsize = varNodes[i]->range();
VarColorMap::iterator it = colorMap.find (dsize);
if (it == colorMap.end()) {
it = colorMap.insert (make_pair (
dsize, vector<Color> (dsize+1,-1))).first;
}
unsigned idx;
if (varNodes[i]->hasEvidence()) {
idx = varNodes[i]->getEvidence();
} else {
idx = dsize;
}
vector<Color>& stateColors = it->second;
if (stateColors[idx] == -1) {
stateColors[idx] = getFreeColor();
}
setColor (varNodes[i], stateColors[idx]);
}
const FacNodes& facNodes = groundFg_->facNodes();
for (unsigned i = 0; i < facNodes.size(); i++) {
facNodes[i]->factor().setDistId (Util::maxUnsigned());
}
// FIXME FIXME FIXME : pfl should give correct dist ids.
if (checkForIdenticalFactors || true) {
unsigned groupCount = 1;
for (unsigned i = 0; i < facNodes.size(); i++) {
Factor& f1 = facNodes[i]->factor();
if (f1.distId() != Util::maxUnsigned()) {
continue;
}
f1.setDistId (groupCount);
for (unsigned j = i + 1; j < facNodes.size(); j++) {
Factor& f2 = facNodes[j]->factor();
if (f2.distId() != Util::maxUnsigned()) {
continue;
}
if (f1.size() == f2.size() &&
f1.ranges() == f2.ranges() &&
f1.params() == f2.params()) {
f2.setDistId (groupCount);
}
}
groupCount ++;
}
}
// create the initial factor colors
DistColorMap distColors;
for (unsigned i = 0; i < facNodes.size(); i++) {
unsigned distId = facNodes[i]->factor().distId();
DistColorMap::iterator it = distColors.find (distId);
if (it == distColors.end()) {
it = distColors.insert (make_pair (distId, getFreeColor())).first;
}
setColor (facNodes[i], it->second);
}
}
void
CFactorGraph::createGroups (void)
{
VarSignMap varGroups;
FacSignMap facGroups;
unsigned nIters = 0;
bool groupsHaveChanged = true;
const VarNodes& varNodes = groundFg_->varNodes();
const FacNodes& facNodes = groundFg_->facNodes();
while (groupsHaveChanged || nIters == 1) {
nIters ++;
unsigned prevFactorGroupsSize = facGroups.size();
facGroups.clear();
// set a new color to the factors with the same signature
for (unsigned i = 0; i < facNodes.size(); i++) {
const Signature& signature = getSignature (facNodes[i]);
FacSignMap::iterator it = facGroups.find (signature);
if (it == facGroups.end()) {
it = facGroups.insert (make_pair (signature, FacNodes())).first;
}
it->second.push_back (facNodes[i]);
}
for (FacSignMap::iterator it = facGroups.begin();
it != facGroups.end(); it++) {
Color newColor = getFreeColor();
FacNodes& groupMembers = it->second;
for (unsigned i = 0; i < groupMembers.size(); i++) {
setColor (groupMembers[i], newColor);
}
}
// set a new color to the variables with the same signature
unsigned prevVarGroupsSize = varGroups.size();
varGroups.clear();
for (unsigned i = 0; i < varNodes.size(); i++) {
const Signature& signature = getSignature (varNodes[i]);
VarSignMap::iterator it = varGroups.find (signature);
if (it == varGroups.end()) {
it = varGroups.insert (make_pair (signature, VarNodes())).first;
}
it->second.push_back (varNodes[i]);
}
for (VarSignMap::iterator it = varGroups.begin();
it != varGroups.end(); it++) {
Color newColor = getFreeColor();
VarNodes& groupMembers = it->second;
for (unsigned i = 0; i < groupMembers.size(); i++) {
setColor (groupMembers[i], newColor);
}
}
groupsHaveChanged = prevVarGroupsSize != varGroups.size()
|| prevFactorGroupsSize != facGroups.size();
}
printGroups (varGroups, facGroups);
createClusters (varGroups, facGroups);
}
void
CFactorGraph::createClusters (
const VarSignMap& varGroups,
const FacSignMap& facGroups)
{
varClusters_.reserve (varGroups.size());
for (VarSignMap::const_iterator it = varGroups.begin();
it != varGroups.end(); it++) {
const VarNodes& groupVars = it->second;
VarCluster* vc = new VarCluster (groupVars);
for (unsigned i = 0; i < groupVars.size(); i++) {
vid2VarCluster_.insert (make_pair (groupVars[i]->varId(), vc));
}
varClusters_.push_back (vc);
}
facClusters_.reserve (facGroups.size());
for (FacSignMap::const_iterator it = facGroups.begin();
it != facGroups.end(); it++) {
FacNode* groupFactor = it->second[0];
const VarNodes& neighs = groupFactor->neighbors();
VarClusters varClusters;
varClusters.reserve (neighs.size());
for (unsigned i = 0; i < neighs.size(); i++) {
VarId vid = neighs[i]->varId();
varClusters.push_back (vid2VarCluster_.find (vid)->second);
}
facClusters_.push_back (new FacCluster (it->second, varClusters));
}
}
const Signature&
CFactorGraph::getSignature (const VarNode* varNode)
{
Signature& sign = varSignatures_[varNode->getIndex()];
vector<Color>::iterator it = sign.colors.begin();
const FacNodes& neighs = varNode->neighbors();
for (unsigned i = 0; i < neighs.size(); i++) {
*it = getColor (neighs[i]);
it ++;
*it = neighs[i]->factor().indexOf (varNode->varId());
it ++;
}
*it = getColor (varNode);
return sign;
}
const Signature&
CFactorGraph::getSignature (const FacNode* facNode)
{
Signature& sign = facSignatures_[facNode->getIndex()];
vector<Color>::iterator it = sign.colors.begin();
const VarNodes& neighs = facNode->neighbors();
for (unsigned i = 0; i < neighs.size(); i++) {
*it = getColor (neighs[i]);
it ++;
}
*it = getColor (facNode);
return sign;
}
FactorGraph*
CFactorGraph::getGroundFactorGraph (void) const
{
FactorGraph* fg = new FactorGraph();
for (unsigned i = 0; i < varClusters_.size(); i++) {
VarNode* var = varClusters_[i]->getGroundVarNodes()[0];
VarNode* newVar = new VarNode (var);
varClusters_[i]->setRepresentativeVariable (newVar);
fg->addVarNode (newVar);
}
for (unsigned i = 0; i < facClusters_.size(); i++) {
const VarClusters& myVarClusters = facClusters_[i]->getVarClusters();
Vars myGroundVars;
myGroundVars.reserve (myVarClusters.size());
for (unsigned j = 0; j < myVarClusters.size(); j++) {
VarNode* v = myVarClusters[j]->getRepresentativeVariable();
myGroundVars.push_back (v);
}
FacNode* fn = new FacNode (Factor (myGroundVars,
facClusters_[i]->getGroundFactors()[0]->factor().params()));
facClusters_[i]->setRepresentativeFactor (fn);
fg->addFacNode (fn);
for (unsigned j = 0; j < myGroundVars.size(); j++) {
fg->addEdge (static_cast<VarNode*> (myGroundVars[j]), fn);
}
}
return fg;
}
unsigned
CFactorGraph::getEdgeCount (
const FacCluster* fc,
const VarCluster* vc) const
{
unsigned count = 0;
VarId vid = vc->getGroundVarNodes().front()->varId();
const FacNodes& clusterGroundFactors = fc->getGroundFactors();
for (unsigned i = 0; i < clusterGroundFactors.size(); i++) {
if (clusterGroundFactors[i]->factor().contains (vid)) {
count ++;
}
}
// CVarNodes vars = vc->getGroundVarNodes();
// for (unsigned i = 1; i < vars.size(); i++) {
// VarNode* var = vc->getGroundVarNodes()[i];
// unsigned count2 = 0;
// for (unsigned i = 0; i < clusterGroundFactors.size(); i++) {
// if (clusterGroundFactors[i]->getPosition (var) != -1) {
// count2 ++;
// }
// }
// if (count != count2) { cout << "oops!" << endl; abort(); }
// }
return count;
}
void
CFactorGraph::printGroups (
const VarSignMap& varGroups,
const FacSignMap& facGroups) const
{
unsigned count = 1;
cout << "variable groups:" << endl;
for (VarSignMap::const_iterator it = varGroups.begin();
it != varGroups.end(); it++) {
const VarNodes& groupMembers = it->second;
if (groupMembers.size() > 0) {
cout << count << ": " ;
for (unsigned i = 0; i < groupMembers.size(); i++) {
cout << groupMembers[i]->label() << " " ;
}
count ++;
cout << endl;
}
}
count = 1;
cout << endl << "factor groups:" << endl;
for (FacSignMap::const_iterator it = facGroups.begin();
it != facGroups.end(); it++) {
const FacNodes& groupMembers = it->second;
if (groupMembers.size() > 0) {
cout << ++count << ": " ;
for (unsigned i = 0; i < groupMembers.size(); i++) {
cout << groupMembers[i]->getLabel() << " " ;
}
count ++;
cout << endl;
}
}
}

247
packages/CLPBN/clpbn/bp/CFactorGraph.h
View File

@ -1,247 +0,0 @@
#ifndef HORUS_CFACTORGRAPH_H
#define HORUS_CFACTORGRAPH_H
#include <unordered_map>
#include "FactorGraph.h"
#include "Factor.h"
#include "Horus.h"
class VarCluster;
class FacCluster;
class Distribution;
class Signature;
class SignatureHash;
typedef long Color;
typedef unordered_map<unsigned, vector<Color>> VarColorMap;
typedef unordered_map<unsigned, Color> DistColorMap;
typedef unordered_map<VarId, VarCluster*> VarId2VarCluster;
typedef vector<VarCluster*> VarClusters;
typedef vector<FacCluster*> FacClusters;
typedef unordered_map<Signature, VarNodes, SignatureHash> VarSignMap;
typedef unordered_map<Signature, FacNodes, SignatureHash> FacSignMap;
struct Signature
{
Signature (unsigned size) : colors(size) { }
bool operator< (const Signature& sig) const
{
if (colors.size() < sig.colors.size()) {
return true;
} else if (colors.size() > sig.colors.size()) {
return false;
} else {
for (unsigned i = 0; i < colors.size(); i++) {
if (colors[i] < sig.colors[i]) {
return true;
} else if (colors[i] > sig.colors[i]) {
return false;
}
}
}
return false;
}
bool operator== (const Signature& sig) const
{
if (colors.size() != sig.colors.size()) {
return false;
}
for (unsigned i = 0; i < colors.size(); i++) {
if (colors[i] != sig.colors[i]) {
return false;
}
}
return true;
}
vector<Color> colors;
};
struct SignatureHash
{
size_t operator() (const Signature &sig) const
{
size_t val = hash<size_t>()(sig.colors.size());
for (unsigned i = 0; i < sig.colors.size(); i++) {
val ^= hash<size_t>()(sig.colors[i]);
}
return val;
}
};
class VarCluster
{
public:
VarCluster (const VarNodes& vs)
{
for (unsigned i = 0; i < vs.size(); i++) {
groundVars_.push_back (vs[i]);
}
}
void addFacCluster (FacCluster* fc)
{
facClusters_.push_back (fc);
}
const FacClusters& getFacClusters (void) const
{
return facClusters_;
}
VarNode* getRepresentativeVariable (void) const { return representVar_; }
void setRepresentativeVariable (VarNode* v) { representVar_ = v; }
const VarNodes& getGroundVarNodes (void) const { return groundVars_; }
private:
VarNodes groundVars_;
FacClusters facClusters_;
VarNode* representVar_;
};
class FacCluster
{
public:
FacCluster (const FacNodes& groundFactors, const VarClusters& vcs)
{
groundFactors_ = groundFactors;
varClusters_ = vcs;
for (unsigned i = 0; i < varClusters_.size(); i++) {
varClusters_[i]->addFacCluster (this);
}
}
const VarClusters& getVarClusters (void) const
{
return varClusters_;
}
bool containsGround (const FacNode* fn)
{
for (unsigned i = 0; i < groundFactors_.size(); i++) {
if (groundFactors_[i] == fn) {
return true;
}
}
return false;
}
FacNode* getRepresentativeFactor (void) const
{
return representFactor_;
}
void setRepresentativeFactor (FacNode* fn)
{
representFactor_ = fn;
}
const FacNodes& getGroundFactors (void) const
{
return groundFactors_;
}
private:
FacNodes groundFactors_;
VarClusters varClusters_;
FacNode* representFactor_;
};
class CFactorGraph
{
public:
CFactorGraph (const FactorGraph&);
~CFactorGraph (void);
const VarClusters& getVarClusters (void) { return varClusters_; }
const FacClusters& getFacClusters (void) { return facClusters_; }
VarNode* getEquivalentVariable (VarId vid)
{
VarCluster* vc = vid2VarCluster_.find (vid)->second;
return vc->getRepresentativeVariable();
}
FactorGraph* getGroundFactorGraph (void) const;
unsigned getEdgeCount (const FacCluster*, const VarCluster*) const;
static bool checkForIdenticalFactors;
private:
Color getFreeColor (void)
{
++ freeColor_;
return freeColor_ - 1;
}
Color getColor (const VarNode* vn) const
{
return varColors_[vn->getIndex()];
}
Color getColor (const FacNode* fn) const {
return facColors_[fn->getIndex()];
}
void setColor (const VarNode* vn, Color c)
{
varColors_[vn->getIndex()] = c;
}
void setColor (const FacNode* fn, Color c)
{
facColors_[fn->getIndex()] = c;
}
VarCluster* getVariableCluster (VarId vid) const
{
return vid2VarCluster_.find (vid)->second;
}
void setInitialColors (void);
void createGroups (void);
void createClusters (const VarSignMap&, const FacSignMap&);
const Signature& getSignature (const VarNode*);
const Signature& getSignature (const FacNode*);
void printGroups (const VarSignMap&, const FacSignMap&) const;
Color freeColor_;
vector<Color> varColors_;
vector<Color> facColors_;
vector<Signature> varSignatures_;
vector<Signature> facSignatures_;
VarClusters varClusters_;
FacClusters facClusters_;
VarId2VarCluster vid2VarCluster_;
const FactorGraph* groundFg_;
};
#endif // HORUS_CFACTORGRAPH_H

244
packages/CLPBN/clpbn/bp/CbpSolver.cpp
View File

@ -1,244 +0,0 @@
#include "CbpSolver.h"
CbpSolver::CbpSolver (const FactorGraph& fg) : BpSolver (fg)
{
unsigned nGroundVars, nGroundFacs, nWithoutNeighs;
if (Constants::COLLECT_STATS) {
nGroundVars = fg_->varNodes().size();
nGroundFacs = fg_->facNodes().size();
const VarNodes& vars = fg_->varNodes();
nWithoutNeighs = 0;
for (unsigned i = 0; i < vars.size(); i++) {
const FacNodes& factors = vars[i]->neighbors();
if (factors.size() == 1 && factors[0]->neighbors().size() == 1) {
nWithoutNeighs ++;
}
}
}
cfg_ = new CFactorGraph (fg);
fg_ = cfg_->getGroundFactorGraph();
if (Constants::COLLECT_STATS) {
unsigned nClusterVars = fg_->varNodes().size();
unsigned nClusterFacs = fg_->facNodes().size();
Statistics::updateCompressingStatistics (nGroundVars,
nGroundFacs, nClusterVars, nClusterFacs, nWithoutNeighs);
}
Util::printHeader ("Uncompressed Factor Graph");
fg.print();
Util::printHeader ("Compressed Factor Graph");
fg_->print();
}
CbpSolver::~CbpSolver (void)
{
delete cfg_;
delete fg_;
for (unsigned i = 0; i < links_.size(); i++) {
delete links_[i];
}
links_.clear();
}
Params
CbpSolver::getPosterioriOf (VarId vid)
{
if (runned_ == false) {
runSolver();
}
assert (cfg_->getEquivalentVariable (vid));
VarNode* var = cfg_->getEquivalentVariable (vid);
Params probs;
if (var->hasEvidence()) {
probs.resize (var->range(), LogAware::noEvidence());
probs[var->getEvidence()] = LogAware::withEvidence();
} else {
probs.resize (var->range(), LogAware::multIdenty());
const SpLinkSet& links = ninf(var)->getLinks();
if (Globals::logDomain) {
for (unsigned i = 0; i < links.size(); i++) {
CbpSolverLink* l = static_cast<CbpSolverLink*> (links[i]);
Util::add (probs, l->poweredMessage());
}
LogAware::normalize (probs);
Util::fromLog (probs);
} else {
for (unsigned i = 0; i < links.size(); i++) {
CbpSolverLink* l = static_cast<CbpSolverLink*> (links[i]);
Util::multiply (probs, l->poweredMessage());
}
LogAware::normalize (probs);
}
}
return probs;
}
Params
CbpSolver::getJointDistributionOf (const VarIds& jointVids)
{
VarIds eqVarIds;
for (unsigned i = 0; i < jointVids.size(); i++) {
VarNode* vn = cfg_->getEquivalentVariable (jointVids[i]);
eqVarIds.push_back (vn->varId());
}
return BpSolver::getJointDistributionOf (eqVarIds);
}
void
CbpSolver::createLinks (void)
{
const FacClusters& fcs = cfg_->getFacClusters();
for (unsigned i = 0; i < fcs.size(); i++) {
const VarClusters& vcs = fcs[i]->getVarClusters();
for (unsigned j = 0; j < vcs.size(); j++) {
unsigned c = cfg_->getEdgeCount (fcs[i], vcs[j]);
links_.push_back (new CbpSolverLink (
fcs[i]->getRepresentativeFactor(),
vcs[j]->getRepresentativeVariable(), c));
}
}
}
void
CbpSolver::maxResidualSchedule (void)
{
if (nIters_ == 1) {
for (unsigned i = 0; i < links_.size(); i++) {
calculateMessage (links_[i]);
SortedOrder::iterator it = sortedOrder_.insert (links_[i]);
linkMap_.insert (make_pair (links_[i], it));
if (Constants::DEBUG >= 2 && Constants::DEBUG < 5) {
cout << "calculating " << links_[i]->toString() << endl;
}
}
return;
}
for (unsigned c = 0; c < links_.size(); c++) {
if (Constants::DEBUG >= 2) {
cout << endl << "current residuals:" << endl;
for (SortedOrder::iterator it = sortedOrder_.begin();
it != sortedOrder_.end(); it ++) {
cout << " " << setw (30) << left << (*it)->toString();
cout << "residual = " << (*it)->getResidual() << endl;
}
}
SortedOrder::iterator it = sortedOrder_.begin();
SpLink* link = *it;
if (Constants::DEBUG >= 2) {
cout << "updating " << (*sortedOrder_.begin())->toString() << endl;
}
if (link->getResidual() < BpOptions::accuracy) {
return;
}
link->updateMessage();
link->clearResidual();
sortedOrder_.erase (it);
linkMap_.find (link)->second = sortedOrder_.insert (link);
// update the messages that depend on message source --> destin
const FacNodes& factorNeighbors = link->getVariable()->neighbors();
for (unsigned i = 0; i < factorNeighbors.size(); i++) {
const SpLinkSet& links = ninf(factorNeighbors[i])->getLinks();
for (unsigned j = 0; j < links.size(); j++) {
if (links[j]->getVariable() != link->getVariable()) {
if (Constants::DEBUG >= 2 && Constants::DEBUG < 5) {
cout << " calculating " << links[j]->toString() << endl;
}
calculateMessage (links[j]);
SpLinkMap::iterator iter = linkMap_.find (links[j]);
sortedOrder_.erase (iter->second);
iter->second = sortedOrder_.insert (links[j]);
}
}
}
// in counting bp, the message that a variable X sends to
// to a factor F depends on the message that F sent to the X
const SpLinkSet& links = ninf(link->getFactor())->getLinks();
for (unsigned i = 0; i < links.size(); i++) {
if (links[i]->getVariable() != link->getVariable()) {
if (Constants::DEBUG >= 2 && Constants::DEBUG < 5) {
cout << " calculating " << links[i]->toString() << endl;
}
calculateMessage (links[i]);
SpLinkMap::iterator iter = linkMap_.find (links[i]);
sortedOrder_.erase (iter->second);
iter->second = sortedOrder_.insert (links[i]);
}
}
}
}
Params
CbpSolver::getVar2FactorMsg (const SpLink* link) const
{
Params msg;
const VarNode* src = link->getVariable();
const FacNode* dst = link->getFactor();
const CbpSolverLink* l = static_cast<const CbpSolverLink*> (link);
if (src->hasEvidence()) {
msg.resize (src->range(), LogAware::noEvidence());
double value = link->getMessage()[src->getEvidence()];
msg[src->getEvidence()] = LogAware::pow (value, l->nrEdges() - 1);
} else {
msg = link->getMessage();
LogAware::pow (msg, l->nrEdges() - 1);
}
if (Constants::DEBUG >= 5) {
cout << " " << "init: " << msg << endl;
}
const SpLinkSet& links = ninf(src)->getLinks();
if (Globals::logDomain) {
for (unsigned i = 0; i < links.size(); i++) {
if (links[i]->getFactor() != dst) {
CbpSolverLink* l = static_cast<CbpSolverLink*> (links[i]);
Util::add (msg, l->poweredMessage());
}
}
} else {
for (unsigned i = 0; i < links.size(); i++) {
if (links[i]->getFactor() != dst) {
CbpSolverLink* l = static_cast<CbpSolverLink*> (links[i]);
Util::multiply (msg, l->poweredMessage());
if (Constants::DEBUG >= 5) {
cout << " msg from " << l->getFactor()->getLabel() << ": " ;
cout << l->poweredMessage() << endl;
}
}
}
}
if (Constants::DEBUG >= 5) {
cout << " result = " << msg << endl;
}
return msg;
}
void
CbpSolver::printLinkInformation (void) const
{
for (unsigned i = 0; i < links_.size(); i++) {
CbpSolverLink* l = static_cast<CbpSolverLink*> (links_[i]);
cout << l->toString() << ":" << endl;
cout << " curr msg = " << l->getMessage() << endl;
cout << " next msg = " << l->getNextMessage() << endl;
cout << " powered = " << l->poweredMessage() << endl;
cout << " residual = " << l->getResidual() << endl;
}
}

60
packages/CLPBN/clpbn/bp/CbpSolver.h
View File

@ -1,60 +0,0 @@
#ifndef HORUS_CBP_H
#define HORUS_CBP_H
#include "BpSolver.h"
#include "CFactorGraph.h"
class Factor;
class CbpSolverLink : public SpLink
{
public:
CbpSolverLink (FacNode* fn, VarNode* vn, unsigned c)
: SpLink (fn, vn), nrEdges_(c),
pwdMsg_(vn->range(), LogAware::one()) { }
unsigned nrEdges (void) const { return nrEdges_; }
const Params& poweredMessage (void) const { return pwdMsg_; }
void updateMessage (void)
{
pwdMsg_ = *nextMsg_;
swap (currMsg_, nextMsg_);
msgSended_ = true;
LogAware::pow (pwdMsg_, nrEdges_);
}
private:
unsigned nrEdges_;
Params pwdMsg_;
};
class CbpSolver : public BpSolver
{
public:
CbpSolver (const FactorGraph& fg);
~CbpSolver (void);
Params getPosterioriOf (VarId);
Params getJointDistributionOf (const VarIds&);
private:
void createLinks (void);
void maxResidualSchedule (void);
Params getVar2FactorMsg (const SpLink*) const;
void printLinkInformation (void) const;
CFactorGraph* cfg_;
};
#endif // HORUS_CBP_H

1148
packages/CLPBN/clpbn/bp/ConstraintTree.cpp
View File

File diff suppressed because it is too large Load Diff

303
packages/CLPBN/clpbn/bp/ElimGraph.cpp
View File

@ -1,303 +0,0 @@
#include <limits>
#include <fstream>
#include "ElimGraph.h"
ElimHeuristic ElimGraph::elimHeuristic_ = MIN_NEIGHBORS;
ElimGraph::ElimGraph (const vector<Factor*>& factors)
{
for (unsigned i = 0; i < factors.size(); i++) {
const VarIds& vids = factors[i]->arguments();
for (unsigned j = 0; j < vids.size() - 1; j++) {
EgNode* n1 = getEgNode (vids[j]);
if (n1 == 0) {
n1 = new EgNode (vids[j], factors[i]->range (j));
addNode (n1);
}
for (unsigned k = j + 1; k < vids.size(); k++) {
EgNode* n2 = getEgNode (vids[k]);
if (n2 == 0) {
n2 = new EgNode (vids[k], factors[i]->range (k));
addNode (n2);
}
if (neighbors (n1, n2) == false) {
addEdge (n1, n2);
}
}
}
if (vids.size() == 1) {
if (getEgNode (vids[0]) == 0) {
addNode (new EgNode (vids[0], factors[i]->range (0)));
}
}
}
}
ElimGraph::~ElimGraph (void)
{
for (unsigned i = 0; i < nodes_.size(); i++) {
delete nodes_[i];
}
}
VarIds
ElimGraph::getEliminatingOrder (const VarIds& exclude)
{
VarIds elimOrder;
marked_.resize (nodes_.size(), false);
for (unsigned i = 0; i < exclude.size(); i++) {
assert (getEgNode (exclude[i]));
EgNode* node = getEgNode (exclude[i]);
marked_[*node] = true;
}
unsigned nVarsToEliminate = nodes_.size() - exclude.size();
for (unsigned i = 0; i < nVarsToEliminate; i++) {
EgNode* node = getLowestCostNode();
marked_[*node] = true;
elimOrder.push_back (node->varId());
connectAllNeighbors (node);
}
return elimOrder;
}
void
ElimGraph::print (void) const
{
for (unsigned i = 0; i < nodes_.size(); i++) {
cout << "node " << nodes_[i]->label() << " neighs:" ;
vector<EgNode*> neighs = nodes_[i]->neighbors();
for (unsigned j = 0; j < neighs.size(); j++) {
cout << " " << neighs[j]->label();
}
cout << endl;
}
}
void
ElimGraph::exportToGraphViz (
const char* fileName,
bool showNeighborless,
const VarIds& highlightVarIds) const
{
ofstream out (fileName);
if (!out.is_open()) {
cerr << "error: cannot open file to write at " ;
cerr << "Markov::exportToDotFile()" << endl;
abort();
}
out << "strict graph {" << endl;
for (unsigned i = 0; i < nodes_.size(); i++) {
if (showNeighborless || nodes_[i]->neighbors().size() != 0) {
out << '"' << nodes_[i]->label() << '"' << endl;
}
}
for (unsigned i = 0; i < highlightVarIds.size(); i++) {
EgNode* node =getEgNode (highlightVarIds[i]);
if (node) {
out << '"' << node->label() << '"' ;
out << " [shape=box3d]" << endl;
} else {
cout << "error: invalid variable id: " << highlightVarIds[i] << endl;
abort();
}
}
for (unsigned i = 0; i < nodes_.size(); i++) {
vector<EgNode*> neighs = nodes_[i]->neighbors();
for (unsigned j = 0; j < neighs.size(); j++) {
out << '"' << nodes_[i]->label() << '"' << " -- " ;
out << '"' << neighs[j]->label() << '"' << endl;
}
}
out << "}" << endl;
out.close();
}
VarIds
ElimGraph::getEliminationOrder (
const vector<Factor*> factors,
VarIds excludedVids)
{
ElimGraph graph (factors);
// graph.print();
// graph.exportToGraphViz ("_egg.dot");
return graph.getEliminatingOrder (excludedVids);
}
void
ElimGraph::addNode (EgNode* n)
{
nodes_.push_back (n);
n->setIndex (nodes_.size() - 1);
varMap_.insert (make_pair (n->varId(), n));
}
EgNode*
ElimGraph::getEgNode (VarId vid) const
{
unordered_map<VarId, EgNode*>::const_iterator it;
it = varMap_.find (vid);
return (it != varMap_.end()) ? it->second : 0;
}
EgNode*
ElimGraph::getLowestCostNode (void) const
{
EgNode* bestNode = 0;
unsigned minCost = std::numeric_limits<unsigned>::max();
for (unsigned i = 0; i < nodes_.size(); i++) {
if (marked_[i]) continue;
unsigned cost = 0;
switch (elimHeuristic_) {
case MIN_NEIGHBORS:
cost = getNeighborsCost (nodes_[i]);
break;
case MIN_WEIGHT:
cost = getWeightCost (nodes_[i]);
break;
case MIN_FILL:
cost = getFillCost (nodes_[i]);
break;
case WEIGHTED_MIN_FILL:
cost = getWeightedFillCost (nodes_[i]);
break;
default:
assert (false);
}
if (cost < minCost) {
bestNode = nodes_[i];
minCost = cost;
}
}
assert (bestNode);
return bestNode;
}
unsigned
ElimGraph::getNeighborsCost (const EgNode* n) const
{
unsigned cost = 0;
const vector<EgNode*>& neighs = n->neighbors();
for (unsigned i = 0; i < neighs.size(); i++) {
if (marked_[*neighs[i]] == false) {
cost ++;
}
}
return cost;
}
unsigned
ElimGraph::getWeightCost (const EgNode* n) const
{
unsigned cost = 1;
const vector<EgNode*>& neighs = n->neighbors();
for (unsigned i = 0; i < neighs.size(); i++) {
if (marked_[*neighs[i]] == false) {
cost *= neighs[i]->range();
}
}
return cost;
}
unsigned
ElimGraph::getFillCost (const EgNode* n) const
{
unsigned cost = 0;
const vector<EgNode*>& neighs = n->neighbors();
if (neighs.size() > 0) {
for (unsigned i = 0; i < neighs.size() - 1; i++) {
if (marked_[*neighs[i]] == true) continue;
for (unsigned j = i+1; j < neighs.size(); j++) {
if (marked_[*neighs[j]] == true) continue;
if (!neighbors (neighs[i], neighs[j])) {
cost ++;
}
}
}
}
return cost;
}
unsigned
ElimGraph::getWeightedFillCost (const EgNode* n) const
{
unsigned cost = 0;
const vector<EgNode*>& neighs = n->neighbors();
if (neighs.size() > 0) {
for (unsigned i = 0; i < neighs.size() - 1; i++) {
if (marked_[*neighs[i]] == true) continue;
for (unsigned j = i+1; j < neighs.size(); j++) {
if (marked_[*neighs[j]] == true) continue;
if (!neighbors (neighs[i], neighs[j])) {
cost += neighs[i]->range() * neighs[j]->range();
}
}
}
}
return cost;
}
void
ElimGraph::connectAllNeighbors (const EgNode* n)
{
const vector<EgNode*>& neighs = n->neighbors();
if (neighs.size() > 0) {
for (unsigned i = 0; i < neighs.size() - 1; i++) {
if (marked_[*neighs[i]] == true) continue;
for (unsigned j = i+1; j < neighs.size(); j++) {
if (marked_[*neighs[j]] == true) continue;
if (!neighbors (neighs[i], neighs[j])) {
addEdge (neighs[i], neighs[j]);
}
}
}
}
}
bool
ElimGraph::neighbors (const EgNode* n1, const EgNode* n2) const
{
const vector<EgNode*>& neighs = n1->neighbors();
for (unsigned i = 0; i < neighs.size(); i++) {
if (neighs[i] == n2) {
return true;
}
}
return false;
}

88
packages/CLPBN/clpbn/bp/ElimGraph.h
View File

@ -1,88 +0,0 @@
#ifndef HORUS_ELIMGRAPH_H
#define HORUS_ELIMGRAPH_H
#include "unordered_map"
#include "FactorGraph.h"
#include "Horus.h"
using namespace std;
enum ElimHeuristic
{
MIN_NEIGHBORS,
MIN_WEIGHT,
MIN_FILL,
WEIGHTED_MIN_FILL
};
class EgNode : public Var
{
public:
EgNode (VarId vid, unsigned range) : Var (vid, range) { }
void addNeighbor (EgNode* n) { neighs_.push_back (n); }
const vector<EgNode*>& neighbors (void) const { return neighs_; }
private:
vector<EgNode*> neighs_;
};
class ElimGraph
{
public:
ElimGraph (const vector<Factor*>&); // TODO
~ElimGraph (void);
VarIds getEliminatingOrder (const VarIds&);
void print (void) const;
void exportToGraphViz (const char*, bool = true,
const VarIds& = VarIds()) const;
static VarIds getEliminationOrder (const vector<Factor*>, VarIds);
static void setEliminationHeuristic (ElimHeuristic h)
{
elimHeuristic_ = h;
}
private:
void addEdge (EgNode* n1, EgNode* n2)
{
assert (n1 != n2);
n1->addNeighbor (n2);
n2->addNeighbor (n1);
}
void addNode (EgNode*);
EgNode* getEgNode (VarId) const;
EgNode* getLowestCostNode (void) const;
unsigned getNeighborsCost (const EgNode*) const;
unsigned getWeightCost (const EgNode*) const;
unsigned getFillCost (const EgNode*) const;
unsigned getWeightedFillCost (const EgNode*) const;
void connectAllNeighbors (const EgNode*);
bool neighbors (const EgNode*, const EgNode*) const;
vector<EgNode*> nodes_;
vector<bool> marked_;
unordered_map<VarId, EgNode*> varMap_;
static ElimHeuristic elimHeuristic_;
};
#endif // HORUS_ELIMGRAPH_H

265
packages/CLPBN/clpbn/bp/Factor.cpp
View File

@ -1,265 +0,0 @@
#include <cstdlib>
#include <cassert>
#include <algorithm>
#include <iostream>
#include <sstream>
#include "Factor.h"
#include "Indexer.h"
Factor::Factor (const Factor& g)
{
copyFromFactor (g);
}
Factor::Factor (
const VarIds& vids,
const Ranges& ranges,
const Params& params,
unsigned distId)
{
args_ = vids;
ranges_ = ranges;
params_ = params;
distId_ = distId;
assert (params_.size() == Util::expectedSize (ranges_));
}
Factor::Factor (
const Vars& vars,
const Params& params,
unsigned distId)
{
for (unsigned i = 0; i < vars.size(); i++) {
args_.push_back (vars[i]->varId());
ranges_.push_back (vars[i]->range());
}
params_ = params;
distId_ = distId;
assert (params_.size() == Util::expectedSize (ranges_));
}
void
Factor::sumOutAllExcept (VarId vid)
{
assert (indexOf (vid) != -1);
while (args_.back() != vid) {
sumOutLastVariable();
}
while (args_.front() != vid) {
sumOutFirstVariable();
}
}
void
Factor::sumOutAllExcept (const VarIds& vids)
{
for (int i = 0; i < (int)args_.size(); i++) {
if (Util::contains (vids, args_[i]) == false) {
sumOut (args_[i]);
i --;
}
}
}
void
Factor::sumOut (VarId vid)
{
int idx = indexOf (vid);
assert (idx != -1);
if (vid == args_.back()) {
sumOutLastVariable(); // optimization
return;
}
if (vid == args_.front()) {
sumOutFirstVariable(); // optimization
return;
}
// number of parameters separating a different state of `var',
// with the states of the remaining variables fixed
unsigned varOffset = 1;
// number of parameters separating a different state of the variable
// on the left of `var', with the states of the remaining vars fixed
unsigned leftVarOffset = 1;
for (int i = args_.size() - 1; i > idx; i--) {
varOffset *= ranges_[i];
leftVarOffset *= ranges_[i];
}
leftVarOffset *= ranges_[idx];
unsigned offset = 0;
unsigned count1 = 0;
unsigned count2 = 0;
unsigned newpsSize = params_.size() / ranges_[idx];
Params newps;
newps.reserve (newpsSize);
while (newps.size() < newpsSize) {
double sum = LogAware::addIdenty();
for (unsigned i = 0; i < ranges_[idx]; i++) {
if (Globals::logDomain) {
sum = Util::logSum (sum, params_[offset]);
} else {
sum += params_[offset];
}
offset += varOffset;
}
newps.push_back (sum);
count1 ++;
if (idx == (int)args_.size() - 1) {
offset = count1 * ranges_[idx];
} else {
if (((offset - varOffset + 1) % leftVarOffset) == 0) {
count1 = 0;
count2 ++;
}
offset = (leftVarOffset * count2) + count1;
}
}
args_.erase (args_.begin() + idx);
ranges_.erase (ranges_.begin() + idx);
params_ = newps;
}
void
Factor::sumOutFirstVariable (void)
{
unsigned range = ranges_.front();
unsigned sep = params_.size() / range;
if (Globals::logDomain) {
for (unsigned i = sep; i < params_.size(); i++) {
params_[i % sep] = Util::logSum (params_[i % sep], params_[i]);
}
} else {
for (unsigned i = sep; i < params_.size(); i++) {
params_[i % sep] += params_[i];
}
}
params_.resize (sep);
args_.erase (args_.begin());
ranges_.erase (ranges_.begin());
}
void
Factor::sumOutLastVariable (void)
{
unsigned range = ranges_.back();
unsigned idx1 = 0;
unsigned idx2 = 0;
if (Globals::logDomain) {
while (idx1 < params_.size()) {
params_[idx2] = params_[idx1];
idx1 ++;
for (unsigned j = 1; j < range; j++) {
params_[idx2] = Util::logSum (params_[idx2], params_[idx1]);
idx1 ++;
}
idx2 ++;
}
} else {
while (idx1 < params_.size()) {
params_[idx2] = params_[idx1];
idx1 ++;
for (unsigned j = 1; j < range; j++) {
params_[idx2] += params_[idx1];
idx1 ++;
}
idx2 ++;
}
}
params_.resize (idx2);
args_.pop_back();
ranges_.pop_back();
}
void
Factor::multiply (Factor& g)
{
if (args_.size() == 0) {
copyFromFactor (g);
return;
}
TFactor<VarId>::multiply (g);
}
void
Factor::reorderAccordingVarIds (void)
{
VarIds sortedVarIds = args_;
sort (sortedVarIds.begin(), sortedVarIds.end());
reorderArguments (sortedVarIds);
}
string
Factor::getLabel (void) const
{
stringstream ss;
ss << "f(" ;
for (unsigned i = 0; i < args_.size(); i++) {
if (i != 0) ss << "," ;
ss << Var (args_[i], ranges_[i]).label();
}
ss << ")" ;
return ss.str();
}
void
Factor::print (void) const
{
Vars vars;
for (unsigned i = 0; i < args_.size(); i++) {
vars.push_back (new Var (args_[i], ranges_[i]));
}
vector<string> jointStrings = Util::getStateLines (vars);
for (unsigned i = 0; i < params_.size(); i++) {
cout << "[" << distId_ << "] f(" << jointStrings[i] << ")" ;
cout << " = " << params_[i] << endl;
}
cout << endl;
for (unsigned i = 0; i < vars.size(); i++) {
delete vars[i];
}
}
void
Factor::copyFromFactor (const Factor& g)
{
args_ = g.arguments();
ranges_ = g.ranges();
params_ = g.params();
distId_ = g.distId();
}

288
packages/CLPBN/clpbn/bp/Factor.h
View File

@ -1,288 +0,0 @@
#ifndef HORUS_FACTOR_H
#define HORUS_FACTOR_H
#include <vector>
#include "Var.h"
#include "Indexer.h"
#include "Util.h"
using namespace std;
template <typename T>
class TFactor
{
public:
const vector<T>& arguments (void) const { return args_; }
vector<T>& arguments (void) { return args_; }
const Ranges& ranges (void) const { return ranges_; }
const Params& params (void) const { return params_; }
Params& params (void) { return params_; }
unsigned nrArguments (void) const { return args_.size(); }
unsigned size (void) const { return params_.size(); }
unsigned distId (void) const { return distId_; }
void setDistId (unsigned id) { distId_ = id; }
void normalize (void) { LogAware::normalize (params_); }
void setParams (const Params& newParams)
{
params_ = newParams;
assert (params_.size() == Util::expectedSize (ranges_));
}
int indexOf (const T& t) const
{
int idx = -1;
for (unsigned i = 0; i < args_.size(); i++) {
if (args_[i] == t) {
idx = i;
break;
}
}
return idx;
}
const T& argument (unsigned idx) const
{
assert (idx < args_.size());
return args_[idx];
}
T& argument (unsigned idx)
{
assert (idx < args_.size());
return args_[idx];
}
unsigned range (unsigned idx) const
{
assert (idx < ranges_.size());
return ranges_[idx];
}
void multiply (TFactor<T>& g)
{
const vector<T>& g_args = g.arguments();
const Ranges& g_ranges = g.ranges();
const Params& g_params = g.params();
if (args_ == g_args) {
// optimization: if the factors contain the same set of args,
// we can do a 1 to 1 operation on the parameters
if (Globals::logDomain) {
Util::add (params_, g_params);
} else {
Util::multiply (params_, g_params);
}
} else {
bool sharedArgs = false;
vector<unsigned> gvarpos;
for (unsigned i = 0; i < g_args.size(); i++) {
int idx = indexOf (g_args[i]);
if (idx == -1) {
insertArgument (g_args[i], g_ranges[i]);
gvarpos.push_back (args_.size() - 1);
} else {
sharedArgs = true;
gvarpos.push_back (idx);
}
}
if (sharedArgs == false) {
// optimization: if the original factors doesn't have common args,
// we don't need to marry the states of the common args
unsigned count = 0;
for (unsigned i = 0; i < params_.size(); i++) {
if (Globals::logDomain) {
params_[i] += g_params[count];
} else {
params_[i] *= g_params[count];
}
count ++;
if (count >= g_params.size()) {
count = 0;
}
}
} else {
StatesIndexer indexer (ranges_, false);
while (indexer.valid()) {
unsigned g_li = 0;
unsigned prod = 1;
for (int j = gvarpos.size() - 1; j >= 0; j--) {
g_li += indexer[gvarpos[j]] * prod;
prod *= g_ranges[j];
}
if (Globals::logDomain) {
params_[indexer] += g_params[g_li];
} else {
params_[indexer] *= g_params[g_li];
}
++ indexer;
}
}
}
}
void absorveEvidence (const T& arg, unsigned evidence)
{
int idx = indexOf (arg);
assert (idx != -1);
assert (evidence < ranges_[idx]);
Params copy = params_;
params_.clear();
params_.reserve (copy.size() / ranges_[idx]);
StatesIndexer indexer (ranges_);
for (unsigned i = 0; i < evidence; i++) {
indexer.increment (idx);
}
while (indexer.valid()) {
params_.push_back (copy[indexer]);
indexer.incrementExcluding (idx);
}
args_.erase (args_.begin() + idx);
ranges_.erase (ranges_.begin() + idx);
}
void reorderArguments (const vector<T> newArgs)
{
assert (newArgs.size() == args_.size());
if (newArgs == args_) {
return; // already in the wanted order
}
Ranges newRanges;
vector<unsigned> positions;
for (unsigned i = 0; i < newArgs.size(); i++) {
unsigned idx = indexOf (newArgs[i]);
newRanges.push_back (ranges_[idx]);
positions.push_back (idx);
}
unsigned N = ranges_.size();
Params newParams (params_.size());
for (unsigned i = 0; i < params_.size(); i++) {
unsigned li = i;
// calculate vector index corresponding to linear index
vector<unsigned> vi (N);
for (int k = N-1; k >= 0; k--) {
vi[k] = li % ranges_[k];
li /= ranges_[k];
}
// convert permuted vector index to corresponding linear index
unsigned prod = 1;
unsigned new_li = 0;
for (int k = N - 1; k >= 0; k--) {
new_li += vi[positions[k]] * prod;
prod *= ranges_[positions[k]];
}
newParams[new_li] = params_[i];
}
args_ = newArgs;
ranges_ = newRanges;
params_ = newParams;
}
bool contains (const T& arg) const
{
return Util::contains (args_, arg);
}
bool contains (const vector<T>& args) const
{
for (unsigned i = 0; i < args_.size(); i++) {
if (contains (args[i]) == false) {
return false;
}
}
return true;
}
protected:
vector<T> args_;
Ranges ranges_;
Params params_;
unsigned distId_;
private:
void insertArgument (const T& arg, unsigned range)
{
assert (indexOf (arg) == -1);
Params copy = params_;
params_.clear();
params_.reserve (copy.size() * range);
for (unsigned i = 0; i < copy.size(); i++) {
for (unsigned reps = 0; reps < range; reps++) {
params_.push_back (copy[i]);
}
}
args_.push_back (arg);
ranges_.push_back (range);
}
void insertArguments (const vector<T>& args, const Ranges& ranges)
{
Params copy = params_;
unsigned nrStates = 1;
for (unsigned i = 0; i < args.size(); i++) {
assert (indexOf (args[i]) == -1);
args_.push_back (args[i]);
ranges_.push_back (ranges[i]);
nrStates *= ranges[i];
}
params_.clear();
params_.reserve (copy.size() * nrStates);
for (unsigned i = 0; i < copy.size(); i++) {
for (unsigned reps = 0; reps < nrStates; reps++) {
params_.push_back (copy[i]);
}
}
}
};
class Factor : public TFactor<VarId>
{
public:
Factor (void) { }
Factor (const Factor&);
Factor (const VarIds&, const Ranges&, const Params&,
unsigned = Util::maxUnsigned());
Factor (const Vars&, const Params&,
unsigned = Util::maxUnsigned());
void sumOutAllExcept (VarId);
void sumOutAllExcept (const VarIds&);
void sumOut (VarId);
void sumOutFirstVariable (void);
void sumOutLastVariable (void);
void multiply (Factor&);
void reorderAccordingVarIds (void);
string getLabel (void) const;
void print (void) const;
private:
void copyFromFactor (const Factor& f);
};
#endif // HORUS_FACTOR_H

711
packages/CLPBN/clpbn/bp/FoveSolver.cpp
View File

@ -1,711 +0,0 @@
#include <algorithm>
#include <set>
#include "FoveSolver.h"
#include "Histogram.h"
#include "Util.h"
vector<LiftedOperator*>
LiftedOperator::getValidOps (
ParfactorList& pfList,
const Grounds& query)
{
vector<LiftedOperator*> validOps;
vector<SumOutOperator*> sumOutOps;
vector<CountingOperator*> countOps;
vector<GroundOperator*> groundOps;
sumOutOps = SumOutOperator::getValidOps (pfList, query);
countOps = CountingOperator::getValidOps (pfList);
groundOps = GroundOperator::getValidOps (pfList);
validOps.insert (validOps.end(), sumOutOps.begin(), sumOutOps.end());
validOps.insert (validOps.end(), countOps.begin(), countOps.end());
validOps.insert (validOps.end(), groundOps.begin(), groundOps.end());
return validOps;
}
void
LiftedOperator::printValidOps (
ParfactorList& pfList,
const Grounds& query)
{
vector<LiftedOperator*> validOps;
validOps = LiftedOperator::getValidOps (pfList, query);
for (unsigned i = 0; i < validOps.size(); i++) {
cout << "-> " << validOps[i]->toString() << endl;
delete validOps[i];
}
}
unsigned
SumOutOperator::getCost (void)
{
TinySet<unsigned> groupSet;
ParfactorList::const_iterator pfIter = pfList_.begin();
while (pfIter != pfList_.end()) {
if ((*pfIter)->containsGroup (group_)) {
vector<unsigned> groups = (*pfIter)->getAllGroups();
groupSet |= TinySet<unsigned> (groups);
}
++ pfIter;
}
unsigned cost = 1;
for (unsigned i = 0; i < groupSet.size(); i++) {
pfIter = pfList_.begin();
while (pfIter != pfList_.end()) {
if ((*pfIter)->containsGroup (groupSet[i])) {
int idx = (*pfIter)->indexOfGroup (groupSet[i]);
cost *= (*pfIter)->range (idx);
break;
}
++ pfIter;
}
}
return cost;
}
void
SumOutOperator::apply (void)
{
vector<ParfactorList::iterator> iters
= parfactorsWithGroup (pfList_, group_);
Parfactor* product = *(iters[0]);
pfList_.remove (iters[0]);
for (unsigned i = 1; i < iters.size(); i++) {
product->multiply (**(iters[i]));
pfList_.removeAndDelete (iters[i]);
}
if (product->nrArguments() == 1) {
delete product;
return;
}
int fIdx = product->indexOfGroup (group_);
LogVarSet excl = product->exclusiveLogVars (fIdx);
if (product->constr()->isCountNormalized (excl)) {
product->sumOut (fIdx);
pfList_.addShattered (product);
} else {
Parfactors pfs = FoveSolver::countNormalize (product, excl);
for (unsigned i = 0; i < pfs.size(); i++) {
pfs[i]->sumOut (fIdx);
pfList_.add (pfs[i]);
}
delete product;
}
}
vector<SumOutOperator*>
SumOutOperator::getValidOps (
ParfactorList& pfList,
const Grounds& query)
{
vector<SumOutOperator*> validOps;
set<unsigned> allGroups;
ParfactorList::const_iterator it = pfList.begin();
while (it != pfList.end()) {
const ProbFormulas& formulas = (*it)->arguments();
for (unsigned i = 0; i < formulas.size(); i++) {
allGroups.insert (formulas[i].group());
}
++ it;
}
set<unsigned>::const_iterator groupIt = allGroups.begin();
while (groupIt != allGroups.end()) {
if (validOp (*groupIt, pfList, query)) {
validOps.push_back (new SumOutOperator (*groupIt, pfList));
}
++ groupIt;
}
return validOps;
}
string
SumOutOperator::toString (void)
{
stringstream ss;
vector<ParfactorList::iterator> pfIters;
pfIters = parfactorsWithGroup (pfList_, group_);
int idx = (*pfIters[0])->indexOfGroup (group_);
ProbFormula f = (*pfIters[0])->argument (idx);
TupleSet tupleSet = (*pfIters[0])->constr()->tupleSet (f.logVars());
ss << "sum out " << f.functor() << "/" << f.arity();
ss << "|" << tupleSet << " (group " << group_ << ")";
ss << " [cost=" << getCost() << "]" << endl;
return ss.str();
}
bool
SumOutOperator::validOp (
unsigned group,
ParfactorList& pfList,
const Grounds& query)
{
vector<ParfactorList::iterator> pfIters;
pfIters = parfactorsWithGroup (pfList, group);
if (isToEliminate (*pfIters[0], group, query) == false) {
return false;
}
unordered_map<unsigned, unsigned> groupToRange;
for (unsigned i = 0; i < pfIters.size(); i++) {
int fIdx = (*pfIters[i])->indexOfGroup (group);
if ((*pfIters[i])->argument (fIdx).contains (
(*pfIters[i])->elimLogVars()) == false) {
return false;
}
vector<unsigned> ranges = (*pfIters[i])->ranges();
vector<unsigned> groups = (*pfIters[i])->getAllGroups();
for (unsigned i = 0; i < groups.size(); i++) {
unordered_map<unsigned, unsigned>::iterator it;
it = groupToRange.find (groups[i]);
if (it == groupToRange.end()) {
groupToRange.insert (make_pair (groups[i], ranges[i]));
} else {
if (it->second != ranges[i]) {
return false;
}
}
}
}
return true;
}
vector<ParfactorList::iterator>
SumOutOperator::parfactorsWithGroup (
ParfactorList& pfList,
unsigned group)
{
vector<ParfactorList::iterator> iters;
ParfactorList::iterator pflIt = pfList.begin();
while (pflIt != pfList.end()) {
if ((*pflIt)->containsGroup (group)) {
iters.push_back (pflIt);
}
++ pflIt;
}
return iters;
}
bool
SumOutOperator::isToEliminate (
Parfactor* g,
unsigned group,
const Grounds& query)
{
int fIdx = g->indexOfGroup (group);
const ProbFormula& formula = g->argument (fIdx);
bool toElim = true;
for (unsigned i = 0; i < query.size(); i++) {
if (formula.functor() == query[i].functor() &&
formula.arity() == query[i].arity()) {
g->constr()->moveToTop (formula.logVars());
if (g->constr()->containsTuple (query[i].args())) {
toElim = false;
break;
}
}
}
return toElim;
}
unsigned
CountingOperator::getCost (void)
{
unsigned cost = 0;
int fIdx = (*pfIter_)->indexOfLogVar (X_);
unsigned range = (*pfIter_)->range (fIdx);
unsigned size = (*pfIter_)->size() / range;
TinySet<unsigned> counts;
counts = (*pfIter_)->constr()->getConditionalCounts (X_);
for (unsigned i = 0; i < counts.size(); i++) {
cost += size * HistogramSet::nrHistograms (counts[i], range);
}
return cost;
}
void
CountingOperator::apply (void)
{
if ((*pfIter_)->constr()->isCountNormalized (X_)) {
(*pfIter_)->countConvert (X_);
} else {
Parfactor* pf = *pfIter_;
pfList_.remove (pfIter_);
Parfactors pfs = FoveSolver::countNormalize (pf, X_);
for (unsigned i = 0; i < pfs.size(); i++) {
unsigned condCount = pfs[i]->constr()->getConditionalCount (X_);
bool cartProduct = pfs[i]->constr()->isCarteesianProduct (
pfs[i]->countedLogVars() | X_);
if (condCount > 1 && cartProduct) {
pfs[i]->countConvert (X_);
}
pfList_.add (pfs[i]);
}
delete pf;
}
}
vector<CountingOperator*>
CountingOperator::getValidOps (ParfactorList& pfList)
{
vector<CountingOperator*> validOps;
ParfactorList::iterator it = pfList.begin();
while (it != pfList.end()) {
LogVarSet candidates = (*it)->uncountedLogVars();
for (unsigned i = 0; i < candidates.size(); i++) {
if (validOp (*it, candidates[i])) {
validOps.push_back (new CountingOperator (
it, candidates[i], pfList));
}
}
++ it;
}
return validOps;
}
string
CountingOperator::toString (void)
{
stringstream ss;
ss << "count convert " << X_ << " in " ;
ss << (*pfIter_)->getLabel();
ss << " [cost=" << getCost() << "]" << endl;
Parfactors pfs = FoveSolver::countNormalize (*pfIter_, X_);
if ((*pfIter_)->constr()->isCountNormalized (X_) == false) {
for (unsigned i = 0; i < pfs.size(); i++) {
ss << " º " << pfs[i]->getLabel() << endl;
}
}
for (unsigned i = 0; i < pfs.size(); i++) {
delete pfs[i];
}
return ss.str();
}
bool
CountingOperator::validOp (Parfactor* g, LogVar X)
{
if (g->nrFormulas (X) != 1) {
return false;
}
int fIdx = g->indexOfLogVar (X);
if (g->argument (fIdx).isCounting()) {
return false;
}
bool countNormalized = g->constr()->isCountNormalized (X);
if (countNormalized) {
unsigned condCount = g->constr()->getConditionalCount (X);
bool cartProduct = g->constr()->isCarteesianProduct (
g->countedLogVars() | X);
if (condCount == 1 || cartProduct == false) {
return false;
}
}
return true;
}
unsigned
GroundOperator::getCost (void)
{
unsigned cost = 0;
bool isCountingLv = (*pfIter_)->countedLogVars().contains (X_);
if (isCountingLv) {
int fIdx = (*pfIter_)->indexOfLogVar (X_);
unsigned currSize = (*pfIter_)->size();
unsigned nrHists = (*pfIter_)->range (fIdx);
unsigned range = (*pfIter_)->argument (fIdx).range();
unsigned nrSymbols = (*pfIter_)->constr()->getConditionalCount (X_);
cost = (currSize / nrHists) * (std::pow (range, nrSymbols));
} else {
cost = (*pfIter_)->constr()->nrSymbols (X_) * (*pfIter_)->size();
}
return cost;
}
void
GroundOperator::apply (void)
{
bool countedLv = (*pfIter_)->countedLogVars().contains (X_);
Parfactor* pf = *pfIter_;
pfList_.remove (pfIter_);
if (countedLv) {
pf->fullExpand (X_);
pfList_.add (pf);
} else {
ConstraintTrees cts = pf->constr()->ground (X_);
for (unsigned i = 0; i < cts.size(); i++) {
pfList_.add (new Parfactor (pf, cts[i]));
}
delete pf;
}
}
vector<GroundOperator*>
GroundOperator::getValidOps (ParfactorList& pfList)
{
vector<GroundOperator*> validOps;
ParfactorList::iterator pfIter = pfList.begin();
while (pfIter != pfList.end()) {
LogVarSet set = (*pfIter)->logVarSet();
for (unsigned i = 0; i < set.size(); i++) {
if ((*pfIter)->constr()->isSingleton (set[i]) == false) {
validOps.push_back (new GroundOperator (pfIter, set[i], pfList));
}
}
++ pfIter;
}
return validOps;
}
string
GroundOperator::toString (void)
{
stringstream ss;
((*pfIter_)->countedLogVars().contains (X_))
? ss << "full expanding "
: ss << "grounding " ;
ss << X_ << " in " << (*pfIter_)->getLabel();
ss << " [cost=" << getCost() << "]" << endl;
return ss.str();
}
Params
FoveSolver::getPosterioriOf (const Ground& query)
{
return getJointDistributionOf ({query});
}
Params
FoveSolver::getJointDistributionOf (const Grounds& query)
{
runSolver (query);
(*pfList_.begin())->normalize();
Params params = (*pfList_.begin())->params();
if (Globals::logDomain) {
Util::fromLog (params);
}
return params;
}
void
FoveSolver::absorveEvidence (
ParfactorList& pfList,
ObservedFormulas& obsFormulas)
{
for (unsigned i = 0; i < obsFormulas.size(); i++) {
Parfactors newPfs;
ParfactorList::iterator it = pfList.begin();
while (it != pfList.end()) {
Parfactor* pf = *it;
it = pfList.remove (it);
Parfactors absorvedPfs = absorve (obsFormulas[i], pf);
if (absorvedPfs.empty() == false) {
if (absorvedPfs.size() == 1 && absorvedPfs[0] == 0) {
// just remove pf;
} else {
Util::addToVector (newPfs, absorvedPfs);
}
delete pf;
} else {
it = pfList.insertShattered (it, pf);
++ it;
}
}
pfList.add (newPfs);
}
if (Constants::DEBUG >= 2 && obsFormulas.empty() == false) {
Util::printAsteriskLine();
cout << "AFTER EVIDENCE ABSORVED" << endl;
for (unsigned i = 0; i < obsFormulas.size(); i++) {
cout << " -> " << obsFormulas[i] << endl;
}
Util::printAsteriskLine();
pfList.print();
}
}
Parfactors
FoveSolver::countNormalize (
Parfactor* g,
const LogVarSet& set)
{
Parfactors normPfs;
if (set.empty()) {
normPfs.push_back (new Parfactor (*g));
} else {
ConstraintTrees normCts = g->constr()->countNormalize (set);
for (unsigned i = 0; i < normCts.size(); i++) {
normPfs.push_back (new Parfactor (g, normCts[i]));
}
}
return normPfs;
}
void
FoveSolver::runSolver (const Grounds& query)
{
shatterAgainstQuery (query);
runWeakBayesBall (query);
while (true) {
if (Constants::DEBUG >= 2) {
Util::printDashedLine();
pfList_.print();
LiftedOperator::printValidOps (pfList_, query);
}
LiftedOperator* op = getBestOperation (query);
if (op == 0) {
break;
}
if (Constants::DEBUG >= 2) {
cout << "best operation: " << op->toString() << endl;
}
op->apply();
delete op;
}
assert (pfList_.size() > 0);
if (pfList_.size() > 1) {
ParfactorList::iterator pfIter = pfList_.begin();
pfIter ++;
while (pfIter != pfList_.end()) {
(*pfList_.begin())->multiply (**pfIter);
++ pfIter;
}
}
(*pfList_.begin())->reorderAccordingGrounds (query);
}
LiftedOperator*
FoveSolver::getBestOperation (const Grounds& query)
{
unsigned bestCost;
LiftedOperator* bestOp = 0;
vector<LiftedOperator*> validOps;
validOps = LiftedOperator::getValidOps (pfList_, query);
for (unsigned i = 0; i < validOps.size(); i++) {
unsigned cost = validOps[i]->getCost();
if ((bestOp == 0) || (cost < bestCost)) {
bestOp = validOps[i];
bestCost = cost;
}
}
for (unsigned i = 0; i < validOps.size(); i++) {
if (validOps[i] != bestOp) {
delete validOps[i];
}
}
return bestOp;
}
void
FoveSolver::runWeakBayesBall (const Grounds& query)
{
queue<unsigned> todo; // groups to process
set<unsigned> done; // processed or in queue
for (unsigned i = 0; i < query.size(); i++) {
ParfactorList::iterator it = pfList_.begin();
while (it != pfList_.end()) {
int group = (*it)->findGroup (query[i]);
if (group != -1) {
todo.push (group);
done.insert (group);
break;
}
++ it;
}
}
set<Parfactor*> requiredPfs;
while (todo.empty() == false) {
unsigned group = todo.front();
ParfactorList::iterator it = pfList_.begin();
while (it != pfList_.end()) {
if (Util::contains (requiredPfs, *it) == false &&
(*it)->containsGroup (group)) {
vector<unsigned> groups = (*it)->getAllGroups();
for (unsigned i = 0; i < groups.size(); i++) {
if (Util::contains (done, groups[i]) == false) {
todo.push (groups[i]);
done.insert (groups[i]);
}
}
requiredPfs.insert (*it);
}
++ it;
}
todo.pop();
}
ParfactorList::iterator it = pfList_.begin();
while (it != pfList_.end()) {
if (Util::contains (requiredPfs, *it) == false) {
it = pfList_.removeAndDelete (it);
} else {
++ it;
}
}
if (Constants::DEBUG >= 2) {
Util::printHeader ("REQUIRED PARFACTORS");
pfList_.print();
}
}
void
FoveSolver::shatterAgainstQuery (const Grounds& query)
{
for (unsigned i = 0; i < query.size(); i++) {
if (query[i].isAtom()) {
continue;
}
bool found = false;
Parfactors newPfs;
ParfactorList::iterator it = pfList_.begin();
while (it != pfList_.end()) {
if ((*it)->containsGround (query[i])) {
found = true;
std::pair<ConstraintTree*, ConstraintTree*> split =
(*it)->constr()->split (query[i].args(), query[i].arity());
ConstraintTree* commCt = split.first;
ConstraintTree* exclCt = split.second;
newPfs.push_back (new Parfactor (*it, commCt));
if (exclCt->empty() == false) {
newPfs.push_back (new Parfactor (*it, exclCt));
} else {
delete exclCt;
}
it = pfList_.removeAndDelete (it);
} else {
++ it;
}
}
if (found == false) {
cerr << "error: could not find a parfactor with ground " ;
cerr << "`" << query[i] << "'" << endl;
exit (0);
}
pfList_.add (newPfs);
}
if (Constants::DEBUG >= 2) {
cout << endl;
Util::printAsteriskLine();
cout << "SHATTERED AGAINST THE QUERY" << endl;
for (unsigned i = 0; i < query.size(); i++) {
cout << " -> " << query[i] << endl;
}
Util::printAsteriskLine();
pfList_.print();
}
}
Parfactors
FoveSolver::absorve (
ObservedFormula& obsFormula,
Parfactor* g)
{
Parfactors absorvedPfs;
const ProbFormulas& formulas = g->arguments();
for (unsigned i = 0; i < formulas.size(); i++) {
if (obsFormula.functor() == formulas[i].functor() &&
obsFormula.arity() == formulas[i].arity()) {
if (obsFormula.isAtom()) {
if (formulas.size() > 1) {
g->absorveEvidence (formulas[i], obsFormula.evidence());
} else {
// hack to erase parfactor g
absorvedPfs.push_back (0);
}
break;
}
g->constr()->moveToTop (formulas[i].logVars());
std::pair<ConstraintTree*, ConstraintTree*> res
= g->constr()->split (&(obsFormula.constr()), formulas[i].arity());
ConstraintTree* commCt = res.first;
ConstraintTree* exclCt = res.second;
if (commCt->empty() == false) {
if (formulas.size() > 1) {
LogVarSet excl = g->exclusiveLogVars (i);
Parfactors countNormPfs = countNormalize (g, excl);
for (unsigned j = 0; j < countNormPfs.size(); j++) {
countNormPfs[j]->absorveEvidence (
formulas[i], obsFormula.evidence());
absorvedPfs.push_back (countNormPfs[j]);
}
} else {
delete commCt;
}
if (exclCt->empty() == false) {
absorvedPfs.push_back (new Parfactor (g, exclCt));
} else {
delete exclCt;
}
if (absorvedPfs.empty()) {
// hack to erase parfactor g
absorvedPfs.push_back (0);
}
break;
} else {
delete commCt;
delete exclCt;
}
}
}
return absorvedPfs;
}

76
packages/CLPBN/clpbn/bp/Horus.h
View File

@ -1,76 +0,0 @@
#ifndef HORUS_HORUS_H
#define HORUS_HORUS_H
#include <limits>
#include <vector>
#define DISALLOW_COPY_AND_ASSIGN(TypeName) \
TypeName(const TypeName&); \
void operator=(const TypeName&)
using namespace std;
class Var;
class Factor;
class VarNode;
class FacNode;
typedef vector<double> Params;
typedef unsigned VarId;
typedef vector<VarId> VarIds;
typedef vector<Var*> Vars;
typedef vector<VarNode*> VarNodes;
typedef vector<FacNode*> FacNodes;
typedef vector<Factor*> Factors;
typedef vector<string> States;
typedef vector<unsigned> Ranges;
enum InfAlgorithms
{
VE, // variable elimination
BP, // belief propagation
CBP // counting belief propagation
};
namespace Globals {
extern bool logDomain;
extern InfAlgorithms infAlgorithm;
};
namespace Constants {
// level of debug information
const unsigned DEBUG = 0;
const int NO_EVIDENCE = -1;
// number of digits to show when printing a parameter
const unsigned PRECISION = 5;
const bool COLLECT_STATS = false;
};
namespace BpOptions
{
enum Schedule {
SEQ_FIXED,
SEQ_RANDOM,
PARALLEL,
MAX_RESIDUAL
};
extern Schedule schedule;
extern double accuracy;
extern unsigned maxIter;
}
#endif // HORUS_HORUS_H

171
packages/CLPBN/clpbn/bp/HorusCli.cpp
View File

@ -1,171 +0,0 @@
#include <cstdlib>
#include <iostream>
#include <sstream>
#include "FactorGraph.h"
#include "VarElimSolver.h"
#include "BpSolver.h"
#include "CbpSolver.h"
using namespace std;
void processArguments (FactorGraph&, int, const char* []);
void runSolver (const FactorGraph&, const VarIds&);
const string USAGE = "usage: \
./hcli ve|bp|cbp NETWORK_FILE [VARIABLE | OBSERVED_VARIABLE=EVIDENCE]..." ;
int
main (int argc, const char* argv[])
{
if (argc <= 1) {
cerr << "error: no solver specified" << endl;
cerr << "error: no graphical model specified" << endl;
cerr << USAGE << endl;
exit (0);
}
if (argc <= 2) {
cerr << "error: no graphical model specified" << endl;
cerr << USAGE << endl;
exit (0);
}
string solver (argv[1]);
if (solver == "ve") {
Globals::infAlgorithm = InfAlgorithms::VE;
} else if (solver == "bp") {
Globals::infAlgorithm = InfAlgorithms::BP;
} else if (solver == "cbp") {
Globals::infAlgorithm = InfAlgorithms::CBP;
} else {
cerr << "error: unknow solver `" << solver << "'" << endl ;
cerr << USAGE << endl;
exit(0);
}
string fileName (argv[2]);
string extension = fileName.substr (
fileName.find_last_of ('.') + 1);
FactorGraph fg;
if (extension == "uai") {
fg.readFromUaiFormat (fileName.c_str());
} else if (extension == "fg") {
fg.readFromLibDaiFormat (fileName.c_str());
} else {
cerr << "error: the graphical model must be defined either " ;
cerr << "in a UAI or libDAI file" << endl;
exit (0);
}
processArguments (fg, argc, argv);
return 0;
}
void
processArguments (FactorGraph& fg, int argc, const char* argv[])
{
VarIds queryIds;
for (int i = 3; i < argc; i++) {
const string& arg = argv[i];
if (arg.find ('=') == std::string::npos) {
if (!Util::isInteger (arg)) {
cerr << "error: `" << arg << "' " ;
cerr << "is not a valid variable id" ;
cerr << endl;
exit (0);
}
VarId vid;
stringstream ss;
ss << arg;
ss >> vid;
VarNode* queryVar = fg.getVarNode (vid);
if (queryVar) {
queryIds.push_back (vid);
} else {
cerr << "error: there isn't a variable with " ;
cerr << "`" << vid << "' as id" ;
cerr << endl;
exit (0);
}
} else {
size_t pos = arg.find ('=');
if (arg.substr (0, pos).empty()) {
cerr << "error: missing left argument" << endl;
cerr << USAGE << endl;
exit (0);
}
if (arg.substr (pos + 1).empty()) {
cerr << "error: missing right argument" << endl;
cerr << USAGE << endl;
exit (0);
}
if (!Util::isInteger (arg.substr (0, pos))) {
cerr << "error: `" << arg.substr (0, pos) << "' " ;
cerr << "is not a variable id" ;
cerr << endl;
exit (0);
}
VarId vid;
stringstream ss;
ss << arg.substr (0, pos);
ss >> vid;
VarNode* var = fg.getVarNode (vid);
if (var) {
if (!Util::isInteger (arg.substr (pos + 1))) {
cerr << "error: `" << arg.substr (pos + 1) << "' " ;
cerr << "is not a state index" ;
cerr << endl;
exit (0);
}
int stateIndex;
stringstream ss;
ss << arg.substr (pos + 1);
ss >> stateIndex;
if (var->isValidState (stateIndex)) {
var->setEvidence (stateIndex);
} else {
cerr << "error: `" << stateIndex << "' " ;
cerr << "is not a valid state index for variable " ;
cerr << "`" << var->varId() << "'" ;
cerr << endl;
exit (0);
}
} else {
cerr << "error: there isn't a variable with " ;
cerr << "`" << vid << "' as id" ;
cerr << endl;
exit (0);
}
}
}
runSolver (fg, queryIds);
}
void
runSolver (const FactorGraph& fg, const VarIds& queryIds)
{
Solver* solver = 0;
switch (Globals::infAlgorithm) {
case InfAlgorithms::VE:
solver = new VarElimSolver (fg);
break;
case InfAlgorithms::BP:
solver = new BpSolver (fg);
break;
case InfAlgorithms::CBP:
solver = new CbpSolver (fg);
break;
default:
assert (false);
}
if (queryIds.size() == 0) {
solver->printAllPosterioris();
} else {
solver->printAnswer (queryIds);
}
delete solver;
}

296
packages/CLPBN/clpbn/bp/Indexer.h
View File

@ -1,296 +0,0 @@
#ifndef HORUS_STATESINDEXER_H
#define HORUS_STATESINDEXER_H
#include <algorithm>
#include <numeric>
#include <functional>
#include <sstream>
#include <iomanip>
#include "Var.h"
#include "Util.h"
class StatesIndexer
{
public:
StatesIndexer (const Ranges& ranges, bool calcOffsets = true)
{
size_ = 1;
indices_.resize (ranges.size(), 0);
ranges_ = ranges;
for (unsigned i = 0; i < ranges.size(); i++) {
size_ *= ranges[i];
}
li_ = 0;
if (calcOffsets) {
calculateOffsets();
}
}
StatesIndexer (const Vars& vars, bool calcOffsets = true)
{
size_ = 1;
indices_.resize (vars.size(), 0);
ranges_.reserve (vars.size());
for (unsigned i = 0; i < vars.size(); i++) {
ranges_.push_back (vars[i]->range());
size_ *= vars[i]->range();
}
li_ = 0;
if (calcOffsets) {
calculateOffsets();
}
}
void increment (void)
{
for (int i = ranges_.size() - 1; i >= 0; i--) {
indices_[i] ++;
if (indices_[i] != ranges_[i]) {
break;
} else {
indices_[i] = 0;
}
}
li_ ++;
}
void increment (unsigned dim)
{
assert (dim < ranges_.size());
assert (ranges_.size() == offsets_.size());
assert (indices_[dim] < ranges_[dim]);
indices_[dim] ++;
li_ += offsets_[dim];
}
void incrementExcluding (unsigned skipDim)
{
assert (ranges_.size() == offsets_.size());
for (int i = ranges_.size() - 1; i >= 0; i--) {
if (i != (int)skipDim) {
indices_[i] ++;
li_ += offsets_[i];
if (indices_[i] != ranges_[i]) {
return;
} else {
indices_[i] = 0;
li_ -= offsets_[i] * ranges_[i];
}
}
}
li_ = size_;
}
unsigned linearIndex (void) const
{
return li_;
}
const vector<unsigned>& indices (void) const
{
return indices_;
}
StatesIndexer& operator ++ (void)
{
increment();
return *this;
}
operator unsigned (void) const
{
return li_;
}
unsigned operator[] (unsigned dim) const
{
assert (valid());
assert (dim < ranges_.size());
return indices_[dim];
}
bool valid (void) const
{
return li_ < size_;
}
void reset (void)
{
std::fill (indices_.begin(), indices_.end(), 0);
li_ = 0;
}
void reset (unsigned dim)
{
indices_[dim] = 0;
li_ -= offsets_[dim] * ranges_[dim];
}
unsigned size (void) const
{
return size_ ;
}
friend ostream& operator<< (ostream &os, const StatesIndexer& idx)
{
os << "(" << std::setw (2) << std::setfill('0') << idx.li_ << ") " ;
os << idx.indices_;
return os;
}
private:
void calculateOffsets (void)
{
unsigned prod = 1;
offsets_.resize (ranges_.size());
for (int i = ranges_.size() - 1; i >= 0; i--) {
offsets_[i] = prod;
prod *= ranges_[i];
}
}
unsigned li_;
unsigned size_;
vector<unsigned> indices_;
vector<unsigned> ranges_;
vector<unsigned> offsets_;
};
class MapIndexer
{
public:
MapIndexer (const Ranges& ranges, const vector<bool>& mapDims)
{
assert (ranges.size() == mapDims.size());
unsigned prod = 1;
offsets_.resize (ranges.size());
for (int i = ranges.size() - 1; i >= 0; i--) {
if (mapDims[i]) {
offsets_[i] = prod;
prod *= ranges[i];
}
}
indices_.resize (ranges.size(), 0);
ranges_ = ranges;
index_ = 0;
valid_ = true;
}
MapIndexer (const Ranges& ranges, unsigned ignoreDim)
{
unsigned prod = 1;
offsets_.resize (ranges.size());
for (int i = ranges.size() - 1; i >= 0; i--) {
if (i != (int)ignoreDim) {
offsets_[i] = prod;
prod *= ranges[i];
}
}
indices_.resize (ranges.size(), 0);
ranges_ = ranges;
index_ = 0;
valid_ = true;
}
/*
MapIndexer (
const VarIds& loopVids,
const Ranges& loopRanges,
const VarIds& mapVids,
const Ranges& mapRanges)
{
unsigned prod = 1;
vector<unsigned> offsets (mapRanges.size());
for (int i = mapRanges.size() - 1; i >= 0; i--) {
offsets[i] = prod;
prod *= mapRanges[i];
}
offsets_.reserve (loopVids.size());
for (unsigned i = 0; i < loopVids.size(); i++) {
VarIds::const_iterator it =
std::find (mapVids.begin(), mapVids.end(), loopVids[i]);
if (it != mapVids.end()) {
offsets_.push_back (offsets[it - mapVids.begin()]);
} else {
offsets_.push_back (0);
}
}
indices_.resize (loopVids.size(), 0);
ranges_ = loopRanges;
index_ = 0;
size_ = prod;
}
*/
MapIndexer& operator ++ (void)
{
assert (valid_);
for (int i = ranges_.size() - 1; i >= 0; i--) {
indices_[i] ++;
index_ += offsets_[i];
if (indices_[i] != ranges_[i]) {
return *this;
} else {
indices_[i] = 0;
index_ -= offsets_[i] * ranges_[i];
}
}
valid_ = false;
return *this;
}
unsigned mappedIndex (void) const
{
return index_;
}
operator unsigned (void) const
{
return index_;
}
unsigned operator[] (unsigned dim) const
{
assert (valid());
assert (dim < ranges_.size());
return indices_[dim];
}
bool valid (void) const
{
return valid_;
}
void reset (void)
{
std::fill (indices_.begin(), indices_.end(), 0);
index_ = 0;
}
friend ostream& operator<< (ostream &os, const MapIndexer& idx)
{
os << "(" << std::setw (2) << std::setfill('0') << idx.index_ << ") " ;
os << idx.indices_;
return os;
}
private:
unsigned index_;
bool valid_;
vector<unsigned> ranges_;
vector<unsigned> indices_;
vector<unsigned> offsets_;
};
#endif // HORUS_STATESINDEXER_H

685
packages/CLPBN/clpbn/bp/Parfactor.cpp
View File

@ -1,685 +0,0 @@
#include "Parfactor.h"
#include "Histogram.h"
#include "Indexer.h"
#include "Util.h"
#include "Horus.h"
Parfactor::Parfactor (
const ProbFormulas& formulas,
const Params& params,
const Tuples& tuples,
unsigned distId)
{
args_ = formulas;
params_ = params;
distId_ = distId;
LogVars logVars;
for (unsigned i = 0; i < args_.size(); i++) {
ranges_.push_back (args_[i].range());
const LogVars& lvs = args_[i].logVars();
for (unsigned j = 0; j < lvs.size(); j++) {
if (Util::contains (logVars, lvs[j]) == false) {
logVars.push_back (lvs[j]);
}
}
}
constr_ = new ConstraintTree (logVars, tuples);
assert (params_.size() == Util::expectedSize (ranges_));
}
Parfactor::Parfactor (const Parfactor* g, const Tuple& tuple)
{
args_ = g->arguments();
params_ = g->params();
ranges_ = g->ranges();
distId_ = g->distId();
constr_ = new ConstraintTree (g->logVars(), {tuple});
assert (params_.size() == Util::expectedSize (ranges_));
}
Parfactor::Parfactor (const Parfactor* g, ConstraintTree* constr)
{
args_ = g->arguments();
params_ = g->params();
ranges_ = g->ranges();
distId_ = g->distId();
constr_ = constr;
assert (params_.size() == Util::expectedSize (ranges_));
}
Parfactor::Parfactor (const Parfactor& g)
{
args_ = g.arguments();
params_ = g.params();
ranges_ = g.ranges();
distId_ = g.distId();
constr_ = new ConstraintTree (*g.constr());
assert (params_.size() == Util::expectedSize (ranges_));
}
Parfactor::~Parfactor (void)
{
delete constr_;
}
LogVarSet
Parfactor::countedLogVars (void) const
{
LogVarSet set;
for (unsigned i = 0; i < args_.size(); i++) {
if (args_[i].isCounting()) {
set.insert (args_[i].countedLogVar());
}
}
return set;
}
LogVarSet
Parfactor::uncountedLogVars (void) const
{
return constr_->logVarSet() - countedLogVars();
}
LogVarSet
Parfactor::elimLogVars (void) const
{
LogVarSet requiredToElim = constr_->logVarSet();
requiredToElim -= constr_->singletons();
requiredToElim -= countedLogVars();
return requiredToElim;
}
LogVarSet
Parfactor::exclusiveLogVars (unsigned fIdx) const
{
assert (fIdx < args_.size());
LogVarSet remaining;
for (unsigned i = 0; i < args_.size(); i++) {
if (i != fIdx) {
remaining |= args_[i].logVarSet();
}
}
return args_[fIdx].logVarSet() - remaining;
}
void
Parfactor::setConstraintTree (ConstraintTree* newTree)
{
delete constr_;
constr_ = newTree;
}
void
Parfactor::sumOut (unsigned fIdx)
{
assert (fIdx < args_.size());
assert (args_[fIdx].contains (elimLogVars()));
LogVarSet excl = exclusiveLogVars (fIdx);
if (args_[fIdx].isCounting()) {
LogAware::pow (params_, constr_->getConditionalCount (
excl - args_[fIdx].countedLogVar()));
} else {
LogAware::pow (params_, constr_->getConditionalCount (excl));
}
if (args_[fIdx].isCounting()) {
unsigned N = constr_->getConditionalCount (
args_[fIdx].countedLogVar());
unsigned R = args_[fIdx].range();
vector<double> numAssigns = HistogramSet::getNumAssigns (N, R);
StatesIndexer sindexer (ranges_, fIdx);
while (sindexer.valid()) {
unsigned h = sindexer[fIdx];
if (Globals::logDomain) {
params_[sindexer] += numAssigns[h];
} else {
params_[sindexer] *= numAssigns[h];
}
++ sindexer;
}
}
Params copy = params_;
params_.clear();
params_.resize (copy.size() / ranges_[fIdx], LogAware::addIdenty());
MapIndexer indexer (ranges_, fIdx);
if (Globals::logDomain) {
for (unsigned i = 0; i < copy.size(); i++) {
params_[indexer] = Util::logSum (params_[indexer], copy[i]);
++ indexer;
}
} else {
for (unsigned i = 0; i < copy.size(); i++) {
params_[indexer] += copy[i];
++ indexer;
}
}
args_.erase (args_.begin() + fIdx);
ranges_.erase (ranges_.begin() + fIdx);
constr_->remove (excl);
}
void
Parfactor::multiply (Parfactor& g)
{
alignAndExponentiate (this, &g);
TFactor<ProbFormula>::multiply (g);
constr_->join (g.constr(), true);
}
void
Parfactor::countConvert (LogVar X)
{
int fIdx = indexOfLogVar (X);
assert (fIdx != -1);
assert (constr_->isCountNormalized (X));
assert (constr_->getConditionalCount (X) > 1);
assert (constr_->isCarteesianProduct (countedLogVars() | X));
unsigned N = constr_->getConditionalCount (X);
unsigned R = ranges_[fIdx];
unsigned H = HistogramSet::nrHistograms (N, R);
vector<Histogram> histograms = HistogramSet::getHistograms (N, R);
StatesIndexer indexer (ranges_);
vector<Params> sumout (params_.size() / R);
unsigned count = 0;
while (indexer.valid()) {
sumout[count].reserve (R);
for (unsigned r = 0; r < R; r++) {
sumout[count].push_back (params_[indexer]);
indexer.increment (fIdx);
}
count ++;
indexer.reset (fIdx);
indexer.incrementExcluding (fIdx);
}
params_.clear();
params_.reserve (sumout.size() * H);
ranges_[fIdx] = H;
MapIndexer mapIndexer (ranges_, fIdx);
while (mapIndexer.valid()) {
double prod = LogAware::multIdenty();
unsigned i = mapIndexer.mappedIndex();
unsigned h = mapIndexer[fIdx];
for (unsigned r = 0; r < R; r++) {
if (Globals::logDomain) {
prod += LogAware::pow (sumout[i][r], histograms[h][r]);
} else {
prod *= LogAware::pow (sumout[i][r], histograms[h][r]);
}
}
params_.push_back (prod);
++ mapIndexer;
}
args_[fIdx].setCountedLogVar (X);
}
void
Parfactor::expand (LogVar X, LogVar X_new1, LogVar X_new2)
{
int fIdx = indexOfLogVar (X);
assert (fIdx != -1);
assert (args_[fIdx].isCounting());
unsigned N1 = constr_->getConditionalCount (X_new1);
unsigned N2 = constr_->getConditionalCount (X_new2);
unsigned N = N1 + N2;
unsigned R = args_[fIdx].range();
unsigned H1 = HistogramSet::nrHistograms (N1, R);
unsigned H2 = HistogramSet::nrHistograms (N2, R);
vector<Histogram> histograms = HistogramSet::getHistograms (N, R);
vector<Histogram> histograms1 = HistogramSet::getHistograms (N1, R);
vector<Histogram> histograms2 = HistogramSet::getHistograms (N2, R);
vector<unsigned> sumIndexes;
sumIndexes.reserve (H1 * H2);
for (unsigned i = 0; i < H1; i++) {
for (unsigned j = 0; j < H2; j++) {
Histogram hist = histograms1[i];
std::transform (
hist.begin(), hist.end(),
histograms2[j].begin(),
hist.begin(),
plus<int>());
sumIndexes.push_back (HistogramSet::findIndex (hist, histograms));
}
}
expandPotential (fIdx, H1 * H2, sumIndexes);
args_.insert (args_.begin() + fIdx + 1, args_[fIdx]);
args_[fIdx].rename (X, X_new1);
args_[fIdx + 1].rename (X, X_new2);
ranges_.insert (ranges_.begin() + fIdx + 1, H2);
ranges_[fIdx] = H1;
}
void
Parfactor::fullExpand (LogVar X)
{
int fIdx = indexOfLogVar (X);
assert (fIdx != -1);
assert (args_[fIdx].isCounting());
unsigned N = constr_->getConditionalCount (X);
unsigned R = args_[fIdx].range();
vector<Histogram> originHists = HistogramSet::getHistograms (N, R);
vector<Histogram> expandHists = HistogramSet::getHistograms (1, R);
vector<unsigned> sumIndexes;
sumIndexes.reserve (N * R);
Ranges expandRanges (N, R);
StatesIndexer indexer (expandRanges);
while (indexer.valid()) {
vector<unsigned> hist (R, 0);
for (unsigned n = 0; n < N; n++) {
std::transform (
hist.begin(), hist.end(),
expandHists[indexer[n]].begin(),
hist.begin(),
plus<int>());
}
sumIndexes.push_back (HistogramSet::findIndex (hist, originHists));
++ indexer;
}
expandPotential (fIdx, std::pow (R, N), sumIndexes);
ProbFormula f = args_[fIdx];
args_.erase (args_.begin() + fIdx);
ranges_.erase (ranges_.begin() + fIdx);
LogVars newLvs = constr_->expand (X);
assert (newLvs.size() == N);
for (unsigned i = 0 ; i < N; i++) {
ProbFormula newFormula (f.functor(), f.logVars(), f.range());
newFormula.rename (X, newLvs[i]);
args_.insert (args_.begin() + fIdx + i, newFormula);
ranges_.insert (ranges_.begin() + fIdx + i, R);
}
}
void
Parfactor::reorderAccordingGrounds (const Grounds& grounds)
{
ProbFormulas newFormulas;
for (unsigned i = 0; i < grounds.size(); i++) {
for (unsigned j = 0; j < args_.size(); j++) {
if (grounds[i].functor() == args_[j].functor() &&
grounds[i].arity() == args_[j].arity()) {
constr_->moveToTop (args_[j].logVars());
if (constr_->containsTuple (grounds[i].args())) {
newFormulas.push_back (args_[j]);
break;
}
}
}
assert (newFormulas.size() == i + 1);
}
reorderArguments (newFormulas);
}
void
Parfactor::absorveEvidence (const ProbFormula& formula, unsigned evidence)
{
int fIdx = indexOf (formula);
assert (fIdx != -1);
LogVarSet excl = exclusiveLogVars (fIdx);
assert (args_[fIdx].isCounting() == false);
assert (constr_->isCountNormalized (excl));
LogAware::pow (params_, constr_->getConditionalCount (excl));
TFactor<ProbFormula>::absorveEvidence (formula, evidence);
constr_->remove (excl);
}
void
Parfactor::setNewGroups (void)
{
for (unsigned i = 0; i < args_.size(); i++) {
args_[i].setGroup (ProbFormula::getNewGroup());
}
}
void
Parfactor::applySubstitution (const Substitution& theta)
{
for (unsigned i = 0; i < args_.size(); i++) {
LogVars& lvs = args_[i].logVars();
for (unsigned j = 0; j < lvs.size(); j++) {
lvs[j] = theta.newNameFor (lvs[j]);
}
if (args_[i].isCounting()) {
LogVar clv = args_[i].countedLogVar();
args_[i].setCountedLogVar (theta.newNameFor (clv));
}
}
constr_->applySubstitution (theta);
}
int
Parfactor::findGroup (const Ground& ground) const
{
int group = -1;
for (unsigned i = 0; i < args_.size(); i++) {
if (args_[i].functor() == ground.functor() &&
args_[i].arity() == ground.arity()) {
constr_->moveToTop (args_[i].logVars());
if (constr_->containsTuple (ground.args())) {
group = args_[i].group();
break;
}
}
}
return group;
}
bool
Parfactor::containsGround (const Ground& ground) const
{
return findGroup (ground) != -1;
}
bool
Parfactor::containsGroup (unsigned group) const
{
for (unsigned i = 0; i < args_.size(); i++) {
if (args_[i].group() == group) {
return true;
}
}
return false;
}
unsigned
Parfactor::nrFormulas (LogVar X) const
{
unsigned count = 0;
for (unsigned i = 0; i < args_.size(); i++) {
if (args_[i].contains (X)) {
count ++;
}
}
return count;
}
int
Parfactor::indexOfLogVar (LogVar X) const
{
int idx = -1;
assert (nrFormulas (X) == 1);
for (unsigned i = 0; i < args_.size(); i++) {
if (args_[i].contains (X)) {
idx = i;
break;
}
}
return idx;
}
int
Parfactor::indexOfGroup (unsigned group) const
{
int pos = -1;
for (unsigned i = 0; i < args_.size(); i++) {
if (args_[i].group() == group) {
pos = i;
break;
}
}
return pos;
}
vector<unsigned>
Parfactor::getAllGroups (void) const
{
vector<unsigned> groups (args_.size());
for (unsigned i = 0; i < args_.size(); i++) {
groups[i] = args_[i].group();
}
return groups;
}
string
Parfactor::getLabel (void) const
{
stringstream ss;
ss << "phi(" ;
for (unsigned i = 0; i < args_.size(); i++) {
if (i != 0) ss << "," ;
ss << args_[i];
}
ss << ")" ;
ConstraintTree copy (*constr_);
copy.moveToTop (copy.logVarSet().elements());
ss << "|" << copy.tupleSet();
return ss.str();
}
void
Parfactor::print (bool printParams) const
{
cout << "Formulas: " ;
for (unsigned i = 0; i < args_.size(); i++) {
if (i != 0) cout << ", " ;
cout << args_[i];
}
cout << endl;
if (args_[0].group() != Util::maxUnsigned()) {
vector<string> groups;
for (unsigned i = 0; i < args_.size(); i++) {
groups.push_back (string ("g") + Util::toString (args_[i].group()));
}
cout << "Groups: " << groups << endl;
}
cout << "LogVars: " << constr_->logVarSet() << endl;
cout << "Ranges: " << ranges_ << endl;
if (printParams == false) {
cout << "Params: " << params_ << endl;
}
ConstraintTree copy (*constr_);
copy.moveToTop (copy.logVarSet().elements());
cout << "Tuples: " << copy.tupleSet() << endl;
if (printParams) {
vector<string> jointStrings;
StatesIndexer indexer (ranges_);
while (indexer.valid()) {
stringstream ss;
for (unsigned i = 0; i < args_.size(); i++) {
if (i != 0) ss << ", " ;
if (args_[i].isCounting()) {
unsigned N = constr_->getConditionalCount (
args_[i].countedLogVar());
HistogramSet hs (N, args_[i].range());
unsigned c = 0;
while (c < indexer[i]) {
hs.nextHistogram();
c ++;
}
ss << hs;
} else {
ss << indexer[i];
}
}
jointStrings.push_back (ss.str());
++ indexer;
}
for (unsigned i = 0; i < params_.size(); i++) {
cout << "f(" << jointStrings[i] << ")" ;
cout << " = " << params_[i] << endl;
}
}
cout << endl;
}
void
Parfactor::expandPotential (
int fIdx,
unsigned newRange,
const vector<unsigned>& sumIndexes)
{
unsigned size = (params_.size() / ranges_[fIdx]) * newRange;
Params copy = params_;
params_.clear();
params_.reserve (size);
unsigned prod = 1;
vector<unsigned> offsets_ (ranges_.size());
for (int i = ranges_.size() - 1; i >= 0; i--) {
offsets_[i] = prod;
prod *= ranges_[i];
}
unsigned index = 0;
ranges_[fIdx] = newRange;
vector<unsigned> indices (ranges_.size(), 0);
for (unsigned k = 0; k < size; k++) {
params_.push_back (copy[index]);
for (int i = ranges_.size() - 1; i >= 0; i--) {
indices[i] ++;
if (i == fIdx) {
assert (indices[i] - 1 < sumIndexes.size());
int diff = sumIndexes[indices[i]] - sumIndexes[indices[i] - 1];
index += diff * offsets_[i];
} else {
index += offsets_[i];
}
if (indices[i] != ranges_[i]) {
break;
} else {
if (i == fIdx) {
int diff = sumIndexes[0] - sumIndexes[indices[i]];
index += diff * offsets_[i];
} else {
index -= offsets_[i] * ranges_[i];
}
indices[i] = 0;
}
}
}
}
void
Parfactor::alignAndExponentiate (Parfactor* g1, Parfactor* g2)
{
LogVars X_1, X_2;
const ProbFormulas& formulas1 = g1->arguments();
const ProbFormulas& formulas2 = g2->arguments();
for (unsigned i = 0; i < formulas1.size(); i++) {
for (unsigned j = 0; j < formulas2.size(); j++) {
if (formulas1[i].group() == formulas2[j].group()) {
Util::addToVector (X_1, formulas1[i].logVars());
Util::addToVector (X_2, formulas2[j].logVars());
}
}
}
LogVarSet Y_1 = g1->logVarSet() - LogVarSet (X_1);
LogVarSet Y_2 = g2->logVarSet() - LogVarSet (X_2);
assert (g1->constr()->isCountNormalized (Y_1));
assert (g2->constr()->isCountNormalized (Y_2));
unsigned condCount1 = g1->constr()->getConditionalCount (Y_1);
unsigned condCount2 = g2->constr()->getConditionalCount (Y_2);
LogAware::pow (g1->params(), 1.0 / condCount2);
LogAware::pow (g2->params(), 1.0 / condCount1);
// this must be done in the end or else X_1 and X_2
// will refer the old log var names in the code above
align (g1, X_1, g2, X_2);
}
void
Parfactor::align (
Parfactor* g1, const LogVars& alignLvs1,
Parfactor* g2, const LogVars& alignLvs2)
{
LogVar freeLogVar = 0;
Substitution theta1;
Substitution theta2;
const LogVarSet& allLvs1 = g1->logVarSet();
for (unsigned i = 0; i < allLvs1.size(); i++) {
theta1.add (allLvs1[i], freeLogVar);
++ freeLogVar;
}
const LogVarSet& allLvs2 = g2->logVarSet();
for (unsigned i = 0; i < allLvs2.size(); i++) {
theta2.add (allLvs2[i], freeLogVar);
++ freeLogVar;
}
assert (alignLvs1.size() == alignLvs2.size());
for (unsigned i = 0; i < alignLvs1.size(); i++) {
theta1.rename (alignLvs1[i], theta2.newNameFor (alignLvs2[i]));
}
g1->applySubstitution (theta1);
g2->applySubstitution (theta2);
}

37
packages/CLPBN/clpbn/bp/Solver.cpp
View File

@ -1,37 +0,0 @@
#include "Solver.h"
#include "Util.h"
void
Solver::printAnswer (const VarIds& vids)
{
Vars unobservedVars;
VarIds unobservedVids;
for (unsigned i = 0; i < vids.size(); i++) {
VarNode* vn = fg.getVarNode (vids[i]);
if (vn->hasEvidence() == false) {
unobservedVars.push_back (vn);
unobservedVids.push_back (vids[i]);
}
}
Params res = solveQuery (unobservedVids);
vector<string> stateLines = Util::getStateLines (unobservedVars);
for (unsigned i = 0; i < res.size(); i++) {
cout << "P(" << stateLines[i] << ") = " ;
cout << std::setprecision (Constants::PRECISION) << res[i];
cout << endl;
}
cout << endl;
}
void
Solver::printAllPosterioris (void)
{
const VarNodes& vars = fg.varNodes();
for (unsigned i = 0; i < vars.size(); i++) {
printAnswer ({vars[i]->varId()});
}
}

4
packages/CLPBN/clpbn/bp/TODO
View File

@ -1,4 +0,0 @@
TODO
- add a way to calculate combinations and factorials with large numbers
- refactor sumOut in parfactor -> is really ugly code
- Indexer: start receiving ranges as constant reference

200
packages/CLPBN/clpbn/bp/TinySet.h
View File

@ -1,200 +0,0 @@
#ifndef HORUS_TINYSET_H
#define HORUS_TINYSET_H
#include <vector>
#include <algorithm>
using namespace std;
template <typename T>
class TinySet
{
public:
TinySet (void) {}
TinySet (const T& t)
{
elements_.push_back (t);
}
TinySet (const vector<T>& elements)
{
elements_.reserve (elements.size());
for (unsigned i = 0; i < elements.size(); i++) {
insert (elements[i]);
}
}
TinySet (const TinySet<T>& s) : elements_(s.elements_) { }
void insert (const T& t)
{
typename vector<T>::iterator it =
std::lower_bound (elements_.begin(), elements_.end(), t);
if (it == elements_.end() || *it != t) {
elements_.insert (it, t);
}
}
void remove (const T& t)
{
typename vector<T>::iterator it =
std::lower_bound (elements_.begin(), elements_.end(), t);
if (it != elements_.end()) {
elements_.erase (it);
}
}
/* set union */
TinySet operator| (const TinySet& s) const
{
TinySet res;
std::set_union (
elements_.begin(),
elements_.end(),
s.elements_.begin(),
s.elements_.end(),
std::back_inserter (res.elements_));
return res;
}
/* set intersection */
TinySet operator& (const TinySet& s) const
{
TinySet res;
std::set_intersection (
elements_.begin(),
elements_.end(),
s.elements_.begin(),
s.elements_.end(),
std::back_inserter (res.elements_));
return res;
}
/* set difference */
TinySet operator- (const TinySet& s) const
{
TinySet res;
std::set_difference (
elements_.begin(),
elements_.end(),
s.elements_.begin(),
s.elements_.end(),
std::back_inserter (res.elements_));
return res;
}
TinySet& operator|= (const TinySet& s)
{
return *this = (*this | s);
}
TinySet& operator&= (const TinySet& s)
{
return *this = (*this & s);
}
TinySet& operator-= (const TinySet& s)
{
return *this = (*this - s);
}
bool contains (const T& t) const
{
return std::binary_search (
elements_.begin(), elements_.end(), t);
}
bool contains (const TinySet& s) const
{
return std::includes (
elements_.begin(),
elements_.end(),
s.elements_.begin(),
s.elements_.end());
}
bool in (const TinySet& s) const
{
return std::includes (
s.elements_.begin(),
s.elements_.end(),
elements_.begin(),
elements_.end());
}
bool intersects (const TinySet& s) const
{
return (*this & s).size() > 0;
}
T operator[] (unsigned i) const
{
return elements_[i];
}
const vector<T>& elements (void) const
{
return elements_;
}
T front (void) const
{
return elements_.front();
}
T back (void) const
{
return elements_.back();
}
unsigned size (void) const
{
return elements_.size();
}
bool empty (void) const
{
return elements_.size() == 0;
}
typedef typename std::vector<T>::const_iterator const_iterator;
const_iterator begin (void) const
{
return elements_.begin();
}
const_iterator end (void) const
{
return elements_.end();
}
friend bool operator== (const TinySet& s1, const TinySet& s2)
{
return s1.elements_ == s2.elements_;
}
friend bool operator!= (const TinySet& s1, const TinySet& s2)
{
return s1.elements_ != s2.elements_;
}
friend std::ostream& operator << (std::ostream& out, const TinySet<T>& s)
{
out << "{" ;
for (unsigned i = 0; i < s.size(); i++) {
out << ((i != 0) ? "," : "") << s.elements()[i];
}
out << "}" ;
return out;
}
protected:
vector<T> elements_;
};
#endif // HORUS_TINYSET_H

502
packages/CLPBN/clpbn/bp/Util.cpp
View File

@ -1,502 +0,0 @@
#include <limits>
#include <sstream>
#include <fstream>
#include "Util.h"
#include "Indexer.h"
namespace Globals {
bool logDomain = false;
//InfAlgs infAlgorithm = InfAlgorithms::VE;
//InfAlgs infAlgorithm = InfAlgorithms::BN_BP;
//InfAlgs infAlgorithm = InfAlgorithms::FG_BP;
InfAlgorithms infAlgorithm = InfAlgorithms::CBP;
};
namespace BpOptions {
Schedule schedule = BpOptions::Schedule::SEQ_FIXED;
//Schedule schedule = BpOptions::Schedule::SEQ_RANDOM;
//Schedule schedule = BpOptions::Schedule::PARALLEL;
//Schedule schedule = BpOptions::Schedule::MAX_RESIDUAL;
double accuracy = 0.0001;
unsigned maxIter = 1000;
}
vector<NetInfo> Statistics::netInfo_;
vector<CompressInfo> Statistics::compressInfo_;
unsigned Statistics::primaryNetCount_;
namespace Util {
void
toLog (Params& v)
{
for (unsigned i = 0; i < v.size(); i++) {
v[i] = log (v[i]);
}
}
void
fromLog (Params& v)
{
for (unsigned i = 0; i < v.size(); i++) {
v[i] = exp (v[i]);
}
}
double
factorial (double num)
{
double result = 1.0;
for (int i = 1; i <= num; i++) {
result *= i;
}
return result;
}
unsigned
nrCombinations (unsigned n, unsigned r)
{
assert (n >= r);
unsigned prod = 1;
for (int i = (int)n; i > (int)(n - r); i--) {
prod *= i;
}
return (prod / factorial (r));
}
unsigned
expectedSize (const Ranges& ranges)
{
unsigned prod = 1;
for (unsigned i = 0; i < ranges.size(); i++) {
prod *= ranges[i];
}
return prod;
}
unsigned
getNumberOfDigits (int number)
{
unsigned count = 1;
while (number >= 10) {
number /= 10;
count ++;
}
return count;
}
bool
isInteger (const string& s)
{
stringstream ss1 (s);
stringstream ss2;
int integer;
ss1 >> integer;
ss2 << integer;
return (ss1.str() == ss2.str());
}
string
parametersToString (const Params& v, unsigned precision)
{
stringstream ss;
ss.precision (precision);
ss << "[" ;
for (unsigned i = 0; i < v.size(); i++) {
if (i != 0) ss << ", " ;
ss << v[i];
}
ss << "]" ;
return ss.str();
}
vector<string>
getStateLines (const Vars& vars)
{
StatesIndexer idx (vars);
vector<string> jointStrings;
while (idx.valid()) {
stringstream ss;
for (unsigned i = 0; i < vars.size(); i++) {
if (i != 0) ss << ", " ;
ss << vars[i]->label() << "=" << vars[i]->states()[(idx[i])];
}
jointStrings.push_back (ss.str());
++ idx;
}
return jointStrings;
}
void
printHeader (string header, std::ostream& os)
{
printAsteriskLine (os);
os << header << endl;
printAsteriskLine (os);
}
void
printSubHeader (string header, std::ostream& os)
{
printDashedLine (os);
os << header << endl;
printDashedLine (os);
}
void
printAsteriskLine (std::ostream& os)
{
os << "********************************" ;
os << "********************************" ;
os << endl;
}
void
printDashedLine (std::ostream& os)
{
os << "--------------------------------" ;
os << "--------------------------------" ;
os << endl;
}
}
namespace LogAware {
void
normalize (Params& v)
{
double sum;
if (Globals::logDomain) {
sum = LogAware::addIdenty();
for (unsigned i = 0; i < v.size(); i++) {
sum = Util::logSum (sum, v[i]);
}
assert (sum != -numeric_limits<double>::infinity());
for (unsigned i = 0; i < v.size(); i++) {
v[i] -= sum;
}
} else {
sum = 0.0;
for (unsigned i = 0; i < v.size(); i++) {
sum += v[i];
}
assert (sum != 0.0);
for (unsigned i = 0; i < v.size(); i++) {
v[i] /= sum;
}
}
}
double
getL1Distance (const Params& v1, const Params& v2)
{
assert (v1.size() == v2.size());
double dist = 0.0;
if (Globals::logDomain) {
for (unsigned i = 0; i < v1.size(); i++) {
dist += abs (exp(v1[i]) - exp(v2[i]));
}
} else {
for (unsigned i = 0; i < v1.size(); i++) {
dist += abs (v1[i] - v2[i]);
}
}
return dist;
}
double
getMaxNorm (const Params& v1, const Params& v2)
{
assert (v1.size() == v2.size());
double max = 0.0;
if (Globals::logDomain) {
for (unsigned i = 0; i < v1.size(); i++) {
double diff = abs (exp(v1[i]) - exp(v2[i]));
if (diff > max) {
max = diff;
}
}
} else {
for (unsigned i = 0; i < v1.size(); i++) {
double diff = abs (v1[i] - v2[i]);
if (diff > max) {
max = diff;
}
}
}
return max;
}
double
pow (double p, unsigned expoent)
{
return Globals::logDomain ? p * expoent : std::pow (p, expoent);
}
double
pow (double p, double expoent)
{
// assumes that `expoent' is never in log domain
return Globals::logDomain ? p * expoent : std::pow (p, expoent);
}
void
pow (Params& v, unsigned expoent)
{
if (expoent == 1) {
return;
}
if (Globals::logDomain) {
for (unsigned i = 0; i < v.size(); i++) {
v[i] *= expoent;
}
} else {
for (unsigned i = 0; i < v.size(); i++) {
v[i] = std::pow (v[i], expoent);
}
}
}
void
pow (Params& v, double expoent)
{
// assumes that `expoent' is never in log domain
if (Globals::logDomain) {
for (unsigned i = 0; i < v.size(); i++) {
v[i] *= expoent;
}
} else {
for (unsigned i = 0; i < v.size(); i++) {
v[i] = std::pow (v[i], expoent);
}
}
}
}
unsigned
Statistics::getSolvedNetworksCounting (void)
{
return netInfo_.size();
}
void
Statistics::incrementPrimaryNetworksCounting (void)
{
primaryNetCount_ ++;
}
unsigned
Statistics::getPrimaryNetworksCounting (void)
{
return primaryNetCount_;
}
void
Statistics::updateStatistics (
unsigned size,
bool loopy,
unsigned nIters,
double time)
{
netInfo_.push_back (NetInfo (size, loopy, nIters, time));
}
void
Statistics::printStatistics (void)
{
cout << getStatisticString();
}
void
Statistics::writeStatistics (const char* fileName)
{
ofstream out (fileName);
if (!out.is_open()) {
cerr << "error: cannot open file to write at " ;
cerr << "Statistics::writeStats()" << endl;
abort();
}
out << getStatisticString();
out.close();
}
void
Statistics::updateCompressingStatistics (
unsigned nrGroundVars,
unsigned nrGroundFactors,
unsigned nrClusterVars,
unsigned nrClusterFactors,
unsigned nrNeighborless) {
compressInfo_.push_back (CompressInfo (nrGroundVars, nrGroundFactors,
nrClusterVars, nrClusterFactors, nrNeighborless));
}
string
Statistics::getStatisticString (void)
{
stringstream ss2, ss3, ss4, ss1;
ss1 << "running mode: " ;
switch (Globals::infAlgorithm) {
case InfAlgorithms::VE: ss1 << "ve" << endl; break;
case InfAlgorithms::BP: ss1 << "bp" << endl; break;
case InfAlgorithms::CBP: ss1 << "cbp" << endl; break;
}
ss1 << "message schedule: " ;
switch (BpOptions::schedule) {
case BpOptions::Schedule::SEQ_FIXED:
ss1 << "sequential fixed" << endl;
break;
case BpOptions::Schedule::SEQ_RANDOM:
ss1 << "sequential random" << endl;
break;
case BpOptions::Schedule::PARALLEL:
ss1 << "parallel" << endl;
break;
case BpOptions::Schedule::MAX_RESIDUAL:
ss1 << "max residual" << endl;
break;
}
ss1 << "max iterations: " << BpOptions::maxIter << endl;
ss1 << "accuracy " << BpOptions::accuracy << endl;
ss1 << endl << endl;
Util::printSubHeader ("Network information", ss2);
ss2 << left;
ss2 << setw (15) << "Network Size" ;
ss2 << setw (9) << "Loopy" ;
ss2 << setw (15) << "Iterations" ;
ss2 << setw (15) << "Solving Time" ;
ss2 << endl;
unsigned nLoopyNets = 0;
unsigned nUnconvergedRuns = 0;
double totalSolvingTime = 0.0;
for (unsigned i = 0; i < netInfo_.size(); i++) {
ss2 << setw (15) << netInfo_[i].size;
if (netInfo_[i].loopy) {
ss2 << setw (9) << "yes";
nLoopyNets ++;
} else {
ss2 << setw (9) << "no";
}
if (netInfo_[i].nIters == 0) {
ss2 << setw (15) << "n/a" ;
} else {
ss2 << setw (15) << netInfo_[i].nIters;
if (netInfo_[i].nIters > BpOptions::maxIter) {
nUnconvergedRuns ++;
}
}
ss2 << setw (15) << netInfo_[i].time;
totalSolvingTime += netInfo_[i].time;
ss2 << endl;
}
ss2 << endl << endl;
unsigned c1 = 0, c2 = 0, c3 = 0, c4 = 0;
if (compressInfo_.size() > 0) {
Util::printSubHeader ("Compress information", ss3);
ss3 << left;
ss3 << "Ground Cluster Ground Cluster Neighborless" << endl;
ss3 << "Vars Vars Factors Factors Vars" << endl;
for (unsigned i = 0; i < compressInfo_.size(); i++) {
ss3 << setw (9) << compressInfo_[i].nrGroundVars;
ss3 << setw (10) << compressInfo_[i].nrClusterVars;
ss3 << setw (10) << compressInfo_[i].nrGroundFactors;
ss3 << setw (10) << compressInfo_[i].nrClusterFactors;
ss3 << setw (10) << compressInfo_[i].nrNeighborless;
ss3 << endl;
c1 += compressInfo_[i].nrGroundVars - compressInfo_[i].nrNeighborless;
c2 += compressInfo_[i].nrClusterVars;
c3 += compressInfo_[i].nrGroundFactors - compressInfo_[i].nrNeighborless;
c4 += compressInfo_[i].nrClusterFactors;
if (compressInfo_[i].nrNeighborless != 0) {
c2 --;
c4 --;
}
}
ss3 << endl << endl;
}
ss4 << "primary networks: " << primaryNetCount_ << endl;
ss4 << "solved networks: " << netInfo_.size() << endl;
ss4 << "loopy networks: " << nLoopyNets << endl;
ss4 << "unconverged runs: " << nUnconvergedRuns << endl;
ss4 << "total solving time: " << totalSolvingTime << endl;
if (compressInfo_.size() > 0) {
double pc1 = (1.0 - (c2 / (double)c1)) * 100.0;
double pc2 = (1.0 - (c4 / (double)c3)) * 100.0;
ss4 << setprecision (5);
ss4 << "variable compression: " << pc1 << "%" << endl;
ss4 << "factor compression: " << pc2 << "%" << endl;
}
ss4 << endl << endl;
ss1 << ss4.str() << ss2.str() << ss3.str();
return ss1.str();
}

376
packages/CLPBN/clpbn/bp/Util.h
View File

@ -1,376 +0,0 @@
#ifndef HORUS_UTIL_H
#define HORUS_UTIL_H
#include <cmath>
#include <cassert>
#include <limits>
#include <algorithm>
#include <vector>
#include <set>
#include <queue>
#include <unordered_map>
#include <sstream>
#include <iostream>
#include "Horus.h"
using namespace std;
namespace Util {
template <typename T> void addToVector (vector<T>&, const vector<T>&);
template <typename T> void addToSet (set<T>&, const vector<T>&);
template <typename T> void addToQueue (queue<T>&, const vector<T>&);
template <typename T> bool contains (const vector<T>&, const T&);
template <typename T> bool contains (const set<T>&, const T&);
template <typename K, typename V> bool contains (
const unordered_map<K, V>&, const K&);
template <typename T> std::string toString (const T&);
void toLog (Params&);
void fromLog (Params&);
double logSum (double, double);
void multiply (Params&, const Params&);
void multiply (Params&, const Params&, unsigned);
void add (Params&, const Params&);
void add (Params&, const Params&, unsigned);
double factorial (double);
unsigned nrCombinations (unsigned, unsigned);
unsigned expectedSize (const Ranges&);
unsigned getNumberOfDigits (int);
bool isInteger (const string&);
string parametersToString (const Params&, unsigned = Constants::PRECISION);
vector<string> getStateLines (const Vars&);
void printHeader (string, std::ostream& os = std::cout);
void printSubHeader (string, std::ostream& os = std::cout);
void printAsteriskLine (std::ostream& os = std::cout);
void printDashedLine (std::ostream& os = std::cout);
unsigned maxUnsigned (void);
};
template <typename T> void
Util::addToVector (vector<T>& v, const vector<T>& elements)
{
v.insert (v.end(), elements.begin(), elements.end());
}
template <typename T> void
Util::addToSet (set<T>& s, const vector<T>& elements)
{
s.insert (elements.begin(), elements.end());
}
template <typename T> void
Util::addToQueue (queue<T>& q, const vector<T>& elements)
{
for (unsigned i = 0; i < elements.size(); i++) {
q.push (elements[i]);
}
}
template <typename T> bool
Util::contains (const vector<T>& v, const T& e)
{
return std::find (v.begin(), v.end(), e) != v.end();
}
template <typename T> bool
Util::contains (const set<T>& s, const T& e)
{
return s.find (e) != s.end();
}
template <typename K, typename V> bool
Util::contains (const unordered_map<K, V>& m, const K& k)
{
return m.find (k) != m.end();
}
template <typename T> std::string
Util::toString (const T& t)
{
std::stringstream ss;
ss << t;
return ss.str();
}
template <typename T>
std::ostream& operator << (std::ostream& os, const vector<T>& v)
{
os << "[" ;
for (unsigned i = 0; i < v.size(); i++) {
os << ((i != 0) ? ", " : "") << v[i];
}
os << "]" ;
return os;
}
namespace {
const double INF = -numeric_limits<double>::infinity();
};
inline double
Util::logSum (double x, double y)
{
return log (exp (x) + exp (y));
assert (isfinite (x) && isfinite (y));
// If one value is much smaller than the other, keep the larger value.
if (x < (y - log (1e200))) {
return y;
}
if (y < (x - log (1e200))) {
return x;
}
double diff = x - y;
assert (isfinite (diff) && isfinite (x) && isfinite (y));
if (!isfinite (exp (diff))) {
// difference is too large
return x > y ? x : y;
}
// otherwise return the sum.
return y + log (static_cast<double>(1.0) + exp (diff));
}
inline void
Util::multiply (Params& v1, const Params& v2)
{
assert (v1.size() == v2.size());
for (unsigned i = 0; i < v1.size(); i++) {
v1[i] *= v2[i];
}
}
inline void
Util::multiply (Params& v1, const Params& v2, unsigned repetitions)
{
for (unsigned count = 0; count < v1.size(); ) {
for (unsigned i = 0; i < v2.size(); i++) {
for (unsigned r = 0; r < repetitions; r++) {
v1[count] *= v2[i];
count ++;
}
}
}
}
inline void
Util::add (Params& v1, const Params& v2)
{
assert (v1.size() == v2.size());
for (unsigned i = 0; i < v1.size(); i++) {
v1[i] += v2[i];
}
}
inline void
Util::add (Params& v1, const Params& v2, unsigned repetitions)
{
for (unsigned count = 0; count < v1.size(); ) {
for (unsigned i = 0; i < v2.size(); i++) {
for (unsigned r = 0; r < repetitions; r++) {
v1[count] += v2[i];
count ++;
}
}
}
}
inline unsigned
Util::maxUnsigned (void)
{
return numeric_limits<unsigned>::max();
}
namespace LogAware {
inline double
one()
{
return Globals::logDomain ? 0.0 : 1.0;
}
inline double
zero() {
return Globals::logDomain ? INF : 0.0 ;
}
inline double
addIdenty()
{
return Globals::logDomain ? INF : 0.0;
}
inline double
multIdenty()
{
return Globals::logDomain ? 0.0 : 1.0;
}
inline double
withEvidence()
{
return Globals::logDomain ? 0.0 : 1.0;
}
inline double
noEvidence() {
return Globals::logDomain ? INF : 0.0;
}
inline double
tl (double v)
{
return Globals::logDomain ? log (v) : v;
}
inline double
fl (double v)
{
return Globals::logDomain ? exp (v) : v;
}
void normalize (Params&);
double getL1Distance (const Params&, const Params&);
double getMaxNorm (const Params&, const Params&);
double pow (double, unsigned);
double pow (double, double);
void pow (Params&, unsigned);
void pow (Params&, double);
};
struct NetInfo
{
NetInfo (unsigned size, bool loopy, unsigned nIters, double time)
{
this->size = size;
this->loopy = loopy;
this->nIters = nIters;
this->time = time;
}
unsigned size;
bool loopy;
unsigned nIters;
double time;
};
struct CompressInfo
{
CompressInfo (unsigned a, unsigned b, unsigned c, unsigned d, unsigned e)
{
nrGroundVars = a;
nrGroundFactors = b;
nrClusterVars = c;
nrClusterFactors = d;
nrNeighborless = e;
}
unsigned nrGroundVars;
unsigned nrGroundFactors;
unsigned nrClusterVars;
unsigned nrClusterFactors;
unsigned nrNeighborless;
};
class Statistics
{
public:
static unsigned getSolvedNetworksCounting (void);
static void incrementPrimaryNetworksCounting (void);
static unsigned getPrimaryNetworksCounting (void);
static void updateStatistics (unsigned, bool, unsigned, double);
static void printStatistics (void);
static void writeStatistics (const char*);
static void updateCompressingStatistics (
unsigned, unsigned, unsigned, unsigned, unsigned);
private:
static string getStatisticString (void);
static vector<NetInfo> netInfo_;
static vector<CompressInfo> compressInfo_;
static unsigned primaryNetCount_;
};
#endif // HORUS_UTIL_H

35
packages/CLPBN/clpbn/bp/benchmarks/benchs.sh
View File

@ -1,35 +0,0 @@
if [ $1 ] && [ $1 == "clear" ]; then
rm *~
rm -f school/*.log school/*~
rm -f city/*.log city/*~
rm -f workshop_attrs/*.log workshop_attrs/*~
fi
function run_solver
{
constraint=$1
solver_flag=true
if [ -n "$2" ]; then
if [ $SOLVER = hve ]; then
extra_flag=clpbn_horus:set_horus_flag\(elim_heuristic,$2\)
elif [ $SOLVER = bp ]; then
extra_flag=clpbn_horus:set_horus_flag\(schedule,$2\)
elif [ $SOLVER = cbp ]; then
extra_flag=clpbn_horus:set_horus_flag\(schedule,$2\)
else
echo "unknow flag $2"
fi
fi
/usr/bin/time -o $LOG_FILE -a -f "real:%E\tuser:%U\tsys:%S" \
$YAP << EOF >> $LOG_FILE 2>> ignore.$LOG_FILE
[$NETWORK].
[$constraint].
clpbn_horus:set_solver($SOLVER).
clpbn_horus:set_horus_flag(use_logarithms, true).
$solver_flag.
$QUERY.
open("$LOG_FILE", 'append', S), format(S, '$constraint: ~15+ ', []), close(S).
EOF
}

17
packages/CLPBN/clpbn/bp/benchmarks/city/bp_tests.sh
View File

@ -1,17 +0,0 @@
#!/bin/bash
source city.sh
source ../benchs.sh
SOLVER="bp"
YAP=~/bin/$SHORTNAME-$SOLVER
LOG_FILE=$SOLVER.log
#LOG_FILE=results`date "+ %H:%M:%S %d-%m-%Y"`.
rm -f $LOG_FILE
rm -f ignore.$LOG_FILE
run_all_graphs "bp(shedule=seq_fixed) " seq_fixed

17
packages/CLPBN/clpbn/bp/benchmarks/city/cbp_tests.sh
View File

@ -1,17 +0,0 @@
#!/bin/bash
source city.sh
source ../benchs.sh
SOLVER="cbp"
YAP=~/bin/$SHORTNAME-$SOLVER
LOG_FILE=$SOLVER.log
#LOG_FILE=results`date "+ %H:%M:%S %d-%m-%Y"`.
rm -f $LOG_FILE
rm -f ignore.$LOG_FILE
run_all_graphs "cbp(shedule=seq_fixed) " seq_fixed

25
packages/CLPBN/clpbn/bp/benchmarks/city/city.sh
View File

@ -1,25 +0,0 @@
#!/bin/bash
NETWORK="'../../examples/city'"
SHORTNAME="city"
QUERY="is_joe_guilty(X)"
function run_all_graphs
{
cp ~/bin/yap $YAP
echo -n "**********************************" >> $LOG_FILE
echo "**********************************" >> $LOG_FILE
echo "results for solver $1" >> $LOG_FILE
echo -n "**********************************" >> $LOG_FILE
echo "**********************************" >> $LOG_FILE
run_solver city_5 $2
#run_solver city_1000 $2
#run_solver city_5000 $2
#run_solver city_10000 $2
#run_solver city_50000 $2
#run_solver city_100000 $2
#run_solver city_500000 $2
#run_solver city_1000000 $2
}

17
packages/CLPBN/clpbn/bp/benchmarks/city/fove_tests.sh
View File

@ -1,17 +0,0 @@
#!/bin/bash
source city.sh
source ../benchs.sh
SOLVER="fove"
YAP=~/bin/$SHORTNAME-$SOLVER
LOG_FILE=$SOLVER.log
#LOG_FILE=results`date "+ %H:%M:%S %d-%m-%Y"`.
rm -f $LOG_FILE
rm -f ignore.$LOG_FILEE
run_all_graphs "fove "

17
packages/CLPBN/clpbn/bp/benchmarks/city/hve_tests.sh
View File

@ -1,17 +0,0 @@
#!/bin/bash
source city.sh
source ../benchs.sh
SOLVER="hve"
YAP=~/bin/$SHORTNAME-$SOLVER
LOG_FILE=$SOLVER.log
#LOG_FILE=results`date "+ %H:%M:%S %d-%m-%Y"`.
rm -f $LOG_FILE
rm -f ignore.$LOG_FILE
run_all_graphs "hve(elim_heuristic=min_neighbors) " min_neighbors

11
packages/CLPBN/clpbn/bp/benchmarks/workshop_attrs/bp_tests.sh
View File

@ -1,11 +0,0 @@
#!/bin/bash
source wa.sh
source ../benchs.sh
SOLVER="bp"
YAP=~/bin/$SHORTNAME-$SOLVER
run_all_graphs "bp(shedule=seq_fixed) " seq_fixed

11
packages/CLPBN/clpbn/bp/benchmarks/workshop_attrs/cbp_tests.sh
View File

@ -1,11 +0,0 @@
#!/bin/bash
source wa.sh
source ../benchs.sh
SOLVER="cbp"
YAP=~/bin/$SHORTNAME-$SOLVER
run_all_graphs "cbp(shedule=seq_fixed) " seq_fixed

12
packages/CLPBN/clpbn/bp/benchmarks/workshop_attrs/fove_tests.sh
View File

@ -1,12 +0,0 @@
#!/bin/bash
source wa.sh
source ../benchs.sh
SOLVER="fove"
YAP=~/bin/$SHORTNAME-$SOLVER
run_all_graphs "fove "

11
packages/CLPBN/clpbn/bp/benchmarks/workshop_attrs/hve_tests.sh
View File

@ -1,11 +0,0 @@
#!/bin/bash
source wa.sh
source ../benchs.sh
SOLVER="hve"
YAP=~/bin/$SHORTNAME-$SOLVER
run_all_graphs "hve(elim_heuristic=min_neighbors) " min_neighbors

33
packages/CLPBN/clpbn/bp/benchmarks/workshop_attrs/wa.sh
View File

@ -1,33 +0,0 @@
#!/bin/bash
NETWORK="'../../examples/workshop_attrs'"
SHORTNAME="wa"
QUERY="series(X)"
function run_all_graphs
{
LOG_FILE=$SOLVER.log
#LOG_FILE=results`date "+ %H:%M:%S %d-%m-%Y"`.
rm -f $LOG_FILE
rm -f ignore.$LOG_FILE
cp ~/bin/yap $YAP
echo -n "**********************************" >> $LOG_FILE
echo "**********************************" >> $LOG_FILE
echo "results for solver $1" >> $LOG_FILE
echo -n "**********************************" >> $LOG_FILE
echo "**********************************" >> $LOG_FILE
run_solver pop_10 $2
#run_solver pop_1000 $2
#run_solver pop_5000 $2
#run_solver pop_10000 $2
#run_solver pop_50000 $2
#run_solver pop_100000 $2
#run_solver pop_500000 $2
#run_solver pop_1000000 $2
}

41
packages/CLPBN/clpbn/bp/examples/burglary-alarm.yap
View File

@ -1,41 +0,0 @@
:- use_module(library(pfl)).
%:- set_pfl_flag(solver,ve).
:- set_pfl_flag(solver,bp), clpbn_horus:set_horus_flag(inf_alg,ve).
%:- set_pfl_flag(solver,bp), clpbn_horus:set_horus_flag(inf_alg,bp).
%:- set_pfl_flag(solver,fove).
% :- yap_flag(write_strings, off).
bayes burglary::[b1,b3] ; [0.001, 0.999] ; [].
bayes earthquake::[e1,e2] ; [0.002, 0.998]; [].
bayes alarm::[a1,a2] , burglary, earthquake ; [0.95, 0.94, 0.29, 0.001, 0.05, 0.06, 0.71, 0.999] ; [].
bayes john_calls::[j1,j2] , alarm ; [0.9, 0.05, 0.1, 0.95] ; [].
bayes mary_calls::[m1,m2] , alarm ; [0.7, 0.01, 0.3, 0.99] ; [].
b_cpt([0.001, 0.999]).
e_cpt([0.002, 0.998]).
a_cpt([0.95, 0.94, 0.29, 0.001,
0.05, 0.06, 0.71, 0.999]).
jc_cpt([0.9, 0.05,
0.1, 0.95]).
mc_cpt([0.7, 0.01,
0.3, 0.99]).
% ?- alarm(A).
?- john_calls(J), mary_calls(m1).
%?- john_calls(J), mary_calls(m1), alarm(a1).
%?- john_calls(J), alarm(a1).

15
packages/CLPBN/clpbn/bp/examples/cbp_example.uai
View File

@ -1,15 +0,0 @@
# example in counting belief propagation paper
MARKOV
3
2 2 2
2
2 0 1
2 2 1
4
1.2 1.4 2.0 0.4
4
1.2 1.4 2.0 0.4

31
packages/CLPBN/clpbn/bp/examples/comp_workshops.yap
View File

@ -1,31 +0,0 @@
:- use_module(library(pfl)).
:- clpbn_horus:set_solver(fove).
%:- clpbn_horus:set_solver(hve).
%:- clpbn_horus:set_solver(bp).
%:- clpbn_horus:set_solver(cbp).
:- yap_flag(write_strings, off).
c(p1,w1).
c(p1,w2).
c(p1,w3).
c(p2,w1).
c(p2,w2).
c(p2,w3).
c(p3,w1).
c(p3,w2).
c(p3,w3).
c(p4,w1).
c(p4,w2).
c(p4,w3).
c(p5,w1).
c(p5,w2).
c(p5,w3).
markov attends(P)::[t,f] , hot(W)::[t,f] ; [0.1, 0.2, 0.3, 0.4] ; [c(P,W)].
markov attends(P)::[t,f], series::[t,f] ; [0.5, 0.6, 0.7, 0.8] ; [c(P,_)].
% ?- series(X).

24
packages/CLPBN/clpbn/bp/examples/smokers.yap
View File

@ -1,24 +0,0 @@
:- use_module(library(pfl)).
:- clpbn_horus:set_solver(fove).
%:- clpbn_horus:set_solver(hve).
%:- clpbn_horus:set_solver(bp).
%:- clpbn_horus:set_solver(cbp).
:- yap_flag(write_strings, off).
friends(P1, P2) :-
people(P1),
people(P2),
P1 \= P2.
people @ 3.
markov smokes(P)::[t,f], cancer(P)::[t,f] ; [0.1, 0.2, 0.3, 0.4] ; [people(P)].
markov friend(P1,P2)::[t,f], smokes(P1)::[t,f], smokes(P2)::[t,f] ;
[0.5, 0.6, 0.7, 0.8, 0.5, 0.6, 0.7, 0.8] ; [friends(P1, P2)].
% ?- smokes(p1, t), smokes(p2, f), friend(p1, p2, X).

27
packages/CLPBN/clpbn/bp/examples/workshop_attrs.yap
View File

@ -1,27 +0,0 @@
:- use_module(library(pfl)).
%:- clpbn_horus:set_solver(fove).
%:- clpbn_horus:set_solver(hve).
:- clpbn_horus:set_solver(bp).
%:- clpbn_horus:set_solver(cbp).
:- yap_flag(write_strings, off).
people @ 3.
markov attends(P)::[t,f], attr1::[t,f] ; [0.11, 0.2, 0.3, 0.4] ; [people(P)].
markov attends(P)::[t,f], attr2::[t,f] ; [0.1, 0.22, 0.3, 0.4] ; [people(P)].
markov attends(P)::[t,f], attr3::[t,f] ; [0.1, 0.2, 0.33, 0.4] ; [people(P)].
markov attends(P)::[t,f], attr4::[t,f] ; [0.1, 0.2, 0.3, 0.44] ; [people(P)].
markov attends(P)::[t,f], attr5::[t,f] ; [0.1, 0.2, 0.3, 0.45] ; [people(P)].
markov attends(P)::[t,f], attr6::[t,f] ; [0.1, 0.2, 0.3, 0.46] ; [people(P)].
markov attends(P)::[t,f], series::[t,f] ; [0.5, 0.6, 0.7, 0.87] ; [people(P)].
% ?- series(X).

31
packages/CLPBN/clpbn/ground_factors.yap
View File

@ -41,20 +41,30 @@ do_network([], _, _, _) :- !.
do_network(QueryVars, EVars, Keys, Factors) :-
retractall(currently_defined(_)),
retractall(f(_,_,_,_)),
writeln(keys:Keys),
run_through_factors(QueryVars),
run_through_factors(EVars),
findall(K, currently_defined(K), Keys),
writeln(keys2:Keys),
ground_all_keys(QueryVars, Keys),
ground_all_keys(EVars, Keys),
findall(f(FType,FId,FKeys,FCPT), f(FType,FId,FKeys,FCPT), Factors).
match([], _Keys).
match([V|GVars], Keys) :-
clpbn:get_atts(V,[key(GKey)]), !,
member(GKey, Keys), ground(GKey),
match(GVars, Keys).
match([_V|GVars], Keys) :-
match(GVars, Keys).
run_through_factors([]).
run_through_factors([Var|_QueryVars]) :-
clpbn:get_atts(Var,[key(K)]),
find_factors(K),
fail.
run_through_factors([_|QueryVars]) :-
run_through_factors(QueryVars).
ground_all_keys([], _).
ground_all_keys([V|GVars], AllKeys) :-
clpbn:get_atts(V,[key(Key)]),
\+ ground(Key), !,
member(Key, AllKeys),
ground_all_keys(GVars, AllKeys).
ground_all_keys([_V|GVars], AllKeys) :-
ground_all_keys(GVars, AllKeys).
%
@ -99,6 +109,7 @@ keys([Var|QueryVars], [Key|QueryKeys]) :-
initialize_evidence([]).
initialize_evidence([V|EVars]) :-
clpbn:get_atts(V, [key(K)]),
ground(K),
assert(currently_defined(K)),
initialize_evidence(EVars).
@ -106,7 +117,7 @@ initialize_evidence([V|EVars]) :-
% gets key K, and collects factors that define it
find_factors(K) :-
\+ currently_defined(K),
assert(currently_defined(K)),
( ground(K) -> assert(currently_defined(K)) ; true),
defined_in_factor(K, ParFactor),
add_factor(ParFactor, Ks),
member(K1, Ks),

70
packages/CLPBN/clpbn/horus.yap
View File

@ -1,61 +1,63 @@
/*******************************************************
Interface with C++
Horus Interface
********************************************************/
:- module(clpbn_horus,
[set_solver/1,
create_lifted_network/3,
create_ground_network/4,
set_parfactors_params/2,
set_factors_params/2,
run_lifted_solver/3,
run_ground_solver/3,
set_vars_information/2,
set_horus_flag/2,
free_parfactors/1,
free_ground_network/1
set_horus_flag/1,
cpp_create_lifted_network/3,
cpp_create_ground_network/4,
cpp_set_parfactors_params/2,
cpp_set_factors_params/2,
cpp_run_lifted_solver/3,
cpp_run_ground_solver/3,
cpp_set_vars_information/2,
cpp_set_horus_flag/2,
cpp_free_parfactors/1,
cpp_free_ground_network/1
]).
:- use_module(library(clpbn),
[set_clpbn_flag/2]).
patch_things_up :-
assert_static(clpbn_horus:set_horus_flag(_,_)).
assert_static(clpbn_horus:cpp_set_horus_flag(_,_)).
warning :-
format(user_error,"Horus library not installed: cannot use bp, fove~n.",[]).
:- catch(load_foreign_files([horus], [], init_predicates), _, patch_things_up) -> true ; warning.
:- catch(load_foreign_files([horus], [], init_predicates), _, patch_things_up)
-> true ; warning.
set_solver(ve) :- pfl:set_pfl_flag(solver,ve).
set_solver(jt) :- pfl:set_pfl_flag(solver,jt).
set_solver(gibbs) :- pfl:set_pfl_flag(solver,gibbs).
set_solver(fove) :- pfl:set_pfl_flag(solver,fove).
set_solver(hve) :- pfl:set_pfl_flag(solver,bp), set_horus_flag(inf_alg, ve).
set_solver(bp) :- pfl:set_pfl_flag(solver,bp), set_horus_flag(inf_alg, bp).
set_solver(cbp) :- pfl:set_pfl_flag(solver,bp), set_horus_flag(inf_alg, cbp).
set_solver(ve) :- set_clpbn_flag(solver,ve).
set_solver(jt) :- set_clpbn_flag(solver,jt).
set_solver(gibbs) :- set_clpbn_flag(solver,gibbs).
set_solver(fove) :- set_clpbn_flag(solver,fove), set_horus_flag(lifted_solver, fove).
set_solver(lbp) :- set_clpbn_flag(solver,fove), set_horus_flag(lifted_solver, lbp).
set_solver(hve) :- set_clpbn_flag(solver,bp), set_horus_flag(ground_solver, ve).
set_solver(bp) :- set_clpbn_flag(solver,bp), set_horus_flag(ground_solver, bp).
set_solver(cbp) :- set_clpbn_flag(solver,bp), set_horus_flag(ground_solver, cbp).
set_solver(S) :- throw(error('unknow solver ', S)).
%:- set_horus_flag(inf_alg, ve).
%:- set_horus_flag(inf_alg, bp).
%: -set_horus_flag(inf_alg, cbp).
set_horus_flag(K,V) :- cpp_set_horus_flag(K,V).
:- set_horus_flag(schedule, seq_fixed).
%:- set_horus_flag(schedule, seq_random).
%:- set_horus_flag(schedule, parallel).
%:- set_horus_flag(schedule, max_residual).
:- set_horus_flag(accuracy, 0.0001).
:- cpp_set_horus_flag(schedule, seq_fixed).
%:- cpp_set_horus_flag(schedule, seq_random).
%:- cpp_set_horus_flag(schedule, parallel).
%:- cpp_set_horus_flag(schedule, max_residual).
:- set_horus_flag(max_iter, 1000).
:- cpp_set_horus_flag(accuracy, 0.0001).
:- set_horus_flag(order_factor_variables, false).
%:- set_horus_flag(order_factor_variables, true).
:- cpp_set_horus_flag(max_iter, 1000).
:- set_horus_flag(use_logarithms, false).
% :- set_horus_flag(use_logarithms, true).
:- cpp_set_horus_flag(use_logarithms, false).
% :- cpp_set_horus_flag(use_logarithms, true).

119
packages/CLPBN/clpbn/bp.yap → packages/CLPBN/clpbn/horus_ground.yap
View File

@ -1,19 +1,27 @@
/*******************************************************
Belief Propagation and Variable Elimination Interface
Interface to Horus Ground Solvers. Used by:
- Variable Elimination
- Belief Propagation
- Counting Belief Propagation
********************************************************/
:- module(clpbn_bp,
[bp/3,
check_if_bp_done/1,
init_bp_solver/4,
run_bp_solver/3,
call_bp_ground/6,
finalize_bp_solver/1
:- module(clpbn_horus_ground,
[call_horus_ground_solver/6,
check_if_horus_ground_solver_done/1,
init_horus_ground_solver/4,
run_horus_ground_solver/3,
finalize_horus_ground_solver/1
]).
:- use_module(horus,
[cpp_create_ground_network/4,
cpp_set_factors_params/2,
cpp_run_ground_solver/3,
cpp_set_vars_information/2,
cpp_free_ground_network/1
]).
:- use_module(library('clpbn/dists'),
[dist/4,
@ -22,25 +30,20 @@
get_dist_params/2
]).
:- use_module(library('clpbn/display'),
[clpbn_bind_vals/3]).
:- use_module(library('clpbn/aggregates'),
[check_for_agg_vars/2]).
:- use_module(library(charsio),
[term_to_atom/2]).
:- use_module(library(pfl),
[skolem/2,
get_pfl_parameters/2
]).
:- use_module(library(lists)).
:- use_module(library(atts)).
@ -48,45 +51,36 @@
:- use_module(library(bhash)).
:- use_module(horus,
[create_ground_network/4,
set_factors_params/2,
run_ground_solver/3,
set_vars_information/2,
free_ground_network/1
]).
call_bp_ground(QueryVars, QueryKeys, AllKeys, Factors, Evidence, Output) :-
writeln(here:Factors),
call_horus_ground_solver(QueryVars, QueryKeys, AllKeys, Factors, Evidence, Output) :-
b_hash_new(Hash0),
keys_to_ids(AllKeys, 0, Hash0, Hash),
get_factors_type(Factors, Type),
evidence_to_ids(Evidence, Hash, EvidenceIds),
factors_to_ids(Factors, Hash, FactorIds),
writeln(type:Type), writeln(''),
writeln(allKeys:AllKeys), writeln(''),
writeln(factors:Factors), writeln(''),
writeln(factorIds:FactorIds), writeln(''),
writeln(evidence:Evidence), writeln(''),
writeln(evidenceIds:EvidenceIds), writeln(''),
create_ground_network(Type, FactorIds, EvidenceIds, Network),
%writeln(type:Type), writeln(''),
%writeln(allKeys:AllKeys), writeln(''),
%sort(AllKeys,SKeys),writeln(allKeys:SKeys), writeln(''),
%writeln(factors:Factors), writeln(''),
%writeln(factorIds:FactorIds), writeln(''),
%writeln(evidence:Evidence), writeln(''),
%writeln(evidenceIds:EvidenceIds), writeln(''),
cpp_create_ground_network(Type, FactorIds, EvidenceIds, Network),
%get_vars_information(AllKeys, StatesNames),
%set_vars_information(AllKeys, StatesNames),
%terms_to_atoms(AllKeys, KeysAtoms),
%cpp_set_vars_information(KeysAtoms, StatesNames),
run_solver(ground(Network,Hash), QueryKeys, Solutions),
writeln(answer:Solutions),
clpbn_bind_vals([QueryVars], Solutions, Output),
free_ground_network(Network).
cpp_free_ground_network(Network).
run_solver(ground(Network,Hash), QueryKeys, Solutions) :-
%get_dists_parameters(DistIds, DistsParams),
%set_factors_params(Network, DistsParams),
%cpp_set_factors_params(Network, DistsParams),
list_of_keys_to_ids(QueryKeys, Hash, QueryIds),
writeln(queryKeys:QueryKeys), writeln(''),
writeln(queryIds:QueryIds), writeln(''),
%writeln(queryKeys:QueryKeys), writeln(''),
%writeln(queryIds:QueryIds), writeln(''),
list_of_keys_to_ids(QueryKeys, Hash, QueryIds),
run_ground_solver(Network, [QueryIds], Solutions).
cpp_run_ground_solver(Network, [QueryIds], Solutions).
keys_to_ids([], _, Hash, Hash).
@ -132,31 +126,40 @@ get_vars_information(Key.QueryKeys, Domain.StatesNames) :-
get_vars_information(QueryKeys, StatesNames).
finalize_bp_solver(bp(Network, _)) :-
free_ground_network(Network).
terms_to_atoms([], []).
terms_to_atoms(K.Ks, Atom.As) :-
term_to_atom(K,Atom),
terms_to_atoms(Ks,As).
bp([[]],_,_) :- !.
bp([QueryVars], AllVars, Output) :-
init_bp_solver(_, AllVars, _, Network),
run_bp_solver([QueryVars], LPs, Network),
finalize_bp_solver(Network),
clpbn_bind_vals([QueryVars], LPs, Output).
finalize_horus_ground_solver(bp(Network, _)) :-
cpp_free_ground_network(Network).
init_bp_solver(_, AllVars0, _, bp(BayesNet, DistIds)) :-
%check_for_agg_vars(AllVars0, AllVars),
get_vars_info(AllVars0, VarsInfo, DistIds0),
sort(DistIds0, DistIds),
create_ground_network(VarsInfo, BayesNet),
true.
init_horus_ground_solver(_, _AllVars0, _, bp(_BayesNet, _DistIds)) :- !.
run_horus_ground_solver(_QueryVars, _Solutions, bp(_Network, _DistIds)) :- !.
run_bp_solver(QueryVars, Solutions, bp(Network, DistIds)) :-
get_dists_parameters(DistIds, DistsParams),
set_factors_params(Network, DistsParams),
vars_to_ids(QueryVars, QueryVarsIds),
run_ground_solver(Network, QueryVarsIds, Solutions).
%bp([[]],_,_) :- !.
%bp([QueryVars], AllVars, Output) :-
% init_horus_ground_solver(_, AllVars, _, Network),
% run_horus_ground_solver([QueryVars], LPs, Network),
% finalize_horus_ground_solver(Network),
% clpbn_bind_vals([QueryVars], LPs, Output).
%
%init_horus_ground_solver(_, AllVars0, _, bp(BayesNet, DistIds)) :-
% %check_for_agg_vars(AllVars0, AllVars),
% get_vars_info(AllVars0, VarsInfo, DistIds0),
% sort(DistIds0, DistIds),
% cpp_create_ground_network(VarsInfo, BayesNet),
% true.
%
%
%run_horus_ground_solver(QueryVars, Solutions, bp(Network, DistIds)) :-
% get_dists_parameters(DistIds, DistsParams),
% cpp_set_factors_params(Network, DistsParams),
% vars_to_ids(QueryVars, QueryVarsIds),
% cpp_run_ground_solver(Network, QueryVarsIds, Solutions).
get_dists_parameters([],[]).

64
packages/CLPBN/clpbn/fove.yap → packages/CLPBN/clpbn/horus_lifted.yap
View File

@ -1,27 +1,31 @@
/*******************************************************
First Order Variable Elimination Interface
Interface to Horus Lifted Solvers. Used by:
- Lifted Variable Elimination
********************************************************/
:- module(clpbn_fove,
[fove/3,
check_if_fove_done/1,
init_fove_solver/4,
run_fove_solver/3,
finalize_fove_solver/1
:- 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
]).
:- use_module(horus,
[cpp_create_lifted_network/3,
cpp_set_parfactors_params/2,
cpp_run_lifted_solver/3,
cpp_free_parfactors/1
]).
:- use_module(library('clpbn/display'),
[clpbn_bind_vals/3]).
:- use_module(library('clpbn/dists'),
[get_dist_params/2]).
:- use_module(library(pfl),
[factor/6,
skolem/2,
@ -29,30 +33,22 @@
]).
:- use_module(horus,
[create_lifted_network/3,
set_parfactors_params/2,
run_lifted_solver/3,
free_parfactors/1
]).
fove([[]], _, _) :- !.
fove([QueryVars], AllVars, Output) :-
init_fove_solver(_, AllVars, _, ParfactorList),
run_fove_solver([QueryVars], LPs, ParfactorList),
finalize_fove_solver(ParfactorList),
call_horus_lifted_solver([[]], _, _) :- !.
call_horus_lifted_solver([QueryVars], AllVars, Output) :-
init_horus_lifted_solver(_, AllVars, _, ParfactorList),
run_horus_lifted_solver([QueryVars], LPs, ParfactorList),
finalize_horus_lifted_solver(ParfactorList),
clpbn_bind_vals([QueryVars], LPs, Output).
init_fove_solver(_, AllAttVars, _, fove(ParfactorList, DistIds)) :-
init_horus_lifted_solver(_, AllAttVars, _, fove(ParfactorList, DistIds)) :-
get_parfactors(Parfactors),
get_dist_ids(Parfactors, DistIds0),
sort(DistIds0, DistIds),
get_observed_vars(AllAttVars, ObservedVars),
writeln(parfactors:Parfactors:'\n'),
writeln(evidence:ObservedVars:'\n'),
create_lifted_network(Parfactors,ObservedVars,ParfactorList).
%writeln(parfactors:Parfactors:'\n'),
%writeln(evidence:ObservedVars:'\n'),
cpp_create_lifted_network(Parfactors,ObservedVars,ParfactorList).
:- table get_parfactors/1.
@ -138,15 +134,15 @@ get_dists_parameters([Id|Ids], [dist(Id, Params)|DistsInfo]) :-
get_dists_parameters(Ids, DistsInfo).
run_fove_solver(QueryVarsAtts, Solutions, fove(ParfactorList, DistIds)) :-
run_horus_lifted_solver(QueryVarsAtts, Solutions, fove(ParfactorList, DistIds)) :-
get_query_vars(QueryVarsAtts, QueryVars),
writeln(queryVars:QueryVars), writeln(''),
%writeln(queryVars:QueryVars), writeln(''),
get_dists_parameters(DistIds, DistsParams),
writeln(dists:DistsParams), writeln(''),
set_parfactors_params(ParfactorList, DistsParams),
run_lifted_solver(ParfactorList, QueryVars, Solutions).
%writeln(dists:DistsParams), writeln(''),
cpp_set_parfactors_params(ParfactorList, DistsParams),
cpp_run_lifted_solver(ParfactorList, QueryVars, Solutions).
finalize_fove_solver(fove(ParfactorList, _)) :-
free_parfactors(ParfactorList).
finalize_horus_lifted_solver(fove(ParfactorList, _)) :-
cpp_free_parfactors(ParfactorList).

25
packages/CLPBN/examples/City/db_128.yap
View File

@ -1,25 +0,0 @@
%conservative_city(nyc, t).
hair_color(joe, t).
car_color(joe, t).
shoe_size(joe, f).
/* Steps:
1. generate N facts lives(I, nyc), 0 <= I < N.
2. generate evidence on descn for N people, *** except for 1 ***
3. Run query ?- guilty(joe, Guilty), witness(joe, t), descn(2,t), descn(3, f), descn(4, f).
query(Guilty) :-
guilty(joe, Guilty),
witness(joe, t),
descn(2,t),
descn(3,f),
descn(4,f), ....
*/

60
packages/CLPBN/examples/City/schema.yap
View File

@ -1,60 +0,0 @@
/* base file for school database. Supposed to be called from school_*.yap */
conservative_city(City, Cons) :-
cons_table(City, ConsDist),
{ Cons = cons(City) with p([y,n], ConsDist) }.
gender(X, Gender) :-
gender_table(City, GenderDist),
{ Gender = gender(City) with p([m,f], GenderDist) }.
hair_color(X, Color) :-
lives(X, City),
conservative_city(City, Cons),
gender(X, Gender),
color_table(X,ColorTable),
{ Color = color(X) with
p([t,f], ColorTable,[Gender,Cons]) }.
car_color(X, Color) :-
hair_color(City, HColor),
ccolor_table(X,CColorTable),
{ Color = ccolor(X) with
p([t,f], CColorTable,[HColor]) }.
height(X, Height) :-
gender(X, Gender),
height_table(X,HeightTable),
{ Height = height(X) with
p([t,f], HeightTable,[Gender]) }.
shoe_size(X, Shoesize) :-
height(X, Height),
shoe_size_table(X,ShoesizeTable),
{ Shoesize = shoe_size(X) with
p([t,f], ShoesizeTable,[Height]) }.
guilty(X, Guilt) :-
guilt_table(X, GuiltDist),
{ Guilt = guilt(X) with p([y,n], GuiltDist) }.
descn(X, Descn) :-
car_color(X, Car),
hair_color(X, Hair),
height(X, Height),
guilty(X, Guilt),
descn_table(X, DescTable),
{ Descn = descn(X) with
p([t,f], DescTable,[Car,Hair,Height,Guilt]) }.
witness(City, Witness) :-
descn(joe, DescnJ),
descn(1, Descn1),
wit_table(WitTable),
{ Witness = wit(City) with
p([t,f], WitTable,[DescnJ, Descn1]) }.

35
packages/CLPBN/examples/City/tables.yap
View File

@ -1,35 +0,0 @@
cons_table(amsterdam,[0.2,
0.8]) :- !.
cons_table(_, [0.8,
0.2]).
color_table(_,
/* tm tf fm ff */
[ 0.05, 0.1, 0.3, 0.5 ,
0.95, 0.9, 0.7, 0.5 ]).
ccolor_table(_,
/* t f */
[ 0.9, 0.2 ,
0.1, 0.8 ]).
height_table(_,
/* m f */
[ 0.6, 0.4 ,
0.4, 0.6 ]).
shoe_size_table(_,
/* t f */
[ 0.9, 0.1 ,
0.1, 0.9 ]).
A: professor's ability;
B: student's grade (for course registration).
*/
descn_table(_,
/* color, hair, height, guilt */
/* ttttt tttf ttft ttff tfttt tftf tfft tfff ttttt fttf ftft ftff ffttt fftf ffft ffff */
/*t*/ [0.99, 0.99, 0.99, 0.99, 0.99, 0.99, 0.99, 0.99, 0.99, 0.99, 0.99, 0.99, 0.99, 0.99, 0.99, 0.99,
/*f*/ 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01 ]).

0
packages/CLPBN/clpbn/bp/examples/burglary-alarm.fg → packages/CLPBN/examples/burglary-alarm.fg
View File

0
packages/CLPBN/clpbn/bp/examples/burglary-alarm.uai → packages/CLPBN/examples/burglary-alarm.uai
View File

23
packages/CLPBN/examples/burglary-alarm.yap Normal file
View File

@ -0,0 +1,23 @@
:- use_module(library(pfl)).
%:- set_solver(fove).
%:- set_solver(hve).
%:- set_solver(bp).
%:- set_solver(cbp).
:- yap_flag(write_strings, off).
bayes burglary::[b1,b2] ; [0.001, 0.999] ; [].
bayes earthquake::[e1,e2] ; [0.002, 0.998]; [].
bayes alarm::[a1,a2], burglary, earthquake ;
[0.95, 0.94, 0.29, 0.001, 0.05, 0.06, 0.71, 0.999] ;
[].
bayes john_calls::[j1,j2], alarm ; [0.9, 0.05, 0.1, 0.95] ; [].
bayes mary_calls::[m1,m2], alarm ; [0.7, 0.01, 0.3, 0.99] ; [].
% ?- john_calls(J), mary_calls(m1).

27
packages/CLPBN/clpbn/bp/examples/city.yap → packages/CLPBN/examples/city.yap
View File

@ -1,20 +1,23 @@
:- use_module(library(pfl)).
:- clpbn_horus:set_solver(fove).
%:- clpbn_horus:set_solver(hve).
:- clpbn_horus:set_solver(bp).
%:- clpbn_horus:set_solver(cbp).
%:- set_solver(fove).
%:- set_solver(hve).
%:- set_solver(bp).
%:- set_solver(cbp).
:- multifile people/2.
:- multifile ev/1.
people(joe,nyc).
people(p2, nyc).
people(p3, nyc).
people(p4, nyc).
people(p5, nyc).
ev(descn(p2, t)).
ev(descn(p3, t)).
% :- [city_7].
ev(descn(p4, t)).
ev(descn(p5, t)).
bayes city_conservativeness(C)::[y,n] ; cons_table(C) ; [people(_,C)].
@ -34,12 +37,12 @@ bayes descn(P)::[t,f], car_color(P), hair_color(P), height(P), guilty(P) ; descn
bayes witness(C)::[t,f], descn(Joe), descn(P2) ; wit_table ; [people(_,C), Joe=joe, P2=p2].
cons_table(amsterdam, [0.2, 0.8]) :- !.
% FIXME
%cons_table(amsterdam, [0.2, 0.8]) :- !.
cons_table(_, [0.8, 0.2]).
gender_table(_, [0.55, 0.44]).
gender_table(_, [0.55, 0.45]).
hair_color_table(_,
@ -73,8 +76,8 @@ guilty_table(_, [0.23, 0.77]).
descn_table(_,
/* color, hair, height, guilt */
/* ttttt tttf ttft ttff tfttt tftf tfft tfff ttttt fttf ftft ftff ffttt fftf ffft ffff */
[ 0.99, 0.5, 0.23, 0.88, 0.41, 0.3, 0.76, 0.87, 0.44, 0.43, 0.29, 0.72, 0.33, 0.91, 0.95, 0.92,
0.01, 0.5, 0.77, 0.12, 0.59, 0.7, 0.24, 0.13, 0.56, 0.57, 0.61, 0.28, 0.77, 0.09, 0.05, 0.08]).
[ 0.99, 0.5, 0.23, 0.88, 0.41, 0.3, 0.76, 0.87, 0.44, 0.43, 0.29, 0.72, 0.23, 0.91, 0.95, 0.92,
0.01, 0.5, 0.77, 0.12, 0.59, 0.7, 0.24, 0.13, 0.56, 0.57, 0.71, 0.28, 0.77, 0.09, 0.05, 0.08]).
wit_table([0.2, 0.45, 0.24, 0.34,

33
packages/CLPBN/examples/comp_workshops.yap Normal file
View File

@ -0,0 +1,33 @@
:- use_module(library(pfl)).
%:- set_solver(fove).
%:- set_solver(hve).
%:- set_solver(bp).
%:- set_solver(cbp).
:- yap_flag(write_strings, off).
:- multifile c/2.
c(p1,w1).
c(p1,w2).
c(p1,w3).
c(p2,w1).
c(p2,w2).
c(p2,w3).
c(p3,w1).
c(p3,w2).
c(p3,w3).
c(p4,w1).
c(p4,w2).
c(p4,w3).
c(p5,w1).
c(p5,w2).
c(p5,w3).
markov attends(P)::[t,f], hot(W)::[t,f] ; [0.2, 0.8, 0.8, 0.8] ; [c(P,W)].
markov attends(P)::[t,f], series::[t,f] ; [0.501, 0.499, 0.499, 0.499] ; [c(P,_)].
% ?- series(X).

0
packages/CLPBN/clpbn/bp/examples/fail.yap → packages/CLPBN/examples/fail1.yap
View File

21
packages/CLPBN/examples/fail2.yap Normal file
View File

@ -0,0 +1,21 @@
:- use_module(library(pfl)).
:- set_solver(fove).
%:- set_solver(hve).
%:- set_solver(bp).
%:- set_solver(cbp).
:- yap_flag(write_strings, off).
:- clpbn_horus:set_horus_flag(verbosity,5).
people(p1,p1).
people(p1,p2).
people(p2,p1).
people(p2,p2).
markov p(A,A)::[t,f] ; [1.0,4.5] ; [people(A,_)].
markov p(A,B)::[t,f] ; [1.0,4.5] ; [people(A,B)].
?- p(p1,p1,X).

31
packages/CLPBN/examples/social_domain1.yap Normal file
View File

@ -0,0 +1,31 @@
:- use_module(library(pfl)).
%:- set_solver(fove).
%:- set_solver(hve).
%:- set_solver(bp).
%:- set_solver(cbp).
:- yap_flag(write_strings, off).
:- multifile people/1.
people @ 5.
people(X,Y) :-
people(X),
people(Y),
X \== Y.
markov smokes(X)::[t,f]; [1.0, 4.0552]; [people(X)].
markov cancer(X)::[t,f]; [1.0, 9.9742]; [people(X)].
markov friends(X,Y)::[t,f] ; [1.0, 99.48432] ; [people(X,Y)].
markov smokes(X)::[t,f], cancer(X)::[t,f] ; [4.48169, 4.48169, 1.0, 4.48169] ; [people(X)].
markov friends(X,Y)::[t,f], smokes(X)::[t,f], smokes(Y)::[t,f] ;
[3.004166, 3.004166, 3.004166, 3.004166, 3.004166, 1.0, 1.0, 3.004166] ; [people(X,Y)].
% ?- friends(p1,p2,X).

31
packages/CLPBN/examples/social_domain2.yap Normal file
View File

@ -0,0 +1,31 @@
:- use_module(library(pfl)).
%:- set_solver(fove).
%:- set_solver(hve).
%:- set_solver(bp).
%:- set_solver(cbp).
:- yap_flag(write_strings, off).
:- multifile people/1.
people @ 5.
people(X,Y) :-
people(X),
people(Y).
% X \== Y.
markov smokes(X)::[t,f]; [1.0, 4.0552]; [people(X)].
markov asthma(X)::[t,f]; [1.0, 9.9742] ; [people(X)].
markov friends(X,Y)::[t,f]; [1.0, 99.48432] ; [people(X,Y)].
markov asthma(X)::[t,f], smokes(X)::[t,f]; [4.48169, 4.48169, 1.0, 4.48169] ; [people(X)].
markov asthma(X)::[t,f], friends(X,Y)::[t,f], smokes(Y)::[t,f];
[3.004166, 3.004166, 3.004166, 3.004166, 3.004166, 1.0, 1.0, 3.004166] ; [people(X,Y)].
% ?- smokes(p1,t), smokes(p2,t), friends(p1,p2,X)

29
packages/CLPBN/examples/workshop_attrs.yap Normal file
View File

@ -0,0 +1,29 @@
:- use_module(library(pfl)).
%:- set_solver(fove).
%:- set_solver(hve).
%:- set_solver(bp).
%:- set_solver(cbp).
:- yap_flag(write_strings, off).
:- multifile people/1.
people @ 5.
markov attends(P)::[t,f], attr1::[t,f] ; [0.7, 0.3, 0.3, 0.3] ; [people(P)].
markov attends(P)::[t,f], attr2::[t,f] ; [0.7, 0.3, 0.3, 0.3] ; [people(P)].
markov attends(P)::[t,f], attr3::[t,f] ; [0.7, 0.3, 0.3, 0.3] ; [people(P)].
markov attends(P)::[t,f], attr4::[t,f] ; [0.7, 0.3, 0.3, 0.3] ; [people(P)].
markov attends(P)::[t,f], attr5::[t,f] ; [0.7, 0.3, 0.3, 0.3] ; [people(P)].
markov attends(P)::[t,f], attr6::[t,f] ; [0.7, 0.3, 0.3, 0.3] ; [people(P)].
markov attends(P)::[t,f], series::[t,f] ; [0.501, 0.499, 0.499, 0.499] ; [people(P)].
% ?- series(X).

19
packages/CLPBN/clpbn/bp/BayesBall.cpp → packages/CLPBN/horus/BayesBall.cpp
View File

@ -9,14 +9,12 @@
#include "Util.h"
FactorGraph*
BayesBall::getMinimalFactorGraph (const VarIds& queryIds)
{
assert (fg_.isFromBayesNetwork());
assert (fg_.bayesianFactors());
Scheduling scheduling;
for (unsigned i = 0; i < queryIds.size(); i++) {
for (size_t i = 0; i < queryIds.size(); i++) {
assert (dag_.getNode (queryIds[i]));
DAGraphNode* n = dag_.getNode (queryIds[i]);
scheduling.push (ScheduleInfo (n, false, true));
@ -60,11 +58,11 @@ void
BayesBall::constructGraph (FactorGraph* fg) const
{
const FacNodes& facNodes = fg_.facNodes();
for (unsigned i = 0; i < facNodes.size(); i++) {
for (size_t i = 0; i < facNodes.size(); i++) {
const DAGraphNode* n = dag_.getNode (
facNodes[i]->factor().argument (0));
if (n->isMarkedOnTop()) {
fg->addFactor (Factor (facNodes[i]->factor()));
fg->addFactor (facNodes[i]->factor());
} else if (n->hasEvidence() && n->isVisited()) {
VarIds varIds = { facNodes[i]->factor().argument (0) };
Ranges ranges = { facNodes[i]->factor().range (0) };
@ -73,5 +71,14 @@ BayesBall::constructGraph (FactorGraph* fg) const
fg->addFactor (Factor (varIds, ranges, params));
}
}
const VarNodes& varNodes = fg_.varNodes();
for (size_t i = 0; i < varNodes.size(); i++) {
if (varNodes[i]->hasEvidence()) {
VarNode* vn = fg->getVarNode (varNodes[i]->varId());
if (vn) {
vn->setEvidence (varNodes[i]->getEvidence());
}
}
}
}

4
packages/CLPBN/clpbn/bp/BayesBall.h → packages/CLPBN/horus/BayesBall.h
View File

@ -64,7 +64,7 @@ BayesBall::scheduleParents (const DAGraphNode* n, Scheduling& sch) const
{
const vector<DAGraphNode*>& ps = n->parents();
for (vector<DAGraphNode*>::const_iterator it = ps.begin();
it != ps.end(); it++) {
it != ps.end(); ++it) {
sch.push (ScheduleInfo (*it, false, true));
}
}
@ -76,7 +76,7 @@ BayesBall::scheduleChilds (const DAGraphNode* n, Scheduling& sch) const
{
const vector<DAGraphNode*>& cs = n->childs();
for (vector<DAGraphNode*>::const_iterator it = cs.begin();
it != cs.end(); it++) {
it != cs.end(); ++it) {
sch.push (ScheduleInfo (*it, true, false));
}
}

10
packages/CLPBN/clpbn/bp/BayesNet.cpp → packages/CLPBN/horus/BayesNet.cpp
View File

@ -57,7 +57,7 @@ DAGraph::getNode (VarId vid)
void
DAGraph::setIndexes (void)
{
for (unsigned i = 0; i < nodes_.size(); i++) {
for (size_t i = 0; i < nodes_.size(); i++) {
nodes_[i]->setIndex (i);
}
}
@ -67,7 +67,7 @@ DAGraph::setIndexes (void)
void
DAGraph::clear (void)
{
for (unsigned i = 0; i < nodes_.size(); i++) {
for (size_t i = 0; i < nodes_.size(); i++) {
nodes_[i]->clear();
}
}
@ -85,7 +85,7 @@ DAGraph::exportToGraphViz (const char* fileName)
}
out << "digraph {" << endl;
out << "ranksep=1" << endl;
for (unsigned i = 0; i < nodes_.size(); i++) {
for (size_t i = 0; i < nodes_.size(); i++) {
out << nodes_[i]->varId() ;
out << " [" ;
out << "label=\"" << nodes_[i]->label() << "\"" ;
@ -94,9 +94,9 @@ DAGraph::exportToGraphViz (const char* fileName)
}
out << "]" << endl;
}
for (unsigned i = 0; i < nodes_.size(); i++) {
for (size_t i = 0; i < nodes_.size(); i++) {
const vector<DAGraphNode*>& childs = nodes_[i]->childs();
for (unsigned j = 0; j < childs.size(); j++) {
for (size_t j = 0; j < childs.size(); j++) {
out << nodes_[i]->varId() << " -> " << childs[j]->varId();
out << " [style=bold]" << endl ;
}

0
packages/CLPBN/clpbn/bp/BayesNet.h → packages/CLPBN/horus/BayesNet.h
View File

502
packages/CLPBN/horus/BpSolver.cpp Normal file
View File

@ -0,0 +1,502 @@
#include <cassert>
#include <limits>
#include <algorithm>
#include <iostream>
#include "BpSolver.h"
#include "FactorGraph.h"
#include "Factor.h"
#include "Indexer.h"
#include "Horus.h"
BpSolver::BpSolver (const FactorGraph& fg) : Solver (fg)
{
runned_ = false;
}
BpSolver::~BpSolver (void)
{
for (size_t i = 0; i < varsI_.size(); i++) {
delete varsI_[i];
}
for (size_t i = 0; i < facsI_.size(); i++) {
delete facsI_[i];
}
for (size_t i = 0; i < links_.size(); i++) {
delete links_[i];
}
}
Params
BpSolver::solveQuery (VarIds queryVids)
{
assert (queryVids.empty() == false);
return queryVids.size() == 1
? getPosterioriOf (queryVids[0])
: getJointDistributionOf (queryVids);
}
void
BpSolver::printSolverFlags (void) const
{
stringstream ss;
ss << "belief propagation [" ;
ss << "schedule=" ;
typedef BpOptions::Schedule Sch;
switch (BpOptions::schedule) {
case Sch::SEQ_FIXED: ss << "seq_fixed"; break;
case Sch::SEQ_RANDOM: ss << "seq_random"; break;
case Sch::PARALLEL: ss << "parallel"; break;
case Sch::MAX_RESIDUAL: ss << "max_residual"; break;
}
ss << ",max_iter=" << Util::toString (BpOptions::maxIter);
ss << ",accuracy=" << Util::toString (BpOptions::accuracy);
ss << ",log_domain=" << Util::toString (Globals::logDomain);
ss << "]" ;
cout << ss.str() << endl;
}
Params
BpSolver::getPosterioriOf (VarId vid)
{
if (runned_ == false) {
runSolver();
}
assert (fg.getVarNode (vid));
VarNode* var = fg.getVarNode (vid);
Params probs;
if (var->hasEvidence()) {
probs.resize (var->range(), LogAware::noEvidence());
probs[var->getEvidence()] = LogAware::withEvidence();
} else {
probs.resize (var->range(), LogAware::multIdenty());
const BpLinks& links = ninf(var)->getLinks();
if (Globals::logDomain) {
for (size_t i = 0; i < links.size(); i++) {
probs += links[i]->message();
}
LogAware::normalize (probs);
Util::exp (probs);
} else {
for (size_t i = 0; i < links.size(); i++) {
probs *= links[i]->message();
}
LogAware::normalize (probs);
}
}
return probs;
}
Params
BpSolver::getJointDistributionOf (const VarIds& jointVarIds)
{
if (runned_ == false) {
runSolver();
}
VarNode* vn = fg.getVarNode (jointVarIds[0]);
const FacNodes& facNodes = vn->neighbors();
size_t idx = facNodes.size();
for (size_t i = 0; i < facNodes.size(); i++) {
if (facNodes[i]->factor().contains (jointVarIds)) {
idx = i;
break;
}
}
if (idx == facNodes.size()) {
return getJointByConditioning (jointVarIds);
} else {
Factor res (facNodes[idx]->factor());
const BpLinks& links = ninf(facNodes[idx])->getLinks();
for (size_t i = 0; i < links.size(); i++) {
Factor msg ({links[i]->varNode()->varId()},
{links[i]->varNode()->range()},
getVarToFactorMsg (links[i]));
res.multiply (msg);
}
res.sumOutAllExcept (jointVarIds);
res.reorderArguments (jointVarIds);
res.normalize();
Params jointDist = res.params();
if (Globals::logDomain) {
Util::exp (jointDist);
}
return jointDist;
}
}
void
BpSolver::runSolver (void)
{
initializeSolver();
nIters_ = 0;
while (!converged() && nIters_ < BpOptions::maxIter) {
nIters_ ++;
if (Globals::verbosity > 1) {
Util::printHeader (string ("Iteration ") + Util::toString (nIters_));
}
switch (BpOptions::schedule) {
case BpOptions::Schedule::SEQ_RANDOM:
std::random_shuffle (links_.begin(), links_.end());
// no break
case BpOptions::Schedule::SEQ_FIXED:
for (size_t i = 0; i < links_.size(); i++) {
calculateAndUpdateMessage (links_[i]);
}
break;
case BpOptions::Schedule::PARALLEL:
for (size_t i = 0; i < links_.size(); i++) {
calculateMessage (links_[i]);
}
for (size_t i = 0; i < links_.size(); i++) {
updateMessage(links_[i]);
}
break;
case BpOptions::Schedule::MAX_RESIDUAL:
maxResidualSchedule();
break;
}
}
if (Globals::verbosity > 0) {
if (nIters_ < BpOptions::maxIter) {
cout << "Sum-Product converged in " ;
cout << nIters_ << " iterations" << endl;
} else {
cout << "The maximum number of iterations was hit, terminating..." ;
cout << endl;
}
cout << endl;
}
runned_ = true;
}
void
BpSolver::createLinks (void)
{
const FacNodes& facNodes = fg.facNodes();
for (size_t i = 0; i < facNodes.size(); i++) {
const VarNodes& neighbors = facNodes[i]->neighbors();
for (size_t j = 0; j < neighbors.size(); j++) {
links_.push_back (new BpLink (facNodes[i], neighbors[j]));
}
}
}
void
BpSolver::maxResidualSchedule (void)
{
if (nIters_ == 1) {
for (size_t i = 0; i < links_.size(); i++) {
calculateMessage (links_[i]);
SortedOrder::iterator it = sortedOrder_.insert (links_[i]);
linkMap_.insert (make_pair (links_[i], it));
}
return;
}
for (size_t c = 0; c < links_.size(); c++) {
if (Globals::verbosity > 1) {
cout << "current residuals:" << endl;
for (SortedOrder::iterator it = sortedOrder_.begin();
it != sortedOrder_.end(); ++it) {
cout << " " << setw (30) << left << (*it)->toString();
cout << "residual = " << (*it)->residual() << endl;
}
}
SortedOrder::iterator it = sortedOrder_.begin();
BpLink* link = *it;
if (link->residual() < BpOptions::accuracy) {
return;
}
updateMessage (link);
link->clearResidual();
sortedOrder_.erase (it);
linkMap_.find (link)->second = sortedOrder_.insert (link);
// update the messages that depend on message source --> destin
const FacNodes& factorNeighbors = link->varNode()->neighbors();
for (size_t i = 0; i < factorNeighbors.size(); i++) {
if (factorNeighbors[i] != link->facNode()) {
const BpLinks& links = ninf(factorNeighbors[i])->getLinks();
for (size_t j = 0; j < links.size(); j++) {
if (links[j]->varNode() != link->varNode()) {
calculateMessage (links[j]);
BpLinkMap::iterator iter = linkMap_.find (links[j]);
sortedOrder_.erase (iter->second);
iter->second = sortedOrder_.insert (links[j]);
}
}
}
}
if (Globals::verbosity > 1) {
Util::printDashedLine();
}
}
}
void
BpSolver::calcFactorToVarMsg (BpLink* link)
{
FacNode* src = link->facNode();
const VarNode* dst = link->varNode();
const BpLinks& links = ninf(src)->getLinks();
// calculate the product of messages that were sent
// to factor `src', except from var `dst'
unsigned reps = 1;
unsigned msgSize = Util::sizeExpected (src->factor().ranges());
Params msgProduct (msgSize, LogAware::multIdenty());
if (Globals::logDomain) {
for (size_t i = links.size(); i-- > 0; ) {
if (links[i]->varNode() != dst) {
if (Constants::SHOW_BP_CALCS) {
cout << " message from " << links[i]->varNode()->label();
cout << ": " ;
}
Util::apply_n_times (msgProduct, getVarToFactorMsg (links[i]),
reps, std::plus<double>());
if (Constants::SHOW_BP_CALCS) {
cout << endl;
}
}
reps *= links[i]->varNode()->range();
}
} else {
for (size_t i = links.size(); i-- > 0; ) {
if (links[i]->varNode() != dst) {
if (Constants::SHOW_BP_CALCS) {
cout << " message from " << links[i]->varNode()->label();
cout << ": " ;
}
Util::apply_n_times (msgProduct, getVarToFactorMsg (links[i]),
reps, std::multiplies<double>());
if (Constants::SHOW_BP_CALCS) {
cout << endl;
}
}
reps *= links[i]->varNode()->range();
}
}
Factor result (src->factor().arguments(),
src->factor().ranges(), msgProduct);
result.multiply (src->factor());
if (Constants::SHOW_BP_CALCS) {
cout << " message product: " << msgProduct << endl;
cout << " original factor: " << src->factor().params() << endl;
cout << " factor product: " << result.params() << endl;
}
result.sumOutAllExcept (dst->varId());
if (Constants::SHOW_BP_CALCS) {
cout << " marginalized: " << result.params() << endl;
}
link->nextMessage() = result.params();
LogAware::normalize (link->nextMessage());
if (Constants::SHOW_BP_CALCS) {
cout << " curr msg: " << link->message() << endl;
cout << " next msg: " << link->nextMessage() << endl;
}
}
Params
BpSolver::getVarToFactorMsg (const BpLink* link) const
{
const VarNode* src = link->varNode();
Params msg;
if (src->hasEvidence()) {
msg.resize (src->range(), LogAware::noEvidence());
msg[src->getEvidence()] = LogAware::withEvidence();
} else {
msg.resize (src->range(), LogAware::one());
}
if (Constants::SHOW_BP_CALCS) {
cout << msg;
}
BpLinks::const_iterator it;
const BpLinks& links = ninf (src)->getLinks();
if (Globals::logDomain) {
for (it = links.begin(); it != links.end(); ++it) {
msg += (*it)->message();
if (Constants::SHOW_BP_CALCS) {
cout << " x " << (*it)->message();
}
}
msg -= link->message();
} else {
for (it = links.begin(); it != links.end(); ++it) {
msg *= (*it)->message();
if (Constants::SHOW_BP_CALCS) {
cout << " x " << (*it)->message();
}
}
msg /= link->message();
}
if (Constants::SHOW_BP_CALCS) {
cout << " = " << msg;
}
return msg;
}
Params
BpSolver::getJointByConditioning (const VarIds& jointVarIds) const
{
VarNodes jointVars;
for (size_t i = 0; i < jointVarIds.size(); i++) {
assert (fg.getVarNode (jointVarIds[i]));
jointVars.push_back (fg.getVarNode (jointVarIds[i]));
}
FactorGraph* tempFg = new FactorGraph (fg);
BpSolver solver (*tempFg);
solver.runSolver();
Params prevBeliefs = solver.getPosterioriOf (jointVarIds[0]);
VarIds observedVids = {jointVars[0]->varId()};
for (size_t i = 1; i < jointVarIds.size(); i++) {
assert (jointVars[i]->hasEvidence() == false);
Params newBeliefs;
Vars observedVars;
Ranges observedRanges;
for (size_t j = 0; j < observedVids.size(); j++) {
observedVars.push_back (tempFg->getVarNode (observedVids[j]));
observedRanges.push_back (observedVars.back()->range());
}
Indexer indexer (observedRanges, false);
while (indexer.valid()) {
for (size_t j = 0; j < observedVars.size(); j++) {
observedVars[j]->setEvidence (indexer[j]);
}
BpSolver solver (*tempFg);
solver.runSolver();
Params beliefs = solver.getPosterioriOf (jointVarIds[i]);
for (size_t k = 0; k < beliefs.size(); k++) {
newBeliefs.push_back (beliefs[k]);
}
++ indexer;
}
int count = -1;
for (size_t j = 0; j < newBeliefs.size(); j++) {
if (j % jointVars[i]->range() == 0) {
count ++;
}
newBeliefs[j] *= prevBeliefs[count];
}
prevBeliefs = newBeliefs;
observedVids.push_back (jointVars[i]->varId());
}
return prevBeliefs;
}
void
BpSolver::initializeSolver (void)
{
const VarNodes& varNodes = fg.varNodes();
varsI_.reserve (varNodes.size());
for (size_t i = 0; i < varNodes.size(); i++) {
varsI_.push_back (new SPNodeInfo());
}
const FacNodes& facNodes = fg.facNodes();
facsI_.reserve (facNodes.size());
for (size_t i = 0; i < facNodes.size(); i++) {
facsI_.push_back (new SPNodeInfo());
}
createLinks();
for (size_t i = 0; i < links_.size(); i++) {
FacNode* src = links_[i]->facNode();
VarNode* dst = links_[i]->varNode();
ninf (dst)->addBpLink (links_[i]);
ninf (src)->addBpLink (links_[i]);
}
}
bool
BpSolver::converged (void)
{
if (links_.size() == 0) {
return true;
}
if (nIters_ == 0) {
return false;
}
if (Globals::verbosity > 2) {
cout << endl;
}
if (nIters_ == 1) {
if (Globals::verbosity > 1) {
cout << "no residuals" << endl << endl;
}
return false;
}
bool converged = true;
if (BpOptions::schedule == BpOptions::Schedule::MAX_RESIDUAL) {
double maxResidual = (*(sortedOrder_.begin()))->residual();
if (maxResidual > BpOptions::accuracy) {
converged = false;
} else {
converged = true;
}
} else {
for (size_t i = 0; i < links_.size(); i++) {
double residual = links_[i]->residual();
if (Globals::verbosity > 1) {
cout << links_[i]->toString() + " residual = " << residual << endl;
}
if (residual > BpOptions::accuracy) {
converged = false;
if (Globals::verbosity < 2) {
break;
}
}
}
if (Globals::verbosity > 1) {
cout << endl;
}
}
return converged;
}
void
BpSolver::printLinkInformation (void) const
{
for (size_t i = 0; i < links_.size(); i++) {
BpLink* l = links_[i];
cout << l->toString() << ":" << endl;
cout << " curr msg = " ;
cout << l->message() << endl;
cout << " next msg = " ;
cout << l->nextMessage() << endl;
cout << " residual = " << l->residual() << endl;
}
}

70
packages/CLPBN/clpbn/bp/BpSolver.h → packages/CLPBN/horus/BpSolver.h
View File

@ -13,34 +13,31 @@
using namespace std;
class SpLink
class BpLink
{
public:
SpLink (FacNode* fn, VarNode* vn)
BpLink (FacNode* fn, VarNode* vn)
{
fac_ = fn;
var_ = vn;
v1_.resize (vn->range(), LogAware::tl (1.0 / vn->range()));
v2_.resize (vn->range(), LogAware::tl (1.0 / vn->range()));
v1_.resize (vn->range(), LogAware::log (1.0 / vn->range()));
v2_.resize (vn->range(), LogAware::log (1.0 / vn->range()));
currMsg_ = &v1_;
nextMsg_ = &v2_;
msgSended_ = false;
residual_ = 0.0;
}
virtual ~SpLink (void) { };
virtual ~BpLink (void) { };
FacNode* getFactor (void) const { return fac_; }
FacNode* facNode (void) const { return fac_; }
VarNode* getVariable (void) const { return var_; }
VarNode* varNode (void) const { return var_; }
const Params& getMessage (void) const { return *currMsg_; }
const Params& message (void) const { return *currMsg_; }
Params& getNextMessage (void) { return *nextMsg_; }
Params& nextMessage (void) { return *nextMsg_; }
bool messageWasSended (void) const { return msgSended_; }
double getResidual (void) const { return residual_; }
double residual (void) const { return residual_; }
void clearResidual (void) { residual_ = 0.0; }
@ -52,7 +49,6 @@ class SpLink
virtual void updateMessage (void)
{
swap (currMsg_, nextMsg_);
msgSended_ = true;
}
string toString (void) const
@ -71,20 +67,19 @@ class SpLink
Params v2_;
Params* currMsg_;
Params* nextMsg_;
bool msgSended_;
double residual_;
};
typedef vector<SpLink*> SpLinkSet;
typedef vector<BpLink*> BpLinks;
class SPNodeInfo
{
public:
void addSpLink (SpLink* link) { links_.push_back (link); }
const SpLinkSet& getLinks (void) { return links_; }
void addBpLink (BpLink* link) { links_.push_back (link); }
const BpLinks& getLinks (void) { return links_; }
private:
SpLinkSet links_;
BpLinks links_;
};
@ -97,6 +92,8 @@ class BpSolver : public Solver
Params solveQuery (VarIds);
virtual void printSolverFlags (void) const;
virtual Params getPosterioriOf (VarId);
virtual Params getJointDistributionOf (const VarIds&);
@ -108,9 +105,9 @@ class BpSolver : public Solver
virtual void maxResidualSchedule (void);
virtual void calculateFactor2VariableMsg (SpLink*);
virtual void calcFactorToVarMsg (BpLink*);
virtual Params getVar2FactorMsg (const SpLink*) const;
virtual Params getVarToFactorMsg (const BpLink*) const;
virtual Params getJointByConditioning (const VarIds&) const;
@ -124,64 +121,63 @@ class BpSolver : public Solver
return facsI_[fac->getIndex()];
}
void calculateAndUpdateMessage (SpLink* link, bool calcResidual = true)
void calculateAndUpdateMessage (BpLink* link, bool calcResidual = true)
{
if (Constants::DEBUG >= 3) {
if (Globals::verbosity > 2) {
cout << "calculating & updating " << link->toString() << endl;
}
calculateFactor2VariableMsg (link);
calcFactorToVarMsg (link);
if (calcResidual) {
link->updateResidual();
}
link->updateMessage();
}
void calculateMessage (SpLink* link, bool calcResidual = true)
void calculateMessage (BpLink* link, bool calcResidual = true)
{
if (Constants::DEBUG >= 3) {
if (Globals::verbosity > 2) {
cout << "calculating " << link->toString() << endl;
}
calculateFactor2VariableMsg (link);
calcFactorToVarMsg (link);
if (calcResidual) {
link->updateResidual();
}
}
void updateMessage (SpLink* link)
void updateMessage (BpLink* link)
{
link->updateMessage();
if (Constants::DEBUG >= 3) {
if (Globals::verbosity > 2) {
cout << "updating " << link->toString() << endl;
}
}
struct CompareResidual
{
inline bool operator() (const SpLink* link1, const SpLink* link2)
inline bool operator() (const BpLink* link1, const BpLink* link2)
{
return link1->getResidual() > link2->getResidual();
return link1->residual() > link2->residual();
}
};
SpLinkSet links_;
BpLinks links_;
unsigned nIters_;
vector<SPNodeInfo*> varsI_;
vector<SPNodeInfo*> facsI_;
bool runned_;
const FactorGraph* fg_;
typedef multiset<SpLink*, CompareResidual> SortedOrder;
typedef multiset<BpLink*, CompareResidual> SortedOrder;
SortedOrder sortedOrder_;
typedef unordered_map<SpLink*, SortedOrder::iterator> SpLinkMap;
SpLinkMap linkMap_;
typedef unordered_map<BpLink*, SortedOrder::iterator> BpLinkMap;
BpLinkMap linkMap_;
private:
void initializeSolver (void);
bool converged (void);
void printLinkInformation (void) const;
virtual void printLinkInformation (void) const;
};
#endif // HORUS_BPSOLVER_H

400
packages/CLPBN/horus/CbpSolver.cpp Normal file
View File

@ -0,0 +1,400 @@
#include "CbpSolver.h"
#include "WeightedBpSolver.h"
bool CbpSolver::checkForIdenticalFactors = true;
CbpSolver::CbpSolver (const FactorGraph& fg)
: Solver (fg), freeColor_(0)
{
findIdenticalFactors();
setInitialColors();
createGroups();
compressedFg_ = getCompressedFactorGraph();
solver_ = new WeightedBpSolver (*compressedFg_, getWeights());
}
CbpSolver::~CbpSolver (void)
{
delete solver_;
delete compressedFg_;
for (size_t i = 0; i < varClusters_.size(); i++) {
delete varClusters_[i];
}
for (size_t i = 0; i < facClusters_.size(); i++) {
delete facClusters_[i];
}
}
void
CbpSolver::printSolverFlags (void) const
{
stringstream ss;
ss << "counting bp [" ;
ss << "schedule=" ;
typedef BpOptions::Schedule Sch;
switch (BpOptions::schedule) {
case Sch::SEQ_FIXED: ss << "seq_fixed"; break;
case Sch::SEQ_RANDOM: ss << "seq_random"; break;
case Sch::PARALLEL: ss << "parallel"; break;
case Sch::MAX_RESIDUAL: ss << "max_residual"; break;
}
ss << ",max_iter=" << BpOptions::maxIter;
ss << ",accuracy=" << BpOptions::accuracy;
ss << ",log_domain=" << Util::toString (Globals::logDomain);
ss << ",chkif=" <<
Util::toString (CbpSolver::checkForIdenticalFactors);
ss << "]" ;
cout << ss.str() << endl;
}
Params
CbpSolver::solveQuery (VarIds queryVids)
{
assert (queryVids.empty() == false);
Params res;
if (queryVids.size() == 1) {
res = solver_->getPosterioriOf (getRepresentative (queryVids[0]));
} else {
VarNode* vn = fg.getVarNode (queryVids[0]);
const FacNodes& facNodes = vn->neighbors();
size_t idx = facNodes.size();
for (size_t i = 0; i < facNodes.size(); i++) {
if (facNodes[i]->factor().contains (queryVids)) {
idx = i;
break;
}
cout << endl;
}
if (idx == facNodes.size()) {
cerr << "error: only joint distributions on variables of some " ;
cerr << "clique are supported with the current solver" ;
cerr << endl;
exit (1);
}
VarIds representatives;
for (size_t i = 0; i < queryVids.size(); i++) {
representatives.push_back (getRepresentative (queryVids[i]));
}
res = solver_->getJointDistributionOf (representatives);
}
return res;
}
void
CbpSolver::findIdenticalFactors()
{
const FacNodes& facNodes = fg.facNodes();
if (checkForIdenticalFactors == false ||
facNodes.size() == 1) {
return;
}
for (size_t i = 0; i < facNodes.size(); i++) {
facNodes[i]->factor().setDistId (Util::maxUnsigned());
}
unsigned groupCount = 1;
for (size_t i = 0; i < facNodes.size() - 1; i++) {
Factor& f1 = facNodes[i]->factor();
if (f1.distId() != Util::maxUnsigned()) {
continue;
}
f1.setDistId (groupCount);
for (size_t j = i + 1; j < facNodes.size(); j++) {
Factor& f2 = facNodes[j]->factor();
if (f2.distId() != Util::maxUnsigned()) {
continue;
}
if (f1.size() == f2.size() &&
f1.ranges() == f2.ranges() &&
f1.params() == f2.params()) {
f2.setDistId (groupCount);
}
}
groupCount ++;
}
}
void
CbpSolver::setInitialColors (void)
{
varColors_.resize (fg.nrVarNodes());
facColors_.resize (fg.nrFacNodes());
// create the initial variable colors
VarColorMap colorMap;
const VarNodes& varNodes = fg.varNodes();
for (size_t i = 0; i < varNodes.size(); i++) {
unsigned range = varNodes[i]->range();
VarColorMap::iterator it = colorMap.find (range);
if (it == colorMap.end()) {
it = colorMap.insert (make_pair (
range, Colors (range + 1, -1))).first;
}
unsigned idx = varNodes[i]->hasEvidence()
? varNodes[i]->getEvidence()
: range;
Colors& stateColors = it->second;
if (stateColors[idx] == -1) {
stateColors[idx] = getNewColor();
}
setColor (varNodes[i], stateColors[idx]);
}
const FacNodes& facNodes = fg.facNodes();
// create the initial factor colors
DistColorMap distColors;
for (size_t i = 0; i < facNodes.size(); i++) {
unsigned distId = facNodes[i]->factor().distId();
DistColorMap::iterator it = distColors.find (distId);
if (it == distColors.end()) {
it = distColors.insert (make_pair (distId, getNewColor())).first;
}
setColor (facNodes[i], it->second);
}
}
void
CbpSolver::createGroups (void)
{
VarSignMap varGroups;
FacSignMap facGroups;
unsigned nIters = 0;
bool groupsHaveChanged = true;
const VarNodes& varNodes = fg.varNodes();
const FacNodes& facNodes = fg.facNodes();
while (groupsHaveChanged || nIters == 1) {
nIters ++;
// set a new color to the variables with the same signature
size_t prevVarGroupsSize = varGroups.size();
varGroups.clear();
for (size_t i = 0; i < varNodes.size(); i++) {
const VarSignature& signature = getSignature (varNodes[i]);
VarSignMap::iterator it = varGroups.find (signature);
if (it == varGroups.end()) {
it = varGroups.insert (make_pair (signature, VarNodes())).first;
}
it->second.push_back (varNodes[i]);
}
for (VarSignMap::iterator it = varGroups.begin();
it != varGroups.end(); ++it) {
Color newColor = getNewColor();
VarNodes& groupMembers = it->second;
for (size_t i = 0; i < groupMembers.size(); i++) {
setColor (groupMembers[i], newColor);
}
}
size_t prevFactorGroupsSize = facGroups.size();
facGroups.clear();
// set a new color to the factors with the same signature
for (size_t i = 0; i < facNodes.size(); i++) {
const FacSignature& signature = getSignature (facNodes[i]);
FacSignMap::iterator it = facGroups.find (signature);
if (it == facGroups.end()) {
it = facGroups.insert (make_pair (signature, FacNodes())).first;
}
it->second.push_back (facNodes[i]);
}
for (FacSignMap::iterator it = facGroups.begin();
it != facGroups.end(); ++it) {
Color newColor = getNewColor();
FacNodes& groupMembers = it->second;
for (size_t i = 0; i < groupMembers.size(); i++) {
setColor (groupMembers[i], newColor);
}
}
groupsHaveChanged = prevVarGroupsSize != varGroups.size()
|| prevFactorGroupsSize != facGroups.size();
}
// printGroups (varGroups, facGroups);
createClusters (varGroups, facGroups);
}
void
CbpSolver::createClusters (
const VarSignMap& varGroups,
const FacSignMap& facGroups)
{
varClusters_.reserve (varGroups.size());
for (VarSignMap::const_iterator it = varGroups.begin();
it != varGroups.end(); ++it) {
const VarNodes& groupVars = it->second;
VarCluster* vc = new VarCluster (groupVars);
for (size_t i = 0; i < groupVars.size(); i++) {
vid2VarCluster_.insert (make_pair (groupVars[i]->varId(), vc));
}
varClusters_.push_back (vc);
}
facClusters_.reserve (facGroups.size());
for (FacSignMap::const_iterator it = facGroups.begin();
it != facGroups.end(); ++it) {
FacNode* groupFactor = it->second[0];
const VarNodes& neighs = groupFactor->neighbors();
VarClusters varClusters;
varClusters.reserve (neighs.size());
for (size_t i = 0; i < neighs.size(); i++) {
VarId vid = neighs[i]->varId();
varClusters.push_back (vid2VarCluster_.find (vid)->second);
}
facClusters_.push_back (new FacCluster (it->second, varClusters));
}
}
VarSignature
CbpSolver::getSignature (const VarNode* varNode)
{
const FacNodes& neighs = varNode->neighbors();
VarSignature sign;
sign.reserve (neighs.size() + 1);
for (size_t i = 0; i < neighs.size(); i++) {
sign.push_back (make_pair (
getColor (neighs[i]),
neighs[i]->factor().indexOf (varNode->varId())));
}
std::sort (sign.begin(), sign.end());
sign.push_back (make_pair (getColor (varNode), 0));
return sign;
}
FacSignature
CbpSolver::getSignature (const FacNode* facNode)
{
const VarNodes& neighs = facNode->neighbors();
FacSignature sign;
sign.reserve (neighs.size() + 1);
for (size_t i = 0; i < neighs.size(); i++) {
sign.push_back (getColor (neighs[i]));
}
sign.push_back (getColor (facNode));
return sign;
}
FactorGraph*
CbpSolver::getCompressedFactorGraph (void)
{
FactorGraph* fg = new FactorGraph();
for (size_t i = 0; i < varClusters_.size(); i++) {
VarNode* newVar = new VarNode (varClusters_[i]->first());
varClusters_[i]->setRepresentative (newVar);
fg->addVarNode (newVar);
}
for (size_t i = 0; i < facClusters_.size(); i++) {
Vars vars;
const VarClusters& clusters = facClusters_[i]->varClusters();
for (size_t j = 0; j < clusters.size(); j++) {
vars.push_back (clusters[j]->representative());
}
const Factor& groundFac = facClusters_[i]->first()->factor();
FacNode* fn = new FacNode (Factor (
vars, groundFac.params(), groundFac.distId()));
facClusters_[i]->setRepresentative (fn);
fg->addFacNode (fn);
for (size_t j = 0; j < vars.size(); j++) {
fg->addEdge (static_cast<VarNode*> (vars[j]), fn);
}
}
return fg;
}
vector<vector<unsigned>>
CbpSolver::getWeights (void) const
{
vector<vector<unsigned>> weights;
weights.reserve (facClusters_.size());
for (size_t i = 0; i < facClusters_.size(); i++) {
const VarClusters& neighs = facClusters_[i]->varClusters();
weights.push_back ({ });
weights.back().reserve (neighs.size());
for (size_t j = 0; j < neighs.size(); j++) {
weights.back().push_back (getWeight (
facClusters_[i], neighs[j], j));
}
}
return weights;
}
unsigned
CbpSolver::getWeight (
const FacCluster* fc,
const VarCluster* vc,
size_t index) const
{
unsigned weight = 0;
VarId reprVid = vc->representative()->varId();
VarNode* groundVar = fg.getVarNode (reprVid);
const FacNodes& neighs = groundVar->neighbors();
for (size_t i = 0; i < neighs.size(); i++) {
FacNodes::const_iterator it;
it = std::find (fc->members().begin(), fc->members().end(), neighs[i]);
if (it != fc->members().end() &&
(*it)->factor().indexOf (reprVid) == index) {
weight ++;
}
}
return weight;
}
void
CbpSolver::printGroups (
const VarSignMap& varGroups,
const FacSignMap& facGroups) const
{
unsigned count = 1;
cout << "variable groups:" << endl;
for (VarSignMap::const_iterator it = varGroups.begin();
it != varGroups.end(); ++it) {
const VarNodes& groupMembers = it->second;
if (groupMembers.size() > 0) {
cout << count << ": " ;
for (size_t i = 0; i < groupMembers.size(); i++) {
cout << groupMembers[i]->label() << " " ;
}
count ++;
cout << endl;
}
}
count = 1;
cout << endl << "factor groups:" << endl;
for (FacSignMap::const_iterator it = facGroups.begin();
it != facGroups.end(); ++it) {
const FacNodes& groupMembers = it->second;
if (groupMembers.size() > 0) {
cout << ++count << ": " ;
for (size_t i = 0; i < groupMembers.size(); i++) {
cout << groupMembers[i]->getLabel() << " " ;
}
count ++;
cout << endl;
}
}
}

183
packages/CLPBN/horus/CbpSolver.h Normal file
View File

@ -0,0 +1,183 @@
#ifndef HORUS_CBPSOLVER_H
#define HORUS_CBPSOLVER_H
#include <unordered_map>
#include "Solver.h"
#include "FactorGraph.h"
#include "Util.h"
#include "Horus.h"
class VarCluster;
class FacCluster;
class VarSignHash;
class FacSignHash;
class WeightedBpSolver;
typedef long Color;
typedef vector<Color> Colors;
typedef vector<std::pair<Color,unsigned>> VarSignature;
typedef vector<Color> FacSignature;
typedef unordered_map<unsigned, Color> DistColorMap;
typedef unordered_map<unsigned, Colors> VarColorMap;
typedef unordered_map<VarSignature, VarNodes, VarSignHash> VarSignMap;
typedef unordered_map<FacSignature, FacNodes, FacSignHash> FacSignMap;
typedef vector<VarCluster*> VarClusters;
typedef vector<FacCluster*> FacClusters;
typedef unordered_map<VarId, VarCluster*> VarId2VarCluster;
struct VarSignHash
{
size_t operator() (const VarSignature &sig) const
{
size_t val = hash<size_t>()(sig.size());
for (size_t i = 0; i < sig.size(); i++) {
val ^= hash<size_t>()(sig[i].first);
val ^= hash<size_t>()(sig[i].second);
}
return val;
}
};
struct FacSignHash
{
size_t operator() (const FacSignature &sig) const
{
size_t val = hash<size_t>()(sig.size());
for (size_t i = 0; i < sig.size(); i++) {
val ^= hash<size_t>()(sig[i]);
}
return val;
}
};
class VarCluster
{
public:
VarCluster (const VarNodes& vs) : members_(vs) { }
const VarNode* first (void) const { return members_.front(); }
const VarNodes& members (void) const { return members_; }
VarNode* representative (void) const { return repr_; }
void setRepresentative (VarNode* vn) { repr_ = vn; }
private:
VarNodes members_;
VarNode* repr_;
};
class FacCluster
{
public:
FacCluster (const FacNodes& fcs, const VarClusters& vcs)
: members_(fcs), varClusters_(vcs) { }
const FacNode* first (void) const { return members_.front(); }
const FacNodes& members (void) const { return members_; }
VarClusters& varClusters (void) { return varClusters_; }
FacNode* representative (void) const { return repr_; }
void setRepresentative (FacNode* fn) { repr_ = fn; }
private:
FacNodes members_;
VarClusters varClusters_;
FacNode* repr_;
};
class CbpSolver : public Solver
{
public:
CbpSolver (const FactorGraph& fg);
~CbpSolver (void);
void printSolverFlags (void) const;
Params solveQuery (VarIds);
static bool checkForIdenticalFactors;
private:
Color getNewColor (void)
{
++ freeColor_;
return freeColor_ - 1;
}
Color getColor (const VarNode* vn) const
{
return varColors_[vn->getIndex()];
}
Color getColor (const FacNode* fn) const
{
return facColors_[fn->getIndex()];
}
void setColor (const VarNode* vn, Color c)
{
varColors_[vn->getIndex()] = c;
}
void setColor (const FacNode* fn, Color c)
{
facColors_[fn->getIndex()] = c;
}
void findIdenticalFactors (void);
void setInitialColors (void);
void createGroups (void);
void createClusters (const VarSignMap&, const FacSignMap&);
VarSignature getSignature (const VarNode*);
FacSignature getSignature (const FacNode*);
void printGroups (const VarSignMap&, const FacSignMap&) const;
VarId getRepresentative (VarId vid)
{
assert (Util::contains (vid2VarCluster_, vid));
VarCluster* vc = vid2VarCluster_.find (vid)->second;
return vc->representative()->varId();
}
FactorGraph* getCompressedFactorGraph (void);
vector<vector<unsigned>> getWeights (void) const;
unsigned getWeight (const FacCluster*,
const VarCluster*, size_t index) const;
Color freeColor_;
Colors varColors_;
Colors facColors_;
VarClusters varClusters_;
FacClusters facClusters_;
VarId2VarCluster vid2VarCluster_;
const FactorGraph* compressedFg_;
WeightedBpSolver* solver_;
};
#endif // HORUS_CBPSOLVER_H

1130
packages/CLPBN/horus/ConstraintTree.cpp Normal file
View File

File diff suppressed because it is too large Load Diff

Some files were not shown because too many files have changed in this diff Show More