diogo/yap-6.3
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Merge branch 'master' of /cygdrive/z/vitor/Yap/yap-6.3

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This commit is contained in:
U-WIN-U2045GN0RNQ\Vítor Santos Costa 2011-07-25 17:09:43 +01:00
commit 4fe1833ece
81 changed files with 4239 additions and 2447 deletions
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7
C/absmi.c
View File

@ -2081,8 +2081,13 @@ Yap_absmi(int inp)
goto failloop;
} else
#endif /* FROZEN_STACKS */
if (IN_BETWEEN(H0,pt1,H) && IsAttVar(pt1))
if (IN_BETWEEN(H0,pt1,H)) {
if (IsAttVar(pt1)) {
goto failloop;
} else if (*pt1 == (CELL)FunctorBigInt) {
Yap_CleanOpaqueVariable(pt1);
}
}
#ifdef FROZEN_STACKS /* TRAIL */
/* don't reset frozen variables */
if (pt0 < TR_FZ)

14
C/amasm.c
View File

@ -252,7 +252,7 @@ STATIC_PROTO(yamop *a_if, (op_numbers, union clause_obj *, int, yamop *, int, st
STATIC_PROTO(yamop *a_cut, (clause_info *,yamop *, int, struct intermediates *));
#ifdef YAPOR
STATIC_PROTO(yamop *a_try, (op_numbers, CELL, CELL, int, int, yamop *, int, struct intermediates *));
STATIC_PROTO(yamop *a_either, (op_numbers, CELL, CELL, int, int, yamop *, int, struct intermediates *));
STATIC_PROTO(yamop *a_either, (op_numbers, CELL, CELL, int, yamop *, int, struct intermediates *));
#else
STATIC_PROTO(yamop *a_try, (op_numbers, CELL, CELL, yamop *, int, struct intermediates *));
STATIC_PROTO(yamop *a_either, (op_numbers, CELL, CELL, yamop *, int, struct intermediates *));
@ -2155,7 +2155,7 @@ a_try(op_numbers opcode, CELL lab, CELL opr, int nofalts, int hascut, yamop *cod
#endif
#ifdef YAPOR
INIT_YAMOP_LTT(code_p, nofalts);
if (hascut)
if (cip->clause_has_cut)
PUT_YAMOP_CUT(code_p);
if (ap->PredFlags & SequentialPredFlag)
PUT_YAMOP_SEQ(code_p);
@ -2167,7 +2167,7 @@ a_try(op_numbers opcode, CELL lab, CELL opr, int nofalts, int hascut, yamop *cod
static yamop *
#ifdef YAPOR
a_either(op_numbers opcode, CELL opr, CELL lab, int nofalts, int hascut, yamop *code_p, int pass_no, struct intermediates *cip)
a_either(op_numbers opcode, CELL opr, CELL lab, int nofalts, yamop *code_p, int pass_no, struct intermediates *cip)
#else
a_either(op_numbers opcode, CELL opr, CELL lab, yamop *code_p, int pass_no, struct intermediates *cip)
#endif /* YAPOR */
@ -2179,7 +2179,7 @@ a_either(op_numbers opcode, CELL opr, CELL lab, yamop *code_p, int pass_no, stru
code_p->u.Osblp.p0 = cip->CurrentPred;
#ifdef YAPOR
INIT_YAMOP_LTT(code_p, nofalts);
if (hascut)
if (cip->clause_has_cut)
PUT_YAMOP_CUT(code_p);
if (cip->CurrentPred->PredFlags & SequentialPredFlag)
PUT_YAMOP_SEQ(code_p);
@ -3583,7 +3583,7 @@ do_pass(int pass_no, yamop **entry_codep, int assembling, int *clause_has_blobsp
}
code_p = a_either(_either,
-Signed(RealEnvSize) - CELLSIZE * cip->cpc->rnd2,
Unsigned(cip->code_addr) + cip->label_offset[cip->cpc->rnd1], 0, 0, code_p, pass_no, cip);
Unsigned(cip->code_addr) + cip->label_offset[cip->cpc->rnd1], 0, code_p, pass_no, cip);
#else
code_p = a_either(_either,
-Signed(RealEnvSize) - CELLSIZE * cip->cpc->rnd2,
@ -3596,7 +3596,7 @@ do_pass(int pass_no, yamop **entry_codep, int assembling, int *clause_has_blobsp
either_inst[either_cont++] = code_p;
code_p = a_either(_or_else,
-Signed(RealEnvSize) - CELLSIZE * cip->cpc->rnd2,
Unsigned(cip->code_addr) + cip->label_offset[cip->cpc->rnd1], 0, 0, code_p, pass_no, cip);
Unsigned(cip->code_addr) + cip->label_offset[cip->cpc->rnd1], 0, code_p, pass_no, cip);
#else
code_p = a_either(_or_else,
-Signed(RealEnvSize) - CELLSIZE * cip->cpc->rnd2,
@ -3608,7 +3608,7 @@ do_pass(int pass_no, yamop **entry_codep, int assembling, int *clause_has_blobsp
#ifdef YAPOR
if (pass_no)
either_inst[either_cont++] = code_p;
code_p = a_either(_or_last, 0, 0, 0, 0, code_p, pass_no, cip);
code_p = a_either(_or_last, 0, 0, 0, code_p, pass_no, cip);
if (pass_no) {
int cont = 1;
do {

57
C/bignum.c
View File

@ -25,9 +25,10 @@ static char SccsId[] = "%W% %G%";
#include <string.h>
#endif
#include "YapHeap.h"
#ifdef USE_GMP
#include "YapHeap.h"
#include "eval.h"
#include "alloc.h"
@ -59,6 +60,7 @@ Yap_MkBigIntTerm(MP_INT *big)
return AbsAppl(ret);
}
MP_INT *
Yap_BigIntOfTerm(Term t)
{
@ -127,9 +129,60 @@ Yap_RatTermToApplTerm(Term t)
return Yap_MkApplTerm(FunctorRDiv,2,ts);
}
#endif
Term
Yap_AllocExternalDataInStack(CELL tag, size_t bytes)
{
CACHE_REGS
Int nlimbs;
MP_INT *dst = (MP_INT *)(H+2);
CELL *ret = H;
nlimbs = ALIGN_YAPTYPE(bytes,CELL)/CellSize;
if (nlimbs > (ASP-ret)-1024) {
return TermNil;
}
H[0] = (CELL)FunctorBigInt;
H[1] = tag;
dst->_mp_size = 0;
dst->_mp_alloc = nlimbs;
H = (CELL *)(dst+1)+nlimbs;
H[0] = EndSpecials;
H++;
if (tag != EXTERNAL_BLOB) {
TrailTerm(TR) = AbsPair(ret);
TR++;
}
return AbsAppl(ret);
}
int Yap_CleanOpaqueVariable(CELL *pt)
{
CELL blob_info, blob_tag;
MP_INT *blobp;
#ifdef DEBUG
/* sanity checking */
if (pt[0] != (CELL)FunctorBigInt) {
Yap_Error(SYSTEM_ERROR, TermNil, "CleanOpaqueVariable bad call");
return FALSE;
}
#endif
blob_tag = pt[1];
if (blob_tag < USER_BLOB_START ||
blob_tag >= USER_BLOB_END) {
Yap_Error(SYSTEM_ERROR, AbsAppl(pt), "clean opaque: bad blob with tag " UInt_FORMAT ,blob_tag);
return FALSE;
}
blob_info = blob_tag - USER_BLOB_START;
if (!GLOBAL_OpaqueHandlers)
return FALSE;
blobp = (MP_INT *)(pt+2);
if (!GLOBAL_OpaqueHandlers[blob_info].fail_handler)
return TRUE;
return (GLOBAL_OpaqueHandlers[blob_info].fail_handler)((void *)(blobp+1));
}
Term
Yap_MkULLIntTerm(YAP_ULONG_LONG n)
{

84
C/c_interface.c
View File

@ -390,6 +390,8 @@ X_API Bool STD_PROTO(YAP_IsDbRefTerm,(Term));
X_API Bool STD_PROTO(YAP_IsAtomTerm,(Term));
X_API Bool STD_PROTO(YAP_IsPairTerm,(Term));
X_API Bool STD_PROTO(YAP_IsApplTerm,(Term));
X_API Bool STD_PROTO(YAP_IsExternalDataInStackTerm,(Term));
X_API Bool STD_PROTO(YAP_IsOpaqueObjectTerm,(Term, int));
X_API Term STD_PROTO(YAP_MkIntTerm,(Int));
X_API Term STD_PROTO(YAP_MkBigNumTerm,(void *));
X_API Term STD_PROTO(YAP_MkRationalTerm,(void *));
@ -463,7 +465,7 @@ X_API IOSTREAM *STD_PROTO(YAP_TermToStream,(Term));
X_API IOSTREAM *STD_PROTO(YAP_InitConsult,(int, char *));
X_API void STD_PROTO(YAP_EndConsult,(IOSTREAM *));
X_API Term STD_PROTO(YAP_Read, (IOSTREAM *));
X_API void STD_PROTO(YAP_Write, (Term, int (*)(wchar_t), int));
X_API void STD_PROTO(YAP_Write, (Term, IOSTREAM *, int));
X_API Term STD_PROTO(YAP_CopyTerm, (Term));
X_API Term STD_PROTO(YAP_WriteBuffer, (Term, char *, unsigned int, int));
X_API char *STD_PROTO(YAP_CompileClause, (Term));
@ -536,13 +538,11 @@ X_API Term STD_PROTO(YAP_ModuleUser,(void));
X_API Int STD_PROTO(YAP_NumberOfClausesForPredicate,(PredEntry *));
X_API int STD_PROTO(YAP_MaxOpPriority,(Atom, Term));
X_API int STD_PROTO(YAP_OpInfo,(Atom, Term, int, int *, int *));
static int (*do_putcf)(wchar_t);
static int do_yap_putc(int streamno,wchar_t ch) {
do_putcf(ch);
return(ch);
}
X_API Term STD_PROTO(YAP_AllocExternalDataInStack,(size_t));
X_API void *STD_PROTO(YAP_ExternalDataInStackFromTerm,(Term));
X_API int STD_PROTO(YAP_NewOpaqueType,(void *));
X_API Term STD_PROTO(YAP_NewOpaqueObject,(int, size_t));
X_API void *STD_PROTO(YAP_OpaqueObjectFromTerm,(Term));
static int
dogc(void)
@ -1677,7 +1677,6 @@ YAP_ExecuteOnCut(PredEntry *pe, CPredicate exec_code, struct cut_c_str *top)
if (pe->PredFlags & CArgsPredFlag) {
val = execute_cargs_back(pe, exec_code, ctx PASS_REGS);
} else {
fprintf(stderr,"ctx=%p\n",ctx);
val = ((codev)(args-LCL0,0,ctx));
}
/* make sure we clean up the frames left by the user */
@ -2314,6 +2313,65 @@ YAP_RunGoal(Term t)
return(out);
}
X_API Term
YAP_AllocExternalDataInStack(size_t bytes)
{
Term t = Yap_AllocExternalDataInStack(EXTERNAL_BLOB, bytes);
if (t == TermNil)
return 0L;
return t;
}
X_API Bool
YAP_IsExternalDataInStackTerm(Term t)
{
return IsExternalBlobTerm(t, EXTERNAL_BLOB);
}
X_API void *
YAP_ExternalDataInStackFromTerm(Term t)
{
return ExternalBlobFromTerm (t);
}
int YAP_NewOpaqueType(void *f)
{
int i;
if (!GLOBAL_OpaqueHandlers) {
GLOBAL_OpaqueHandlers = malloc(sizeof(opaque_handler_t)*(USER_BLOB_END-USER_BLOB_START));
if (!GLOBAL_OpaqueHandlers) {
/* no room */
return -1;
}
} else if (GLOBAL_OpaqueHandlersCount == USER_BLOB_END-USER_BLOB_START) {
/* all types used */
return -1;
}
i = GLOBAL_OpaqueHandlersCount++;
memcpy(GLOBAL_OpaqueHandlers+i,f,sizeof(opaque_handler_t));
return i+USER_BLOB_START;
}
Term YAP_NewOpaqueObject(int tag, size_t bytes)
{
Term t = Yap_AllocExternalDataInStack((CELL)tag, bytes);
if (t == TermNil)
return 0L;
return t;
}
X_API Bool
YAP_IsOpaqueObjectTerm(Term t, int tag)
{
return IsExternalBlobTerm(t, (CELL)tag);
}
X_API void *
YAP_OpaqueObjectFromTerm(Term t)
{
return ExternalBlobFromTerm (t);
}
X_API Term
YAP_RunGoalOnce(Term t)
{
@ -2369,7 +2427,6 @@ YAP_RestartGoal(void)
BACKUP_MACHINE_REGS();
if (LOCAL_AllowRestart) {
P = (yamop *)FAILCODE;
do_putcf = myputc;
LOCAL_PrologMode = UserMode;
out = Yap_exec_absmi(TRUE);
LOCAL_PrologMode = UserCCallMode;
@ -2589,12 +2646,11 @@ YAP_Read(IOSTREAM *inp)
}
X_API void
YAP_Write(Term t, int (*myputc)(wchar_t), int flags)
YAP_Write(Term t, IOSTREAM *stream, int flags)
{
BACKUP_MACHINE_REGS();
do_putcf = myputc; /* */
Yap_plwrite (t, do_yap_putc, flags, 1200);
Yap_dowrite (t, stream, flags, 1200);
RECOVER_MACHINE_REGS();
}
@ -2774,6 +2830,7 @@ YAP_Init(YAP_init_args *yap_init)
Yap_init_yapor_global_local_memory();
LOCAL = REMOTE(0);
#endif /* YAPOR_COPY || YAPOR_COW || YAPOR_SBA */
GLOBAL_PrologShouldHandleInterrupts = yap_init->PrologShouldHandleInterrupts;
Yap_InitSysbits(); /* init signal handling and time, required by later functions */
GLOBAL_argv = yap_init->Argv;
GLOBAL_argc = yap_init->Argc;
@ -2821,7 +2878,6 @@ YAP_Init(YAP_init_args *yap_init)
} else {
Heap = yap_init->HeapSize;
}
GLOBAL_PrologShouldHandleInterrupts = yap_init->PrologShouldHandleInterrupts;
Yap_InitWorkspace(Heap, Stack, Trail, Atts,
yap_init->MaxTableSpaceSize,
yap_init->NumberWorkers,

2
C/compiler.c
View File

@ -735,7 +735,7 @@ c_arg(Int argno, Term t, unsigned int arity, unsigned int level, compiler_struct
} else if (IsPairTerm(t)) {
cglobs->space_used += 2;
if (optimizer_on && level < 6) {
#if !defined(THREADS)
#if !defined(THREADS) && !defined(YAPOR)
/* discard code sharing because we cannot write on shared stuff */
if (!(cglobs->cint.CurrentPred->PredFlags & (DynamicPredFlag|LogUpdatePredFlag))) {
if (try_store_as_dbterm(t, argno, arity, level, cglobs))

4
C/exec.c
View File

@ -961,7 +961,7 @@ exec_absmi(int top USES_REGS)
restore_H();
/* set stack */
ASP = (CELL *)PROTECT_FROZEN_B(B);
Yap_StartSlots( PASS_REGS1 );
Yap_PopSlots();
LOCK(LOCAL_SignalLock);
/* forget any signals active, we're reborne */
LOCAL_ActiveSignals = 0;
@ -991,9 +991,9 @@ exec_absmi(int top USES_REGS)
LOCAL_PrologMode = UserMode;
}
} else {
Yap_CloseSlots( PASS_REGS1 );
LOCAL_PrologMode = UserMode;
}
Yap_CloseSlots( PASS_REGS1 );
YENV = ASP;
YENV[E_CB] = Unsigned (B);
out = Yap_absmi(0);

4
C/grow.c
View File

@ -399,7 +399,7 @@ AdjustTrail(int adjusting_heap, int thread_copying USES_REGS)
#if defined(YAPOR_THREADS)
}
#endif
/* moving the trail is simple */
/* moving the trail is simple, yeaahhh! */
while (ptt != tr_base) {
register CELL reg = TrailTerm(ptt-1);
#ifdef FROZEN_STACKS
@ -420,8 +420,6 @@ AdjustTrail(int adjusting_heap, int thread_copying USES_REGS)
} else if (IsPairTerm(reg)) {
TrailTerm(ptt) = AdjustPair(reg PASS_REGS);
#ifdef MULTI_ASSIGNMENT_VARIABLES /* does not work with new structures */
/* check it whether we are protecting a
multi-assignment */
} else if (IsApplTerm(reg)) {
TrailTerm(ptt) = AdjustAppl(reg PASS_REGS);
#endif

33
C/heapgc.c
View File

@ -1325,7 +1325,7 @@ mark_variable(CELL_PTR current USES_REGS)
sz++;
#if DEBUG
if (next[sz] != EndSpecials) {
fprintf(stderr,"[ Error: could not find EndSpecials at blob %p type %lx ]\n", next, next[1]);
fprintf(stderr,"[ Error: could not find EndSpecials at blob %p type " UInt_FORMAT " ]\n", next, next[1]);
}
#endif
MARK(next+sz);
@ -1658,13 +1658,22 @@ mark_trail(tr_fr_ptr trail_ptr, tr_fr_ptr trail_base, CELL *gc_H, choiceptr gc_B
#endif
}
} else if (IsPairTerm(trail_cell)) {
/* can safely ignore this */
/* cannot safely ignore this */
CELL *cptr = RepPair(trail_cell);
if (IN_BETWEEN(LOCAL_GlobalBase,cptr,H) &&
GlobalIsAttVar(cptr)) {
if (IN_BETWEEN(LOCAL_GlobalBase,cptr,H)) {
if (GlobalIsAttVar(cptr)) {
TrailTerm(trail_base) = (CELL)cptr;
mark_external_reference(&TrailTerm(trail_base) PASS_REGS);
TrailTerm(trail_base) = trail_cell;
} else if (*cptr == (CELL)FunctorBigInt) {
TrailTerm(trail_base) = AbsAppl(cptr);
mark_external_reference(&TrailTerm(trail_base) PASS_REGS);
TrailTerm(trail_base) = trail_cell;
}
#ifdef DEBUG
else
fprintf(GLOBAL_stderr,"OOPS in GC: weird trail entry at %p:" UInt_FORMAT "\n", &TrailTerm(trail_base), (CELL)cptr);
#endif
}
}
#if MULTI_ASSIGNMENT_VARIABLES
@ -1904,11 +1913,11 @@ mark_choicepoints(register choiceptr gc_B, tr_fr_ptr saved_TR, int very_verbose
PredEntry *pe = Yap_PredForChoicePt(gc_B);
#if defined(ANALYST) || defined(DEBUG)
if (pe == NULL) {
fprintf(GLOBAL_stderr,"%% marked %ld (%s)\n", LOCAL_total_marked, Yap_op_names[opnum]);
fprintf(GLOBAL_stderr,"%% marked " UInt_FORMAT " (%s)\n", LOCAL_total_marked, Yap_op_names[opnum]);
} else if (pe->ArityOfPE) {
fprintf(GLOBAL_stderr,"%% %s/%d marked %ld (%s)\n", RepAtom(NameOfFunctor(pe->FunctorOfPred))->StrOfAE, pe->ArityOfPE, LOCAL_total_marked, Yap_op_names[opnum]);
fprintf(GLOBAL_stderr,"%% %s/%d marked " UInt_FORMAT " (%s)\n", RepAtom(NameOfFunctor(pe->FunctorOfPred))->StrOfAE, pe->ArityOfPE, LOCAL_total_marked, Yap_op_names[opnum]);
} else {
fprintf(GLOBAL_stderr,"%% %s marked %ld (%s)\n", RepAtom((Atom)(pe->FunctorOfPred))->StrOfAE, LOCAL_total_marked, Yap_op_names[opnum]);
fprintf(GLOBAL_stderr,"%% %s marked " UInt_FORMAT " (%s)\n", RepAtom((Atom)(pe->FunctorOfPred))->StrOfAE, LOCAL_total_marked, Yap_op_names[opnum]);
}
#else
if (pe == NULL) {
@ -2450,12 +2459,20 @@ sweep_trail(choiceptr gc_B, tr_fr_ptr old_TR USES_REGS)
CELL *pt0 = RepPair(trail_cell);
CELL flags;
if (IN_BETWEEN(LOCAL_GlobalBase, pt0, H) && GlobalIsAttVar(pt0)) {
if (IN_BETWEEN(LOCAL_GlobalBase, pt0, H)) {
if (GlobalIsAttVar(pt0)) {
TrailTerm(dest) = trail_cell;
/* be careful with partial gc */
if (HEAP_PTR(TrailTerm(dest))) {
into_relocation_chain(&TrailTerm(dest), GET_NEXT(trail_cell) PASS_REGS);
}
} else if (*pt0 == (CELL)FunctorBigInt) {
TrailTerm(dest) = trail_cell;
/* be careful with partial gc */
if (HEAP_PTR(TrailTerm(dest))) {
into_relocation_chain(&TrailTerm(dest), GET_NEXT(trail_cell) PASS_REGS);
}
}
dest++;
trail_ptr++;
continue;

23
H/TermExt.h
View File

@ -86,7 +86,9 @@ typedef enum
CLAUSE_LIST = 0x40,
BLOB_STRING = 0x80, /* SWI style strings */
BLOB_WIDE_STRING = 0x81, /* SWI style strings */
EXTERNAL_BLOB = 0x100 /* for SWI emulation */
EXTERNAL_BLOB = 0x100, /* generic data */
USER_BLOB_START = 0x1000, /* user defined blob */
USER_BLOB_END = 0x1100 /* end of user defined blob */
}
big_blob_type;
@ -438,6 +440,25 @@ IsLargeNumTerm (Term t)
&& (FunctorOfTerm (t) >= FunctorLongInt)));
}
inline EXTERN int IsExternalBlobTerm (Term, CELL);
inline EXTERN int
IsExternalBlobTerm (Term t, CELL tag)
{
return (int) (IsApplTerm (t) &&
FunctorOfTerm (t) == FunctorBigInt &&
RepAppl(t)[1] == tag);
}
inline EXTERN void *ExternalBlobFromTerm (Term);
inline EXTERN void *
ExternalBlobFromTerm (Term t)
{
MP_INT *base = (MP_INT *)(RepAppl(t)+2);
return (void *) (base+1);
}

6
H/YapHeap.h
View File

@ -33,6 +33,12 @@ typedef int (*SWI_PLGetStreamPositionFunction)(void *);
#include "../include/dswiatoms.h"
typedef int (*Opaque_CallOnFail)(void *);
typedef struct opaque_handler_struct {
Opaque_CallOnFail fail_handler;
} opaque_handler_t;
#ifndef INT_KEYS_DEFAULT_SIZE
#define INT_KEYS_DEFAULT_SIZE 256
#endif

2
H/Yapproto.h
View File

@ -120,6 +120,8 @@ int STD_PROTO(Yap_IsStringTerm, (Term));
int STD_PROTO(Yap_IsWideStringTerm, (Term));
Term STD_PROTO(Yap_RatTermToApplTerm, (Term));
void STD_PROTO(Yap_InitBigNums, (void));
Term STD_PROTO(Yap_AllocExternalDataInStack, (CELL, size_t));
int STD_PROTO(Yap_CleanOpaqueVariable, (CELL *));
/* c_interface.c */
Int STD_PROTO(YAP_Execute,(struct pred_entry *, CPredicate));

2
H/dglobals.h
View File

@ -102,6 +102,8 @@
#define GLOBAL_Executable Yap_global->Executable_
#endif
#define GLOBAL_OpaqueHandlersCount Yap_global->OpaqueHandlersCount_
#define GLOBAL_OpaqueHandlers Yap_global->OpaqueHandlers_
#if __simplescalar__
#define GLOBAL_pwd Yap_global->pwd_
#endif

2
H/hglobals.h
View File

@ -102,6 +102,8 @@ typedef struct global_data {
char Executable_[YAP_FILENAME_MAX];
#endif
int OpaqueHandlersCount_;
struct opaque_handler_struct* OpaqueHandlers_;
#if __simplescalar__
char pwd_[YAP_FILENAME_MAX];
#endif

2
H/iglobals.h
View File

@ -102,6 +102,8 @@ static void InitGlobal(void) {
#endif
GLOBAL_OpaqueHandlersCount = 0;
GLOBAL_OpaqueHandlers = NULL;
#if __simplescalar__
#endif

2
H/rglobals.h
View File

@ -102,6 +102,8 @@ static void RestoreGlobal(void) {
#endif
#if __simplescalar__
#endif

3
H/yapio.h
View File

@ -67,6 +67,7 @@
#define YP_FILE FILE
int STD_PROTO(YP_putc,(int, int));
void STD_PROTO(Yap_dowrite, (Term, IOSTREAM *, int, int));
#else
@ -96,8 +97,6 @@ int STD_PROTO(YP_putc,(int, int));
#define fclose ERR_fclose
#define fflush ERR_fflush
/* flags for files in IOSTREAM struct */
#define _YP_IO_WRITE 1
#define _YP_IO_READ 2

60
MYDDAS/myddas_odbc.c
View File

@ -154,18 +154,6 @@ static int SQLBINDCOL(SQLHSTMT sthandle,
return TRUE;
}
static int SQLFREESTMT(SQLHSTMT sthandle,
SQLUSMALLINT opt,
char * print)
{
SQLRETURN retcode;
retcode = SQLFreeStmt(sthandle,opt);
if (retcode != SQL_SUCCESS && retcode != SQL_SUCCESS_WITH_INFO)
return odbc_error(SQL_HANDLE_STMT, sthandle, "SQLFreeStmt", print);
return TRUE;
}
static int SQLNUMRESULTCOLS(SQLHSTMT sthandle,
SQLSMALLINT * ncols,
char * print)
@ -421,8 +409,9 @@ c_db_odbc_query( USES_REGS1 ) {
/* +1 because of '\0' */
bind_space = malloc(sizeof(char)*(ColumnSizePtr+1));
data_info = malloc(sizeof(SQLINTEGER));
if (!SQLBINDCOL(hstmt,i,SQL_C_CHAR,bind_space,(ColumnSizePtr+1),data_info,"db_query"))
if (!SQLBINDCOL(hstmt,i,SQL_C_CHAR,bind_space,(ColumnSizePtr+1),data_info,"db_query")) {
return FALSE;
}
properties[0] = MkIntegerTerm((Int)bind_space);
properties[2] = MkIntegerTerm((Int)data_info);
@ -444,7 +433,7 @@ c_db_odbc_query( USES_REGS1 ) {
{
if (!SQLCLOSECURSOR(hstmt,"db_query"))
return FALSE;
if (!SQLFREESTMT(hstmt,SQL_CLOSE,"db_query"))
if (!SQLFREEHANDLE(SQL_HANDLE_STMT, hstmt, "db_query"))
return FALSE;
return FALSE;
}
@ -466,7 +455,7 @@ c_db_odbc_number_of_fields( USES_REGS1 ) {
char sql[256];
SQLSMALLINT number_fields;
sprintf(sql,"DESCRIBE %s",relation);
sprintf(sql,"SELECT column_name from INFORMATION_SCHEMA.COLUMNS where table_name = \'%s\'",relation);
if (!SQLALLOCHANDLE(SQL_HANDLE_STMT, hdbc, &hstmt, "db_number_of_fields"))
return FALSE;
@ -482,7 +471,7 @@ c_db_odbc_number_of_fields( USES_REGS1 ) {
if (!SQLCLOSECURSOR(hstmt,"db_number_of_fields"))
return FALSE;
if (!SQLFREESTMT(hstmt,SQL_CLOSE,"db_number_of_fields"))
if (!SQLFREEHANDLE(SQL_HANDLE_STMT, hstmt, "db_number_of_fields"))
return FALSE;
if (!Yap_unify(arg_fields, MkIntegerTerm(number_fields)))
@ -506,7 +495,7 @@ c_db_odbc_get_attributes_types( USES_REGS1 ) {
Term head, list;
list = arg_types_list;
sprintf(sql,"DESCRIBE %s",relation);
sprintf(sql,"SELECT column_name,data_type FROM INFORMATION_SCHEMA.COLUMNS where table_name = \'%s\'",relation);
if (!SQLALLOCHANDLE(SQL_HANDLE_STMT, hdbc, &hstmt, "db_get_attributes_types"))
return FALSE;
@ -547,7 +536,7 @@ c_db_odbc_get_attributes_types( USES_REGS1 ) {
if (!SQLCLOSECURSOR(hstmt,"db_get_attributes_types"))
return FALSE;
if (!SQLFREESTMT(hstmt,SQL_CLOSE, "db_get_attributes_types"))
if (!SQLFREEHANDLE(SQL_HANDLE_STMT, hstmt, "db_get_attributes_types"))
return FALSE;
return TRUE;
}
@ -585,12 +574,31 @@ c_db_odbc_row_cut( USES_REGS1 ) {
if (!SQLCLOSECURSOR(hstmt,"db_row_cut"))
return FALSE;
if (!SQLFREESTMT(hstmt,SQL_CLOSE,"db_row_cut"))
if (!SQLFREEHANDLE(SQL_HANDLE_STMT, hstmt, "db_row_cut"))
return FALSE;
return TRUE;
}
static int
release_list_args(Term arg_list_args, Term arg_bind_list, const char *error_msg)
{
Term list = arg_list_args;
Term list_bind = arg_bind_list;
while (IsPairTerm(list_bind))
{
Term head_bind = HeadOfTerm(list_bind);
list = TailOfTerm(list);
list_bind = TailOfTerm(list_bind);
free((char *)IntegerOfTerm(ArgOfTerm(1,head_bind)));
free((SQLINTEGER *)IntegerOfTerm(ArgOfTerm(3,head_bind)));
}
return TRUE;
}
/* db_row: ResultSet x BindList x ListOfArgs -> */
static Int
c_db_odbc_row( USES_REGS1 ) {
@ -611,8 +619,11 @@ c_db_odbc_row( USES_REGS1 ) {
{
if (!SQLCLOSECURSOR(hstmt,"db_row"))
return FALSE;
if (!SQLFREESTMT(hstmt,SQL_CLOSE,"db_row"))
if (!SQLFREEHANDLE(SQL_HANDLE_STMT, hstmt, "db_row"))
return FALSE;
if (!release_list_args(arg_list_args, arg_bind_list, "db_row")) {
return FALSE;
}
cut_fail();
return FALSE;
@ -699,7 +710,7 @@ c_db_odbc_number_of_fields_in_query( USES_REGS1 ) {
if (!Yap_unify(arg_fields, MkIntegerTerm(number_cols))){
if (!SQLCLOSECURSOR(hstmt,"db_number_of_fields_in_query"))
return FALSE;
if (!SQLFREESTMT(hstmt,SQL_CLOSE, "db_number_of_fields_in_query"))
if (!SQLFREEHANDLE(SQL_HANDLE_STMT, hstmt, "db_number_of_fields_in_query"))
return FALSE;
return FALSE;
@ -707,7 +718,7 @@ c_db_odbc_number_of_fields_in_query( USES_REGS1 ) {
if (!SQLCLOSECURSOR(hstmt,"db_number_of_fields_in_query"))
return FALSE;
if (!SQLFREESTMT(hstmt,SQL_CLOSE, "db_number_of_fields_in_query"))
if (!SQLFREEHANDLE(SQL_HANDLE_STMT, hstmt, "db_number_of_fields_in_query"))
return FALSE;
return TRUE;
@ -775,7 +786,7 @@ c_db_odbc_get_fields_properties( USES_REGS1 ) {
if (!SQLCLOSECURSOR(hstmt2,"db_get_fields_properties"))
return FALSE;
if (!SQLFREESTMT(hstmt2,SQL_CLOSE,"db_get_fields_properties"))
if (!SQLFREEHANDLE(SQL_HANDLE_STMT, hstmt2, "db_get_fields_properties"))
return FALSE;
for (i=1;i<=num_fields;i++)
@ -816,9 +827,8 @@ c_db_odbc_get_fields_properties( USES_REGS1 ) {
if (!SQLCLOSECURSOR(hstmt,"db_get_fields_properties"))
return FALSE;
if (!SQLFREESTMT(hstmt,SQL_CLOSE,"db_get_fields_properties"))
if (!SQLFREEHANDLE(SQL_HANDLE_STMT, hstmt2, "db_get_fields_properties"))
return FALSE;
return TRUE;
}

7
configure vendored
View File

@ -9927,6 +9927,9 @@ mkdir -p packages/clib/maildrop
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/clpqr
mkdir -p packages/cplint
mkdir -p packages/cplint/approx
@ -10619,8 +10622,8 @@ esac
cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
# Files that config.status was made for.
config_files="`echo $ac_config_files`"
config_headers="`echo $ac_config_headers`"
config_files="$ac_config_files"
config_headers="$ac_config_headers"
_ACEOF

3
configure.in
View File

@ -2103,6 +2103,9 @@ mkdir -p packages/clib/maildrop
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/clpqr
mkdir -p packages/cplint
mkdir -p packages/cplint/approx

80
docs/yap.tex
View File

@ -16811,13 +16811,29 @@ only two boolean flags are accepted: @code{YAPC_ENABLE_GC} and
@code{YAPC_ENABLE_AGC}. The first enables/disables the standard garbage
collector, the second does the same for the atom garbage collector.`
@item @code{YAP_TERM} YAP_AllocExternalDataInStack(@code{size_t bytes})
@item @code{void *} YAP_ExternalDataInStackFromTerm(@code{YAP_Term t})
@item @code{YAP_Bool} YAP_IsExternalDataInStackTerm(@code{YAP_Term t})
@findex YAP_AllocExternalDataInStack (C-Interface function)
The next routines allow one to store external data in the Prolog
execution stack. The first routine reserves space for @var{sz} bytes
and returns an opaque handle. The second routines receives the handle
and returns a pointer to the data. The last routine checks if a term
is an opaque handle.
Data will be automatically reclaimed during
backtracking. Also, this storage is opaque to the Prolog garbage compiler,
so it should not be used to store Prolog terms. On the other hand, it
may be useful to store arrays in a compact way, or pointers to external objects.
@item @code{int} YAP_HaltRegisterHook(@code{YAP_halt_hook f, void *closure})
@findex YAP_HaltRegisterHook (C-Interface function)
Register the function @var{f} to be called if YAP is halted. The
function is called with two arguments: the exit code of the process (@code{0}
if this cannot be determined on your operating system) and the closure
argument @var{closure}.
function is called with two arguments: the exit code of the process
(@code{0} if this cannot be determined on your operating system) and
the closure argument @var{closure}.
@c See also @code{at_halt/1}.
@end table
@ -16850,6 +16866,7 @@ implementing the predicate and @var{arity} is its arity.
@findex YAP_UserBackCutCPredicate (C-Interface function)
@findex YAP_PRESERVE_DATA (C-Interface function)
@findex YAP_PRESERVED_DATA (C-Interface function)
@findex YAP_PRESERVED_DATA_CUT (C-Interface function)
@findex YAP_cutsucceed (C-Interface function)
@findex YAP_cutfail (C-Interface function)
For the second kind of predicates we need three C functions. The first one
@ -16915,11 +16932,15 @@ static int start_n100(void)
@end example
The routine starts by getting the dereference value of the argument.
The call to @code{YAP_PRESERVE_DATA} is used to initialize the memory which will
hold the information to be preserved across backtracking. The first
argument is the variable we shall use, and the second its type. Note
that we can only use @code{YAP_PRESERVE_DATA} once, so often we will
want the variable to be a structure.
The call to @code{YAP_PRESERVE_DATA} is used to initialize the memory
which will hold the information to be preserved across
backtracking. The first argument is the variable we shall use, and the
second its type. Note that we can only use @code{YAP_PRESERVE_DATA}
once, so often we will want the variable to be a structure. This data
is visible to the garbage collector, so it should consist of Prolog
terms, as in the example. It is also correct to store pointers to
objects external to YAP stacks, as the garbage collector will ignore
such references.
If the argument of the predicate is a variable, the routine initializes the
structure to be preserved across backtracking with the information
@ -16988,6 +17009,34 @@ when pruning the execution of the predicate, @var{arity} is the
predicate arity, and @var{sizeof} is the size of the data to be
preserved in the stack. In this example, we would have something like
@example
void
init_n100(void)
@{
YAP_UserBackCutCPredicate("n100", start_n100, continue_n100, cut_n100, 1, 1);
@}
@end example
The argument before last is the predicate's arity. Notice again the
last argument to the call. function argument gives the extra space we
want to use for @code{PRESERVED_DATA}. Space is given in cells, where
a cell is the same size as a pointer. The garbage collector has access
to this space, hence users should use it either to store terms or to
store pointers to objects outside the stacks.
The code for @code{cut_n100} could be:
@example
static int cut_n100(void)
@{
YAP_PRESERVED_DATA_CUT(n100_data,n100_data_type*);
fprintf("n100 cut with counter %ld\n", YAP_IntOfTerm(n100_data->next_solution));
return TRUE;
@}
@end example
Notice that we have to use @code{YAP_PRESERVED_DATA_CUT}: this is
because the Prolog engine is at a different state during cut.
If no work is required at cut, we can use:
@example
void
init_n100(void)
@ -16995,8 +17044,7 @@ init_n100(void)
YAP_UserBackCutCPredicate("n100", start_n100, continue_n100, NULL, 1, 1);
@}
@end example
Notice that we do not actually need to do anything on receiving a cut in
this case.
in this case no code is executed at cut time.
@node Loading Objects, Save&Rest, Writing C, C-Interface
@section Loading Object Files
@ -17272,9 +17320,9 @@ Associate the term @var{value} with the atom @var{at}. The term
@var{value} must be a constant. This functionality is used by YAP as a
simple way for controlling and communicating with the Prolog run-time.
@item @code{YAP_Term} YAP_Read(@code{int (*)(void)} @var{GetC})
@item @code{YAP_Term} YAP_Read(@code{IOSTREAM *Stream})
@findex YAP_Read/1
Parse a Term using the function @var{GetC} to input characters.
Parse a @var{Term} from the stream @var{Stream}.
@item @code{YAP_Term} YAP_Write(@code{YAP_Term} @var{t})
@findex YAP_CopyTerm/1
@ -17282,13 +17330,13 @@ Copy a Term @var{t} and all associated constraints. May call the garbage
collector and returns @code{0L} on error (such as no space being
available).
@item @code{void} YAP_Write(@code{YAP_Term} @var{t}, @code{void (*)(int)}
@var{PutC}, @code{int} @var{flags})
@item @code{void} YAP_Write(@code{YAP_Term} @var{t}, @code{IOSTREAM}
@var{stream}, @code{int} @var{flags})
@findex YAP_Write/3
Write a Term @var{t} using the function @var{PutC} to output
Write a Term @var{t} using the stream @var{stream} to output
characters. The term is written according to a mask of the following
flags in the @code{flag} argument: @code{YAP_WRITE_QUOTED},
@code{YAP_WRITE_HANDLE_VARS}, and @code{YAP_WRITE_IGNORE_OPS}.
@code{YAP_WRITE_HANDLE_VARS}, @code{YAP_WRITE_USE_PORTRAY}, and @code{YAP_WRITE_IGNORE_OPS}.
@item @code{void} YAP_WriteBuffer(@code{YAP_Term} @var{t}, @code{char *}
@var{buff}, @code{unsigned int}

17
include/YapInterface.h
View File

@ -237,7 +237,7 @@ extern X_API void PROTO(YAP_UserBackCPredicate,(CONST char *, YAP_Bool (*)(void)
/* void UserBackCPredicate(char *name, int *init(), int *cont(), int *cut(), int
arity, int extra) */
extern X_API void PROTO(YAP_UserBackCutCPredicate,(char *, YAP_Bool (*)(void), YAP_Bool (*)(void), YAP_Bool (*)(void), YAP_Arity, unsigned int));
extern X_API void PROTO(YAP_UserBackCutCPredicate,(CONST char *, YAP_Bool (*)(void), YAP_Bool (*)(void), YAP_Bool (*)(void), YAP_Arity, unsigned int));
/* void CallProlog(YAP_Term t) */
extern X_API YAP_Bool PROTO(YAP_CallProlog,(YAP_Term t));
@ -245,9 +245,9 @@ extern X_API YAP_Bool PROTO(YAP_CallProlog,(YAP_Term t));
/* void cut_fail(void) */
extern X_API void PROTO(YAP_cut_up,(void));
#define YAP_cut_succeed() { YAP_cut_up(); return TRUE; }
#define YAP_cut_succeed() do { YAP_cut_up(); return TRUE; } while(0)
#define YAP_cut_fail() { YAP_cut_up(); return FALSE; }
#define YAP_cut_fail() do { YAP_cut_up(); return FALSE; } while(0)
/* void *AllocSpaceFromYAP_(int) */
extern X_API void *PROTO(YAP_AllocSpaceFromYap,(unsigned int));
@ -555,6 +555,17 @@ extern X_API int PROTO(YAP_MaxOpPriority,(YAP_Atom, YAP_Term));
/* int YAP_OpInfo(Atom, Term, int, int *, int *) */
extern X_API int PROTO(YAP_OpInfo,(YAP_Atom, YAP_Term, int, int *, int *));
/* YAP_Bool YAP_IsExternalDataInStackTerm(YAP_Term) */
extern X_API YAP_Bool PROTO(YAP_IsExternalDataInStackTerm,(YAP_Term));
extern X_API YAP_opaque_tag_t PROTO(YAP_NewOpaqueType,(struct YAP_opaque_handler_struct *));
extern X_API YAP_Bool PROTO(YAP_IsOpaqueObjectTerm,(YAP_Term, YAP_opaque_tag_t));
extern X_API YAP_Term PROTO(YAP_NewOpaqueObject,(YAP_opaque_tag_t, size_t));
extern X_API void *PROTO(YAP_OpaqueObjectFromTerm,(YAP_Term));
#define YAP_InitCPred(N,A,F) YAP_UserCPredicate(N,F,A)
__END_DECLS

13
include/yap_structs.h
View File

@ -101,9 +101,10 @@ typedef double YAP_Float;
#define YAP_FULL_BOOT_FROM_PROLOG 4
#define YAP_BOOT_ERROR -1
#define YAP_WRITE_QUOTED 0
#define YAP_WRITE_HANDLE_VARS 1
#define YAP_WRITE_QUOTED 1
#define YAP_WRITE_IGNORE_OPS 2
#define YAP_WRITE_HANDLE_VARS 2
#define YAP_WRITE_USE_PORTRAY 8
#define YAP_CONSULT_MODE 0
#define YAP_RECONSULT_MODE 1
@ -204,6 +205,14 @@ typedef int (*YAP_agc_hook)(void *_Atom);
typedef void (*YAP_halt_hook)(int exit_code, void *closure);
typedef int YAP_opaque_tag_t;
typedef int (*YAP_Opaque_CallOnFail)(void *);
typedef struct YAP_opaque_handler_struct {
YAP_Opaque_CallOnFail fail_handler;
} YAP_opaque_handler_t;
/********* execution mode ***********************/
typedef enum

6
library/MYDDAS/myddas_prolog2sql.ypp
View File

@ -241,6 +241,8 @@ tokenize_arguments([FirstArg|RestArgs],[TokFirstArg|TokRestArgs]):-
%
% --------------------------------------------------------------------------------------
:- dynamic attribute/4.
query_generation([],_,[]).
query_generation([Conjunction|Conjunctions],ProjectionTerm,[Query|Queries]):-
@ -1157,9 +1159,9 @@ column_atom(att(RangeVar,Attribute),QueryList,Diff):-
column_atom(Attribute,X2,Diff).
column_atom(rel(Relation,RangeVar),QueryList,Diff):-
column_atom('`',QueryList,X0),
column_atom('',QueryList,X0),
column_atom(Relation,X0,X1),
column_atom('` ',X1,X2),
column_atom(' ',X1,X2),
column_atom(RangeVar,X2,Diff).
column_atom('$const$'(String),QueryList,Diff):-

10
library/lammpi/prologterms2c.c
View File

@ -142,12 +142,6 @@ p2c_putc(const int c) {
/*
* Function used by YAP to read a char from a string
*/
static int
p2c_getc(void) {
if( BUFFER_POS < BUFFER_LEN )
return BUFFER_PTR[BUFFER_POS++];
return -1;
}
/*
* Writes a term to a stream.
*/
@ -177,7 +171,7 @@ read_term_from_stream(const int fd) {
if ( size> BUFFER_SIZE)
expand_buffer(size-BUFFER_SIZE);
read(fd,BUFFER_PTR,size); // read term from stream
return YAP_Read( p2c_getc );
return YAP_ReadBuffer( BUFFER_PTR , NULL);
}
/*********************************************************************************************
* Conversion: Prolog Term->char[] and char[]->Prolog Term
@ -229,7 +223,7 @@ string2term(char *const ptr,const size_t *size) {
}
BUFFER_POS=0;
LOCAL_ErrorMessage=NULL;
t = YAP_Read(p2c_getc);
t = YAP_ReadBuffer( BUFFER_PTR , NULL );
if ( t==FALSE ) {
write_msg(__FUNCTION__,__FILE__,__LINE__,"FAILED string2term>>>>size:%d %d %s\n",BUFFER_SIZE,strlen(BUFFER_PTR),LOCAL_ErrorMessage);
exit(1);

16
library/mpi/mpi.c
View File

@ -30,7 +30,6 @@ static char *rcsid = "$Header: /Users/vitor/Yap/yap-cvsbackup/library/mpi/mpi.c,
#include <string.h>
#include <mpi.h>
Term STD_PROTO(YAP_Read, (int (*)(void)));
void STD_PROTO(YAP_Write, (Term, void (*)(int), int));
STATIC_PROTO (Int p_mpi_open, (void));
@ -105,15 +104,6 @@ mpi_putc(Int ch)
}
}
static Int
mpi_getc(void)
{
if( bufptr < bufsize ) return buf[bufptr++];
else return -1;
}
/*
* C Predicates
@ -301,7 +291,7 @@ p_mpi_receive() /* mpi_receive(-data, ?orig, ?tag) */
/* parse received string into a Prolog term */
bufptr = 0;
t = YAP_Read( mpi_getc );
t = YAP_ReadBuffer( buf, NULL );
if( t == TermNil ) {
retv = FALSE;
@ -384,7 +374,7 @@ p_mpi_bcast3() /* mpi_bcast( ?data, +root, +max_size ) */
bufptr = 0;
/* parse received string into a Prolog term */
return Yap_unify( YAP_Read(mpi_getc), ARG1 );
return Yap_unify( YAP_ReadBuffer( buf, NULL ), ARG1 );
}
}
@ -464,7 +454,7 @@ p_mpi_bcast2() /* mpi_bcast( ?data, +root ) */
bufstrlen = strlen(buf);
bufptr = 0;
return Yap_unify(YAP_Read( mpi_getc ), ARG1);
return Yap_unify(YAP_ReadBuffer( buf, NULL ), ARG1);
}
}

2
misc/GLOBALS
View File

@ -120,6 +120,8 @@ char* DIRNAME =NULL
char Executable[YAP_FILENAME_MAX] void
#endif
int OpaqueHandlersCount =0
struct opaque_handler_struct* OpaqueHandlers =NULL
#if __simplescalar__
char pwd[YAP_FILENAME_MAX] void

149
packages/CLPBN/clpbn/bp/BPNodeInfo.cpp Executable file
View File

@ -0,0 +1,149 @@
#include <cassert>
#include <cmath>
#include <iostream>
#include "BPNodeInfo.h"
#include "BPSolver.h"
BPNodeInfo::BPNodeInfo (BayesNode* node)
{
node_ = node;
ds_ = node->getDomainSize();
piValsCalc_ = false;
ldValsCalc_ = false;
nPiMsgsRcv_ = 0;
nLdMsgsRcv_ = 0;
piVals_.resize (ds_, 1);
ldVals_.resize (ds_, 1);
const BnNodeSet& childs = node->getChilds();
for (unsigned i = 0; i < childs.size(); i++) {
cmsgs_.insert (make_pair (childs[i], false));
}
const BnNodeSet& parents = node->getParents();
for (unsigned i = 0; i < parents.size(); i++) {
pmsgs_.insert (make_pair (parents[i], false));
}
}
ParamSet
BPNodeInfo::getBeliefs (void) const
{
double sum = 0.0;
ParamSet beliefs (ds_);
for (unsigned xi = 0; xi < ds_; xi++) {
double prod = piVals_[xi] * ldVals_[xi];
beliefs[xi] = prod;
sum += prod;
}
assert (sum);
//normalize the beliefs
for (unsigned xi = 0; xi < ds_; xi++) {
beliefs[xi] /= sum;
}
return beliefs;
}
bool
BPNodeInfo::readyToSendPiMsgTo (const BayesNode* child) const
{
for (unsigned i = 0; i < inChildLinks_.size(); i++) {
if (inChildLinks_[i]->getSource() != child
&& !inChildLinks_[i]->messageWasSended()) {
return false;
}
}
return true;
}
bool
BPNodeInfo::readyToSendLambdaMsgTo (const BayesNode* parent) const
{
for (unsigned i = 0; i < inParentLinks_.size(); i++) {
if (inParentLinks_[i]->getSource() != parent
&& !inParentLinks_[i]->messageWasSended()) {
return false;
}
}
return true;
}
double
BPNodeInfo::getPiValue (unsigned idx) const
{
assert (idx >=0 && idx < ds_);
return piVals_[idx];
}
void
BPNodeInfo::setPiValue (unsigned idx, Param value)
{
assert (idx >=0 && idx < ds_);
piVals_[idx] = value;
}
double
BPNodeInfo::getLambdaValue (unsigned idx) const
{
assert (idx >=0 && idx < ds_);
return ldVals_[idx];
}
void
BPNodeInfo::setLambdaValue (unsigned idx, Param value)
{
assert (idx >=0 && idx < ds_);
ldVals_[idx] = value;
}
double
BPNodeInfo::getBeliefChange (void)
{
double change = 0.0;
if (oldBeliefs_.size() == 0) {
oldBeliefs_ = getBeliefs();
change = 9999999999.0;
} else {
ParamSet currentBeliefs = getBeliefs();
for (unsigned xi = 0; xi < ds_; xi++) {
change += abs (currentBeliefs[xi] - oldBeliefs_[xi]);
}
oldBeliefs_ = currentBeliefs;
}
return change;
}
bool
BPNodeInfo::receivedBottomInfluence (void) const
{
// if all lambda values are equal, then neither
// this node neither its descendents have evidence,
// we can use this to don't send lambda messages his parents
bool childInfluenced = false;
for (unsigned xi = 1; xi < ds_; xi++) {
if (ldVals_[xi] != ldVals_[0]) {
childInfluenced = true;
break;
}
}
return childInfluenced;
}

82
packages/CLPBN/clpbn/bp/BPNodeInfo.h Executable file
View File

@ -0,0 +1,82 @@
#ifndef BP_BP_NODE_H
#define BP_BP_NODE_H
#include <vector>
#include <map>
#include "BPSolver.h"
#include "BayesNode.h"
#include "Shared.h"
//class Edge;
using namespace std;
class BPNodeInfo
{
public:
BPNodeInfo (int);
BPNodeInfo (BayesNode*);
ParamSet getBeliefs (void) const;
double getPiValue (unsigned) const;
void setPiValue (unsigned, Param);
double getLambdaValue (unsigned) const;
void setLambdaValue (unsigned, Param);
double getBeliefChange (void);
bool receivedBottomInfluence (void) const;
ParamSet& getPiValues (void) { return piVals_; }
ParamSet& getLambdaValues (void) { return ldVals_; }
bool arePiValuesCalculated (void) { return piValsCalc_; }
bool areLambdaValuesCalculated (void) { return ldValsCalc_; }
void markPiValuesAsCalculated (void) { piValsCalc_ = true; }
void markLambdaValuesAsCalculated (void) { ldValsCalc_ = true; }
void incNumPiMsgsRcv (void) { nPiMsgsRcv_ ++; }
void incNumLambdaMsgsRcv (void) { nLdMsgsRcv_ ++; }
bool receivedAllPiMessages (void)
{
return node_->getParents().size() == nPiMsgsRcv_;
}
bool receivedAllLambdaMessages (void)
{
return node_->getChilds().size() == nLdMsgsRcv_;
}
bool readyToSendPiMsgTo (const BayesNode*) const ;
bool readyToSendLambdaMsgTo (const BayesNode*) const;
CEdgeSet getIncomingParentLinks (void) { return inParentLinks_; }
CEdgeSet getIncomingChildLinks (void) { return inChildLinks_; }
CEdgeSet getOutcomingParentLinks (void) { return outParentLinks_; }
CEdgeSet getOutcomingChildLinks (void) { return outChildLinks_; }
void addIncomingParentLink (Edge* l) { inParentLinks_.push_back (l); }
void addIncomingChildLink (Edge* l) { inChildLinks_.push_back (l); }
void addOutcomingParentLink (Edge* l) { outParentLinks_.push_back (l); }
void addOutcomingChildLink (Edge* l) { outChildLinks_.push_back (l); }
private:
DISALLOW_COPY_AND_ASSIGN (BPNodeInfo);
ParamSet piVals_; // pi values
ParamSet ldVals_; // lambda values
ParamSet oldBeliefs_;
unsigned nPiMsgsRcv_;
unsigned nLdMsgsRcv_;
bool piValsCalc_;
bool ldValsCalc_;
EdgeSet inParentLinks_;
EdgeSet inChildLinks_;
EdgeSet outParentLinks_;
EdgeSet outChildLinks_;
unsigned ds_;
const BayesNode* node_;
map<const BayesNode*, bool> pmsgs_;
map<const BayesNode*, bool> cmsgs_;
};
#endif //BP_BP_NODE_H

884
packages/CLPBN/clpbn/bp/BPSolver.cpp
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File diff suppressed because it is too large Load Diff

514
packages/CLPBN/clpbn/bp/BPSolver.h
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@ -1,259 +1,106 @@
#ifndef BP_BPSOLVER_H
#define BP_BPSOLVER_H
#ifndef BP_BP_SOLVER_H
#define BP_BP_SOLVER_H
#include <vector>
#include <string>
#include <set>
#include "Solver.h"
#include "BayesNet.h"
#include "BpNode.h"
#include "BPNodeInfo.h"
#include "Shared.h"
using namespace std;
class BPSolver;
class BPNodeInfo;
static const string PI = "pi" ;
static const string LD = "ld" ;
enum MessageType {PI_MSG, LAMBDA_MSG};
class BPSolver;
struct Edge
enum MessageType {PI_MSG, LAMBDA_MSG};
enum JointCalcType {CHAIN_RULE, JUNCTION_NODE};
class Edge
{
public:
Edge (BayesNode* s, BayesNode* d, MessageType t)
{
source = s;
destination = d;
type = t;
source_ = s;
destin_ = d;
type_ = t;
if (type_ == PI_MSG) {
currMsg_.resize (s->getDomainSize(), 1);
nextMsg_.resize (s->getDomainSize(), 1);
} else {
currMsg_.resize (d->getDomainSize(), 1);
nextMsg_.resize (d->getDomainSize(), 1);
}
string getId (void) const
msgSended_ = false;
residual_ = 0.0;
}
//void setMessage (ParamSet msg)
//{
// Util::normalize (msg);
// residual_ = Util::getMaxNorm (currMsg_, msg);
// currMsg_ = msg;
//}
void setNextMessage (CParamSet msg)
{
stringstream ss;
type == PI_MSG ? ss << PI : ss << LD;
ss << source->getVarId() << "." << destination->getVarId();
return ss.str();
nextMsg_ = msg;
Util::normalize (nextMsg_);
residual_ = Util::getMaxNorm (currMsg_, nextMsg_);
}
void updateMessage (void)
{
currMsg_ = nextMsg_;
if (DL >= 3) {
cout << "updating " << toString() << endl;
}
msgSended_ = true;
}
void updateResidual (void)
{
residual_ = Util::getMaxNorm (currMsg_, nextMsg_);
}
string toString (void) const
{
stringstream ss;
type == PI_MSG ? ss << PI << "(" : ss << LD << "(" ;
ss << source->getLabel() << " --> " ;
ss << destination->getLabel();
ss << ")" ;
if (type_ == PI_MSG) {
ss << PI;
} else if (type_ == LAMBDA_MSG) {
ss << LD;
} else {
abort();
}
ss << "(" << source_->getLabel();
ss << " --> " << destin_->getLabel() << ")" ;
return ss.str();
}
BayesNode* source;
BayesNode* destination;
MessageType type;
static BPSolver* klass;
BayesNode* getSource (void) const { return source_; }
BayesNode* getDestination (void) const { return destin_; }
MessageType getMessageType (void) const { return type_; }
CParamSet getMessage (void) const { return currMsg_; }
bool messageWasSended (void) const { return msgSended_; }
double getResidual (void) const { return residual_; }
void clearResidual (void) { residual_ = 0.0; }
private:
BayesNode* source_;
BayesNode* destin_;
MessageType type_;
ParamSet currMsg_;
ParamSet nextMsg_;
bool msgSended_;
double residual_;
};
/*
class BPMessage
{
BPMessage (BayesNode* parent, BayesNode* child)
{
parent_ = parent;
child_ = child;
currPiMsg_.resize (child->getDomainSize(), 1);
currLdMsg_.resize (parent->getDomainSize(), 1);
nextLdMsg_.resize (parent->getDomainSize(), 1);
nextPiMsg_.resize (child->getDomainSize(), 1);
piResidual_ = 1.0;
ldResidual_ = 1.0;
}
Param getPiMessageValue (int idx) const
{
assert (idx >=0 && idx < child->getDomainSize());
return currPiMsg_[idx];
}
Param getLambdaMessageValue (int idx) const
{
assert (idx >=0 && idx < parent->getDomainSize());
return currLdMsg_[idx];
}
const ParamSet& getPiMessage (void) const
{
return currPiMsg_;
}
const ParamSet& getLambdaMessage (void) const
{
return currLdMsg_;
}
ParamSet& piNextMessageReference (void)
{
return nextPiMsg_;
}
ParamSet& lambdaNextMessageReference (const BayesNode* source)
{
return nextLdMsg_;
}
void updatePiMessage (void)
{
currPiMsg_ = nextPiMsg_;
Util::normalize (currPiMsg_);
}
void updateLambdaMessage (void)
{
currLdMsg_ = nextLdMsg_;
Util::normalize (currLdMsg_);
}
double getPiResidual (void)
{
return piResidual_;
}
double getLambdaResidual (void)
{
return ldResidual_;
}
void updatePiResidual (void)
{
piResidual_ = Util::getL1dist (currPiMsg_, nextPiMsg_);
}
void updateLambdaResidual (void)
{
ldResidual_ = Util::getL1dist (currLdMsg_, nextLdMsg_);
}
void clearPiResidual (void)
{
piResidual_ = 0.0;
}
void clearLambdaResidual (void)
{
ldResidual_ = 0.0;
}
BayesNode* parent_;
BayesNode* child_;
ParamSet currPiMsg_; // current pi messages
ParamSet currLdMsg_; // current lambda messages
ParamSet nextPiMsg_;
ParamSet nextLdMsg_;
Param piResidual_;
Param ldResidual_;
};
class NodeInfo
{
NodeInfo (BayesNode* node)
{
node_ = node;
piVals_.resize (node->getDomainSize(), 1);
ldVals_.resize (node->getDomainSize(), 1);
}
ParamSet getBeliefs (void) const
{
double sum = 0.0;
ParamSet beliefs (node_->getDomainSize());
for (int xi = 0; xi < node_->getDomainSize(); xi++) {
double prod = piVals_[xi] * ldVals_[xi];
beliefs[xi] = prod;
sum += prod;
}
assert (sum);
//normalize the beliefs
for (int xi = 0; xi < node_->getDomainSize(); xi++) {
beliefs[xi] /= sum;
}
return beliefs;
}
double getPiValue (int idx) const
{
assert (idx >=0 && idx < node_->getDomainSize());
return piVals_[idx];
}
void setPiValue (int idx, double value)
{
assert (idx >=0 && idx < node_->getDomainSize());
piVals_[idx] = value;
}
double getLambdaValue (int idx) const
{
assert (idx >=0 && idx < node_->getDomainSize());
return ldVals_[idx];
}
void setLambdaValue (int idx, double value)
{
assert (idx >=0 && idx < node_->getDomainSize());
ldVals_[idx] = value;
}
ParamSet& getPiValues (void)
{
return piVals_;
}
ParamSet& getLambdaValues (void)
{
return ldVals_;
}
double getBeliefChange (void)
{
double change = 0.0;
if (oldBeliefs_.size() == 0) {
oldBeliefs_ = getBeliefs();
change = MAX_CHANGE_;
} else {
ParamSet currentBeliefs = getBeliefs();
for (int xi = 0; xi < node_->getDomainSize(); xi++) {
change += abs (currentBeliefs[xi] - oldBeliefs_[xi]);
}
oldBeliefs_ = currentBeliefs;
}
return change;
}
bool hasReceivedChildInfluence (void) const
{
// if all lambda values are equal, then neither
// this node neither its descendents have evidence,
// we can use this to don't send lambda messages his parents
bool childInfluenced = false;
for (int xi = 1; xi < node_->getDomainSize(); xi++) {
if (ldVals_[xi] != ldVals_[0]) {
childInfluenced = true;
break;
}
}
return childInfluenced;
}
BayesNode* node_;
ParamSet piVals_; // pi values
ParamSet ldVals_; // lambda values
ParamSet oldBeliefs_;
};
*/
bool compareResidual (const Edge&, const Edge&);
class BPSolver : public Solver
{
public:
@ -261,190 +108,85 @@ class BPSolver : public Solver
~BPSolver (void);
void runSolver (void);
ParamSet getPosterioriOf (const Variable* var) const;
ParamSet getJointDistribution (const NodeSet&) const;
ParamSet getPosterioriOf (Vid) const;
ParamSet getJointDistributionOf (const VidSet&);
private:
DISALLOW_COPY_AND_ASSIGN (BPSolver);
void initializeSolver (void);
void incorporateEvidence (BayesNode*);
void runPolyTreeSolver (void);
void polyTreePiMessage (BayesNode*, BayesNode*);
void polyTreeLambdaMessage (BayesNode*, BayesNode*);
void runGenericSolver (void);
void runLoopySolver (void);
void maxResidualSchedule (void);
bool converged (void) const;
void updatePiValues (BayesNode*);
void updateLambdaValues (BayesNode*);
void calculateNextPiMessage (BayesNode*, BayesNode*);
void calculateNextLambdaMessage (BayesNode*, BayesNode*);
ParamSet calculateNextLambdaMessage (Edge* edge);
ParamSet calculateNextPiMessage (Edge* edge);
ParamSet getJointByJunctionNode (const VidSet&) const;
ParamSet getJointByChainRule (const VidSet&) const;
void printMessageStatusOf (const BayesNode*) const;
void printAllMessageStatus (void) const;
// inlines
void updatePiMessage (BayesNode*, BayesNode*);
void updateLambdaMessage (BayesNode*, BayesNode*);
void calculateNextMessage (const Edge&);
void updateMessage (const Edge&);
void updateValues (const Edge&);
double getResidual (const Edge&) const;
void updateResidual (const Edge&);
void clearResidual (const Edge&);
BpNode* M (const BayesNode*) const;
friend bool compareResidual (const Edge&, const Edge&);
ParamSet getMessage (Edge* edge)
{
if (DL >= 3) {
cout << " calculating " << edge->toString() << endl;
}
if (edge->getMessageType() == PI_MSG) {
return calculateNextPiMessage (edge);
} else if (edge->getMessageType() == LAMBDA_MSG) {
return calculateNextLambdaMessage (edge);
} else {
abort();
}
return ParamSet();
}
void updateValues (Edge* edge)
{
if (!edge->getDestination()->hasEvidence()) {
if (edge->getMessageType() == PI_MSG) {
updatePiValues (edge->getDestination());
} else if (edge->getMessageType() == LAMBDA_MSG) {
updateLambdaValues (edge->getDestination());
} else {
abort();
}
}
}
BPNodeInfo* M (const BayesNode* node) const
{
assert (node);
assert (node == bn_->getBayesNode (node->getVarId()));
assert (node->getIndex() < nodesI_.size());
return nodesI_[node->getIndex()];
}
const BayesNet* bn_;
vector<BpNode*> msgs_;
Schedule schedule_;
int nIter_;
int maxIter_;
double accuracy_;
vector<Edge> updateOrder_;
bool forceGenericSolver_;
vector<BPNodeInfo*> nodesI_;
unsigned nIter_;
vector<Edge*> links_;
bool useAlwaysLoopySolver_;
JointCalcType jointCalcType_;
struct compare
{
inline bool operator() (const Edge& e1, const Edge& e2)
inline bool operator() (const Edge* e1, const Edge* e2)
{
return compareResidual (e1, e2);
return e1->getResidual() > e2->getResidual();
}
};
typedef multiset<Edge, compare> SortedOrder;
typedef multiset<Edge*, compare> SortedOrder;
SortedOrder sortedOrder_;
typedef unordered_map<string, SortedOrder::iterator> EdgeMap;
typedef map<Edge*, SortedOrder::iterator> EdgeMap;
EdgeMap edgeMap_;
};
inline void
BPSolver::updatePiMessage (BayesNode* source, BayesNode* destination)
{
M(source)->updatePiMessage(destination);
}
inline void
BPSolver::updateLambdaMessage (BayesNode* source, BayesNode* destination)
{
M(destination)->updateLambdaMessage(source);
}
inline void
BPSolver::calculateNextMessage (const Edge& e)
{
if (DL >= 1) {
cout << "calculating " << e.toString() << endl;
}
if (e.type == PI_MSG) {
calculateNextPiMessage (e.source, e.destination);
} else {
calculateNextLambdaMessage (e.source, e.destination);
}
}
inline void
BPSolver::updateMessage (const Edge& e)
{
if (DL >= 1) {
cout << "updating " << e.toString() << endl;
}
if (e.type == PI_MSG) {
M(e.source)->updatePiMessage(e.destination);
} else {
M(e.destination)->updateLambdaMessage(e.source);
}
}
inline void
BPSolver::updateValues (const Edge& e)
{
if (!e.destination->hasEvidence()) {
if (e.type == PI_MSG) {
updatePiValues (e.destination);
} else {
updateLambdaValues (e.destination);
}
}
}
inline double
BPSolver::getResidual (const Edge& e) const
{
if (e.type == PI_MSG) {
return M(e.source)->getPiResidual(e.destination);
} else {
return M(e.destination)->getLambdaResidual(e.source);
}
}
inline void
BPSolver::updateResidual (const Edge& e)
{
if (e.type == PI_MSG) {
M(e.source)->updatePiResidual(e.destination);
} else {
M(e.destination)->updateLambdaResidual(e.source);
}
}
inline void
BPSolver::clearResidual (const Edge& e)
{
if (e.type == PI_MSG) {
M(e.source)->clearPiResidual(e.destination);
} else {
M(e.destination)->clearLambdaResidual(e.source);
}
}
inline bool
compareResidual (const Edge& e1, const Edge& e2)
{
double residual1;
double residual2;
if (e1.type == PI_MSG) {
residual1 = Edge::klass->M(e1.source)->getPiResidual(e1.destination);
} else {
residual1 = Edge::klass->M(e1.destination)->getLambdaResidual(e1.source);
}
if (e2.type == PI_MSG) {
residual2 = Edge::klass->M(e2.source)->getPiResidual(e2.destination);
} else {
residual2 = Edge::klass->M(e2.destination)->getLambdaResidual(e2.source);
}
return residual1 > residual2;
}
inline BpNode*
BPSolver::M (const BayesNode* node) const
{
assert (node);
assert (node == bn_->getNode (node->getVarId()));
assert (node->getIndex() < msgs_.size());
return msgs_[node->getIndex()];
}
#endif
#endif //BP_BP_SOLVER_H

338
packages/CLPBN/clpbn/bp/BayesNet.cpp
View File

@ -1,30 +1,24 @@
#include <cstdlib>
#include <cassert>
#include <iostream>
#include <fstream>
#include <sstream>
#include <iomanip>
#include <cassert>
#include <cstdlib>
#include <map>
#include "xmlParser/xmlParser.h"
#include "BayesNet.h"
BayesNet::BayesNet (void)
{
}
BayesNet::BayesNet (const char* fileName)
{
map<string, Domain> domains;
XMLNode xMainNode = XMLNode::openFileHelper (fileName, "BIF");
// only the first network is parsed, others are ignored
XMLNode xNode = xMainNode.getChildNode ("NETWORK");
int nVars = xNode.nChildNode ("VARIABLE");
for (int i = 0; i < nVars; i++) {
unsigned nVars = xNode.nChildNode ("VARIABLE");
for (unsigned i = 0; i < nVars; i++) {
XMLNode var = xNode.getChildNode ("VARIABLE", i);
string type = var.getAttribute ("TYPE");
if (type != "nature") {
@ -32,9 +26,9 @@ BayesNet::BayesNet (const char* fileName)
abort();
}
Domain domain;
string label = var.getChildNode("NAME").getText();
int domainSize = var.nChildNode ("OUTCOME");
for (int j = 0; j < domainSize; j++) {
string varLabel = var.getChildNode("NAME").getText();
unsigned dsize = var.nChildNode ("OUTCOME");
for (unsigned j = 0; j < dsize; j++) {
if (var.getChildNode("OUTCOME", j).getText() == 0) {
stringstream ss;
ss << j + 1;
@ -43,37 +37,37 @@ BayesNet::BayesNet (const char* fileName)
domain.push_back (var.getChildNode("OUTCOME", j).getText());
}
}
domains.insert (make_pair (label, domain));
domains.insert (make_pair (varLabel, domain));
}
int nDefs = xNode.nChildNode ("DEFINITION");
unsigned nDefs = xNode.nChildNode ("DEFINITION");
if (nVars != nDefs) {
cerr << "error: different number of variables and definitions";
cerr << endl;
cerr << "error: different number of variables and definitions" << endl;
abort();
}
queue<int> indexes;
for (int i = 0; i < nDefs; i++) {
queue<unsigned> indexes;
for (unsigned i = 0; i < nDefs; i++) {
indexes.push (i);
}
while (!indexes.empty()) {
int index = indexes.front();
unsigned index = indexes.front();
indexes.pop();
XMLNode def = xNode.getChildNode ("DEFINITION", index);
string label = def.getChildNode("FOR").getText();
string varLabel = def.getChildNode("FOR").getText();
map<string, Domain>::const_iterator iter;
iter = domains.find (label);
iter = domains.find (varLabel);
if (iter == domains.end()) {
cerr << "error: unknow variable `" << label << "'" << endl;
cerr << "error: unknow variable `" << varLabel << "'" << endl;
abort();
}
bool processItLatter = false;
NodeSet parents;
int nParams = iter->second.size();
BnNodeSet parents;
unsigned nParams = iter->second.size();
for (int j = 0; j < def.nChildNode ("GIVEN"); j++) {
string parentLabel = def.getChildNode("GIVEN", j).getText();
BayesNode* parentNode = getNode (parentLabel);
BayesNode* parentNode = getBayesNode (parentLabel);
if (parentNode) {
nParams *= parentNode->getDomainSize();
parents.push_back (parentNode);
@ -95,7 +89,7 @@ BayesNet::BayesNet (const char* fileName)
}
if (!processItLatter) {
int count = 0;
unsigned count = 0;
ParamSet params (nParams);
stringstream s (def.getChildNode("TABLE").getText());
while (!s.eof() && count < nParams) {
@ -104,11 +98,11 @@ BayesNet::BayesNet (const char* fileName)
}
if (count != nParams) {
cerr << "error: invalid number of parameters " ;
cerr << "for variable `" << label << "'" << endl;
cerr << "for variable `" << varLabel << "'" << endl;
abort();
}
params = reorderParameters (params, iter->second.size());
addNode (label, iter->second, parents, params);
addNode (varLabel, iter->second, parents, params);
}
}
setIndexes();
@ -118,7 +112,6 @@ BayesNet::BayesNet (const char* fileName)
BayesNet::~BayesNet (void)
{
Statistics::writeStats();
for (unsigned i = 0; i < nodes_.size(); i++) {
delete nodes_[i];
}
@ -127,25 +120,25 @@ BayesNet::~BayesNet (void)
BayesNode*
BayesNet::addNode (unsigned varId)
BayesNet::addNode (Vid vid)
{
indexMap_.insert (make_pair (varId, nodes_.size()));
nodes_.push_back (new BayesNode (varId));
indexMap_.insert (make_pair (vid, nodes_.size()));
nodes_.push_back (new BayesNode (vid));
return nodes_.back();
}
BayesNode*
BayesNet::addNode (unsigned varId,
BayesNet::addNode (Vid vid,
unsigned dsize,
int evidence,
NodeSet& parents,
BnNodeSet& parents,
Distribution* dist)
{
indexMap_.insert (make_pair (varId, nodes_.size()));
indexMap_.insert (make_pair (vid, nodes_.size()));
nodes_.push_back (new BayesNode (
varId, dsize, evidence, parents, dist));
vid, dsize, evidence, parents, dist));
return nodes_.back();
}
@ -154,7 +147,7 @@ BayesNet::addNode (unsigned varId,
BayesNode*
BayesNet::addNode (string label,
Domain domain,
NodeSet& parents,
BnNodeSet& parents,
ParamSet& params)
{
indexMap_.insert (make_pair (nodes_.size(), nodes_.size()));
@ -169,9 +162,9 @@ BayesNet::addNode (string label,
BayesNode*
BayesNet::getNode (unsigned varId) const
BayesNet::getBayesNode (Vid vid) const
{
IndexMap::const_iterator it = indexMap_.find(varId);
IndexMap::const_iterator it = indexMap_.find (vid);
if (it == indexMap_.end()) {
return 0;
} else {
@ -182,7 +175,7 @@ BayesNet::getNode (unsigned varId) const
BayesNode*
BayesNet::getNode (string label) const
BayesNet::getBayesNode (string label) const
{
BayesNode* node = 0;
for (unsigned i = 0; i < nodes_.size(); i++) {
@ -196,6 +189,15 @@ BayesNet::getNode (string label) const
Variable*
BayesNet::getVariable (Vid vid) const
{
return getBayesNode (vid);
}
void
BayesNet::addDistribution (Distribution* dist)
{
@ -219,15 +221,15 @@ BayesNet::getDistribution (unsigned distId) const
const NodeSet&
BayesNet::getNodes (void) const
const BnNodeSet&
BayesNet::getBayesNodes (void) const
{
return nodes_;
}
int
unsigned
BayesNet::getNumberOfNodes (void) const
{
return nodes_.size();
@ -235,10 +237,10 @@ BayesNet::getNumberOfNodes (void) const
NodeSet
BnNodeSet
BayesNet::getRootNodes (void) const
{
NodeSet roots;
BnNodeSet roots;
for (unsigned i = 0; i < nodes_.size(); i++) {
if (nodes_[i]->isRoot()) {
roots.push_back (nodes_[i]);
@ -249,10 +251,10 @@ BayesNet::getRootNodes (void) const
NodeSet
BnNodeSet
BayesNet::getLeafNodes (void) const
{
NodeSet leafs;
BnNodeSet leafs;
for (unsigned i = 0; i < nodes_.size(); i++) {
if (nodes_[i]->isLeaf()) {
leafs.push_back (nodes_[i]);
@ -276,30 +278,32 @@ BayesNet::getVariables (void) const
BayesNet*
BayesNet::pruneNetwork (BayesNode* queryNode) const
BayesNet::getMinimalRequesiteNetwork (Vid vid) const
{
NodeSet queryNodes;
queryNodes.push_back (queryNode);
return pruneNetwork (queryNodes);
return getMinimalRequesiteNetwork (VidSet() = {vid});
}
BayesNet*
BayesNet::pruneNetwork (const NodeSet& interestedVars) const
BayesNet::getMinimalRequesiteNetwork (const VidSet& queryVids) const
{
/*
cout << "interested vars: " ;
for (unsigned i = 0; i < interestedVars.size(); i++) {
cout << interestedVars[i]->getLabel() << " " ;
BnNodeSet queryVars;
for (unsigned i = 0; i < queryVids.size(); i++) {
assert (getBayesNode (queryVids[i]));
queryVars.push_back (getBayesNode (queryVids[i]));
}
cout << endl;
*/
// cout << "query vars: " ;
// for (unsigned i = 0; i < queryVars.size(); i++) {
// cout << queryVars[i]->getLabel() << " " ;
// }
// cout << endl;
vector<StateInfo*> states (nodes_.size(), 0);
Scheduling scheduling;
for (NodeSet::const_iterator it = interestedVars.begin();
it != interestedVars.end(); it++) {
for (BnNodeSet::const_iterator it = queryVars.begin();
it != queryVars.end(); it++) {
scheduling.push (ScheduleInfo (*it, false, true));
}
@ -378,18 +382,18 @@ BayesNet::constructGraph (BayesNet* bn,
states[i]->markedOnTop;
}
if (isRequired) {
NodeSet parents;
BnNodeSet parents;
if (states[i]->markedOnTop) {
const NodeSet& ps = nodes_[i]->getParents();
const BnNodeSet& ps = nodes_[i]->getParents();
for (unsigned j = 0; j < ps.size(); j++) {
BayesNode* parent = bn->getNode (ps[j]->getVarId());
BayesNode* parent = bn->getBayesNode (ps[j]->getVarId());
if (!parent) {
parent = bn->addNode (ps[j]->getVarId());
}
parents.push_back (parent);
}
}
BayesNode* node = bn->getNode (nodes_[i]->getVarId());
BayesNode* node = bn->getBayesNode (nodes_[i]->getVarId());
if (node) {
node->setData (nodes_[i]->getDomainSize(),
nodes_[i]->getEvidence(), parents,
@ -411,65 +415,6 @@ BayesNet::constructGraph (BayesNet* bn,
bn->setIndexes();
}
/*
void
BayesNet::constructGraph (BayesNet* bn,
const vector<StateInfo*>& states) const
{
for (unsigned i = 0; i < nodes_.size(); i++) {
if (states[i]) {
if (nodes_[i]->hasEvidence() && states[i]->visited) {
NodeSet parents;
if (states[i]->markedOnTop) {
const NodeSet& ps = nodes_[i]->getParents();
for (unsigned j = 0; j < ps.size(); j++) {
BayesNode* parent = bn->getNode (ps[j]->getVarId());
if (parent == 0) {
parent = bn->addNode (ps[j]->getVarId());
}
parents.push_back (parent);
}
}
BayesNode* n = bn->getNode (nodes_[i]->getVarId());
if (n) {
n->setData (nodes_[i]->getDomainSize(),
nodes_[i]->getEvidence(), parents,
nodes_[i]->getDistribution());
} else {
bn->addNode (nodes_[i]->getVarId(),
nodes_[i]->getDomainSize(),
nodes_[i]->getEvidence(), parents,
nodes_[i]->getDistribution());
}
} else if (states[i]->markedOnTop) {
NodeSet parents;
const NodeSet& ps = nodes_[i]->getParents();
for (unsigned j = 0; j < ps.size(); j++) {
BayesNode* parent = bn->getNode (ps[j]->getVarId());
if (parent == 0) {
parent = bn->addNode (ps[j]->getVarId());
}
parents.push_back (parent);
}
BayesNode* n = bn->getNode (nodes_[i]->getVarId());
if (n) {
n->setData (nodes_[i]->getDomainSize(),
nodes_[i]->getEvidence(), parents,
nodes_[i]->getDistribution());
} else {
bn->addNode (nodes_[i]->getVarId(),
nodes_[i]->getDomainSize(),
nodes_[i]->getEvidence(), parents,
nodes_[i]->getDistribution());
}
}
}
}
}*/
bool
@ -480,70 +425,6 @@ BayesNet::isSingleConnected (void) const
vector<DomainConf>
BayesNet::getDomainConfigurationsOf (const NodeSet& nodes)
{
int nConfs = 1;
for (unsigned i = 0; i < nodes.size(); i++) {
nConfs *= nodes[i]->getDomainSize();
}
vector<DomainConf> confs (nConfs);
for (int i = 0; i < nConfs; i++) {
confs[i].resize (nodes.size());
}
int nReps = 1;
for (int i = nodes.size() - 1; i >= 0; i--) {
int index = 0;
while (index < nConfs) {
for (int j = 0; j < nodes[i]->getDomainSize(); j++) {
for (int r = 0; r < nReps; r++) {
confs[index][i] = j;
index++;
}
}
}
nReps *= nodes[i]->getDomainSize();
}
return confs;
}
vector<string>
BayesNet::getInstantiations (const NodeSet& parents_)
{
int nParents = parents_.size();
int rowSize = 1;
for (unsigned i = 0; i < parents_.size(); i++) {
rowSize *= parents_[i]->getDomainSize();
}
int nReps = 1;
vector<string> headers (rowSize);
for (int i = nParents - 1; i >= 0; i--) {
Domain domain = parents_[i]->getDomain();
int index = 0;
while (index < rowSize) {
for (int j = 0; j < parents_[i]->getDomainSize(); j++) {
for (int r = 0; r < nReps; r++) {
if (headers[index] != "") {
headers[index] = domain[j] + "," + headers[index];
} else {
headers[index] = domain[j];
}
index++;
}
}
}
nReps *= parents_[i]->getDomainSize();
}
return headers;
}
void
BayesNet::setIndexes (void)
{
@ -565,7 +446,7 @@ BayesNet::freeDistributions (void)
void
BayesNet::printNetwork (void) const
BayesNet::printGraphicalModel (void) const
{
for (unsigned i = 0; i < nodes_.size(); i++) {
cout << *nodes_[i];
@ -575,32 +456,11 @@ BayesNet::printNetwork (void) const
void
BayesNet::printNetworkToFile (const char* fileName) const
{
string s = "../../" ;
s += fileName;
ofstream out (s.c_str());
if (!out.is_open()) {
cerr << "error: cannot open file to write at " ;
cerr << "BayesNet::printToFile()" << endl;
abort();
}
for (unsigned i = 0; i < nodes_.size(); i++) {
out << *nodes_[i];
}
out.close();
}
void
BayesNet::exportToDotFile (const char* fileName,
BayesNet::exportToDotFormat (const char* fileName,
bool showNeighborless,
const NodeSet& highlightNodes) const
CVidSet& highlightVids) const
{
string s = "../../" ;
s+= fileName;
ofstream out (s.c_str());
ofstream out (fileName);
if (!out.is_open()) {
cerr << "error: cannot open file to write at " ;
cerr << "BayesNet::exportToDotFile()" << endl;
@ -608,13 +468,6 @@ BayesNet::exportToDotFile (const char* fileName,
}
out << "digraph \"" << fileName << "\" {" << endl;
for (unsigned i = 0; i < nodes_.size(); i++) {
const NodeSet& childs = nodes_[i]->getChilds();
for (unsigned j = 0; j < childs.size(); j++) {
out << '"' << nodes_[i]->getLabel() << '"' << " -> " ;
out << '"' << childs[j]->getLabel() << '"' << endl;
}
}
for (unsigned i = 0; i < nodes_.size(); i++) {
if (showNeighborless || nodes_[i]->hasNeighbors()) {
@ -627,9 +480,24 @@ BayesNet::exportToDotFile (const char* fileName,
}
}
for (unsigned i = 0; i < highlightNodes.size(); i++) {
out << '"' << highlightNodes[i]->getLabel() << '"' ;
out << " [shape=box]" << endl;
for (unsigned i = 0; i < highlightVids.size(); i++) {
BayesNode* node = getBayesNode (highlightVids[i]);
if (node) {
out << '"' << node->getLabel() << '"' ;
// out << " [shape=polygon, sides=6]" << endl;
out << " [shape=box3d]" << endl;
} else {
cout << "error: invalid variable id: " << highlightVids[i] << endl;
abort();
}
}
for (unsigned i = 0; i < nodes_.size(); i++) {
const BnNodeSet& childs = nodes_[i]->getChilds();
for (unsigned j = 0; j < childs.size(); j++) {
out << '"' << nodes_[i]->getLabel() << '"' << " -> " ;
out << '"' << childs[j]->getLabel() << '"' << endl;
}
}
out << "}" << endl;
@ -639,11 +507,9 @@ BayesNet::exportToDotFile (const char* fileName,
void
BayesNet::exportToBifFile (const char* fileName) const
BayesNet::exportToBifFormat (const char* fileName) const
{
string s = "../../" ;
s += fileName;
ofstream out (s.c_str());
ofstream out (fileName);
if(!out.is_open()) {
cerr << "error: cannot open file to write at " ;
cerr << "BayesNet::exportToBifFile()" << endl;
@ -666,7 +532,7 @@ BayesNet::exportToBifFile (const char* fileName) const
for (unsigned i = 0; i < nodes_.size(); i++) {
out << "<DEFINITION>" << endl;
out << "\t<FOR>" << nodes_[i]->getLabel() << "</FOR>" << endl;
const NodeSet& parents = nodes_[i]->getParents();
const BnNodeSet& parents = nodes_[i]->getParents();
for (unsigned j = 0; j < parents.size(); j++) {
out << "\t<GIVEN>" << parents[j]->getLabel();
out << "</GIVEN>" << endl;
@ -731,8 +597,8 @@ vector<int>
BayesNet::getAdjacentNodes (int v) const
{
vector<int> adjacencies;
const NodeSet& parents = nodes_[v]->getParents();
const NodeSet& childs = nodes_[v]->getChilds();
const BnNodeSet& parents = nodes_[v]->getParents();
const BnNodeSet& childs = nodes_[v]->getChilds();
for (unsigned i = 0; i < parents.size(); i++) {
adjacencies.push_back (parents[i]->getIndex());
}
@ -745,8 +611,8 @@ BayesNet::getAdjacentNodes (int v) const
ParamSet
BayesNet::reorderParameters (const ParamSet& params,
int domainSize) const
BayesNet::reorderParameters (CParamSet params,
unsigned domainSize) const
{
// the interchange format for bayesian networks keeps the probabilities
// in the following order:
@ -773,15 +639,15 @@ BayesNet::reorderParameters (const ParamSet& params,
ParamSet
BayesNet::revertParameterReorder (const ParamSet& params,
int domainSize) const
BayesNet::revertParameterReorder (CParamSet params,
unsigned domainSize) const
{
unsigned count = 0;
unsigned rowSize = params.size() / domainSize;
ParamSet reordered;
while (reordered.size() < params.size()) {
unsigned idx = count;
for (int i = 0; i < domainSize; i++) {
for (unsigned i = 0; i < domainSize; i++) {
reordered.push_back (params[idx]);
idx += rowSize;
}

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

@ -4,8 +4,6 @@
#include <vector>
#include <queue>
#include <list>
#include <string>
#include <unordered_map>
#include <map>
#include "GraphicalModel.h"
@ -46,42 +44,42 @@ struct StateInfo
typedef vector<Distribution*> DistSet;
typedef queue<ScheduleInfo, list<ScheduleInfo> > Scheduling;
typedef unordered_map<unsigned, unsigned> Histogram;
typedef unordered_map<unsigned, double> Times;
typedef map<unsigned, unsigned> Histogram;
typedef map<unsigned, double> Times;
class BayesNet : public GraphicalModel
{
public:
BayesNet (void);
BayesNet (void) {};
BayesNet (const char*);
~BayesNet (void);
BayesNode* addNode (unsigned);
BayesNode* addNode (unsigned, unsigned, int, NodeSet&, Distribution*);
BayesNode* addNode (string, Domain, NodeSet&, ParamSet&);
BayesNode* getNode (unsigned) const;
BayesNode* getNode (string) const;
BayesNode* addNode (unsigned, unsigned, int, BnNodeSet&,
Distribution*);
BayesNode* addNode (string, Domain, BnNodeSet&, ParamSet&);
BayesNode* getBayesNode (Vid) const;
BayesNode* getBayesNode (string) const;
Variable* getVariable (Vid) const;
void addDistribution (Distribution*);
Distribution* getDistribution (unsigned) const;
const NodeSet& getNodes (void) const;
int getNumberOfNodes (void) const;
NodeSet getRootNodes (void) const;
NodeSet getLeafNodes (void) const;
const BnNodeSet& getBayesNodes (void) const;
unsigned getNumberOfNodes (void) const;
BnNodeSet getRootNodes (void) const;
BnNodeSet getLeafNodes (void) const;
VarSet getVariables (void) const;
BayesNet* pruneNetwork (BayesNode*) const;
BayesNet* pruneNetwork (const NodeSet& queryNodes) const;
void constructGraph (BayesNet*, const vector<StateInfo*>&) const;
BayesNet* getMinimalRequesiteNetwork (Vid) const;
BayesNet* getMinimalRequesiteNetwork (const VidSet&) const;
void constructGraph (BayesNet*,
const vector<StateInfo*>&) const;
bool isSingleConnected (void) const;
static vector<DomainConf> getDomainConfigurationsOf (const NodeSet&);
static vector<string> getInstantiations (const NodeSet& nodes);
void setIndexes (void);
void freeDistributions (void);
void printNetwork (void) const;
void printNetworkToFile (const char*) const;
void exportToDotFile (const char*, bool = true,
const NodeSet& = NodeSet()) const;
void exportToBifFile (const char*) const;
void printGraphicalModel (void) const;
void exportToDotFormat (const char*, bool = true,
CVidSet = VidSet()) const;
void exportToBifFormat (const char*) const;
static Histogram histogram_;
static Times times_;
@ -93,12 +91,12 @@ class BayesNet : public GraphicalModel
bool containsUndirectedCycle (int, int,
vector<bool>&)const;
vector<int> getAdjacentNodes (int) const ;
ParamSet reorderParameters (const ParamSet&, int) const;
ParamSet revertParameterReorder (const ParamSet&, int) const;
ParamSet reorderParameters (CParamSet, unsigned) const;
ParamSet revertParameterReorder (CParamSet, unsigned) const;
void scheduleParents (const BayesNode*, Scheduling&) const;
void scheduleChilds (const BayesNode*, Scheduling&) const;
NodeSet nodes_;
BnNodeSet nodes_;
DistSet dists_;
IndexMap indexMap_;
};
@ -108,8 +106,8 @@ class BayesNet : public GraphicalModel
inline void
BayesNet::scheduleParents (const BayesNode* n, Scheduling& sch) const
{
const NodeSet& ps = n->getParents();
for (NodeSet::const_iterator it = ps.begin(); it != ps.end(); it++) {
const BnNodeSet& ps = n->getParents();
for (BnNodeSet::const_iterator it = ps.begin(); it != ps.end(); it++) {
sch.push (ScheduleInfo (*it, false, true));
}
}
@ -119,11 +117,11 @@ BayesNet::scheduleParents (const BayesNode* n, Scheduling& sch) const
inline void
BayesNet::scheduleChilds (const BayesNode* n, Scheduling& sch) const
{
const NodeSet& cs = n->getChilds();
for (NodeSet::const_iterator it = cs.begin(); it != cs.end(); it++) {
const BnNodeSet& cs = n->getChilds();
for (BnNodeSet::const_iterator it = cs.begin(); it != cs.end(); it++) {
sch.push (ScheduleInfo (*it, true, false));
}
}
#endif
#endif //BP_BAYES_NET_H

62
packages/CLPBN/clpbn/bp/BayesNode.cpp
View File

@ -1,23 +1,18 @@
#include <cstdlib>
#include <cassert>
#include <iostream>
#include <sstream>
#include <iomanip>
#include <cassert>
#include <cstdlib>
#include "BayesNode.h"
BayesNode::BayesNode (unsigned varId) : Variable (varId)
{
}
BayesNode::BayesNode (unsigned varId,
BayesNode::BayesNode (Vid vid,
unsigned dsize,
int evidence,
const NodeSet& parents,
Distribution* dist) : Variable(varId, dsize, evidence)
const BnNodeSet& parents,
Distribution* dist) : Variable (vid, dsize, evidence)
{
parents_ = parents;
dist_ = dist;
@ -28,13 +23,13 @@ BayesNode::BayesNode (unsigned varId,
BayesNode::BayesNode (unsigned varId,
BayesNode::BayesNode (Vid vid,
string label,
const Domain& domain,
const NodeSet& parents,
Distribution* dist) : Variable(varId, domain)
const BnNodeSet& parents,
Distribution* dist) : Variable (vid, domain,
NO_EVIDENCE, label)
{
label_ = new string (label);
parents_ = parents;
dist_ = dist;
for (unsigned int i = 0; i < parents.size(); i++) {
@ -47,11 +42,11 @@ BayesNode::BayesNode (unsigned varId,
void
BayesNode::setData (unsigned dsize,
int evidence,
const NodeSet& parents,
const BnNodeSet& parents,
Distribution* dist)
{
setDomainSize (dsize);
evidence_ = evidence;
setEvidence (evidence);
parents_ = parents;
dist_ = dist;
for (unsigned int i = 0; i < parents.size(); i++) {
@ -135,19 +130,18 @@ BayesNode::getCptEntries (void)
{
if (dist_->entries.size() == 0) {
unsigned rowSize = getRowSize();
unsigned nParents = parents_.size();
vector<DomainConf> confs (rowSize);
vector<DConf> confs (rowSize);
for (unsigned i = 0; i < rowSize; i++) {
confs[i].resize (nParents);
confs[i].resize (parents_.size());
}
int nReps = 1;
for (int i = nParents - 1; i >= 0; i--) {
unsigned nReps = 1;
for (int i = parents_.size() - 1; i >= 0; i--) {
unsigned index = 0;
while (index < rowSize) {
for (int j = 0; j < parents_[i]->getDomainSize(); j++) {
for (int r = 0; r < nReps; r++) {
for (unsigned j = 0; j < parents_[i]->getDomainSize(); j++) {
for (unsigned r = 0; r < nReps; r++) {
confs[index][i] = j;
index++;
}
@ -184,7 +178,7 @@ BayesNode::cptEntryToString (const CptEntry& entry) const
{
stringstream ss;
ss << "p(" ;
const DomainConf& conf = entry.getParentConfigurations();
const DConf& conf = entry.getDomainConfiguration();
int row = entry.getParameterIndex() / getRowSize();
ss << getDomain()[row];
if (parents_.size() > 0) {
@ -207,7 +201,7 @@ BayesNode::cptEntryToString (int row, const CptEntry& entry) const
{
stringstream ss;
ss << "p(" ;
const DomainConf& conf = entry.getParentConfigurations();
const DConf& conf = entry.getDomainConfiguration();
ss << getDomain()[row];
if (parents_.size() > 0) {
ss << "|" ;
@ -227,16 +221,16 @@ BayesNode::cptEntryToString (int row, const CptEntry& entry) const
vector<string>
BayesNode::getDomainHeaders (void) const
{
int nParents = parents_.size();
int rowSize = getRowSize();
int nReps = 1;
unsigned nParents = parents_.size();
unsigned rowSize = getRowSize();
unsigned nReps = 1;
vector<string> headers (rowSize);
for (int i = nParents - 1; i >= 0; i--) {
Domain domain = parents_[i]->getDomain();
int index = 0;
unsigned index = 0;
while (index < rowSize) {
for (int j = 0; j < parents_[i]->getDomainSize(); j++) {
for (int r = 0; r < nReps; r++) {
for (unsigned j = 0; j < parents_[i]->getDomainSize(); j++) {
for (unsigned r = 0; r < nReps; r++) {
if (headers[index] != "") {
headers[index] = domain[j] + "," + headers[index];
} else {
@ -270,7 +264,7 @@ operator << (ostream& o, const BayesNode& node)
o << endl;
o << "Parents: " ;
const NodeSet& parents = node.getParents();
const BnNodeSet& parents = node.getParents();
if (parents.size() != 0) {
for (unsigned int i = 0; i < parents.size() - 1; i++) {
o << parents[i]->getLabel() << ", " ;
@ -280,7 +274,7 @@ operator << (ostream& o, const BayesNode& node)
o << endl;
o << "Childs: " ;
const NodeSet& childs = node.getChilds();
const BnNodeSet& childs = node.getChilds();
if (childs.size() != 0) {
for (unsigned int i = 0; i < childs.size() - 1; i++) {
o << childs[i]->getLabel() << ", " ;

75
packages/CLPBN/clpbn/bp/BayesNode.h
View File

@ -1,9 +1,7 @@
#ifndef BP_BAYESNODE_H
#define BP_BAYESNODE_H
#ifndef BP_BAYES_NODE_H
#define BP_BAYES_NODE_H
#include <vector>
#include <string>
#include <sstream>
#include "Variable.h"
#include "CptEntry.h"
@ -16,11 +14,12 @@ using namespace std;
class BayesNode : public Variable
{
public:
BayesNode (unsigned);
BayesNode (unsigned, unsigned, int, const NodeSet&, Distribution*);
BayesNode (unsigned, string, const Domain&, const NodeSet&, Distribution*);
BayesNode (Vid vid) : Variable (vid) {}
BayesNode (Vid, unsigned, int, const BnNodeSet&, Distribution*);
BayesNode (Vid, string, const Domain&, const BnNodeSet&, Distribution*);
void setData (unsigned, int, const NodeSet&, Distribution*);
void setData (unsigned, int, const BnNodeSet&,
Distribution*);
void addChild (BayesNode*);
Distribution* getDistribution (void);
const ParamSet& getParameters (void);
@ -34,11 +33,21 @@ class BayesNode : public Variable
int getIndexOfParent (const BayesNode*) const;
string cptEntryToString (const CptEntry&) const;
string cptEntryToString (int, const CptEntry&) const;
// inlines
const NodeSet& getParents (void) const;
const NodeSet& getChilds (void) const;
double getProbability (int, const CptEntry& entry);
unsigned getRowSize (void) const;
const BnNodeSet& getParents (void) const { return parents_; }
const BnNodeSet& getChilds (void) const { return childs_; }
unsigned getRowSize (void) const
{
return dist_->params.size() / getDomainSize();
}
double getProbability (int row, const CptEntry& entry)
{
int col = entry.getParameterIndex();
int idx = (row * getRowSize()) + col;
return dist_->params[idx];
}
private:
DISALLOW_COPY_AND_ASSIGN (BayesNode);
@ -46,46 +55,12 @@ class BayesNode : public Variable
Domain getDomainHeaders (void) const;
friend ostream& operator << (ostream&, const BayesNode&);
NodeSet parents_;
NodeSet childs_;
BnNodeSet parents_;
BnNodeSet childs_;
Distribution* dist_;
};
ostream& operator << (ostream&, const BayesNode&);
inline const NodeSet&
BayesNode::getParents (void) const
{
return parents_;
}
inline const NodeSet&
BayesNode::getChilds (void) const
{
return childs_;
}
inline double
BayesNode::getProbability (int row, const CptEntry& entry)
{
int col = entry.getParameterIndex();
int idx = (row * getRowSize()) + col;
return dist_->params[idx];
}
inline unsigned
BayesNode::getRowSize (void) const
{
return dist_->params.size() / getDomainSize();
}
#endif
#endif //BP_BAYES_NODE_H

198
packages/CLPBN/clpbn/bp/CountingBP.cpp Normal file
View File

@ -0,0 +1,198 @@
#include "CountingBP.h"
CountingBP::~CountingBP (void)
{
delete lfg_;
delete fg_;
for (unsigned i = 0; i < links_.size(); i++) {
delete links_[i];
}
links_.clear();
}
ParamSet
CountingBP::getPosterioriOf (Vid vid) const
{
FgVarNode* var = lfg_->getEquivalentVariable (vid);
ParamSet probs;
if (var->hasEvidence()) {
probs.resize (var->getDomainSize(), 0.0);
probs[var->getEvidence()] = 1.0;
} else {
probs.resize (var->getDomainSize(), 1.0);
CLinkSet links = varsI_[var->getIndex()]->getLinks();
for (unsigned i = 0; i < links.size(); i++) {
ParamSet msg = links[i]->getMessage();
CountingBPLink* l = static_cast<CountingBPLink*> (links[i]);
Util::pow (msg, l->getNumberOfEdges());
for (unsigned j = 0; j < msg.size(); j++) {
probs[j] *= msg[j];
}
}
Util::normalize (probs);
}
return probs;
}
void
CountingBP::initializeSolver (void)
{
lfg_ = new LiftedFG (*fg_);
unsigned nUncVars = fg_->getFgVarNodes().size();
unsigned nUncFactors = fg_->getFactors().size();
CFgVarSet vars = fg_->getFgVarNodes();
unsigned nNeighborLessVars = 0;
for (unsigned i = 0; i < vars.size(); i++) {
CFactorSet factors = vars[i]->getFactors();
if (factors.size() == 1 && factors[0]->getFgVarNodes().size() == 1) {
nNeighborLessVars ++;
}
}
// cout << "UNCOMPRESSED FACTOR GRAPH" << endl;
// fg_->printGraphicalModel();
fg_->exportToDotFormat ("uncompress.dot");
FactorGraph *temp;
temp = fg_;
fg_ = lfg_->getCompressedFactorGraph();
unsigned nCompVars = fg_->getFgVarNodes().size();
unsigned nCompFactors = fg_->getFactors().size();
Statistics::updateCompressingStats (nUncVars,
nUncFactors,
nCompVars,
nCompFactors,
nNeighborLessVars);
cout << "COMPRESSED FACTOR GRAPH" << endl;
fg_->printGraphicalModel();
//fg_->exportToDotFormat ("compress.dot");
SPSolver::initializeSolver();
}
void
CountingBP::createLinks (void)
{
const FactorClusterSet fcs = lfg_->getFactorClusters();
for (unsigned i = 0; i < fcs.size(); i++) {
const VarClusterSet vcs = fcs[i]->getVarClusters();
for (unsigned j = 0; j < vcs.size(); j++) {
unsigned c = lfg_->getGroundEdgeCount (fcs[i], vcs[j]);
links_.push_back (
new CountingBPLink (fcs[i]->getRepresentativeFactor(),
vcs[j]->getRepresentativeVariable(), c));
//cout << (links_.back())->toString() << " edge count =" << c << endl;
}
}
return;
}
void
CountingBP::deleteJunction (Factor* f, FgVarNode*)
{
f->freeDistribution();
}
void
CountingBP::maxResidualSchedule (void)
{
if (nIter_ == 1) {
for (unsigned i = 0; i < links_.size(); i++) {
links_[i]->setNextMessage (getFactor2VarMsg (links_[i]));
SortedOrder::iterator it = sortedOrder_.insert (links_[i]);
linkMap_.insert (make_pair (links_[i], it));
if (DL >= 2 && DL < 5) {
cout << "calculating " << links_[i]->toString() << endl;
}
}
return;
}
for (unsigned c = 0; c < links_.size(); c++) {
if (DL >= 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();
Link* link = *it;
if (DL >= 2) {
cout << "updating " << (*sortedOrder_.begin())->toString() << endl;
}
if (link->getResidual() < SolverOptions::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
CFactorSet factorNeighbors = link->getVariable()->getFactors();
for (unsigned i = 0; i < factorNeighbors.size(); i++) {
CLinkSet links = factorsI_[factorNeighbors[i]->getIndex()]->getLinks();
for (unsigned j = 0; j < links.size(); j++) {
if (links[j]->getVariable() != link->getVariable()) { //FIXMEFIXME
if (DL >= 2 && DL < 5) {
cout << " calculating " << links[j]->toString() << endl;
}
links[j]->setNextMessage (getFactor2VarMsg (links[j]));
LinkMap::iterator iter = linkMap_.find (links[j]);
sortedOrder_.erase (iter->second);
iter->second = sortedOrder_.insert (links[j]);
}
}
}
}
}
ParamSet
CountingBP::getVar2FactorMsg (const Link* link) const
{
const FgVarNode* src = link->getVariable();
const Factor* dest = link->getFactor();
ParamSet msg;
if (src->hasEvidence()) {
cout << "has evidence" << endl;
msg.resize (src->getDomainSize(), 0.0);
msg[src->getEvidence()] = link->getMessage()[src->getEvidence()];
cout << "-> " << link->getVariable()->getLabel() << " " << link->getFactor()->getLabel() << endl;
cout << "-> p2s " << Util::parametersToString (msg) << endl;
} else {
msg = link->getMessage();
}
const CountingBPLink* l = static_cast<const CountingBPLink*> (link);
Util::pow (msg, l->getNumberOfEdges() - 1);
CLinkSet links = varsI_[src->getIndex()]->getLinks();
for (unsigned i = 0; i < links.size(); i++) {
if (links[i]->getFactor() != dest) {
ParamSet msgFromFactor = links[i]->getMessage();
CountingBPLink* l = static_cast<CountingBPLink*> (links[i]);
Util::pow (msgFromFactor, l->getNumberOfEdges());
for (unsigned j = 0; j < msgFromFactor.size(); j++) {
msg[j] *= msgFromFactor[j];
}
}
}
return msg;
}

45
packages/CLPBN/clpbn/bp/CountingBP.h Normal file
View File

@ -0,0 +1,45 @@
#ifndef BP_COUNTING_BP_H
#define BP_COUNTING_BP_H
#include "SPSolver.h"
#include "LiftedFG.h"
class Factor;
class FgVarNode;
class CountingBPLink : public Link
{
public:
CountingBPLink (Factor* f, FgVarNode* v, unsigned c) : Link (f, v)
{
edgeCount_ = c;
}
unsigned getNumberOfEdges (void) const { return edgeCount_; }
private:
unsigned edgeCount_;
};
class CountingBP : public SPSolver
{
public:
CountingBP (FactorGraph& fg) : SPSolver (fg) { }
~CountingBP (void);
ParamSet getPosterioriOf (Vid) const;
private:
void initializeSolver (void);
void createLinks (void);
void deleteJunction (Factor*, FgVarNode*);
void maxResidualSchedule (void);
ParamSet getVar2FactorMsg (const Link*) const;
LiftedFG* lfg_;
};
#endif // BP_COUNTING_BP_H

62
packages/CLPBN/clpbn/bp/CptEntry.h
View File

@ -1,5 +1,5 @@
#ifndef BP_CPTENTRY_H
#define BP_CPTENTRY_H
#ifndef BP_CPT_ENTRY_H
#define BP_CPT_ENTRY_H
#include <vector>
@ -10,62 +10,34 @@ using namespace std;
class CptEntry
{
public:
CptEntry (unsigned, const vector<unsigned>&);
unsigned getParameterIndex (void) const;
const vector<unsigned>& getParentConfigurations (void) const;
bool matchConstraints (const DomainConstr&) const;
bool matchConstraints (const vector<DomainConstr>&) const;
private:
unsigned index_;
vector<unsigned> confs_;
};
inline
CptEntry::CptEntry (unsigned index, const vector<unsigned>& confs)
CptEntry (unsigned index, const DConf& conf)
{
index_ = index;
confs_ = confs;
conf_ = conf;
}
unsigned getParameterIndex (void) const { return index_; }
const DConf& getDomainConfiguration (void) const { return conf_; }
inline unsigned
CptEntry::getParameterIndex (void) const
bool matchConstraints (const DConstraint& constr) const
{
return index_;
return conf_[constr.first] == constr.second;
}
inline const vector<unsigned>&
CptEntry::getParentConfigurations (void) const
{
return confs_;
}
inline bool
CptEntry::matchConstraints (const DomainConstr& constr) const
{
return confs_[constr.first] == constr.second;
}
inline bool
CptEntry::matchConstraints (const vector<DomainConstr>& constrs) const
bool matchConstraints (const vector<DConstraint>& constrs) const
{
for (unsigned j = 0; j < constrs.size(); j++) {
if (confs_[constrs[j].first] != constrs[j].second) {
if (conf_[constrs[j].first] != constrs[j].second) {
return false;
}
}
return true;
}
#endif
private:
unsigned index_;
DConf conf_;
};
#endif //BP_CPT_ENTRY_H

11
packages/CLPBN/clpbn/bp/Distribution.h
View File

@ -2,8 +2,8 @@
#define BP_DISTRIBUTION_H
#include <vector>
#include <string>
#include "CptEntry.h"
#include "Shared.h"
using namespace std;
@ -11,16 +11,18 @@ using namespace std;
struct Distribution
{
public:
Distribution (unsigned id)
Distribution (unsigned id, bool shared = false)
{
this->id = id;
this->params = params;
this->shared = shared;
}
Distribution (const ParamSet& params)
Distribution (const ParamSet& params, bool shared = false)
{
this->id = -1;
this->params = params;
this->shared = shared;
}
void updateParameters (const ParamSet& params)
@ -31,10 +33,11 @@ struct Distribution
unsigned id;
ParamSet params;
vector<CptEntry> entries;
bool shared;
private:
DISALLOW_COPY_AND_ASSIGN (Distribution);
};
#endif
#endif //BP_DISTRIBUTION_H

411
packages/CLPBN/clpbn/bp/Factor.cpp
View File

@ -1,37 +1,37 @@
#include <iostream>
#include <sstream>
#include <cstdlib>
#include <cassert>
#include <iostream>
#include <sstream>
#include "Factor.h"
#include "FgVarNode.h"
int Factor::indexCount_ = 0;
Factor::Factor (FgVarNode* var) {
vs_.push_back (var);
int nParams = var->getDomainSize();
// create a uniform distribution
double val = 1.0 / nParams;
ps_ = ParamSet (nParams, val);
id_ = indexCount_;
indexCount_ ++;
Factor::Factor (const Factor& g)
{
copyFactor (g);
}
Factor::Factor (const FgVarSet& vars) {
vs_ = vars;
Factor::Factor (FgVarNode* var)
{
Factor (FgVarSet() = {var});
}
Factor::Factor (const FgVarSet& vars)
{
vars_ = vars;
int nParams = 1;
for (unsigned i = 0; i < vs_.size(); i++) {
nParams *= vs_[i]->getDomainSize();
for (unsigned i = 0; i < vars_.size(); i++) {
nParams *= vars_[i]->getDomainSize();
}
// create a uniform distribution
double val = 1.0 / nParams;
ps_ = ParamSet (nParams, val);
id_ = indexCount_;
indexCount_ ++;
dist_ = new Distribution (ParamSet (nParams, val));
}
@ -39,10 +39,17 @@ Factor::Factor (const FgVarSet& vars) {
Factor::Factor (FgVarNode* var,
const ParamSet& params)
{
vs_.push_back (var);
ps_ = params;
id_ = indexCount_;
indexCount_ ++;
vars_.push_back (var);
dist_ = new Distribution (params);
}
Factor::Factor (FgVarSet& vars,
Distribution* dist)
{
vars_ = vars;
dist_ = dist;
}
@ -50,42 +57,8 @@ Factor::Factor (FgVarNode* var,
Factor::Factor (const FgVarSet& vars,
const ParamSet& params)
{
vs_ = vars;
ps_ = params;
id_ = indexCount_;
indexCount_ ++;
}
const FgVarSet&
Factor::getFgVarNodes (void) const
{
return vs_;
}
FgVarSet&
Factor::getFgVarNodes (void)
{
return vs_;
}
const ParamSet&
Factor::getParameters (void) const
{
return ps_;
}
ParamSet&
Factor::getParameters (void)
{
return ps_;
vars_ = vars;
dist_ = new Distribution (params);
}
@ -93,75 +66,95 @@ Factor::getParameters (void)
void
Factor::setParameters (const ParamSet& params)
{
//cout << "ps size: " << ps_.size() << endl;
//cout << "params size: " << params.size() << endl;
assert (ps_.size() == params.size());
ps_ = params;
assert (dist_->params.size() == params.size());
dist_->updateParameters (params);
}
Factor&
Factor::operator= (const Factor& g)
void
Factor::copyFactor (const Factor& g)
{
FgVarSet vars = g.getFgVarNodes();
ParamSet params = g.getParameters();
return *this;
vars_ = g.getFgVarNodes();
dist_ = new Distribution (g.getDistribution()->params);
}
Factor&
Factor::operator*= (const Factor& g)
void
Factor::multiplyByFactor (const Factor& g, const vector<CptEntry>* entries)
{
FgVarSet gVs = g.getFgVarNodes();
if (vars_.size() == 0) {
copyFactor (g);
return;
}
const FgVarSet& gVs = g.getFgVarNodes();
const ParamSet& gPs = g.getParameters();
bool factorsAreEqual = true;
if (gVs.size() == vars_.size()) {
for (unsigned i = 0; i < vars_.size(); i++) {
if (gVs[i] != vars_[i]) {
factorsAreEqual = false;
break;
}
}
} else {
factorsAreEqual = false;
}
if (factorsAreEqual) {
// optimization: if the factors contain the same set of variables,
// we can do 1 to 1 operations on the parameteres
for (unsigned i = 0; i < dist_->params.size(); i++) {
dist_->params[i] *= gPs[i];
}
} else {
bool hasCommonVars = false;
vector<int> varIndexes;
vector<unsigned> gVsIndexes;
for (unsigned i = 0; i < gVs.size(); i++) {
int idx = getIndexOf (gVs[i]);
if (idx == -1) {
insertVariable (gVs[i]);
varIndexes.push_back (vs_.size() - 1);
gVsIndexes.push_back (vars_.size() - 1);
} else {
hasCommonVars = true;
varIndexes.push_back (idx);
gVsIndexes.push_back (idx);
}
}
if (hasCommonVars) {
vector<unsigned> gVsOffsets (gVs.size());
gVsOffsets[gVs.size() - 1] = 1;
for (int i = gVs.size() - 2; i >= 0; i--) {
gVsOffsets[i] = gVsOffsets[i + 1] * gVs[i + 1]->getDomainSize();
}
if (hasCommonVars) {
vector<int> offsets (gVs.size());
offsets[gVs.size() - 1] = 1;
for (int i = gVs.size() - 2; i >= 0; i--) {
offsets[i] = offsets[i + 1] * gVs[i + 1]->getDomainSize();
if (entries == 0) {
entries = &getCptEntries();
}
vector<CptEntry> entries = getCptEntries();
for (unsigned i = 0; i < entries.size(); i++) {
int idx = 0;
const DomainConf conf = entries[i].getParentConfigurations();
for (unsigned j = 0; j < varIndexes.size(); j++) {
idx += offsets[j] * conf[varIndexes[j]];
for (unsigned i = 0; i < entries->size(); i++) {
unsigned idx = 0;
const DConf& conf = (*entries)[i].getDomainConfiguration();
for (unsigned j = 0; j < gVsIndexes.size(); j++) {
idx += gVsOffsets[j] * conf[ gVsIndexes[j] ];
}
//cout << "ps_[" << i << "] = " << ps_[i] << " * " ;
//cout << gPs[idx] << " , idx = " << idx << endl;
ps_[i] = ps_[i] * gPs[idx];
dist_->params[i] = dist_->params[i] * gPs[idx];
}
} else {
// if the originally factors doesn't have common factors.
// we don't have to make domain comparations
unsigned idx = 0;
for (unsigned i = 0; i < ps_.size(); i++) {
//cout << "ps_[" << i << "] = " << ps_[i] << " * " ;
//cout << gPs[idx] << " , idx = " << idx << endl;
ps_[i] = ps_[i] * gPs[idx];
idx ++;
if (idx >= gPs.size()) {
idx = 0;
// optimization: if the original factors doesn't have common variables,
// we don't need to marry the states of the common variables
unsigned count = 0;
for (unsigned i = 0; i < dist_->params.size(); i++) {
dist_->params[i] *= gPs[count];
count ++;
if (count >= gPs.size()) {
count = 0;
}
}
}
}
return *this;
}
@ -169,81 +162,109 @@ Factor::operator*= (const Factor& g)
void
Factor::insertVariable (FgVarNode* var)
{
int c = 0;
ParamSet newPs (ps_.size() * var->getDomainSize());
for (unsigned i = 0; i < ps_.size(); i++) {
for (int j = 0; j < var->getDomainSize(); j++) {
newPs[c] = ps_[i];
c ++;
assert (getIndexOf (var) == -1);
ParamSet newPs;
newPs.reserve (dist_->params.size() * var->getDomainSize());
for (unsigned i = 0; i < dist_->params.size(); i++) {
for (unsigned j = 0; j < var->getDomainSize(); j++) {
newPs.push_back (dist_->params[i]);
}
}
vs_.push_back (var);
ps_ = newPs;
vars_.push_back (var);
dist_->updateParameters (newPs);
}
void
Factor::marginalizeVariable (const FgVarNode* var) {
int varIndex = getIndexOf (var);
marginalizeVariable (varIndex);
}
void
Factor::marginalizeVariable (unsigned varIndex)
Factor::removeVariable (const FgVarNode* var)
{
assert (varIndex >= 0 && varIndex < vs_.size());
int distOffset = 1;
int leftVarOffset = 1;
for (unsigned i = vs_.size() - 1; i > varIndex; i--) {
distOffset *= vs_[i]->getDomainSize();
leftVarOffset *= vs_[i]->getDomainSize();
}
leftVarOffset *= vs_[varIndex]->getDomainSize();
int varIndex = getIndexOf (var);
assert (varIndex >= 0 && varIndex < (int)vars_.size());
// 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 = vars_.size() - 1; i > varIndex; i--) {
varOffset *= vars_[i]->getDomainSize();
leftVarOffset *= vars_[i]->getDomainSize();
}
leftVarOffset *= vars_[varIndex]->getDomainSize();
unsigned offset = 0;
unsigned count1 = 0;
unsigned count2 = 0;
unsigned newPsSize = dist_->params.size() / vars_[varIndex]->getDomainSize();
int ds = vs_[varIndex]->getDomainSize();
int count = 0;
int offset = 0;
int startIndex = 0;
int currDomainIdx = 0;
unsigned newPsSize = ps_.size() / ds;
ParamSet newPs;
newPs.reserve (newPsSize);
stringstream ss;
ss << "marginalizing " << vs_[varIndex]->getLabel();
ss << " from factor " << getLabel() << endl;
// stringstream ss;
// ss << "marginalizing " << vars_[varIndex]->getLabel();
// ss << " from factor " << getLabel() << endl;
while (newPs.size() < newPsSize) {
ss << " sum = ";
// ss << " sum = ";
double sum = 0.0;
for (int j = 0; j < ds; j++) {
if (j != 0) ss << " + ";
ss << ps_[offset];
sum = sum + ps_[offset];
offset = offset + distOffset;
for (unsigned i = 0; i < vars_[varIndex]->getDomainSize(); i++) {
// if (i != 0) ss << " + ";
// ss << dist_->params[offset];
sum += dist_->params[offset];
offset += varOffset;
}
newPs.push_back (sum);
count ++;
if (varIndex == vs_.size() - 1) {
offset = count * ds;
count1 ++;
if (varIndex == (int)vars_.size() - 1) {
offset = count1 * vars_[varIndex]->getDomainSize();
} else {
offset = offset - distOffset + 1;
if ((offset % leftVarOffset) == 0) {
currDomainIdx ++;
startIndex = leftVarOffset * currDomainIdx;
offset = startIndex;
count = 0;
} else {
offset = startIndex + count;
if (((offset - varOffset + 1) % leftVarOffset) == 0) {
count1 = 0;
count2 ++;
}
offset = (leftVarOffset * count2) + count1;
}
ss << " = " << sum << endl;
// ss << " = " << sum << endl;
}
// cout << ss.str() << endl;
ps_ = newPs;
vs_.erase (vs_.begin() + varIndex);
vars_.erase (vars_.begin() + varIndex);
dist_->updateParameters (newPs);
}
const vector<CptEntry>&
Factor::getCptEntries (void) const
{
if (dist_->entries.size() == 0) {
vector<DConf> confs (dist_->params.size());
for (unsigned i = 0; i < dist_->params.size(); i++) {
confs[i].resize (vars_.size());
}
unsigned nReps = 1;
for (int i = vars_.size() - 1; i >= 0; i--) {
unsigned index = 0;
while (index < dist_->params.size()) {
for (unsigned j = 0; j < vars_[i]->getDomainSize(); j++) {
for (unsigned r = 0; r < nReps; r++) {
confs[index][i] = j;
index++;
}
}
}
nReps *= vars_[i]->getDomainSize();
}
dist_->entries.clear();
dist_->entries.reserve (dist_->params.size());
for (unsigned i = 0; i < dist_->params.size(); i++) {
dist_->entries.push_back (CptEntry (i, confs[i]));
}
}
return dist_->entries;
}
@ -252,11 +273,10 @@ string
Factor::getLabel (void) const
{
stringstream ss;
ss << "f(" ;
// ss << "Φ(" ;
for (unsigned i = 0; i < vs_.size(); i++) {
ss << "Φ(" ;
for (unsigned i = 0; i < vars_.size(); i++) {
if (i != 0) ss << "," ;
ss << "v" << vs_[i]->getVarId();
ss << vars_[i]->getLabel();
}
ss << ")" ;
return ss.str();
@ -264,62 +284,24 @@ Factor::getLabel (void) const
string
Factor::toString (void) const
void
Factor::printFactor (void)
{
stringstream ss;
ss << "vars: " ;
for (unsigned i = 0; i < vs_.size(); i++) {
if (i != 0) ss << ", " ;
ss << "v" << vs_[i]->getVarId();
ss << getLabel() << endl;
ss << "--------------------" << endl;
VarSet vs;
for (unsigned i = 0; i < vars_.size(); i++) {
vs.push_back (vars_[i]);
}
ss << endl;
vector<CptEntry> entries = getCptEntries();
vector<string> domainConfs = Util::getInstantiations (vs);
const vector<CptEntry>& entries = getCptEntries();
for (unsigned i = 0; i < entries.size(); i++) {
ss << "Φ(" ;
char s = 'a' ;
const DomainConf& conf = entries[i].getParentConfigurations();
for (unsigned j = 0; j < conf.size(); j++) {
if (j != 0) ss << "," ;
ss << s << conf[j] + 1;
s++;
ss << "Φ(" << domainConfs[i] << ")" ;
unsigned idx = entries[i].getParameterIndex();
ss << " = " << dist_->params[idx] << endl;
}
ss << ") = " << ps_[entries[i].getParameterIndex()] << endl;
}
return ss.str();
}
vector<CptEntry>
Factor::getCptEntries (void) const
{
vector<DomainConf> confs (ps_.size());
for (unsigned i = 0; i < ps_.size(); i++) {
confs[i].resize (vs_.size());
}
int nReps = 1;
for (int i = vs_.size() - 1; i >= 0; i--) {
unsigned index = 0;
while (index < ps_.size()) {
for (int j = 0; j < vs_[i]->getDomainSize(); j++) {
for (int r = 0; r < nReps; r++) {
confs[index][i] = j;
index++;
}
}
}
nReps *= vs_[i]->getDomainSize();
}
vector<CptEntry> entries;
for (unsigned i = 0; i < ps_.size(); i++) {
for (unsigned j = 0; j < vs_.size(); j++) {
}
entries.push_back (CptEntry (i, confs[i]));
}
return entries;
cout << ss.str();
}
@ -327,20 +309,11 @@ Factor::getCptEntries (void) const
int
Factor::getIndexOf (const FgVarNode* var) const
{
for (unsigned i = 0; i < vs_.size(); i++) {
if (vs_[i] == var) {
for (unsigned i = 0; i < vars_.size(); i++) {
if (vars_[i] == var) {
return i;
}
}
return -1;
}
Factor operator* (const Factor& f, const Factor& g)
{
Factor r = f;
r *= g;
return r;
}

45
packages/CLPBN/clpbn/bp/Factor.h
View File

@ -3,43 +3,46 @@
#include <vector>
#include "Distribution.h"
#include "CptEntry.h"
using namespace std;
class FgVarNode;
class Distribution;
class Factor
{
public:
Factor (void) { }
Factor (const Factor&);
Factor (FgVarNode*);
Factor (const FgVarSet&);
Factor (CFgVarSet);
Factor (FgVarNode*, const ParamSet&);
Factor (const FgVarSet&, const ParamSet&);
Factor (FgVarSet&, Distribution*);
Factor (CFgVarSet, CParamSet);
const FgVarSet& getFgVarNodes (void) const;
FgVarSet& getFgVarNodes (void);
const ParamSet& getParameters (void) const;
ParamSet& getParameters (void);
void setParameters (const ParamSet&);
Factor& operator= (const Factor& f);
Factor& operator*= (const Factor& f);
void setParameters (CParamSet);
void copyFactor (const Factor& f);
void multiplyByFactor (const Factor& f, const vector<CptEntry>* = 0);
void insertVariable (FgVarNode* index);
void marginalizeVariable (const FgVarNode* var);
void marginalizeVariable (unsigned);
void removeVariable (const FgVarNode* var);
const vector<CptEntry>& getCptEntries (void) const;
string getLabel (void) const;
string toString (void) const;
void printFactor (void);
private:
vector<CptEntry> getCptEntries() const;
CFgVarSet getFgVarNodes (void) const { return vars_; }
CParamSet getParameters (void) const { return dist_->params; }
Distribution* getDistribution (void) const { return dist_; }
unsigned getIndex (void) const { return index_; }
void setIndex (unsigned index) { index_ = index; }
void freeDistribution (void) { delete dist_; dist_ = 0;}
int getIndexOf (const FgVarNode*) const;
FgVarSet vs_;
ParamSet ps_;
int id_;
static int indexCount_;
private:
FgVarSet vars_;
Distribution* dist_;
unsigned index_;
};
Factor operator* (const Factor&, const Factor&);
#endif
#endif //BP_FACTOR_H

258
packages/CLPBN/clpbn/bp/FactorGraph.cpp
View File

@ -1,23 +1,26 @@
#include <cstdlib>
#include <vector>
#include <set>
#include <iostream>
#include <fstream>
#include <sstream>
#include <vector>
#include <cstdlib>
#include "FactorGraph.h"
#include "FgVarNode.h"
#include "Factor.h"
#include "BayesNet.h"
FactorGraph::FactorGraph (const char* fileName)
{
string line;
ifstream is (fileName);
if (!is.is_open()) {
cerr << "error: cannot read from file " + std::string (fileName) << endl;
abort();
}
string line;
while (is.peek() == '#' || is.peek() == '\n') getline (is, line);
getline (is, line);
if (line != "MARKOV") {
@ -39,7 +42,7 @@ FactorGraph::FactorGraph (const char* fileName)
while (is.peek() == '#' || is.peek() == '\n') getline (is, line);
for (int i = 0; i < nVars; i++) {
varNodes_.push_back (new FgVarNode (i, domainSizes[i]));
addVariable (new FgVarNode (i, domainSizes[i]));
}
int nFactors;
@ -50,11 +53,11 @@ FactorGraph::FactorGraph (const char* fileName)
is >> nFactorVars;
FgVarSet factorVars;
for (int j = 0; j < nFactorVars; j++) {
int varId;
is >> varId;
FgVarNode* var = getVariableById (varId);
if (var == 0) {
cerr << "error: invalid variable identifier (" << varId << ")" << endl;
int vid;
is >> vid;
FgVarNode* var = getFgVarNode (vid);
if (!var) {
cerr << "error: invalid variable identifier (" << vid << ")" << endl;
abort();
}
factorVars.push_back (var);
@ -87,6 +90,33 @@ FactorGraph::FactorGraph (const char* fileName)
FactorGraph::FactorGraph (const BayesNet& bn)
{
const BnNodeSet& nodes = bn.getBayesNodes();
for (unsigned i = 0; i < nodes.size(); i++) {
FgVarNode* varNode = new FgVarNode (nodes[i]);
varNode->setIndex (i);
addVariable (varNode);
}
for (unsigned i = 0; i < nodes.size(); i++) {
const BnNodeSet& parents = nodes[i]->getParents();
if (!(nodes[i]->hasEvidence() && parents.size() == 0)) {
FgVarSet factorVars = { varNodes_[nodes[i]->getIndex()] };
for (unsigned j = 0; j < parents.size(); j++) {
factorVars.push_back (varNodes_[parents[j]->getIndex()]);
}
Factor* f = new Factor (factorVars, nodes[i]->getDistribution());
factors_.push_back (f);
for (unsigned j = 0; j < factorVars.size(); j++) {
factorVars[j]->addFactor (f);
}
}
}
}
FactorGraph::~FactorGraph (void)
{
for (unsigned i = 0; i < varNodes_.size(); i++) {
@ -99,18 +129,67 @@ FactorGraph::~FactorGraph (void)
FgVarSet
FactorGraph::getFgVarNodes (void) const
void
FactorGraph::addVariable (FgVarNode* varNode)
{
return varNodes_;
varNodes_.push_back (varNode);
varNode->setIndex (varNodes_.size() - 1);
indexMap_.insert (make_pair (varNode->getVarId(), varNodes_.size() - 1));
}
vector<Factor*>
FactorGraph::getFactors (void) const
void
FactorGraph::removeVariable (const FgVarNode* var)
{
return factors_;
if (varNodes_[varNodes_.size() - 1] == var) {
varNodes_.pop_back();
} else {
for (unsigned i = 0; i < varNodes_.size(); i++) {
if (varNodes_[i] == var) {
varNodes_.erase (varNodes_.begin() + i);
return;
}
}
assert (false);
}
indexMap_.erase (indexMap_.find (var->getVarId()));
}
void
FactorGraph::addFactor (Factor* f)
{
factors_.push_back (f);
const FgVarSet& factorVars = f->getFgVarNodes();
for (unsigned i = 0; i < factorVars.size(); i++) {
factorVars[i]->addFactor (f);
}
}
void
FactorGraph::removeFactor (const Factor* f)
{
const FgVarSet& factorVars = f->getFgVarNodes();
for (unsigned i = 0; i < factorVars.size(); i++) {
if (factorVars[i]) {
factorVars[i]->removeFactor (f);
}
}
if (factors_[factors_.size() - 1] == f) {
factors_.pop_back();
} else {
for (unsigned i = 0; i < factors_.size(); i++) {
if (factors_[i] == f) {
factors_.erase (factors_.begin() + i);
return;
}
}
assert (false);
}
}
@ -127,47 +206,142 @@ FactorGraph::getVariables (void) const
FgVarNode*
FactorGraph::getVariableById (unsigned id) const
Variable*
FactorGraph::getVariable (Vid vid) const
{
for (unsigned i = 0; i < varNodes_.size(); i++) {
if (varNodes_[i]->getVarId() == id) {
return varNodes_[i];
}
}
return 0;
}
FgVarNode*
FactorGraph::getVariableByLabel (string label) const
{
for (unsigned i = 0; i < varNodes_.size(); i++) {
stringstream ss;
ss << "v" << varNodes_[i]->getVarId();
if (ss.str() == label) {
return varNodes_[i];
}
}
return 0;
return getFgVarNode (vid);
}
void
FactorGraph::printFactorGraph (void) const
FactorGraph::setIndexes (void)
{
for (unsigned i = 0; i < varNodes_.size(); i++) {
varNodes_[i]->setIndex (i);
}
for (unsigned i = 0; i < factors_.size(); i++) {
factors_[i]->setIndex (i);
}
}
void
FactorGraph::freeDistributions (void)
{
set<Distribution*> dists;
for (unsigned i = 0; i < factors_.size(); i++) {
dists.insert (factors_[i]->getDistribution());
}
for (set<Distribution*>::iterator it = dists.begin();
it != dists.end(); it++) {
delete *it;
}
}
void
FactorGraph::printGraphicalModel (void) const
{
for (unsigned i = 0; i < varNodes_.size(); i++) {
cout << "variable number " << varNodes_[i]->getIndex() << endl;
cout << "Id = " << varNodes_[i]->getVarId() << endl;
cout << "Label = " << varNodes_[i]->getLabel() << endl;
cout << "Domain size = " << varNodes_[i]->getDomainSize() << endl;
cout << "Evidence = " << varNodes_[i]->getEvidence() << endl;
cout << endl;
cout << "Factors = " ;
for (unsigned j = 0; j < varNodes_[i]->getFactors().size(); j++) {
cout << varNodes_[i]->getFactors()[j]->getLabel() << " " ;
}
cout << endl << endl;
}
cout << endl;
for (unsigned i = 0; i < factors_.size(); i++) {
cout << factors_[i]->toString() << endl;
factors_[i]->printFactor();
cout << endl;
}
}
void
FactorGraph::exportToDotFormat (const char* fileName) const
{
ofstream out (fileName);
if (!out.is_open()) {
cerr << "error: cannot open file to write at " ;
cerr << "FactorGraph::exportToDotFile()" << endl;
abort();
}
out << "graph \"" << fileName << "\" {" << endl;
for (unsigned i = 0; i < varNodes_.size(); i++) {
if (varNodes_[i]->hasEvidence()) {
out << '"' << varNodes_[i]->getLabel() << '"' ;
out << " [style=filled, fillcolor=yellow]" << endl;
}
}
for (unsigned i = 0; i < factors_.size(); i++) {
out << '"' << factors_[i]->getLabel() << '"' ;
out << " [label=\"" << factors_[i]->getLabel() << "\\n(";
out << factors_[i]->getDistribution()->id << ")" << "\"" ;
out << ", shape=box]" << endl;
}
for (unsigned i = 0; i < factors_.size(); i++) {
CFgVarSet myVars = factors_[i]->getFgVarNodes();
for (unsigned j = 0; j < myVars.size(); j++) {
out << '"' << factors_[i]->getLabel() << '"' ;
out << " -- " ;
out << '"' << myVars[j]->getLabel() << '"' << endl;
}
}
out << "}" << endl;
out.close();
}
void
FactorGraph::exportToUaiFormat (const char* fileName) const
{
ofstream out (fileName);
if (!out.is_open()) {
cerr << "error: cannot open file to write at " ;
cerr << "FactorGraph::exportToUaiFormat()" << endl;
abort();
}
out << "MARKOV" << endl;
out << varNodes_.size() << endl;
for (unsigned i = 0; i < varNodes_.size(); i++) {
out << varNodes_[i]->getDomainSize() << " " ;
}
out << endl;
out << factors_.size() << endl;
for (unsigned i = 0; i < factors_.size(); i++) {
CFgVarSet factorVars = factors_[i]->getFgVarNodes();
out << factorVars.size();
for (unsigned j = 0; j < factorVars.size(); j++) {
out << " " << factorVars[j]->getIndex();
}
out << endl;
}
for (unsigned i = 0; i < factors_.size(); i++) {
CParamSet params = factors_[i]->getParameters();
out << endl << params.size() << endl << " " ;
for (unsigned j = 0; j < params.size(); j++) {
out << params[j] << " " ;
}
out << endl;
}
out.close();
}

44
packages/CLPBN/clpbn/bp/FactorGraph.h
View File

@ -1,8 +1,7 @@
#ifndef BP_FACTORGRAPH_H
#define BP_FACTORGRAPH_H
#ifndef BP_FACTOR_GRAPH_H
#define BP_FACTOR_GRAPH_H
#include <vector>
#include <string>
#include "GraphicalModel.h"
#include "Shared.h"
@ -11,25 +10,48 @@ using namespace std;
class FgVarNode;
class Factor;
class BayesNet;
class FactorGraph : public GraphicalModel
{
public:
FactorGraph (const char* fileName);
FactorGraph (void) {};
FactorGraph (const char*);
FactorGraph (const BayesNet&);
~FactorGraph (void);
FgVarSet getFgVarNodes (void) const;
vector<Factor*> getFactors (void) const;
void addVariable (FgVarNode*);
void removeVariable (const FgVarNode*);
void addFactor (Factor*);
void removeFactor (const Factor*);
VarSet getVariables (void) const;
FgVarNode* getVariableById (unsigned) const;
FgVarNode* getVariableByLabel (string) const;
void printFactorGraph (void) const;
Variable* getVariable (unsigned) const;
void setIndexes (void);
void freeDistributions (void);
void printGraphicalModel (void) const;
void exportToDotFormat (const char*) const;
void exportToUaiFormat (const char*) const;
const FgVarSet& getFgVarNodes (void) const { return varNodes_; }
const FactorSet& getFactors (void) const { return factors_; }
FgVarNode* getFgVarNode (Vid vid) const
{
IndexMap::const_iterator it = indexMap_.find (vid);
if (it == indexMap_.end()) {
return 0;
} else {
return varNodes_[it->second];
}
}
private:
DISALLOW_COPY_AND_ASSIGN (FactorGraph);
FgVarSet varNodes_;
vector<Factor*> factors_;
FactorSet factors_;
IndexMap indexMap_;
};
#endif
#endif // BP_FACTOR_GRAPH_H

29
packages/CLPBN/clpbn/bp/FgVarNode.h
View File

@ -1,8 +1,7 @@
#ifndef BP_VARIABLE_H
#define BP_VARIABLE_H
#ifndef BP_FG_VAR_NODE_H
#define BP_FG_VAR_NODE_H
#include <vector>
#include <string>
#include "Variable.h"
#include "Shared.h"
@ -14,15 +13,31 @@ class Factor;
class FgVarNode : public Variable
{
public:
FgVarNode (int varId, int dsize) : Variable (varId, dsize) { }
FgVarNode (unsigned vid, unsigned dsize) : Variable (vid, dsize) { }
FgVarNode (const Variable* v) : Variable (v) { }
void addFactor (Factor* f) { factors_.push_back (f); }
vector<Factor*> getFactors (void) const { return factors_; }
CFactorSet getFactors (void) const { return factors_; }
void removeFactor (const Factor* f)
{
if (factors_[factors_.size() -1] == f) {
factors_.pop_back();
} else {
for (unsigned i = 0; i < factors_.size(); i++) {
if (factors_[i] == f) {
factors_.erase (factors_.begin() + i);
return;
}
}
assert (false);
}
}
private:
DISALLOW_COPY_AND_ASSIGN (FgVarNode);
// members
vector<Factor*> factors_;
FactorSet factors_;
};
#endif // BP_VARIABLE_H
#endif // BP_FG_VAR_NODE_H

11
packages/CLPBN/clpbn/bp/GraphicalModel.h
View File

@ -1,5 +1,5 @@
#ifndef BP_GRAPHICALMODEL_H
#define BP_GRAPHICALMODEL_H
#ifndef BP_GRAPHICAL_MODEL_H
#define BP_GRAPHICAL_MODEL_H
#include "Variable.h"
#include "Shared.h"
@ -9,9 +9,10 @@ using namespace std;
class GraphicalModel
{
public:
virtual ~GraphicalModel (void) {};
virtual Variable* getVariable (Vid) const = 0;
virtual VarSet getVariables (void) const = 0;
private:
virtual void printGraphicalModel (void) const = 0;
};
#endif
#endif // BP_GRAPHICAL_MODEL_H

124
packages/CLPBN/clpbn/bp/HorusCli.cpp
View File

@ -1,17 +1,19 @@
#include <iostream>
#include <cstdlib>
#include <iostream>
#include <sstream>
#include "BayesNet.h"
#include "BPSolver.h"
#include "FactorGraph.h"
#include "SPSolver.h"
#include "BPSolver.h"
#include "CountingBP.h"
using namespace std;
void BayesianNetwork (int, const char* []);
void markovNetwork (int, const char* []);
void runSolver (Solver*, const VarSet&);
const string USAGE = "usage: \
./hcli FILE [VARIABLE | OBSERVED_VARIABLE=EVIDENCE]..." ;
@ -20,13 +22,39 @@ const string USAGE = "usage: \
int
main (int argc, const char* argv[])
{
/*
FactorGraph fg;
FgVarNode* varNode1 = new FgVarNode (0, 2);
FgVarNode* varNode2 = new FgVarNode (1, 2);
FgVarNode* varNode3 = new FgVarNode (2, 2);
fg.addVariable (varNode1);
fg.addVariable (varNode2);
fg.addVariable (varNode3);
Distribution* dist = new Distribution (ParamSet() = {1.2, 1.4, 2.0, 0.4});
fg.addFactor (new Factor (FgVarSet() = {varNode1, varNode2}, dist));
fg.addFactor (new Factor (FgVarSet() = {varNode3, varNode2}, dist));
//fg.printGraphicalModel();
//SPSolver sp (fg);
//sp.runSolver();
//sp.printAllPosterioris();
//ParamSet p = sp.getJointDistributionOf (VidSet() = {0, 1, 2});
//cout << Util::parametersToString (p) << endl;
CountingBP cbp (fg);
//cbp.runSolver();
//cbp.printAllPosterioris();
ParamSet p2 = cbp.getJointDistributionOf (VidSet() = {0, 1, 2});
cout << Util::parametersToString (p2) << endl;
fg.freeDistributions();
Statistics::printCompressingStats ("compressing.stats");
return 0;
*/
if (!argv[1]) {
cerr << "error: no graphical model specified" << endl;
cerr << USAGE << endl;
exit (0);
}
string fileName = argv[1];
string extension = fileName.substr (fileName.find_last_of ('.') + 1);
const string& fileName = argv[1];
const string& extension = fileName.substr (fileName.find_last_of ('.') + 1);
if (extension == "xml") {
BayesianNetwork (argc, argv);
} else if (extension == "uai") {
@ -45,13 +73,13 @@ void
BayesianNetwork (int argc, const char* argv[])
{
BayesNet bn (argv[1]);
//bn.printNetwork();
//bn.printGraphicalModel();
NodeSet queryVars;
VarSet queryVars;
for (int i = 2; i < argc; i++) {
string arg = argv[i];
const string& arg = argv[i];
if (arg.find ('=') == std::string::npos) {
BayesNode* queryVar = bn.getNode (arg);
BayesNode* queryVar = bn.getBayesNode (arg);
if (queryVar) {
queryVars.push_back (queryVar);
} else {
@ -62,8 +90,8 @@ BayesianNetwork (int argc, const char* argv[])
}
} else {
size_t pos = arg.find ('=');
string label = arg.substr (0, pos);
string state = arg.substr (pos + 1);
const string& label = arg.substr (0, pos);
const string& state = arg.substr (pos + 1);
if (label.empty()) {
cerr << "error: missing left argument" << endl;
cerr << USAGE << endl;
@ -74,7 +102,7 @@ BayesianNetwork (int argc, const char* argv[])
cerr << USAGE << endl;
exit (0);
}
BayesNode* node = bn.getNode (label);
BayesNode* node = bn.getBayesNode (label);
if (node) {
if (node->isValidState (state)) {
node->setEvidence (state);
@ -94,19 +122,16 @@ BayesianNetwork (int argc, const char* argv[])
}
}
BPSolver solver (bn);
if (queryVars.size() == 0) {
solver.runSolver();
solver.printAllPosterioris();
} else if (queryVars.size() == 1) {
solver.runSolver();
solver.printPosterioriOf (queryVars[0]);
Solver* solver;
if (SolverOptions::convertBn2Fg) {
FactorGraph* fg = new FactorGraph (bn);
fg->printGraphicalModel();
solver = new SPSolver (*fg);
runSolver (solver, queryVars);
delete fg;
} else {
Domain domain = BayesNet::getInstantiations(queryVars);
ParamSet params = solver.getJointDistribution (queryVars);
for (unsigned i = 0; i < params.size(); i++) {
cout << domain[i] << "\t" << params[i] << endl;
}
solver = new BPSolver (bn);
runSolver (solver, queryVars);
}
bn.freeDistributions();
}
@ -117,11 +142,11 @@ void
markovNetwork (int argc, const char* argv[])
{
FactorGraph fg (argv[1]);
//fg.printFactorGraph();
//fg.printGraphicalModel();
VarSet queryVars;
for (int i = 2; i < argc; i++) {
string arg = argv[i];
const string& arg = argv[i];
if (arg.find ('=') == std::string::npos) {
if (!Util::isInteger (arg)) {
cerr << "error: `" << arg << "' " ;
@ -129,16 +154,16 @@ markovNetwork (int argc, const char* argv[])
cerr << endl;
exit (0);
}
unsigned varId;
Vid vid;
stringstream ss;
ss << arg;
ss >> varId;
Variable* queryVar = fg.getVariableById (varId);
ss >> vid;
Variable* queryVar = fg.getFgVarNode (vid);
if (queryVar) {
queryVars.push_back (queryVar);
} else {
cerr << "error: there isn't a variable with " ;
cerr << "`" << varId << "' as id" ;
cerr << "`" << vid << "' as id" ;
cerr << endl;
exit (0);
}
@ -160,11 +185,11 @@ markovNetwork (int argc, const char* argv[])
cerr << endl;
exit (0);
}
unsigned varId;
Vid vid;
stringstream ss;
ss << arg.substr (0, pos);
ss >> varId;
Variable* var = fg.getVariableById (varId);
ss >> vid;
Variable* var = fg.getFgVarNode (vid);
if (var) {
if (!Util::isInteger (arg.substr (pos + 1))) {
cerr << "error: `" << arg.substr (pos + 1) << "' " ;
@ -176,7 +201,6 @@ markovNetwork (int argc, const char* argv[])
stringstream ss;
ss << arg.substr (pos + 1);
ss >> stateIndex;
cout << "si: " << stateIndex << endl;
if (var->isValidStateIndex (stateIndex)) {
var->setEvidence (stateIndex);
} else {
@ -188,27 +212,35 @@ markovNetwork (int argc, const char* argv[])
}
} else {
cerr << "error: there isn't a variable with " ;
cerr << "`" << varId << "' as id" ;
cerr << "`" << vid << "' as id" ;
cerr << endl;
exit (0);
}
}
}
Solver* solver = new SPSolver (fg);
runSolver (solver, queryVars);
fg.freeDistributions();
}
SPSolver solver (fg);
void
runSolver (Solver* solver, const VarSet& queryVars)
{
VidSet vids;
for (unsigned i = 0; i < queryVars.size(); i++) {
vids.push_back (queryVars[i]->getVarId());
}
if (queryVars.size() == 0) {
solver.runSolver();
solver.printAllPosterioris();
solver->runSolver();
solver->printAllPosterioris();
} else if (queryVars.size() == 1) {
solver.runSolver();
solver.printPosterioriOf (queryVars[0]);
solver->runSolver();
solver->printPosterioriOf (vids[0]);
} else {
assert (false); //FIXME
//Domain domain = BayesNet::getInstantiations(queryVars);
//ParamSet params = solver.getJointDistribution (queryVars);
//for (unsigned i = 0; i < params.size(); i++) {
// cout << domain[i] << "\t" << params[i] << endl;
//}
solver->printJointDistributionOf (vids);
}
delete solver;
}

179
packages/CLPBN/clpbn/bp/HorusYap.cpp
View File

@ -1,41 +1,39 @@
#include <cstdlib>
#include <vector>
#include <iostream>
#include <sstream>
#include <vector>
#include <string>
#include <YapInterface.h>
#include "callgrind.h"
#include "BayesNet.h"
#include "BayesNode.h"
#include "FactorGraph.h"
#include "BPSolver.h"
#include "SPSolver.h"
#include "CountingBP.h"
using namespace std;
int
createNetwork (void)
{
Statistics::numCreatedNets ++;
cout << "creating network number " << Statistics::numCreatedNets << endl;
if (Statistics::numCreatedNets == 1) {
//CALLGRIND_START_INSTRUMENTATION;
}
BayesNet* bn = new BayesNet();
//Statistics::numCreatedNets ++;
//cout << "creating network number " << Statistics::numCreatedNets << endl;
BayesNet* bn = new BayesNet();
YAP_Term varList = YAP_ARG1;
while (varList != YAP_TermNil()) {
YAP_Term var = YAP_HeadOfTerm (varList);
unsigned varId = (unsigned) YAP_IntOfTerm (YAP_ArgOfTerm (1, var));
Vid vid = (Vid) YAP_IntOfTerm (YAP_ArgOfTerm (1, var));
unsigned dsize = (unsigned) YAP_IntOfTerm (YAP_ArgOfTerm (2, var));
int evidence = (int) YAP_IntOfTerm (YAP_ArgOfTerm (3, var));
YAP_Term parentL = YAP_ArgOfTerm (4, var);
unsigned distId = (unsigned) YAP_IntOfTerm (YAP_ArgOfTerm (5, var));
NodeSet parents;
BnNodeSet parents;
while (parentL != YAP_TermNil()) {
unsigned parentId = (unsigned) YAP_IntOfTerm (YAP_HeadOfTerm (parentL));
BayesNode* parent = bn->getNode (parentId);
BayesNode* parent = bn->getBayesNode (parentId);
if (!parent) {
parent = bn->addNode (parentId);
}
@ -47,23 +45,20 @@ createNetwork (void)
dist = new Distribution (distId);
bn->addDistribution (dist);
}
BayesNode* node = bn->getNode (varId);
BayesNode* node = bn->getBayesNode (vid);
if (node) {
node->setData (dsize, evidence, parents, dist);
} else {
bn->addNode (varId, dsize, evidence, parents, dist);
bn->addNode (vid, dsize, evidence, parents, dist);
}
varList = YAP_TailOfTerm (varList);
}
bn->setIndexes();
if (Statistics::numCreatedNets == 1688) {
Statistics::writeStats();
// if (Statistics::numCreatedNets == 1688) {
// Statistics::writeStats();
//CALLGRIND_STOP_INSTRUMENTATION;
//CALLGRIND_DUMP_STATS;
// exit (0);
}
// }
YAP_Int p = (YAP_Int) (bn);
return YAP_Unify (YAP_MkIntTerm (p), YAP_ARG2);
}
@ -77,7 +72,7 @@ setExtraVarsInfo (void)
YAP_Term varsInfoL = YAP_ARG2;
while (varsInfoL != YAP_TermNil()) {
YAP_Term head = YAP_HeadOfTerm (varsInfoL);
unsigned varId = YAP_IntOfTerm (YAP_ArgOfTerm (1, head));
Vid vid = YAP_IntOfTerm (YAP_ArgOfTerm (1, head));
YAP_Atom label = YAP_AtomOfTerm (YAP_ArgOfTerm (2, head));
YAP_Term domainL = YAP_ArgOfTerm (3, head);
Domain domain;
@ -86,7 +81,7 @@ setExtraVarsInfo (void)
domain.push_back ((char*) YAP_AtomName (atom));
domainL = YAP_TailOfTerm (domainL);
}
BayesNode* node = bn->getNode (varId);
BayesNode* node = bn->getBayesNode (vid);
assert (node);
node->setLabel ((char*) YAP_AtomName (label));
node->setDomain (domain);
@ -112,6 +107,11 @@ setParameters (void)
paramL = YAP_TailOfTerm (paramL);
}
bn->getDistribution(distId)->updateParameters(params);
if (Statistics::numCreatedNets == 4) {
cout << "dist " << distId << " parameters:" ;
cout << Util::parametersToString (params);
cout << endl;
}
distList = YAP_TailOfTerm (distList);
}
return TRUE;
@ -124,71 +124,113 @@ runSolver (void)
{
BayesNet* bn = (BayesNet*) YAP_IntOfTerm (YAP_ARG1);
YAP_Term taskList = YAP_ARG2;
vector<NodeSet> tasks;
NodeSet marginalVars;
vector<VidSet> tasks;
VidSet marginalVids;
while (taskList != YAP_TermNil()) {
if (YAP_IsPairTerm (YAP_HeadOfTerm (taskList))) {
NodeSet jointVars;
VidSet jointVids;
YAP_Term jointList = YAP_HeadOfTerm (taskList);
while (jointList != YAP_TermNil()) {
unsigned varId = (unsigned) YAP_IntOfTerm (YAP_HeadOfTerm (jointList));
assert (bn->getNode (varId));
jointVars.push_back (bn->getNode (varId));
Vid vid = (unsigned) YAP_IntOfTerm (YAP_HeadOfTerm (jointList));
assert (bn->getBayesNode (vid));
jointVids.push_back (vid);
jointList = YAP_TailOfTerm (jointList);
}
tasks.push_back (jointVars);
tasks.push_back (jointVids);
} else {
unsigned varId = (unsigned) YAP_IntOfTerm (YAP_HeadOfTerm (taskList));
BayesNode* node = bn->getNode (varId);
assert (node);
tasks.push_back (NodeSet() = {node});
marginalVars.push_back (node);
Vid vid = (unsigned) YAP_IntOfTerm (YAP_HeadOfTerm (taskList));
assert (bn->getBayesNode (vid));
tasks.push_back (VidSet() = {vid});
marginalVids.push_back (vid);
}
taskList = YAP_TailOfTerm (taskList);
}
/*
cout << "tasks to resolve:" << endl;
for (unsigned i = 0; i < tasks.size(); i++) {
cout << "i" << ": " ;
if (tasks[i].size() == 1) {
cout << tasks[i][0]->getVarId() << endl;
} else {
for (unsigned j = 0; j < tasks[i].size(); j++) {
cout << tasks[i][j]->getVarId() << " " ;
}
cout << endl;
}
}
*/
cerr << "prunning now..." << endl;
BayesNet* prunedNet = bn->pruneNetwork (marginalVars);
bn->printNetworkToFile ("net.txt");
BPSolver solver (*prunedNet);
cerr << "solving marginals now..." << endl;
solver.runSolver();
cerr << "calculating joints now ..." << endl;
// cout << "inference tasks:" << endl;
// for (unsigned i = 0; i < tasks.size(); i++) {
// cout << "i" << ": " ;
// if (tasks[i].size() == 1) {
// cout << tasks[i][0] << endl;
// } else {
// for (unsigned j = 0; j < tasks[i].size(); j++) {
// cout << tasks[i][j] << " " ;
// }
// cout << endl;
// }
// }
Solver* solver = 0;
GraphicalModel* gm = 0;
VidSet vids;
const BnNodeSet& nodes = bn->getBayesNodes();
for (unsigned i = 0; i < nodes.size(); i++) {
vids.push_back (nodes[i]->getVarId());
}
if (marginalVids.size() != 0) {
bn->exportToDotFormat ("bn unbayes.dot");
BayesNet* mrn = bn->getMinimalRequesiteNetwork (marginalVids);
mrn->exportToDotFormat ("bn bayes.dot");
//BayesNet* mrn = bn->getMinimalRequesiteNetwork (vids);
if (SolverOptions::convertBn2Fg) {
gm = new FactorGraph (*mrn);
if (SolverOptions::compressFactorGraph) {
solver = new CountingBP (*static_cast<FactorGraph*> (gm));
} else {
solver = new SPSolver (*static_cast<FactorGraph*> (gm));
}
if (SolverOptions::runBayesBall) {
delete mrn;
}
} else {
gm = mrn;
solver = new BPSolver (*static_cast<BayesNet*> (gm));
}
solver->runSolver();
}
vector<ParamSet> results;
results.reserve (tasks.size());
for (unsigned i = 0; i < tasks.size(); i++) {
if (tasks[i].size() == 1) {
BayesNode* node = prunedNet->getNode (tasks[i][0]->getVarId());
results.push_back (solver.getPosterioriOf (node));
results.push_back (solver->getPosterioriOf (tasks[i][0]));
} else {
BPSolver solver2 (*bn);
cout << "calculating an join dist on: " ;
for (unsigned j = 0; j < tasks[i].size(); j++) {
cout << tasks[i][j]->getVarId() << " " ;
static int count = 0;
cout << "calculating joint... " << count ++ << endl;
//if (count == 5225) {
// Statistics::printCompressingStats ("compressing.stats");
//}
Solver* solver2 = 0;
GraphicalModel* gm2 = 0;
bn->exportToDotFormat ("joint.dot");
BayesNet* mrn2;
if (SolverOptions::runBayesBall) {
mrn2 = bn->getMinimalRequesiteNetwork (tasks[i]);
} else {
mrn2 = bn;
}
cout << "..." << endl;
results.push_back (solver2.getJointDistribution (tasks[i]));
if (SolverOptions::convertBn2Fg) {
gm2 = new FactorGraph (*mrn2);
if (SolverOptions::compressFactorGraph) {
solver2 = new CountingBP (*static_cast<FactorGraph*> (gm2));
} else {
solver2 = new SPSolver (*static_cast<FactorGraph*> (gm2));
}
if (SolverOptions::runBayesBall) {
delete mrn2;
}
} else {
gm2 = mrn2;
solver2 = new BPSolver (*static_cast<BayesNet*> (gm2));
}
results.push_back (solver2->getJointDistributionOf (tasks[i]));
delete solver2;
delete gm2;
}
}
delete prunedNet;
delete solver;
delete gm;
YAP_Term list = YAP_TermNil();
for (int i = results.size() - 1; i >= 0; i--) {
@ -210,8 +252,9 @@ runSolver (void)
int
deleteBayesNet (void)
freeBayesNetwork (void)
{
//Statistics::printCompressingStats ("../../compressing.stats");
BayesNet* bn = (BayesNet*) YAP_IntOfTerm (YAP_ARG1);
bn->freeDistributions();
delete bn;
@ -227,6 +270,6 @@ init_predicates (void)
YAP_UserCPredicate ("set_extra_vars_info", setExtraVarsInfo, 2);
YAP_UserCPredicate ("set_parameters", setParameters, 2);
YAP_UserCPredicate ("run_solver", runSolver, 3);
YAP_UserCPredicate ("delete_bayes_net", deleteBayesNet, 1);
YAP_UserCPredicate ("free_bayesian_network", freeBayesNetwork, 1);
}

278
packages/CLPBN/clpbn/bp/LiftedFG.cpp Normal file
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@ -0,0 +1,278 @@
#include "LiftedFG.h"
#include "FgVarNode.h"
#include "Factor.h"
#include "Distribution.h"
LiftedFG::LiftedFG (const FactorGraph& fg)
{
groundFg_ = &fg;
freeColor_ = 0;
const FgVarSet& varNodes = fg.getFgVarNodes();
const FactorSet& factors = fg.getFactors();
varColors_.resize (varNodes.size());
factorColors_.resize (factors.size());
for (unsigned i = 0; i < factors.size(); i++) {
factors[i]->setIndex (i);
}
// create the initial variable colors
VarColorMap colorMap;
for (unsigned i = 0; i < varNodes.size(); i++) {
unsigned dsize = varNodes[i]->getDomainSize();
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]);
}
// create the initial factor colors
DistColorMap distColors;
for (unsigned i = 0; i < factors.size(); i++) {
Distribution* dist = factors[i]->getDistribution();
DistColorMap::iterator it = distColors.find (dist);
if (it == distColors.end()) {
it = distColors.insert (make_pair (dist, getFreeColor())).first;
}
setColor (factors[i], it->second);
}
VarSignMap varGroups;
FactorSignMap factorGroups;
bool groupsHaveChanged = true;
unsigned nIter = 0;
while (groupsHaveChanged || nIter == 1) {
nIter ++;
if (Statistics::numCreatedNets == 4) {
cout << "--------------------------------------------" << endl;
cout << "Iteration " << nIter << endl;
cout << "--------------------------------------------" << endl;
}
unsigned prevFactorGroupsSize = factorGroups.size();
factorGroups.clear();
// set a new color to the factors with the same signature
for (unsigned i = 0; i < factors.size(); i++) {
const string& signatureId = getSignatureId (factors[i]);
// cout << factors[i]->getLabel() << " signature: " ;
// cout<< signatureId << endl;
FactorSignMap::iterator it = factorGroups.find (signatureId);
if (it == factorGroups.end()) {
it = factorGroups.insert (make_pair (signatureId, FactorSet())).first;
}
it->second.push_back (factors[i]);
}
if (nIter > 0)
for (FactorSignMap::iterator it = factorGroups.begin();
it != factorGroups.end(); it++) {
Color newColor = getFreeColor();
FactorSet& 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 string& signatureId = getSignatureId (varNodes[i]);
VarSignMap::iterator it = varGroups.find (signatureId);
// cout << varNodes[i]->getLabel() << " signature: " ;
// cout << signatureId << endl;
if (it == varGroups.end()) {
it = varGroups.insert (make_pair (signatureId, FgVarSet())).first;
}
it->second.push_back (varNodes[i]);
}
if (nIter > 0)
for (VarSignMap::iterator it = varGroups.begin();
it != varGroups.end(); it++) {
Color newColor = getFreeColor();
FgVarSet& groupMembers = it->second;
for (unsigned i = 0; i < groupMembers.size(); i++) {
setColor (groupMembers[i], newColor);
}
}
//if (nIter >= 3) cout << "bigger than three: " << nIter << endl;
groupsHaveChanged = prevVarGroupsSize != varGroups.size()
|| prevFactorGroupsSize != factorGroups.size();
}
printGroups (varGroups, factorGroups);
for (VarSignMap::iterator it = varGroups.begin();
it != varGroups.end(); it++) {
CFgVarSet vars = it->second;
VarCluster* vc = new VarCluster (vars);
for (unsigned i = 0; i < vars.size(); i++) {
vid2VarCluster_.insert (make_pair (vars[i]->getVarId(), vc));
}
varClusters_.push_back (vc);
}
for (FactorSignMap::iterator it = factorGroups.begin();
it != factorGroups.end(); it++) {
VarClusterSet varClusters;
Factor* groundFactor = it->second[0];
FgVarSet groundVars = groundFactor->getFgVarNodes();
for (unsigned i = 0; i < groundVars.size(); i++) {
Vid vid = groundVars[i]->getVarId();
varClusters.push_back (vid2VarCluster_.find (vid)->second);
}
factorClusters_.push_back (new FactorCluster (it->second, varClusters));
}
}
LiftedFG::~LiftedFG (void)
{
for (unsigned i = 0; i < varClusters_.size(); i++) {
delete varClusters_[i];
}
for (unsigned i = 0; i < factorClusters_.size(); i++) {
delete factorClusters_[i];
}
}
string
LiftedFG::getSignatureId (FgVarNode* var) const
{
stringstream ss;
CFactorSet myFactors = var->getFactors();
ss << myFactors.size();
for (unsigned i = 0; i < myFactors.size(); i++) {
ss << "." << getColor (myFactors[i]);
ss << "." << myFactors[i]->getIndexOf(var);
}
ss << "." << getColor (var);
return ss.str();
}
string
LiftedFG::getSignatureId (Factor* factor) const
{
stringstream ss;
CFgVarSet myVars = factor->getFgVarNodes();
ss << myVars.size();
for (unsigned i = 0; i < myVars.size(); i++) {
ss << "." << getColor (myVars[i]);
}
ss << "." << getColor (factor);
return ss.str();
}
FactorGraph*
LiftedFG::getCompressedFactorGraph (void)
{
FactorGraph* fg = new FactorGraph();
for (unsigned i = 0; i < varClusters_.size(); i++) {
FgVarNode* var = varClusters_[i]->getGroundFgVarNodes()[0];
FgVarNode* newVar = new FgVarNode (var);
newVar->setIndex (i);
varClusters_[i]->setRepresentativeVariable (newVar);
fg->addVariable (newVar);
}
for (unsigned i = 0; i < factorClusters_.size(); i++) {
FgVarSet myGroundVars;
const VarClusterSet& myVarClusters = factorClusters_[i]->getVarClusters();
for (unsigned j = 0; j < myVarClusters.size(); j++) {
myGroundVars.push_back (myVarClusters[j]->getRepresentativeVariable());
}
Factor* newFactor = new Factor (myGroundVars,
factorClusters_[i]->getGroundFactors()[0]->getDistribution());
factorClusters_[i]->setRepresentativeFactor (newFactor);
fg->addFactor (newFactor);
}
return fg;
}
unsigned
LiftedFG::getGroundEdgeCount (FactorCluster* fc, VarCluster* vc) const
{
CFactorSet clusterGroundFactors = fc->getGroundFactors();
FgVarNode* var = vc->getGroundFgVarNodes()[0];
unsigned count = 0;
for (unsigned i = 0; i < clusterGroundFactors.size(); i++) {
if (clusterGroundFactors[i]->getIndexOf (var) != -1) {
count ++;
}
}
/*
CFgVarSet vars = vc->getGroundFgVarNodes();
for (unsigned i = 1; i < vars.size(); i++) {
FgVarNode* var = vc->getGroundFgVarNodes()[i];
unsigned count2 = 0;
for (unsigned i = 0; i < clusterGroundFactors.size(); i++) {
if (clusterGroundFactors[i]->getIndexOf (var) != -1) {
count2 ++;
}
}
if (count != count2) { cout << "oops!" << endl; abort(); }
}
*/
return count;
}
void
LiftedFG::printGroups (const VarSignMap& varGroups,
const FactorSignMap& factorGroups) const
{
cout << "variable groups:" << endl;
unsigned count = 0;
for (VarSignMap::const_iterator it = varGroups.begin();
it != varGroups.end(); it++) {
const FgVarSet& groupMembers = it->second;
if (groupMembers.size() > 0) {
cout << ++count << ": " ;
//if (groupMembers.size() > 1) {
for (unsigned i = 0; i < groupMembers.size(); i++) {
cout << groupMembers[i]->getLabel() << " " ;
}
//}
cout << endl;
}
}
cout << endl;
cout << "factor groups:" << endl;
count = 0;
for (FactorSignMap::const_iterator it = factorGroups.begin();
it != factorGroups.end(); it++) {
const FactorSet& groupMembers = it->second;
if (groupMembers.size() > 0) {
cout << ++count << ": " ;
//if (groupMembers.size() > 1) {
for (unsigned i = 0; i < groupMembers.size(); i++) {
cout << groupMembers[i]->getLabel() << " " ;
}
//}
cout << endl;
}
}
}

152
packages/CLPBN/clpbn/bp/LiftedFG.h Normal file
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@ -0,0 +1,152 @@
#ifndef BP_LIFTED_FG_H
#define BP_LIFTED_FG_H
#include <unordered_map>
#include "FactorGraph.h"
#include "FgVarNode.h"
#include "Factor.h"
#include "Shared.h"
class VarCluster;
class FactorCluster;
class Distribution;
typedef long Color;
typedef vector<Color> Signature;
typedef vector<VarCluster*> VarClusterSet;
typedef vector<FactorCluster*> FactorClusterSet;
typedef map<string, FgVarSet> VarSignMap;
typedef map<string, FactorSet> FactorSignMap;
typedef map<unsigned, vector<Color> > VarColorMap;
typedef map<Distribution*, Color> DistColorMap;
typedef map<Vid, VarCluster*> Vid2VarCluster;
class VarCluster
{
public:
VarCluster (CFgVarSet vs)
{
for (unsigned i = 0; i < vs.size(); i++) {
groundVars_.push_back (vs[i]);
}
}
void addFactorCluster (FactorCluster* fc)
{
factorClusters_.push_back (fc);
}
const FactorClusterSet& getFactorClusters (void) const
{
return factorClusters_;
}
FgVarNode* getRepresentativeVariable (void) const { return representVar_; }
void setRepresentativeVariable (FgVarNode* v) { representVar_ = v; }
CFgVarSet getGroundFgVarNodes (void) const { return groundVars_; }
private:
FgVarSet groundVars_;
FactorClusterSet factorClusters_;
FgVarNode* representVar_;
};
class FactorCluster
{
public:
FactorCluster (CFactorSet groundFactors, const VarClusterSet& vcs)
{
groundFactors_ = groundFactors;
varClusters_ = vcs;
for (unsigned i = 0; i < varClusters_.size(); i++) {
varClusters_[i]->addFactorCluster (this);
}
}
const VarClusterSet& getVarClusters (void) const
{
return varClusters_;
}
bool containsGround (const Factor* f)
{
for (unsigned i = 0; i < groundFactors_.size(); i++) {
if (groundFactors_[i] == f) {
return true;
}
}
return false;
}
Factor* getRepresentativeFactor (void) const { return representFactor_; }
void setRepresentativeFactor (Factor* f) { representFactor_ = f; }
CFactorSet getGroundFactors (void) const { return groundFactors_; }
private:
FactorSet groundFactors_;
VarClusterSet varClusters_;
Factor* representFactor_;
};
class LiftedFG
{
public:
LiftedFG (const FactorGraph&);
~LiftedFG (void);
FactorGraph* getCompressedFactorGraph (void);
unsigned getGroundEdgeCount (FactorCluster*, VarCluster*) const;
void printGroups (const VarSignMap& varGroups,
const FactorSignMap& factorGroups) const;
FgVarNode* getEquivalentVariable (Vid vid)
{
VarCluster* vc = vid2VarCluster_.find (vid)->second;
return vc->getRepresentativeVariable();
}
const VarClusterSet& getVariableClusters (void) { return varClusters_; }
const FactorClusterSet& getFactorClusters (void) { return factorClusters_; }
private:
string getSignatureId (FgVarNode*) const;
string getSignatureId (Factor*) const;
Color getFreeColor (void) { return ++freeColor_ -1; }
Color getColor (FgVarNode* v) const { return varColors_[v->getIndex()]; }
Color getColor (Factor* f) const { return factorColors_[f->getIndex()]; }
void setColor (FgVarNode* v, Color c)
{
varColors_[v->getIndex()] = c;
}
void setColor (Factor* f, Color c)
{
factorColors_[f->getIndex()] = c;
}
VarCluster* getVariableCluster (Vid vid) const
{
return vid2VarCluster_.find (vid)->second;
}
Color freeColor_;
vector<Color> varColors_;
vector<Color> factorColors_;
VarClusterSet varClusters_;
FactorClusterSet factorClusters_;
Vid2VarCluster vid2VarCluster_;
const FactorGraph* groundFg_;
};
#endif // BP_LIFTED_FG_H

39
packages/CLPBN/clpbn/bp/Makefile.in
View File

@ -50,17 +50,19 @@ CWD=$(PWD)
HEADERS = \
$(srcdir)/GraphicalModel.h \
$(srcdir)/Variable.h \
$(srcdir)/Distribution.h \
$(srcdir)/BayesNet.h \
$(srcdir)/BayesNode.h \
$(srcdir)/Distribution.h \
$(srcdir)/LiftedFG.h \
$(srcdir)/CptEntry.h \
$(srcdir)/FactorGraph.h \
$(srcdir)/FgVarNode.h \
$(srcdir)/Factor.h \
$(srcdir)/Solver.h \
$(srcdir)/BPSolver.h \
$(srcdir)/BpNode.h \
$(srcdir)/BPNodeInfo.h \
$(srcdir)/SPSolver.h \
$(srcdir)/CountingBP.h \
$(srcdir)/Shared.h \
$(srcdir)/xmlParser/xmlParser.h
@ -69,9 +71,12 @@ CPP_SOURCES = \
$(srcdir)/BayesNode.cpp \
$(srcdir)/FactorGraph.cpp \
$(srcdir)/Factor.cpp \
$(srcdir)/LiftedFG.cpp \
$(srcdir)/BPSolver.cpp \
$(srcdir)/BpNode.cpp \
$(srcdir)/BPNodeInfo.cpp \
$(srcdir)/SPSolver.cpp \
$(srcdir)/CountingBP.cpp \
$(srcdir)/Util.cpp \
$(srcdir)/HorusYap.cpp \
$(srcdir)/HorusCli.cpp \
$(srcdir)/xmlParser/xmlParser.cpp
@ -82,22 +87,38 @@ OBJS = \
FactorGraph.o \
Factor.o \
BPSolver.o \
BpNode.o \
BPNodeInfo.o \
SPSolver.o \
HorusYap.o \
xmlParser.o
Util.o \
LiftedFG.o \
CountingBP.o \
HorusYap.o
HCLI_OBJS = \
BayesNet.o \
BayesNode.o \
FactorGraph.o \
Factor.o \
BPSolver.o \
BPNodeInfo.o \
SPSolver.o \
Util.o \
LiftedFG.o \
CountingBP.o \
HorusCli.o \
xmlParser/xmlParser.o
SOBJS=horus.@SO@
all: $(SOBJS)
all: $(SOBJS) hcli
# default rule
%.o : $(srcdir)/%.cpp
$(CXX) -c $(CXXFLAGS) $< -o $@
xmlParser.o : $(srcdir)/xmlParser/xmlParser.cpp
xmlParser/xmlParser.o : $(srcdir)/xmlParser/xmlParser.cpp
$(CXX) -c $(CXXFLAGS) $< -o $@
@ -105,7 +126,7 @@ xmlParser.o : $(srcdir)/xmlParser/xmlParser.cpp
@DO_SECOND_LD@ @SHLIB_CXX_LD@ -o horus.@SO@ $(OBJS) @EXTRA_LIBS_FOR_SWIDLLS@
hcli: $(OBJS)
hcli: $(HCLI_OBJS)
$(CXX) -o hcli $(HCLI_OBJS)

513
packages/CLPBN/clpbn/bp/SPSolver.cpp
View File

@ -1,38 +1,77 @@
#include <cassert>
#include <algorithm>
#include <limits>
#include <iostream>
#include "SPSolver.h"
#include "FactorGraph.h"
#include "FgVarNode.h"
#include "Factor.h"
SPSolver* Link::klass = 0;
#include "Shared.h"
SPSolver::SPSolver (const FactorGraph& fg) : Solver (&fg)
SPSolver::SPSolver (FactorGraph& fg) : Solver (&fg)
{
fg_ = &fg;
accuracy_ = 0.0001;
maxIter_ = 10000;
//schedule_ = S_SEQ_FIXED;
//schedule_ = S_SEQ_RANDOM;
//schedule_ = S_SEQ_PARALLEL;
schedule_ = S_MAX_RESIDUAL;
Link::klass = this;
FgVarSet vars = fg_->getFgVarNodes();
for (unsigned i = 0; i < vars.size(); i++) {
msgs_.push_back (new MessageBanket (vars[i]));
}
}
SPSolver::~SPSolver (void)
{
for (unsigned i = 0; i < msgs_.size(); i++) {
delete msgs_[i];
for (unsigned i = 0; i < varsI_.size(); i++) {
delete varsI_[i];
}
for (unsigned i = 0; i < factorsI_.size(); i++) {
delete factorsI_[i];
}
for (unsigned i = 0; i < links_.size(); i++) {
delete links_[i];
}
}
void
SPSolver::runTreeSolver (void)
{
CFactorSet factors = fg_->getFactors();
bool finish = false;
while (!finish) {
finish = true;
for (unsigned i = 0; i < factors.size(); i++) {
CLinkSet links = factorsI_[factors[i]->getIndex()]->getLinks();
for (unsigned j = 0; j < links.size(); j++) {
if (!links[j]->messageWasSended()) {
if (readyToSendMessage(links[j])) {
links[j]->setNextMessage (getFactor2VarMsg (links[j]));
links[j]->updateMessage();
}
finish = false;
}
}
}
}
}
bool
SPSolver::readyToSendMessage (const Link* link) const
{
CFgVarSet factorVars = link->getFactor()->getFgVarNodes();
for (unsigned i = 0; i < factorVars.size(); i++) {
if (factorVars[i] != link->getVariable()) {
CLinkSet links = varsI_[factorVars[i]->getIndex()]->getLinks();
for (unsigned j = 0; j < links.size(); j++) {
if (links[j]->getFactor() != link->getFactor() &&
!links[j]->messageWasSended()) {
return false;
}
}
}
}
return true;
}
@ -40,62 +79,54 @@ SPSolver::~SPSolver (void)
void
SPSolver::runSolver (void)
{
initializeSolver();
runTreeSolver();
return;
nIter_ = 0;
vector<Factor*> factors = fg_->getFactors();
for (unsigned i = 0; i < factors.size(); i++) {
FgVarSet neighbors = factors[i]->getFgVarNodes();
for (unsigned j = 0; j < neighbors.size(); j++) {
updateOrder_.push_back (Link (factors[i], neighbors[j]));
}
}
while (!converged() && nIter_ < SolverOptions::maxIter) {
while (!converged() && nIter_ < maxIter_) {
if (DL >= 1) {
nIter_ ++;
if (DL >= 2) {
cout << endl;
cout << "****************************************" ;
cout << "****************************************" ;
cout << endl;
cout << " Iteration " << nIter_ + 1 << endl;
cout << " Iteration " << nIter_ << endl;
cout << "****************************************" ;
cout << "****************************************" ;
cout << endl;
}
switch (schedule_) {
case S_SEQ_RANDOM:
random_shuffle (updateOrder_.begin(), updateOrder_.end());
switch (SolverOptions::schedule) {
case SolverOptions::S_SEQ_RANDOM:
random_shuffle (links_.begin(), links_.end());
// no break
case S_SEQ_FIXED:
for (unsigned c = 0; c < updateOrder_.size(); c++) {
Link& link = updateOrder_[c];
calculateNextMessage (link.source, link.destination);
updateMessage (updateOrder_[c]);
case SolverOptions::S_SEQ_FIXED:
for (unsigned i = 0; i < links_.size(); i++) {
links_[i]->setNextMessage (getFactor2VarMsg (links_[i]));
links_[i]->updateMessage();
}
break;
case S_PARALLEL:
for (unsigned c = 0; c < updateOrder_.size(); c++) {
Link link = updateOrder_[c];
calculateNextMessage (link.source, link.destination);
case SolverOptions::S_PARALLEL:
for (unsigned i = 0; i < links_.size(); i++) {
links_[i]->setNextMessage (getFactor2VarMsg (links_[i]));
}
for (unsigned c = 0; c < updateOrder_.size(); c++) {
Link link = updateOrder_[c];
updateMessage (updateOrder_[c]);
for (unsigned i = 0; i < links_.size(); i++) {
links_[i]->updateMessage();
}
break;
case S_MAX_RESIDUAL:
case SolverOptions::S_MAX_RESIDUAL:
maxResidualSchedule();
break;
}
nIter_++;
}
if (DL >= 2) {
cout << endl;
if (DL >= 1) {
if (nIter_ < maxIter_) {
if (nIter_ < SolverOptions::maxIter) {
cout << "Loopy Sum-Product converged in " ;
cout << nIter_ << " iterations" << endl;
} else {
@ -108,56 +139,166 @@ SPSolver::runSolver (void)
ParamSet
SPSolver::getPosterioriOf (const Variable* var) const
SPSolver::getPosterioriOf (Vid vid) const
{
assert (var);
assert (var == fg_->getVariableById (var->getVarId()));
assert (var->getIndex() < msgs_.size());
assert (fg_->getFgVarNode (vid));
FgVarNode* var = fg_->getFgVarNode (vid);
ParamSet probs;
ParamSet probs (var->getDomainSize(), 1);
if (var->hasEvidence()) {
for (unsigned i = 0; i < probs.size(); i++) {
if ((int)i != var->getEvidence()) {
probs[i] = 0;
}
}
probs.resize (var->getDomainSize(), 0.0);
probs[var->getEvidence()] = 1.0;
} else {
MessageBanket* mb = msgs_[var->getIndex()];
const FgVarNode* varNode = fg_->getFgVarNodes()[var->getIndex()];
vector<Factor*> neighbors = varNode->getFactors();
for (unsigned i = 0; i < neighbors.size(); i++) {
const Message& msg = mb->getMessage (neighbors[i]);
probs.resize (var->getDomainSize(), 1.0);
CLinkSet links = varsI_[var->getIndex()]->getLinks();
for (unsigned i = 0; i < links.size(); i++) {
CParamSet msg = links[i]->getMessage();
for (unsigned j = 0; j < msg.size(); j++) {
probs[j] *= msg[j];
}
}
Util::normalize (probs);
}
return probs;
}
ParamSet
SPSolver::getJointDistributionOf (const VidSet& jointVids)
{
FgVarSet jointVars;
unsigned dsize = 1;
for (unsigned i = 0; i < jointVids.size(); i++) {
FgVarNode* varNode = fg_->getFgVarNode (jointVids[i]);
dsize *= varNode->getDomainSize();
jointVars.push_back (varNode);
}
unsigned maxVid = std::numeric_limits<unsigned>::max();
FgVarNode* junctionVar = new FgVarNode (maxVid, dsize);
FgVarSet factorVars = { junctionVar };
for (unsigned i = 0; i < jointVars.size(); i++) {
factorVars.push_back (jointVars[i]);
}
unsigned nParams = dsize * dsize;
ParamSet params (nParams);
for (unsigned i = 0; i < nParams; i++) {
unsigned row = i / dsize;
unsigned col = i % dsize;
if (row == col) {
params[i] = 1;
} else {
params[i] = 0;
}
}
Distribution* dist = new Distribution (params, maxVid);
Factor* newFactor = new Factor (factorVars, dist);
fg_->addVariable (junctionVar);
fg_->addFactor (newFactor);
runSolver();
ParamSet results = getPosterioriOf (maxVid);
deleteJunction (newFactor, junctionVar);
return results;
}
void
SPSolver::initializeSolver (void)
{
fg_->setIndexes();
CFgVarSet vars = fg_->getFgVarNodes();
for (unsigned i = 0; i < varsI_.size(); i++) {
delete varsI_[i];
}
varsI_.reserve (vars.size());
for (unsigned i = 0; i < vars.size(); i++) {
varsI_.push_back (new SPNodeInfo());
}
CFactorSet factors = fg_->getFactors();
for (unsigned i = 0; i < factorsI_.size(); i++) {
delete factorsI_[i];
}
factorsI_.reserve (factors.size());
for (unsigned i = 0; i < factors.size(); i++) {
factorsI_.push_back (new SPNodeInfo());
}
for (unsigned i = 0; i < links_.size(); i++) {
delete links_[i];
}
createLinks();
for (unsigned i = 0; i < links_.size(); i++) {
Factor* source = links_[i]->getFactor();
FgVarNode* dest = links_[i]->getVariable();
varsI_[dest->getIndex()]->addLink (links_[i]);
factorsI_[source->getIndex()]->addLink (links_[i]);
}
}
void
SPSolver::createLinks (void)
{
CFactorSet factors = fg_->getFactors();
for (unsigned i = 0; i < factors.size(); i++) {
CFgVarSet neighbors = factors[i]->getFgVarNodes();
for (unsigned j = 0; j < neighbors.size(); j++) {
links_.push_back (new Link (factors[i], neighbors[j]));
}
}
}
void
SPSolver::deleteJunction (Factor* f, FgVarNode* v)
{
fg_->removeFactor (f);
f->freeDistribution();
delete f;
fg_->removeVariable (v);
delete v;
}
bool
SPSolver::converged (void)
{
// this can happen if the graph is fully disconnected
if (links_.size() == 0) {
return true;
}
if (nIter_ == 0 || nIter_ == 1) {
return false;
}
bool converged = true;
for (unsigned i = 0; i < updateOrder_.size(); i++) {
double residual = getResidual (updateOrder_[i]);
if (DL >= 1) {
cout << updateOrder_[i].toString();
cout << " residual = " << residual << endl;
}
if (residual > accuracy_) {
if (SolverOptions::schedule == SolverOptions::S_MAX_RESIDUAL) {
Param maxResidual = (*(sortedOrder_.begin()))->getResidual();
if (maxResidual < SolverOptions::accuracy) {
converged = true;
} else {
converged = false;
if (DL == 0) {
break;
}
} else {
for (unsigned i = 0; i < links_.size(); i++) {
double residual = links_[i]->getResidual();
if (DL >= 2) {
cout << links_[i]->toString() + " residual = " << residual << endl;
}
if (residual > SolverOptions::accuracy) {
converged = false;
if (DL == 0) break;
}
}
}
@ -169,127 +310,161 @@ SPSolver::converged (void)
void
SPSolver::maxResidualSchedule (void)
{
if (nIter_ == 0) {
for (unsigned c = 0; c < updateOrder_.size(); c++) {
Link& l = updateOrder_[c];
calculateNextMessage (l.source, l.destination);
if (DL >= 1) {
cout << updateOrder_[c].toString() << " residual = " ;
cout << getResidual (updateOrder_[c]) << endl;
if (nIter_ == 1) {
for (unsigned i = 0; i < links_.size(); i++) {
links_[i]->setNextMessage (getFactor2VarMsg (links_[i]));
SortedOrder::iterator it = sortedOrder_.insert (links_[i]);
linkMap_.insert (make_pair (links_[i], it));
if (DL >= 2 && DL < 5) {
cout << "calculating " << links_[i]->toString() << endl;
}
}
sort (updateOrder_.begin(), updateOrder_.end(), compareResidual);
} else {
return;
}
for (unsigned c = 0; c < updateOrder_.size(); c++) {
Link& link = updateOrder_.front();
updateMessage (link);
resetResidual (link);
for (unsigned c = 0; c < links_.size(); c++) {
if (DL >= 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;
}
}
// update the messages that depend on message source --> destination
vector<Factor*> fstLevelNeighbors = link.destination->getFactors();
for (unsigned i = 0; i < fstLevelNeighbors.size(); i++) {
if (fstLevelNeighbors[i] != link.source) {
FgVarSet sndLevelNeighbors;
sndLevelNeighbors = fstLevelNeighbors[i]->getFgVarNodes();
for (unsigned j = 0; j < sndLevelNeighbors.size(); j++) {
if (sndLevelNeighbors[j] != link.destination) {
calculateNextMessage (fstLevelNeighbors[i], sndLevelNeighbors[j]);
SortedOrder::iterator it = sortedOrder_.begin();
Link* link = *it;
if (DL >= 2) {
cout << "updating " << (*sortedOrder_.begin())->toString() << endl;
}
if (link->getResidual() < SolverOptions::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
CFactorSet factorNeighbors = link->getVariable()->getFactors();
for (unsigned i = 0; i < factorNeighbors.size(); i++) {
if (factorNeighbors[i] != link->getFactor()) {
CLinkSet links = factorsI_[factorNeighbors[i]->getIndex()]->getLinks();
for (unsigned j = 0; j < links.size(); j++) {
if (links[j]->getVariable() != link->getVariable()) {
if (DL >= 2 && DL < 5) {
cout << " calculating " << links[j]->toString() << endl;
}
links[j]->setNextMessage (getFactor2VarMsg (links[j]));
LinkMap::iterator iter = linkMap_.find (links[j]);
sortedOrder_.erase (iter->second);
iter->second = sortedOrder_.insert (links[j]);
}
}
}
}
sort (updateOrder_.begin(), updateOrder_.end(), compareResidual);
}
}
}
void
SPSolver::updateMessage (const Link& link)
ParamSet
SPSolver::getFactor2VarMsg (const Link* link) const
{
updateMessage (link.source, link.destination);
}
void
SPSolver::updateMessage (const Factor* src, const FgVarNode* dest)
{
msgs_[dest->getIndex()]->updateMessage (src);
/* cout << src->getLabel() << " --> " << dest->getLabel() << endl;
cout << " m: " ;
Message msg = msgs_[dest->getIndex()]->getMessage (src);
for (unsigned i = 0; i < msg.size(); i++) {
if (i != 0) cout << ", " ;
cout << msg[i];
}
cout << endl;
*/
}
void
SPSolver::calculateNextMessage (const Link& link)
{
calculateNextMessage (link.source, link.destination);
}
void
SPSolver::calculateNextMessage (const Factor* src, const FgVarNode* dest)
{
FgVarSet neighbors = src->getFgVarNodes();
// calculate the product of MessageBankets sended
const Factor* src = link->getFactor();
const FgVarNode* dest = link->getVariable();
CFgVarSet neighbors = src->getFgVarNodes();
CLinkSet links = factorsI_[src->getIndex()]->getLinks();
// calculate the product of messages that were sent
// to factor `src', except from var `dest'
Factor result = *src;
Factor result (*src);
Factor temp;
if (DL >= 5) {
cout << "calculating " ;
cout << src->getLabel() << " --> " << dest->getLabel();
cout << endl;
}
for (unsigned i = 0; i < neighbors.size(); i++) {
if (neighbors[i] != dest) {
Message msg (neighbors[i]->getDomainSize(), 1);
calculateVarFactorMessage (neighbors[i], src, msg);
result *= Factor (neighbors[i], msg);
if (links[i]->getVariable() != dest) {
if (DL >= 5) {
cout << " message from " << links[i]->getVariable()->getLabel();
cout << ": " ;
ParamSet p = getVar2FactorMsg (links[i]);
cout << endl;
Factor temp2 (links[i]->getVariable(), p);
temp.multiplyByFactor (temp2);
temp2.freeDistribution();
} else {
Factor temp2 (links[i]->getVariable(), getVar2FactorMsg (links[i]));
temp.multiplyByFactor (temp2);
temp2.freeDistribution();
}
}
// marginalize all vars except `dest'
for (unsigned i = 0; i < neighbors.size(); i++) {
if (neighbors[i] != dest) {
result.marginalizeVariable (neighbors[i]);
}
if (links.size() >= 2) {
result.multiplyByFactor (temp, &(src->getCptEntries()));
if (DL >= 5) {
cout << " message product: " ;
cout << Util::parametersToString (temp.getParameters()) << endl;
cout << " factor product: " ;
cout << Util::parametersToString (src->getParameters());
cout << " x " ;
cout << Util::parametersToString (temp.getParameters());
cout << " = " ;
cout << Util::parametersToString (result.getParameters()) << endl;
}
temp.freeDistribution();
}
for (unsigned i = 0; i < links.size(); i++) {
if (links[i]->getVariable() != dest) {
result.removeVariable (links[i]->getVariable());
}
}
msgs_[dest->getIndex()]->setNextMessage (src, result.getParameters());
if (DL >= 5) {
cout << " final message: " ;
cout << Util::parametersToString (result.getParameters()) << endl << endl;
}
ParamSet msg = result.getParameters();
result.freeDistribution();
return msg;
}
void
SPSolver::calculateVarFactorMessage (const FgVarNode* src,
const Factor* dest,
Message& placeholder) const
ParamSet
SPSolver::getVar2FactorMsg (const Link* link) const
{
assert (src->getDomainSize() == (int)placeholder.size());
const FgVarNode* src = link->getVariable();
const Factor* dest = link->getFactor();
ParamSet msg;
if (src->hasEvidence()) {
for (unsigned i = 0; i < placeholder.size(); i++) {
if ((int)i != src->getEvidence()) {
placeholder[i] = 0.0;
msg.resize (src->getDomainSize(), 0.0);
msg[src->getEvidence()] = 1.0;
if (DL >= 5) {
cout << Util::parametersToString (msg);
}
} else {
placeholder[i] = 1.0;
}
}
} else {
MessageBanket* mb = msgs_[src->getIndex()];
vector<Factor*> neighbors = src->getFactors();
for (unsigned i = 0; i < neighbors.size(); i++) {
if (neighbors[i] != dest) {
const Message& fromFactor = mb->getMessage (neighbors[i]);
for (unsigned j = 0; j < fromFactor.size(); j++) {
placeholder[j] *= fromFactor[j];
}
}
}
msg.resize (src->getDomainSize(), 1.0);
}
if (DL >= 5) {
cout << Util::parametersToString (msg);
}
CLinkSet links = varsI_[src->getIndex()]->getLinks();
for (unsigned i = 0; i < links.size(); i++) {
if (links[i]->getFactor() != dest) {
CParamSet msgFromFactor = links[i]->getMessage();
for (unsigned j = 0; j < msgFromFactor.size(); j++) {
msg[j] *= msgFromFactor[j];
}
if (DL >= 5) {
cout << " x " << Util::parametersToString (msgFromFactor);
}
}
}
if (DL >= 5) {
cout << " = " << Util::parametersToString (msg);
}
return msg;
}

217
packages/CLPBN/clpbn/bp/SPSolver.h
View File

@ -1,10 +1,8 @@
#ifndef BP_SPSOLVER_H
#define BP_SPSOLVER_H
#ifndef BP_SP_SOLVER_H
#define BP_SP_SOLVER_H
#include <cmath>
#include <map>
#include <vector>
#include <string>
#include <set>
#include "Solver.h"
#include "FgVarNode.h"
@ -15,157 +13,118 @@ using namespace std;
class FactorGraph;
class SPSolver;
struct Link
class Link
{
Link (Factor* s, FgVarNode* d)
public:
Link (Factor* f, FgVarNode* v)
{
source = s;
destination = d;
factor_ = f;
var_ = v;
currMsg_.resize (v->getDomainSize(), 1);
nextMsg_.resize (v->getDomainSize(), 1);
msgSended_ = false;
residual_ = 0.0;
}
void setMessage (ParamSet msg)
{
Util::normalize (msg);
residual_ = Util::getMaxNorm (currMsg_, msg);
currMsg_ = msg;
}
void setNextMessage (CParamSet msg)
{
nextMsg_ = msg;
Util::normalize (nextMsg_);
residual_ = Util::getMaxNorm (currMsg_, nextMsg_);
}
void updateMessage (void)
{
currMsg_ = nextMsg_;
msgSended_ = true;
}
string toString (void) const
{
stringstream ss;
ss << source->getLabel() << " --> " ;
ss << destination->getLabel();
ss << factor_->getLabel();
ss << " -- " ;
ss << var_->getLabel();
return ss.str();
}
Factor* source;
FgVarNode* destination;
static SPSolver* klass;
};
class MessageBanket
{
public:
MessageBanket (const FgVarNode* var)
{
vector<Factor*> sources = var->getFactors();
for (unsigned i = 0; i < sources.size(); i++) {
indexMap_.insert (make_pair (sources[i], i));
currMsgs_.push_back (Message(var->getDomainSize(), 1));
nextMsgs_.push_back (Message(var->getDomainSize(), -10));
residuals_.push_back (0.0);
}
}
void updateMessage (const Factor* source)
{
unsigned idx = getIndex(source);
currMsgs_[idx] = nextMsgs_[idx];
}
void setNextMessage (const Factor* source, const Message& msg)
{
unsigned idx = getIndex(source);
nextMsgs_[idx] = msg;
residuals_[idx] = computeResidual (source);
}
const Message& getMessage (const Factor* source) const
{
return currMsgs_[getIndex(source)];
}
double getResidual (const Factor* source) const
{
return residuals_[getIndex(source)];
}
void resetResidual (const Factor* source)
{
residuals_[getIndex(source)] = 0.0;
}
Factor* getFactor (void) const { return factor_; }
FgVarNode* getVariable (void) const { return var_; }
CParamSet getMessage (void) const { return currMsg_; }
bool messageWasSended (void) const { return msgSended_; }
double getResidual (void) const { return residual_; }
void clearResidual (void) { residual_ = 0.0; }
private:
double computeResidual (const Factor* source)
{
double change = 0.0;
unsigned idx = getIndex (source);
const Message& currMessage = currMsgs_[idx];
const Message& nextMessage = nextMsgs_[idx];
for (unsigned i = 0; i < currMessage.size(); i++) {
change += abs (currMessage[i] - nextMessage[i]);
}
return change;
}
unsigned getIndex (const Factor* factor) const
{
assert (factor);
assert (indexMap_.find(factor) != indexMap_.end());
return indexMap_.find(factor)->second;
}
typedef map<const Factor*, unsigned> IndexMap;
IndexMap indexMap_;
vector<Message> currMsgs_;
vector<Message> nextMsgs_;
vector<double> residuals_;
Factor* factor_;
FgVarNode* var_;
ParamSet currMsg_;
ParamSet nextMsg_;
bool msgSended_;
double residual_;
};
class SPNodeInfo
{
public:
void addLink (Link* link) { links_.push_back (link); }
CLinkSet getLinks (void) { return links_; }
private:
LinkSet links_;
};
class SPSolver : public Solver
{
public:
SPSolver (const FactorGraph&);
~SPSolver (void);
SPSolver (FactorGraph&);
virtual ~SPSolver (void);
void runSolver (void);
ParamSet getPosterioriOf (const Variable* var) const;
virtual ParamSet getPosterioriOf (Vid) const;
ParamSet getJointDistributionOf (CVidSet);
private:
protected:
virtual void initializeSolver (void);
void runTreeSolver (void);
bool readyToSendMessage (const Link*) const;
virtual void createLinks (void);
virtual void deleteJunction (Factor*, FgVarNode*);
bool converged (void);
void maxResidualSchedule (void);
void updateMessage (const Link&);
void updateMessage (const Factor*, const FgVarNode*);
void calculateNextMessage (const Link&);
void calculateNextMessage (const Factor*, const FgVarNode*);
void calculateVarFactorMessage (
const FgVarNode*, const Factor*, Message&) const;
double getResidual (const Link&) const;
void resetResidual (const Link&) const;
friend bool compareResidual (const Link&, const Link&);
virtual void maxResidualSchedule (void);
virtual ParamSet getFactor2VarMsg (const Link*) const;
virtual ParamSet getVar2FactorMsg (const Link*) const;
const FactorGraph* fg_;
vector<MessageBanket*> msgs_;
Schedule schedule_;
int nIter_;
double accuracy_;
int maxIter_;
vector<Link> updateOrder_;
struct CompareResidual {
inline bool operator() (const Link* link1, const Link* link2)
{
return link1->getResidual() > link2->getResidual();
}
};
FactorGraph* fg_;
LinkSet links_;
vector<SPNodeInfo*> varsI_;
vector<SPNodeInfo*> factorsI_;
unsigned nIter_;
typedef multiset<Link*, CompareResidual> SortedOrder;
SortedOrder sortedOrder_;
inline double
SPSolver::getResidual (const Link& link) const
{
MessageBanket* mb = Link::klass->msgs_[link.destination->getIndex()];
return mb->getResidual (link.source);
}
typedef map<Link*, SortedOrder::iterator> LinkMap;
LinkMap linkMap_;
};
inline void
SPSolver::resetResidual (const Link& link) const
{
MessageBanket* mb = Link::klass->msgs_[link.destination->getIndex()];
mb->resetResidual (link.source);
}
inline bool
compareResidual (const Link& link1, const Link& link2)
{
MessageBanket* mb1 = Link::klass->msgs_[link1.destination->getIndex()];
MessageBanket* mb2 = Link::klass->msgs_[link2.destination->getIndex()];
return mb1->getResidual(link1.source) > mb2->getResidual(link2.source);
}
#endif
#endif // BP_SP_SOLVER_H

229
packages/CLPBN/clpbn/bp/Shared.h
View File

@ -2,14 +2,15 @@
#define BP_SHARED_H
#include <cmath>
#include <iostream>
#include <fstream>
#include <cassert>
#include <vector>
#include <map>
#include <unordered_map>
// Macro to disallow the copy constructor and operator= functions
#include <iostream>
#include <fstream>
#include <iomanip>
#define DISALLOW_COPY_AND_ASSIGN(TypeName) \
TypeName(const TypeName&); \
void operator=(const TypeName&)
@ -19,26 +20,46 @@ using namespace std;
class Variable;
class BayesNode;
class FgVarNode;
class Factor;
class Link;
class Edge;
typedef double Param;
typedef vector<Param> ParamSet;
typedef vector<Param> Message;
typedef const ParamSet& CParamSet;
typedef unsigned Vid;
typedef vector<Vid> VidSet;
typedef const VidSet& CVidSet;
typedef vector<Variable*> VarSet;
typedef vector<BayesNode*> NodeSet;
typedef vector<BayesNode*> BnNodeSet;
typedef const BnNodeSet& CBnNodeSet;
typedef vector<FgVarNode*> FgVarSet;
typedef const FgVarSet& CFgVarSet;
typedef vector<Factor*> FactorSet;
typedef const FactorSet& CFactorSet;
typedef vector<Link*> LinkSet;
typedef const LinkSet& CLinkSet;
typedef vector<Edge*> EdgeSet;
typedef const EdgeSet& CEdgeSet;
typedef vector<string> Domain;
typedef vector<unsigned> DomainConf;
typedef pair<unsigned, unsigned> DomainConstr;
typedef unordered_map<unsigned, unsigned> IndexMap;
typedef vector<unsigned> DConf;
typedef pair<unsigned, unsigned> DConstraint;
typedef map<unsigned, unsigned> IndexMap;
//extern unsigned DL;
// level of debug information
static const unsigned DL = 0;
// number of digits to show when printing a parameter
static const unsigned PRECISION = 10;
static const int NO_EVIDENCE = -1;
// shared by bp and sp solver
// number of digits to show when printing a parameter
static const unsigned PRECISION = 5;
static const bool EXPORT_TO_DOT = false;
static const unsigned EXPORT_MIN_SIZE = 30;
namespace SolverOptions
{
enum Schedule
{
S_SEQ_FIXED,
@ -46,34 +67,115 @@ enum Schedule
S_PARALLEL,
S_MAX_RESIDUAL
};
extern bool runBayesBall;
extern bool convertBn2Fg;
extern bool compressFactorGraph;
extern Schedule schedule;
extern double accuracy;
extern unsigned maxIter;
}
namespace Util
{
void normalize (ParamSet&);
void pow (ParamSet&, unsigned);
double getL1dist (CParamSet, CParamSet);
double getMaxNorm (CParamSet, CParamSet);
bool isInteger (const string&);
string parametersToString (CParamSet);
vector<DConf> getDomainConfigurations (const VarSet&);
vector<string> getInstantiations (const VarSet&);
};
struct NetInfo
{
NetInfo (unsigned c, double t)
NetInfo (void)
{
counting = c;
solvingTime = t;
counting = 0;
nIters = 0;
solvingTime = 0.0;
}
unsigned counting;
double solvingTime;
unsigned nIters;
};
struct CompressInfo
{
CompressInfo (unsigned a, unsigned b, unsigned c,
unsigned d, unsigned e) {
nUncVars = a;
nUncFactors = b;
nCompVars = c;
nCompFactors = d;
nNeighborlessVars = e;
}
unsigned nUncVars;
unsigned nUncFactors;
unsigned nCompVars;
unsigned nCompFactors;
unsigned nNeighborlessVars;
};
typedef map<unsigned, NetInfo> StatisticMap;
class Statistics
{
public:
static void updateStats (unsigned size, double time)
static void updateStats (unsigned size, unsigned nIters, double time)
{
StatisticMap::iterator it = stats_.find (size);
if (it == stats_.end()) {
stats_.insert (make_pair (size, NetInfo (1, 0.0)));
it = (stats_.insert (make_pair (size, NetInfo()))).first;
} else {
it->second.counting ++;
it->second.nIters += nIters;
it->second.solvingTime += time;
totalOfIterations += nIters;
if (nIters > maxIterations) {
maxIterations = nIters;
}
}
}
static void updateCompressingStats (unsigned nUncVars,
unsigned nUncFactors,
unsigned nCompVars,
unsigned nCompFactors,
unsigned nNeighborlessVars) {
compressInfo_.push_back (CompressInfo (
nUncVars, nUncFactors, nCompVars, nCompFactors, nNeighborlessVars));
}
static void printCompressingStats (const char* fileName)
{
ofstream out (fileName);
if (!out.is_open()) {
cerr << "error: cannot open file to write at " ;
cerr << "BayesNet::printCompressingStats()" << endl;
abort();
}
out << "--------------------------------------" ;
out << "--------------------------------------" << endl;
out << " Compression Stats" << endl;
out << "--------------------------------------" ;
out << "--------------------------------------" << endl;
out << left;
out << "Uncompress Compressed Uncompress Compressed Neighborless";
out << endl;
out << "Vars Vars Factors Factors Vars" ;
out << endl;
for (unsigned i = 0; i < compressInfo_.size(); i++) {
out << setw (13) << compressInfo_[i].nUncVars;
out << setw (13) << compressInfo_[i].nCompVars;
out << setw (13) << compressInfo_[i].nUncFactors;
out << setw (13) << compressInfo_[i].nCompFactors;
out << setw (13) << compressInfo_[i].nNeighborlessVars;
out << endl;
}
}
@ -84,20 +186,12 @@ class Statistics
return it->second.counting;
}
static void updateIterations (unsigned nIters)
{
totalOfIterations += nIters;
if (nIters > maxIterations) {
maxIterations = nIters;
}
}
static void writeStats (void)
{
ofstream out ("../../stats.txt");
if (!out.is_open()) {
cerr << "error: cannot open file to write at " ;
cerr << "Statistics:::updateStats()" << endl;
cerr << "Statistics::updateStats()" << endl;
abort();
}
unsigned avgIterations = 0;
@ -117,17 +211,24 @@ class Statistics
out << " average iterations: " << avgIterations << endl;
out << "total solving time " << totalSolvingTime << endl;
out << endl;
out << "Network Size\tCounting\tSolving Time\tAverage Time" << endl;
out << left << endl;
out << setw (15) << "Network Size" ;
out << setw (15) << "Counting" ;
out << setw (15) << "Solving Time" ;
out << setw (15) << "Average Time" ;
out << setw (15) << "#Iterations" ;
out << endl;
for (StatisticMap::iterator it = stats_.begin();
it != stats_.end(); it++) {
out << it->first;
out << "\t\t" << it->second.counting;
out << "\t\t" << it->second.solvingTime;
out << setw (15) << it->first;
out << setw (15) << it->second.counting;
out << setw (15) << it->second.solvingTime;
if (it->second.counting > 0) {
out << "\t\t" << it->second.solvingTime / it->second.counting;
out << setw (15) << it->second.solvingTime / it->second.counting;
} else {
out << "\t\t0.0" ;
out << setw (15) << "0.0" ;
}
out << setw (15) << it->second.nIters;
out << endl;
}
out.close();
@ -142,62 +243,8 @@ class Statistics
static StatisticMap stats_;
static unsigned maxIterations;
static unsigned totalOfIterations;
static vector<CompressInfo> compressInfo_;
};
class Util
{
public:
static void normalize (ParamSet& v)
{
double 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;
}
}
static double getL1dist (const ParamSet& v1, const ParamSet& v2)
{
assert (v1.size() == v2.size());
double dist = 0.0;
for (unsigned i = 0; i < v1.size(); i++) {
dist += abs (v1[i] - v2[i]);
}
return dist;
}
static double getMaxNorm (const ParamSet& v1, const ParamSet& v2)
{
assert (v1.size() == v2.size());
double max = 0.0;
for (unsigned i = 0; i < v1.size(); i++) {
double diff = abs (v1[i] - v2[i]);
if (diff > max) {
max = diff;
}
}
return max;
}
static bool isInteger (const string& s)
{
stringstream ss1 (s);
stringstream ss2;
int integer;
ss1 >> integer;
ss2 << integer;
return (ss1.str() == ss2.str());
}
};
//unsigned Statistics::totalOfIterations = 0;
#endif
#endif //BP_SHARED_H

48
packages/CLPBN/clpbn/bp/Solver.h
View File

@ -15,19 +15,30 @@ class Solver
{
gm_ = gm;
}
virtual ~Solver() {} // to call subclass destructor
virtual void runSolver (void) = 0;
virtual ParamSet getPosterioriOf (const Variable*) const = 0;
virtual ParamSet getPosterioriOf (Vid) const = 0;
virtual ParamSet getJointDistributionOf (const VidSet&) = 0;
void printPosterioriOf (const Variable* var) const
void printAllPosterioris (void) const
{
VarSet vars = gm_->getVariables();
for (unsigned i = 0; i < vars.size(); i++) {
printPosterioriOf (vars[i]->getVarId());
}
}
void printPosterioriOf (Vid vid) const
{
Variable* var = gm_->getVariable (vid);
cout << endl;
cout << setw (20) << left << var->getLabel() << "posteriori" ;
cout << endl;
cout << "------------------------------" ;
cout << endl;
const Domain& domain = var->getDomain();
ParamSet results = getPosterioriOf (var);
for (int xi = 0; xi < var->getDomainSize(); xi++) {
ParamSet results = getPosterioriOf (vid);
for (unsigned xi = 0; xi < var->getDomainSize(); xi++) {
cout << setw (20) << domain[xi];
cout << setprecision (PRECISION) << results[xi];
cout << endl;
@ -35,16 +46,35 @@ class Solver
cout << endl;
}
void printAllPosterioris (void) const
void printJointDistributionOf (const VidSet& vids)
{
VarSet vars = gm_->getVariables();
for (unsigned i = 0; i < vars.size(); i++) {
printPosterioriOf (vars[i]);
const ParamSet& jointDist = getJointDistributionOf (vids);
cout << endl;
cout << "joint distribution of " ;
VarSet vars;
for (unsigned i = 0; i < vids.size() - 1; i++) {
Variable* var = gm_->getVariable (vids[i]);
cout << var->getLabel() << ", " ;
vars.push_back (var);
}
Variable* var = gm_->getVariable (vids[vids.size() - 1]);
cout << var->getLabel() ;
vars.push_back (var);
cout << endl;
cout << "------------------------------" ;
cout << endl;
const vector<string>& domainConfs = Util::getInstantiations (vars);
for (unsigned i = 0; i < jointDist.size(); i++) {
cout << left << setw (20) << domainConfs[i];
cout << setprecision (PRECISION) << jointDist[i];
cout << endl;
}
cout << endl;
}
private:
const GraphicalModel* gm_;
};
#endif
#endif //BP_SOLVER_H

191
packages/CLPBN/clpbn/bp/Util.cpp Normal file
View File

@ -0,0 +1,191 @@
#include <sstream>
#include "Variable.h"
#include "Shared.h"
namespace SolverOptions {
bool runBayesBall = false;
bool convertBn2Fg = true;
bool compressFactorGraph = true;
Schedule schedule = S_SEQ_FIXED;
//Schedule schedule = S_SEQ_RANDOM;
//Schedule schedule = S_PARALLEL;
//Schedule schedule = S_MAX_RESIDUAL;
double accuracy = 0.0001;
unsigned maxIter = 1000; //FIXME
}
unsigned Statistics::numCreatedNets = 0;
unsigned Statistics::numSolvedPolyTrees = 0;
unsigned Statistics::numSolvedLoopyNets = 0;
unsigned Statistics::numUnconvergedRuns = 0;
unsigned Statistics::maxIterations = 0;
unsigned Statistics::totalOfIterations = 0;
vector<CompressInfo> Statistics::compressInfo_;
StatisticMap Statistics::stats_;
namespace Util {
void
normalize (ParamSet& v)
{
double 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;
}
}
void
pow (ParamSet& v, unsigned expoent)
{
for (unsigned i = 0; i < v.size(); i++) {
double value = 1;
for (unsigned j = 0; j < expoent; j++) {
value *= v[i];
}
v[i] = value;
}
}
double
getL1dist (const ParamSet& v1, const ParamSet& v2)
{
assert (v1.size() == v2.size());
double dist = 0.0;
for (unsigned i = 0; i < v1.size(); i++) {
dist += abs (v1[i] - v2[i]);
}
return dist;
}
double
getMaxNorm (const ParamSet& v1, const ParamSet& v2)
{
assert (v1.size() == v2.size());
double max = 0.0;
for (unsigned i = 0; i < v1.size(); i++) {
double diff = abs (v1[i] - v2[i]);
if (diff > max) {
max = diff;
}
}
return max;
}
bool
isInteger (const string& s)
{
stringstream ss1 (s);
stringstream ss2;
int integer;
ss1 >> integer;
ss2 << integer;
return (ss1.str() == ss2.str());
}
string
parametersToString (CParamSet v)
{
stringstream ss;
ss << "[" ;
for (unsigned i = 0; i < v.size() - 1; i++) {
ss << v[i] << ", " ;
}
if (v.size() != 0) {
ss << v[v.size() - 1];
}
ss << "]" ;
return ss.str();
}
vector<DConf>
getDomainConfigurations (const VarSet& vars)
{
unsigned nConfs = 1;
for (unsigned i = 0; i < vars.size(); i++) {
nConfs *= vars[i]->getDomainSize();
}
vector<DConf> confs (nConfs);
for (unsigned i = 0; i < nConfs; i++) {
confs[i].resize (vars.size());
}
unsigned nReps = 1;
for (int i = vars.size() - 1; i >= 0; i--) {
unsigned index = 0;
while (index < nConfs) {
for (unsigned j = 0; j < vars[i]->getDomainSize(); j++) {
for (unsigned r = 0; r < nReps; r++) {
confs[index][i] = j;
index++;
}
}
}
nReps *= vars[i]->getDomainSize();
}
return confs;
}
vector<string>
getInstantiations (const VarSet& vars)
{
//FIXME handle variables without domain
/*
char c = 'a' ;
const DConf& conf = entries[i].getDomainConfiguration();
for (unsigned j = 0; j < conf.size(); j++) {
if (j != 0) ss << "," ;
ss << c << conf[j] + 1;
c ++;
}
*/
unsigned rowSize = 1;
for (unsigned i = 0; i < vars.size(); i++) {
rowSize *= vars[i]->getDomainSize();
}
vector<string> headers (rowSize);
unsigned nReps = 1;
for (int i = vars.size() - 1; i >= 0; i--) {
Domain domain = vars[i]->getDomain();
unsigned index = 0;
while (index < rowSize) {
for (unsigned j = 0; j < vars[i]->getDomainSize(); j++) {
for (unsigned r = 0; r < nReps; r++) {
if (headers[index] != "") {
headers[index] = domain[j] + ", " + headers[index];
} else {
headers[index] = domain[j];
}
index++;
}
}
}
nReps *= vars[i]->getDomainSize();
}
return headers;
}
}

81
packages/CLPBN/clpbn/bp/Variable.h
View File

@ -1,9 +1,10 @@
#ifndef BP_GENERIC_VARIABLE_H
#define BP_GENERIC_VARIABLE_H
#ifndef BP_VARIABLE_H
#define BP_VARIABLE_H
#include <algorithm>
#include <sstream>
#include <algorithm>
#include "Shared.h"
using namespace std;
@ -12,52 +13,80 @@ class Variable
{
public:
Variable (unsigned varId)
Variable (const Variable* v)
{
this->varId_ = varId;
vid_ = v->getVarId();
dsize_ = v->getDomainSize();
if (v->hasDomain()) {
domain_ = v->getDomain();
dsize_ = domain_.size();
} else {
dsize_ = v->getDomainSize();
}
evidence_ = v->getEvidence();
if (v->hasLabel()) {
label_ = new string (v->getLabel());
} else {
label_ = 0;
}
}
Variable (Vid vid)
{
this->vid_ = vid;
this->dsize_ = 0;
this->evidence_ = -1;
this->evidence_ = NO_EVIDENCE;
this->label_ = 0;
}
Variable (unsigned varId, unsigned dsize, int evidence = -1)
Variable (Vid vid, unsigned dsize, int evidence = NO_EVIDENCE,
const string& lbl = string())
{
assert (dsize != 0);
assert (evidence < (int)dsize);
this->varId_ = varId;
this->vid_ = vid;
this->dsize_ = dsize;
this->evidence_ = evidence;
if (!lbl.empty()) {
this->label_ = new string (lbl);
} else {
this->label_ = 0;
}
}
Variable (unsigned varId, const Domain& domain, int evidence = -1)
Variable (Vid vid, const Domain& domain, int evidence = NO_EVIDENCE,
const string& lbl = string())
{
assert (!domain.empty());
assert (evidence < (int)domain.size());
this->varId_ = varId;
this->vid_ = vid;
this->dsize_ = domain.size();
this->domain_ = domain;
this->evidence_ = evidence;
if (!lbl.empty()) {
this->label_ = new string (lbl);
} else {
this->label_ = 0;
}
}
~Variable (void)
{
delete label_;
}
unsigned getVarId (void) const { return varId_; }
unsigned getVarId (void) const { return vid_; }
unsigned getIndex (void) const { return index_; }
void setIndex (unsigned idx) { index_ = idx; }
int getDomainSize (void) const { return dsize_; }
bool hasEvidence (void) const { return evidence_ != -1; }
unsigned getDomainSize (void) const { return dsize_; }
bool hasEvidence (void) const { return evidence_ != NO_EVIDENCE; }
int getEvidence (void) const { return evidence_; }
bool hasDomain (void) { return !domain_.empty(); }
bool hasLabel (void) { return label_ != 0; }
bool hasDomain (void) const { return !domain_.empty(); }
bool hasLabel (void) const { return label_ != 0; }
bool isValidStateIndex (int index)
{
return index >= 0 && index < dsize_;
return index >= 0 && index < (int)dsize_;
}
bool isValidState (const string& state)
@ -70,7 +99,7 @@ class Variable
assert (dsize_ != 0);
if (domain_.size() == 0) {
Domain d;
for (int i = 0; i < dsize_; i++) {
for (unsigned i = 0; i < dsize_; i++) {
stringstream ss;
ss << "x" << i ;
d.push_back (ss.str());
@ -110,7 +139,7 @@ class Variable
}
}
void setLabel (string label)
void setLabel (const string& label)
{
label_ = new string (label);
}
@ -119,25 +148,25 @@ class Variable
{
if (label_ == 0) {
stringstream ss;
ss << "v" << varId_;
ss << "v" << vid_;
return ss.str();
} else {
return *label_;
}
}
protected:
unsigned varId_;
string* label_;
unsigned index_;
int evidence_;
private:
DISALLOW_COPY_AND_ASSIGN (Variable);
Vid vid_;
unsigned dsize_;
int evidence_;
Domain domain_;
int dsize_;
string* label_;
unsigned index_;
};
#endif // BP_GENERIC_VARIABLE_H
#endif // BP_VARIABLE_H

34
packages/CLPBN/clpbn/bp/examples/1parentNchilds.yap Executable file
View File

@ -0,0 +1,34 @@
:- use_module(library(clpbn)).
:- set_clpbn_flag(solver, bp).
%
% R
% / | \
% / | \
% A B C
%
r(R) :-
{ R = r with p([t, f], [0.35, 0.65]) }.
a(A) :-
r(R),
child_dist(R,Dist),
{ A = a with Dist }.
b(B) :-
r(R),
child_dist(R,Dist),
{ B = b with Dist }.
c(C) :-
r(R),
child_dist(R,Dist),
{ C = c with Dist }.
child_dist(R, p([t, f], [0.3, 0.4, 0.25, 0.05], [R])).

53
packages/CLPBN/clpbn/bp/examples/bp-example.xml Executable file
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@ -0,0 +1,53 @@
<?xml version="1.0" encoding="US-ASCII"?>
<!--
A B
\ /
\ /
C
-->
<BIF VERSION="0.3">
<NETWORK>
<NAME>Neapolitan</NAME>
<VARIABLE TYPE="nature">
<NAME>A</NAME>
<OUTCOME>a1</OUTCOME>
<OUTCOME>a2</OUTCOME>
</VARIABLE>
<VARIABLE TYPE="nature">
<NAME>B</NAME>
<OUTCOME>b1</OUTCOME>
<OUTCOME>b2</OUTCOME>
</VARIABLE>
<VARIABLE TYPE="nature">
<NAME>C</NAME>
<OUTCOME>c1</OUTCOME>
<OUTCOME>c2</OUTCOME>
</VARIABLE>
<DEFINITION>
<FOR>A</FOR>
<TABLE> .695 .305 </TABLE>
</DEFINITION>
<DEFINITION>
<FOR>B</FOR>
<TABLE> .25 .75 </TABLE>
</DEFINITION>
<DEFINITION>
<FOR>C</FOR>
<GIVEN>A</GIVEN>
<GIVEN>B</GIVEN>
<TABLE> .2 .8 .45 .55 .32 .68 .7 .3 </TABLE>
</DEFINITION>
</NETWORK>
</BIF>

4
packages/CLPBN/clpbn/bp/examples/burglary-alarm.uai
View File

@ -9,10 +9,10 @@ MARKOV
2 4 2
2
.001 .009
.001 .999
2
.002 .008
.002 .998
8
.95 .94 .29 .001

4
packages/CLPBN/clpbn/bp/examples/burglary-alarm.xml
View File

@ -49,12 +49,12 @@
<DEFINITION>
<FOR>B</FOR>
<TABLE> .001 .009 </TABLE>
<TABLE> .001 .999 </TABLE>
</DEFINITION>
<DEFINITION>
<FOR>E</FOR>
<TABLE> .002 .008 </TABLE>
<TABLE> .002 .998 </TABLE>
</DEFINITION>
<DEFINITION>

57
packages/CLPBN/clpbn/bp/examples/burglary-alarm.yap
View File

@ -1,54 +1,29 @@
:- use_module(library(clpbn)).
:- set_clpbn_flag(solver, vel).
:- set_clpbn_flag(solver, bp).
%
% B E
% \ /
% \ /
% A
% / \
% / \
% J M
%
r(R) :- r_cpt(RCpt),
{ R = r with p([r1, r2], RCpt) }.
t(T) :- t_cpt(TCpt),
{ T = t with p([t1, t2], TCpt) }.
b(B) :-
b_table(BDist),
{ B = b with p([b1, b2], BDist) }.
a(A) :- r(R), t(T), a_cpt(ACpt),
{ A = a with p([a1, a2], ACpt, [R, T]) }.
e(E) :-
e_table(EDist),
{ E = e with p([e1, e2], EDist) }.
j(J) :- a(A), j_cpt(JCpt),
{ J = j with p([j1, j2], JCpt, [A]) }.
a(A) :-
b(B),
e(E),
a_table(ADist),
{ A = a with p([a1, a2], ADist, [B, E]) }.
m(M) :- a(A), m_cpt(MCpt),
{ M = m with p([m1, m2], MCpt, [A]) }.
j(J):-
a(A),
j_table(JDist),
{ J = j with p([j1, j2], JDist, [A]) }.
m(M):-
a(A),
m_table(MDist),
{ M = m with p([m1, m2], MDist, [A]) }.
b_table([0.001, 0.009]).
e_table([0.002, 0.008]).
a_table([0.95, 0.94, 0.29, 0.001,
r_cpt([0.001, 0.999]).
t_cpt([0.002, 0.998]).
a_cpt([0.95, 0.94, 0.29, 0.001,
0.05, 0.06, 0.71, 0.999]).
j_table([0.9, 0.05,
j_cpt([0.9, 0.05,
0.1, 0.95]).
m_table([0.7, 0.01,
m_cpt([0.7, 0.01,
0.3, 0.99]).

15
packages/CLPBN/clpbn/bp/examples/convergence.xml
View File

@ -16,34 +16,37 @@
<VARIABLE TYPE="nature">
<NAME>A</NAME>
<OUTCOME></OUTCOME>
<OUTCOME>a1</OUTCOME>
<OUTCOME>a2</OUTCOME>
</VARIABLE>
<VARIABLE TYPE="nature">
<NAME>B</NAME>
<OUTCOME></OUTCOME>
<OUTCOME>b1</OUTCOME>
<OUTCOME>b2</OUTCOME>
</VARIABLE>
<VARIABLE TYPE="nature">
<NAME>C</NAME>
<OUTCOME></OUTCOME>
<OUTCOME>c1</OUTCOME>
<OUTCOME>c2</OUTCOME>
</VARIABLE>
<DEFINITION>
<FOR>A</FOR>
<TABLE>1</TABLE>
<TABLE>.695 .305</TABLE>
</DEFINITION>
<DEFINITION>
<FOR>B</FOR>
<TABLE>1</TABLE>
<TABLE>0.25 0.75</TABLE>
</DEFINITION>
<DEFINITION>
<FOR>C</FOR>
<GIVEN>A</GIVEN>
<GIVEN>B</GIVEN>
<TABLE>1</TABLE>
<TABLE>0.2 0.8 0.45 0.55 0.32 0.68 0.7 0.3</TABLE>
</DEFINITION>
</NETWORK>

67
packages/CLPBN/clpbn/bp/examples/lambda fail.xml Executable file
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@ -0,0 +1,67 @@
<?xml version="1.0" encoding="US-ASCII"?>
<!--
P1 P2 P3
\ | /
\ | /
-
C
-->
<BIF VERSION="0.3">
<NETWORK>
<NAME>Simple Convergence</NAME>
<VARIABLE TYPE="nature">
<NAME>P1</NAME>
<OUTCOME>p1</OUTCOME>
<OUTCOME>p2</OUTCOME>
</VARIABLE>
<VARIABLE TYPE="nature">
<NAME>P2</NAME>
<OUTCOME>p1</OUTCOME>
<OUTCOME>p2</OUTCOME>
<OUTCOME>p3</OUTCOME>
</VARIABLE>
<VARIABLE TYPE="nature">
<NAME>P3</NAME>
<OUTCOME>p1</OUTCOME>
<OUTCOME>p2</OUTCOME>
</VARIABLE>
<VARIABLE TYPE="nature">
<NAME>C</NAME>
<OUTCOME>c1</OUTCOME>
<OUTCOME>c2</OUTCOME>
</VARIABLE>
<DEFINITION>
<FOR>P1</FOR>
<TABLE>.695 .305</TABLE>
</DEFINITION>
<DEFINITION>
<FOR>P2</FOR>
<TABLE>0.2 0.3 0.5</TABLE>
</DEFINITION>
<DEFINITION>
<FOR>P3</FOR>
<TABLE>0.25 0.75</TABLE>
</DEFINITION>
<DEFINITION>
<FOR>C</FOR>
<GIVEN>P1</GIVEN>
<GIVEN>P2</GIVEN>
<GIVEN>P3</GIVEN>
<TABLE>0.2 0.8 0.45 0.55 0.32 0.68 0.7 0.3 0.3 0.7 0.55 0.45 0.22 0.78 0.25 0.75 0.11 0.89 0.34 0.66 0.1 0.9 0.6 0.4</TABLE>
</DEFINITION>
</NETWORK>
</BIF>

1
packages/CLPBN/clpbn/bp/examples/neapolitan.yap
View File

@ -2,6 +2,7 @@
:- use_module(library(clpbn)).
:- set_clpbn_flag(solver, bp).
%:- set_clpbn_flag(solver, jt).
%
% B F

17
packages/CLPBN/clpbn/bp/examples/sp-example.uai Executable file
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@ -0,0 +1,17 @@
MARKOV
3
2 2 2
3
1 0
1 1
3 2 0 1
2
.695 .305
2
.25 .75
8
0.2 0.45 0.32 0.7
0.8 0.55 0.68 0.3

128
packages/CLPBN/clpbn/bp/examples/test_bn.xml Executable file
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@ -0,0 +1,128 @@
<?xml version="1.0" encoding="US-ASCII"?>
<!--
A B C
\ | /
\ | /
D
/ | \
/ | \
E F G
-->
<BIF VERSION="0.3">
<NETWORK>
<NAME>Node with several parents and childs</NAME>
<VARIABLE TYPE="nature">
<NAME>A</NAME>
<OUTCOME>a1</OUTCOME>
<OUTCOME>a2</OUTCOME>
</VARIABLE>
<VARIABLE TYPE="nature">
<NAME>B</NAME>
<OUTCOME>b1</OUTCOME>
<OUTCOME>b2</OUTCOME>
<OUTCOME>b3</OUTCOME>
<OUTCOME>b4</OUTCOME>
</VARIABLE>
<VARIABLE TYPE="nature">
<NAME>C</NAME>
<OUTCOME>c1</OUTCOME>
<OUTCOME>c2</OUTCOME>
<OUTCOME>c3</OUTCOME>
</VARIABLE>
<VARIABLE TYPE="nature">
<NAME>D</NAME>
<OUTCOME>d1</OUTCOME>
<OUTCOME>d2</OUTCOME>
<OUTCOME>d3</OUTCOME>
</VARIABLE>
<VARIABLE TYPE="nature">
<NAME>E</NAME>
<OUTCOME>e1</OUTCOME>
<OUTCOME>e2</OUTCOME>
<OUTCOME>e3</OUTCOME>
<OUTCOME>e4</OUTCOME>
</VARIABLE>
<VARIABLE TYPE="nature">
<NAME>F</NAME>
<OUTCOME>f1</OUTCOME>
<OUTCOME>f2</OUTCOME>
<OUTCOME>f3</OUTCOME>
</VARIABLE>
<VARIABLE TYPE="nature">
<NAME>G</NAME>
<OUTCOME>g1</OUTCOME>
<OUTCOME>g2</OUTCOME>
</VARIABLE>
<DEFINITION>
<FOR>A</FOR>
<TABLE> .1 .2 </TABLE>
</DEFINITION>
<DEFINITION>
<FOR>B</FOR>
<TABLE> .01 .02 .03 .04 </TABLE>
</DEFINITION>
<DEFINITION>
<FOR>C</FOR>
<TABLE> .11 .22 .33 </TABLE>
</DEFINITION>
<DEFINITION>
<FOR>D</FOR>
<GIVEN>A</GIVEN>
<GIVEN>B</GIVEN>
<GIVEN>C</GIVEN>
<TABLE>
.522 .008 .99 .01 .2 .8 .003 .457 .423 .007 .92 .04 .5 .232 .033 .227 .112 .048 .91 .21 .24 .18 .005 .227
.212 .04 .59 .21 .6 .1 .023 .215 .913 .017 .96 .01 .55 .422 .013 .417 .272 .068 .61 .11 .26 .28 .205 .322
.142 .028 .19 .11 .5 .67 .013 .437 .163 .067 .12 .06 .1 .262 .063 .167 .512 .028 .11 .41 .14 .68 .015 .92
</TABLE>
</DEFINITION>
<DEFINITION>
<FOR>E</FOR>
<GIVEN>D</GIVEN>
<TABLE>
.111 .11 .1
.222 .22 .2
.333 .33 .3
.444 .44 .4
</TABLE>
</DEFINITION>
<DEFINITION>
<FOR>F</FOR>
<GIVEN>D</GIVEN>
<TABLE>
.112 .111 .110
.223 .222 .221
.334 .333 .332
</TABLE>
</DEFINITION>
<DEFINITION>
<FOR>G</FOR>
<GIVEN>D</GIVEN>
<TABLE>
.101 .102 .103
.201 .202 .203
</TABLE>
</DEFINITION>
</NETWORK>
</BIF>

36
packages/CLPBN/clpbn/bp/examples/test_mk.uai Executable file
View File

@ -0,0 +1,36 @@
MARKOV
5
4 2 3 2 3
7
1 0
1 1
1 2
1 3
1 4
2 0 1
4 1 2 3 4
4
0.1 0.7 0.43 0.22
2
0.2 0.6
3
0.3 0.5 0.2
2
0.15 0.75
3
0.25 0.45 0.15
8
0.210 0.333 0.457 0.4
0.811 0.000 0.189 0.89
36
0.1 0.15 0.2 0.25 0.3 0.45 0.5 0.55 0.65 0.7 0.75 0.9
0.11 0.22 0.33 0.44 0.55 0.66 0.77 0.88 0.91 0.93 0.95 0.97
0.42 0.22 0.33 0.44 0.15 0.36 0.27 0.28 0.21 0.13 0.25 0.17

69
packages/CLPBN/clpbn/bp/examples/ve_example.xml Executable file
View File

@ -0,0 +1,69 @@
<?xml version="1.0" encoding="US-ASCII"?>
<!--
A B
\ /
\ /
C
|
|
D
-->
<BIF VERSION="0.3">
<NETWORK>
<NAME>Simple Loop</NAME>
<VARIABLE TYPE="nature">
<NAME>A</NAME>
<OUTCOME>a1</OUTCOME>
<OUTCOME>a2</OUTCOME>
</VARIABLE>
<VARIABLE TYPE="nature">
<NAME>B</NAME>
<OUTCOME>b1</OUTCOME>
<OUTCOME>b2</OUTCOME>
</VARIABLE>
<VARIABLE TYPE="nature">
<NAME>C</NAME>
<OUTCOME>c1</OUTCOME>
<OUTCOME>c2</OUTCOME>
</VARIABLE>
<VARIABLE TYPE="nature">
<NAME>D</NAME>
<OUTCOME>d1</OUTCOME>
<OUTCOME>d2</OUTCOME>
</VARIABLE>
<DEFINITION>
<FOR>A</FOR>
<TABLE> .001 .009 </TABLE>
</DEFINITION>
<DEFINITION>
<FOR>B</FOR>
<TABLE> .002 .008 </TABLE>
</DEFINITION>
<DEFINITION>
<FOR>C</FOR>
<GIVEN>A</GIVEN>
<GIVEN>B</GIVEN>
<TABLE> .95 .05 .94 .06 .29 .71 .001 .999 </TABLE>
</DEFINITION>
<DEFINITION>
<FOR>D</FOR>
<GIVEN>C</GIVEN>
<TABLE> .9 .1 .05 .95 </TABLE>
</DEFINITION>
</NETWORK>
</BIF>

9
packages/PLStream/pl-write.c
View File

@ -884,6 +884,15 @@ writePrimitive(term_t t, write_options *options)
return writeString(t, options);
#endif /* O_STRING */
#if __YAP_PROLOG__
{
number n;
n.type = V_INTEGER;
n.value.i = 0;
return WriteNumber(&n, options);
}
#endif
assert(0);
fail;
}

30
packages/PLStream/pl-yap.c
View File

@ -1121,6 +1121,9 @@ Yap_StreamPosition(IOSTREAM *st)
return StreamPosition(st);
}
IOSTREAM *STD_PROTO(Yap_Scurin, (void));
int STD_PROTO(Yap_dowrite, (Term, IOSTREAM *, int, int));
IOSTREAM *
Yap_Scurin(void)
{
@ -1128,6 +1131,32 @@ Yap_Scurin(void)
return Scurin;
}
int
Yap_dowrite(Term t, IOSTREAM *stream, int flags, int priority)
/* term to be written */
/* consumer */
/* write options */
{
CACHE_REGS
int swi_flags;
int res;
Int slot = Yap_InitSlot(t PASS_REGS);
swi_flags = 0;
if (flags & Quote_illegal_f)
swi_flags |= PL_WRT_QUOTED;
if (flags & Handle_vars_f)
swi_flags |= PL_WRT_NUMBERVARS;
if (flags & Use_portray_f)
swi_flags |= PL_WRT_PORTRAY;
if (flags & Ignore_ops_f)
swi_flags |= PL_WRT_IGNOREOPS;
res = PL_write_term(stream, slot, priority, swi_flags);
Yap_RecoverSlots(1 PASS_REGS);
return res;
}
#if THREADS
@ -1178,6 +1207,7 @@ error:
return rc;
}
int
recursiveMutexInit(recursiveMutex *m)
{

2
packages/RDF

@ -1 +1 @@
Subproject commit cee6c346ba77e046ef1873b9d8c88c52c3baae2d
Subproject commit a5d2a3755f86ebffd8eb6e2a6921790d299eab30

2
packages/clib

@ -1 +1 @@
Subproject commit f6fce313722d2f69e5ce6074f304ce05065bbf40
Subproject commit a6f0f4ec7d5fd51ca8b268b8392da9b20bfd1b44

2
packages/http

@ -1 +1 @@
Subproject commit 3f7eee803d46071f10804010f7266b3864bab7e6
Subproject commit 2a0843683e8790d8129fa4bad99c82a5fcaf441b

2
packages/plunit

@ -1 +1 @@
Subproject commit aa90b8f8a67e605e82566b719a8f20d125598bd2
Subproject commit 2daa5b9942a9fc22005ec48b6560f8596f33d995

2
packages/semweb

@ -1 +1 @@
Subproject commit 2229eb3807b21497ffd680686ceeeddeac9f57fb
Subproject commit e3c7eb9a9a54d6a9069396ecd1c3b537a8f6165a

2
packages/sgml

@ -1 +1 @@
Subproject commit babcbfe9cc5ab269cd5fd4f024e9d57bd3d0a8db
Subproject commit f1c3ef54f4d9431ba5b4188cb72ca3056d20b202

59
packages/tai/Makefile.in
View File

@ -1,59 +0,0 @@
#
# default base directory for YAP installation
# (EROOT for architecture-dependent files)
#
prefix = @prefix@
exec_prefix = @exec_prefix@
ROOTDIR = $(prefix)
EROOTDIR = @exec_prefix@
abs_top_builddir = @abs_top_builddir@
#
# where the binary should be
#
BINDIR = $(EROOTDIR)/bin
#
# where YAP should look for libraries
#
LIBDIR=@libdir@
YAPLIBDIR=@libdir@/Yap
#
#
DEFS=@DEFS@ -D_YAP_NOT_INSTALLED_=1
CC=@CC@
CFLAGS= @SHLIB_CFLAGS@ $(YAP_EXTRAS) $(DEFS) -I$(srcdir) -I../.. -I$(srcdir)/../../include -I$(srcdir)/../PLStream -I$(srcdir)/../PLStream/windows -I$(srcdir)/../../H
#
#
# You shouldn't need to change what follows.
#
INSTALL=@INSTALL@
INSTALL_DATA=@INSTALL_DATA@
INSTALL_PROGRAM=@INSTALL_PROGRAM@
SHELL=/bin/sh
RANLIB=@RANLIB@
srcdir=@srcdir@
SO=@SO@
#4.1VPATH=@srcdir@:@srcdir@/OPTYap
CWD=$(PWD)
#
OBJS=pl-tai.o
SOBJS=pl-tai.@SO@
#in some systems we just create a single object, in others we need to
# create a libray
all: $(SOBJS)
pl-tai.o: $(srcdir)/pl-tai.c
(cd libtai ; $(MAKE))
$(CC) -c $(CFLAGS) $(srcdir)/pl-tai.c -o pl-tai.o
@DO_SECOND_LD@pl-tai.@SO@: pl-tai.o
@DO_SECOND_LD@ @SHLIB_LD@ $(LDFLAGS) -o pl-tai.@SO@ pl-tai.o libtai/libtai.a @EXTRA_LIBS_FOR_SWIDLLS@
install: all
$(INSTALL_PROGRAM) $(SOBJS) $(DESTDIR)$(YAPLIBDIR)
clean:
rm -f *.o *~ $(OBJS) $(SOBJS) *.BAK
-(cd libtai && $(MAKE) clean)

2
packages/zlib

@ -1 +1 @@
Subproject commit deea4bfdf7041387e91eca37978a5c8db9287eda
Subproject commit 109bf1d224009dc049ab12a0fbbb50511ef8e1fb

2
pl/consult.yap
View File

@ -1050,6 +1050,8 @@ make :-
fail.
make.
make_library_index(_Directory).
'$file_name'(Stream,F) :-
stream_property(Stream, file_name(F)), !.
'$file_name'(user_input,user_output).

2
pl/debug.yap
View File

@ -495,7 +495,7 @@ debugging :-
'$continue_debugging'(no, '$execute_nonstop'(G,M)).
'$spycall'(G, M, CalledFromDebugger, InRedo) :-
'$flags'(G,M,F,F),
F /\ 0x18402000 =\= 0, !, % dynamic procedure, logical semantics, user-C, or source
F /\ 0x08402000 =\= 0, !, % dynamic procedure, logical semantics, or source
% use the interpreter
CP is '$last_choice_pt',
'$clause'(G, M, Cl, _),

31
pl/errors.yap
View File

@ -245,22 +245,15 @@ print_message(Severity, Msg) :-
'$notrace'(user:portray_message(Severity, Msg)), !.
% This predicate has more hooks than a pirate ship!
print_message(Severity, Term) :-
(
(
'$oncenotrace'(user:generate_message_hook(Term, [], Lines)) ->
true
;
'$oncenotrace'(prolog:message(Term, Lines, [])) ->
true
;
'$messages':generate_message(Term, Lines, [])
)
-> ( nonvar(Term),
% first step at hook processing
'$message_to_lines'(Term, Lines),
( nonvar(Term),
'$oncenotrace'(user:message_hook(Term, Severity, Lines))
-> !
; !, '$print_system_message'(Term, Severity, Lines)
)
).
->
true
;
'$print_system_message'(Term, Severity, Lines)
), !.
print_message(silent, _) :- !.
print_message(_, error(syntax_error(syntax_error(_,between(_,L,_),_,_,_,_,StreamName)),_)) :- !,
format(user_error,'SYNTAX ERROR at ~a, close to ~d~n',[StreamName,L]).
@ -271,6 +264,14 @@ print_message(_, loaded(A, F, _, Time, Space)) :- !,
print_message(_, Term) :-
format(user_error,'~q~n',[Term]).
'$message_to_lines'(Term, Lines) :-
'$oncenotrace'(user:generate_message_hook(Term, [], Lines)), !.
'$message_to_lines'(Term, Lines) :-
'$oncenotrace'(prolog:message(Term, Lines, [])), !.
'$message_to_lines'(Term, Lines) :-
'$messages':generate_message(Term, Lines, []), !.
% print_system_message(+Term, +Level, +Lines)
%
% Print the message if the user did not intecept the message.

14
pl/messages.yap
View File

@ -69,6 +69,10 @@ generate_message(debug) --> !,
[ debug ].
generate_message(trace) --> !,
[ trace ].
generate_message(error(Error,Context)) -->
{ Error = existence_error(procedure,_) }, !,
system_message(error(Error,Context)),
stack_dump(error(Error,Context)).
generate_message(error(Error,context(Cause,Extra))) -->
system_message(error(Error,Cause)),
stack_dump(error(Error,context(Cause,Extra))).
@ -130,8 +134,6 @@ system_message(no_match(P)) -->
[ 'No matching predicate for ~w.' - [P] ].
system_message(leash([A|B])) -->
[ 'Leashing set to ~w.' - [[A|B]] ].
system_message(existence_error(prolog_flag,F)) -->
[ 'Prolog Flag ~w: new Prolog flags must be created using create_prolog_flag/3.' - [F] ].
system_message(singletons([SV],P)) -->
[ 'Singleton variable ~s in ~q.' - [SV,P] ].
system_message(singletons(SVs,P)) -->
@ -159,14 +161,18 @@ system_message(error(context_error(Goal,Who),Where)) -->
system_message(error(domain_error(DomainType,Opt), Where)) -->
[ 'DOMAIN ERROR- ~w: ' - Where],
domain_error(DomainType, Opt).
system_message(error(existence_error(directory,Key), Where)) -->
[ 'EXISTENCE ERROR- ~w: ~w not an existing directory' - [Where,Key] ].
system_message(error(existence_error(key,Key), Where)) -->
[ 'EXISTENCE ERROR- ~w: ~w not an existing key' - [Where,Key] ].
system_message(existence_error(prolog_flag,F)) -->
[ 'Prolog Flag ~w: new Prolog flags must be created using create_prolog_flag/3.' - [F] ].
system_message(error(existence_error(prolog_flag,P), Where)) --> !,
[ 'EXISTENCE ERROR- ~w: prolog flag ~w is undefined' - [Where,P] ].
system_message(error(existence_error(procedure,P), context(Call,Parent))) --> !,
[ 'EXISTENCE ERROR- procedure ~w is undefined, called from context ~w~n Goal was ~w' - [P,Parent,Call] ].
system_message(error(existence_error(stream,Stream), Where)) -->
[ 'EXISTENCE ERROR- ~w: ~w not an open stream' - [Where,Stream] ].
system_message(error(existence_error(key,Key), Where)) -->
[ 'EXISTENCE ERROR- ~w: ~w not an existing key' - [Where,Key] ].
system_message(error(existence_error(thread,Thread), Where)) -->
[ 'EXISTENCE ERROR- ~w: ~w not a running thread' - [Where,Thread] ].
system_message(error(existence_error(variable,Var), Where)) -->