From c804d105b6e73440c85c79786b477bf840308fa0 Mon Sep 17 00:00:00 2001
From: Theofrastos Mantadelis <theo@herbie.cs.kuleuven.be>
Date: Wed, 3 Nov 2010 19:22:11 +0100
Subject: [PATCH] Some ProbLog improvements related with tabling efficiency,
 more to come soon

---
 packages/ProbLog/problog.yap                | 804 ++++++++++----------
 packages/ProbLog/problog/logger.yap         |  56 +-
 packages/ProbLog/problog/nestedtries.yap    | 423 ++++++++++
 packages/ProbLog/problog/tabling.yap        |   5 +-
 packages/ProbLog/problog/timer.yap          |  30 +-
 packages/ProbLog/problog/tptree.yap         | 221 +++---
 packages/ProbLog/problog/utils_learning.yap |  47 +-
 packages/ProbLog/problog_learning.yap       |  28 +-
 8 files changed, 1025 insertions(+), 589 deletions(-)
 create mode 100644 packages/ProbLog/problog/nestedtries.yap

diff --git a/packages/ProbLog/problog.yap b/packages/ProbLog/problog.yap
index fe47bad99..b7083adcf 100644
--- a/packages/ProbLog/problog.yap
+++ b/packages/ProbLog/problog.yap
@@ -2,8 +2,8 @@
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %
-%  $Date: 2010-10-06 12:56:13 +0200 (Wed, 06 Oct 2010) $
-%  $Revision: 4877 $
+%  $Date: 2010-10-21 10:47:36 +0200 (Thu, 21 Oct 2010) $
+%  $Revision: 4970 $
 %
 %  This file is part of ProbLog
 %  http://dtai.cs.kuleuven.be/problog
@@ -14,7 +14,7 @@
 %  Katholieke Universiteit Leuven
 %
 %  Main authors of this file:
-%  Angelika Kimmig, Vitor Santos Costa,Bernd Gutmann,
+%  Angelika Kimmig, Vitor Santos Costa, Bernd Gutmann,
 %  Theofrastos Mantadelis, Guy Van den Broeck
 %
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -300,21 +300,17 @@
 :- style_check(all).
 :- yap_flag(unknown,error).
 
-:- set_prolog_flag(to_chars_mode,quintus).
-
 % general yap modules
-:- use_module(library(charsio)).
-:- use_module(library(lists)).
-:- use_module(library(terms)).
-:- use_module(library(random)).		% PM doesn't seem to be used!
-:- use_module(library(system)).
-:- use_module(library(rbtrees)).	% PM doesn't seem to be used!
+:- use_module(library(lists), [append/3,member/2,memberchk/2,reverse/2,select/3,nth1/3,nth1/4,nth0/4]).
+:- use_module(library(terms), [variable_in_term/2] ).
+:- use_module(library(random), [random/1]).
+:- use_module(library(system), [tmpnam/1,shell/2,delete_file/1,delete_file/2]).
 :- use_module(library(ordsets), [list_to_ord_set/2, ord_insert/3, ord_union/3]).
 
 % problog related modules
 :- use_module('problog/variables').
 :- use_module('problog/extlists').
-:- use_module('problog/gflags', [flag_store/2]).
+:- use_module('problog/gflags').
 :- use_module('problog/flags').
 :- use_module('problog/print').
 :- use_module('problog/os').
@@ -323,6 +319,8 @@
 :- use_module('problog/sampling').
 :- use_module('problog/intervals').
 :- use_module('problog/mc_DNF_sampling').
+:- use_module('problog/timer').
+:- use_module('problog/utils').
 :- catch(use_module('problog/ad_converter'),_,true).
 :- catch(use_module('problog/variable_elimination'),_,true).
 
@@ -344,7 +342,6 @@
 :- dynamic(tunable_fact/2).
 :- dynamic(non_ground_fact/1).
 :- dynamic(continuous_fact/1).
-%:- dynamic(problog_dir/1).
 % global, manipulated via problog_control/2
 :- dynamic(up/0).
 :- dynamic(limit/0).
@@ -368,14 +365,11 @@
 :- dynamic(answer/1).
 % to keep track of the groundings for non-ground facts
 :- dynamic(grounding_is_known/2).
-
 % for decisions
 :- dynamic(decision_fact/2).
-
 % for fact where the proabability is a variable
 :- dynamic(dynamic_probability_fact/1).
 :- dynamic(dynamic_probability_fact_extract/2).
-
 % for storing continuous parts of proofs (Hybrid ProbLog)
 :- dynamic([hybrid_proof/3, hybrid_proof/4]).
 :- dynamic(hybrid_proof_disjoint/4).
@@ -384,6 +378,8 @@
 % and this module provides the predicate X::Y to iterate over them
 :- multifile('::'/2).
 
+:- multifile(user:term_expansion/1).
+
 % directory where problogbdd executable is located
 % automatically set during loading -- assumes it is in same place as this file (problog.yap)
 :- getcwd(PD), set_problog_path(PD).
@@ -566,6 +562,7 @@ generate_atoms(N, A):-
 % dynamic predicate problog_predicate(Name,Arity) keeps track of predicates that already have wrapper clause
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
+% converts annotated disjunctions - if loaded
 term_expansion_intern(A, B, C):-
   catch(term_expansion_intern_ad(A, B, C), _, false).
 
@@ -617,12 +614,69 @@ term_expansion_intern((Annotation :: Head :- Body), Module, problog:ExpandedClau
 	).
 
 
-/* this can slow down prolog time by several orders if there's lots of them
-user:term_expansion(P::Goal,Goal) :-
-	P \= t(_),
-	P =:= 1,
-	!.
-*/
+
+
+% handles continuous facts
+term_expansion_intern(Head :: Goal,Module,problog:ProbFact) :-
+	nonvar(Head),
+	Head=(X,Distribution),
+	!,
+	(
+	 Distribution=gaussian(Mu,Sigma)
+	->
+	 true;
+	 ( throw(unknown_distribution)
+	 )
+	),
+
+	 (
+	  variable_in_term_exactly_once(Goal,X)
+	 ->
+	  true;
+	  (
+	   throw(variable)
+	  )
+	 ),
+
+	copy_term(((X,Distribution) :: Goal), ((X2,Distribution2) :: Goal2)),
+	% bind_the_variable
+	X2=Distribution2,
+
+	% find position in term
+	Goal2=..[Name|Args],
+	once(nth1(Pos,Args,Distribution2)),
+
+	length(Args,Arity),
+	atomic_concat([problogcontinuous_,Name],ProblogName),
+	probclause_id(ID),
+	
+	% is it a tunable fact?
+	(
+	 (number(Mu),number(Sigma))
+	->
+	 NewArgs=Args;
+	 (
+	  Mu_Random is 0.1, % random*4-2,
+	  Sigma_Random is 0.4, % random*2+0.5,
+	  nth1(Pos,Args,_,KeepArgs),
+	  nth1(Pos,NewArgs,gaussian(Mu_Random,Sigma_Random),KeepArgs),
+	  assertz(tunable_fact(ID,gaussian(Mu,Sigma)))
+	 )
+	),
+	ProbFact =.. [ProblogName,ID|NewArgs],
+
+	(
+	 ground(Goal)
+	->
+	 true;
+	 assertz(non_ground_fact(ID))
+	),
+	assertz(continuous_fact(ID)),
+	problog_continuous_predicate(Name, Arity, Pos,ProblogName,Module).
+
+
+
+	
 
 % handles probabilistic facts
 term_expansion_intern(P :: Goal,Module,problog:ProbFact) :-
@@ -704,71 +758,11 @@ sample_initial_value_for_tunable_fact(LogP) :-
 
 
 
-% Hybrid ProbLog stuff
-
-is_valid_gaussian(X) :-
-	compound(X),
-	X=gaussian(Mu,Sigma),
-	(
-	 ((number(Mu),number(Sigma));(Mu=t(_),Sigma=t(_)))
-	->
-	 true;
-	 throw(invalid_gaussian(X))
-	).
-
-:- multifile(user:term_expansion/1).
-
-user:term_expansion(Goal, problog:ProbFact) :-
-	compound(Goal),
-	Goal=..[Name|Args],
-	once( (nth(Pos,Args,GaussianArg),is_valid_gaussian(GaussianArg)) ),
-
-	%Goal contains a Gaussian, there is some work to do
-
-	( % check for a second Gaussian
-	 (nth(Pos2,Args,GaussianArg2),Pos2\=Pos,is_valid_gaussian(GaussianArg2))
-	->
-	  (
-	   format(user_error,'We only support continous atoms with at most one Gaussian inside.~n',[]),
-	   format(user_error,'Your program contains the atom ~w with more than one.~n',[]),
-	   throw(unsupported_multivariate_gaussian(Goal))
-	  );
-	  true
-	),
-
-	functor(Goal, Name, Arity),
-	atomic_concat([problogcontinuous_,Name],ProblogName),
-	probclause_id(ID),
-
-	GaussianArg=gaussian(Mu_Arg,Sigma_Arg),
-
-	% is it a tunable fact?
-	(
-	 (number(Mu_Arg),number(Sigma_Arg))
-	->
-	 NewArgs=Args;
-	 (
-	  Mu_Random is 0.1, % random*4-2,
-	  Sigma_Random is 0.4, % random*2+0.5,
-	  nth(Pos,Args,_,KeepArgs),
-	  nth(Pos,NewArgs,gaussian(Mu_Random,Sigma_Random),KeepArgs),
-	  assertz(tunable_fact(ID,gaussian(Mu_Arg,Sigma_Arg)))
-	 )
-	),
-	ProbFact =.. [ProblogName,ID|NewArgs],
-
-	(
-	 ground(Goal)
-	->
-	 true;
-	 assertz(non_ground_fact(ID))
-	),
-	assertz(continuous_fact(ID)),
-	problog_continuous_predicate(Name, Arity, Pos,ProblogName).
+%
 
 
 % introduce wrapper clause if predicate seen first time
-problog_continuous_predicate(Name, Arity,ContinuousArgumentPosition,_) :-
+problog_continuous_predicate(Name, Arity,ContinuousArgumentPosition,_,_) :-
 	problog_continuous_predicate(Name, Arity,OldContinuousArgumentPosition),
 	!,
 	(
@@ -784,7 +778,7 @@ problog_continuous_predicate(Name, Arity,ContinuousArgumentPosition,_) :-
 	  throw(continuous_argument(not_unique_position))
 	 )
 	).
-problog_continuous_predicate(Name, Arity, ContinuousArgumentPosition, ProblogName) :-
+problog_continuous_predicate(Name, Arity, ContinuousArgumentPosition, ProblogName,Module) :-
 
 	LBefore is ContinuousArgumentPosition-1,
 	LAfter is Arity-ContinuousArgumentPosition,
@@ -798,9 +792,8 @@ problog_continuous_predicate(Name, Arity, ContinuousArgumentPosition, ProblogNam
 
 
 	ProbFact =.. [ProblogName,ID|ProbArgs],
-	prolog_load_context(module,Mod),
 
-	assertz( (Mod:OriginalGoal :- ProbFact,
+	assertz( (Module:OriginalGoal :- ProbFact,
 		                   % continuous facts always get a grounding ID, even when they are actually ground
 		                   % this simplifies the BDD script generation
 		                     non_ground_fact_grounding_id(ProbFact,Ground_ID),
@@ -812,6 +805,9 @@ problog_continuous_predicate(Name, Arity, ContinuousArgumentPosition, ProblogNam
 	ArityPlus1 is Arity+1,
 	dynamic(problog:ProblogName/ArityPlus1).
 
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% predicates for the user to manipulate continuous facts
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 in_interval(ID,Low,High) :-
 	number(Low),
@@ -834,7 +830,9 @@ interval_merge((_ID,GroundID,_Type),Interval) :-
 	b_setval(Key,NewInterval).
 
 
-
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% assert/retract for probabilistic facts
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 problog_assert(P::Goal) :-
 	problog_assert(user,P::Goal).
@@ -849,6 +847,10 @@ problog_retractall(Goal) :-
 	ProbLogGoal=..[F2|Args2],
 	retractall(problog:ProbLogGoal).
 
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% 
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
 
 % introduce wrapper clause if predicate seen first time
 problog_predicate(Name, Arity, _,_) :-
@@ -874,6 +876,39 @@ problog_predicate(Name, Arity, ProblogName,Mod) :-
 	ArityPlus2 is Arity+2,
 	dynamic(problog:ProblogName/ArityPlus2).
 
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% Generating and storing the grounding IDs for
+% non-ground probabilistic facts
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+non_ground_fact_grounding_id(Goal,ID) :-
+	ground(Goal),
+	!,
+	(
+	 grounding_is_known(Goal,ID)
+	->
+	 true;
+	 (
+	  nb_getval(non_ground_fact_grounding_id_counter,ID),
+	  ID2 is ID+1,
+	  nb_setval(non_ground_fact_grounding_id_counter,ID2),
+	  assertz(grounding_is_known(Goal,ID))
+	 )
+	).
+non_ground_fact_grounding_id(Goal,_) :-	
+	format(user_error,'The current program uses non-ground facts.~n', []),
+	format(user_error,'If you query those, you may only query fully-grounded versions of the fact.~n',[]),
+	format(user_error,'Within the current proof, you queried for ~q which is not ground.~2n', [Goal]),
+	throw(error(non_ground_fact(Goal))).
+
+reset_non_ground_facts :-
+	required(keep_ground_ids),
+	!.
+reset_non_ground_facts :-
+	nb_setval(non_ground_fact_grounding_id_counter,0),
+	retractall(grounding_is_known(_,_)).
+
+:- initialization(reset_non_ground_facts).
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % Getting the ID for any kind of ground fact
@@ -947,78 +982,40 @@ probclause_id(ID) :-
 	C1 is ID+1,
 	nb_setval(probclause_counter,C1), !.
 
-non_ground_fact_grounding_id(Goal,ID) :-
-	(
-	    ground(Goal)
-	->
-	    true;
-	    (
-		format(user_error,'The current program uses non-ground facts.~n', []),
-		format(user_error,'If you query those, you may only query fully-grounded versions of the fact.~n',[]),
-		format(user_error,'Within the current proof, you queried for ~q which is not ground.~n~n', [Goal]),
-		throw(error(non_ground_fact(Goal)))
-	    )
-	),
-	(
-	    grounding_is_known(Goal,ID)
-	->
-	    true;
-	    (
-		nb_getval(non_ground_fact_grounding_id_counter,ID),
-		ID2 is ID+1,
-		nb_setval(non_ground_fact_grounding_id_counter,ID2),
-		assertz(grounding_is_known(Goal,ID))
-	    )
-	).
 
-reset_non_ground_facts :-
-  (required(keep_ground_ids) ->
-      true
-  ;
-      nb_setval(non_ground_fact_grounding_id_counter,0),
-      retractall(grounding_is_known(_,_))
-  ).
-
-:- initialization(reset_non_ground_facts).
 
 % backtrack over all probabilistic facts
 % must come before term_expansion
-P::Goal :-
-    probabilistic_fact(P,Goal,_).
+Prob::Goal :-
+    probabilistic_fact(Prob,Goal,_).
 
 % backtrack over all probabilistic facts
-probabilistic_fact(P2,Goal,ID) :-
+probabilistic_fact(Prob,Goal,ID) :-
+	ground(Goal),
+	!,
+	Goal =.. [F|Args],
+	atomic_concat('problog_',F,F2),
+	append([ID|Args],[LProb],Args2),
+	Goal2 =..[F2|Args2],
+	length(Args2,N),
+	current_predicate(F2/N),
+	Goal2,
+	number(LProb),
+	Prob is exp(LProb).
+probabilistic_fact(Prob,Goal,ID) :-
+	get_internal_fact(ID,ProblogTerm,_ProblogName,_ProblogArity),
+	ProblogTerm =.. [F,_ID|Args],
+	append(Args2,[LProb],Args),
+	name(F,[_p,_r,_o,_b,_l,_o,_g,_|F2Chars]),
+	name(F2,F2Chars),
+	Goal =.. [F2|Args2],
 	(
-	 ground(Goal)
+	 dynamic_probability_fact(ID)
 	->
-	 (
-	  Goal =.. [F|Args],
-	  atomic_concat('problog_',F,F2),
-	  append([ID|Args],[P],Args2),
-	  Goal2 =..[F2|Args2],
-	  length(Args2,N),
-	  current_predicate(F2/N),
-	  call(Goal2),
-	  number(P),
-	  P2 is exp(P)
-	 );
-	 (
-	  get_internal_fact(ID,ProblogTerm,_ProblogName,_ProblogArity),
-	  ProblogTerm =.. [F,_ID|Args],
-	  append(Args2,[P],Args),
-	  name(F,[_p,_r,_o,_b,_l,_o,_g,_|F2Chars]),
-	  name(F2,F2Chars),
-	  Goal =.. [F2|Args2],
-	  (
-	   dynamic_probability_fact(ID)
-	  ->
-	   P2=p;
-	   P2 is exp(P)
-	  )
-	 )
+	 Prob=p;
+	 Prob is exp(LProb)
 	).
 
-
 % generates unique IDs for proofs
 proof_id(ID) :-
 	nb_getval(problog_proof_id,ID),
@@ -1044,17 +1041,17 @@ get_fact_probability(A, Prob) :-
   once(append(Part1, [95|Part2], A_Codes)), % 95 = '_'
   number_codes(ID, Part1), !,
   % let's check whether Part2 contains an 'l' (l=low)
-  (member(108, Part2) ->
-    fail
+  \+ memberchk(108,Part2),
+  number_codes(Grounding_ID, Part2),
+  (
+   dynamic_probability_fact(ID)
+  ->
+   grounding_is_known(Goal, Grounding_ID),
+   dynamic_probability_fact_extract(Goal, Prob)
   ;
-    number_codes(Grounding_ID, Part2),
-    (dynamic_probability_fact(ID) ->
-      grounding_is_known(Goal, Grounding_ID),
-      dynamic_probability_fact_extract(Goal, Prob)
-    ;
-      get_fact_probability(ID, Prob)
-    )
-  ).
+   get_fact_probability(ID, Prob)
+  ),
+  !.
 get_fact_probability(ID,Prob) :-
   ground(ID),
   prob_for_id(ID,Prob,_),
@@ -1093,9 +1090,9 @@ set_fact_probability(ID,Prob) :-
 	get_internal_fact(ID,ProblogTerm,ProblogName,ProblogArity),
 	retract(ProblogTerm),
 	ProblogTerm =.. [ProblogName|ProblogTermArgs],
-	nth(ProblogArity,ProblogTermArgs,_,KeepArgs),
+	nth1(ProblogArity,ProblogTermArgs,_,KeepArgs),
 	NewLogProb is log(Prob),
-	nth(ProblogArity,NewProblogTermArgs,NewLogProb,KeepArgs),
+	nth1(ProblogArity,NewProblogTermArgs,NewLogProb,KeepArgs),
 	NewProblogTerm =.. [ProblogName|NewProblogTermArgs],
 	assertz(NewProblogTerm).
 
@@ -1176,7 +1173,7 @@ get_fact(ID,OutsideTerm) :-
 	ProblogTerm =.. [_Functor,ID|Args],
 	atomic_concat('problog_',OutsideFunctor,ProblogName),
 	Last is ProblogArity-1,
-	nth(Last,Args,_LogProb,OutsideArgs),
+	nth1(Last,Args,_LogProb,OutsideArgs),
 	OutsideTerm =.. [OutsideFunctor|OutsideArgs].
 % ID of instance of non-ground fact: get fact from grounding table
 get_fact(ID,OutsideTerm) :-
@@ -1216,73 +1213,82 @@ get_fact_list([ID|IDs],[Fact|Facts]) :-
 %       else update state and succeed
 %
 % do not maintain gloabl variables in montecarlo mode
-add_to_proof(ID, Prob) :-
-  (problog_control(check, mc) ->
-    montecarlo_check(ID)
-  ;
-    b_getval(problog_steps,MaxSteps),
-    b_getval(problog_probability, CurrentP),
-    nb_getval(problog_threshold, CurrentThreshold),
-    b_getval(problog_current_proof, IDs),
-    %%%% Bernd, changes for negated ground facts
-    \+ open_end_memberchk(not(ID),IDs),
-    %%%% Bernd, changes for negated ground facts
-    (MaxSteps =< 0 ->
-      fail
-    ;
-      (open_end_memberchk(ID, IDs) -> %Theo
-        true
-      ;
-        open_end_add(ID, IDs, NIDs), %Theo
-        % \+ prune_check(NIDs, Trie_Completed_Proofs),
-        multiply_probabilities(CurrentP, Prob, NProb),
-        (NProb < CurrentThreshold ->
-          upper_bound(NIDs),
-          fail
-        ;
-          b_setval(problog_probability, NProb),
-          b_setval(problog_current_proof, NIDs)
-        )
-      ),
-      Steps is MaxSteps - 1,
-      b_setval(problog_steps, Steps)
-    )
-  ).
+add_to_proof(ID, _LogProb) :-
+	problog_control(check, mc),
+	!,
+	montecarlo_check(ID).
+add_to_proof(ID, LogProb) :-
+	b_getval(problog_steps,MaxSteps),
+	MaxSteps>0,
+	b_getval(problog_probability, CurrentLogProb),
+	nb_getval(problog_threshold, CurrentThreshold),
+	b_getval(problog_current_proof, IDs),
+	
+	% check whether negation of this fact is already used in proof
+	\+ open_end_memberchk(not(ID),IDs),
+	
+	(  % check whether this fact is already used in proof  
+	   open_end_memberchk(ID, IDs)
+	->	
+	   true;
+	   (
+	    open_end_add(ID, IDs, NIDs),
+	    NewLogProb is CurrentLogProb+LogProb,
+	    (
+	     NewLogProb < CurrentThreshold
+	    ->
+	     (
+	      upper_bound(NIDs),
+	      fail
+	     );
+	     (
+	      b_setval(problog_probability, NewLogProb),
+	      b_setval(problog_current_proof, NIDs)
+	     )
+	    )
+	   )
+	),
+	Steps is MaxSteps - 1,
+	b_setval(problog_steps, Steps).
 
-%%%% Bernd, changes for negated ground facts
-add_to_proof_negated(ID, Prob) :-
-  (problog_control(check, mc) ->
-    % the sample has to fail if the fact is negated
-    \+ montecarlo_check(ID)
-  ;
-    b_getval(problog_steps, MaxSteps),
-    b_getval(problog_probability, CurrentP),
-    nb_getval(problog_threshold, CurrentThreshold),
-    b_getval(problog_current_proof, IDs),
-    \+ open_end_memberchk(ID, IDs),
-    (MaxSteps =< 0 ->
-      fail
-    ;
-      (open_end_memberchk(not(ID), IDs) ->
-        true
-      ;
-        open_end_add(not(ID), IDs, NIDs), %Theo
-        % \+ prune_check(NIDs, Trie_Completed_Proofs),
-        InverseProb is log(1 - exp(Prob)),
-        multiply_probabilities(CurrentP, InverseProb, NProb),
-        (NProb < CurrentThreshold ->
-          upper_bound(NIDs),  %% checkme
-          fail
-        ;
-          b_setval(problog_probability, NProb),
-          b_setval(problog_current_proof, NIDs)
-        )
-      ),
-      Steps is MaxSteps - 1,
-      b_setval(problog_steps, Steps)
-    )
-  ).
-%%%% Bernd, changes for negated ground facts
+add_to_proof_negated(ID, _) :-
+	problog_control(check, mc),
+	!,
+	% the sample has to fail if the fact is negated
+	\+ montecarlo_check(ID).
+add_to_proof_negated(ID, LogProb) :-
+	b_getval(problog_steps, MaxSteps),
+	MaxSteps>0,
+	b_getval(problog_probability, CurrentLogProb),
+	nb_getval(problog_threshold, CurrentThreshold),
+	b_getval(problog_current_proof, IDs),
+
+	% check whether unnegated fact is already used in proof
+	\+ open_end_memberchk(ID, IDs),
+	
+	( % check wether negation of this fact is already used in proof
+	 open_end_memberchk(not(ID), IDs)
+	->
+	 true;
+	 (
+	  open_end_add(not(ID), IDs, NIDs),
+	  NewLogProb is CurrentLogProb + log(1-exp(LogProb)),
+	  (
+	   NewLogProb < CurrentThreshold
+	  ->
+	   (
+	    upper_bound(NIDs),
+	    fail
+	   );
+	   (
+	    b_setval(problog_probability, NewLogProb),
+	    b_setval(problog_current_proof, NIDs)
+	   )
+	  )
+	 )
+	),
+	Steps is MaxSteps - 1,
+	b_setval(problog_steps, Steps).
 
 %Hybrid
 add_continuous_to_proof(ID,GroundID) :-
@@ -1376,15 +1382,12 @@ split_g_id([A|B],[A|FactID],GroundingID) :-
 %
 % List always length>=1 -> don't need []=true-case for tries
 upper_bound(List) :-
-  problog_control(on, limit),
-  problog_control(check, up),
-  nb_getval(problog_stopped_proofs, Trie_Stopped_Proofs),
-  open_end_close_end(List, R),
-% (prune_check(R, Trie_Stopped_Proofs) -> true; insert_ptree(R, Trie_Stopped_Proofs)).
-  insert_ptree(R, Trie_Stopped_Proofs).
-
-multiply_probabilities(CurrentLogP, LogProb, NLogProb) :-
-  NLogProb is CurrentLogP + LogProb.
+	problog_control(on, limit),
+	problog_control(check, up),
+	nb_getval(problog_stopped_proofs, Trie_Stopped_Proofs),
+	open_end_close_end(List, R),
+	% (prune_check(R, Trie_Stopped_Proofs) -> true; insert_ptree(R, Trie_Stopped_Proofs)).
+	insert_ptree(R, Trie_Stopped_Proofs).
 
 % this is called by all inference methods before the actual ProbLog goal
 % to set up environment for proving
@@ -1404,7 +1407,20 @@ init_problog(Threshold) :-
 	b_setval(problog_continuous_facts_used,[]),
 	retractall(hybrid_proof(_,_,_)),
 	retractall(hybrid_proof(_,_,_,_)),
-	retractall(hybrid_proof_disjoint(_,_,_,_)).
+	retractall(hybrid_proof_disjoint(_,_,_,_)),
+
+	% reset all timers in case a query failed before
+	timer_reset(variable_elimination_time),
+	timer_reset(bdd_script_time),
+	timer_reset(bdd_generation_time),
+	timer_reset(script_gen_time_naive),
+	timer_reset(bdd_gen_time_naive),
+	timer_reset(script_gen_time_builtin),
+	timer_reset(bdd_gen_time_builtin),
+	timer_reset(script_gen_time_dec),
+	timer_reset(bdd_gen_time_dec),
+	timer_reset(sld_time),
+	timer_reset(build_tree_low).
 
 % idea: proofs that are refinements of known proof can be pruned as they don't add probability mass
 % note that current ptree implementation doesn't provide the check as there's no efficient method known so far...
@@ -1471,14 +1487,12 @@ problog_statistics(Stat, Result):-
 	problog_var_get(Stat, Result).
 
 generate_order_by_prob_fact_appearance(Order, FileName):-
-  open(FileName, 'write', Stream),
-  forall(member(PF, Order), (
-    ptree:get_var_name(PF, Name),
-    format(Stream, "@~w~n", [Name]))),
-/*  findall(_, (recorded(variable_elimination, prob_fact(PF, _), _),
-    ptree:get_var_name(PF, Name),
-    format(Stream, "@~w~n", [Name])), _),*/
-  close(Stream).
+	open(FileName, 'write', Stream),
+	forall(member(PF, Order), (
+				   ptree:get_var_name(PF, Name),
+				   format(Stream, "@~w~n", [Name])
+				  )),
+	close(Stream).
 
 get_order(Trie, Order):-
 	findall(List, ptree:traverse_ptree(Trie, List), Proofs),
@@ -1528,11 +1542,11 @@ eval_dnf(OriTrie1, Prob, Status) :-
 
 
   ((problog_flag(variable_elimination, true), nb_getval(problog_nested_tries, false)) ->
-    statistics(walltime, _),
+    timer_start(variable_elimination_time),
     trie_check_for_and_cluster(OriTrie),
-    statistics(walltime, [_, VariableEliminationTime]),
+    timer_stop(variable_elimination_time,Variable_Elimination_Time),
+    problog_var_set(variable_elimination_time, Variable_Elimination_Time),
     trie_replace_and_cluster(OriTrie, Trie),
-    problog_var_set(variable_elimination_time, VariableEliminationTime),
     variable_elimination_stats(Clusters, OrigPF, CompPF),
     problog_var_set(variable_elimination_stats, compress(Clusters, OrigPF, CompPF)),
     clean_up
@@ -1576,7 +1590,7 @@ eval_dnf(OriTrie1, Prob, Status) :-
   convert_filename_to_working_path(BDDParFileFlag, BDDParFile),
   % old reduction method doesn't support nested tries
   ((problog_flag(use_old_trie, true), nb_getval(problog_nested_tries, false)) ->
-    statistics(walltime, _),
+    timer_start(bdd_script_time),
     (problog_control(check, remember) ->
       bdd_ptree_map(Trie, BDDFile, BDDParFile, Mapping),
       convert_filename_to_working_path(save_map, MapFile),
@@ -1587,14 +1601,14 @@ eval_dnf(OriTrie1, Prob, Status) :-
     ;
       bdd_ptree(Trie, BDDFile, BDDParFile)
     ),
-    statistics(walltime, [_, ScriptGenerationTime]),
-    problog_var_set(bdd_script_time, ScriptGenerationTime),
+    timer_stop(bdd_script_time,BDD_Script_Time),
+    problog_var_set(bdd_script_time, BDD_Script_Time),
 
-    statistics(walltime, _),
+    timer_start(bdd_generation_time),
     execute_bdd_tool(BDDFile, BDDParFile, Prob_old, Status_old),
-    statistics(walltime,[_, BDDGenerationTime]),
-    (Status_old = ok ->
-      problog_var_set(bdd_generation_time, BDDGenerationTime),
+    timer_stop(bdd_generation_time,BDD_Generation_Time),
+    (Status_old == ok ->
+      problog_var_set(bdd_generation_time, BDD_Generation_Time),
       problog_var_set(probability, Prob_old)
     ;
       problog_var_set(bdd_generation_time, fail),
@@ -1605,18 +1619,17 @@ eval_dnf(OriTrie1, Prob, Status) :-
   ),
   % naive method with nested trie support but not loops
   ((problog_flag(use_naive_trie, true); (problog_flag(use_old_trie, true), nb_getval(problog_nested_tries, true))) ->
-    statistics(walltime, _),
-%     atomic_concat([BDDFile, '_naive'], BDDFile_naive),
+   timer_start(script_gen_time_naive),
     BDDFile = BDDFile_naive,
     nested_ptree_to_BDD_script(Trie, BDDFile_naive, BDDParFile),
-    statistics(walltime, [_, ScriptGenerationTime_naive]),
-    problog_var_set(bdd_script_time(naive), ScriptGenerationTime_naive),
+    timer_stop(script_gen_time_naive,Script_Gen_Time_Naive),
+    problog_var_set(bdd_script_time(naive), Script_Gen_Time_Naive),
 
-    statistics(walltime, _),
+     timer_start(bdd_gen_time_naive),
     execute_bdd_tool(BDDFile_naive, BDDParFile, Prob_naive, Status_naive),
-    statistics(walltime,[_, BDDGenerationTime_naive]),
-    (Status_naive = ok ->
-      problog_var_set(bdd_generation_time(naive), BDDGenerationTime_naive),
+     timer_stop(bdd_gen_time_naive,BDD_Gen_Time_Naive),
+    (Status_naive == ok ->
+      problog_var_set(bdd_generation_time(naive),BDD_Gen_Time_Naive),
       problog_var_set(probability(naive), Prob_naive)
     ;
       problog_var_set(bdd_generation_time(naive), fail),
@@ -1625,9 +1638,6 @@ eval_dnf(OriTrie1, Prob, Status) :-
   ;
     true
   ),
-%   problog_statistics,
-%   print_nested_ptree(Trie),
-%   findall(_,(problog_chktabled(_ID, _T), writeln(problog_chktabled(_ID, _T))),_),
   % reduction method with depth_breadth trie support
   problog_flag(db_trie_opt_lvl, ROptLevel),
   problog_flag(db_min_prefix, MinPrefix),
@@ -1640,8 +1650,7 @@ eval_dnf(OriTrie1, Prob, Status) :-
   forall(member(OptLevel, Levels), (
     (problog_flag(use_db_trie, true) ->
       tries:trie_db_opt_min_prefix(MinPrefix),
-      statistics(walltime, _),
-%       atomic_concat([BDDFile, '_builtin_', OptLevel], BDDFile_builtin),
+      timer_start(script_gen_time_builtin),
       BDDFile = BDDFile_builtin,
       (nb_getval(problog_nested_tries, false) ->
         trie_to_bdd_trie(Trie, DBTrie, BDDFile_builtin, OptLevel, BDDParFile)
@@ -1657,16 +1666,17 @@ eval_dnf(OriTrie1, Prob, Status) :-
       problog_var_set(dbtrie_statistics(Builtin), tries(memory(FM), tries(FT), entries(FE), nodes(FN))),
 
       delete_ptree(DBTrie),
-      statistics(walltime, [_, ScriptGenerationTime_builtin]),
-      problog_var_set(bdd_script_time(Builtin), ScriptGenerationTime_builtin),
+      timer_stop(script_gen_time_builtin,Script_Gen_Time_Builtin),
+  
+      problog_var_set(bdd_script_time(Builtin), Script_Gen_Time_Builtin),
 
-      statistics(walltime, _),
+      timer_start(bdd_gen_time_builtin),
       execute_bdd_tool(BDDFile_builtin, BDDParFile, Prob_builtin, Status_builtin),
-      statistics(walltime,[_, BDDGenerationTime_builtin]),
+      timer_stop(bdd_gen_time_builtin,BDD_Gen_Time_Builtin),
       ptree_db_trie_opt_performed(LVL1, LVL2, LV3),
       problog_var_set(db_trie_opts_performed(Builtin), opt_perform(LVL1, LVL2, LV3)),
-      (Status_builtin = ok ->
-        problog_var_set(bdd_generation_time(Builtin), BDDGenerationTime_builtin),
+      (Status_builtin == ok ->
+        problog_var_set(bdd_generation_time(Builtin), BDD_Gen_Time_Builtin),
         problog_var_set(probability(Builtin), Prob_builtin)
       ;
         problog_var_set(bdd_generation_time(Builtin), fail),
@@ -1679,18 +1689,17 @@ eval_dnf(OriTrie1, Prob, Status) :-
 
   % decomposition method
   (problog_flag(use_dec_trie, true) ->
-    statistics(walltime, _),
-%     atomic_concat([BDDFile, '_dec'], BDDFile_dec),
     BDDFile = BDDFile_dec,
+    timer_start(script_gen_time_dec),
     ptree_decomposition(Trie, BDDFile_dec, BDDParFile),
-    statistics(walltime, [_, ScriptGenerationTime_dec]),
-    problog_var_set(bdd_script_time(dec), ScriptGenerationTime_dec),
+    timer_stop(script_gen_time_dec,Script_Gen_Time_Dec),
+    problog_var_set(bdd_script_time(dec), Script_Gen_Time_Dec),
 
-    statistics(walltime, _),
+    timer_start(bdd_gen_time_dec),
     execute_bdd_tool(BDDFile_dec, BDDParFile, Prob_dec, Status_dec),
-    statistics(walltime,[_, BDDGenerationTime_dec]),
-    (Status_dec = ok ->
-      problog_var_set(bdd_generation_time(dec), BDDGenerationTime_dec),
+    timer_stop(bdd_gen_time_dec,BDD_Gen_Time_Dec),
+    (Status_dec == ok ->
+      problog_var_set(bdd_generation_time(dec), BDD_Gen_Time_Dec),
       problog_var_set(probability(dec), Prob_dec)
     ;
       problog_var_set(bdd_generation_time(dec), fail),
@@ -1948,13 +1957,13 @@ compute_bounds(LP, UP, Status) :-
 problog_low(Goal, Threshold, _, _) :-
 	init_problog_low(Threshold),
 	problog_control(off, up),
-	statistics(walltime, _),
+	timer_start(sld_time),
 	problog_call(Goal),
 	add_solution,
 	fail.
 problog_low(_, _, LP, Status) :-
-	statistics(walltime, [_,E]), %theo
-	problog_var_set(sld_time, E),
+	timer_stop(sld_time,SLD_Time),
+	problog_var_set(sld_time, SLD_Time),
 	nb_getval(problog_completed_proofs, Trie_Completed_Proofs),
 	eval_dnf(Trie_Completed_Proofs, LP, Status),
 	(problog_flag(verbose, true)->
@@ -2046,13 +2055,7 @@ evalStep(Ans,Status) :-
 	nb_getval(problog_stopped_proofs, Trie_Stopped_Proofs),
 	count_ptree(Trie_Completed_Proofs, NProofs),
 	count_ptree(Trie_Stopped_Proofs, NCands),
-	(
-	 problog_flag(verbose,true)
-	->
-	 format(user,'~w proofs, ~w stopped derivations~n',[NProofs,NCands]);
-	 true
-	),
-	flush_output(user),
+	format_if_verbose(user,'~w proofs, ~w stopped derivations~n',[NProofs,NCands]),
 	eval_lower(NProofs,Low,StatusLow),
 	(
 	 StatusLow \== ok
@@ -2073,8 +2076,7 @@ evalStep(Ans,Status) :-
       Status = StatusUp
     ;
       Diff is Up-Low,
-      (problog_flag(verbose,true) -> format(user,'difference:  ~6f~n',[Diff]);true),
-      flush_output(user),
+      format_if_verbose(user,'difference:  ~6f~n',[Diff]),
       ((Diff < Delta; Diff =:= 0) -> Ans = 1; Ans = 0),
       Status = ok
     )
@@ -2088,13 +2090,12 @@ eval_lower(N,P,Status) :-
 	N > 0,
 	low(OldN,_),
 	N \= OldN,
-  nb_getval(problog_completed_proofs, Trie_Completed_Proofs),
+	nb_getval(problog_completed_proofs, Trie_Completed_Proofs),
 	eval_dnf(Trie_Completed_Proofs,P,Status),
-	(Status = ok ->
+	(Status == ok ->
 	    retract(low(_,_)),
 	    assertz(low(N,P)),
-	    (problog_flag(verbose,true) -> format(user,'lower bound: ~6f~n',[P]);true),
-	    flush_output(user)
+	    format_if_verbose(user,'lower bound: ~6f~n',[P])
 	;
 	true).
 
@@ -2113,12 +2114,11 @@ eval_upper(N,UpP,ok) :-
   nb_setval(problog_all_proofs, Trie_All_Proofs),
   eval_dnf(Trie_All_Proofs,UpP,StatusUp),
   delete_ptree(Trie_All_Proofs),
-  (StatusUp = ok ->
+  (StatusUp == ok ->
     retract(up(_,_)),
     assertz(up(N,UpP))
   ;
-    (problog_flag(verbose,true) -> format(user,'~w - continue using old up~n',[StatusUp]);true),
-    flush_output(user),
+     format_if_verbose(user,'~w - continue using old up~n',[StatusUp]),
     up(_,UpP)
   ).
 
@@ -2150,17 +2150,14 @@ init_problog_max(Threshold) :-
 update_max :-
   b_getval(problog_probability, CurrP),
   max_probability(MaxP),
-  (CurrP =< MaxP ->
-    fail
-  ;
-    b_getval(problog_current_proof, IDs),
-    open_end_close_end(IDs, R),
-    retractall(max_proof(_)),
-    assertz(max_proof(R)),
-    nb_setval(problog_threshold, CurrP),
-    retractall(max_probability(_)),
-    assertz(max_probability(CurrP))
-  ).
+  CurrP>MaxP,
+  b_getval(problog_current_proof, IDs),
+  open_end_close_end(IDs, R),
+  retractall(max_proof(_)),
+  assertz(max_proof(R)),
+  nb_setval(problog_threshold, CurrP),
+  retractall(max_probability(_)),
+  assertz(max_probability(CurrP)).
 
 problog_max_id(Goal, _Prob, _Clauses) :-
 	problog_call(Goal),
@@ -2276,12 +2273,10 @@ problog_kbest_id(Goal, K) :-
 update_kbest(K) :-
 	b_getval(problog_probability,NewLogProb),
 	current_kbest(LogThreshold,_,_),
-	(NewLogProb>=LogThreshold ->
-	    b_getval(problog_current_proof,RevProof),
-	    open_end_close_end(RevProof,Proof),
-	    update_current_kbest(K,NewLogProb,Proof)
-	;
-	    fail).
+	NewLogProb>=LogThreshold,
+	b_getval(problog_current_proof,RevProof),
+	open_end_close_end(RevProof,Proof),
+	update_current_kbest(K,NewLogProb,Proof).
 
 update_current_kbest(_,NewLogProb,Cl) :-
 	current_kbest(_,List,_),
@@ -2312,7 +2307,7 @@ sorted_insert(A-LA,[B1-LB1|B], [B1-LB1|C] ) :-
 % keeps all entries with lowest probability, even if implying a total of more than k
 cutoff(List,Len,1,List,Len) :- !.
 cutoff([P-L|List],Length,First,[P-L|List],Length) :-
-	nth(First,[P-L|List],PF-_),
+	nth1(First,[P-L|List],PF-_),
 	PF=:=P,
 	!.
 cutoff([_|List],Length,First,NewList,NewLength) :-
@@ -2442,69 +2437,48 @@ problog_montecarlo(Goal,Delta,Prob) :-
 	close_static_array(mc_sample).
 
 montecarlo(Goal,Delta,K,File) :-
-%        reset_static_array(mc_sample),
 	clean_sample,
 	problog_control(on,mc),
 	open(File,write,Log),
 	format(Log,'# goal: ~q~n#delta: ~w~n',[Goal,Delta]),
 	format(Log,'# num_programs  prob   low   high  diff  time~2n',[]),
 	close(Log),
-	statistics(walltime,[T1,_]),
-	(problog_flag(verbose,true) -> format('search for ~q~n',[Goal]);true),
-	montecarlo(Goal,Delta,K,0,File,0,T1),
+	timer_start(monte_carlo),
+	format_if_verbose(user,'search for ~q~n',[Goal]),
+	montecarlo(Goal,Delta,K,0,File,0),
+	timer_stop(monte_carlo,_Monte_Carlo_Time),
 	problog_control(off,mc).
 
 % calculate values after K samples
-montecarlo(Goal,Delta,K,SamplesSoFar,File,PositiveSoFar,InitialTime) :-
-  SamplesNew is SamplesSoFar+1,
-  SamplesNew mod K =:= 0,
-  !,
-  copy_term(Goal,GoalC),
-  (mc_prove(GoalC) -> Next is PositiveSoFar+1; Next=PositiveSoFar),
-  Prob is Next/SamplesNew,
-  statistics(walltime,[T2,_]),
-  Time is (T2-InitialTime),%/1000,
-
-  problog_convergence_check(Time, Prob, SamplesNew, Delta, _Epsilon, Converged),
-  ((Converged = true; Converged = terminate) ->
-    (problog_flag(verbose,true) ->
-      format('Runtime ~w ms~2n',[Time])
-    ;
-      true
-    ),
-    assertz(mc_prob(Prob))
-  ;
-    montecarlo(Goal,Delta,K,SamplesNew,File,Next,InitialTime)
-  ).
-
-
-%   Epsilon is 2*sqrt(Prob*(1-Prob)/SamplesNew),
-%   Low is Prob-Epsilon,
-%   High is Prob+Epsilon,
-%   Diff is 2*Epsilon,
-%   (problog_flag(verbose,true) -> format('~n~w samples~nestimated probability ~w~n95 percent confidence interval [~w,~w]~n',[SamplesNew,Prob,Low,High]);true),
-%   open(File,append,Log),
-%   format(Log,'~w  ~8f  ~8f  ~8f  ~8f  ~3f~n',[SamplesNew,Prob,Low,High,Diff,Time]),
-%   close(Log),
-
-
-%   ((Diff<Delta; Diff =:= 0) ->
-%     (problog_flag(verbose,true) ->
-%       format('Runtime ~w sec~2n',[Time])
-%     ;
-%       true
-%     ),
-%     assertz(mc_prob(Prob))
-%   ;
-%     montecarlo(Goal,Delta,K,SamplesNew,File,Next,InitialTime)
-%   ).
+montecarlo(Goal,Delta,K,SamplesSoFar,File,PositiveSoFar) :-
+	SamplesNew is SamplesSoFar+1,
+	SamplesNew mod K =:= 0,
+	!,
+	copy_term(Goal,GoalC),
+	(
+	 mc_prove(GoalC)
+	->
+	 Next is PositiveSoFar+1;
+	 Next=PositiveSoFar
+	),
+	Prob is Next/SamplesNew,
+	timer_elapsed(monte_carlo,Time),
 
+	problog_convergence_check(Time, Prob, SamplesNew, Delta, _Epsilon, Converged),
+	(
+	 (Converged == true; Converged == terminate)
+	->
+	 format_if_verbose(user,'Runtime ~w ms~2n',[Time]),
+	 assertz(mc_prob(Prob))
+	;
+	 montecarlo(Goal,Delta,K,SamplesNew,File,Next)
+	).
 % continue until next K samples done
-montecarlo(Goal,Delta,K,SamplesSoFar,File,PositiveSoFar,InitialTime) :-
+montecarlo(Goal,Delta,K,SamplesSoFar,File,PositiveSoFar) :-
 	SamplesNew is SamplesSoFar+1,
 	copy_term(Goal,GoalC),
 	(mc_prove(GoalC) -> Next is PositiveSoFar+1; Next=PositiveSoFar),
-	montecarlo(Goal,Delta,K,SamplesNew,File,Next,InitialTime).
+	montecarlo(Goal,Delta,K,SamplesNew,File,Next).
 
 mc_prove(A) :- !,
 	(get_some_proof(A) ->
@@ -2586,10 +2560,8 @@ problog_kbest_answers_id(Goal, K) :-
 update_kbest_answers(Goal,K) :-
 	b_getval(problog_probability,NewLogProb),
 	current_kbest(LogThreshold,_,_),
-	(NewLogProb>=LogThreshold ->
-	    update_current_kbest_answers(K,NewLogProb,Goal)
-	;
-	    fail).
+	NewLogProb>=LogThreshold,
+	update_current_kbest_answers(K,NewLogProb,Goal).
 
 update_current_kbest_answers(_,NewLogProb,Goal) :-
 	current_kbest(_,List,_),
@@ -2700,7 +2672,7 @@ eval_bdd_forest(N,Probs,Status) :-
 	    Status = timeout
 	;
 	    statistics(walltime,[_,E3]),
-		(problog_flag(verbose,true) -> format(user,'~w ms BDD processing~n',[E3]);true),
+	        format_if_verbose(user,'~w ms BDD processing~n',[E3]),
 		see(ResultFile),
 		read_probs(N,Probs),
 		seen,
@@ -2763,14 +2735,14 @@ build_trie(low(Threshold), Goal, _) :-
   number(Threshold),
   init_problog_low(Threshold),
   problog_control(off, up),
-  statistics(walltime, _),
+  timer_start(build_tree_low),
   problog_call(Goal),
   add_solution,
   fail.
 build_trie(low(Threshold), _, Trie) :-
   number(Threshold),
-  statistics(walltime, [_,E]),
-  problog_var_set(sld_time, E),
+  timer_stop(build_tree_low,Build_Tree_Low),
+  problog_var_set(sld_time, Build_Tree_Low),
   nb_getval(problog_completed_proofs, Trie).
   % don't clear tabling; tables can be reused by other query
 
@@ -2957,11 +2929,11 @@ write_bdd_struct_script(Trie,BDDFile,Variables) :-
 
   % decomposition method
   (problog_flag(use_dec_trie, true) ->
-    statistics(walltime, _),
     atomic_concat([BDDFile, '_dec'], BDDFile_dec),
+    timer_start(script_gen_time_dec),
     ptree_decomposition_struct(Trie, BDDFile_dec, Variables),
-    statistics(walltime, [_, ScriptGenerationTime_dec]),
-    problog_var_set(bdd_script_time(dec), ScriptGenerationTime_dec)
+    timer_stop(script_gen_time_dec,Script_Gen_Time_Dec),
+    problog_var_set(bdd_script_time(dec), Script_Gen_Time_Dec)
     % omitted call to execute_bdd_tool
   ;
     true
@@ -3018,37 +2990,33 @@ write_bdd_forest([Goal|Rest],VarsAcc,VarsTot,N):-
 
 % Write files
 write_nth_bdd_struct_script(N,Trie,Vars) :-
-  bdd_forest_file(N,BDDFile),
-  write_bdd_struct_script(Trie,BDDFile,Vars).
+	bdd_forest_file(N,BDDFile),
+	write_bdd_struct_script(Trie,BDDFile,Vars).
 
 write_global_bdd_file(NbVars,L) :-
-  bdd_file(BDDFile),
-  open(BDDFile,'write',BDDFileStream),
-  tell(BDDFileStream),
-  format('@BDD2~n~w~n~w~n~w~n',[NbVars,0,L]),
-  write_global_bdd_file_line(1,L),
-  write_global_bdd_file_query(1,L),
-  flush_output,
-  told.
+	bdd_file(BDDFile),
+	open(BDDFile,'write',BDDFileStream),
+	format(BDDFileStream,'@BDD2~n~w~n~w~n~w~n',[NbVars,0,L]),
+	write_global_bdd_file_line(1,L,BDDFileStream),
+	write_global_bdd_file_query(1,L,BDDFileStream),
+	close(BDDFileStream).
 
-write_global_bdd_file_line(I,Max) :-
-  (I>Max ->
-      true
-  ;
-      bdd_forest_file(I,BDDFile),
-      format("L~q = <~w>~n",[I,BDDFile]),
-      I2 is I+1,
-      write_global_bdd_file_line(I2,Max)
-  ).
+write_global_bdd_file_line(I,Max,_Handle) :-
+	I>Max,
+	!.
+write_global_bdd_file_line(I,Max,Handle) :-
+	bdd_forest_file(I,BDDFile),
+	format(Handle,'L~q = <~w>~n',[I,BDDFile]),
+	I2 is I+1,
+	write_global_bdd_file_line(I2,Max,Handle).
 
-write_global_bdd_file_query(I,Max) :-
-  (I=Max ->
-      format("L~q~n",[I])
-  ;
-      format("L~q,",[I]),
-      I2 is I+1,
-      write_global_bdd_file_query(I2,Max)
-  ).
+write_global_bdd_file_query(Max,Max,Handle) :-
+	!,
+	format(Handle,'L~q~n',[Max]).
+write_global_bdd_file_query(I,Max,Handle) :-
+	format(Handle,'L~q,',[I]),
+	I2 is I+1,
+	write_global_bdd_file_query(I2,Max,Handle).
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % Filename specifications
@@ -3057,19 +3025,19 @@ write_global_bdd_file_query(I,Max) :-
 bdd_forest_file(N,BDDFile) :-
 	problog_flag(bdd_file,BDDFileFlag),
 	atomic_concat([BDDFileFlag,'_',N],BDDFileFlagWithN),
-    convert_filename_to_working_path(BDDFileFlagWithN, BDDFile).
+	convert_filename_to_working_path(BDDFileFlagWithN, BDDFile).
 
 bdd_files(BDDFile,BDDParFile) :-
 	bdd_file(BDDFile),
 	bdd_par_file(BDDParFile).
 
 bdd_file(BDDFile) :-
-    problog_flag(bdd_file, BDDFileFlag),
-    convert_filename_to_working_path(BDDFileFlag, BDDFile).
+	problog_flag(bdd_file, BDDFileFlag),
+	convert_filename_to_working_path(BDDFileFlag, BDDFile).
 
 bdd_par_file(BDDParFile) :-
-    problog_flag(bdd_par_file, BDDParFileFlag),
-    convert_filename_to_working_path(BDDParFileFlag, BDDParFile).
+	problog_flag(bdd_par_file, BDDParFileFlag),
+	convert_filename_to_working_path(BDDParFileFlag, BDDParFile).
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % Persistent Ground IDs
@@ -3109,6 +3077,16 @@ required(Feature) :-
 	catch(b_getval(Feature_Required,Val),error(existence_error(variable,Feature_Required),_),fail),
 	Val == required.
 
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% 
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+format_if_verbose(H,T,L) :-
+	problog_flag(verbose,true),
+	!,
+	format(H,T,L).
+format_if_verbose(_,_,_).
+
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % Should go to dtproblog.yap
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
diff --git a/packages/ProbLog/problog/logger.yap b/packages/ProbLog/problog/logger.yap
index 4a1795e80..cfd68feb3 100644
--- a/packages/ProbLog/problog/logger.yap
+++ b/packages/ProbLog/problog/logger.yap
@@ -2,8 +2,8 @@
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %
-%  $Date: 2010-09-30 13:50:45 +0200 (Thu, 30 Sep 2010) $
-%  $Revision: 4857 $
+%  $Date: 2010-10-11 14:14:11 +0200 (Mon, 11 Oct 2010) $
+%  $Revision: 4892 $
 %
 %  This file is part of ProbLog
 %  http://dtai.cs.kuleuven.be/problog
@@ -206,7 +206,6 @@
 
 
 :- module(logger,[logger_define_variable/2,
-	          logger_define_variables/2,
 	          logger_set_filename/1,
 		  logger_set_delimiter/1,
 		  logger_set_variable/2,
@@ -238,25 +237,35 @@
 %= +Name, +Type
 %========================================================================
 
-logger_define_variable(Name,int) :-
+logger_define_variable(Name,Type) :-
+	bb_get(logger_variables,Variables),
+	member((Name,_),Variables),
+	!,
+	throw(error(variable_redefined(logger_define_variable(Name,Type)))).
+logger_define_variable(Name,Type) :-
+	ground(Name),
+	atomic(Name),
+	!,
+	logger_define_variable_intern(Type,Name).
+logger_define_variable(Name,Type) :-
+	throw(error(illegal_variable_name(logger_define_variable(Name,Type)))).
+
+logger_define_variable_intern(int,Name) :-
 	!,
-	is_variable_already_defined(Name),
 	bb_delete(logger_variables,OldVariables),
 	append(OldVariables,[(Name,int)],NewVariables),
 	bb_put(logger_variables,NewVariables),
 	atom_concat(logger_data_,Name,Key),
 	bb_put(Key,null).
-logger_define_variable(Name,float) :-
+logger_define_variable_intern(float,Name) :-
 	!,
-	is_variable_already_defined(Name),
 	bb_delete(logger_variables,OldVariables),
 	append(OldVariables,[(Name,float)],NewVariables),
 	bb_put(logger_variables,NewVariables),
 	atom_concat(logger_data_,Name,Key),
 	bb_put(Key,null).
-logger_define_variable(Name,time) :-
+logger_define_variable_intern(time,Name) :-
 	!,
-	is_variable_already_defined(Name),
 	bb_delete(logger_variables,OldVariables),
 	append(OldVariables,[(Name,time)],NewVariables),
 	bb_put(logger_variables,NewVariables),
@@ -264,34 +273,9 @@ logger_define_variable(Name,time) :-
 	atom_concat(logger_start_time_,Name,Key2),
 	bb_put(Key,null),
 	bb_put(Key2,null).
-logger_define_variable(Name,Unknown) :-
-	is_variable_already_defined(Name),
-	write('logger_define_variable, unknown type '),
-	write(Unknown),
-	write(' for variable '),
-	write(Name),
-	nl,
-	fail.
+logger_define_variable_intern(Type,Name) :-
+	throw(error(unknown_variable_type(logger_define_variable(Name,Type)))).
 
-is_variable_already_defined(Name) :-
-	bb_get(logger_variables,Variables),
-	member((Name,_),Variables),!,
-	write('logger_define_variable, Variable '),
-	write(Name),
-	write(' is already defined!\n'),
-	fail;
-	true.
-
-%========================================================================
-%= 
-%=
-%= +ListOfNames, +Type
-%========================================================================
-
-logger_define_variables([],_).
-logger_define_variables([H|T],Type) :-
-	logger_define_variable(H,Type),
-	logger_define_variables(T,Type).
 
 %========================================================================
 %= Set the filename, to which the output should be appended
diff --git a/packages/ProbLog/problog/nestedtries.yap b/packages/ProbLog/problog/nestedtries.yap
new file mode 100644
index 000000000..abeb512d2
--- /dev/null
+++ b/packages/ProbLog/problog/nestedtries.yap
@@ -0,0 +1,423 @@
+%%% -*- Mode: Prolog; -*-
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+%  $Date: 2010-11-03 19:13:53 +0100 (Wed, 03 Nov 2010) $
+%  $Revision: 4986 $
+%
+%  This file is part of ProbLog
+%  http://dtai.cs.kuleuven.be/problog
+%
+%  ProbLog was developed at Katholieke Universiteit Leuven
+%
+%  Copyright 2008, 2009, 2010
+%  Katholieke Universiteit Leuven
+%
+%  Main authors of this file:
+%  Theofrastos Mantadelis
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Artistic License 2.0
+%
+% Copyright (c) 2000-2006, The Perl Foundation.
+%
+% Everyone is permitted to copy and distribute verbatim copies of this
+% license document, but changing it is not allowed.  Preamble
+%
+% This license establishes the terms under which a given free software
+% Package may be copied, modified, distributed, and/or
+% redistributed. The intent is that the Copyright Holder maintains some
+% artistic control over the development of that Package while still
+% keeping the Package available as open source and free software.
+%
+% You are always permitted to make arrangements wholly outside of this
+% license directly with the Copyright Holder of a given Package. If the
+% terms of this license do not permit the full use that you propose to
+% make of the Package, you should contact the Copyright Holder and seek
+% a different licensing arrangement.  Definitions
+%
+% "Copyright Holder" means the individual(s) or organization(s) named in
+% the copyright notice for the entire Package.
+%
+% "Contributor" means any party that has contributed code or other
+% material to the Package, in accordance with the Copyright Holder's
+% procedures.
+%
+% "You" and "your" means any person who would like to copy, distribute,
+% or modify the Package.
+%
+% "Package" means the collection of files distributed by the Copyright
+% Holder, and derivatives of that collection and/or of those files. A
+% given Package may consist of either the Standard Version, or a
+% Modified Version.
+%
+% "Distribute" means providing a copy of the Package or making it
+% accessible to anyone else, or in the case of a company or
+% organization, to others outside of your company or organization.
+%
+% "Distributor Fee" means any fee that you charge for Distributing this
+% Package or providing support for this Package to another party. It
+% does not mean licensing fees.
+%
+% "Standard Version" refers to the Package if it has not been modified,
+% or has been modified only in ways explicitly requested by the
+% Copyright Holder.
+%
+% "Modified Version" means the Package, if it has been changed, and such
+% changes were not explicitly requested by the Copyright Holder.
+%
+% "Original License" means this Artistic License as Distributed with the
+% Standard Version of the Package, in its current version or as it may
+% be modified by The Perl Foundation in the future.
+%
+% "Source" form means the source code, documentation source, and
+% configuration files for the Package.
+%
+% "Compiled" form means the compiled bytecode, object code, binary, or
+% any other form resulting from mechanical transformation or translation
+% of the Source form.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Permission for Use and Modification Without Distribution
+%
+% (1) You are permitted to use the Standard Version and create and use
+% Modified Versions for any purpose without restriction, provided that
+% you do not Distribute the Modified Version.
+%
+% Permissions for Redistribution of the Standard Version
+%
+% (2) You may Distribute verbatim copies of the Source form of the
+% Standard Version of this Package in any medium without restriction,
+% either gratis or for a Distributor Fee, provided that you duplicate
+% all of the original copyright notices and associated disclaimers. At
+% your discretion, such verbatim copies may or may not include a
+% Compiled form of the Package.
+%
+% (3) You may apply any bug fixes, portability changes, and other
+% modifications made available from the Copyright Holder. The resulting
+% Package will still be considered the Standard Version, and as such
+% will be subject to the Original License.
+%
+% Distribution of Modified Versions of the Package as Source
+%
+% (4) You may Distribute your Modified Version as Source (either gratis
+% or for a Distributor Fee, and with or without a Compiled form of the
+% Modified Version) provided that you clearly document how it differs
+% from the Standard Version, including, but not limited to, documenting
+% any non-standard features, executables, or modules, and provided that
+% you do at least ONE of the following:
+%
+% (a) make the Modified Version available to the Copyright Holder of the
+% Standard Version, under the Original License, so that the Copyright
+% Holder may include your modifications in the Standard Version.  (b)
+% ensure that installation of your Modified Version does not prevent the
+% user installing or running the Standard Version. In addition, the
+% modified Version must bear a name that is different from the name of
+% the Standard Version.  (c) allow anyone who receives a copy of the
+% Modified Version to make the Source form of the Modified Version
+% available to others under (i) the Original License or (ii) a license
+% that permits the licensee to freely copy, modify and redistribute the
+% Modified Version using the same licensing terms that apply to the copy
+% that the licensee received, and requires that the Source form of the
+% Modified Version, and of any works derived from it, be made freely
+% available in that license fees are prohibited but Distributor Fees are
+% allowed.
+%
+% Distribution of Compiled Forms of the Standard Version or
+% Modified Versions without the Source
+%
+% (5) You may Distribute Compiled forms of the Standard Version without
+% the Source, provided that you include complete instructions on how to
+% get the Source of the Standard Version. Such instructions must be
+% valid at the time of your distribution. If these instructions, at any
+% time while you are carrying out such distribution, become invalid, you
+% must provide new instructions on demand or cease further
+% distribution. If you provide valid instructions or cease distribution
+% within thirty days after you become aware that the instructions are
+% invalid, then you do not forfeit any of your rights under this
+% license.
+%
+% (6) You may Distribute a Modified Version in Compiled form without the
+% Source, provided that you comply with Section 4 with respect to the
+% Source of the Modified Version.
+%
+% Aggregating or Linking the Package
+%
+% (7) You may aggregate the Package (either the Standard Version or
+% Modified Version) with other packages and Distribute the resulting
+% aggregation provided that you do not charge a licensing fee for the
+% Package. Distributor Fees are permitted, and licensing fees for other
+% components in the aggregation are permitted. The terms of this license
+% apply to the use and Distribution of the Standard or Modified Versions
+% as included in the aggregation.
+%
+% (8) You are permitted to link Modified and Standard Versions with
+% other works, to embed the Package in a larger work of your own, or to
+% build stand-alone binary or bytecode versions of applications that
+% include the Package, and Distribute the result without restriction,
+% provided the result does not expose a direct interface to the Package.
+%
+% Items That are Not Considered Part of a Modified Version
+%
+% (9) Works (including, but not limited to, modules and scripts) that
+% merely extend or make use of the Package, do not, by themselves, cause
+% the Package to be a Modified Version. In addition, such works are not
+% considered parts of the Package itself, and are not subject to the
+% terms of this license.
+%
+% General Provisions
+%
+% (10) Any use, modification, and distribution of the Standard or
+% Modified Versions is governed by this Artistic License. By using,
+% modifying or distributing the Package, you accept this license. Do not
+% use, modify, or distribute the Package, if you do not accept this
+% license.
+%
+% (11) If your Modified Version has been derived from a Modified Version
+% made by someone other than you, you are nevertheless required to
+% ensure that your Modified Version complies with the requirements of
+% this license.
+%
+% (12) This license does not grant you the right to use any trademark,
+% service mark, tradename, or logo of the Copyright Holder.
+%
+% (13) This license includes the non-exclusive, worldwide,
+% free-of-charge patent license to make, have made, use, offer to sell,
+% sell, import and otherwise transfer the Package with respect to any
+% patent claims licensable by the Copyright Holder that are necessarily
+% infringed by the Package. If you institute patent litigation
+% (including a cross-claim or counterclaim) against any party alleging
+% that the Package constitutes direct or contributory patent
+% infringement, then this Artistic License to you shall terminate on the
+% date that such litigation is filed.
+%
+% (14) Disclaimer of Warranty: THE PACKAGE IS PROVIDED BY THE COPYRIGHT
+% HOLDER AND CONTRIBUTORS "AS IS' AND WITHOUT ANY EXPRESS OR IMPLIED
+% WARRANTIES. THE IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
+% PARTICULAR PURPOSE, OR NON-INFRINGEMENT ARE DISCLAIMED TO THE EXTENT
+% PERMITTED BY YOUR LOCAL LAW. UNLESS REQUIRED BY LAW, NO COPYRIGHT
+% HOLDER OR CONTRIBUTOR WILL BE LIABLE FOR ANY DIRECT, INDIRECT,
+% INCIDENTAL, OR CONSEQUENTIAL DAMAGES ARISING IN ANY WAY OUT OF THE USE
+% OF THE PACKAGE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% nested tries handling
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+:- module(nestedtries, [nested_trie_to_depth_breadth_trie/4]).
+
+:- use_module(library(ordsets), [list_to_ord_set/2, ord_subset/2]). % this two might be better to do a custom fast implementation
+:- use_module(library(lists), [memberchk/2, delete/3]).
+:- use_module(library(tries), [trie_to_depth_breadth_trie/6, trie_get_depth_breadth_reduction_entry/1, trie_dup/2, trie_close/1, trie_open/1, trie_replace_nested_trie/3, trie_remove_entry/1, trie_get_entry/2, trie_put_entry/3, trie_traverse/2]).
+
+:- use_module(flags, [problog_define_flag/5, problog_flag/2]).
+
+:- style_check(all).
+:- yap_flag(unknown,error).
+
+:- initialization((
+%   problog_define_flag(subset_check,    problog_flag_validate_boolean, 'perform subset check in nested tries', true, nested_tries),
+  problog_define_flag(loop_refine_ancs, problog_flag_validate_boolean, 'refine ancestors if no loop exists', true, nested_tries)
+%   problog_define_flag(trie_preprocess, problog_flag_validate_boolean, 'perform a preprocess step to nested tries', false, nested_tries),
+%   problog_define_flag(refine_anclst,   problog_flag_validate_boolean, 'refine the ancestor list with their childs', false, nested_tries),
+%   problog_define_flag(anclst_represent,problog_flag_validate_in_list([list, integer]), 'represent the ancestor list', list, nested_tries)
+)).
+
+
+trie_replace_entry(_Trie, Entry, _E, false):-
+  !, trie_remove_entry(Entry).
+trie_replace_entry(Trie, Entry, E, true):-
+  !, trie_get_entry(Entry, Proof),
+  delete(Proof, E, NewProof),
+  (NewProof == [] ->
+    trie_delete(Trie),
+    trie_put_entry(Trie, [true], _)
+  ;
+    trie_remove_entry(Entry),
+    trie_put_entry(Trie, NewProof, _)
+  ).
+trie_replace_entry(Trie, _Entry, t(ID), R):-
+  trie_replace_nested_trie(Trie, ID, R).
+
+trie_delete(Trie):-
+  trie_traverse(Trie, R),
+  trie_remove_entry(R),
+  fail.
+trie_delete(_Trie).
+
+is_state(Variable):-
+  Variable == true, !.
+is_state(Variable):-
+  Variable == false.
+is_state(Variable):-
+  nonvar(Variable),
+  Variable = not(NestedVariable),
+  is_state(NestedVariable).
+
+is_trie(Trie, ID):-
+  nonvar(Trie),
+  Trie = t(ID), !.
+is_trie(Trie, ID):-
+  nonvar(Trie),
+  Trie = not(NestedTrie),
+  is_trie(NestedTrie, ID).
+
+is_label(Label, ID):-
+  atom(Label), !,
+  atomic_concat('L', ID, Label).
+is_label(Label, ID):-
+  nonvar(Label),
+  Label = not(NestedLabel),
+  is_label(NestedLabel, ID).
+
+% Ancestor related stuff
+
+initialise_ancestors(0):-
+  problog_flag(anclst_represent, integer).
+initialise_ancestors([]):-
+  problog_flag(anclst_represent, list).
+
+add_to_ancestors(ID, Ancestors, NewAncestors):-
+  integer(Ancestors), !,
+  NewAncestors is (1 << (ID - 1)) \/ Ancestors.
+add_to_ancestors(ID, Ancestors, NewAncestors):-
+  is_list(Ancestors),
+  list_to_ord_set([ID|Ancestors], NewAncestors).
+
+ancestor_subset_check(SubAncestors, Ancestors):-
+  integer(SubAncestors), !,
+  SubAncestors is Ancestors /\ SubAncestors.
+ancestor_subset_check(SubAncestors, Ancestors):-
+  is_list(SubAncestors),
+  ord_subset(SubAncestors, Ancestors).
+
+ancestor_loop_refine(Loop, Ancestors, 0):-
+  var(Loop), integer(Ancestors), !.
+ancestor_loop_refine(Loop, Ancestors, []):-
+  var(Loop), is_list(Ancestors), !.
+ancestor_loop_refine(true, Ancestors, Ancestors).
+
+% Cycle check related stuff
+% missing synonym check
+
+cycle_check(ID, Ancestors):-
+  integer(Ancestors), !,
+  Bit is 1 << (ID - 1),
+  Bit is Bit /\ Ancestors.
+cycle_check(ID, Ancestors):-
+  is_list(Ancestors),
+  memberchk(ID, Ancestors).
+
+preprocess(Index, DepthBreadthTrie, OptimizationLevel, StartCount, FinalEndCount):-
+  problog:problog_chktabled(Index, Trie), !,
+  trie_dup(Trie, CopyTrie),
+  initialise_ancestors(Ancestors),
+  make_nested_trie_base_cases(CopyTrie, t(Index), DepthBreadthTrie, OptimizationLevel, StartCount, EndCount, Ancestors),
+  trie_close(CopyTrie),
+  Next is Index + 1,
+  preprocess(Next, DepthBreadthTrie, OptimizationLevel, EndCount, FinalEndCount).
+preprocess(_, _, _, FinalEndCount, FinalEndCount).
+
+make_nested_trie_base_cases(Trie, t(ID), DepthBreadthTrie, OptimizationLevel, StartCount, FinalEndCount, Ancestors):-
+  trie_to_depth_breadth_trie(Trie, DepthBreadthTrie, Label, OptimizationLevel, StartCount, EndCount),
+  (is_trie(Label, SID) ->
+    trie_get_depth_breadth_reduction_entry(NestedEntry),
+    trie_replace_entry(Trie, NestedEntry, Label, false),
+    add_to_ancestors(SID, Ancestors, NewAncestors),
+    make_nested_trie_base_cases(Trie, t(ID), DepthBreadthTrie, OptimizationLevel, EndCount, FinalEndCount, NewAncestors)
+  ;
+    FinalEndCount = EndCount,
+    get_set_trie(ID, Label, Ancestors)
+  ).
+
+nested_trie_to_depth_breadth_trie(Trie, DepthBreadthTrie, FinalLabel, OptimizationLevel):-
+  integer(OptimizationLevel),
+  trie_open(DepthBreadthTrie),
+  (problog_flag(trie_preprocess, true) ->
+    preprocess(1, DepthBreadthTrie, OptimizationLevel, 0, StartCount)
+  ;
+    StartCount = 0
+  ),
+  initialise_ancestors(Ancestors),
+%   initialise_ancestors(Childs),
+  (problog_flag(loop_refine_ancs, true) ->
+    trie_2_dbtrie_init(Trie, DepthBreadthTrie, OptimizationLevel, StartCount, _, Ancestors, FinalLabel, _)
+  ;
+    trie_2_dbtrie_init(Trie, DepthBreadthTrie, OptimizationLevel, StartCount, _, Ancestors, FinalLabel, true)
+  ),
+  eraseall(problog_trie_table).
+
+trie_2_dbtrie_init(ID, DepthBreadthTrie, OptimizationLevel, StartCount, EndCount, Ancestors, Label, ContainLoop):-
+  get_trie_pointer(ID, Trie),
+  trie_dup(Trie, CopyTrie),
+  trie_2_dbtrie_intern(CopyTrie, DepthBreadthTrie, OptimizationLevel, StartCount, EndCount, Ancestors, Label, ContainLoop),
+  trie_close(CopyTrie).
+
+trie_2_dbtrie_intern(Trie, DepthBreadthTrie, OptimizationLevel, StartCount, FinalEndCount, Ancestors, TrieLabel, ContainLoop):-
+  trie_to_depth_breadth_trie(Trie, DepthBreadthTrie, Label, OptimizationLevel, StartCount, EndCount),
+  (is_trie(Label, ID) ->             % Label might have issues with negation
+    trie_get_depth_breadth_reduction_entry(NestedEntry),
+    % check if Trie introduces a loop
+    (cycle_check(ID, Ancestors) ->
+      ContainLoop = true,
+      NewLabel = false,
+      NewEndCount = EndCount
+    ;
+      % check if Trie is resolved and extract it
+      (get_set_trie(ID, NewLabel, Ancestors) ->
+        NewEndCount = EndCount
+      ;
+        % calculate the nested trie
+        add_to_ancestors(ID, Ancestors, NewAncestors), % to be able to support 2 representations
+        trie_2_dbtrie_init(ID, DepthBreadthTrie, OptimizationLevel, EndCount, NewEndCount, NewAncestors, NewLabel, NewContainLoop),
+        ancestor_loop_refine(NewContainLoop, Ancestors, RefinedAncestors),
+        get_set_trie(ID, NewLabel, RefinedAncestors),
+        ContainLoop = NewContainLoop
+      )
+    ),
+    trie_replace_entry(Trie, NestedEntry, t(ID), NewLabel), % should be careful to verify that it works also with not(t(ID))
+    trie_2_dbtrie_intern(Trie, DepthBreadthTrie, OptimizationLevel, NewEndCount, FinalEndCount, Ancestors, TrieLabel, ContainLoop)
+  ;
+    % else we can terminate and return
+    FinalEndCount = EndCount,
+    TrieLabel = Label
+  ).
+
+% predicate to check/remember resolved tries
+% no refiment of ancestor list included
+
+get_trie_pointer(ID, Trie):-
+  problog:problog_chktabled(ID, Trie), !.
+get_trie_pointer(Trie, Trie).
+
+get_set_trie(Trie, Label, Ancestors):-
+  recorded(problog_trie_table, store(Trie, StoredAncestors, Label), _),
+  (problog_flag(subset_check, true) ->
+    ancestor_subset_check(StoredAncestors, Ancestors)
+  ;
+    StoredAncestors == Ancestors
+  ), !.
+get_set_trie(Trie, Label, Ancestors):-
+  ground(Label),
+  recordz(problog_trie_table, store(Trie, Ancestors, Label), _).
+
+
+% chk_negated([H|T], ID):-
+%   simplify(H, not(t(ID))), !.
+% chk_negated([_|T], ID):-
+%   chk_negated(T, ID).
+
+
+/*
+chk_negated([], ID, ID).
+chk_negated([H|T], ID, not(ID)):-
+  simplify(H, not(t(ID))), !.
+chk_negated([H|T], ID, ID):-
+  simplify(H, t(ID)), !.
+chk_negated([_|T], ID, FID):-
+  chk_negated(T, ID, FID).*/
diff --git a/packages/ProbLog/problog/tabling.yap b/packages/ProbLog/problog/tabling.yap
index 7ba047a96..118bb5f27 100644
--- a/packages/ProbLog/problog/tabling.yap
+++ b/packages/ProbLog/problog/tabling.yap
@@ -2,8 +2,8 @@
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %
-%  $Date: 2010-10-06 12:56:13 +0200 (Wed, 06 Oct 2010) $
-%  $Revision: 4877 $
+%  $Date: 2010-11-03 19:08:13 +0100 (Wed, 03 Nov 2010) $
+%  $Revision: 4984 $
 %
 %  This file is part of ProbLog
 %  http://dtai.cs.kuleuven.be/problog
@@ -445,6 +445,7 @@ problog_neg(M:G):-
   functor(G, Name, Arity),
   \+ problog_tabled(M:Name/Arity),
   \+ problog:problog_predicate(Name, Arity),
+  \+ (Name == problog_neg, Arity == 1),
   throw(problog_neg_error('Error: goal must be dynamic and tabled', M:G)).
 problog_neg(M:G):-
   % exact inference
diff --git a/packages/ProbLog/problog/timer.yap b/packages/ProbLog/problog/timer.yap
index b0aed892e..d8d6617d6 100644
--- a/packages/ProbLog/problog/timer.yap
+++ b/packages/ProbLog/problog/timer.yap
@@ -2,8 +2,8 @@
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %
-%  $Date: 2010-09-28 21:04:43 +0200 (Tue, 28 Sep 2010) $
-%  $Revision: 4838 $
+%  $Date: 2010-10-15 17:09:55 +0200 (Fri, 15 Oct 2010) $
+%  $Revision: 4939 $
 %
 %  This file is part of ProbLog
 %  http://dtai.cs.kuleuven.be/problog
@@ -208,9 +208,10 @@
 :- module(timer,[timer_start/1,    % +ID
 		 timer_stop/2,     % +ID,-Duration
 		 timer_pause/1,    % +ID
-		 timer_pause/2,    % +ID
-		 timer_resume/1]). % +ID
-
+		 timer_pause/2,    % +ID,-Duration
+		 timer_resume/1,   % +ID
+		 timer_elapsed/2,  % +ID, -Duration
+		 timer_reset/1]).  % +ID
 :- yap_flag(unknown,error).
 :- style_check(single_var).
 
@@ -228,6 +229,11 @@ timer_start(Name) :-
 	 assertz(timer(Name,StartTime))
 	).
 
+timer_start_forced(Name) :-
+	retractall(timer(Name,_)),
+	statistics(walltime,[StartTime,_]),
+	assertz(timer(Name,StartTime)).
+
 timer_stop(Name,Duration) :-
 	(
 	 retract(timer(Name,StartTime))
@@ -270,3 +276,17 @@ timer_resume(Name):-
 	 
 	 throw(timer_not_paused(timer_resume(Name)))
 	).
+
+timer_elapsed(Name,Duration) :-
+	(
+	 timer(Name,StartTime)
+	->
+	 statistics(walltime,[StopTime,_]),
+	 Duration is StopTime-StartTime;
+
+	 throw(timer_not_started(timer_elapsed(Name,Duration)))
+	).
+
+timer_reset(Name) :-
+	retractall(timer(Name,_)),
+	retractall(timer_paused(Name,_)).
\ No newline at end of file
diff --git a/packages/ProbLog/problog/tptree.yap b/packages/ProbLog/problog/tptree.yap
index c6e4d0740..9ff552589 100644
--- a/packages/ProbLog/problog/tptree.yap
+++ b/packages/ProbLog/problog/tptree.yap
@@ -2,8 +2,8 @@
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %
-%  $Date: 2010-09-28 21:04:43 +0200 (Tue, 28 Sep 2010) $
-%  $Revision: 4838 $
+%  $Date: 2010-11-03 19:08:13 +0100 (Wed, 03 Nov 2010) $
+%  $Revision: 4984 $
 %
 %  This file is part of ProbLog
 %  http://dtai.cs.kuleuven.be/problog
@@ -247,11 +247,15 @@
 % load library modules
 :- use_module(library(tries)).
 :- use_module(library(lists), [append/3, member/2, memberchk/2, delete/3]).
-:- use_module(library(system), [delete_file/1, shell/1, tmpnam/1]).
+:- use_module(library(system), [tmpnam/1]).
 :- use_module(library(ordsets), [ord_intersection/3, ord_union/3]).
 
+
+
 % load our own modules
 :- use_module(flags).
+:- use_module(utils).
+:- use_module(nestedtries, [nested_trie_to_depth_breadth_trie/4]).
 
 % switch on all tests to reduce bug searching time
 :- style_check(all).
@@ -463,30 +467,31 @@ name_vars([A|B]) :-
 
 nested_ptree_to_BDD_struct_script(Trie, BDDFileName, Variables):-
   tmpnam(TmpFile1),
-  tmpnam(TmpFile2),
   open(TmpFile1, 'write', BDDS),
-  (generate_BDD_from_trie(Trie, Inter, BDDS) ->
-    next_intermediate_step(TMP), InterCNT is TMP - 1,
-    write(BDDS, Inter), nl(BDDS),
+
+  (
+   generate_BDD_from_trie(Trie, Inter, BDDS)
+  ->
+   (
+    next_intermediate_step(TMP),
+    InterCNT is TMP - 1,
+    format(BDDS,'~q~n',[Inter]),
     close(BDDS),
-    (get_used_vars(Variables, VarCNT);VarCNT = 0),
-    open(TmpFile2, 'write', HEADERS),
-    write(HEADERS, '@BDD1'), nl(HEADERS),
-    write(HEADERS, VarCNT), nl(HEADERS),
-    write(HEADERS, 0), nl(HEADERS),
-    write(HEADERS, InterCNT), nl(HEADERS),
-    close(HEADERS),
-    atomic_concat(['cat ', TmpFile2, ' ', TmpFile1, ' > ', BDDFileName], CMD),
-    shell(CMD),
-    delete_file(TmpFile1),
-    delete_file(TmpFile2),
+    (
+     get_used_vars(Variables, VarCNT)
+    ->
+     true;
+     VarCNT = 0
+    ),
+    create_bdd_file_with_header(BDDFileName,VarCNT,InterCNT,TmpFile1),
+    delete_file_silent(TmpFile1),
     cleanup_BDD_generation
-  ;
+   );(
     close(BDDS),
-    (delete_file(TmpFile1);true),
-    (delete_file(TmpFile2);true),
+    delete_file_silent(TmpFile1),
     cleanup_BDD_generation,
     fail
+   )
   ).
 
 trie_to_bdd_struct_trie(A, B, OutputFile, OptimizationLevel, Variables) :-
@@ -528,7 +533,8 @@ trie_to_bdd_struct_trie(A, B, OutputFile, OptimizationLevel, Variables) :-
   ).
 
 nested_trie_to_bdd_struct_trie(A, B, OutputFile, OptimizationLevel, Variables):-
-  trie_nested_to_depth_breadth_trie(A, B, LL, OptimizationLevel, problog:problog_chktabled),
+  %trie_nested_to_depth_breadth_trie(A, B, LL, OptimizationLevel, problog:problog_chktabled),
+  nested_trie_to_depth_breadth_trie(A, B, LL, OptimizationLevel),
   (is_label(LL) ->
     retractall(deref(_,_)),
     (problog_flag(deref_terms, true) ->
@@ -571,15 +577,20 @@ nested_trie_to_bdd_struct_trie(A, B, OutputFile, OptimizationLevel, Variables):-
     write(1), nl,
     write(0), nl,
     write(1), nl,
-    get_var_name(LL, NLL),
-    write('L1 = '),write(NLL),nl,
+    simplify(LL, FLL),
+    (FLL = not(_) ->
+      write('L1 = ~')
+    ;
+      write('L1 = ')
+    ),
+    get_var_name(FLL, NLL),
+    write(NLL),nl,
     write('L1'), nl,
     told
   ).
 
 ptree_decomposition_struct(Trie, BDDFileName, Variables) :-
   tmpnam(TmpFile1),
-  tmpnam(TmpFile2),
   nb_setval(next_inter_step, 1),
   variables_in_dbtrie(Trie, Variables),
   length(Variables, VarCnt),
@@ -599,16 +610,8 @@ ptree_decomposition_struct(Trie, BDDFileName, Variables) :-
     write('L1'), nl
   ),
   told,
-  tell(TmpFile2),
-  write('@BDD1'),nl,
-  write(VarCnt),nl,
-  write('0'),nl,
-  write(LCnt),nl,
-  told,
-  atomic_concat(['cat ', TmpFile2, ' ', TmpFile1, ' > ', BDDFileName], CMD),
-  shell(CMD),
-  delete_file(TmpFile1),
-  delete_file(TmpFile2).
+  create_bdd_file_with_header(BDDFileName,VarCnt,LCnt,TmpFile1),
+  delete_file_silent(TmpFile1).
 
 %%%%%%%%%%%%%%%%%%%%%%%%
 % write BDD info for given ptree to file
@@ -696,10 +699,10 @@ bdd_vars_script_intern(A) :-
 	).
 bdd_vars_script_intern2(A) :-
 	get_var_name(A,NameA),
-	atom_chars(A,A_Chars),
+	atom_codes(A,A_Codes),
 
-	once(append(Part1,[95|Part2],A_Chars)),	% 95 = '_'
-	number_chars(ID,Part1),
+	once(append(Part1,[95|Part2],A_Codes)),	% 95 = '_'
+	number_codes(ID,Part1),
 
 	(	     % let's check whether Part2 contains an 'l' (l=low)
          member(108,Part2)
@@ -709,7 +712,7 @@ bdd_vars_script_intern2(A) :-
 	   format('@~w~n0~n0~n~12f;~12f~n',[NameA,Mu,Sigma])
 	 );
          (
-	  number_chars(Grounding_ID,Part2),
+	  number_codes(Grounding_ID,Part2),
       (problog:decision_fact(ID,_) ->
           % it's a non-ground decision
           (problog:problog_control(check,internal_strategy) ->
@@ -987,8 +990,44 @@ get_next_name(Name) :-
 % create BDD-var as fact id prefixed by x
 % learning.yap relies on this format!
 % when changing, also adapt test_var_name/1 below
+
+
+simplify_list(List, SList):-
+  findall(NEL, (member(El, List), simplify(El, NEL)), SList).
+
+simplify(not(false), true):- !.
+simplify(not(true), false):- !.
+simplify(not(not(A)), B):-
+  !, simplify(A, B).
+simplify(A, A).
+
+
+
+simplify(not(false), true):- !.
+simplify(not(true), false):- !.
+simplify(not(not(A)), B):-
+  !, simplify(A, B).
+simplify(A, A).
+
+get_var_name(true, 'TRUE'):- !.
+get_var_name(false, 'FALSE'):- !.
+get_var_name(Variable, Name):-
+  atomic(Variable), !,
+  atomic_concat([x, Variable], Name),
+  (recorded(map, m(Variable, Name), _) ->
+    true
+  ;
+    recorda(map, m(Variable, Name), _)
+  ).
+get_var_name(not(A), NameA):-
+  get_var_name(A, NameA).
+
+
+/*
 get_var_name(true, 'TRUE') :-!.
 get_var_name(false, 'FALSE') :-!.
+get_var_name(not(A), NameA):-
+  !, get_var_name(A, NameA).
 get_var_name(A, NameA) :-
 	atomic_concat([x, A], NameA),
 	(
@@ -997,7 +1036,7 @@ get_var_name(A, NameA) :-
 	    true
 	;
 	    recorda(map, m(A, NameA), _)
-	).
+	).*/
 
 % test used by base case of compression mapping to detect single-variable tree
 % has to match above naming scheme
@@ -1060,39 +1099,29 @@ spacy_print(Msg, Level, Space):-
 :- dynamic(generated_trie/2).
 :- dynamic(next_intermediate_step/1).
 
-%
-% This needs to be modified
-% Include nasty code of temporary file usage
-% also it is OS depended (requires the cat utility)
-%
 
 nested_ptree_to_BDD_script(Trie, BDDFileName, VarFileName):-
   tmpnam(TmpFile1),
-  tmpnam(TmpFile2),
   open(TmpFile1, 'write', BDDS),
   (generate_BDD_from_trie(Trie, Inter, BDDS) ->
     next_intermediate_step(TMP), InterCNT is TMP - 1,
     write(BDDS, Inter), nl(BDDS),
     close(BDDS),
-    (get_used_vars(Vars, VarCNT);VarCNT = 0),
-    open(TmpFile2, 'write', HEADERS),
-    write(HEADERS, '@BDD1'), nl(HEADERS),
-    write(HEADERS, VarCNT), nl(HEADERS),
-    write(HEADERS, 0), nl(HEADERS),
-    write(HEADERS, InterCNT), nl(HEADERS),
-    close(HEADERS),
-    atomic_concat(['cat ', TmpFile2, ' ', TmpFile1, ' > ', BDDFileName], CMD),
-    shell(CMD),
-    delete_file(TmpFile1),
-    delete_file(TmpFile2),
+    (
+     get_used_vars(Vars, VarCNT)
+    ->
+     true;
+     VarCNT = 0
+    ),
+    create_bdd_file_with_header(BDDFileName,VarCNT,InterCNT,TmpFile1),
+    delete_file_silent(TmpFile1),
     open(VarFileName, 'write', VarStream),
     bddvars_to_script(Vars, VarStream),
     close(VarStream),
     cleanup_BDD_generation
   ;
     close(BDDS),
-    (delete_file(TmpFile1);true),
-    (delete_file(TmpFile2);true),
+    delete_file_silent(TmpFile1),
     cleanup_BDD_generation,
     fail
   ).
@@ -1136,7 +1165,7 @@ write_bdd_lineterm([LineTerm|LineTerms], Operator, Stream):-
 
 generate_line([], [], Inter, _Stream):-
   !, get_next_intermediate_step(Inter).
-generate_line([neg(t(Hash))|L], [TrieInter|T] , Inter, Stream):-
+generate_line([not(t(Hash))|L], [TrieInter|T] , Inter, Stream):-
   !, problog:problog_chktabled(Hash, Trie),
   generate_BDD_from_trie(Trie, TrieInterTmp, Stream),
   atomic_concat(['~', TrieInterTmp], TrieInter),
@@ -1159,11 +1188,11 @@ bddvars_to_script([H|T], Stream):-
   (number(H) ->
     CurVar = H
   ;
-    atom_chars(H, H_Chars),
+    atom_codes(H, H_Codes),
     % 95 = '_'
-    append(Part1, [95|Part2], H_Chars),
-    number_chars(CurVar, Part1),
-    number_chars(Grounding_ID, Part2)
+    append(Part1, [95|Part2], H_Codes),
+    number_codes(CurVar, Part1),
+    number_codes(Grounding_ID, Part2)
   ),
   (problog:dynamic_probability_fact(CurVar) ->
     problog:grounding_is_known(Goal, Grounding_ID),
@@ -1198,16 +1227,17 @@ make_bdd_var(V, VName):-
   get_var_name(V, VName),
   add_to_vars(V).
 
+
 add_to_vars(V):-
-  clause(get_used_vars(Vars, _Cnt), true),
-  memberchk(V, Vars),!.
+	clause(get_used_vars(Vars, _Cnt), true),
+	memberchk(V, Vars),!.
 add_to_vars(V):-
-  clause(get_used_vars(Vars, Cnt), true), !,
-  retract(get_used_vars(Vars, Cnt)),
-  NewCnt is Cnt + 1,
-  assertz(get_used_vars([V|Vars], NewCnt)).
+	clause(get_used_vars(Vars, Cnt), true), !,
+	retract(get_used_vars(Vars, Cnt)),
+	NewCnt is Cnt + 1,
+	assertz(get_used_vars([V|Vars], NewCnt)).
 add_to_vars(V):-
-  assertz(get_used_vars([V], 1)).
+	assertz(get_used_vars([V], 1)).
 
 
 %%%%%%%%%%%%%%% depth breadth builtin support %%%%%%%%%%%%%%%%%
@@ -1310,7 +1340,8 @@ is_state(true).
 is_state(false).
 
 nested_trie_to_bdd_trie(A, B, OutputFile, OptimizationLevel, FileParam):-
-  trie_nested_to_depth_breadth_trie(A, B, LL, OptimizationLevel, problog:problog_chktabled),
+%   trie_nested_to_depth_breadth_trie(A, B, LL, OptimizationLevel, problog:problog_chktabled),
+  nested_trie_to_depth_breadth_trie(A, B, LL, OptimizationLevel),
   (is_label(LL) ->
     retractall(deref(_,_)),
     (problog_flag(deref_terms, true) ->
@@ -1352,16 +1383,24 @@ nested_trie_to_bdd_trie(A, B, OutputFile, OptimizationLevel, FileParam):-
     ;
       Edges = [LL]
     ),
+    writeln(Edges),
     tell(FileParam),
-    bdd_vars_script(Edges),
+    simplify_list(Edges, SEdges),
+    bdd_vars_script(SEdges),
     told,
     tell(OutputFile),
     write('@BDD1'), nl,
     write(1), nl,
     write(0), nl,
     write(1), nl,
-    get_var_name(LL, NLL),
-    write('L1 = '),write(NLL),nl,
+    (LL = not(_) ->
+      write('L1 = ~')
+    ;
+      write('L1 = ')
+    ),
+    simplify(LL, FLL),
+    get_var_name(FLL, NLL),
+    write(NLL),nl,
     write('L1'), nl,
     told
   ).
@@ -1792,7 +1831,6 @@ seperate([H|T], Labels, [H|Vars]):-
 
 ptree_decomposition(Trie, BDDFileName, VarFileName) :-
   tmpnam(TmpFile1),
-  tmpnam(TmpFile2),
   nb_setval(next_inter_step, 1),
   variables_in_dbtrie(Trie, T),
   length(T, VarCnt),
@@ -1815,16 +1853,8 @@ ptree_decomposition(Trie, BDDFileName, VarFileName) :-
     write('L1'), nl
   ),
   told,
-  tell(TmpFile2),
-  write('@BDD1'),nl,
-  write(VarCnt),nl,
-  write('0'),nl,
-  write(LCnt),nl,
-  told,
-  atomic_concat(['cat ', TmpFile2, ' ', TmpFile1, ' > ', BDDFileName], CMD),
-  shell(CMD),
-  delete_file(TmpFile1),
-  delete_file(TmpFile2).
+  create_bdd_file_with_header(BDDFileName,VarCnt,LCnt,TmpFile1),
+  delete_file_silent(TmpFile1).
 
 get_next_inter_step(I):-
   nb_getval(next_inter_step, I),
@@ -2012,3 +2042,22 @@ mark_deref(DB_Trie):-
 mark_deref(_).
 
 % end of Theo
+
+create_bdd_file_with_header(BDD_File_Name,VarCount,IntermediateSteps,TmpFile) :-
+	open(BDD_File_Name,write,H),
+	% this is the header of the BDD script for problogbdd
+	format(H, '@BDD1~n~q~n0~n~q~n',[VarCount,IntermediateSteps]),
+
+	% append the content of the file TmpFile
+	open(TmpFile,read,H2),
+
+	(
+	 repeat,
+	 get_byte(H2,C),
+	 put_byte(H,C),
+	 at_end_of_stream(H2),
+	 !
+	),
+	close(H2),
+	
+	close(H).
\ No newline at end of file
diff --git a/packages/ProbLog/problog/utils_learning.yap b/packages/ProbLog/problog/utils_learning.yap
index 697add8b9..85402a6b2 100644
--- a/packages/ProbLog/problog/utils_learning.yap
+++ b/packages/ProbLog/problog/utils_learning.yap
@@ -2,8 +2,8 @@
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %
-%  $Date: 2010-09-29 13:24:43 +0200 (Wed, 29 Sep 2010) $
-%  $Revision: 4845 $
+%  $Date: 2010-10-20 18:06:47 +0200 (Wed, 20 Oct 2010) $
+%  $Revision: 4969 $
 %
 %  This file is part of ProbLog
 %  http://dtai.cs.kuleuven.be/problog
@@ -205,9 +205,7 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 :- module(utils_learning, [empty_bdd_directory/0,
-			   empty_output_directory/0,
-			   delete_file_silent/1,
-			   slice_n/4]).
+			   empty_output_directory/0]).
 
 
 % load library modules
@@ -217,6 +215,7 @@
 % load our own modules
 :- use_module(os).
 :- use_module(flags).
+:- use_module(utils).
 
 %========================================================================
 %= 
@@ -246,19 +245,8 @@ empty_output_directory :-
 	concat_path_with_filename(Path,'log.dat',F1),
 	concat_path_with_filename(Path,'out.dat',F2),
 	
-	(
-	 file_exists(F1)
-	->
-	 delete_file_silent(F1);
-	 true
-	),
-
-	(
-	 file_exists(F2)
-	->
-	 delete_file_silent(F2);
-	 true
-	),
+	delete_file_silent(F1),
+	delete_file_silent(F2),
 
 	atom_codes('values_', PF1),           % 'values_*_q_*.dat'
 	atom_codes('factprobs_', PF2),        % 'factprobs_*.pl'
@@ -272,16 +260,7 @@ empty_output_directory :-
 empty_output_directory :-
 	throw(error(problog_flag_does_not_exist(output_directory))).
 
-%========================================================================
-%= 
-%= 
-%========================================================================
 
-delete_file_silent(File) :-
-	file_exists(File),
-	delete_file(File),
-	!.
-delete_file_silent(_).
 
 %========================================================================
 %= 
@@ -304,17 +283,3 @@ delete_files_with_matching_prefix([Name|T],Path,Prefixes) :-
 
 	delete_files_with_matching_prefix(T,Path,Prefixes).
 
-%========================================================================
-%= Split a list into the first n elements and the tail
-%= +List +Integer -Prefix -Residuum
-%========================================================================
-
-
-slice_n([],_,[],[]) :-
-	!.
-slice_n([H|T],N,[H|T2],T3) :-
-	N>0,
-	!,
-	N2 is N-1,
-	slice_n(T,N2,T2,T3).
-slice_n(L,_,[],L).
diff --git a/packages/ProbLog/problog_learning.yap b/packages/ProbLog/problog_learning.yap
index b8c2ff1f0..82a350075 100644
--- a/packages/ProbLog/problog_learning.yap
+++ b/packages/ProbLog/problog_learning.yap
@@ -2,8 +2,8 @@
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %
-%  $Date: 2010-10-05 16:52:13 +0200 (Tue, 05 Oct 2010) $
-%  $Revision: 4869 $
+%  $Date: 2010-10-20 18:06:47 +0200 (Wed, 20 Oct 2010) $
+%  $Revision: 4969 $
 %
 %  This file is part of ProbLog
 %  http://dtai.cs.kuleuven.be/problog
@@ -225,6 +225,7 @@
 :- use_module('problog/os').
 :- use_module('problog/print_learning').
 :- use_module('problog/utils_learning').
+:- use_module('problog/utils').
 
 % used to indicate the state of the system
 :- dynamic(values_correct/0).
@@ -549,11 +550,12 @@ init_learning :-
 	!.
 init_learning :-
 	check_examples,
-
+	
+	empty_output_directory,
 	logger_write_header,
 
 	format_learning(1,'Initializing everything~n',[]),
-	empty_output_directory,
+
 
         %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 	% Delete the BDDs from the previous run if they should
@@ -1031,6 +1033,7 @@ mse_testset :-
 	 (
 	  format_learning(2,'MSE_Test ',[]),
 	  update_values,
+	  bb_put(llh_test_queries,0.0),
 	  findall(SquaredError,
 		  (user:test_example(QueryID,_Query,QueryProb,Type),
 		   once(update_query(QueryID,'+',probability)),
@@ -1041,7 +1044,10 @@ mse_testset :-
 		   ->
 		    SquaredError is (CurrentProb-QueryProb)**2;
 		    SquaredError = 0.0
-		   )
+		   ),
+		   bb_get(llh_test_queries,Old_LLH_Test_Queries),
+		   New_LLH_Test_Queries is Old_LLH_Test_Queries+log(CurrentProb),
+		   bb_put(llh_test_queries,New_LLH_Test_Queries)
 		  ),
 		  AllSquaredErrors),
 	  
@@ -1050,10 +1056,12 @@ mse_testset :-
 	  min_list(AllSquaredErrors,MinError),
 	  max_list(AllSquaredErrors,MaxError),
 	  MSE is SumAllSquaredErrors/Length,
+	  bb_delete(llh_test_queries,LLH_Test_Queries),
 
 	  logger_set_variable(mse_testset,MSE),
 	  logger_set_variable(mse_min_testset,MinError),
 	  logger_set_variable(mse_max_testset,MaxError),
+	  logger_set_variable(llh_test_queries,LLH_Test_Queries),
 	  format_learning(2,' (~8f)~n',[MSE])
 	 ); true
 	).
@@ -1232,6 +1240,7 @@ gradient_descent :-
 	bb_put(mse_train_sum, 0.0),
 	bb_put(mse_train_min, 0.0),
 	bb_put(mse_train_max, 0.0),
+	bb_put(llh_training_queries, 0.0),
 	
 	problog_flag(alpha,Alpha),
 	logger_set_variable(alpha,Alpha),
@@ -1267,12 +1276,15 @@ gradient_descent :-
 	  bb_get(mse_train_sum,Old_MSE_Train_Sum),
 	  bb_get(mse_train_min,Old_MSE_Train_Min),
 	  bb_get(mse_train_max,Old_MSE_Train_Max),
+	  bb_get(llh_training_queries,Old_LLH_Training_Queries),
 	  New_MSE_Train_Sum is Old_MSE_Train_Sum+Squared_Error,
 	  New_MSE_Train_Min is min(Old_MSE_Train_Min,Squared_Error),
 	  New_MSE_Train_Max is max(Old_MSE_Train_Max,Squared_Error),
+	  New_LLH_Training_Queries is Old_LLH_Training_Queries+log(BDDProb),
 	  bb_put(mse_train_sum,New_MSE_Train_Sum),
 	  bb_put(mse_train_min,New_MSE_Train_Min),
 	  bb_put(mse_train_max,New_MSE_Train_Max),
+	  bb_put(llh_training_queries,New_LLH_Training_Queries),
 	  
 
 
@@ -1368,11 +1380,13 @@ gradient_descent :-
 	bb_delete(mse_train_sum,MSE_Train_Sum),
 	bb_delete(mse_train_min,MSE_Train_Min),
 	bb_delete(mse_train_max,MSE_Train_Max),
+	bb_delete(llh_training_queries,LLH_Training_Queries),
 	MSE is MSE_Train_Sum/Example_Count,
 
 	logger_set_variable(mse_trainingset,MSE),
 	logger_set_variable(mse_min_trainingset,MSE_Train_Min),
 	logger_set_variable(mse_max_trainingset,MSE_Train_Max),
+	logger_set_variable(llh_training_queries,LLH_Training_Queries),
 
 	format_learning(2,'~n',[]),
 
@@ -1670,7 +1684,9 @@ init_logger :-
 	logger_define_variable(ground_truth_mindiff,float),
 	logger_define_variable(ground_truth_maxdiff,float),
 	logger_define_variable(learning_rate,float),
-	logger_define_variable(alpha,float).
+	logger_define_variable(alpha,float),
+	logger_define_variable(llh_training_queries,float),
+	logger_define_variable(llh_test_queries,float).
 
 :- initialization(init_flags).
 :- initialization(init_logger).