% used for EC_rule generalization: cover()<50 :-use_module(library(ordsets)). %:-['testInput']. set(evDepth,7). /*********************Inconsistent Check ************************/ % T is discarded once cover one negative example coverNeg(NegList):- member(NegEI,NegList), ex(NegEI,E,0), %%write('one Negative example'),%write(NegEI), set(evDepth,DepthLimit), depth_bound_call(user:E, DepthLimit). /*********************Integrity Constraint ************************/ /***************Count Coverage (RELATIVE) *********/ % only check those from check list unCoverRecord([],[]). unCoverRecord([Index|CheckList],NUnCoverList):- %write('%%%%% covering'),%write(Index), (integer(Index)-> ex(Index,E,PosNegSign), ((set(etoB,yes),PosNegSign==1)-> retract(ex(Index,E,PosNegSign)); Flag=0 % Flag is for later added ); % not necessarily positive -- used for count FalseNeg E=Index ), %%write(E), %%write('%%%%% covering'), set(evDepth,DepthLimit), %%write('%%%%% covering'), (depth_bound_call(user:E, DepthLimit)-> NUnCoverList=UnCoverList; NUnCoverList=[Index|UnCoverList] ), (Flag==0 -> Foo2=1; % do nothing assert(ex(Index,E,PosNegSign)) ), %%write('%%%%% finish this example'),nl, unCoverRecord(CheckList,UnCoverList). /***************SCORE ********************/ % Sequentially compute each T: add T, score it, remove T0 tCompScore([],0). tCompScore([ClaI|T],NTScore):- tCompScore(T,TScore), claInterpreter(ClaI,Cla), length(Cla,HL), NTScore is TScore+HL. % score = TComplex+NumUnCover(Overall) % {PreSocre,PreUnCover,T} % {Score,UnCover,NewTSoFar,T} scoreTs(PosList,NegList,TSoFar,[],[]). scoreTs(PosList,NegList,TSoFar,[T|Ts],NScoredTs):- scoreTs(PosList,NegList,TSoFar,Ts,ScoredTs), %write('^^^Start scoring this T: Clause under inspection'), %write(T), nl, addTI(TSoFar,[],RefTSoFar),%write('TSoFar'),%write(TSoFar),%write('&&&'), addTI(T,RefTSoFar,RefAllT),%write('???Problem here'),%write(RefAllT),nl, %nl,nl,%write(TSoFar), %write('ADDing '), %%print_list(T),nl,listing, ((coverNeg(NegList);once(integrityConstraint))-> % expensive to check redundancy, so remove as much as possible at this stage %write('---inconsistent---'),nl, removeRefT(RefAllT,UselessT), NScoredTs=ScoredTs; %write('----Fine'),nl, %write('$$$$Check Redundant'), removeRedundant(RefAllT,NewRefAllT), %write('$$$$Finish'),nl, unCoverRecord(PosList,UnCover), %write('for this example'),%write(UnCover),nl, length(UnCover,K), removeRefT(NewRefAllT,NewAllT), tCompScore(NewAllT,TComplex), Score is TComplex+K, NScoredTs=[{Score,UnCover,NewAllT,T}|ScoredTs], % T itself is useless in the next gene--but to debug increamental write('')%write('Finish this score'),%write({Score,UnCover,NewAllT,T}),nl ). %%write('^^^ finish'),%write({Score,UnCover,NewAllT,T}),nl. /*************** START *******************/ % AllPEs initial set of PE (sampled for training--different from that for GenEList-include that not in AllPE) assembleHs(AllPEs,[],[]). assembleHs(AllPEs,[_-{T,GenEList}|Ts],[{Score,UnCover,[],T}|NewTs]):- assembleHs(AllPEs,Ts,NewTs), ord_subtract(AllPEs,GenEList,UnCover). noGenAssemble(AllPEs,[],[]). noGenAssemble(AllPEs,[{_,T}|Ts],[{Score,AllPEs,[],T}|NewTs]):- noGenAssemble(AllPEs,Ts,NewTs). %set(depthLimit,DepthLimit):-numMap(20,DepthLimit). cover([],_,FinalT,FinalT). % All Cover cover(EIs,_,FinalT,FinalT):- length(EIs, RemainedNum),RemainedNum < 50,!. % only 100 remained cover([EI|UnCover],NegList,TSoFar,FinalT):- set(depthLimit,DepthLimit), singleE(DepthLimit,EI,Ts), %nl,keggMapping(EI,KeggRID),%write(KeggRID),%write('*********Hypothesis for this example is '), %write(Ts),nl,%length(Ts,K),%write(K),nl, %%write('@@@@@@@Input for evaluation'), %write(UnCover),nl,%write(NegList),nl,nl, %%write('__________Start Scoring'),nl, evOneGen(Ts,TSoFar,UnCover,NegList,{NUnCover,NewTSoFar}), %write('--- Those remain uncover are'), %write(NUnCover),nl,maplist(keggMapping,NUnCover,RIDs),%write(RIDs),nl, %maplist(%writeReaction,RIDs), %%write('T So Far are : '), nl,%print_list(NewTSoFar),nl,%listing,nl, %%write('finish this one eGen evaluation, and '), %length([EIndex|UnCover],Num), %length(NUnCover,NNum), %NewCoveredNum is Num-NNum, %write(NewCoveredNum), %%write(' more are covered, while remain uncover is: '), %%write(NUnCover),nl, %%write(NewTSoFar),nl, cover(NUnCover,NegList,NewTSoFar,FinalT). keggMapping(EI,KeggRID):- ex(EI,E,PosNegSign), E=reactionClass(RID,_),concept_accession(RID,'KEGG',KeggRID,false). outputList([],[]). outputList([X|Rest],[X|Rest]):- set(depthLimit,DepthLimit), %write(X),%write('~~~~~~!!!!!!!!'), outputList(Rest,Rest). % no worry about cover uncover--PosList evOneGen(Ts,TSoFar,PosList,NegList,{UnCovered,NewTSoFar}):- scoreTs(PosList,NegList,TSoFar,Ts,ScoredTs),%write('^&^&^&^& finish scoring'),nl, %sort(ScoredTs,[{Min,UnCovered,NewTSoFar,BestT}|RestTs]), %%write('best for this examples is '),nl,%write({Min,UnCovered,NewTSoFar,BestT}), %%write('?2'), sort(ScoredTs,SortedTs),%write('?1'),write(SortedTs), SortedTs=[{Score,UnCovered,NewTSoFar,ChosenT}|Rest],%write({Score,UnCovered,NewTSoFar,ChosenT}),nl, %minSets(SortedTs,MinSet), %first5(SortedTs,MinSet), %print_list(MinSet), %print_list([{Score,UnCovered,NewTSoFar,ChosenT}|Rest]), %member({Score,UnCovered,NewTSoFar,ChosenT},SortedTs), %addT(NewTSoFar,TRef), %%print_list([{Min,UnCovered,NewTSoFar,BestT}|RestTs]), nl. first5([A,B,C,D,E|R],[A,B,C,D,E]). minSets([{Min,UnCovered,NewTSoFar,ChosenT}|Lists],[{Min,UnCovered,NewTSoFar,ChosenT}|Same]):- (once(append(Same,[{Score1,UnCovered1,NewTSoFar1,ChosenT1}|ListB],Lists),Score1\==Min),!;Same=[]). % find the first one that is not the same as Min % format("Here0~n",[]), %coverTest(EI):- c:- %write('abc start greedy search now'), statistics(cputime,[Total1,Previous]), tell('ec1_March_4.txt'), numbersList(1,483,PosEIs), NegEIs=[], %tell('odd.txt'), %cover([EI|[2,3,4,5,6,7,8]],[9,10,11,12,13,14,15,16],[],FinalT), % both even and odd %cover([EI|[4,6,8]],[9,10,11,12,13,14,15,16],[],FinalT), % both even and odd %cover([EI|[4,6,8]],[9,11,13,15],[],FinalT), % only odd % %tell('inoue.txt'), %PosEIs=[1,2,3],NegEIs=[], %tell('metaLogAbduction.txt'), %numbersList(1,20,PosEIs), %PosEIs=[1,2,3,4,5,6,8,9,10,11,13,12,14,15,16,17,18,19,20], /*tell('animal.txt'), %numbersList(1,16,PosEIs), PosEIs=[1,2,3,4,5,6,7,8,9,10,11,13,12,14,15,16], numbersList(17,58,NegEIs),*/ %tell('grammar.txt'), %numbersList(1,40,PosEIs0), %permutation(PosEIs0,PosEIs), %PosEIs=[1,19], %PosEIs=[21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,1,2,3,4,5,6,8,9,10,11,13,12,14,15,16,17,18,19,20], %numbersList(41,48,NegEIs), %tell('odd_even.txt'), %PosEIs=[19,5,7,11,1],NegEIs=[2,6,8,12,20], %PosEIs=[1,3,5,7,9,11,13,15,17,19],NegEIs=[2,4,6,8,10,12,14,16,18,20], cover(PosEIs,NegEIs,[],FinalTI), statistics(cputime,[Total2,Now]), TimeTaken is Now-Previous, %write('Final Learning Result'),nl, tInterpreter(FinalTI,FinalT), %print_list(FinalT), %write('Total Time Taken is '), %write(TimeTaken), nl.%told. % change that in evOneGen (from choosing only head to one of (member)) all:- %write('Find all possible HYPOTHESES'), statistics(cputime,[Total1,Previous]), %tell('ec1.txt'), %numbersList(1,483,EIs), %cover(EIs,[],[],FinalT), %tell('odd.txt'), %cover([EI|[2,3,4,5,6,7,8]],[9,10,11,12,13,14,15,16],[],FinalT), % both even and odd %cover([EI|[4,6,8]],[9,10,11,12,13,14,15,16],[],FinalT), % both even and odd %cover([EI|[4,6,8]],[9,11,13,15],[],FinalT), % only odd % tell('inoueAll.txt'), PosEIs=[1,2,3],NegEIs=[], %tell('metaLogAbduction.txt'), %numbersList(1,20,PosEIs), %PosEIs=[1,2,3,4,5,6,8,9,10,11,13,12,14,15,16,17,18,19,20], /*tell('animal.txt'), %numbersList(1,16,PosEIs), PosEIs=[1,2,3,4,5,6,7,8,9,10,11,13,12,14,15,16], numbersList(17,58,NegEIs),*/ %tell('grammar.txt'), %numbersList(1,26,PosEIs), %numbersList(27,33,NegEIs), findall(FinalTI, (cover(PosEIs,NegEIs,[],FinalTI), nl%tInterpreter(FinalTI,FinalT) ), AllPossibilities), length(AllPossibilities,AllNum),%write(AllNum), statistics(cputime,[Total2,Now]), TimeTaken is Now-Previous, %write('All Learning Result'),nl, %writeTheories(AllPossibilities), %write('Total Time Taken is '), %write(TimeTaken), told.