% Similar to genT.pl, the programs in this file generate hypotheses for training examples, however, rather than using covering, each example is used as a seed, and then crossproduct /*-------No Cross Product (simply go through each one) -------*/ % if put them together, then it becomes a big program. %OneTs=[[[enzymeState-]],[enzymeState-],[enzymeState-]]], % test product tno:- %numbersList(1,10,EIs), % %tell('tomato_crossProduct.txt'), PosEIs= [1,4,5,7,10,11], %[1,3,4,5,6,7,10,11,12], %[1,3,4,5,6,7,8,9,10,11],[1,4,5,7,9] learnAll(PosEIs,FinalT), write('Final suggested hypothesis is '),write(FinalT), /* genAll(EIs,Ts,TotalNum),write('Total is '), write(TotalNum),nl, Ts=[OneTs|RestTs], n1(OneTs,[],[],InitialCountedResult), setsCrossProduct(RestTs,InitialCountedResult,AllH), %sorteach(AllH,SortedHs), allScoring(AllH,AllScoredH), nl,sort(AllScoredH,SortedAllH),write('OK'),nl,print_list(SortedAllH), length(AllH,K), write('After'),write(K), */ nl. %told. norlate:- AspartateBioSynthesisPathway=[91,92,93,103], learnAll(AspartateBioSynthesisPathway,FinalT). norlateTCA:- TCA_cycle=[91,92,105,108]. cnrMid:- TCA_cycle=[47,48,61,64], learnAll(TCA_cycle,FinalT). learnAll(EIs,FinalTI):- tell('candidateH_genAll.pl'), genAll_signedTIs(EIs,EITIs,TotalNum), told, consult('candidateH_genAll.pl'), %allSetsCrossProduct(EIsTs,[[]],Result), crossProductlyCombine_and_check(EITIs,[[]],Result), tell('tomato_AspartateCandidates.txt'), print_list(Result), length(Result,RNum),write('Total is '), write({TotalNum,RNum}),nl,told. /* Ts=[OneTs|RestTs], n1(OneTs,[],[],InitialCountedResult), setsCrossProduct(RestTs,InitialCountedResult,AllH), %sorteach(AllH,SortedHs), allScoring(AllH,AllScoredH), nl,sort(AllScoredH,SortedAllH),nl,print_list(SortedAllH), length(AllH,K), write('After'),write(K), SortedAllH=[Score-FinalT0|_], nl,write(Score-FinalT0),nl, maplist(extractECNumState,FinalT0,FinalTI), nl. */ extractECNumState(Sign-Counter-{EC_Number,State},[enzyme_state-{EC_Number,State}]). sorteach([],[]). sorteach([Ele|Eles],[SortedEle|SortedEles]):- sorteach(Eles,SortedEles), sort(Ele,SortedEle). % twoSetsProduct() % cross product is simply recursively multiply two sets. s:- T0=[[]], EsTs=[ [ [[e1t1c1],[e1t1c2]], [[e1t2c2]] ], % one e1 [ [[e2t1c1],[e2t1c2]], [[e2t2c2]] ] % one e2 ], allSetsCrossProduct(EsTs,T0,Result), print_list(Result). %allSetsCrossProduct([[[[e1t1c1],[e1t1c2]], [[e1t2c2]]], [[[e2t1c1],[e2t1c2]],[[e2t2c2]]]],[[]],Result). allSetsCrossProduct([],Result,Result). allSetsCrossProduct([Set|RestSets],ResultSoFar,Result):- twoSetsProduct(Set,ResultSoFar,[],NewResultSoFar), allSetsCrossProduct(RestSets,NewResultSoFar,Result). twoSetsProduct([],Set2,Result,Result). twoSetsProduct([Ele1|Set1],Set2,ResultSoFar,Result):- maplist(combine(Ele1),Set2,NewEles), append(NewEles,ResultSoFar,NewResultSoFar), twoSetsProduct(Set1,Set2,NewResultSoFar,Result). combine(Ele1,Ele2,NewEle):- append(Ele1,Ele2,NewEle). %,!. %combine(Ele1,Ele2,NewEle):- % Ele2 is a list, while Ele1 is not. % append([Ele1],Ele2,NewEle),!. %combine(Ele1,Ele2,[Ele1,Ele2]). % the input is a list of EI-TIs crossProductlyCombine_and_check([],FinalHs,FinalHs). crossProductlyCombine_and_check([EI-TIs|EIs],Hs_sofar,FinalHs):- findall(NewH_sofar, ( member(TI,TIs), candidateH0(EI,TI,OneEIT), member(H_sofar,Hs_sofar),combineCheck(OneEIT,H_sofar,NewH_sofar) ), NewHs_sofar), crossProductlyCombine_and_check(EIs,NewHs_sofar,FinalHs). myAppend([],List2,List2). myAppend([Ele|List1],List2,[Ele|Result]):- myAppend(List1,List2,Result). combineCheck([],H,H). combineCheck([OneEIFact|OneEIT],H_sofar,H):- insertFact_to_Hsofar_noRedundant(OneEIFact,H_sofar,NewH_sofar), combineCheck(OneEIT,NewH_sofar,H). % add one clause to T insertFact_to_Hsofar_noRedundant(OneEIFact,H_sofar,H_sofar):- OneEIFact=[rs-{ReactionID,LimitingType,State,Time}], member([rs-{ReactionID,LimitingType2,State2,Time}],H_sofar),!, % get it State2==State. /* ((State2==State)-> %, LimitingType2==LimitingType Foo=1; write(OneEIFact), write('to be Added to'),write(H_sofar),fail ). % require them the same; not to added -- ensure no redundant */ insertFact_to_Hsofar_noRedundant(OneEIFact,H_sofar,[OneEIFact|H_sofar]). /* Even simple by using forAll(P,Q):- \+ (P, \+Q). numbersList(1,10,PosEIs), forAll(member(EI,PosEIs),g(EI,T)), */ as:- tell('H_for_ALLexs.txt'), statistics(cputime,[Total1,Previous]), set(depthLimit,DepthLimit), %numbersList(1,5,EIs), EIs=[1,2,3,5,7,9,10], continueEs(DepthLimit,EIs,RecordAll), length(RecordAll,K), nl,write('The total number of hypotheses is'), write(K),nl, statistics(cputime,[Total2,Now]), TimeTaken is Now-Previous, write('Total Time Taken is '), %write(TimeTaken), told. continueEs(DepthLimit,EIs,RecordAll):- findall(Tr, ( oneByone(DepthLimit,EIs,[],Tr),%write('OneTr'),write(Tr),nl,write('PreRemove'),listing,removeRefT(Tr),write('AfterRemove'),listing, %consistentCheck(Tr,FinalT), nl %tInterpreter(Tr,T) %,write('*** One theory'),nl, %write(Tr),nl, % track the ID of clauses in B %print_list(T),nl,nl ), RecordAll). oneByone(_,[],Tr,Tr). oneByone(DepthLimit,[EI|EIs],TrSoFar,Tr):- continueGenEx(DepthLimit,EI,TrSoFar,NewTrSoFar), %noRedundantAdd(OneTr,TrSoFar,NewTrSoFar), % check integrity constraint; oneByone(DepthLimit,EIs,NewTrSoFar,Tr). %1. add. Ref is included in Tr noRedundantAdd([],TrSoFar,TrSoFar). noRedundantAdd([ClauseIndex|OneTr],TrSoFar,NewTrSoFar):- hInterpreter(ClauseIndex,Clause), %(partialMem(ClauseIndex,TrSoFar,Sign),!; redundantCheck(Clause,Sign) ,%), (Sign==redundant-> write('Redundant HERE'),%listing,nl, UpdatedTrSoFar=TrSoFar; length(Clause,K),assertaH(K,Clause,Ref), UpdatedTrSoFar=[Ref-ClauseIndex|TrSoFar] ), noRedundantAdd(OneTr,UpdatedTrSoFar,NewTrSoFar). partialMem(ClauseIndex,[],nonRedundant). partialMem(ClauseIndex,[Ref-ClauseIndex|TrSoFar],redundant):- !. partialMem(ClauseIndex,[Ref-ClauseIndex2|TrSoFar],Sign):- partialMem(ClauseIndex,TrSoFar,Sign). %2. check, after adding one. intergrety, if violate, then cancel and stop; while if not, then continue % if violate the integrity constraint, then removeT(Ref),fail. (force it to fail) /*------- Cross Product-------*/ setsCrossProduct([],Result,Result). setsCrossProduct([Set|RestSets],ResultSoFar,Result):- nn(Set,ResultSoFar,[],NewResultSoFar), setsCrossProduct(RestSets,NewResultSoFar,Result). %nn(SetA,[],[],CountedResult):-!,n1(SetA,[],[],CountedResult). nn(SetA,[],Result,Result). nn(SetA,[Ele|SetB],ResultSoFar,Result):- n1(SetA,Ele,ResultSoFar,NewResultSoFar), nn(SetA,SetB,NewResultSoFar,Result). n1([],_,Result,Result). n1([Ele1|Set],Ele0,ResultSoFar,Result):- % It can be simple append(Ele1,Ele0,NewEle), but here we discard those inconsistent and count those repeated (add_to_countedResult(Ele1,Ele0,NewEle)-> NewSoFar=[NewEle|ResultSoFar]; NewSoFar=ResultSoFar ), n1(Set,Ele0,NewSoFar,Result). add_to_countedResult([],CountedResult,CountedResult). add_to_countedResult([Fact|T],CountedResultSoFar,CountedResult):- insertOneFact(Fact,CountedResultSoFar,NewSoFar), add_to_countedResult(T,NewSoFar,CountedResult). insertOneFact(Fact,CountedResultSoFar,NewSoFar):- Fact=[enzyme_state-{Sign,EC_Number,State}], append(Pre,[Sign-Counter-{EC_Number,StateStored}|Post],CountedResultSoFar),!, State==StateStored, NewCounter is Counter+1, append(Pre,Post,NewSoFar0), NewSoFar=[Sign-NewCounter-{EC_Number,StateStored}|NewSoFar0]. insertOneFact(Fact,CountedResultSoFar,[Sign-1-{EC_Number,State}|CountedResultSoFar]):- Fact=[enzyme_state-{Sign,EC_Number,State}]. allScoring([],[]). allScoring([H|AllH],[Score-H|AllScoredH]):- allScoring(AllH,AllScoredH), %oneHScoring(H,Score). oneHScoring_ignoreNoChange(H,Score). oneHScoring([],0). oneHScoring([Ele|H],Score):- oneHScoring(H,ScoredSoFar), Ele=Sign-NewCounter-{EC_Number,StateStored}, Score is ScoredSoFar+Sign. oneHScoring_ignoreNoChange([],0). oneHScoring_ignoreNoChange([Ele|H],Score):- oneHScoring_ignoreNoChange(H,ScoredSoFar), Ele=Sign-NewCounter-{EC_Number,State}, (State==no_change-> Score=ScoredSoFar; Score is ScoredSoFar+Sign ).