% this version is only specific for Syngenta % mainly for hypothesis selection based on trees % settings and cross validation are more modules % in terms of tomato input files % use Ondex ID directly -- rather than ex0 % new constraint -- direction of same reaction % mutant and time constraint % score function is specific for the data % For cancer project -- genEIs_T_constraintIncorporated.pl need to be replaced -- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % Load in build-in libraries %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% :-use_module(library(lists)). :-use_module(library(terms)). :-use_module(library(ordsets)). :-use_module(library(rbtrees)). :-use_module(library(random)). :-use_module(library(apply_macros)). %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % mc-TopLog %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% :-['source/settings.pl']. :-['source/genEIs_T_constraintIncorporated.pl']. %_multiE :-['source/topTheory_varConnection.pl']. %:-['source/genTmE.pl']. %:-['source/crossProduct_allEx.pl']. :-['source/nonGroundHBuilder.pl']. :-['source/covering.pl']. %:-['source/covering_syngenta_1.pl']. % used before for ex0 %:-['source/multiECovering.pl']. %:-['source/countingChoosing_temp.pl']. %countingChoosing_onlyCounting %:-['source/allEITs_BayesianCounting.pl']. %:-['source/bayes_syngenta.pl']. %:-['source/countTheory.pl']. % :-['source/insertTheories/decomposed_intoCla_outputed.pl']. %:-['source/insertTheories/decomposed_positionID.pl']. %decomposed_intoCla.pl %:-['source/likelihood_posterial.pl']. %:-['source/score/scoreCla_GE_BOTHTimeMutant_constrainted.pl']. % %:-['source/score/scoreCla_GE_Time_Mutant_constrainted.pl']. %scoreCla_GE %shared_NoLength %scoreTheory_GE_multivariate %:-['source/score/shared_NoLength.pl']. %:-['source/score/scoreTheory_GE_multivariate.pl']. :-['source/cross_validation_sepTrain_and_Test.pl']. % _temp :-['source/exProcess.pl']. :-['source/utilities.pl']. :-['source/programTransform.pl']. % this one haven't been %:-['source/cross_product_thretholdPruning.pl']. %:-['source/hypothesisSelection_preprocssing_smallestShared.pl']. %:-['source/hypothesisSelection_smallestShared.pl']. %:-['source/hypothesisSelection_domainSpecific.pl']. %:-['source/treeConstruction/hypothesisSelection.pl']. :-['source/treeConstruction/coverageNonSorted_fluxRecord.pl']. % coverageSorted_fluxRecord %_beamSearch %:-['source/treeConstruction/differentDescriptionLength/hypothesisSelection_groupingChoosing_keepPreSelection_FluxPassing.pl']. %hypothesisSelection_noEIs_combineCheck %hypothesisSelection_groupingChoosing_noRecordForCombineAndCompeting %:-['source/treeConstruction/differentDescriptionLength/hypothesisSelection_group_ScoreBased.pl']. %hypothesisSelection_groupingChoosing_keepPreSelection_FluxPassing_beamSearch_EIsubsetIgnored %hypothesisSelection_groupingChoosing_keepPreSelection_FluxPassing_beamSearch_fewRecord %:-['source/treeConstruction/differentDescriptionLength/hypothesisSelection1.pl']. :-['source/treeConstruction/differentDescriptionLength/hypothesisSelection_groupingChoosing_keepPreSelection_FluxPassing_beamSearch_EIsubsetIgnored2.pl']. % _newCombinable_2011_9_26 %:-['source/treeConstruction/draw.pl']. %:-['source/claIndex.pl']. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % Data %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % !!!!! remember to change the retract in 'covering.pl' %:-['artificialData/bioNetwork/inoue/ex']. %:-['artificialData/bioNetwork/metalog/hyEx']. %:-['artificialData/bioNetwork/ecRule/ecClass1Ex']. %:-['artificialData/animal/ex']. %:-['artificialData/grammar/grammar']. %:-['artificialData/bioNetwork/reactionReconstruction/ex']. %:-['artificialData/odd_even/ex']. %:-['artificialData/tomato/tomato_learningData/ex']. %:-['artificialData/metalog/hyEx']. %:-['artificialData/tomato/tomato_data.pl']. %:-['artificialData/tomato/archive/11_30/tomato_data.pl']. :-['artificialData/cancer/cancer_data.pl']. %:-['artificialData/hexose/hexose_data.pl']. %:-['artificialData/rsToy/candidateH0.pl']. %:-['artificialData/toy_example.pl']. %:-['artificialData/familyTree/family.pl']. %:-['artificialData/eventCalculus/data.pl']. /* :-['artificialData/odd_even/odd_evenEx']. %:-['artificialData/odd_even/odd_evenTopCla']. :-['artificialData/odd_even/odd_evenTopCla_nonFixLength']. %:-['artificialData/odd_even/singleCla/t']. %:-['artificialData/odd_even/singleCla/t_nonFixLength']. %:-['artificialData/odd_even/singleCla/b']. %:-['artificialData/odd_even/singleCla/odd_even_automa']. %:-['artificialData/odd_even/singleCla/evInputOddEven']. %:-['artificialData/odd_even/theory/t']. :-['artificialData/odd_even/theory/t_nonFixLength']. %:-['artificialData/odd_even/theory/t_nonFixLength_special']. :-['artificialData/odd_even/theory/b']. %:-['artificialData/odd_even/theory/mE/test']. %:-['artificialData/odd_even/theory/mE/t']. %:-['artificialData/odd_even/theory/mE/b']. */ %:-['artificialData/path_edge/path_edgeEx']. %:-['artificialData/path_edge/path_edgeTopCla']. %:-['artificialData/path_edge/experiment/0/t']. %:-['artificialData/path_edge/experiment/0/b']. %:-['artificialData/path_edge/experiment/abduction/t']. %:-['artificialData/path_edge/experiment/abduction/b']. /* %:-['artificialData/path_edge/AILP/path_edge']. %:-['artificialData/path_edge/AILP/evInputPath_edge']. %:-['artificialData/path_edge/abduction/path_edge']. %:-['artificialData/path_edge/abduction/evInputPath_edge']. %:-['artificialData/path_edge/induction/path_edge']. %:-['artificialData/path_edge/induction/path_edge_automa']. %:-['artificialData/path_edge/induction/evInputPath_edge']. */ /* %:-['artificialData/grammar/grammar']. %:-['artificialData/grammar/evInput_grammar']. %:-['artificialData/grammar/AILP/12/grammarLengthLimit']. %:-['artificialData/grammar/AILP/12/grammar']. %:-['artificialData/grammar/AILP/12/evInput_grammar']. */ :- dynamic claID_mapping/2. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % Output Version Information mcTopLog_version(1). mcTopLog_manual('http://www.doc.ic.ac.uk/~dl308/MC-Toplog/user_manual.html'). versionInfo:- nl, nl, write('MC-TopLog Version '), mcTopLog_version(Version), write(Version), nl, mcTopLog_manual(Man), write('Manual: '), write(Man), nl, nl. %training_examples([90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110]). run:- yap_flag(argv,[InputFile1,InputFile2]), consult(InputFile2), training_examples(TrainEIs),%write(TrainEIs), test_examples(TestEIs), (set(etoB,yes)-> maplist(removeTestEI,TestEIs,RemovedEIsDetail); Foo=0 % do nothing ), gen_output_readIn_candiateH(TrainEIs), indentifySharedHs(TrainEIs,T_EITIs), outputToC(TrainEIs,T_EITIs). % ideally, you need to remove training data when learning, but since you :- yap_flag(argv,[TimePoint,Fold_Index0]), %[InputFile1,TimePoint,Fold_Index0]), %[TimePoint,Fold_Index0]=['Day1','10'], getAllEx_oneTimePoint(TimePoint,AllEIs), %atom_number(Fold_Index0,Fold_Index_original), Fold_Index is Fold_Index_original+1, atom_number(Fold_Index0,Fold_Index), get_folds(Fold_Index,AllEIs,OneFoldEIs), %atom_concat(['./artificialData/cancer/experiments/progolH/',TimePoint,'/','hypoonly_',Fold_Index0,'.txt'],FileName), atom_concat(['./artificialData/cancer/experiments/mcTopLogH_GE_gen3-8/',TimePoint,'_',Fold_Index0,'.pl'],FileName), %mcTopLogH_gen3_GE consult(FileName), test_only(OneFoldEIs,Result), tell('oneFoldPrediction.txt'), write(Result),write(' '), told. compression:- yap_flag(argv,[TimePoint,Fold_Index0]), %[TimePoint,Fold_Index0]=['rin_late','20'], atom_concat([TimePoint,'_',Fold_Index0,'.pl'],FileName), consult(FileName), computeCompression(Compression), tell('oneFoldPrediction.txt'), write(Compression),write(' '), told.