python-pebl-doc 1.0.2-3 / usr / share / doc / python-pebl / html / searchindex.js

Search.setIndex({envversion:42,terms:{represent:[18,8],all:[20,18,14,15,22,1,2,3,23,5,12,17,6,19],entropi:[15,5,16,20],edg:[13,5,1,21],osx:23,scratch:6,macosx:25,datum:20,bayesian:[21,22,1,24,5,10,6,19],disc:20,add_network:3,abil:[5,1],follow:[18,15,16,1,23,24,5,12,17,6,19],learnerresult:[24,3,6],row:[21,6],content:7,decid:5,entropy_of_list:15,depend:19,abhik:6,graph:13,linesep:18,nose:[23,19],common:[18,6],program:[1,8,6],under:[1,23],sens:22,ofici:23,stopping_criteria:5,fieldsep:18,datafil:18,sourc:[12,23,19],everi:[22,21],string:[15,18,12,8],yeast:6,fals:[18,16,12,22],than:[14,15,22,23,5,18,6],result2:[3,6],result3:3,mpi:2,util:[15,1],feasibl:5,randomize_network:5,mechan:6,score_network:5,affect:[6,19],exact:[5,1],relev:[5,23],induct:21,recip:15,foo:[15,18,12,23],nestedit:15,list:[8,18,15,22,16,1,2,23,17,12,6,19],iter:[16,10,24,17,5,6],factori:13,"try":[23,20],item:15,lru_cach:15,form:[12,0,21,18],matric:22,maxsiz:[15,5,17,6],small:[24,5,21,8,6],configpars:12,continuousvari:18,dimens:18,newrow:21,smaller:22,intial:19,till:24,naiv:5,seper:17,direct:13,annot:13,threshold:[16,6],zero:18,cln2:6,cln1:6,skip_stat:18,download:[1,23],further:[5,23,6,19],port:0,append:6,belief:1,compat:12,index:[15,7,1],what:23,appear:8,compar:6,cast:12,section:12,learner:[13,5,1,23],calcul:[21,15,22,16,1,6],higuchi:22,children:8,current:[21,2,23,20],delet:15,engin:23,version:[21,23,4,5,6,19],include_default:12,"new":[24,16,1,21,3],net:[22,5,16,3,23],newtork:8,"public":[21,18],metadata:18,genex:18,involv:21,elimin:5,full:[17,25,6],abov:[12,23,6],merged_result:6,simulatedannealinglearn:13,usag:6,gener:[15,23],never:[5,6],privat:23,matplotlib:23,met:[24,22],shouldn:5,let:[4,23],free:[6,19],trunk:[23,19],path:[25,17,8,23],numbin:[18,6,20],modifi:[8,19],sinc:[5,6],valu:[13,20,12,21,18],wait:[17,25],incom:8,convert:12,technolog:25,biologi:6,scatter:2,precis:15,prior:[13,1,2],as_pydot:8,as_list:15,doctest:19,implement:[8,20,21,22,1,24,5,10],gene:[22,6],transact:5,uniformprior:22,via:[8,22,10,24,17,12,5,25],repositori:19,test_taskcontrol:23,appli:[15,5],modul:[7,8,13,18,22,16,10,2,3,24,5,12,6,19],prefer:19,missingdatamaximumentropynetworkevalu:5,filenam:[8,12,3,17,18,6],unix:23,"boolean":8,heurist:1,instal:[7,19],txt:[21,5,12,23,6],nullprior:22,causal:6,select:15,plot:23,from:[17,8,18,21,15,1,3,23,5,12,4,6,19],describ:5,would:[18,12,6],commun:19,incorrect:18,regist:[12,23],two:[8,21,15,22,12,6],coverag:6,subvers:19,few:[23,5,18,3,6],sucessfulli:23,call:[15,18,23],usr:[23,6],criteria:[5,1,17,6],type:13,until:19,more:[0,20,21,22,10,23,24,5,18,25,19],sort:[16,8],hundr:6,relat:[13,4,1,3,19],line:[18,1,12,23,6],probabilist:[21,6],enhanc:19,listlearn:13,gibbs_stat:5,subclass:12,accept:[24,8,6,19],known:[23,6],moin:0,given:[8,21,15,22,16,1,12,6],cach:[15,5,17,6],fromstr:18,must:[15,22,5,18,6,19],religi:19,add_mani:8,none:[0,8,20,18,14,15,22,10,2,3,24,5,12,17],retriev:[5,8,23],multinomi:21,hour:4,alia:18,setup:[23,19],work:[15,22,16,3,23,24,5,18],uniqu:18,remain:6,can:[0,8,20,12,21,18,16,10,3,23,24,5,1,17,25,19],inadequ:6,learn:[1,3,23,24,5,10],meet:2,root:[8,23],ipy1:13,def:15,appropri:[18,23,6],control:[13,18],encapsul:5,useabl:5,give:6,classvariableerror:18,ipython1control:0,sudo:[23,19],indic:[18,12],max_count:[4,17],high:6,critic:19,minimum:[4,17],tab:[18,6,19],heckerman:[24,5,10],serial:[13,17],has_miss:18,rescor:[24,5],tak:14,multipl:[8,14,1,2,5,18,17,6],variou:[1,6],rather:[14,23],anoth:[22,6],six:6,test_xgrid:23,write:[18,5,12],acycl:13,sever:[1,12,23],pure:21,reject:24,instead:[21,23],parameter:19,updat:4,resourc:[4,6,19],singular:6,network1:15,max:[15,5,10,12,17],after:[21,18,19],them:[4,14,23,6],reflect:[20,19],befor:[15,23,24,17,18,6,19],mac:23,edgelist:8,contribut:19,r2815:23,mai:[1,6,20],fromfil:[21,18,3,6],result1:[3,6],data:[13,12,21],parallel:[1,23,6],averag:6,outdir:[3,6],stabil:6,handl:[5,1,21,6],"short":[12,23,6],default_valid:12,otherlearn:6,redend:5,bootstrap:6,credenti:[4,23],correspond:[12,8,6],element:15,issu:[5,19],inform:[0,22,16,10,25,23,24,5,18,6,19],maintain:[5,8],combin:[15,22],allow:[23,6,19],assai:6,first:[21,18,8,23],egg:23,order:[16,18],longer:23,missingdatanetworkevalu:13,missingdata_evalu:5,help:23,ith:18,ec2control:4,somedata:21,over:[0,21,22,25,23,5,18,6],approv:12,becaus:[22,5,23,17,6],maximum_entropy_discret:[18,20],graphviz:[8,23],lst:15,through:[5,16],same:[8,5,22,1,17,18,4,6],husmeier:6,still:22,ieee:22,paramet:13,style:[1,8,19],herskovitz:21,consensu:[16,1,6],how:18,remove_mani:8,better:[24,6],platform:[4,23],window:23,imoto:22,fig:6,creat:[18,5,12,21,19],comprehens:6,hidden:1,main:[5,6],might:[2,6],alter:[5,18],split:2,xgridtaskcontrol:13,good:[15,6,19],"return":[8,18,15,22,16,1,3,24,5,12],greater:[18,23],thei:[1,18,6],python:[21,5,12,19],overal:6,cpickl:5,initi:19,mention:6,tofil:[18,3,6],bar:[15,12],now:[23,19],introduct:7,choic:5,multiprocess:13,name:[18,25,17,22,10,3,23,24,5,12,4,6],realist:6,edit:15,config:13,pyxg:23,probwheel:15,instruct:[23,19],authent:[4,17,23],separ:[18,23],iff:18,random_network:[21,8],mode:19,each:[22,8,6],found:[12,16,1,0,6],intervent:[1,18,6],difficult:5,mean:[17,4,14,5],subset:[21,18,6],domain:18,shortform:15,weight:[15,22],replac:21,hard:[22,1,6],continu:[5,18,6],hetland:15,combinatori:5,search:[7,8,16,10,24,17,12,6],expect:[15,18,6],learner_:3,micrarrai:6,energi:22,intparamet:12,extract:15,out:4,variabl:[13,21],shown:6,network:[13,12,21,19],space:[5,16,6],miss:[13,18,21,20],start_run:3,research:19,profil:6,undon:5,rel:6,reader:6,print:[16,23],merg:[1,18,3,6],correct:5,math:15,statist:[15,1,3,6],dataset:[13,21],xgridcontrol:25,linear:6,navig:23,written:12,regulatori:6,manipul:18,includevar:[18,20],undo:5,standard:[12,19],reason:4,base:[5,18,6,19],dictionari:15,latest:12,put:20,org:[0,15,10,23,24,5],yourpassword:23,likelihood:22,greedi:[13,5],basi:[23,6],tohtml:[3,6],perform:[15,5,18,8,20],kuhara:22,could:[15,12],script:[25,17,23,6],synchron:6,keep:[5,6],localscor:[5,17],perhap:6,"_calc_stat":18,place:[20,18,3,19],descript:12,learner1:6,retain:5,principl:6,confus:22,interact:[12,23],frequent:19,lambda:[5,8],origin:20,pleas:[23,19],rpesent:22,stringrep:18,directli:[5,18,6],perturb:6,feel:[6,19],onc:[16,23],arrai:[16,18],independ:6,number:[17,8,20,18,14,15,3,24,5,12,4,6],edit_dist:15,system:13,datastructur:15,done:[5,23],"long":5,mask:18,wasn:6,stabl:6,poolsiz:[17,14,6],open:5,redund:5,size:[20,14,15,3,17,5,6],min:12,differ:[8,15,1,4,5,6],silent:8,exponenti:15,ndarrai:[18,8],as_dotfil:8,top:[16,1,3,17,12,6],sometim:23,construct:[16,6],silenc:6,definit:13,indata:20,numnetwork:12,termin:[4,23],miyano:22,"final":[4,20,23,19],store:[15,3,8],includ:[20,18,21,1,2,3,23,5,12,17,6,19],ariti:[18,6],shell:[12,23],option:[18,5,12],relationship:6,especi:[6,19],methodolog:19,copi:8,specifi:13,ec2:13,node_posit:8,part:[10,2,25,24,5,12,6],pars:18,consult:[22,10,23,24,5,6,19],kept:17,attract:6,haven:23,testhtmlreport:23,serv:[6,19],molecular:6,instanc:[0,8,18,2,23,24,17,12,4],provid:[10,8,18,15,22,16,1,2,24,4,12,5,6],remov:[5,16,8],requir:[20,12,21,23,5,18,6],biolog:[22,6],structur:[1,18,6],charact:18,project:[23,19],matter:18,extended_properti:15,were:12,posit:8,minut:23,other:[5,18,23,6,20],secret_access_kei:23,html:12,seri:6,pre:20,"function":[13,12,21],comput:[22,1,23,4,5,6],ipclust:23,terribl:18,ran:23,py2:23,pass:[24,5,10,25],mind:6,ani:[10,25,22,1,3,23,24,17,18,5,6,19],packag:[1,23,6],seed:[24,17,10],variable_head:18,manner:5,tcserver:0,consensus_network:16,need:[23,4,5,6],dedic:23,"null":[22,9],fget:15,autoassign:15,fromdata:8,strength:1,burnin:[5,17],recreat:21,stop_run:3,alias:8,check:[18,12,23,6],xgridconfig:23,self:[15,24,2],violat:20,simul:13,contact:[23,6,19],note:[5,18,16,20],also:[8,1,3,23,24,18,6,19],msr:[24,5,10],curent:23,build:19,which:[20,18,22,2,23,24,12,6],tupl:[15,22,8],command:[1,12,23,6],phenotyp:6,data1:6,mit:1,data2:6,even:[15,20,19],begin:[24,18,6],sure:23,node:[8,21,16,23,5,6],distribut:13,normal:[15,18,23,6],track:5,alter_network:5,object:[12,22,16,1,3,18,19],reach:6,most:5,data_:[8,21,10,2,24,5],thi:[17,8,20,18,14,21,9,15,22,16,1,2,3,24,5,12,10,6,19],pair:15,gibbs_sampl:5,adjacency_list:8,"class":[13,12,21],as_str:8,don:[5,23],clear:[5,8,23],start_temp:[17,10],request:18,posterior:13,doe:[5,12,8,6],clear_network:5,runtim:[24,17],determin:[15,21,18,8,6],accompani:19,propos:19,microsoft:[24,5,10],dist:23,cartesian_product:15,example_data:12,edgeset:8,show:6,opposit:15,random:[24,5,8],access_kei:23,bin:[17,18,23,6,20],concurr:[17,14],saccharomyc:6,permiss:1,hack:18,learner2:6,uniform:22,trivial:16,find:23,restart_after_max_unimproved_iter:24,impact:20,cell:6,onli:[20,12,21,15,16,23,5,18,6],explicitli:18,locat:[23,6],just:[9,15,10,24,5,18,25],facil:1,hadn:22,max_tim:[24,17,6],explain:6,configur:13,solut:[23,6],state:5,technic:[24,5,10],network_:5,parametr:12,queu:14,analyz:6,neato:23,anneal:13,analys:1,serialcontrol:9,startswith:12,nosetest:[23,19],hit:15,lst2:15,as_imag:8,get:[15,12,8,23,20],familiar:6,localscorecach:13,express:[5,17,6],stop:[1,3,23,17,5,6],autom:[23,19],amazon:[13,23],cannot:[16,23,6],min_count:[4,17],network2:15,restart:[24,5,17],layout:8,child:21,ipython1:13,consist:[18,19],organ:6,pydot:[8,23],possibl:[21,22,1,2,5,6],baz:15,max_iters_at_temp:[17,10],method:[8,21,15,22,1,5,18,6],numtask:[17,6],whether:[18,12,23],integr:1,contain:[21,15,16,1,3,17,6,19],shh:18,peak:23,telecommun:23,where:[12,23],valid:13,wiki:[24,5,10],conform:[18,12],unobserv:1,set:12,seq:15,list_of_list:15,knowledg:[22,1,6],mutabl:[16,3],datatyp:12,see:[8,12,16,25,23,18,6],sec:[17,25],result:[13,5,12,20],arg:[22,18,3,9],fail:[18,8,23],close:19,simpl:[1,9],gmail:[23,6,19],unzip:15,detect:8,as_dotstr:8,parent:[21,8],has_intervent:18,wikipedia:[24,5,10],below:[5,6],label:[18,6],favor:22,enough:14,score:[22,16,1,2,3,24,5,12,17,6],jth:18,matrixedgelist:8,between:[8,15,10,25,17,12,6],"import":[12,6,19],experi:[23,6],approach:6,email:19,attribut:[15,18],spars:8,syntact:15,kei:[15,17,1,23],numer:18,xrang:18,cycl:[8,6],"0x7f942aec88c0":8,here:[17,6],otherwis:[24,22,5,12],ipython:[0,23],come:20,addit:[18,14,12,23],greedylearn:13,last:[5,6],delimit:[18,6],boto:23,hashabl:15,howev:6,equal:[22,20],subset_bynam:18,tempor:6,destnod:8,etc:[17,5,12,8],tutori:[24,7,5,10,19],atleast:12,agent:[17,25],futher:6,mani:12,com:[15,25,23,6,19],load:[23,5,18,3,6],randomli:15,simpli:[22,21,23,6,19],cancer:[18,6],point:24,color:8,overview:6,gridnumb:23,period:[5,17],height:8,header:6,featur:[1,23,6],non:[18,6,20],discretevari:18,checkout:19,linux:23,respect:8,poll:[17,25],assum:[18,6],pebl:13,quit:6,delta_temp:[17,10],second:[24,17],fortran:23,numpi:18,due:6,empti:15,mark:[15,1],compon:6,much:6,"66a3470f":23,treat:6,classvari:18,immedi:19,strategi:6,fset:15,your_amazon_accesskei:23,"0x7f94304de578":12,both:[18,8,23],rescale_logvalu:15,imag:[8,23],sampler:[5,17],worker:23,ez_setup:23,argument:[15,18,12],fromconfig:[18,5,12],revison:19,doesn:[22,23],func:15,demand:23,cerevisia:6,fileexist:12,present:[22,1],tashiro:22,"case":[16,18,23,6],replic:6,ident:6,multiprocesscontrol:13,tostr:18,properti:[15,8],sourceforg:23,pixel:8,defin:[15,12,4,2],"while":[5,18,6],parsingerror:18,error:[18,12],required_edg:[22,8],exist:[5,12,8],margin:[1,6],ill:18,loop:15,rent:[4,23,6],spawn:14,earli:18,have:[8,20,15,22,16,23,5,6,19],helper:5,metric:15,dotpath:8,"_psize":12,site:[1,19],activ:23,cluster:[4,1,0,23,6],kwarg:[22,18,9],cond:15,conf:22,crash:6,fdel:15,"__init__":[15,19],microarrai:[22,6],decor:[15,8],demostr:6,"_pfilenam":12,make:[20,21,1,23,24,5,19],format:[8,12,1,3,23,17,18],ec2config:23,access:[16,23],quickli:5,binari:[18,23],complex:[5,6],descend:16,easi:23,shah:6,document:[18,19],check_ar:18,start:[24,17,10,3,23],complet:5,exhaust:13,oneof:12,finish:[4,23],sortedscor:16,hostnam:[17,25,23],again:[24,19],optim:6,nest:15,max_iter:[24,17,6],upon:[18,6],assign:15,rais:[18,12],user:[4,1,12,5,23],aneaal:10,improv:[24,17],multimod:6,php:23,chang:[21,10,24,5,17,6,19],recent:[15,23],atmost:12,task:13,least:15,spellman:6,thu:[12,6],smartnetworkevalu:13,without:[15,1,23,24,5,18,17,6],pickl:[17,3],"2gb":6,exampl:13,shortli:6,max_unimproved_iter:[24,17],envis:19,model:[13,1,2],airti:18,dimension:6,usual:[16,23,6],comment:[18,6,19],distanc:15,identifi:6,execut:[1,23],hybrid:6,key_nam:23,rest:[5,21],insid:3,shape:18,observ:[1,18,6],aspect:[22,6],accuraci:15,speed:18,loglikelihood:[22,21],languag:6,previous:5,password:[17,25,23],miscellan:15,expos:8,hint:6,is_acyclic_python:8,except:13,param:[12,10,24,5,18,25],desktop:[23,6],informat:6,rescal:15,add:[8,15,16,3,5,6],discret:[13,18],peblpath:[17,25],guidelin:19,els:[15,12],save:[17,12,3,6,8],approxim:6,smart:5,take:[22,23],ami:23,applic:[1,8,6],spectacular:6,transpar:1,read:[12,1,3,17,18,6,19],big:[14,20],rna:6,caller:5,pollinterv:[17,25,23],localscore_cach:5,missingdataexactnetworkevalu:5,testipython1tc:23,built:6,temperatur:[17,10],grid:[17,25,23],step:[24,17,10,23,20],bit:22,characterist:8,associ:6,lst1:15,licens:1,python2:[15,23],insert:8,ignor:[18,6],png:8,like:[22,16,23,6],specif:[1,12,23,6],arbitrari:15,should:[0,18,21,16,2,3,23,5,12,17,6,19],xgriddeferredresult:25,prohibited_edg:[22,8],simann:13,probabililti:6,integ:[12,8],server:[0,25,23],collect:[3,8],datapoint:20,necessari:[15,23],confid:6,is_acycl:8,popular:23,output:[17,3,23,20],soft:[22,1],manag:[5,1],underli:6,encount:18,www:[25,23],often:22,manual:[23,19],phenomena:6,springer:6,resolv:19,stringparamet:12,enumer:[5,6],sampl:[13,21],"goto":22,logweight:15,guarante:6,successfulli:6,librari:[15,1,12,23,6],win32:23,cooper:21,avoid:5,preliminari:6,pep:19,slide:6,greedy_algorithm:24,when:[14,15,23,4,18,5,6,19],estim:[22,16,6],larg:[15,5,8,6],unit:[23,19],prog:8,condit:13,three:[21,23,6],proc:22,xgrid:13,either:18,machin:[23,6],core:1,process:[20,14,9,23,17,6],previou:[5,6],run:[10,0,14,25,9,17,1,3,23,24,5,4,6,19],power:23,logsum:15,fucntion:15,burn:[5,17],local:[15,24,5,23,6],example4:6,example2:6,example3:6,although:[5,23,6,19],example1:6,immut:16,post:16,test_result:23,impos:6,earlier:23,energy_matrix:22,src:23,about:[0,22,1,25,23,24,5,18,10,6,19],simplest:6,interven:[18,6],constraint:[22,1,2],column:[21,6],memori:[5,6],http:[0,15,10,25,23,24,5,6,19],page:[7,19],outgo:8,book:6,oldrow:21,compil:23,soc:22,effici:[5,21],activest:15,replace_data:21,programat:[1,6],easy_instal:19,automat:[15,12,23],upgrad:23,incorrectarityerror:18,speifi:18,been:6,identif:6,ensur:15,next:23,your:[23,6,19],sparseedgelist:8,nd8rjhnkj:6,fast:21,complianc:19,wai:6,maxim:20,bioinformat:6,support:[23,16,17,6],question:[6,19],submit:23,custom:[5,6],avail:[21,23],width:8,adjac:[22,8],appl:[25,23,6],interfac:[5,16,8],low:6,lot:15,unequ:20,taskcontrol:13,strict:19,unfortun:23,analysi:[5,1,6],zip:15,gibb:[5,17],simplejson:23,offer:8,some:[21,1,2,23,18,6],keyerror:12,histogram:15,knockdown:6,cloud:[4,23],measur:6,overflow:15,realli:5,"true":[18,5,12,16,22],dump:5,your_amazon_secret_access_kei:23,count:2,abhikshah:[23,6,19],input:[15,22,12,20],temp:[17,10],unfortunatli:23,"default":[0,8,18,14,25,9,17,10,2,3,24,5,12,4,6],wish:6,adjacency_matrix:8,hardwar:6,googlecod:[23,19],maximum:[20,15,5,24,17,4],adjacency_matric:16,scipi:[0,23],limit:[17,14,6],sum:15,bioinform:22,highlight:6,problem:23,stochast:6,similar:[15,22,2,6],medic:6,flatten:15,configobj:12,reserv:[4,23],later:[3,6,19],prior_:[24,5,10,2],evalu:13,certain:23,dure:[16,1,19],excludevar:[18,20],inbclud:21,levenshtein:15,repres:[22,16,18,8,6],strongli:19,floatparamet:12,intro:6,sample_head:18,file:[8,18,1,3,23,17,12,4],our:6,config1:6,regul:6,keynam:23,implent:2,probabl:13,logscale_probwheel:15,srcnode:8,unnecessari:5,equat:21,googl:[1,6,19],num_nod:[22,8],orf:6,detail:[1,6],results_sofar:6,expr2:15,expr1:15,futur:[2,3],varieti:1,test:19,squar:[5,17],you:[22,16,23,18,6,19],unlimit:[5,17],logadd:15,poor:6,repeat:24,rang:6,myeval:5,time:[22,17,25,6],restarting_criteria:24,ex1result:6,releas:23,log:[15,22,21,6],consid:[22,19],maxentropy_gibb:5,prepend:6,pool:[14,6],matrix:[22,18,8],svn:[4,23,19],axi:18,sphinx:[23,19],faster:15,algorithm:13,directori:[3,23,19],restore_network:5,cpd:13,visual:[1,8,23],simulated_ann:10,tricki:23,look:[5,23],depth:8,text:[17,18,6],dot:[8,23],caveat:6,far:21,cpt:18,cpu:1,test_ec2:23},objtypes:{"0":"std:confparam","1":"py:module","2":"py:function","3":"py:class","4":"py:method","5":"py:attribute","6":"py:exception"},objnames:{"0":["std","confparam","confparam"],"1":["py","module","Python module"],"2":["py","function","Python function"],"3":["py","class","Python class"],"4":["py","method","Python method"],"5":["py","attribute","Python attribute"],"6":["py","exception","Python exception"]},filenames:["taskcontroller/ipy1","intro","learner/exhaustive","result","taskcontroller/ec2","evaluator","tutorial","index","network","taskcontroller/serial","learner/simanneal","userguide","config","apiref","taskcontroller/multiprocess","util","posterior","paramref","data","devguide","discretizer","cpd","prior","install","learner/greedy","taskcontroller/xgrid"],titles:["<tt class=\"docutils literal\"><span class=\"pre\">taskcontroller.ipy1</span></tt> &#8211; IPython1 task controller","Pebl Introduction","<tt class=\"docutils literal\"><span class=\"pre\">learner.exhaustive</span></tt> &#8211; Exhaustive learners","<tt class=\"docutils literal\"><span class=\"pre\">result</span></tt> &#8211; Learner results","<tt class=\"docutils literal\"><span class=\"pre\">taskcontroller.ec2</span></tt> &#8211; Amazon EC2 task controller","<tt class=\"docutils literal\"><span class=\"pre\">evaluator</span></tt> &#8211; Network evaluators","Tutorial","Pebl Documentation!","<tt class=\"docutils literal\"><span class=\"pre\">network</span></tt> &#8211; Directed Acyclic Graphs","<tt class=\"docutils literal\"><span class=\"pre\">taskcontroller.serial</span></tt> &#8211; Serial task controller","<tt class=\"docutils literal\"><span class=\"pre\">learner.simanneal</span></tt> &#8211; Simulated annealing learner","User Guide","<tt class=\"docutils literal\"><span class=\"pre\">config</span></tt> &#8211; Pebl&#8217;s configuration system","API Reference","<tt class=\"docutils literal\"><span class=\"pre\">taskcontroller.multiprocess</span></tt> &#8211; Multiprocess task controller","&lt;no title&gt;","<tt class=\"docutils literal\"><span class=\"pre\">posterior</span></tt> &#8211; Posterior distribution","Configuration Parameters Reference","<tt class=\"docutils literal\"><span class=\"pre\">data</span></tt> &#8211; Pebl Dataset","Developer&#8217;s Guide","<tt class=\"docutils literal\"><span class=\"pre\">discretizer</span></tt> &#8211; Discretization algorithms","<tt class=\"docutils literal\"><span class=\"pre\">cpd</span></tt> &#8211; Conditional probability distributions","<tt class=\"docutils literal\"><span class=\"pre\">prior</span></tt> &#8211; Prior models","Installation","<tt class=\"docutils literal\"><span class=\"pre\">learner.greedy</span></tt> &#8211; Greedy learner","<tt class=\"docutils literal\"><span class=\"pre\">taskcontroller.xgrid</span></tt> &#8211; Xgrid task controller"],objects:{"pebl.network":{fromdata:[8,2,1,""],random_network:[8,2,1,""],Network:[8,3,1,""],EdgeSet:[8,3,1,""]},"pebl.learner.exhaustive.ListLearner":{split:[2,4,1,""]},"pebl.taskcontroller.multiprocess":{MultiProcessController:[14,3,1,""]},"pebl.taskcontroller.ipy1":{IPython1Controller:[0,3,1,""]},"pebl.cpd":{CPD:[21,3,1,""]},"pebl.taskcontroller.ec2":{EC2Controller:[4,3,1,""]},result:{size:[3,0,1,"-"],format:[3,0,1,"-"],filename:[3,0,1,"-"],outdir:[3,0,1,"-"]},"pebl.prior.Prior":{loglikelihood:[22,4,1,""]},"pebl.data.Dataset":{subset:[18,4,1,""],discretize:[18,4,1,""],subset_byname:[18,4,1,""],shape:[18,5,1,""],check_arities:[18,4,1,""],tofile:[18,4,1,""],has_missing:[18,5,1,""],tostring:[18,4,1,""],has_interventions:[18,5,1,""]},"pebl.result":{merge:[3,2,1,""],fromfile:[3,2,1,""],LearnerResult:[3,3,1,""]},pebl:{network:[8,1,0,"-"],discretizer:[20,1,0,"-"],data:[18,1,0,"-"],cpd:[21,1,0,"-"],util:[15,1,0,"-"],prior:[22,1,0,"-"],posterior:[16,1,0,"-"],result:[3,1,0,"-"],evaluator:[5,1,0,"-"],config:[12,1,0,"-"]},"pebl.util":{normalize:[15,2,1,""],autoassign:[15,2,1,""],unzip:[15,2,1,""],extended_property:[15,2,1,""],probwheel:[15,2,1,""],logsum:[15,2,1,""],cartesian_product:[15,2,1,""],rescale_logvalues:[15,2,1,""],logscale_probwheel:[15,2,1,""],levenshtein:[15,2,1,""],nestediter:[15,2,1,""],cond:[15,2,1,""],flatten:[15,2,1,""],edit_distance:[15,2,1,""],as_list:[15,2,1,""],entropy_of_list:[15,2,1,""],lru_cache:[15,2,1,""],logadd:[15,2,1,""]},"pebl.learner.greedy":{GreedyLearner:[24,3,1,""]},"pebl.learner.simanneal.SimulatedAnnealingLearner":{run:[10,4,1,""]},"pebl.learner.exhaustive":{ListLearner:[2,3,1,""]},"pebl.taskcontroller.serial":{SerialController:[9,3,1,""]},learner:{type:[17,0,1,"-"],numtasks:[17,0,1,"-"]},"pebl.posterior":{Posterior:[16,3,1,""]},gibbs:{burnin:[17,0,1,"-"],stopping_criteria:[5,0,1,"-"],max_iterations:[17,0,1,"-"]},"pebl.posterior.Posterior":{entropy:[16,5,1,""],consensus_network:[16,4,1,""]},"pebl.learner.greedy.GreedyLearner":{run:[24,4,1,""]},xgrid:{pollinterval:[25,0,1,"-"],controller:[25,0,1,"-"],password:[25,0,1,"-"],grid:[25,0,1,"-"],peblpath:[25,0,1,"-"]},"pebl.prior":{UniformPrior:[22,3,1,""],Prior:[22,3,1,""],NullPrior:[22,3,1,""]},"pebl.evaluator.SmartNetworkEvaluator":{score_network:[5,4,1,""],clear_network:[5,4,1,""],restore_network:[5,4,1,""],randomize_network:[5,4,1,""],alter_network:[5,4,1,""]},"pebl.network.EdgeSet":{outgoing:[8,4,1,""],incoming:[8,4,1,""],clear:[8,4,1,""],remove_many:[8,4,1,""],remove:[8,4,1,""],children:[8,4,1,""],add_many:[8,4,1,""],add:[8,4,1,""],parents:[8,4,1,""],adjacency_matrix:[8,5,1,""],adjacency_lists:[8,5,1,""]},"pebl.learner":{exhaustive:[2,1,0,"-"],simanneal:[10,1,0,"-"],greedy:[24,1,0,"-"]},listlearner:{networks:[17,0,1,"-"]},greedy:{seed:[17,0,1,"-"],max_unimproved_iterations:[17,0,1,"-"],max_time:[17,0,1,"-"],max_iterations:[17,0,1,"-"]},ec2:{min_count:[4,0,1,"-"],config:[4,0,1,"-"],max_count:[4,0,1,"-"]},"pebl.cpd.CPD":{replace_data:[21,4,1,""],loglikelihood:[21,4,1,""]},"pebl.config":{IntParameter:[12,3,1,""],FloatParameter:[12,3,1,""],configobj:[12,2,1,""],set:[12,2,1,""],parameters:[12,2,1,""],get:[12,2,1,""],read:[12,2,1,""],StringParameter:[12,3,1,""],oneof:[12,2,1,""],write:[12,2,1,""],atleast:[12,2,1,""],between:[12,2,1,""],atmost:[12,2,1,""],fileexists:[12,2,1,""]},evaluator:{missingdata_evaluator:[5,0,1,"-"]},"pebl.data":{fromconfig:[18,2,1,""],ClassVariable:[18,3,1,""],IncorrectArityError:[18,6,1,""],ClassVariableError:[18,6,1,""],fromstring:[18,2,1,""],ContinuousVariable:[18,3,1,""],Dataset:[18,3,1,""],Sample:[18,3,1,""],merge:[18,2,1,""],ParsingError:[18,6,1,""],Variable:[18,3,1,""],fromfile:[18,2,1,""],DiscreteVariable:[18,3,1,""]},data:{discretize:[17,0,1,"-"],text:[17,0,1,"-"],filename:[17,0,1,"-"]},"pebl.taskcontroller.xgrid":{XgridDeferredResult:[25,3,1,""],XgridController:[25,3,1,""]},multiprocess:{poolsize:[14,0,1,"-"]},ipython1:{controller:[0,0,1,"-"]},"pebl.network.Network":{layout:[8,4,1,""],is_acyclic_python:[8,4,1,""],as_string:[8,4,1,""],as_dotstring:[8,4,1,""],as_image:[8,4,1,""],as_dotfile:[8,4,1,""],as_pydot:[8,4,1,""],is_acyclic:[8,4,1,""],copy:[8,4,1,""]},"pebl.discretizer":{maximum_entropy_discretize:[20,2,1,""]},"pebl.learner.simanneal":{SimulatedAnnealingLearner:[10,3,1,""]},"pebl.result.LearnerResult":{tohtml:[3,4,1,""],stop_run:[3,4,1,""],start_run:[3,4,1,""],posterior:[3,5,1,""],tofile:[3,4,1,""],add_network:[3,4,1,""]},"pebl.taskcontroller":{ec2:[4,1,0,"-"],multiprocess:[14,1,0,"-"],xgrid:[25,1,0,"-"],serial:[9,1,0,"-"],ipy1:[0,1,0,"-"]},simanneal:{seed:[17,0,1,"-"],delta_temp:[17,0,1,"-"],max_iters_at_temp:[17,0,1,"-"],start_temp:[17,0,1,"-"]},localscore_cache:{maxsize:[17,0,1,"-"]},"pebl.taskcontroller.multiprocess.MultiProcessController":{run:[14,4,1,""]},"pebl.evaluator":{fromconfig:[5,2,1,""],MissingDataExactNetworkEvaluator:[5,3,1,""],MissingDataMaximumEntropyNetworkEvaluator:[5,3,1,""],MissingDataNetworkEvaluator:[5,3,1,""],SmartNetworkEvaluator:[5,3,1,""]},"pebl.evaluator.MissingDataNetworkEvaluator":{score_network:[5,4,1,""]},taskcontroller:{type:[17,0,1,"-"]}},titleterms:{missingdatanetworkevalu:5,listlearn:[17,2],edg:8,definit:12,soon:6,code:19,paramet:[0,18,14,17,10,2,3,24,5,12,4,25],depend:23,thank:19,graph:8,configur:[0,18,14,17,10,2,3,24,5,12,4,25],except:18,html:23,bibliographi:6,anneal:10,introduc:6,xgridtaskcontrol:25,format:6,python:23,localscorecach:5,localscore_cach:17,amazon:4,report:[23,19],introduct:1,multiprocess:[17,14],ipython1:[17,0,23],simann:[17,10],factori:[5,12,8],valid:12,set:19,direct:8,valu:5,second:6,sampl:18,result:[23,17,3,6],variabl:18,scale:6,network:[5,8],learner:[24,17,10,2,3],condit:21,xgrid:[17,25,23],refer:[13,17],solv:6,come:6,greedi:[24,17],greedylearn:24,multiprocesscontrol:14,simul:10,prior:22,tutori:6,commit:19,first:6,dude:19,easy_instal:23,dataset:18,api:13,instal:23,guid:[11,19],miss:5,pebl:[7,18,1,23,12,6,19],creat:23,numpi:23,system:12,avail:1,interpret:6,type:12,more:6,"function":[5,18,3,8],option:23,relat:25,specifi:12,posterior:16,bug:19,algorithm:20,annot:18,can:6,learn:6,problem:6,ipy1:0,ec2:[4,17,23],control:[0,14,9,23,4,25],evalu:5,indic:7,file:6,tabl:7,serial:9,guildelin:19,probabl:21,concept:1,develop:[23,19],smartnetworkevalu:5,note:6,acycl:8,discret:20,fourth:6,test:23,document:7,config:12,exhaust:2,distribut:[16,21],user:11,simulatedannealinglearn:10,data:[17,18,6],"class":[0,14,10,2,24,4,18,25],task:[0,14,9,23,4,25],third:6,cpd:21,taskcontrol:[0,14,9,4,17,25],exampl:[12,6],environ:19,model:22}})