[433586]: / doc / _build / html / searchindex.js

Download this file

1 lines (1 with data), 11.8 kB

1
Search.setIndex({docnames:["autoencoder-integration","data-normalization","filtering-and-merging-latent-factors","index","maui","saving-and-loading-models","utils"],envversion:{"sphinx.domains.c":1,"sphinx.domains.changeset":1,"sphinx.domains.cpp":1,"sphinx.domains.javascript":1,"sphinx.domains.math":2,"sphinx.domains.python":1,"sphinx.domains.rst":1,"sphinx.domains.std":1,"sphinx.ext.intersphinx":1,"sphinx.ext.viewcode":1,sphinx:55},filenames:["autoencoder-integration.rst","data-normalization.rst","filtering-and-merging-latent-factors.rst","index.rst","maui.rst","saving-and-loading-models.rst","utils.rst"],objects:{"maui.Maui":{c_index:[4,1,1,""],cluster:[4,1,1,""],compute_auc:[4,1,1,""],compute_roc:[4,1,1,""],fit:[4,1,1,""],fit_transform:[4,1,1,""],get_linear_weights:[4,1,1,""],load:[5,2,1,""],save:[5,2,1,""],select_clinical_factors:[4,1,1,""],transform:[4,1,1,""]},"maui.utils":{compute_harrells_c:[6,2,1,""],compute_roc:[6,2,1,""],correlate_factors_and_features:[6,2,1,""],estimate_kaplan_meier:[6,2,1,""],filter_factors_by_r2:[6,2,1,""],map_factors_to_feaures_using_linear_models:[6,2,1,""],multivariate_logrank_test:[6,2,1,""],scale:[6,2,1,""]},maui:{Maui:[4,0,1,""],utils:[6,3,0,"-"]}},objnames:{"0":["py","class","Python class"],"1":["py","method","Python method"],"2":["py","function","Python function"],"3":["py","module","Python module"]},objtypes:{"0":"py:class","1":"py:method","2":"py:function","3":"py:module"},terms:{"abstract":[],"boolean":[2,4,6],"byte":[],"case":2,"class":[0,2,3,5,6],"default":[2,4,6],"final":[],"function":[0,1,2,4,5,6],"import":3,"int":4,"long":[],"new":5,"null":6,"public":[],"return":[3,4,6],"short":[],"static":[4,5],"switch":[],"true":[2,4,6],"try":[4,6],"while":[0,2,4,6],And:2,But:[],For:[2,3],Its:[],Not:4,One:[2,4],The:[0,2,3,5,6],Then:2,There:[],These:5,Use:[],Used:[2,4],_static:[],abov:[0,2,4,6],absolut:[],accept:[],access:[],accomplish:[2,4,6],accuraci:[4,6],achiev:0,act:[],activ:1,actual:[],add:[],added:[],addit:[],adjust:[2,4,6],after:[0,2],again:5,against:4,age:[2,4,6],all:[1,2,6],allow:0,alpha:[2,4,6],alreadi:[],also:[2,4],altern:[2,6],although:[],alwai:[],ami:4,ami_i:4,among:[4,6],analysi:[2,3,6],ani:[2,6],anoth:[2,6],append:[],appli:[],applic:[],approxim:[],arbitrari:2,architectur:[0,4],area:4,argument:[4,5],arrai:[4,6],assess:2,associ:[4,6],attempt:4,auc:[4,6],auroc:4,autoencod:4,avail:2,averag:4,axi:[2,4,6],back:[],base:[2,3,4,6],baseestim:3,basic:[],batch:[1,4],batch_normalize_embed:4,batch_normalize_input:4,batch_normalize_intermediari:4,batch_siz:4,bayesian:0,becaus:[],been:[2,4,6],befor:2,behav:[],being:[],below:[0,2,4,6],best:[4,6],between:[0,2,4,6],beyond:[],big:0,binari:[],blksize:[],block:[],blockingioerror:[],both:4,bottleneck:0,bottom:0,bound:[],buffer:[],buffer_s:[],bufferediobas:[],bufferedrandom:[],bufferedread:[],bufferedrwpair:[],bufferedwrit:[],builtin:[],bytearrai:[],bytesio:[],c_index:4,call:[0,2,4,5,6],callabl:4,caller:[],calss:2,can:[2,5],cannot:[],captur:2,center:[1,6],certain:[2,4],chang:[],charact:[],characterist:4,check:[2,3],chi:6,choic:[2,6],chosen:[],chunk:[],class_weight:6,classifi:6,client:[],clinic:[2,4,6],clinical_onli:4,close:[],closefd:[],cluster:[2,4,6],cnv:3,codec:[],coeffici:[2,4,6],color:0,column:[2,4,6],come:[1,2],common:[],complet:[2,4],comprehens:[2,3],comput:[2,4,6],compute_auc:4,compute_harrells_c:6,compute_roc:[4,6],concaten:[2,6],concatenated_data:6,connect:[],consid:4,consist:3,constructor:[],contain:[2,4,6],content:[],control:[2,4,6],converg:3,correl:[2,4,6],correlate_factors_and_featur:6,count:[],counterpart:[],covari:[2,4,6],cox:[2,4,6],cox_pen:[2,4,6],cox_penalti:[4,6],coxphfitt:[2,4,6],cph:[2,4,6],creat:[],creation:[],cross:[0,4,6],current:[],curv:[4,6],custom:[],cut:[2,6],cv_fold:[4,6],data:[0,2,3,4,5,6],datafram:[1,2,3,4,6],deal:[],death:[2,4,6],declar:[],decod:[],deep:4,def:[],default_buffer_s:[],defer:[],defin:[2,4,6],dendrogram:[2,4,6],depend:[],deprec:[],deriv:[],describ:[],descriptor:[],desir:3,destdir:[4,5],destin:[4,5],detach:[],determin:[0,2,4,6],devic:[],df1:4,df2:4,df_scale:[],diagnosi:[2,4,6],dict:[4,6],differ:[0,4,6],differenti:6,dimens:[0,2,3],dimension:0,dir:[4,5],direct:0,directli:[2,5],directori:[4,5],disabl:[],disconnect:[],disk:[3,4],distanc:[2,4,6],distance_in:[2,4],distance_metr:[2,4],distance_threshold:[2,4],distinguish:[],distribut:[0,4],diverg:0,document:[],doe:[1,2],doesn:[],down:[2,4],drop:[3,4],drop_unexplanatory_factor:[2,4],dual:6,dummi:[],durat:[2,4,6],duration_column:[2,4,6],dure:1,each:[1,2,4,6],effect:[],effici:0,egg:[],either:[],element:4,embed:[2,4],empti:[],enabl:[],encod:4,end:2,entir:[],entropi:0,eof:[],epoch:[3,4],epsilon_std:4,equal:[],equival:[],error:[],estim:[4,6],estimate_kaplan_mei:6,etc:4,even:2,exampl:[2,3],except:[],exclus:[],exist:[],expect:2,explanatori:2,expos:2,extend:[],extern:4,extra:0,facat:[2,6],fact:1,factor:[0,3,4,6],factorz:[2,4],failur:[],falc:[4,6],fall:[],fals:6,far:[],favtor:[2,4],featur:[1,2,4,6],feature_:6,feed:[1,3],figur:0,file:[4,5],fileexistserror:[],fileio:[],fileno:[],filter:[3,6],filter_factors_by_r2:[2,6],find:4,first:[0,3],fit:[2,3,4,6],fit_intercept:6,fit_transform:[3,4],fix:[],flag:[],flow:0,flush:[],fold:[4,6],follow:0,followup:[2,4,6],form:[2,6],fpr:[4,6],framework:3,from:[0,1,2,3,4,6],full:[],further:[3,5],futur:[],gaussian:0,gener:[],get:[4,6],get_linear_weight:[2,4],getbuff:[],getpreferredencod:[],getvalu:[],gex:3,give:4,given:[4,6],ground:[4,6],group:6,handl:[],harrel:[4,6],has:[2,5,6],have:[2,4,6],hazard:[2,4,6],heatmap:2,hello:[],help:[],here:[2,6],heurist:[],hidden:[0,3,4],hierarch:[2,6],hierarchi:[2,4,6],high:0,hist:3,histori:[],hit:[],hourglass:0,how:2,howev:[],hypothesi:6,ignor:[],imag:[],immedi:[],immin:[],immut:[],implement:[3,5],impli:[],includ:2,incomplet:[],index:[3,4,6],indic:[0,2,4,6],individu:[2,4,6],infer:[3,4],inform:[2,4,6],inherit:[],initi:4,initial_beta_v:4,initial_valu:[],input:[0,1,2,4,6],input_dim:4,insert:0,inspect:3,instanc:[2,5],instanti:[0,3,5],integ:[],integr:[0,4],intend:[],interact:[],intercept_sc:6,interest:2,interfac:[2,6],intermedi:4,interpret:[],introduct:3,involv:5,iobas:[],ioerror:[],isatti:[],isn:[],issu:[],iter:[],its:[],kaplan:6,kappa:4,keep:[2,4,6],kei:[4,6],kept:[],keyword:[],kind:[2,6],km_estim:6,kmean:4,kmeans_kwarg:4,known:[2,4,6],kullback:0,kwarg:4,label:[4,6],larg:2,last:[1,2,4,6],latent:[0,3,4,5,6],later:[2,4,5],layer:[0,1,3,4],lead:[],learn:[0,3,4],learning_r:4,least:6,leav:[],left:0,legal:[],leibler:0,length:[],less:[],level:4,lifelin:[2,4,6],like:[2,4,5,6],limit:1,line:[],line_buff:[],linear:[2,4,6],linearsvc:6,linesep:[],linkag:[2,4,6],linkage_method:[2,4],list:[],load:[3,4],local:[],log:[0,6],look:2,lose:2,loss:[0,4,6],low:[2,4],lower:[0,2],mai:[2,3,4,5],main:3,make:[],mani:[2,4],map:6,map_factors_to_featur:[],map_factors_to_feaures_using_linear_model:6,match:4,mathbf:0,mathcal:0,matplotlib:[2,4],matric:0,matrix:[0,2,4,6],maui:[0,1,2,5],maui_model:[0,3,4,5],max_beta_v:4,max_it:6,maximum:[],mean:[0,2,4,6],meier:6,memori:[],merg:[3,4,6],merge_factor:[2,6],merge_fn:[2,4,6],merge_similar_latent_factor:[2,4],method:[2,4],metric:[2,4,6],middl:[3,4],mini:4,minibatch:1,minim:0,mix:0,modal:[3,4],mode:4,model:[0,2,3,4,6],modul:3,moment:[],more:[2,3],most:[],move:[],mrna:[3,4],much:2,multi:[2,4,6],multi_class:6,multipl:[],multivari:6,multivariate_logrank_test:6,must:4,mut:3,mutat:3,mutual:4,mytabl:[],n_factor:[2,4,6],n_featur:[1,2,3,4,6],n_hidden:[0,3,4],n_init:4,n_job:4,n_latent:[0,3,4,6],n_latent_factor:[4,6],n_sampl:[1,2,3,4,6],name:[2,4,6],need:[1,4],neg:4,network:[0,1,4],neural:[0,1],never:[],newli:[2,6],newlin:[],next:[],node:[3,4],non:[1,4,6],none:[2,4,6],nonzero:[2,4,6],normal:3,note:[],noth:[],number:[2,4,6],numpi:[2,4,6],object:[2,3,4,6],observ:[2,4,6],observed_column:[2,4,6],obtain:4,off:[],offset:[],omic:[2,4,6],omit:[],onc:5,one:[0,2,3,4,5,6],ones:[2,6],onli:[2,4,6],open:[],oper:4,optim:4,optimal_k_method:4,optimal_k_rang:4,option:[2,4],order:[3,6],oserror:[],other:[2,4],otherwis:4,our:[2,3],out:[2,3],output:[0,2,6],over:[],overrid:[],ovr:6,own:[2,6],p_valu:6,page:3,panda:[3,4],paramet:[0,3,5],part:[],pass:0,path:5,patient:[2,6],pdist:[2,4,6],pearson:6,penal:4,penalti:[2,4,6],per:[4,6],perform:[],permit:[],pick:4,pipe:[],place:2,platform:[],plot:[2,3,4,6],plot_dendro:[2,6],plot_dendro_ax:[2,4,6],plot_dendrogram:[2,4],png:[],pointer:[],polici:[],popul:5,pos:[],posit:[4,6],possibl:0,power:2,pre:[2,6],predict:[2,4,6],preprocess:[],previous:[4,5],prior:[0,1],procedur:3,produc:2,proport:[2,4,6],protocol:[],provid:[1,2],put:[],pval_threshold:6,python:[],rais:[],random:[],random_st:6,rang:4,rank:6,rate:[4,6],raw:[],rawio:[],rawiobas:[],reach:[],read1:[],read:[],readabl:[],readal:[],reader:[],readi:[],readinto:[],readlin:[],receiv:4,recogn:[],recommend:[1,2],reconstruct:[0,1],regardless:[],regist:[],regress:[4,6],regular:4,rel:[],relev:[2,4,6],reload:[4,5],relu:4,relu_embed:4,relu_intermediari:4,repeatedli:[],report:[],repres:0,represent:[0,2,4,6],reproduc:4,request:[],requir:5,respect:0,result:4,retain:[],retriev:[],right:0,roc:[4,6],roc_curv:[4,6],run:[2,6],same:[2,6],sampl:[4,6],satisfi:[],save:[3,4],scalar:4,scale:[1,6],scikit:3,scipi:[2,4,6],score:[2,4],scorer:4,search:3,second:0,see:[2,3,4,6],seek:[],seek_cur:[],seek_end:[],seek_set:[],seekabl:[],sel_clin_alpha:4,sel_clin_penalti:4,select:[2,4,6],select_clinical_factor:[2,4,6],self:[2,4,5],sensor:6,separ:[],sequenti:[],seri:[4,6],set:[2,6],sex:[2,4,6],shape:0,should:4,show:[2,4,6],sigmoid:1,signatur:4,signific:4,silhouett:4,similar:[3,6],simpl:[],simpli:[],simultan:[],singl:[2,6],size:[0,4],sklearn:4,snp:4,socket:[],solver:[2,4,6],some:[2,3,4],sometim:0,sourc:[1,2,4,6],space:[2,4,5],spam:[],spatial:[2,4,6],specif:[],specifi:4,sql:[],squar:[2,6],squared_hing:6,squeez:[2,4],stack:[3,4],stage:[2,4,6],standard:[],standardscal:[],start:[],stat:[],state:[],statement:[],statist:6,still:1,store:[4,5],str:[],stream:2,strict:[],string:[],stringio:[],subclass:[],subset:[2,4,6],subtyp:6,success:4,succinct:2,suit:[],supervis:3,suppli:[2,6],support:[2,4,6],surviv:[2,4,6],svm:4,system:[],take:[0,2,5,6],target:5,tell:[],term:0,termin:[],test:6,test_statist:6,text:[],textio:[],textiobas:[],textiowrapp:[],than:[],thei:[2,5],therebi:0,thi:[0,1,2,3,4,6],those:[2,4,6],though:[],three:0,threshold:[2,4,6],through:0,time:[2,4,5,6],timelin:6,togeth:[],tol:6,too:[],top:[],total:[],tpr:[4,6],traiend:3,train:[0,1,2,3,4],transform:[4,5],translat:[],truncat:[],truth:[4,6],tty:[],tumor:[2,4,6],two:[0,3,5],txt:[],type:[],typic:[],unchang:[],under:[4,6],underli:[],unexplanatori:3,uninterest:2,unit:[0,4],univari:[2,4,6],univers:[],unix:[],unless:[],unlik:[],unspecifi:[],unsupervis:2,unsupportedoper:[],until:[],untransl:[],unus:[],updat:[],upon:[],usabl:[],use:[3,4,6],used:[2,3,4,5,6],usefulness:2,uses:[0,1,4],using:[0,2,4,5,6],usual:[],util:[1,2,3,4],vae:4,valid:[4,6],valu:[2,4,6],valueerror:[],vari:0,variabl:0,variat:[3,4],verbos:6,veri:2,version:[],view:0,vignett:[2,3],wai:2,weight:[5,6],well:[4,6],were:5,when:[0,2,4,6],whenc:[],where:[1,2,4,5,6],whether:[2,4,6],which:[0,2,3,4,5,6],whose:[2,4,6],without:2,work:[],would:[],wrap:[],writabl:[],write:[],writeabl:[],writelin:[],writer:[],written:[],x_valid:4,yhat:4,yield:[],your:[2,6],z_clinic:[2,4,6],z_filt:[2,4],z_filter:[2,6],zero:[]},titles:["Multi-modal Autoencoders","Data and Normalization","Filtering and Merging latent factors","Multi-omics Autoencoder Integration (maui)","The Maui Class","Saving and loading models","Maui Utilities"],titleterms:{"class":4,The:4,autoencod:[0,3],content:3,data:1,disk:5,document:[],drop:2,factor:2,filter:2,from:5,indic:3,integr:3,latent:2,load:5,maui:[3,4,6],merg:2,modal:0,model:5,multi:[0,3],normal:1,omic:3,quickstart:3,save:5,similar:2,stack:0,supervis:2,tabl:3,train:5,unexplanatori:2,util:6,variat:0,welcom:[]}})