{"id":"https://openalex.org/W3091633069","doi":"https://doi.org/10.1093/bib/bbaa226","title":"Synthetic observations from deep generative models and binary omics data with limited sample size","display_name":"Synthetic observations from deep generative models and binary omics data with limited sample size","publication_year":2020,"publication_date":"2020-08-24","ids":{"openalex":"https://openalex.org/W3091633069","doi":"https://doi.org/10.1093/bib/bbaa226","mag":"3091633069","pmid":"https://pubmed.ncbi.nlm.nih.gov/33003196"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaa226","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbaa226","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5065221265","display_name":"Jens Nu\u00dfberger","orcid":null},"institutions":[{"id":"https://openalex.org/I4210099379","display_name":"Zimmer Biomet (Germany)","ror":"https://ror.org/016731f38","country_code":"DE","type":"company","lineage":["https://openalex.org/I4210099379","https://openalex.org/I4210115238"]},{"id":"https://openalex.org/I161046081","display_name":"University of Freiburg","ror":"https://ror.org/0245cg223","country_code":"DE","type":"education","lineage":["https://openalex.org/I161046081"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Jens Nu\u00dfberger","raw_affiliation_strings":["Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, Germany"],"affiliations":[{"raw_affiliation_string":"Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, Germany","institution_ids":["https://openalex.org/I4210099379","https://openalex.org/I161046081"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054533062","display_name":"Frederic Boesel","orcid":"https://orcid.org/0009-0006-4773-7554"},"institutions":[{"id":"https://openalex.org/I4210099379","display_name":"Zimmer Biomet (Germany)","ror":"https://ror.org/016731f38","country_code":"DE","type":"company","lineage":["https://openalex.org/I4210099379","https://openalex.org/I4210115238"]},{"id":"https://openalex.org/I161046081","display_name":"University of Freiburg","ror":"https://ror.org/0245cg223","country_code":"DE","type":"education","lineage":["https://openalex.org/I161046081"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Frederic Boesel","raw_affiliation_strings":["Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, Germany"],"affiliations":[{"raw_affiliation_string":"Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, Germany","institution_ids":["https://openalex.org/I4210099379","https://openalex.org/I161046081"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060533947","display_name":"Stefan Lenz","orcid":"https://orcid.org/0000-0001-9135-1743"},"institutions":[{"id":"https://openalex.org/I161046081","display_name":"University of Freiburg","ror":"https://ror.org/0245cg223","country_code":"DE","type":"education","lineage":["https://openalex.org/I161046081"]},{"id":"https://openalex.org/I4210099379","display_name":"Zimmer Biomet (Germany)","ror":"https://ror.org/016731f38","country_code":"DE","type":"company","lineage":["https://openalex.org/I4210099379","https://openalex.org/I4210115238"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Stefan Lenz","raw_affiliation_strings":["Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, Germany"],"affiliations":[{"raw_affiliation_string":"Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, Germany","institution_ids":["https://openalex.org/I4210099379","https://openalex.org/I161046081"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011534196","display_name":"Harald Binder","orcid":"https://orcid.org/0000-0002-5666-8662"},"institutions":[{"id":"https://openalex.org/I161046081","display_name":"University of Freiburg","ror":"https://ror.org/0245cg223","country_code":"DE","type":"education","lineage":["https://openalex.org/I161046081"]},{"id":"https://openalex.org/I4210099379","display_name":"Zimmer Biomet (Germany)","ror":"https://ror.org/016731f38","country_code":"DE","type":"company","lineage":["https://openalex.org/I4210099379","https://openalex.org/I4210115238"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Harald Binder","raw_affiliation_strings":["Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, Germany"],"affiliations":[{"raw_affiliation_string":"Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, Germany","institution_ids":["https://openalex.org/I4210099379","https://openalex.org/I161046081"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5031697244","display_name":"Moritz Hess","orcid":"https://orcid.org/0000-0003-4021-1796"},"institutions":[{"id":"https://openalex.org/I4210099379","display_name":"Zimmer Biomet (Germany)","ror":"https://ror.org/016731f38","country_code":"DE","type":"company","lineage":["https://openalex.org/I4210099379","https://openalex.org/I4210115238"]},{"id":"https://openalex.org/I161046081","display_name":"University of Freiburg","ror":"https://ror.org/0245cg223","country_code":"DE","type":"education","lineage":["https://openalex.org/I161046081"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Moritz Hess","raw_affiliation_strings":["Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, Germany"],"affiliations":[{"raw_affiliation_string":"Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, Germany","institution_ids":["https://openalex.org/I4210099379","https://openalex.org/I161046081"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5031697244"],"corresponding_institution_ids":["https://openalex.org/I161046081","https://openalex.org/I4210099379"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":0.58,"has_fulltext":false,"cited_by_count":12,"citation_normalized_percentile":{"value":0.65292186,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"22","issue":"4","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9991000294685364,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9991000294685364,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10775","display_name":"Generative Adversarial Networks and Image Synthesis","score":0.98580002784729,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9850000143051147,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7037898302078247},{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.7004595994949341},{"id":"https://openalex.org/keywords/imputation","display_name":"Imputation (statistics)","score":0.5408438444137573},{"id":"https://openalex.org/keywords/generative-model","display_name":"Generative model","score":0.5371693968772888},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4983952045440674},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.48777180910110474},{"id":"https://openalex.org/keywords/binary-data","display_name":"Binary data","score":0.4829913377761841},{"id":"https://openalex.org/keywords/binary-number","display_name":"Binary number","score":0.479551762342453},{"id":"https://openalex.org/keywords/sample","display_name":"Sample (material)","score":0.46487998962402344},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.38534438610076904},{"id":"https://openalex.org/keywords/generative-grammar","display_name":"Generative grammar","score":0.371326744556427},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3516828119754791},{"id":"https://openalex.org/keywords/missing-data","display_name":"Missing data","score":0.3190474212169647},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.16764381527900696}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7037898302078247},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.7004595994949341},{"id":"https://openalex.org/C58041806","wikidata":"https://www.wikidata.org/wiki/Q1660484","display_name":"Imputation (statistics)","level":3,"score":0.5408438444137573},{"id":"https://openalex.org/C167966045","wikidata":"https://www.wikidata.org/wiki/Q5532625","display_name":"Generative model","level":3,"score":0.5371693968772888},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4983952045440674},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.48777180910110474},{"id":"https://openalex.org/C2779190172","wikidata":"https://www.wikidata.org/wiki/Q4913888","display_name":"Binary data","level":3,"score":0.4829913377761841},{"id":"https://openalex.org/C48372109","wikidata":"https://www.wikidata.org/wiki/Q3913","display_name":"Binary number","level":2,"score":0.479551762342453},{"id":"https://openalex.org/C198531522","wikidata":"https://www.wikidata.org/wiki/Q485146","display_name":"Sample (material)","level":2,"score":0.46487998962402344},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.38534438610076904},{"id":"https://openalex.org/C39890363","wikidata":"https://www.wikidata.org/wiki/Q36108","display_name":"Generative grammar","level":2,"score":0.371326744556427},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3516828119754791},{"id":"https://openalex.org/C9357733","wikidata":"https://www.wikidata.org/wiki/Q6878417","display_name":"Missing data","level":2,"score":0.3190474212169647},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.16764381527900696},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C94375191","wikidata":"https://www.wikidata.org/wiki/Q11205","display_name":"Arithmetic","level":1,"score":0.0},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018401","descriptor_name":"Sample Size","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018401","descriptor_name":"Sample Size","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018401","descriptor_name":"Sample Size","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbaa226","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbaa226","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:33003196","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33003196","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Peace, Justice and strong institutions","id":"https://metadata.un.org/sdg/16","score":0.41999998688697815}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":40,"referenced_works":["https://openalex.org/W189596042","https://openalex.org/W1912672559","https://openalex.org/W1959608418","https://openalex.org/W1974618278","https://openalex.org/W2042492924","https://openalex.org/W2099057450","https://openalex.org/W2099471712","https://openalex.org/W2099866409","https://openalex.org/W2120575449","https://openalex.org/W2125389028","https://openalex.org/W2225156818","https://openalex.org/W2402144811","https://openalex.org/W2604918751","https://openalex.org/W2801128564","https://openalex.org/W2892055372","https://openalex.org/W2901677030","https://openalex.org/W2921591500","https://openalex.org/W2935703330","https://openalex.org/W2950782073","https://openalex.org/W2951381561","https://openalex.org/W2953384591","https://openalex.org/W2961396908","https://openalex.org/W2963073614","https://openalex.org/W2963679759","https://openalex.org/W2963857374","https://openalex.org/W2963873275","https://openalex.org/W2972569990","https://openalex.org/W2978107983","https://openalex.org/W3101380508","https://openalex.org/W4320013936","https://openalex.org/W6607775107","https://openalex.org/W6640963894","https://openalex.org/W6674887261","https://openalex.org/W6678815747","https://openalex.org/W6713134421","https://openalex.org/W6729966448","https://openalex.org/W6735926176","https://openalex.org/W6746090280","https://openalex.org/W6767271743","https://openalex.org/W6779669310"],"related_works":["https://openalex.org/W2181530120","https://openalex.org/W4211215373","https://openalex.org/W2024529227","https://openalex.org/W1574575415","https://openalex.org/W3144172081","https://openalex.org/W3179858851","https://openalex.org/W3028371478","https://openalex.org/W2081476516","https://openalex.org/W2581984549","https://openalex.org/W3123177881"],"abstract_inverted_index":{"Deep":[0],"generative":[1,96,107],"models":[2],"can":[3,150],"be":[4,39,213,241],"trained":[5],"to":[6,38,155,209,212],"represent":[7],"the":[8,171,200,228],"joint":[9],"distribution":[10],"of":[11,16,47,125,161,176,184],"data,":[12,83,144,219],"such":[13,44,78,115],"as":[14,45,85,116,132,139,141],"measurements":[15],"single":[17],"nucleotide":[18],"polymorphisms":[19],"(SNPs)":[20],"from":[21,31,237],"several":[22,42],"individuals.":[23],"Subsequently,":[24],"synthetic":[25,235],"observations":[26,236],"are":[27],"obtained":[28],"by":[29],"drawing":[30],"this":[32],"distribution.":[33],"This":[34,111,226],"has":[35],"been":[36],"shown":[37],"useful":[40],"for":[41,50,81,153,216,230],"tasks,":[43],"removal":[46],"noise,":[48],"imputation,":[49],"better":[51],"understanding":[52],"underlying":[53],"patterns,":[54],"or":[55],"even":[56,220],"exchanging":[57],"data":[58,239],"under":[59],"privacy":[60],"constraints.":[61],"Yet,":[62],"it":[63],"is":[64,130],"still":[65],"unclear":[66],"how":[67],"well":[68,140,214],"these":[69],"approaches":[70],"work":[71],"with":[72,158,181,191],"limited":[73],"sample":[74,193,224],"size.":[75],"We":[76],"investigate":[77],"settings":[79],"specifically":[80],"binary":[82,217],"e.g.":[84],"relevant":[86],"when":[87,117,164],"considering":[88,118],"SNP":[89,143],"measurements,":[90],"and":[91,106,173,195,205],"evaluate":[92],"three":[93],"frequently":[94],"employed":[95],"modeling":[97],"approaches,":[98,114],"variational":[99],"autoencoders":[100],"(VAEs),":[101],"deep":[102],"Boltzmann":[103],"machines":[104],"(DBMs)":[105],"adversarial":[108],"networks":[109],"(GANs).":[110],"includes":[112],"conditional":[113,121],"gene":[119],"expression":[120],"on":[122],"SNPs.":[123],"Recovery":[124],"pair-wise":[126,197],"odds":[127],"ratios":[128],"(ORs)":[129],"considered":[131],"a":[133,159],"primary":[134],"performance":[135],"criterion.":[136],"For":[137],"simulated":[138],"real":[142],"we":[145],"observe":[146],"that":[147],"DBMs":[148,204],"generally":[149,169],"recover":[151],"structure":[152],"up":[154],"300":[156],"variables,":[157],"tendency":[160],"over-estimating":[162],"ORs":[163],"not":[165],"carefully":[166],"tuned.":[167],"VAEs":[168,206],"get":[170],"direction":[172],"relative":[174],"strength":[175],"pairwise":[177],"relations":[178,198],"right,":[179],"yet":[180],"considerable":[182],"under-estimation":[183],"ORs.":[185],"GANs":[186],"provide":[187],"stable":[188],"results":[189],"only":[190],"larger":[192],"sizes":[194],"strong":[196],"in":[199],"data.":[201],"Taken":[202],"together,":[203],"(in":[207],"contrast":[208],"GANs)":[210],"appear":[211],"suited":[215],"omics":[218,238],"at":[221],"rather":[222],"small":[223],"sizes.":[225],"opens":[227],"way":[229],"many":[231],"potential":[232],"applications":[233],"where":[234],"might":[240],"useful.":[242]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":5}],"updated_date":"2025-11-23T05:10:03.516525","created_date":"2025-10-10T00:00:00"}