{"id":"https://openalex.org/W4205187115","doi":"https://doi.org/10.23919/eusipco54536.2021.9616279","title":"Multiomics Data Integration for Gene Regulatory Network Inference with Exponential Family Embeddings","display_name":"Multiomics Data Integration for Gene Regulatory Network Inference with Exponential Family Embeddings","publication_year":2021,"publication_date":"2021-08-23","ids":{"openalex":"https://openalex.org/W4205187115","doi":"https://doi.org/10.23919/eusipco54536.2021.9616279"},"language":"en","primary_location":{"id":"doi:10.23919/eusipco54536.2021.9616279","is_oa":false,"landing_page_url":"https://doi.org/10.23919/eusipco54536.2021.9616279","pdf_url":null,"source":{"id":"https://openalex.org/S4363607854","display_name":"2021 29th European Signal Processing Conference (EUSIPCO)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2021 29th European Signal Processing Conference (EUSIPCO)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5021469979","display_name":"Surabhi Jagtap","orcid":"https://orcid.org/0000-0001-7599-5434"},"institutions":[{"id":"https://openalex.org/I4210107720","display_name":"CentraleSup\u00e9lec","ror":"https://ror.org/019tcpt25","country_code":"FR","type":"facility","lineage":["https://openalex.org/I277688954","https://openalex.org/I4210107720"]},{"id":"https://openalex.org/I265217849","display_name":"IFP \u00c9nergies nouvelles","ror":"https://ror.org/03gcbhc33","country_code":"FR","type":"facility","lineage":["https://openalex.org/I265217849"]},{"id":"https://openalex.org/I277688954","display_name":"Universit\u00e9 Paris-Saclay","ror":"https://ror.org/03xjwb503","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Surabhi Jagtap","raw_affiliation_strings":["IFP Energies nouvelles, Rueil-Malmaison, France","Universit\u00e9 Paris-Saclay, CentraleSup\u00e9lec, Inria, Gif-Sur-Yvette, France"],"affiliations":[{"raw_affiliation_string":"IFP Energies nouvelles, Rueil-Malmaison, France","institution_ids":["https://openalex.org/I265217849"]},{"raw_affiliation_string":"Universit\u00e9 Paris-Saclay, CentraleSup\u00e9lec, Inria, Gif-Sur-Yvette, France","institution_ids":["https://openalex.org/I4210107720","https://openalex.org/I277688954"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086636153","display_name":"Abdulkadir \u00c7elikkanat","orcid":"https://orcid.org/0000-0001-8912-711X"},"institutions":[{"id":"https://openalex.org/I277688954","display_name":"Universit\u00e9 Paris-Saclay","ror":"https://ror.org/03xjwb503","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954"]},{"id":"https://openalex.org/I4210107720","display_name":"CentraleSup\u00e9lec","ror":"https://ror.org/019tcpt25","country_code":"FR","type":"facility","lineage":["https://openalex.org/I277688954","https://openalex.org/I4210107720"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Abdulkadir Celikkanat","raw_affiliation_strings":["Universit\u00e9 Paris-Saclay, CentraleSup\u00e9lec, Inria, Gif-Sur-Yvette, France"],"affiliations":[{"raw_affiliation_string":"Universit\u00e9 Paris-Saclay, CentraleSup\u00e9lec, Inria, Gif-Sur-Yvette, France","institution_ids":["https://openalex.org/I4210107720","https://openalex.org/I277688954"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5107487179","display_name":"Aurelic Piravre","orcid":null},"institutions":[{"id":"https://openalex.org/I265217849","display_name":"IFP \u00c9nergies nouvelles","ror":"https://ror.org/03gcbhc33","country_code":"FR","type":"facility","lineage":["https://openalex.org/I265217849"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Aurelic Piravre","raw_affiliation_strings":["IFP Energies nouvelles, Rueil-Malmaison, France"],"affiliations":[{"raw_affiliation_string":"IFP Energies nouvelles, Rueil-Malmaison, France","institution_ids":["https://openalex.org/I265217849"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065899022","display_name":"F. Bidard","orcid":null},"institutions":[{"id":"https://openalex.org/I265217849","display_name":"IFP \u00c9nergies nouvelles","ror":"https://ror.org/03gcbhc33","country_code":"FR","type":"facility","lineage":["https://openalex.org/I265217849"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Frederiuue Bidard","raw_affiliation_strings":["IFP Energies nouvelles, Rueil-Malmaison, France"],"affiliations":[{"raw_affiliation_string":"IFP Energies nouvelles, Rueil-Malmaison, France","institution_ids":["https://openalex.org/I265217849"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005435241","display_name":"Laurent Duval","orcid":"https://orcid.org/0000-0002-7732-4666"},"institutions":[{"id":"https://openalex.org/I265217849","display_name":"IFP \u00c9nergies nouvelles","ror":"https://ror.org/03gcbhc33","country_code":"FR","type":"facility","lineage":["https://openalex.org/I265217849"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Laurent Duval","raw_affiliation_strings":["IFP Energies nouvelles, Rueil-Malmaison, France"],"affiliations":[{"raw_affiliation_string":"IFP Energies nouvelles, Rueil-Malmaison, France","institution_ids":["https://openalex.org/I265217849"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5087251228","display_name":"Fragkiskos D. Malliaros","orcid":"https://orcid.org/0000-0002-8770-3969"},"institutions":[{"id":"https://openalex.org/I277688954","display_name":"Universit\u00e9 Paris-Saclay","ror":"https://ror.org/03xjwb503","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954"]},{"id":"https://openalex.org/I4210107720","display_name":"CentraleSup\u00e9lec","ror":"https://ror.org/019tcpt25","country_code":"FR","type":"facility","lineage":["https://openalex.org/I277688954","https://openalex.org/I4210107720"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Fragkiskos D. Malliaros","raw_affiliation_strings":["Universit\u00e9 Paris-Saclay, CentraleSup\u00e9lec, Inria, Gif-Sur-Yvette, France"],"affiliations":[{"raw_affiliation_string":"Universit\u00e9 Paris-Saclay, CentraleSup\u00e9lec, Inria, Gif-Sur-Yvette, France","institution_ids":["https://openalex.org/I4210107720","https://openalex.org/I277688954"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5021469979"],"corresponding_institution_ids":["https://openalex.org/I265217849","https://openalex.org/I277688954","https://openalex.org/I4210107720"],"apc_list":null,"apc_paid":null,"fwci":0.5188,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.55297398,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":null,"issue":null,"first_page":"1221","last_page":"1225"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998999834060669,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998999834060669,"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/T10621","display_name":"Gene Regulatory Network Analysis","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/T10885","display_name":"Gene expression and cancer classification","score":0.9990000128746033,"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/inference","display_name":"Inference","score":0.7844241857528687},{"id":"https://openalex.org/keywords/data-integration","display_name":"Data integration","score":0.65919029712677},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6237090826034546},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.6060993671417236},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.5915811061859131},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.5442431569099426},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.49182772636413574},{"id":"https://openalex.org/keywords/biological-data","display_name":"Biological data","score":0.4299890995025635},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4202684760093689},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.41476064920425415},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.37919607758522034},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.37819308042526245},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3650978207588196},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.30928465723991394},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.22834599018096924},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.19410225749015808},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.19397789239883423},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.08859345316886902}],"concepts":[{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.7844241857528687},{"id":"https://openalex.org/C72634772","wikidata":"https://www.wikidata.org/wiki/Q386824","display_name":"Data integration","level":2,"score":0.65919029712677},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6237090826034546},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.6060993671417236},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.5915811061859131},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.5442431569099426},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.49182772636413574},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.4299890995025635},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4202684760093689},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.41476064920425415},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.37919607758522034},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.37819308042526245},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3650978207588196},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.30928465723991394},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.22834599018096924},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.19410225749015808},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.19397789239883423},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.08859345316886902},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.23919/eusipco54536.2021.9616279","is_oa":false,"landing_page_url":"https://doi.org/10.23919/eusipco54536.2021.9616279","pdf_url":null,"source":{"id":"https://openalex.org/S4363607854","display_name":"2021 29th European Signal Processing Conference (EUSIPCO)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2021 29th European Signal Processing Conference (EUSIPCO)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G7534536118","display_name":null,"funder_award_id":"ANR-20-CE23-0009-01","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"}],"funders":[{"id":"https://openalex.org/F4320320883","display_name":"Agence Nationale de la Recherche","ror":"https://ror.org/00rbzpz17"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":33,"referenced_works":["https://openalex.org/W2101234009","https://openalex.org/W2118258530","https://openalex.org/W2147555013","https://openalex.org/W2147638953","https://openalex.org/W2154851992","https://openalex.org/W2159675211","https://openalex.org/W2177920816","https://openalex.org/W2556519015","https://openalex.org/W2800245987","https://openalex.org/W2904192038","https://openalex.org/W2949447796","https://openalex.org/W2949816873","https://openalex.org/W2951422523","https://openalex.org/W2952631022","https://openalex.org/W2962756421","https://openalex.org/W2964074797","https://openalex.org/W2971865858","https://openalex.org/W2977707586","https://openalex.org/W2978955949","https://openalex.org/W2988716798","https://openalex.org/W2997002213","https://openalex.org/W3003893414","https://openalex.org/W3010144067","https://openalex.org/W3102554291","https://openalex.org/W3104097132","https://openalex.org/W4293651439","https://openalex.org/W4294170691","https://openalex.org/W6675354045","https://openalex.org/W6682691769","https://openalex.org/W6720957491","https://openalex.org/W6744557953","https://openalex.org/W6769944288","https://openalex.org/W6774777834"],"related_works":["https://openalex.org/W2155492529","https://openalex.org/W4252504573","https://openalex.org/W2158714033","https://openalex.org/W4385510321","https://openalex.org/W15348386","https://openalex.org/W2307569040","https://openalex.org/W2131941936","https://openalex.org/W2366067673","https://openalex.org/W78967844","https://openalex.org/W2131550814"],"abstract_inverted_index":{"The":[0],"advent":[1],"of":[2,9,31,73,106],"omics":[3,15,107],"technologies":[4],"have":[5],"enabled":[6],"the":[7,32,90,116,124],"generation":[8],"huge,":[10],"complex,":[11],"heterogeneous,":[12],"and":[13,55,136],"high-dimensional":[14],"data.":[16],"Imposing":[17],"numerous":[18],"challenges":[19],"in":[20,133],"data":[21,24,37],"integration,":[22],"these":[23],"could":[25],"lead":[26],"to":[27,43,66,85,142],"a":[28,74,82,102],"better":[29],"understanding":[30],"organism's":[33],"cellular":[34],"system.":[35],"Omics":[36],"are":[38],"typically":[39],"represented":[40],"as":[41,50],"networks":[42],"study":[44],"relations":[45],"between":[46],"biological":[47,94],"entities,":[48],"such":[49],"protein-protein":[51],"interaction,":[52],"gene":[53,117],"regulation,":[54],"signal":[56],"transduction.":[57],"To":[58],"this":[59,78],"end,":[60],"network":[61,119,144],"embedding":[62],"approaches":[63],"allow":[64],"us":[65],"learn":[67,86],"latent":[68],"feature":[69],"representations":[70],"for":[71,127],"nodes":[72],"graph":[75],"structure.":[76],"In":[77],"study,":[79],"we":[80,129],"propose":[81],"new":[83],"methodology":[84],"embeddings":[87],"by":[88,140],"modeling":[89],"underlying":[91],"interactions":[92],"among":[93],"entities":[95],"(nodes)":[96],"with":[97],"exponential":[98],"family":[99],"distributions":[100],"from":[101],"well":[103],"chosen":[104],"set":[105],"modalities.":[108],"We":[109],"evaluate":[110],"our":[111],"proposed":[112],"method":[113],"based":[114],"on":[115],"regulatory":[118],"(GRN)":[120],"inference":[121],"problem.":[122],"As":[123],"ground":[125],"truth":[126],"evaluation,":[128],"use":[130],"GRN":[131],"available":[132],"public":[134],"databases":[135],"demonstrate":[137],"its":[138],"effectiveness":[139],"comparing":[141],"other":[143],"integration":[145],"approaches.":[146]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2022,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}