{"id":"https://openalex.org/W3204251585","doi":"https://doi.org/10.1093/bib/bbab409","title":"Learning representation for multiple biological networks via a robust graph regularized integration approach","display_name":"Learning representation for multiple biological networks via a robust graph regularized integration approach","publication_year":2021,"publication_date":"2021-09-08","ids":{"openalex":"https://openalex.org/W3204251585","doi":"https://doi.org/10.1093/bib/bbab409","mag":"3204251585","pmid":"https://pubmed.ncbi.nlm.nih.gov/34607360"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbab409","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbab409","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/A5103264194","display_name":"Xiwen Zhang","orcid":"https://orcid.org/0000-0002-9894-9358"},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiwen Zhang","raw_affiliation_strings":["Intelligent Data Center, School of Mathematics, Sun Yat-Sen University, 510275, Guangzhou, China"],"affiliations":[{"raw_affiliation_string":"Intelligent Data Center, School of Mathematics, Sun Yat-Sen University, 510275, Guangzhou, China","institution_ids":["https://openalex.org/I157773358"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100748335","display_name":"Weiwen Wang","orcid":"https://orcid.org/0000-0002-5435-2680"},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Weiwen Wang","raw_affiliation_strings":["Intelligent Data Center, School of Mathematics, Sun Yat-Sen University, 510275, Guangzhou, China"],"affiliations":[{"raw_affiliation_string":"Intelligent Data Center, School of Mathematics, Sun Yat-Sen University, 510275, Guangzhou, China","institution_ids":["https://openalex.org/I157773358"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043031658","display_name":"Chuan-Xian Ren","orcid":null},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chuan-Xian Ren","raw_affiliation_strings":["Intelligent Data Center, School of Mathematics, Sun Yat-Sen University, Guangzhou, 510275, China, and Pazhou Lab, Guangzhou, 510330, China"],"affiliations":[{"raw_affiliation_string":"Intelligent Data Center, School of Mathematics, Sun Yat-Sen University, Guangzhou, 510275, China, and Pazhou Lab, Guangzhou, 510330, China","institution_ids":["https://openalex.org/I157773358"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5102004642","display_name":"Dao\u2010Qing Dai","orcid":"https://orcid.org/0000-0003-4622-8492"},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Dao-Qing Dai","raw_affiliation_strings":["Intelligent Data Center, School of Mathematics, Sun Yat-Sen University, 510275, Guangzhou, China"],"affiliations":[{"raw_affiliation_string":"Intelligent Data Center, School of Mathematics, Sun Yat-Sen University, 510275, Guangzhou, China","institution_ids":["https://openalex.org/I157773358"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5102004642"],"corresponding_institution_ids":["https://openalex.org/I157773358"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":0.3218,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.56367282,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"23","issue":"1","first_page":null,"last_page":null},"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9980999827384949,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"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":0.9980999827384949,"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":0.7651003003120422},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.6940283179283142},{"id":"https://openalex.org/keywords/spurious-relationship","display_name":"Spurious relationship","score":0.6356938481330872},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.629061222076416},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.6109026074409485},{"id":"https://openalex.org/keywords/node","display_name":"Node (physics)","score":0.5788508653640747},{"id":"https://openalex.org/keywords/feature-learning","display_name":"Feature learning","score":0.543605387210846},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5193308591842651},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.46297261118888855},{"id":"https://openalex.org/keywords/categorization","display_name":"Categorization","score":0.4598030149936676},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.45848578214645386},{"id":"https://openalex.org/keywords/noise","display_name":"Noise (video)","score":0.43731489777565},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.33448776602745056},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.32177937030792236},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.129502534866333}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7651003003120422},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.6940283179283142},{"id":"https://openalex.org/C97256817","wikidata":"https://www.wikidata.org/wiki/Q1462316","display_name":"Spurious relationship","level":2,"score":0.6356938481330872},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.629061222076416},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.6109026074409485},{"id":"https://openalex.org/C62611344","wikidata":"https://www.wikidata.org/wiki/Q1062658","display_name":"Node (physics)","level":2,"score":0.5788508653640747},{"id":"https://openalex.org/C59404180","wikidata":"https://www.wikidata.org/wiki/Q17013334","display_name":"Feature learning","level":2,"score":0.543605387210846},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5193308591842651},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.46297261118888855},{"id":"https://openalex.org/C94124525","wikidata":"https://www.wikidata.org/wiki/Q912550","display_name":"Categorization","level":2,"score":0.4598030149936676},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.45848578214645386},{"id":"https://openalex.org/C99498987","wikidata":"https://www.wikidata.org/wiki/Q2210247","display_name":"Noise (video)","level":3,"score":0.43731489777565},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.33448776602745056},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.32177937030792236},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.129502534866333},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0},{"id":"https://openalex.org/C66938386","wikidata":"https://www.wikidata.org/wiki/Q633538","display_name":"Structural engineering","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004058","descriptor_name":"Diffusion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004058","descriptor_name":"Diffusion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004058","descriptor_name":"Diffusion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007858","descriptor_name":"Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007858","descriptor_name":"Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007858","descriptor_name":"Learning","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}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbab409","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbab409","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:34607360","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34607360","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":[],"awards":[{"id":"https://openalex.org/G2265736844","display_name":null,"funder_award_id":"U1611265","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4404956584","display_name":null,"funder_award_id":"61976229","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7389735786","display_name":null,"funder_award_id":"12026601","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8295545977","display_name":null,"funder_award_id":"11631015","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":48,"referenced_works":["https://openalex.org/W1486817521","https://openalex.org/W1530703867","https://openalex.org/W1979537657","https://openalex.org/W1987219048","https://openalex.org/W1992960340","https://openalex.org/W2005126631","https://openalex.org/W2029348196","https://openalex.org/W2045156863","https://openalex.org/W2057793636","https://openalex.org/W2072871705","https://openalex.org/W2087064593","https://openalex.org/W2101770419","https://openalex.org/W2103017472","https://openalex.org/W2105924489","https://openalex.org/W2112014854","https://openalex.org/W2113654464","https://openalex.org/W2114533766","https://openalex.org/W2117235735","https://openalex.org/W2117486996","https://openalex.org/W2123688186","https://openalex.org/W2134962976","https://openalex.org/W2139516171","https://openalex.org/W2153635508","https://openalex.org/W2153838454","https://openalex.org/W2154851992","https://openalex.org/W2256553158","https://openalex.org/W2259538443","https://openalex.org/W2560835477","https://openalex.org/W2607497028","https://openalex.org/W2615066396","https://openalex.org/W2753953057","https://openalex.org/W2767178841","https://openalex.org/W2786016794","https://openalex.org/W2802145570","https://openalex.org/W2911932738","https://openalex.org/W2913710075","https://openalex.org/W2937762029","https://openalex.org/W2952522777","https://openalex.org/W2963460103","https://openalex.org/W2963512530","https://openalex.org/W2977707586","https://openalex.org/W3100188304","https://openalex.org/W3104097132","https://openalex.org/W3137864305","https://openalex.org/W4293651439","https://openalex.org/W6677132398","https://openalex.org/W6730540583","https://openalex.org/W6744557953"],"related_works":["https://openalex.org/W2162899405","https://openalex.org/W3113091479","https://openalex.org/W941090075","https://openalex.org/W2044987316","https://openalex.org/W2237480245","https://openalex.org/W3134374554","https://openalex.org/W2519167559","https://openalex.org/W2075065631","https://openalex.org/W3121164913","https://openalex.org/W2112534124"],"abstract_inverted_index":{"Learning":[0],"node":[1,31,67],"representation":[2,13,68,88,115,132,198],"is":[3,241],"a":[4,87,120,161],"fundamental":[5],"problem":[6],"in":[7,73,103],"biological":[8,93,249],"network":[9,17],"analysis,":[10],"as":[11,27],"compact":[12],"features":[14,199],"reveal":[15],"complicated":[16],"structures":[18,111],"and":[19,30,58,100,129,153,191,209,235],"carry":[20],"useful":[21,245],"information":[22,60],"for":[23,76,91,112],"downstream":[24],"tasks":[25],"such":[26],"link":[28],"prediction":[29],"classification.":[32],"Recently,":[33],"multiple":[34,52,92,248],"networks":[35,63,74,104,128,152,205],"that":[36,221],"profile":[37],"objects":[38,50],"from":[39,51,201,247],"different":[40,62,151,175,207],"aspects":[41],"are":[42,195,213],"increasingly":[43],"accumulated,":[44],"providing":[45,108],"the":[46,55,98,113,136,140,146,168,171,222,238],"opportunity":[47],"to":[48,66,125,160,243],"learn":[49,244],"perspectives.":[53],"However,":[54],"complex":[56],"common":[57,131,147],"specific":[59,157],"across":[61],"pose":[64],"challenges":[65],"methods.":[69],"Moreover,":[70],"ubiquitous":[71],"noise":[72,99,234],"calls":[75],"more":[77],"robust":[78,109,226],"representation.":[79,163],"To":[80],"deal":[81],"with":[82,229],"these":[83],"problems,":[84],"we":[85,96,118],"present":[86],"learning":[89],"method":[90,173,224,240],"networks.":[94,179,250],"First,":[95],"accommodate":[97,155],"spurious":[101],"edges":[102],"using":[105,135,197],"denoised":[106],"diffusion,":[107],"connectivity":[110],"subsequent":[114],"learning.":[116],"Then,":[117],"introduce":[119],"graph":[121],"regularized":[122,137],"integration":[123],"model":[124,142],"combine":[126],"refined":[127],"compute":[130],"features.":[133],"By":[134],"decomposition":[138],"technique,":[139],"proposed":[141,172,223,239],"can":[143],"effectively":[144],"preserve":[145],"structural":[148],"property":[149],"of":[150,170,177,211],"simultaneously":[154],"their":[156],"information,":[158],"leading":[159],"consistent":[162],"A":[164],"simulation":[165],"study":[166],"shows":[167],"superiority":[169],"on":[174,217],"levels":[176,210],"noisy":[178],"Three":[180],"network-based":[181],"inference":[182],"tasks,":[183],"including":[184],"drug-target":[185],"interaction":[186],"prediction,":[187],"gene":[188],"function":[189],"identification":[190],"fine-grained":[192],"species":[193],"categorization,":[194],"conducted":[196],"learned":[200],"our":[202],"method.":[203],"Biological":[204],"at":[206],"scales":[208],"sparsity":[212],"involved.":[214],"Experimental":[215],"results":[216],"real-world":[218],"data":[219],"show":[220],"has":[225],"performance":[227],"compared":[228],"alternatives.":[230],"Overall,":[231],"by":[232],"eliminating":[233],"integrating":[236],"effectively,":[237],"able":[242],"representations":[246]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
