{"id":"https://openalex.org/W4385612899","doi":"https://doi.org/10.1093/bib/bbad278","title":"Identifying spatial domains of spatially resolved transcriptomics via multi-view graph convolutional networks","display_name":"Identifying spatial domains of spatially resolved transcriptomics via multi-view graph convolutional networks","publication_year":2023,"publication_date":"2023-08-07","ids":{"openalex":"https://openalex.org/W4385612899","doi":"https://doi.org/10.1093/bib/bbad278","pmid":"https://pubmed.ncbi.nlm.nih.gov/37544658"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbad278","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbad278","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/A5112975175","display_name":"Xuejing Shi","orcid":null},"institutions":[{"id":"https://openalex.org/I28006308","display_name":"Shandong Normal University","ror":"https://ror.org/01wy3h363","country_code":"CN","type":"education","lineage":["https://openalex.org/I28006308"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xuejing Shi","raw_affiliation_strings":["School of Information Science and Engineering, Shandong Normal University , Jinan, 250358 , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information Science and Engineering, Shandong Normal University , Jinan, 250358 , China","institution_ids":["https://openalex.org/I28006308"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101231370","display_name":"Juntong Zhu","orcid":null},"institutions":[{"id":"https://openalex.org/I28006308","display_name":"Shandong Normal University","ror":"https://ror.org/01wy3h363","country_code":"CN","type":"education","lineage":["https://openalex.org/I28006308"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Juntong Zhu","raw_affiliation_strings":["School of Information Science and Engineering, Shandong Normal University , Jinan, 250358 , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information Science and Engineering, Shandong Normal University , Jinan, 250358 , China","institution_ids":["https://openalex.org/I28006308"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066627747","display_name":"Yahui Long","orcid":"https://orcid.org/0000-0002-2765-3007"},"institutions":[{"id":"https://openalex.org/I115228651","display_name":"Agency for Science, Technology and Research","ror":"https://ror.org/036wvzt09","country_code":"SG","type":"government","lineage":["https://openalex.org/I115228651"]},{"id":"https://openalex.org/I2800824516","display_name":"Singapore Immunology Network","ror":"https://ror.org/03vmmgg57","country_code":"SG","type":"facility","lineage":["https://openalex.org/I115228651","https://openalex.org/I2800824516","https://openalex.org/I2801752549"]}],"countries":["SG"],"is_corresponding":true,"raw_author_name":"Yahui Long","raw_affiliation_strings":["Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR) , 8A Biomedical Grove, 138648 , Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR) , 8A Biomedical Grove, 138648 , Singapore","institution_ids":["https://openalex.org/I2800824516","https://openalex.org/I115228651"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101756728","display_name":"Cheng Liang","orcid":"https://orcid.org/0000-0003-3832-0969"},"institutions":[{"id":"https://openalex.org/I28006308","display_name":"Shandong Normal University","ror":"https://ror.org/01wy3h363","country_code":"CN","type":"education","lineage":["https://openalex.org/I28006308"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Cheng Liang","raw_affiliation_strings":["School of Information Science and Engineering, Shandong Normal University , Jinan, 250358 , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information Science and Engineering, Shandong Normal University , Jinan, 250358 , China","institution_ids":["https://openalex.org/I28006308"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5066627747","https://openalex.org/A5101756728"],"corresponding_institution_ids":["https://openalex.org/I115228651","https://openalex.org/I28006308","https://openalex.org/I2800824516"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":5.92,"has_fulltext":false,"cited_by_count":42,"citation_normalized_percentile":{"value":0.9691706,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"24","issue":"5","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":0.9998000264167786,"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":0.9998000264167786,"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":0.7043625116348267},{"id":"https://openalex.org/keywords/spatial-analysis","display_name":"Spatial analysis","score":0.625652551651001},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5921959280967712},{"id":"https://openalex.org/keywords/spatial-contextual-awareness","display_name":"Spatial contextual awareness","score":0.5032801032066345},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.48552703857421875},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.4535168707370758},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3714792728424072},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.34641605615615845},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3458026647567749},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3242805600166321},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.11834537982940674},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11421403288841248}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7043625116348267},{"id":"https://openalex.org/C159620131","wikidata":"https://www.wikidata.org/wiki/Q1938983","display_name":"Spatial analysis","level":2,"score":0.625652551651001},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5921959280967712},{"id":"https://openalex.org/C64754055","wikidata":"https://www.wikidata.org/wiki/Q7574053","display_name":"Spatial contextual awareness","level":2,"score":0.5032801032066345},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.48552703857421875},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.4535168707370758},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3714792728424072},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.34641605615615845},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3458026647567749},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3242805600166321},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.11834537982940674},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11421403288841248},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"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":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbad278","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbad278","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:37544658","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37544658","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/G3641757492","display_name":null,"funder_award_id":"ZR2023MF119","funder_id":"https://openalex.org/F4320324174","funder_display_name":"Natural Science Foundation of Shandong Province"},{"id":"https://openalex.org/G6851897821","display_name":"\u9762\u5411\u7535\u5b50\u75c5\u5386\u52a8\u6001\u5efa\u6a21\u7684\u53ef\u89e3\u91ca\u6df1\u5ea6\u5b66\u4e60\u65b9\u6cd5\u7814\u7a76","funder_award_id":"62072290","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"},{"id":"https://openalex.org/F4320324174","display_name":"Natural Science Foundation of Shandong Province","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":48,"referenced_works":["https://openalex.org/W2042789810","https://openalex.org/W2073654208","https://openalex.org/W2123273050","https://openalex.org/W2126537932","https://openalex.org/W2131681506","https://openalex.org/W2531563875","https://openalex.org/W2800392236","https://openalex.org/W2899224111","https://openalex.org/W2915848182","https://openalex.org/W2952383043","https://openalex.org/W2953036966","https://openalex.org/W2964015378","https://openalex.org/W2972983657","https://openalex.org/W3021920958","https://openalex.org/W3032266082","https://openalex.org/W3033415403","https://openalex.org/W3036371598","https://openalex.org/W3044030235","https://openalex.org/W3094217342","https://openalex.org/W3099768174","https://openalex.org/W3099810371","https://openalex.org/W3100245636","https://openalex.org/W3108118546","https://openalex.org/W3112563877","https://openalex.org/W3121907939","https://openalex.org/W3126958162","https://openalex.org/W3134482219","https://openalex.org/W3169098619","https://openalex.org/W3181253984","https://openalex.org/W3190202966","https://openalex.org/W3203689742","https://openalex.org/W3210002151","https://openalex.org/W4229033508","https://openalex.org/W4239110337","https://openalex.org/W4280604745","https://openalex.org/W4285388882","https://openalex.org/W4290154117","https://openalex.org/W4306406844","https://openalex.org/W4322738920","https://openalex.org/W4323044112","https://openalex.org/W6685380521","https://openalex.org/W6726873649","https://openalex.org/W6742649196","https://openalex.org/W6779238151","https://openalex.org/W6781035625","https://openalex.org/W6785593542","https://openalex.org/W6785692931","https://openalex.org/W6815484573"],"related_works":["https://openalex.org/W3148227991","https://openalex.org/W1486593826","https://openalex.org/W2771174107","https://openalex.org/W1536965844","https://openalex.org/W2932872266","https://openalex.org/W2344941099","https://openalex.org/W4322212724","https://openalex.org/W2106788855","https://openalex.org/W3081561710","https://openalex.org/W2477413883"],"abstract_inverted_index":{"MOTIVATION:":[0],"Recent":[1],"advances":[2],"in":[3,63,201,226,243],"spatially":[4,219],"resolved":[5],"transcriptomics":[6,184,245],"(ST)":[7],"technologies":[8],"enable":[9],"the":[10,60,104,128,147,154,162,166,227],"measurement":[11],"of":[12,24,35,130,157,165],"gene":[13,22,44,115],"expression":[14,23,45,224],"profiles":[15],"while":[16],"preserving":[17],"cellular":[18],"spatial":[19,28,48,52,77,89,105,158,183,202,211,241,244],"context.":[20],"Linking":[21],"cells":[25],"with":[26,47,59,98,117,169,186,206,222],"their":[27],"distribution":[29],"is":[30,232],"essential":[31],"for":[32,75,153,239],"better":[33],"understanding":[34],"tissue":[36],"microenvironment":[37],"and":[38,144,180,212,235],"biological":[39],"progress.":[40],"However,":[41],"effectively":[42],"combining":[43,114],"data":[46],"information":[49],"to":[50,86,126,139,160],"identify":[51],"domains":[53,78,242],"remains":[54],"challenging.":[55],"RESULTS:":[56],"To":[57],"deal":[58],"above":[61],"issue,":[62],"this":[64],"paper,":[65],"we":[66,91,133],"propose":[67],"a":[68,233],"novel":[69],"unsupervised":[70],"learning":[71],"framework":[72,238],"named":[73],"STMGCN":[74,108,151,175,197,216,231],"identifying":[76,240],"using":[79],"multi-view":[80],"graph":[81,120,122,171],"convolution":[82,123],"networks":[83],"(MGCNs).":[84],"Specifically,":[85],"fully":[87],"exploit":[88],"information,":[90],"first":[92],"construct":[93],"multiple":[94,110,170],"neighbor":[95,119],"graphs":[96],"(views)":[97],"different":[99,131,187],"similarity":[100],"measures":[101],"based":[102],"on":[103,176],"coordinates.":[106],"Then,":[107],"learns":[109],"view-specific":[111,142],"embeddings":[112,143,168],"by":[113],"expressions":[116],"each":[118],"through":[121],"networks.":[124],"Finally,":[125],"capture":[127],"importance":[129],"graphs,":[132],"further":[134],"introduce":[135],"an":[136],"attention":[137],"mechanism":[138],"adaptively":[140],"fuse":[141],"thus":[145],"derive":[146],"final":[148],"spot":[149],"embedding.":[150],"allows":[152],"effective":[155],"utilization":[156],"context":[159],"enhance":[161],"expressive":[163],"power":[164],"latent":[167],"convolutions.":[172],"We":[173],"apply":[174],"two":[177],"simulation":[178],"datasets":[179,185],"five":[181,207],"real":[182],"resolutions":[188],"across":[189],"distinct":[190],"platforms.":[191],"The":[192],"experimental":[193],"results":[194,200],"demonstrate":[195],"that":[196],"obtains":[198],"competitive":[199],"domain":[203],"identification":[204],"compared":[205],"state-of-the-art":[208],"methods,":[209],"including":[210],"non-spatial":[213],"alternatives.":[214],"Besides,":[215],"can":[217],"detect":[218],"variable":[220],"genes":[221],"enriched":[223],"patterns":[225],"identified":[228],"domains.":[229],"Overall,":[230],"powerful":[234],"efficient":[236],"computational":[237],"data.":[246]},"counts_by_year":[{"year":2026,"cited_by_count":8},{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":24},{"year":2023,"cited_by_count":2}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}