{"id":"https://openalex.org/W4384665375","doi":"https://doi.org/10.1093/bib/bbad262","title":"Spatial-MGCN: a novel multi-view graph convolutional network for identifying spatial domains with attention mechanism","display_name":"Spatial-MGCN: a novel multi-view graph convolutional network for identifying spatial domains with attention mechanism","publication_year":2023,"publication_date":"2023-07-18","ids":{"openalex":"https://openalex.org/W4384665375","doi":"https://doi.org/10.1093/bib/bbad262","pmid":"https://pubmed.ncbi.nlm.nih.gov/37466210"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbad262","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbad262","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/A5092492808","display_name":"Bo Wang","orcid":"https://orcid.org/0009-0004-9426-8741"},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Bo Wang","raw_affiliation_strings":["Hunan University College of Computer Science and Electronic Engineering, , Changsha, 410083 , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hunan University College of Computer Science and Electronic Engineering, , Changsha, 410083 , China","institution_ids":["https://openalex.org/I16609230"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026469278","display_name":"Jiawei Luo","orcid":"https://orcid.org/0000-0003-2385-8272"},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Jiawei Luo","raw_affiliation_strings":["Hunan University College of Computer Science and Electronic Engineering, , Changsha, 410083 , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hunan University College of Computer Science and Electronic Engineering, , Changsha, 410083 , China","institution_ids":["https://openalex.org/I16609230"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100414459","display_name":"Ying Liu","orcid":"https://orcid.org/0000-0003-3672-9621"},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Ying Liu","raw_affiliation_strings":["Hunan University College of Computer Science and Electronic Engineering, , Changsha, 410083 , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hunan University College of Computer Science and Electronic Engineering, , Changsha, 410083 , China","institution_ids":["https://openalex.org/I16609230"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5114859464","display_name":"Wanwan Shi","orcid":"https://orcid.org/0000-0003-4730-4610"},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wanwan Shi","raw_affiliation_strings":["Hunan University College of Computer Science and Electronic Engineering, , Changsha, 410083 , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hunan University College of Computer Science and Electronic Engineering, , Changsha, 410083 , China","institution_ids":["https://openalex.org/I16609230"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077277630","display_name":"Zehao Xiong","orcid":"https://orcid.org/0000-0002-6549-9610"},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zehao Xiong","raw_affiliation_strings":["Hunan University College of Computer Science and Electronic Engineering, , Changsha, 410083 , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hunan University College of Computer Science and Electronic Engineering, , Changsha, 410083 , China","institution_ids":["https://openalex.org/I16609230"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071431436","display_name":"Cong Shen","orcid":"https://orcid.org/0000-0001-8505-6406"},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Cong Shen","raw_affiliation_strings":["Hunan University College of Computer Science and Electronic Engineering, , Changsha, 410083 , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hunan University College of Computer Science and Electronic Engineering, , Changsha, 410083 , China","institution_ids":["https://openalex.org/I16609230"]}]},{"author_position":"last","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":false,"raw_author_name":"Yahui Long","raw_affiliation_strings":["Agency for Science, Technology and Research(A*STAR) Singapore Immunology Network(SIgN), , 138648 , Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Agency for Science, Technology and Research(A*STAR) Singapore Immunology Network(SIgN), , 138648 , Singapore","institution_ids":["https://openalex.org/I2800824516","https://openalex.org/I115228651"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5026469278","https://openalex.org/A5100414459"],"corresponding_institution_ids":["https://openalex.org/I16609230"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":9.6872,"has_fulltext":false,"cited_by_count":70,"citation_normalized_percentile":{"value":0.9866562,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"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":0.8950999975204468,"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":0.8950999975204468,"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":0.05290000140666962,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.02160000056028366,"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":0.7209674119949341},{"id":"https://openalex.org/keywords/spatial-analysis","display_name":"Spatial analysis","score":0.6208548545837402},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.6095983982086182},{"id":"https://openalex.org/keywords/spatial-contextual-awareness","display_name":"Spatial contextual awareness","score":0.546233057975769},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4994983673095703},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.47486114501953125},{"id":"https://openalex.org/keywords/encoder","display_name":"Encoder","score":0.45320963859558105},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.4164176881313324},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.2804166078567505},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.13466107845306396}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7209674119949341},{"id":"https://openalex.org/C159620131","wikidata":"https://www.wikidata.org/wiki/Q1938983","display_name":"Spatial analysis","level":2,"score":0.6208548545837402},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6095983982086182},{"id":"https://openalex.org/C64754055","wikidata":"https://www.wikidata.org/wiki/Q7574053","display_name":"Spatial contextual awareness","level":2,"score":0.546233057975769},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4994983673095703},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.47486114501953125},{"id":"https://openalex.org/C118505674","wikidata":"https://www.wikidata.org/wiki/Q42586063","display_name":"Encoder","level":2,"score":0.45320963859558105},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.4164176881313324},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.2804166078567505},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.13466107845306396},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015785","descriptor_name":"Eye Diseases, Hereditary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015785","descriptor_name":"Eye Diseases, Hereditary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015785","descriptor_name":"Eye Diseases, Hereditary","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":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","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":false},{"descriptor_ui":"D040181","descriptor_name":"Genetic Diseases, X-Linked","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040181","descriptor_name":"Genetic Diseases, X-Linked","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040181","descriptor_name":"Genetic Diseases, X-Linked","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbad262","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbad262","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:37466210","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37466210","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/G5539574558","display_name":null,"funder_award_id":"62202152","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6549098544","display_name":null,"funder_award_id":"62032007","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":52,"referenced_works":["https://openalex.org/W1522301498","https://openalex.org/W1974953982","https://openalex.org/W2025398141","https://openalex.org/W2031215175","https://openalex.org/W2033403400","https://openalex.org/W2058487314","https://openalex.org/W2069089843","https://openalex.org/W2073654208","https://openalex.org/W2131681506","https://openalex.org/W2187089797","https://openalex.org/W2344060455","https://openalex.org/W2570088150","https://openalex.org/W2800392236","https://openalex.org/W2902652978","https://openalex.org/W2915848182","https://openalex.org/W2923300855","https://openalex.org/W2941973284","https://openalex.org/W2964015378","https://openalex.org/W3017023874","https://openalex.org/W3021920958","https://openalex.org/W3032266082","https://openalex.org/W3036371598","https://openalex.org/W3039075121","https://openalex.org/W3044030235","https://openalex.org/W3099768174","https://openalex.org/W3100993589","https://openalex.org/W3108118546","https://openalex.org/W3112563877","https://openalex.org/W3124439729","https://openalex.org/W3126958162","https://openalex.org/W3134482219","https://openalex.org/W3140605903","https://openalex.org/W3165120573","https://openalex.org/W3169098619","https://openalex.org/W3216067893","https://openalex.org/W4206826076","https://openalex.org/W4226192560","https://openalex.org/W4229033508","https://openalex.org/W4283815719","https://openalex.org/W4285388882","https://openalex.org/W4285803722","https://openalex.org/W4290154117","https://openalex.org/W4306406844","https://openalex.org/W4313156423","https://openalex.org/W4320489547","https://openalex.org/W4322718355","https://openalex.org/W4322738920","https://openalex.org/W6631190155","https://openalex.org/W6726873649","https://openalex.org/W6774314701","https://openalex.org/W6779238151","https://openalex.org/W6802889560"],"related_works":["https://openalex.org/W3148227991","https://openalex.org/W1486593826","https://openalex.org/W2771174107","https://openalex.org/W1536965844","https://openalex.org/W2344941099","https://openalex.org/W4322212724","https://openalex.org/W2106788855","https://openalex.org/W3081561710","https://openalex.org/W2477413883","https://openalex.org/W2463773089"],"abstract_inverted_index":{"MOTIVATION:":[0],"Recent":[1],"advances":[2],"in":[3,179,193],"spatial":[4,14,18,36,46,62,84,108,127,167,176,197],"transcriptomics":[5],"technologies":[6],"have":[7,42],"enabled":[8],"gene":[9,32,59,104,160],"expression":[10,33,60,105,151,161],"profiles":[11,34,106],"while":[12],"preserving":[13],"context.":[15],"Accurately":[16],"identifying":[17,83],"domains":[19],"is":[20,87,116,145],"crucial":[21],"for":[22,45,82],"downstream":[23],"analysis":[24],"and":[25,35,61,107,126,199],"it":[26],"requires":[27],"the":[28,55,124,149,155,171],"effective":[29],"integration":[30],"of":[31,50,159],"information.":[37],"While":[38],"increasingly":[39],"computational":[40],"methods":[41,191],"been":[43],"developed":[44],"domain":[47],"detection,":[48],"most":[49],"them":[51],"cannot":[52],"adaptively":[53],"learn":[54],"complex":[56],"relationship":[57],"between":[58],"information,":[63,109],"leading":[64],"to":[65,118,147,174],"sub-optimal":[66],"performance.":[67],"RESULTS:":[68],"To":[69],"overcome":[70],"these":[71],"challenges,":[72],"we":[73],"propose":[74],"a":[75,88,112,140,166],"novel":[76],"deep":[77],"learning":[78,173],"method":[79],"named":[80],"Spatial-MGCN":[81,164,188],"domains,":[85],"which":[86],"Multi-view":[89],"Graph":[90],"Convolutional":[91],"Network":[92],"(GCN)":[93],"with":[94],"attention":[95],"mechanism.":[96],"We":[97],"first":[98],"construct":[99],"two":[100],"neighbor":[101,177],"graphs":[102],"using":[103],"respectively.":[110],"Then,":[111],"multi-view":[113],"GCN":[114],"encoder":[115],"designed":[117],"extract":[119],"unique":[120],"embeddings":[121,134],"from":[122],"both":[123,137],"feature":[125],"graphs,":[128],"as":[129,131],"well":[130],"their":[132],"shared":[133],"by":[135,153],"combining":[136],"graphs.":[138],"Finally,":[139],"zero-inflated":[141],"negative":[142],"binomial":[143],"decoder":[144],"used":[146],"reconstruct":[148],"original":[150],"matrix":[152],"capturing":[154],"global":[156],"probability":[157],"distribution":[158],"profiles.":[162],"Moreover,":[163],"incorporates":[165],"regularization":[168],"constraint":[169],"into":[170],"features":[172],"preserve":[175],"information":[178],"an":[180],"end-to-end":[181],"manner.":[182],"The":[183],"experimental":[184],"results":[185],"show":[186],"that":[187],"outperforms":[189],"state-of-the-art":[190],"consistently":[192],"several":[194],"tasks,":[195],"including":[196],"clustering":[198],"trajectory":[200],"inference.":[201]},"counts_by_year":[{"year":2026,"cited_by_count":14},{"year":2025,"cited_by_count":28},{"year":2024,"cited_by_count":27},{"year":2023,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
