{"id":"https://openalex.org/W4366465280","doi":"https://doi.org/10.1093/bib/bbad146","title":"Graph deep learning enabled spatial domains identification for spatial transcriptomics","display_name":"Graph deep learning enabled spatial domains identification for spatial transcriptomics","publication_year":2023,"publication_date":"2023-04-20","ids":{"openalex":"https://openalex.org/W4366465280","doi":"https://doi.org/10.1093/bib/bbad146","pmid":"https://pubmed.ncbi.nlm.nih.gov/37080761"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbad146","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad146","pdf_url":"https://academic.oup.com/bib/article-pdf/24/3/bbad146/50410902/bbad146.pdf","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":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bib/article-pdf/24/3/bbad146/50410902/bbad146.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100416715","display_name":"Teng Liu","orcid":"https://orcid.org/0000-0001-5862-0518"},"institutions":[{"id":"https://openalex.org/I158842170","display_name":"Chongqing University","ror":"https://ror.org/023rhb549","country_code":"CN","type":"education","lineage":["https://openalex.org/I158842170"]},{"id":"https://openalex.org/I50180762","display_name":"Chongqing Three Gorges University","ror":"https://ror.org/05rs3pv16","country_code":"CN","type":"education","lineage":["https://openalex.org/I50180762"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Teng Liu","raw_affiliation_strings":["Clinical Research Center (CRC), Clinical Pathology Center (CPC), Chongqing University Three Gorges Hospital, Chongqing University , Wanzhou, Chongqing, P.R. China"],"affiliations":[{"raw_affiliation_string":"Clinical Research Center (CRC), Clinical Pathology Center (CPC), Chongqing University Three Gorges Hospital, Chongqing University , Wanzhou, Chongqing, P.R. China","institution_ids":["https://openalex.org/I50180762","https://openalex.org/I158842170"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009458572","display_name":"Zhaoyu Fang","orcid":null},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhao-Yu Fang","raw_affiliation_strings":["Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering at Central South University , Hunan, P.R. China"],"affiliations":[{"raw_affiliation_string":"Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering at Central South University , Hunan, P.R. China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100353780","display_name":"Xin Li","orcid":"https://orcid.org/0000-0002-0041-3134"},"institutions":[{"id":"https://openalex.org/I158842170","display_name":"Chongqing University","ror":"https://ror.org/023rhb549","country_code":"CN","type":"education","lineage":["https://openalex.org/I158842170"]},{"id":"https://openalex.org/I50180762","display_name":"Chongqing Three Gorges University","ror":"https://ror.org/05rs3pv16","country_code":"CN","type":"education","lineage":["https://openalex.org/I50180762"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xin Li","raw_affiliation_strings":["Clinical Research Center (CRC), Clinical Pathology Center (CPC), Chongqing University Three Gorges Hospital, Chongqing University , Wanzhou, Chongqing, P.R. China"],"affiliations":[{"raw_affiliation_string":"Clinical Research Center (CRC), Clinical Pathology Center (CPC), Chongqing University Three Gorges Hospital, Chongqing University , Wanzhou, Chongqing, P.R. China","institution_ids":["https://openalex.org/I50180762","https://openalex.org/I158842170"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100781971","display_name":"Lining Zhang","orcid":"https://orcid.org/0000-0002-1047-9313"},"institutions":[{"id":"https://openalex.org/I158842170","display_name":"Chongqing University","ror":"https://ror.org/023rhb549","country_code":"CN","type":"education","lineage":["https://openalex.org/I158842170"]},{"id":"https://openalex.org/I50180762","display_name":"Chongqing Three Gorges University","ror":"https://ror.org/05rs3pv16","country_code":"CN","type":"education","lineage":["https://openalex.org/I50180762"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Li-Ning Zhang","raw_affiliation_strings":["Clinical Research Center (CRC), Clinical Pathology Center (CPC), Chongqing University Three Gorges Hospital, Chongqing University , Wanzhou, Chongqing, P.R. China"],"affiliations":[{"raw_affiliation_string":"Clinical Research Center (CRC), Clinical Pathology Center (CPC), Chongqing University Three Gorges Hospital, Chongqing University , Wanzhou, Chongqing, P.R. China","institution_ids":["https://openalex.org/I50180762","https://openalex.org/I158842170"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083809384","display_name":"Dongsheng Cao","orcid":"https://orcid.org/0000-0003-3604-3785"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Dong-Sheng Cao","raw_affiliation_strings":["Xiangya School of Pharmaceutical Sciences, Central South University , Changsha, 410003, P.R. China"],"affiliations":[{"raw_affiliation_string":"Xiangya School of Pharmaceutical Sciences, Central South University , Changsha, 410003, P.R. China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5021389154","display_name":"Mingzhu Yin","orcid":"https://orcid.org/0000-0002-6964-7131"},"institutions":[{"id":"https://openalex.org/I158842170","display_name":"Chongqing University","ror":"https://ror.org/023rhb549","country_code":"CN","type":"education","lineage":["https://openalex.org/I158842170"]},{"id":"https://openalex.org/I50180762","display_name":"Chongqing Three Gorges University","ror":"https://ror.org/05rs3pv16","country_code":"CN","type":"education","lineage":["https://openalex.org/I50180762"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ming-Zhu Yin","raw_affiliation_strings":["Clinical Research Center (CRC), Clinical Pathology Center (CPC), Chongqing University Three Gorges Hospital, Chongqing University , Wanzhou, Chongqing, P.R. China","Translational Medicine Research Center (TMRC), School of Medicine, Chongqing University , Shapingba, Chongqing, P.R. China"],"affiliations":[{"raw_affiliation_string":"Clinical Research Center (CRC), Clinical Pathology Center (CPC), Chongqing University Three Gorges Hospital, Chongqing University , Wanzhou, Chongqing, P.R. China","institution_ids":["https://openalex.org/I50180762","https://openalex.org/I158842170"]},{"raw_affiliation_string":"Translational Medicine Research Center (TMRC), School of Medicine, Chongqing University , Shapingba, Chongqing, P.R. China","institution_ids":["https://openalex.org/I158842170"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5083809384"],"corresponding_institution_ids":["https://openalex.org/I139660479"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":2.3311,"has_fulltext":true,"cited_by_count":15,"citation_normalized_percentile":{"value":0.8832714,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"24","issue":"3","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"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.992900013923645,"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/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.9319000244140625,"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":0.72216796875},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5646750330924988},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.5505983829498291},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.536711573600769},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.5365880131721497},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.42035791277885437},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.38768625259399414},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.16998529434204102}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.72216796875},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5646750330924988},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.5505983829498291},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.536711573600769},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.5365880131721497},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.42035791277885437},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.38768625259399414},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.16998529434204102}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002450","descriptor_name":"Cell Communication","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002450","descriptor_name":"Cell Communication","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002450","descriptor_name":"Cell Communication","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":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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/bbad146","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad146","pdf_url":"https://academic.oup.com/bib/article-pdf/24/3/bbad146/50410902/bbad146.pdf","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:37080761","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37080761","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":{"id":"doi:10.1093/bib/bbad146","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad146","pdf_url":"https://academic.oup.com/bib/article-pdf/24/3/bbad146/50410902/bbad146.pdf","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"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1121271761","display_name":null,"funder_award_id":"Program","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2087396116","display_name":null,"funder_award_id":"China","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2802911279","display_name":null,"funder_award_id":"Young","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3317480652","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5939423041","display_name":null,"funder_award_id":"Technology","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5994120800","display_name":null,"funder_award_id":"Natural","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7632230142","display_name":null,"funder_award_id":"22173118","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":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4366465280.pdf","grobid_xml":"https://content.openalex.org/works/W4366465280.grobid-xml"},"referenced_works_count":45,"referenced_works":["https://openalex.org/W1974565082","https://openalex.org/W2125310307","https://openalex.org/W2127498532","https://openalex.org/W2156483112","https://openalex.org/W2172085063","https://openalex.org/W2467355029","https://openalex.org/W2768242641","https://openalex.org/W2800392236","https://openalex.org/W2897249806","https://openalex.org/W2915626801","https://openalex.org/W2915848182","https://openalex.org/W2950975031","https://openalex.org/W3004640473","https://openalex.org/W3032266082","https://openalex.org/W3106188259","https://openalex.org/W3108118546","https://openalex.org/W3112563877","https://openalex.org/W3119671877","https://openalex.org/W3134482219","https://openalex.org/W3165120573","https://openalex.org/W3169098619","https://openalex.org/W3171692328","https://openalex.org/W3190202966","https://openalex.org/W3195383593","https://openalex.org/W3198138654","https://openalex.org/W3214865687","https://openalex.org/W4200268966","https://openalex.org/W4210583065","https://openalex.org/W4210853280","https://openalex.org/W4221095552","https://openalex.org/W4229033508","https://openalex.org/W4255584382","https://openalex.org/W4281716652","https://openalex.org/W4283704002","https://openalex.org/W4288419263","https://openalex.org/W4299582267","https://openalex.org/W4306406844","https://openalex.org/W4322718355","https://openalex.org/W6685267192","https://openalex.org/W6746451923","https://openalex.org/W6760045743","https://openalex.org/W6779238151","https://openalex.org/W6800634405","https://openalex.org/W6804850501","https://openalex.org/W6815484573"],"related_works":["https://openalex.org/W4293226380","https://openalex.org/W4375867731","https://openalex.org/W2804364458","https://openalex.org/W4298130764","https://openalex.org/W4226493464","https://openalex.org/W4312417841","https://openalex.org/W3193565141","https://openalex.org/W3133861977","https://openalex.org/W3167935049","https://openalex.org/W3029198973"],"abstract_inverted_index":{"Advancing":[0],"spatially":[1],"resolved":[2],"transcriptomics":[3],"(ST)":[4],"technologies":[5],"help":[6],"biologists":[7],"comprehensively":[8],"understand":[9],"organ":[10],"function":[11],"and":[12,26,69,111],"tissue":[13],"microenvironment.":[14],"Accurate":[15],"spatial":[16,39,70,89],"domain":[17],"identification":[18],"is":[19,42,61,80,98],"the":[20,48,65,75,84,95],"foundation":[21],"for":[22],"delineating":[23],"genome":[24],"heterogeneity":[25],"cellular":[27],"interaction.":[28],"Motivated":[29],"by":[30],"this":[31,45,115],"perspective,":[32],"a":[33],"graph":[34,50,57],"deep":[35,49],"learning":[36],"(GDL)":[37],"based":[38],"clustering":[40],"approach":[41],"constructed":[43],"in":[44,72,114],"paper.":[46],"First,":[47],"infomax":[51],"module":[52],"embedded":[53],"with":[54],"residual":[55],"gated":[56],"convolutional":[58],"neural":[59],"network":[60],"leveraged":[62],"to":[63,82,87,100],"address":[64],"gene":[66],"expression":[67],"profiles":[68],"positions":[71],"ST.":[73],"Then,":[74],"Bayesian":[76],"Gaussian":[77],"mixture":[78],"model":[79],"applied":[81],"handle":[83],"latent":[85],"embeddings":[86],"generate":[88],"domains.":[90],"Designed":[91],"experiments":[92],"certify":[93],"that":[94],"presented":[96],"method":[97],"superior":[99],"other":[101],"state-of-the-art":[102],"GDL-enabled":[103],"techniques":[104],"on":[105],"multiple":[106],"ST":[107],"datasets.":[108],"The":[109],"codes":[110],"dataset":[112],"used":[113],"manuscript":[116],"are":[117],"summarized":[118],"at":[119],"https://github.com/narutoten520/SCGDL.":[120]},"counts_by_year":[{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":1}],"updated_date":"2026-03-22T08:09:32.410652","created_date":"2025-10-10T00:00:00"}
