{"id":"https://openalex.org/W7134807140","doi":"https://doi.org/10.1109/tcbbio.2026.3671964","title":"MSAGCN: Multi-Scale Adaptive Graph Convolutional Network for Integrative Analysis of Single-Cell Spatial Multi-Omics Data","display_name":"MSAGCN: Multi-Scale Adaptive Graph Convolutional Network for Integrative Analysis of Single-Cell Spatial Multi-Omics Data","publication_year":2026,"publication_date":"2026-03-09","ids":{"openalex":"https://openalex.org/W7134807140","doi":"https://doi.org/10.1109/tcbbio.2026.3671964","pmid":"https://pubmed.ncbi.nlm.nih.gov/41801789"},"language":"en","primary_location":{"id":"doi:10.1109/tcbbio.2026.3671964","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2026.3671964","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","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/A5020912808","display_name":"Yating Li","orcid":"https://orcid.org/0009-0001-3993-827X"},"institutions":[{"id":"https://openalex.org/I152033890","display_name":"Hainan Normal University","ror":"https://ror.org/031dhcv14","country_code":"CN","type":"education","lineage":["https://openalex.org/I152033890"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yating Li","raw_affiliation_strings":["School of Information Science and Technology, Hainan Normal University, Haikou, China"],"raw_orcid":"https://orcid.org/0009-0007-1469-7047","affiliations":[{"raw_affiliation_string":"School of Information Science and Technology, Hainan Normal University, Haikou, China","institution_ids":["https://openalex.org/I152033890"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100329989","display_name":"Xi Chen","orcid":"https://orcid.org/0000-0002-8523-3967"},"institutions":[{"id":"https://openalex.org/I152033890","display_name":"Hainan Normal University","ror":"https://ror.org/031dhcv14","country_code":"CN","type":"education","lineage":["https://openalex.org/I152033890"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xingmingyue Chen","raw_affiliation_strings":["School of Information Science and Technology, Hainan Normal University, Haikou, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information Science and Technology, Hainan Normal University, Haikou, China","institution_ids":["https://openalex.org/I152033890"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5128642712","display_name":"Junping Yang","orcid":null},"institutions":[{"id":"https://openalex.org/I152033890","display_name":"Hainan Normal University","ror":"https://ror.org/031dhcv14","country_code":"CN","type":"education","lineage":["https://openalex.org/I152033890"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Junping Yang","raw_affiliation_strings":["School of Information Science and Technology, Hainan Normal University, Haikou, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information Science and Technology, Hainan Normal University, Haikou, China","institution_ids":["https://openalex.org/I152033890"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000194814","display_name":"Xinyue Yu","orcid":"https://orcid.org/0000-0001-5356-5177"},"institutions":[{"id":"https://openalex.org/I152033890","display_name":"Hainan Normal University","ror":"https://ror.org/031dhcv14","country_code":"CN","type":"education","lineage":["https://openalex.org/I152033890"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xinyue Yu","raw_affiliation_strings":["School of Information Science and Technology, Hainan Normal University, Haikou, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information Science and Technology, Hainan Normal University, Haikou, China","institution_ids":["https://openalex.org/I152033890"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000787875","display_name":"Bo Liu","orcid":"https://orcid.org/0000-0002-2802-4405"},"institutions":[{"id":"https://openalex.org/I152033890","display_name":"Hainan Normal University","ror":"https://ror.org/031dhcv14","country_code":"CN","type":"education","lineage":["https://openalex.org/I152033890"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Bo Liu","raw_affiliation_strings":["School of Information Science and Technology, Hainan Normal University, Haikou, China"],"raw_orcid":"https://orcid.org/0000-0002-2802-4405","affiliations":[{"raw_affiliation_string":"School of Information Science and Technology, Hainan Normal University, Haikou, China","institution_ids":["https://openalex.org/I152033890"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5123368488","display_name":"Haixia Long","orcid":null},"institutions":[{"id":"https://openalex.org/I152033890","display_name":"Hainan Normal University","ror":"https://ror.org/031dhcv14","country_code":"CN","type":"education","lineage":["https://openalex.org/I152033890"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Haixia Long","raw_affiliation_strings":["School of Information Science and Technology, Hainan Normal University, Haikou, China"],"raw_orcid":"https://orcid.org/0000-0002-2484-9389","affiliations":[{"raw_affiliation_string":"School of Information Science and Technology, Hainan Normal University, Haikou, China","institution_ids":["https://openalex.org/I152033890"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I152033890"],"apc_list":null,"apc_paid":null,"fwci":3.8362,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.90799063,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"23","issue":"3","first_page":"1160","last_page":"1171"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9948999881744385,"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":0.9948999881744385,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.0007999999797903001,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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":0.0005000000237487257,"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/graph","display_name":"Graph","score":0.5511999726295471},{"id":"https://openalex.org/keywords/spatial-analysis","display_name":"Spatial analysis","score":0.5493999719619751},{"id":"https://openalex.org/keywords/spatial-contextual-awareness","display_name":"Spatial contextual awareness","score":0.5227000117301941},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.4544000029563904},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.42649999260902405},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.4081000089645386},{"id":"https://openalex.org/keywords/perspective","display_name":"Perspective (graphical)","score":0.3734999895095825},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.36570000648498535}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7587000131607056},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5511999726295471},{"id":"https://openalex.org/C159620131","wikidata":"https://www.wikidata.org/wiki/Q1938983","display_name":"Spatial analysis","level":2,"score":0.5493999719619751},{"id":"https://openalex.org/C64754055","wikidata":"https://www.wikidata.org/wiki/Q7574053","display_name":"Spatial contextual awareness","level":2,"score":0.5227000117301941},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5011000037193298},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.4544000029563904},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.44440001249313354},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.42649999260902405},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.4081000089645386},{"id":"https://openalex.org/C12713177","wikidata":"https://www.wikidata.org/wiki/Q1900281","display_name":"Perspective (graphical)","level":2,"score":0.3734999895095825},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.36570000648498535},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.3626999855041504},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3580000102519989},{"id":"https://openalex.org/C53471067","wikidata":"https://www.wikidata.org/wiki/Q7574076","display_name":"Spatial network","level":2,"score":0.33880001306533813},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.3100000023841858},{"id":"https://openalex.org/C27511587","wikidata":"https://www.wikidata.org/wiki/Q2178623","display_name":"Spatial relation","level":2,"score":0.3098999857902527},{"id":"https://openalex.org/C158709400","wikidata":"https://www.wikidata.org/wiki/Q3578586","display_name":"Spatial ecology","level":2,"score":0.30720001459121704},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.2903999984264374},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.27720001339912415},{"id":"https://openalex.org/C67186912","wikidata":"https://www.wikidata.org/wiki/Q367664","display_name":"Data modeling","level":2,"score":0.2680000066757202},{"id":"https://openalex.org/C2986522900","wikidata":"https://www.wikidata.org/wiki/Q2178623","display_name":"Spatial relationship","level":2,"score":0.26460000872612},{"id":"https://openalex.org/C203689450","wikidata":"https://www.wikidata.org/wiki/Q2302053","display_name":"Spatial database","level":3,"score":0.2590000033378601},{"id":"https://openalex.org/C88230418","wikidata":"https://www.wikidata.org/wiki/Q131476","display_name":"Graph theory","level":2,"score":0.25049999356269836}],"mesh":[{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000098422","descriptor_name":"Graph Neural Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000098422","descriptor_name":"Graph Neural Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbbio.2026.3671964","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2026.3671964","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41801789","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41801789","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":"IEEE transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2075623032","display_name":"\u57fa\u4e8e\u6df1\u5ea6\u5b66\u4e60\u7684RNA\u7532\u57fa\u5316\u4f4d\u70b9\u8bc6\u522b\u65b9\u6cd5\u7814\u7a76","funder_award_id":"223QN231","funder_id":"https://openalex.org/F4320322866","funder_display_name":"Natural Science Foundation of Hainan Province"},{"id":"https://openalex.org/G6548824546","display_name":null,"funder_award_id":"62441210","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G685265085","display_name":null,"funder_award_id":"62262019","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6901130845","display_name":"\u56fe\u795e\u7ecf\u7f51\u7edc\u5728\u5355\u7ec6\u80de\u8f6c\u5f55\u7ec4\u6d4b\u5e8f\u6570\u636e\u5206\u6790\u4e2d\u7684\u7814\u7a76","funder_award_id":"823RC488","funder_id":"https://openalex.org/F4320322866","funder_display_name":"Natural Science Foundation of Hainan Province"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320322866","display_name":"Natural Science Foundation of Hainan Province","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":33,"referenced_works":["https://openalex.org/W1523794535","https://openalex.org/W2800392236","https://openalex.org/W2809368942","https://openalex.org/W3100967665","https://openalex.org/W3126958162","https://openalex.org/W3164692211","https://openalex.org/W4285388882","https://openalex.org/W4306194402","https://openalex.org/W4311232381","https://openalex.org/W4311350141","https://openalex.org/W4321611267","https://openalex.org/W4322738920","https://openalex.org/W4322768301","https://openalex.org/W4327675690","https://openalex.org/W4378212119","https://openalex.org/W4378212544","https://openalex.org/W4385515928","https://openalex.org/W4389038260","https://openalex.org/W4389938094","https://openalex.org/W4390615703","https://openalex.org/W4390814844","https://openalex.org/W4390953330","https://openalex.org/W4391840598","https://openalex.org/W4392198237","https://openalex.org/W4399892951","https://openalex.org/W4401843719","https://openalex.org/W4403524525","https://openalex.org/W4406002896","https://openalex.org/W4407931466","https://openalex.org/W4409284406","https://openalex.org/W4409349227","https://openalex.org/W4411186225","https://openalex.org/W4411489604"],"related_works":[],"abstract_inverted_index":{"Single-cell":[0],"spatial":[1,19,39,52,82,90,114,122,147],"multi-omics":[2,123],"sequencing":[3],"technology":[4],"can":[5],"simultaneously":[6],"obtain":[7],"multiple":[8,121],"omics":[9],"data,":[10],"such":[11,132],"as":[12,133],"transcriptome":[13],"and":[14,29,41,80,89,101,105,135,140],"epigenome,":[15],"along":[16],"with":[17,109],"their":[18],"location":[20,91],"information,":[21,92],"providing":[22],"a":[23,37,62,98,113,143],"new":[24,144],"perspectivefor":[25],"deciphering":[26],"cell-cell":[27],"interactions":[28],"tissue":[30],"microenvironments.":[31],"Existing":[32],"modeling":[33],"methods":[34,131],"rely":[35],"on":[36,120],"single":[38],"scale":[40],"non-adaptive":[42],"cross-modality":[43],"fusion":[44],"strategies,":[45],"making":[46],"it":[47],"difficult":[48],"to":[49],"capture":[50],"complex":[51],"heterogeneity.":[53],"To":[54],"address":[55],"the":[56,110,127],"above":[57],"issues,":[58],"this":[59],"paper":[60],"proposes":[61],"graph":[63],"neural":[64],"network":[65],"model":[66,76,129],"named":[67],"Multi-Scale":[68],"Adaptive":[69],"Graph":[70],"Convolutional":[71],"Network,":[72],"MSAGCN.":[73],"The":[74],"MSAGCN":[75,128],"constructs":[77],"feature":[78],"graphs":[79,83],"multi-scale":[81],"by":[84],"leveraging":[85],"cell":[86],"expression":[87],"similarity":[88],"then":[93],"extracts":[94],"omics-specific":[95],"embeddings":[96],"through":[97],"dual-branch":[99],"encoder,":[100],"finally":[102],"obtains":[103],"cross-scale":[104],"cross-modal":[106],"consistent":[107],"representations":[108],"help":[111],"of":[112],"context":[115],"attention":[116],"mechanism.":[117],"Experimental":[118],"results":[119],"datasets":[124],"show":[125],"that":[126],"outperforms":[130],"SpatialGlue":[134],"COSMOS":[136],"in":[137],"overall":[138],"performance":[139],"also":[141],"provides":[142],"tool":[145],"for":[146],"domain":[148],"partitioning.":[149]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2026-03-11T00:00:00"}