{"id":"https://openalex.org/W7163892979","doi":"https://doi.org/10.1021/acs.jcim.6c01121","title":"SpaVGMC: A Unified Representation Learning Framework via Structural and Semantic Alignment in Spatial Transcriptomics","display_name":"SpaVGMC: A Unified Representation Learning Framework via Structural and Semantic Alignment in Spatial Transcriptomics","publication_year":2026,"publication_date":"2026-06-08","ids":{"openalex":"https://openalex.org/W7163892979","doi":"https://doi.org/10.1021/acs.jcim.6c01121","pmid":"https://pubmed.ncbi.nlm.nih.gov/42253102"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.6c01121","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.6c01121","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","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/A5017903391","display_name":"Aman Fan","orcid":"https://orcid.org/0009-0006-9940-572X"},"institutions":[{"id":"https://openalex.org/I202126657","display_name":"Qufu Normal University","ror":"https://ror.org/03ceheh96","country_code":"CN","type":"education","lineage":["https://openalex.org/I202126657"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Aitian Fan","raw_affiliation_strings":["Qufu Normal University","School of Computer Science"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Qufu Normal University","institution_ids":["https://openalex.org/I202126657"]},{"raw_affiliation_string":"School of Computer Science","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5138146457","display_name":"Junliang Shang","orcid":"https://orcid.org/0009-0000-2104-1678"},"institutions":[{"id":"https://openalex.org/I202126657","display_name":"Qufu Normal University","ror":"https://ror.org/03ceheh96","country_code":"CN","type":"education","lineage":["https://openalex.org/I202126657"]},{"id":"https://openalex.org/I4210158179","display_name":"Yellow River Institute of Hydraulic Research","ror":"https://ror.org/0506q7a98","country_code":"CN","type":"government","lineage":["https://openalex.org/I4210155611","https://openalex.org/I4210158179"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Junliang Shang","raw_affiliation_strings":["Qufu Normal University","Rizhao-Qufu Normal University Joint Technology Transfer Center","School of Computer Science","Shandong Key Laboratory of Wetland Ecology and Biodiversity Conservation in the Lower Yellow River"],"raw_orcid":"https://orcid.org/0009-0000-2104-1678","affiliations":[{"raw_affiliation_string":"Qufu Normal University","institution_ids":["https://openalex.org/I202126657"]},{"raw_affiliation_string":"Rizhao-Qufu Normal University Joint Technology Transfer Center","institution_ids":["https://openalex.org/I202126657"]},{"raw_affiliation_string":"School of Computer Science","institution_ids":[]},{"raw_affiliation_string":"Shandong Key Laboratory of Wetland Ecology and Biodiversity Conservation in the Lower Yellow River","institution_ids":["https://openalex.org/I4210158179"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100431071","display_name":"Xiaohan Zhang","orcid":"https://orcid.org/0000-0002-1118-7582"},"institutions":[{"id":"https://openalex.org/I202126657","display_name":"Qufu Normal University","ror":"https://ror.org/03ceheh96","country_code":"CN","type":"education","lineage":["https://openalex.org/I202126657"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaohan Zhang","raw_affiliation_strings":["Qufu Normal University","School of Computer Science"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Qufu Normal University","institution_ids":["https://openalex.org/I202126657"]},{"raw_affiliation_string":"School of Computer Science","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101557490","display_name":"Wenjing Su","orcid":null},"institutions":[{"id":"https://openalex.org/I202126657","display_name":"Qufu Normal University","ror":"https://ror.org/03ceheh96","country_code":"CN","type":"education","lineage":["https://openalex.org/I202126657"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wenjing Su","raw_affiliation_strings":["Qufu Normal University","School of Computer Science"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Qufu Normal University","institution_ids":["https://openalex.org/I202126657"]},{"raw_affiliation_string":"School of Computer Science","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011606369","display_name":"Defu Qiu","orcid":"https://orcid.org/0000-0003-4921-9145"},"institutions":[{"id":"https://openalex.org/I202126657","display_name":"Qufu Normal University","ror":"https://ror.org/03ceheh96","country_code":"CN","type":"education","lineage":["https://openalex.org/I202126657"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Defu Qiu","raw_affiliation_strings":["Qufu Normal University","School of Computer Science"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Qufu Normal University","institution_ids":["https://openalex.org/I202126657"]},{"raw_affiliation_string":"School of Computer Science","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5123594448","display_name":"Hanxiang Wang","orcid":null},"institutions":[{"id":"https://openalex.org/I202126657","display_name":"Qufu Normal University","ror":"https://ror.org/03ceheh96","country_code":"CN","type":"education","lineage":["https://openalex.org/I202126657"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hanxiang Wang","raw_affiliation_strings":["Qufu Normal University","School of Computer Science"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Qufu Normal University","institution_ids":["https://openalex.org/I202126657"]},{"raw_affiliation_string":"School of Computer Science","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101898967","display_name":"Jinxing Liu","orcid":"https://orcid.org/0000-0003-0244-9752"},"institutions":[{"id":"https://openalex.org/I4210164233","display_name":"Health & Life (Taiwan)","ror":"https://ror.org/05nnz8429","country_code":"TW","type":"company","lineage":["https://openalex.org/I4210164233"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Jin-Xing Liu","raw_affiliation_strings":["School of Life Sciences and Health","University of Health and Rehabilitation Sciences"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Life Sciences and Health","institution_ids":["https://openalex.org/I4210164233"]},{"raw_affiliation_string":"University of Health and Rehabilitation Sciences","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5138146457"],"corresponding_institution_ids":["https://openalex.org/I202126657","https://openalex.org/I4210158179"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.78726432,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"66","issue":"12","first_page":"7320","last_page":"7335"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9672999978065491,"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":0.9672999978065491,"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":0.015300000086426735,"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":0.0035000001080334187,"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/inference","display_name":"Inference","score":0.59579998254776},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.5317000150680542},{"id":"https://openalex.org/keywords/feature-learning","display_name":"Feature learning","score":0.517300009727478},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.48890000581741333},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.4586000144481659},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.45419999957084656},{"id":"https://openalex.org/keywords/spatial-analysis","display_name":"Spatial analysis","score":0.44040000438690186},{"id":"https://openalex.org/keywords/mutual-information","display_name":"Mutual information","score":0.4156999886035919},{"id":"https://openalex.org/keywords/probabilistic-logic","display_name":"Probabilistic logic","score":0.3950999975204468}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7268999814987183},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.59579998254776},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5529000163078308},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.5317000150680542},{"id":"https://openalex.org/C59404180","wikidata":"https://www.wikidata.org/wiki/Q17013334","display_name":"Feature learning","level":2,"score":0.517300009727478},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.48890000581741333},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.4586000144481659},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.45419999957084656},{"id":"https://openalex.org/C159620131","wikidata":"https://www.wikidata.org/wiki/Q1938983","display_name":"Spatial analysis","level":2,"score":0.44040000438690186},{"id":"https://openalex.org/C152139883","wikidata":"https://www.wikidata.org/wiki/Q252973","display_name":"Mutual information","level":2,"score":0.4156999886035919},{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.3950999975204468},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.3935000002384186},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3864000141620636},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.3758000135421753},{"id":"https://openalex.org/C184337299","wikidata":"https://www.wikidata.org/wiki/Q1437428","display_name":"Semantics (computer science)","level":2,"score":0.3684000074863434},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.3400000035762787},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.33660000562667847},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.321399986743927},{"id":"https://openalex.org/C2775955345","wikidata":"https://www.wikidata.org/wiki/Q7449071","display_name":"Semantic mapping","level":2,"score":0.30970001220703125},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.2946999967098236},{"id":"https://openalex.org/C38764148","wikidata":"https://www.wikidata.org/wiki/Q17098245","display_name":"Interaction information","level":2,"score":0.29330000281333923},{"id":"https://openalex.org/C155846161","wikidata":"https://www.wikidata.org/wiki/Q1143367","display_name":"Graphical model","level":2,"score":0.2890999913215637},{"id":"https://openalex.org/C89611455","wikidata":"https://www.wikidata.org/wiki/Q6804646","display_name":"Mechanism (biology)","level":2,"score":0.2851000130176544},{"id":"https://openalex.org/C130318100","wikidata":"https://www.wikidata.org/wiki/Q2268914","display_name":"Semantic similarity","level":2,"score":0.27459999918937683},{"id":"https://openalex.org/C19768560","wikidata":"https://www.wikidata.org/wiki/Q320727","display_name":"Dependency (UML)","level":2,"score":0.2639999985694885},{"id":"https://openalex.org/C151876577","wikidata":"https://www.wikidata.org/wiki/Q7049464","display_name":"Nonlinear dimensionality reduction","level":3,"score":0.2565999925136566},{"id":"https://openalex.org/C94124525","wikidata":"https://www.wikidata.org/wiki/Q912550","display_name":"Categorization","level":2,"score":0.2524999976158142}],"mesh":[{"descriptor_ui":"D000098409","descriptor_name":"Representation Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000099285","descriptor_name":"Spatial Transcriptomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.6c01121","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.6c01121","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:42253102","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42253102","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":"Journal of chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Reduced inequalities","id":"https://metadata.un.org/sdg/10","score":0.7271776795387268}],"awards":[{"id":"https://openalex.org/G3938201872","display_name":null,"funder_award_id":"62473179","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4690668261","display_name":null,"funder_award_id":"62472250","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6334930974","display_name":"\u590d\u6742\u75be\u75c5\u5168\u57fa\u56e0\u7ec4SNP\u9ad8\u9636\u4e92\u4f5c\u6a21\u5f0f\u7684\u7f51\u7edc\u6316\u6398\u65b9\u6cd5\u7814\u7a76","funder_award_id":"61972226","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":39,"referenced_works":["https://openalex.org/W1974565082","https://openalex.org/W2033403400","https://openalex.org/W2042789810","https://openalex.org/W2058487314","https://openalex.org/W2085487226","https://openalex.org/W2123273050","https://openalex.org/W2523948971","https://openalex.org/W2543232345","https://openalex.org/W2753908609","https://openalex.org/W2800392236","https://openalex.org/W2809368942","https://openalex.org/W2897249806","https://openalex.org/W2915848182","https://openalex.org/W2923300855","https://openalex.org/W2964121744","https://openalex.org/W2972983657","https://openalex.org/W3036371598","https://openalex.org/W3037329734","https://openalex.org/W3080420240","https://openalex.org/W3108118546","https://openalex.org/W3112563877","https://openalex.org/W3119379269","https://openalex.org/W3126341869","https://openalex.org/W3126958162","https://openalex.org/W3134482219","https://openalex.org/W3165120573","https://openalex.org/W3210002151","https://openalex.org/W4206826076","https://openalex.org/W4226192560","https://openalex.org/W4229033508","https://openalex.org/W4289956737","https://openalex.org/W4297808394","https://openalex.org/W4306406844","https://openalex.org/W4309944312","https://openalex.org/W4322738920","https://openalex.org/W4390814844","https://openalex.org/W4408987264","https://openalex.org/W4409129472","https://openalex.org/W4414660901"],"related_works":[],"abstract_inverted_index":{"Spatial":[0],"transcriptomics":[1,166],"technologies":[2],"profile":[3],"gene":[4],"expression":[5],"within":[6],"its":[7],"native":[8],"spatial":[9,21,80,114,165,177,204],"context,":[10],"offering":[11],"new":[12],"insights":[13],"into":[14],"tissue":[15,184],"organization":[16],"and":[17,33,57,70,82,123,151,157,186,200],"disease.":[18],"However,":[19],"accurate":[20],"domain":[22,178],"identification":[23],"remains":[24],"challenging":[25],"due":[26],"to":[27,135],"local":[28],"oversmoothing,":[29],"impaired":[30],"topological":[31,106],"fidelity,":[32],"insufficient":[34],"modeling":[35,148],"of":[36,76,189],"global":[37,83],"semantic":[38,71,129],"structures.":[39],"To":[40],"address":[41],"these":[42,193],"challenges,":[43],"we":[44],"propose":[45],"SpaVGMC,":[46],"a":[47,92,128,198],"unified":[48],"representation":[49,65,89],"learning":[50,90,141],"framework":[51,61,202],"that":[52,170],"jointly":[53,147],"models":[54],"structural":[55,67,101],"dependencies":[56],"transcriptional":[58,84,136],"semantics.":[59],"The":[60],"integrates":[62],"structured":[63,93],"variational":[64,94],"learning,":[66],"information":[68,102,118],"alignment,":[69,72],"allowing":[73],"the":[74,113,121],"capture":[75],"probabilistic":[77],"uncertainty,":[78],"multiscale":[79],"dependencies,":[81],"organization.":[85],"Specifically,":[86],"SpaVGMC":[87,153,171,196],"formulates":[88],"as":[91,197],"inference":[95],"process":[96],"with":[97,112,183],"context-aware":[98],"message-passing.":[99],"A":[100],"alignment":[103,130],"mechanism":[104,131],"preserves":[105],"fidelity":[107],"by":[108],"aligning":[109],"latent":[110],"embeddings":[111],"graph":[115],"via":[116],"mutual":[117],"at":[119],"both":[120],"edge":[122],"neighborhood":[124],"levels.":[125],"In":[126],"addition,":[127],"organizes":[132],"representations":[133],"according":[134],"similarity":[137],"through":[138],"distribution-aware":[139],"contrastive":[140],"without":[142],"requiring":[143],"data":[144,167],"augmentation.":[145],"By":[146],"representations,":[149],"structures,":[150],"semantics,":[152],"learns":[154],"robust,":[155],"discriminative,":[156],"biologically":[158],"interpretable":[159],"embeddings.":[160],"Extensive":[161],"experiments":[162],"across":[163],"diverse":[164],"sets":[168],"demonstrate":[169],"consistently":[172],"outperforms":[173],"state-of-the-art":[174],"methods":[175],"in":[176],"identification,":[179],"showing":[180],"improved":[181],"agreement":[182],"structures":[185],"enhanced":[187],"detection":[188],"fine-grained":[190],"subdomains.":[191],"Collectively,":[192],"results":[194],"establish":[195],"robust":[199],"scalable":[201],"for":[203],"omics":[205],"analysis.":[206]},"counts_by_year":[],"updated_date":"2026-06-23T06:36:01.041984","created_date":"2026-06-09T00:00:00"}