{"id":"https://openalex.org/W4399162677","doi":"https://doi.org/10.1093/bib/bbae259","title":"SpaNCMG: improving spatial domains identification of spatial transcriptomics using neighborhood-complementary mixed-view graph convolutional network","display_name":"SpaNCMG: improving spatial domains identification of spatial transcriptomics using neighborhood-complementary mixed-view graph convolutional network","publication_year":2024,"publication_date":"2024-05-23","ids":{"openalex":"https://openalex.org/W4399162677","doi":"https://doi.org/10.1093/bib/bbae259","pmid":"https://pubmed.ncbi.nlm.nih.gov/38811360"},"language":"en","primary_location":{"is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae259","pdf_url":"https://academic.oup.com/bib/article-pdf/25/4/bbae259/57981752/bbae259.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":false,"is_indexed_in_scopus":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311647","https://openalex.org/P4310311648"],"host_organization_lineage_names":["University of Oxford","Oxford University Press"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true},"type":"article","type_crossref":"journal-article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bib/article-pdf/25/4/bbae259/57981752/bbae259.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5017349987","display_name":"Zhihao Si","orcid":"https://orcid.org/0000-0002-9141-8976"},"institutions":[{"id":"https://openalex.org/I55654194","display_name":"Inner Mongolia University of Technology","ror":"https://ror.org/05564e019","country_code":"CN","type":"funder","lineage":["https://openalex.org/I55654194"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhihao Si","raw_affiliation_strings":["College of Sciences, Inner Mongolia University of Technology , Hohhot 010051 , China"],"affiliations":[{"raw_affiliation_string":"College of Sciences, Inner Mongolia University of Technology , Hohhot 010051 , China","institution_ids":["https://openalex.org/I55654194"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062770273","display_name":"Hanshuang Li","orcid":"https://orcid.org/0000-0002-5068-4311"},"institutions":[{"id":"https://openalex.org/I2722730","display_name":"Inner Mongolia University","ror":"https://ror.org/0106qb496","country_code":"CN","type":"funder","lineage":["https://openalex.org/I2722730"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hanshuang Li","raw_affiliation_strings":["Inner Mongolia University , Institutes of Biomedical Sciences, College of Life Sciences, , Hohhot 010070 , China","State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, College of Life Sciences, Inner Mongolia University, Hohhot 010070, China"],"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, College of Life Sciences, Inner Mongolia University, Hohhot 010070, China","institution_ids":["https://openalex.org/I2722730"]},{"raw_affiliation_string":"Inner Mongolia University , Institutes of Biomedical Sciences, College of Life Sciences, , Hohhot 010070 , China","institution_ids":["https://openalex.org/I2722730"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101709831","display_name":"Wenjing Shang","orcid":"https://orcid.org/0000-0002-1865-143X"},"institutions":[{"id":"https://openalex.org/I55654194","display_name":"Inner Mongolia University of Technology","ror":"https://ror.org/05564e019","country_code":"CN","type":"funder","lineage":["https://openalex.org/I55654194"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wenjing Shang","raw_affiliation_strings":["College of Sciences, Inner Mongolia University of Technology , Hohhot 010051 , China"],"affiliations":[{"raw_affiliation_string":"College of Sciences, Inner Mongolia University of Technology , Hohhot 010051 , China","institution_ids":["https://openalex.org/I55654194"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101460721","display_name":"Yanan Zhao","orcid":"https://orcid.org/0000-0002-2761-696X"},"institutions":[{"id":"https://openalex.org/I55654194","display_name":"Inner Mongolia University of Technology","ror":"https://ror.org/05564e019","country_code":"CN","type":"funder","lineage":["https://openalex.org/I55654194"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yanan Zhao","raw_affiliation_strings":["College of Sciences, Inner Mongolia University of Technology , Hohhot 010051 , China"],"affiliations":[{"raw_affiliation_string":"College of Sciences, Inner Mongolia University of Technology , Hohhot 010051 , China","institution_ids":["https://openalex.org/I55654194"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113233575","display_name":"Lingjiao Kong","orcid":null},"institutions":[{"id":"https://openalex.org/I55654194","display_name":"Inner Mongolia University of Technology","ror":"https://ror.org/05564e019","country_code":"CN","type":"funder","lineage":["https://openalex.org/I55654194"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lingjiao Kong","raw_affiliation_strings":["College of Sciences, Inner Mongolia University of Technology , Hohhot 010051 , China"],"affiliations":[{"raw_affiliation_string":"College of Sciences, Inner Mongolia University of Technology , Hohhot 010051 , China","institution_ids":["https://openalex.org/I55654194"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012243501","display_name":"Chunshen Long","orcid":"https://orcid.org/0000-0002-1942-5936"},"institutions":[{"id":"https://openalex.org/I2722730","display_name":"Inner Mongolia University","ror":"https://ror.org/0106qb496","country_code":"CN","type":"funder","lineage":["https://openalex.org/I2722730"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chunshen Long","raw_affiliation_strings":["Inner Mongolia University , Institutes of Biomedical Sciences, College of Life Sciences, , Hohhot 010070 , China","State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, College of Life Sciences, Inner Mongolia University, Hohhot 010070, China"],"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, College of Life Sciences, Inner Mongolia University, Hohhot 010070, China","institution_ids":["https://openalex.org/I2722730"]},{"raw_affiliation_string":"Inner Mongolia University , Institutes of Biomedical Sciences, College of Life Sciences, , Hohhot 010070 , China","institution_ids":["https://openalex.org/I2722730"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001300435","display_name":"Yongchun Zuo","orcid":"https://orcid.org/0000-0002-6065-7835"},"institutions":[{"id":"https://openalex.org/I2722730","display_name":"Inner Mongolia University","ror":"https://ror.org/0106qb496","country_code":"CN","type":"funder","lineage":["https://openalex.org/I2722730"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yongchun Zuo","raw_affiliation_strings":["Inner Mongolia University , Institutes of Biomedical Sciences, College of Life Sciences, , Hohhot 010070 , China","State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, College of Life Sciences, Inner Mongolia University, Hohhot 010070, China"],"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, College of Life Sciences, Inner Mongolia University, Hohhot 010070, China","institution_ids":["https://openalex.org/I2722730"]},{"raw_affiliation_string":"Inner Mongolia University , Institutes of Biomedical Sciences, College of Life Sciences, , Hohhot 010070 , China","institution_ids":["https://openalex.org/I2722730"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101985314","display_name":"Zhenxing Feng","orcid":"https://orcid.org/0000-0003-3738-563X"},"institutions":[{"id":"https://openalex.org/I55654194","display_name":"Inner Mongolia University of Technology","ror":"https://ror.org/05564e019","country_code":"CN","type":"funder","lineage":["https://openalex.org/I55654194"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhenxing Feng","raw_affiliation_strings":["College of Sciences, Inner Mongolia University of Technology , Hohhot 010051 , China"],"affiliations":[{"raw_affiliation_string":"College of Sciences, Inner Mongolia University of Technology , Hohhot 010051 , China","institution_ids":["https://openalex.org/I55654194"]}]}],"institution_assertions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.686,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.687246,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":78,"max":89},"biblio":{"volume":"25","issue":"4","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9998,"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":0.9998,"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":[],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7427544},{"id":"https://openalex.org/C159620131","wikidata":"https://www.wikidata.org/wiki/Q1938983","display_name":"Spatial analysis","level":2,"score":0.53780407},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.5365159},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5362987},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.52457094},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.51327944},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4723355},{"id":"https://openalex.org/C70518039","wikidata":"https://www.wikidata.org/wiki/Q16000077","display_name":"Dimensionality reduction","level":2,"score":0.43746275},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.35671687},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.15615514},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.119007796},{"id":"https://openalex.org/C62649853","wikidata":"https://www.wikidata.org/wiki/Q199687","display_name":"Remote sensing","level":1,"score":0.0},{"id":"https://openalex.org/C127313418","wikidata":"https://www.wikidata.org/wiki/Q1069","display_name":"Geology","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017397","descriptor_name":"Prefrontal Cortex","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"","qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae259","pdf_url":"https://academic.oup.com/bib/article-pdf/25/4/bbae259/57981752/bbae259.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":false,"is_indexed_in_scopus":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311647","https://openalex.org/P4310311648"],"host_organization_lineage_names":["University of Oxford","Oxford University Press"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true},{"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11136618","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_indexed_in_scopus":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":["National Institutes of Health"],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true},{"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38811360","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_indexed_in_scopus":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":["National Institutes of Health"],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false}],"best_oa_location":{"is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae259","pdf_url":"https://academic.oup.com/bib/article-pdf/25/4/bbae259/57981752/bbae259.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":false,"is_indexed_in_scopus":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311647","https://openalex.org/P4310311648"],"host_organization_lineage_names":["University of Oxford","Oxford University Press"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/11","display_name":"Sustainable cities and communities","score":0.72}],"grants":[],"datasets":[],"versions":[],"referenced_works_count":42,"referenced_works":["https://openalex.org/W1976455030","https://openalex.org/W2006255103","https://openalex.org/W2022072413","https://openalex.org/W2042789810","https://openalex.org/W2069089843","https://openalex.org/W2089000296","https://openalex.org/W2122111042","https://openalex.org/W2133564696","https://openalex.org/W2471536144","https://openalex.org/W2519132385","https://openalex.org/W2792537872","https://openalex.org/W2800392236","https://openalex.org/W2902652978","https://openalex.org/W2912707296","https://openalex.org/W2915848182","https://openalex.org/W2923300855","https://openalex.org/W2943213517","https://openalex.org/W2944342839","https://openalex.org/W2949177718","https://openalex.org/W2952383043","https://openalex.org/W2964015378","https://openalex.org/W2999899884","https://openalex.org/W3020981980","https://openalex.org/W3021105102","https://openalex.org/W3032266082","https://openalex.org/W3099768174","https://openalex.org/W3108118546","https://openalex.org/W3118987147","https://openalex.org/W3120427588","https://openalex.org/W3134482219","https://openalex.org/W3165120573","https://openalex.org/W3190202966","https://openalex.org/W3214865687","https://openalex.org/W4206826076","https://openalex.org/W4226192560","https://openalex.org/W4229033508","https://openalex.org/W4281716652","https://openalex.org/W4290154117","https://openalex.org/W4353041376","https://openalex.org/W4382877140","https://openalex.org/W4389210152","https://openalex.org/W4390814844"],"related_works":["https://openalex.org/W4293226380","https://openalex.org/W4235240664","https://openalex.org/W3176621072","https://openalex.org/W2965083567","https://openalex.org/W2889616422","https://openalex.org/W2389214306","https://openalex.org/W2095886385","https://openalex.org/W2089704382","https://openalex.org/W1983399550","https://openalex.org/W1838576100"],"abstract_inverted_index":{"Abstract":[0],"The":[1,78,128],"advancement":[2],"of":[3,14,18,27,40,62,117,130,154,161,178,192,224],"spatial":[4,16,44,49,65,176],"transcriptomics":[5],"(ST)":[6],"technology":[7],"contributes":[8],"to":[9,25,46,83,113,142],"a":[10,56,72,103],"more":[11],"profound":[12],"comprehension":[13],"the":[15,38,60,91,97,148,159,162,175,182,189,203,208,218],"properties":[17],"gene":[19,41],"expression":[20,42],"within":[21],"tissues.":[22],"However,":[23],"due":[24],"challenges":[26],"high":[28],"dimensionality,":[29],"pronounced":[30],"noise":[31],"and":[32,43,68,96,121,156,167,187,222,235],"dynamic":[33],"limitations":[34],"in":[35,181],"ST":[36,84],"data,":[37],"integration":[39],"information":[45,93],"accurately":[47,173],"identify":[48],"domains":[50],"remains":[51],"challenging.":[52],"This":[53],"paper":[54],"proposes":[55],"SpaNCMG":[57,131,204,225],"algorithm":[58,79,149],"for":[59,125,231],"purpose":[61],"achieving":[63],"precise":[64],"domain":[66],"description":[67],"localization":[69],"based":[70],"on":[71,132,158],"neighborhood-complementary":[73],"mixed-view":[74],"graph":[75],"convolutional":[76],"network.":[77],"enables":[80],"better":[81],"adaptation":[82],"data":[85],"at":[86,242],"different":[87,118,193],"resolutions":[88],"by":[89],"integrating":[90],"local":[92],"from":[94,100,135],"KNN":[95],"global":[98],"structure":[99,234],"r-radius":[101],"into":[102],"complementary":[104],"neighborhood":[105],"graph.":[106],"It":[107,172],"also":[108,213],"introduces":[109],"an":[110,228],"attention":[111],"mechanism":[112],"achieve":[114],"adaptive":[115],"fusion":[116],"reconstructed":[119],"expressions,":[120],"utilizes":[122],"KPCA":[123],"method":[124],"dimensionality":[126],"reduction.":[127],"application":[129],"five":[133],"datasets":[134,160,198],"four":[136],"sequencing":[137],"platforms":[138],"demonstrates":[139],"superior":[140],"performance":[141],"eight":[143],"existing":[144],"advanced":[145],"methods.":[146],"Specifically,":[147],"achieved":[150],"highest":[151],"ARI":[152],"accuracies":[153],"0.63":[155],"0.52":[157],"human":[163],"dorsolateral":[164],"prefrontal":[165],"cortex":[166],"mouse":[168,183,201],"somatosensory":[169],"cortex,":[170],"respectively.":[171],"identified":[174,207],"locations":[177],"marker":[179],"genes":[180],"olfactory":[184],"bulb":[185],"tissue":[186,210,233],"inferred":[188],"biological":[190],"functions":[191],"regions.":[194],"When":[195],"handling":[196],"larger":[197],"such":[199],"as":[200],"embryos,":[202],"not":[205],"only":[206],"main":[209],"structures":[211],"but":[212],"explored":[214],"unlabeled":[215],"domains.":[216],"Overall,":[217],"good":[219],"generalization":[220],"ability":[221],"scalability":[223],"make":[226],"it":[227],"outstanding":[229],"tool":[230],"understanding":[232],"disease":[236],"mechanisms.":[237],"Our":[238],"codes":[239],"are":[240],"available":[241],"https://github.com/ZhihaoSi/SpaNCMG.":[243]},"abstract_inverted_index_v3":null,"cited_by_api_url":"https://api.openalex.org/works?filter=cites:W4399162677","counts_by_year":[{"year":2024,"cited_by_count":1}],"updated_date":"2025-04-03T23:50:20.440059","created_date":"2024-05-31"}