{"id":"https://openalex.org/W4406047272","doi":"https://doi.org/10.1109/tcbbio.2024.3521983","title":"UPSST: Unsupervised Pathology Domain Identification by Integrating Tissue Morphology, Imputing and Clustering of Spatial Transcriptomics With GAT","display_name":"UPSST: Unsupervised Pathology Domain Identification by Integrating Tissue Morphology, Imputing and Clustering of Spatial Transcriptomics With GAT","publication_year":2025,"publication_date":"2025-01-01","ids":{"openalex":"https://openalex.org/W4406047272","doi":"https://doi.org/10.1109/tcbbio.2024.3521983","pmid":"https://pubmed.ncbi.nlm.nih.gov/40811223"},"language":"en","primary_location":{"id":"doi:10.1109/tcbbio.2024.3521983","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2024.3521983","pdf_url":null,"source":{"id":"https://openalex.org/S5407042751","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"2998-4165","issn":["2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"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/A5058981736","display_name":"Guiyun Chen","orcid":"https://orcid.org/0000-0001-5428-6903"},"institutions":[{"id":"https://openalex.org/I111599522","display_name":"Jiangnan University","ror":"https://ror.org/04mkzax54","country_code":"CN","type":"education","lineage":["https://openalex.org/I111599522"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Guiyun Chen","raw_affiliation_strings":["School of Artificial Intelligence and Computer Science, Jiangnan University, Wuxi, China"],"affiliations":[{"raw_affiliation_string":"School of Artificial Intelligence and Computer Science, Jiangnan University, Wuxi, China","institution_ids":["https://openalex.org/I111599522"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080175335","display_name":"Xiaoyan Hong","orcid":"https://orcid.org/0000-0002-3843-0837"},"institutions":[{"id":"https://openalex.org/I111599522","display_name":"Jiangnan University","ror":"https://ror.org/04mkzax54","country_code":"CN","type":"education","lineage":["https://openalex.org/I111599522"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaoyan Hong","raw_affiliation_strings":["School of Artificial Intelligence and Computer Science, Jiangnan University, Wuxi, China"],"affiliations":[{"raw_affiliation_string":"School of Artificial Intelligence and Computer Science, Jiangnan University, Wuxi, China","institution_ids":["https://openalex.org/I111599522"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100433939","display_name":"Lei Zhang","orcid":"https://orcid.org/0000-0002-6378-1057"},"institutions":[{"id":"https://openalex.org/I4210154454","display_name":"Guizhou Provincial People's Hospital","ror":"https://ror.org/046q1bp69","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210154454"]},{"id":"https://openalex.org/I4210086248","display_name":"Affiliated Hospital of Southwest Medical University","ror":"https://ror.org/0014a0n68","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210086248"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lei Zhang","raw_affiliation_strings":["Department of Vascular Surgery, Zhejiang Provincial People&#x0027;s Hospital Bijie Hospital, Bijie, Guizhou, China","Department of Vascular Surgery, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China"],"affiliations":[{"raw_affiliation_string":"Department of Vascular Surgery, Zhejiang Provincial People&#x0027;s Hospital Bijie Hospital, Bijie, Guizhou, China","institution_ids":["https://openalex.org/I4210154454"]},{"raw_affiliation_string":"Department of Vascular Surgery, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China","institution_ids":["https://openalex.org/I4210086248"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5115762609","display_name":"Longzhen Dinga","orcid":null},"institutions":[{"id":"https://openalex.org/I111599522","display_name":"Jiangnan University","ror":"https://ror.org/04mkzax54","country_code":"CN","type":"education","lineage":["https://openalex.org/I111599522"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Longzhen Ding","raw_affiliation_strings":["School of Artificial Intelligence and Computer Science, Jiangnan University, Wuxi, China"],"affiliations":[{"raw_affiliation_string":"School of Artificial Intelligence and Computer Science, Jiangnan University, Wuxi, China","institution_ids":["https://openalex.org/I111599522"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100440653","display_name":"Lihua Li","orcid":"https://orcid.org/0000-0003-0435-6453"},"institutions":[{"id":"https://openalex.org/I50760025","display_name":"Hangzhou Dianzi University","ror":"https://ror.org/0576gt767","country_code":"CN","type":"education","lineage":["https://openalex.org/I50760025"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lihua Li","raw_affiliation_strings":["Institute of Biomedical Engineering and Instrumentation, Hangzhou Dianzi University, Hangzhou, China"],"affiliations":[{"raw_affiliation_string":"Institute of Biomedical Engineering and Instrumentation, Hangzhou Dianzi University, Hangzhou, China","institution_ids":["https://openalex.org/I50760025"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102177199","display_name":"Chunjuan Jiang","orcid":null},"institutions":[{"id":"https://openalex.org/I4210093194","display_name":"Fudan University Shanghai Cancer Center","ror":"https://ror.org/00my25942","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210093194"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chunjuan Jiang","raw_affiliation_strings":["Department of Nuclear Medicine, Fudan University Shanghai Cancer Center, Shanghai, China"],"affiliations":[{"raw_affiliation_string":"Department of Nuclear Medicine, Fudan University Shanghai Cancer Center, Shanghai, China","institution_ids":["https://openalex.org/I4210093194"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086187414","display_name":"Jiali Nie","orcid":"https://orcid.org/0009-0006-7972-3624"},"institutions":[{"id":"https://openalex.org/I111599522","display_name":"Jiangnan University","ror":"https://ror.org/04mkzax54","country_code":"CN","type":"education","lineage":["https://openalex.org/I111599522"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jianming Ni","raw_affiliation_strings":["Department of Radiology, Jiangnan University Medical Center, Wuxi, China","Department of Medical Imaging, Affiliated Central Hospital of Jiangnan University, Wuxi, China"],"affiliations":[{"raw_affiliation_string":"Department of Radiology, Jiangnan University Medical Center, Wuxi, China","institution_ids":["https://openalex.org/I111599522"]},{"raw_affiliation_string":"Department of Medical Imaging, Affiliated Central Hospital of Jiangnan University, Wuxi, China","institution_ids":["https://openalex.org/I111599522"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080167967","display_name":"Kai Miao","orcid":"https://orcid.org/0000-0003-4832-3354"},"institutions":[{"id":"https://openalex.org/I6469544","display_name":"City University of Macau","ror":"https://ror.org/04gpd4q15","country_code":"MO","type":"education","lineage":["https://openalex.org/I6469544"]},{"id":"https://openalex.org/I204512498","display_name":"University of Macau","ror":"https://ror.org/01r4q9n85","country_code":"MO","type":"education","lineage":["https://openalex.org/I204512498"]}],"countries":["MO"],"is_corresponding":false,"raw_author_name":"Kai Miao","raw_affiliation_strings":["Cancer Center, Faculty of Health Sciences, University of Macau, Taipa, Macau, China","Cancer Center, Faculty of Health Sciences, University of Macau, Macau, China"],"affiliations":[{"raw_affiliation_string":"Cancer Center, Faculty of Health Sciences, University of Macau, Taipa, Macau, China","institution_ids":["https://openalex.org/I204512498"]},{"raw_affiliation_string":"Cancer Center, Faculty of Health Sciences, University of Macau, Macau, China","institution_ids":["https://openalex.org/I6469544","https://openalex.org/I204512498"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100670526","display_name":"Xiang Pan","orcid":"https://orcid.org/0000-0001-6554-1404"},"institutions":[{"id":"https://openalex.org/I4210135985","display_name":"Shanghai University of Medicine and Health Sciences","ror":"https://ror.org/03ns6aq57","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210135985"]},{"id":"https://openalex.org/I111599522","display_name":"Jiangnan University","ror":"https://ror.org/04mkzax54","country_code":"CN","type":"education","lineage":["https://openalex.org/I111599522"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiang Pan","raw_affiliation_strings":["School of Artificial Intelligence and Computer Science, Jiangnan University, Wuxi, China","Shanghai Key Laboratory of Molecular Imaging, Shanghai University of Medicine and Health Sciences, Shanghai, China","Department of Medical Imaging, Affiliated Central Hospital of Jiangnan University, Wuxi, China"],"affiliations":[{"raw_affiliation_string":"School of Artificial Intelligence and Computer Science, Jiangnan University, Wuxi, China","institution_ids":["https://openalex.org/I111599522"]},{"raw_affiliation_string":"Shanghai Key Laboratory of Molecular Imaging, Shanghai University of Medicine and Health Sciences, Shanghai, China","institution_ids":["https://openalex.org/I4210135985"]},{"raw_affiliation_string":"Department of Medical Imaging, Affiliated Central Hospital of Jiangnan University, Wuxi, China","institution_ids":["https://openalex.org/I111599522"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5058981736"],"corresponding_institution_ids":["https://openalex.org/I111599522"],"apc_list":null,"apc_paid":null,"fwci":1.6498,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.80347763,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":99},"biblio":{"volume":"22","issue":"1","first_page":"298","last_page":"309"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9990000128746033,"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":0.9990000128746033,"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":0.9679999947547913,"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/identification","display_name":"Identification (biology)","score":0.6959502696990967},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.589094340801239},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.5416803956031799},{"id":"https://openalex.org/keywords/morphology","display_name":"Morphology (biology)","score":0.5349854826927185},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.522508442401886},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.47582200169563293},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4499059319496155},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.341561496257782},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3320309519767761},{"id":"https://openalex.org/keywords/zoology","display_name":"Zoology","score":0.14772874116897583},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.11046937108039856},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.07828882336616516}],"concepts":[{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.6959502696990967},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.589094340801239},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.5416803956031799},{"id":"https://openalex.org/C499950583","wikidata":"https://www.wikidata.org/wiki/Q183252","display_name":"Morphology (biology)","level":2,"score":0.5349854826927185},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.522508442401886},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.47582200169563293},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4499059319496155},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.341561496257782},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3320309519767761},{"id":"https://openalex.org/C90856448","wikidata":"https://www.wikidata.org/wiki/Q431","display_name":"Zoology","level":1,"score":0.14772874116897583},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.11046937108039856},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.07828882336616516},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbbio.2024.3521983","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2024.3521983","pdf_url":null,"source":{"id":"https://openalex.org/S5407042751","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"2998-4165","issn":["2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"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:40811223","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40811223","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":[{"display_name":"Zero hunger","score":0.44999998807907104,"id":"https://metadata.un.org/sdg/2"}],"awards":[{"id":"https://openalex.org/G2552203565","display_name":null,"funder_award_id":"W2411054","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3557113049","display_name":null,"funder_award_id":"62271178","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7310643791","display_name":null,"funder_award_id":"U21A20521","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"},{"id":"https://openalex.org/F4320322841","display_name":"Universidade de Macau","ror":"https://ror.org/01r4q9n85"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":49,"referenced_works":["https://openalex.org/W2023309229","https://openalex.org/W2042789810","https://openalex.org/W2123491442","https://openalex.org/W2126537932","https://openalex.org/W2129757655","https://openalex.org/W2131681506","https://openalex.org/W2144430639","https://openalex.org/W2151013106","https://openalex.org/W2154228396","https://openalex.org/W2763776271","https://openalex.org/W2770119694","https://openalex.org/W2809368942","https://openalex.org/W2897249806","https://openalex.org/W2906625258","https://openalex.org/W2915848182","https://openalex.org/W2923300855","https://openalex.org/W2928515356","https://openalex.org/W2949067670","https://openalex.org/W2950372712","https://openalex.org/W2951381561","https://openalex.org/W2972983657","https://openalex.org/W2991941214","https://openalex.org/W2999345636","https://openalex.org/W3007402690","https://openalex.org/W3036371598","https://openalex.org/W3094217342","https://openalex.org/W3099768174","https://openalex.org/W3106188259","https://openalex.org/W3108118546","https://openalex.org/W3126958162","https://openalex.org/W3134482219","https://openalex.org/W3164692211","https://openalex.org/W3165120573","https://openalex.org/W3169800083","https://openalex.org/W3190202966","https://openalex.org/W3191029526","https://openalex.org/W4213285121","https://openalex.org/W4220765701","https://openalex.org/W4235169531","https://openalex.org/W4283704002","https://openalex.org/W4290154117","https://openalex.org/W4303986417","https://openalex.org/W4306406844","https://openalex.org/W4309918428","https://openalex.org/W4311666191","https://openalex.org/W4388997570","https://openalex.org/W4390814844","https://openalex.org/W4392868645","https://openalex.org/W6680970901"],"related_works":["https://openalex.org/W2551537403","https://openalex.org/W4298130764","https://openalex.org/W2804364458","https://openalex.org/W579370048","https://openalex.org/W2132641928","https://openalex.org/W4310225030","https://openalex.org/W2090259340","https://openalex.org/W1926736923","https://openalex.org/W2158836806","https://openalex.org/W2393816671"],"abstract_inverted_index":{"Spatial":[0],"transcriptomics":[1,26,67,144],"is":[2,28],"an":[3,75],"emerging":[4],"technology":[5],"that":[6,43],"allows":[7],"for":[8,30,129,142],"analysis":[9],"of":[10,21,80,87,92,108,149],"cellular":[11],"and":[12,34,50,82,106,123,139],"molecular":[13],"heterogeneity":[14,33],"at":[15],"spatial":[16,25,52,66,143],"resolution.":[17],"The":[18],"accurate":[19],"identification":[20,148],"pathological":[22,150],"regions":[23,53,151],"in":[24,111],"data":[27],"essential":[29],"understanding":[31],"tissue":[32,45],"disease":[35],"progression.":[36],"We":[37],"introduce":[38],"UPSST,":[39],"a":[40,55,83,137],"comprehensive":[41],"framework":[42],"integrates":[44],"morphology,":[46],"imputes":[47],"gene":[48],"expression,":[49],"clusters":[51],"using":[54],"graph":[56],"attention":[57],"neural":[58],"network":[59],"(GAT).":[60],"UPSST":[61,116,135],"was":[62],"evaluated":[63],"across":[64],"multiple":[65],"datasets,":[68],"achieving":[69,74],"high":[70,153],"performance,":[71],"such":[72,120],"as":[73,121],"Adjusted":[76],"Rand":[77],"Index":[78,85],"(ARI)":[79],"0.737":[81],"Fowlkes-Mallows":[84],"(FMI)":[86],"0.818":[88],"on":[89],"slice":[90],"151671":[91],"the":[93,104,147],"LIBD":[94],"human":[95],"dorsolateral":[96],"prefrontal":[97],"cortex":[98],"(DLPFC)":[99],"dataset.":[100],"These":[101],"results":[102],"highlight":[103],"robustness":[105],"precision":[107],"our":[109],"approach":[110],"identifying":[112],"pathology":[113],"domains.":[114],"Additionally,":[115],"facilitates":[117],"downstream":[118],"analyses":[119],"differential":[122],"enrichment":[124],"analysis,":[125,145],"which":[126],"are":[127],"crucial":[128],"deriving":[130],"biological":[131],"insights.":[132],"In":[133],"conclusion,":[134],"offers":[136],"powerful":[138],"reliable":[140],"tool":[141],"advancing":[146],"with":[152],"accuracy.":[154]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1}],"updated_date":"2026-03-25T14:56:36.534964","created_date":"2025-10-10T00:00:00"}
