{"id":"https://openalex.org/W4411279214","doi":"https://doi.org/10.1093/bioinformatics/btaf350","title":"Gene spatial integration: enhancing spatial transcriptomics analysis via deep learning and batch effect mitigation","display_name":"Gene spatial integration: enhancing spatial transcriptomics analysis via deep learning and batch effect mitigation","publication_year":2025,"publication_date":"2025-06-01","ids":{"openalex":"https://openalex.org/W4411279214","doi":"https://doi.org/10.1093/bioinformatics/btaf350","pmid":"https://pubmed.ncbi.nlm.nih.gov/40511994"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf350","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf350","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf350/63484357/btaf350.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf350/63484357/btaf350.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5017229179","display_name":"Rian Pratama","orcid":"https://orcid.org/0009-0000-8142-7126"},"institutions":[{"id":"https://openalex.org/I4921948","display_name":"Pusan National University","ror":"https://ror.org/01an57a31","country_code":"KR","type":"education","lineage":["https://openalex.org/I4921948"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Rian Pratama","raw_affiliation_strings":["School of Computer Science and Engineering, Pusan National University , Busan 46241,","School of Computer Science and Engineering, Pusan National University, Busan 46241, South Korea"],"raw_orcid":"https://orcid.org/0009-0000-8142-7126","affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Pusan National University , Busan 46241,","institution_ids":["https://openalex.org/I4921948"]},{"raw_affiliation_string":"School of Computer Science and Engineering, Pusan National University, Busan 46241, South Korea","institution_ids":["https://openalex.org/I4921948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026672731","display_name":"Jason Hilton","orcid":"https://orcid.org/0000-0003-0286-8236"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jason Hilton","raw_affiliation_strings":["Department of Genetics, School of Medicine, Stanford University , Stanford, CA 94304,","Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94304, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genetics, School of Medicine, Stanford University , Stanford, CA 94304,","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94304, United States","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058567429","display_name":"J. Michael Cherry","orcid":"https://orcid.org/0000-0001-9163-5180"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"J Michael Cherry","raw_affiliation_strings":["Department of Genetics, School of Medicine, Stanford University , Stanford, CA 94304,","Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94304, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genetics, School of Medicine, Stanford University , Stanford, CA 94304,","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94304, United States","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5012853928","display_name":"Giltae Song","orcid":"https://orcid.org/0000-0001-8796-4678"},"institutions":[{"id":"https://openalex.org/I4921948","display_name":"Pusan National University","ror":"https://ror.org/01an57a31","country_code":"KR","type":"education","lineage":["https://openalex.org/I4921948"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Giltae Song","raw_affiliation_strings":["Center for Artificial Intelligence Research, Pusan National University , Busan 46241,","School of Computer Science and Engineering, Pusan National University , Busan 46241,","Center for Artificial Intelligence Research, Pusan National University, Busan 46241, South Korea"],"raw_orcid":"https://orcid.org/0000-0001-8796-4678","affiliations":[{"raw_affiliation_string":"Center for Artificial Intelligence Research, Pusan National University , Busan 46241,","institution_ids":["https://openalex.org/I4921948"]},{"raw_affiliation_string":"School of Computer Science and Engineering, Pusan National University , Busan 46241,","institution_ids":["https://openalex.org/I4921948"]},{"raw_affiliation_string":"Center for Artificial Intelligence Research, Pusan National University, Busan 46241, South Korea","institution_ids":["https://openalex.org/I4921948"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.4604,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.81344172,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":98},"biblio":{"volume":"41","issue":"6","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":0.9973000288009644,"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":0.9973000288009644,"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":0.0006000000284984708,"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":0.00039999998989515007,"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":0.5946685075759888},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.4912261366844177},{"id":"https://openalex.org/keywords/spatial-learning","display_name":"Spatial learning","score":0.4359416365623474},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4030296206474304},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3846486806869507},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.30253657698631287},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.25358203053474426},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.18901842832565308},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1730678379535675},{"id":"https://openalex.org/keywords/neuroscience","display_name":"Neuroscience","score":0.08346468210220337}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5946685075759888},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.4912261366844177},{"id":"https://openalex.org/C2985665543","wikidata":"https://www.wikidata.org/wiki/Q3560550","display_name":"Spatial learning","level":3,"score":0.4359416365623474},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4030296206474304},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3846486806869507},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.30253657698631287},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.25358203053474426},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.18901842832565308},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1730678379535675},{"id":"https://openalex.org/C169760540","wikidata":"https://www.wikidata.org/wiki/Q207011","display_name":"Neuroscience","level":1,"score":0.08346468210220337},{"id":"https://openalex.org/C2781161787","wikidata":"https://www.wikidata.org/wiki/Q48360","display_name":"Hippocampus","level":2,"score":0.0}],"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":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","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":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","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":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","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},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaf350","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf350","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf350/63484357/btaf350.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40511994","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40511994","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:12208067","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12208067","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_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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf350","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf350","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf350/63484357/btaf350.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1790733727","display_name":null,"funder_award_id":"IITP-2025-RS-2023-00254177","funder_id":"https://openalex.org/F4320335489","funder_display_name":"Institute for Information and Communications Technology Promotion"},{"id":"https://openalex.org/G4282018984","display_name":null,"funder_award_id":"IITP-2025-RS-2023-00254177","funder_id":"https://openalex.org/F4320328359","funder_display_name":"Ministry of Science and ICT, South Korea"}],"funders":[{"id":"https://openalex.org/F4320320671","display_name":"National Research Foundation","ror":"https://ror.org/05s0g1g46"},{"id":"https://openalex.org/F4320321284","display_name":"Pusan National University","ror":"https://ror.org/01an57a31"},{"id":"https://openalex.org/F4320322120","display_name":"National Research Foundation of Korea","ror":"https://ror.org/013aysd81"},{"id":"https://openalex.org/F4320328359","display_name":"Ministry of Science and ICT, South Korea","ror":"https://ror.org/01wpjm123"},{"id":"https://openalex.org/F4320335489","display_name":"Institute for Information and Communications Technology Promotion","ror":"https://ror.org/01g0hqq23"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4411279214.pdf","grobid_xml":"https://content.openalex.org/works/W4411279214.grobid-xml"},"referenced_works_count":43,"referenced_works":["https://openalex.org/W2069089843","https://openalex.org/W2107665951","https://openalex.org/W2471536144","https://openalex.org/W2533012945","https://openalex.org/W2572375651","https://openalex.org/W2735582123","https://openalex.org/W2805650303","https://openalex.org/W2889326414","https://openalex.org/W2915848182","https://openalex.org/W2948321041","https://openalex.org/W2952383043","https://openalex.org/W2970845521","https://openalex.org/W2977083349","https://openalex.org/W2989830005","https://openalex.org/W3002417351","https://openalex.org/W3002674187","https://openalex.org/W3004640473","https://openalex.org/W3033415403","https://openalex.org/W3036371598","https://openalex.org/W3046027728","https://openalex.org/W3080668573","https://openalex.org/W3100967665","https://openalex.org/W3108118546","https://openalex.org/W3113044156","https://openalex.org/W3126958162","https://openalex.org/W3134482219","https://openalex.org/W3167327839","https://openalex.org/W3178914557","https://openalex.org/W3190202966","https://openalex.org/W3202325557","https://openalex.org/W3203364159","https://openalex.org/W3210002151","https://openalex.org/W4220765701","https://openalex.org/W4225598893","https://openalex.org/W4226192560","https://openalex.org/W4281716652","https://openalex.org/W4283704002","https://openalex.org/W4295750920","https://openalex.org/W4300862018","https://openalex.org/W4306194402","https://openalex.org/W4322738920","https://openalex.org/W4390814844","https://openalex.org/W4392956052"],"related_works":["https://openalex.org/W2399513595","https://openalex.org/W4388386498","https://openalex.org/W2028462563","https://openalex.org/W2982720988","https://openalex.org/W4388725868","https://openalex.org/W2104762330","https://openalex.org/W4379374180","https://openalex.org/W2523545060","https://openalex.org/W4229998356","https://openalex.org/W4392059188"],"abstract_inverted_index":{"MOTIVATION:":[0],"Spatial":[1,121],"transcriptomics":[2],"(ST)":[3],"is":[4,35,292],"a":[5,16,72,92,124,129,245,279],"groundbreaking":[6],"technique":[7],"for":[8,43,96,172],"studying":[9],"the":[10,78,104,135,141,159,182,185,192,198,208,211,217,227,240,260,269],"correlation":[11],"between":[12],"cellular":[13],"organization":[14],"within":[15],"tissue":[17,284],"and":[18,21,33,67,273],"its":[19],"physiological":[20],"pathological":[22],"properties.":[23],"Every":[24],"facet":[25],"of":[26,138,161,175,184,194,210,213,242,262,271,290],"spatial":[27,136,156,162,265],"information,":[28],"including":[29],"cell/spot":[30],"proximity,":[31],"distribution,":[32],"dimensionality,":[34],"significant.":[36],"Most":[37],"methods":[38],"lean":[39],"heavily":[40],"on":[41,103,197],"proximity":[42],"ST":[44,100,186],"analysis,":[45],"each":[46],"resulting":[47],"in":[48,222,250,277,282],"useful":[49],"insights":[50],"but":[51],"still":[52],"leaving":[53],"other":[54],"aspects":[55],"untapped.":[56],"In":[57],"addition,":[58],"samples":[59,177],"procured":[60],"at":[61,294],"different":[62,65,69],"times,":[63],"by":[64,68,82],"donors,":[66],"technologies":[70],"introduce":[71],"batch":[73,274],"effects":[74],"problem":[75],"that":[76],"hinders":[77],"statistical":[79],"approach":[80,132,170],"employed":[81],"most":[83,218],"analysis":[84,114,188,281],"tools.":[85,115],"Addressing":[86],"these":[87],"challenges,":[88],"we":[89],"have":[90],"developed":[91],"deep":[93],"learning":[94,131],"method":[95,109,196,205],"analyzing":[97],"integrated":[98],"multiple":[99,176],"data,":[101],"focusing":[102],"distribution":[105,137,264],"aspect.":[106],"Furthermore,":[107],"our":[108,195,237],"aims":[110],"to":[111,133,154,232,255],"leverage":[112],"single-cell":[113],"RESULTS:":[116],"Our":[117,169,204],"study":[118],"introduces":[119],"Gene":[120],"Integration":[122],"(GSI),":[123],"data":[125,187],"integration":[126,174,272],"pipeline":[127,238],"utilizing":[128],"representation":[130],"extract":[134,155],"genes":[139],"into":[140,164],"same":[142],"feature":[143,167],"space":[144],"as":[145],"gene":[146,165,263],"expression":[147,166],"features.":[148],"We":[149,190,234],"employ":[150],"an":[151],"autoencoder":[152],"network":[153],"embedding,":[157],"facilitating":[158],"projection":[160],"features":[163],"space.":[168],"allows":[171],"seamless":[173],"with":[178,216,239],"minimum":[179],"detriment,":[180],"increasing":[181],"performance":[183,209],"tool.":[189],"show":[191],"application":[193],"human":[199],"dorsolateral":[200],"prefrontal":[201],"cortex":[202],"dataset.":[203],"consistently":[206],"improves":[207],"clustering":[212,241],"Seurat":[214],"tools,":[215],"significant":[219],"increase":[220],"observed":[221],"sample":[223,251],"151673,":[224],"almost":[225],"doubling":[226],"ARI":[228,248],"score":[229,249],"from":[230,253],"0.225":[231],"0.405.":[233],"also":[235,267],"combine":[236],"GraphST,":[243],"achieving":[244],"significantly":[246],"higher":[247],"151672":[252],"0.614":[254],"0.795.":[256],"This":[257],"result":[258],"reveals":[259],"potential":[261],"aspect,":[266],"emphasizes":[268],"impact":[270],"effect":[275],"removal":[276],"developing":[278],"refined":[280],"understanding":[283],"characteristics.":[285],"AVAILABILITY":[286],"AND":[287],"IMPLEMENTATION:":[288],"Implementation":[289],"GSI":[291],"accessible":[293],"https://github.com/Riandanis/Spatial_Integration_GSI.":[295]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
