{"id":"https://openalex.org/W7162299751","doi":"https://doi.org/10.1093/bioinformatics/btag333","title":"A masked generative graph representation learning framework empowering precise spatial domain identification","display_name":"A masked generative graph representation learning framework empowering precise spatial domain identification","publication_year":2026,"publication_date":"2026-05-21","ids":{"openalex":"https://openalex.org/W7162299751","doi":"https://doi.org/10.1093/bioinformatics/btag333","pmid":"https://pubmed.ncbi.nlm.nih.gov/42178226"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btag333","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag333","pdf_url":null,"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://doi.org/10.1093/bioinformatics/btag333","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5081411764","display_name":"C. Wang","orcid":null},"institutions":[{"id":"https://openalex.org/I194450716","display_name":"Jilin University","ror":"https://ror.org/00js3aw79","country_code":"CN","type":"education","lineage":["https://openalex.org/I194450716"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chuyao Wang","raw_affiliation_strings":["Key Laboratory of Symbolic Computation and Knowledge Engineering of the Ministry of Education, College of Computer Science and Technology, Jilin University , Changchun, 130012,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory of Symbolic Computation and Knowledge Engineering of the Ministry of Education, College of Computer Science and Technology, Jilin University , Changchun, 130012,","institution_ids":["https://openalex.org/I194450716"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019382560","display_name":"Tongdong Zhang","orcid":"https://orcid.org/0000-0003-4347-7346"},"institutions":[{"id":"https://openalex.org/I4210121447","display_name":"Center for Excellence in Molecular Cell Science","ror":"https://ror.org/02rrdvm96","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210121447"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Tongdong Zhang","raw_affiliation_strings":["State Key Laboratory of Cell Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences , Shanghai, 200031,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Cell Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences , Shanghai, 200031,","institution_ids":["https://openalex.org/I4210121447"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5136921099","display_name":"Hang Sun","orcid":null},"institutions":[{"id":"https://openalex.org/I194450716","display_name":"Jilin University","ror":"https://ror.org/00js3aw79","country_code":"CN","type":"education","lineage":["https://openalex.org/I194450716"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hang Sun","raw_affiliation_strings":["Key Laboratory of Symbolic Computation and Knowledge Engineering of the Ministry of Education, College of Computer Science and Technology, Jilin University , Changchun, 130012,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory of Symbolic Computation and Knowledge Engineering of the Ministry of Education, College of Computer Science and Technology, Jilin University , Changchun, 130012,","institution_ids":["https://openalex.org/I194450716"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103407122","display_name":"Z W Wu","orcid":null},"institutions":[{"id":"https://openalex.org/I194450716","display_name":"Jilin University","ror":"https://ror.org/00js3aw79","country_code":"CN","type":"education","lineage":["https://openalex.org/I194450716"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhipeng Wu","raw_affiliation_strings":["Key Laboratory of Symbolic Computation and Knowledge Engineering of the Ministry of Education, College of Computer Science and Technology, Jilin University , Changchun, 130012,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory of Symbolic Computation and Knowledge Engineering of the Ministry of Education, College of Computer Science and Technology, Jilin University , Changchun, 130012,","institution_ids":["https://openalex.org/I194450716"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5119247396","display_name":"Shuo Liang","orcid":"https://orcid.org/0009-0009-7115-5433"},"institutions":[{"id":"https://openalex.org/I194450716","display_name":"Jilin University","ror":"https://ror.org/00js3aw79","country_code":"CN","type":"education","lineage":["https://openalex.org/I194450716"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shuo Liang","raw_affiliation_strings":["Key Laboratory of Symbolic Computation and Knowledge Engineering of the Ministry of Education, College of Computer Science and Technology, Jilin University , Changchun, 130012,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory of Symbolic Computation and Knowledge Engineering of the Ministry of Education, College of Computer Science and Technology, Jilin University , Changchun, 130012,","institution_ids":["https://openalex.org/I194450716"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5136919627","display_name":"Xueting Wang","orcid":null},"institutions":[{"id":"https://openalex.org/I194450716","display_name":"Jilin University","ror":"https://ror.org/00js3aw79","country_code":"CN","type":"education","lineage":["https://openalex.org/I194450716"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xueting Wang","raw_affiliation_strings":["Key Laboratory of Symbolic Computation and Knowledge Engineering of the Ministry of Education, College of Computer Science and Technology, Jilin University , Changchun, 130012,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory of Symbolic Computation and Knowledge Engineering of the Ministry of Education, College of Computer Science and Technology, Jilin University , Changchun, 130012,","institution_ids":["https://openalex.org/I194450716"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5136205796","display_name":"Meirong Du","orcid":null},"institutions":[{"id":"https://openalex.org/I4210153623","display_name":"Shanghai First Maternity and Infant Hospital","ror":"https://ror.org/05myyzn85","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210153623"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Meirong Du","raw_affiliation_strings":["Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University , Shanghai, 201204,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University , Shanghai, 201204,","institution_ids":["https://openalex.org/I4210153623"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5136976061","display_name":"Yanchun Liang","orcid":null},"institutions":[{"id":"https://openalex.org/I194450716","display_name":"Jilin University","ror":"https://ror.org/00js3aw79","country_code":"CN","type":"education","lineage":["https://openalex.org/I194450716"]},{"id":"https://openalex.org/I4210165204","display_name":"Zhuhai Institute of Advanced Technology","ror":"https://ror.org/05r1mzq61","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210145761","https://openalex.org/I4210165204"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yanchun Liang","raw_affiliation_strings":["Key Laboratory of Symbolic Computation and Knowledge Engineering of the Ministry of Education, College of Computer Science and Technology, Jilin University , Changchun, 130012,","Zhuhai Sub Laboratory of Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Zhuhai College of Science and Technology , Zhuhai, 519041,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory of Symbolic Computation and Knowledge Engineering of the Ministry of Education, College of Computer Science and Technology, Jilin University , Changchun, 130012,","institution_ids":["https://openalex.org/I194450716"]},{"raw_affiliation_string":"Zhuhai Sub Laboratory of Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Zhuhai College of Science and Technology , Zhuhai, 519041,","institution_ids":["https://openalex.org/I4210165204"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5136956033","display_name":"Xin Gao","orcid":null},"institutions":[{"id":"https://openalex.org/I71920554","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38","country_code":"SA","type":"education","lineage":["https://openalex.org/I71920554"]}],"countries":["SA"],"is_corresponding":false,"raw_author_name":"Xin Gao","raw_affiliation_strings":["King Abdullah University of Science and Technology, Mathematical and Computer Science and Engineering Division, King Abdullah University of Science and Technology (KAUST) , Thuwal, 23955-6900,"],"raw_orcid":"https://orcid.org/0000-0002-7108-3574","affiliations":[{"raw_affiliation_string":"King Abdullah University of Science and Technology, Mathematical and Computer Science and Engineering Division, King Abdullah University of Science and Technology (KAUST) , Thuwal, 23955-6900,","institution_ids":["https://openalex.org/I71920554"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5136903856","display_name":"Qi Tang","orcid":null},"institutions":[{"id":"https://openalex.org/I4210121447","display_name":"Center for Excellence in Molecular Cell Science","ror":"https://ror.org/02rrdvm96","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210121447"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qi Tang","raw_affiliation_strings":["State Key Laboratory of Cell Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences , Shanghai, 200031,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Cell Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences , Shanghai, 200031,","institution_ids":["https://openalex.org/I4210121447"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5136929459","display_name":"Dong Xu","orcid":null},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dong Xu","raw_affiliation_strings":["Department of Electrical Engineering and Computer Science, Bond Life Sciences Center, University of Missouri , Columbia, MO 65211,"],"raw_orcid":"https://orcid.org/0000-0002-4809-0514","affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering and Computer Science, Bond Life Sciences Center, University of Missouri , Columbia, MO 65211,","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052831869","display_name":"Xiaoyue Feng","orcid":"https://orcid.org/0000-0003-3954-1333"},"institutions":[{"id":"https://openalex.org/I194450716","display_name":"Jilin University","ror":"https://ror.org/00js3aw79","country_code":"CN","type":"education","lineage":["https://openalex.org/I194450716"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xiaoyue Feng","raw_affiliation_strings":["Key Laboratory of Symbolic Computation and Knowledge Engineering of the Ministry of Education, College of Computer Science and Technology, Jilin University , Changchun, 130012,"],"raw_orcid":"https://orcid.org/0000-0003-3954-1333","affiliations":[{"raw_affiliation_string":"Key Laboratory of Symbolic Computation and Knowledge Engineering of the Ministry of Education, College of Computer Science and Technology, Jilin University , Changchun, 130012,","institution_ids":["https://openalex.org/I194450716"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068803346","display_name":"An Zeng","orcid":"https://orcid.org/0000-0002-8730-1011"},"institutions":[{"id":"https://openalex.org/I4210121447","display_name":"Center for Excellence in Molecular Cell Science","ror":"https://ror.org/02rrdvm96","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210121447"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"An Zeng","raw_affiliation_strings":["State Key Laboratory of Cell Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences , Shanghai, 200031,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Cell Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences , Shanghai, 200031,","institution_ids":["https://openalex.org/I4210121447"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5136899148","display_name":"Renchu Guan","orcid":null},"institutions":[{"id":"https://openalex.org/I194450716","display_name":"Jilin University","ror":"https://ror.org/00js3aw79","country_code":"CN","type":"education","lineage":["https://openalex.org/I194450716"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Renchu Guan","raw_affiliation_strings":["Key Laboratory of Symbolic Computation and Knowledge Engineering of the Ministry of Education, College of Computer Science and Technology, Jilin University , Changchun, 130012,"],"raw_orcid":"https://orcid.org/0000-0002-7162-7826","affiliations":[{"raw_affiliation_string":"Key Laboratory of Symbolic Computation and Knowledge Engineering of the Ministry of Education, College of Computer Science and Technology, Jilin University , Changchun, 130012,","institution_ids":["https://openalex.org/I194450716"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5052831869","https://openalex.org/A5068803346","https://openalex.org/A5136899148"],"corresponding_institution_ids":["https://openalex.org/I194450716","https://openalex.org/I4210121447"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.61539425,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"42","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":0.9918000102043152,"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":0.9918000102043152,"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":0.0015999999595806003,"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/T11677","display_name":"Congenital heart defects research","score":0.0013000000035390258,"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/domain","display_name":"Domain (mathematical analysis)","score":0.5562000274658203},{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.5393999814987183},{"id":"https://openalex.org/keywords/generative-grammar","display_name":"Generative grammar","score":0.5152000188827515},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5142999887466431},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5103999972343445},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.5016999840736389},{"id":"https://openalex.org/keywords/spatial-analysis","display_name":"Spatial analysis","score":0.4747999906539917},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.4690999984741211},{"id":"https://openalex.org/keywords/feature-learning","display_name":"Feature learning","score":0.4560999870300293}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7452999949455261},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.5562000274658203},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5447999835014343},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.5393999814987183},{"id":"https://openalex.org/C39890363","wikidata":"https://www.wikidata.org/wiki/Q36108","display_name":"Generative grammar","level":2,"score":0.5152000188827515},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5142999887466431},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5103999972343445},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.5016999840736389},{"id":"https://openalex.org/C159620131","wikidata":"https://www.wikidata.org/wiki/Q1938983","display_name":"Spatial analysis","level":2,"score":0.4747999906539917},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.4690999984741211},{"id":"https://openalex.org/C59404180","wikidata":"https://www.wikidata.org/wiki/Q17013334","display_name":"Feature learning","level":2,"score":0.4560999870300293},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4284000098705292},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.414000004529953},{"id":"https://openalex.org/C167966045","wikidata":"https://www.wikidata.org/wiki/Q5532625","display_name":"Generative model","level":3,"score":0.3970000147819519},{"id":"https://openalex.org/C2777402240","wikidata":"https://www.wikidata.org/wiki/Q6783436","display_name":"Masking (illustration)","level":2,"score":0.384799987077713},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3472000062465668},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.3379000127315521},{"id":"https://openalex.org/C116409475","wikidata":"https://www.wikidata.org/wiki/Q1385056","display_name":"External Data Representation","level":2,"score":0.3377000093460083},{"id":"https://openalex.org/C64754055","wikidata":"https://www.wikidata.org/wiki/Q7574053","display_name":"Spatial contextual awareness","level":2,"score":0.33239999413490295},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.31119999289512634},{"id":"https://openalex.org/C207685749","wikidata":"https://www.wikidata.org/wiki/Q2088941","display_name":"Domain knowledge","level":2,"score":0.29429998993873596},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.2761000096797943},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.27480000257492065},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.26739999651908875},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.26100000739097595}],"mesh":[{"descriptor_ui":"D000098409","descriptor_name":"Representation Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098409","descriptor_name":"Representation Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098842","descriptor_name":"Generative Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098842","descriptor_name":"Generative Artificial Intelligence","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":false},{"descriptor_ui":"D000099285","descriptor_name":"Spatial Transcriptomics","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btag333","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag333","pdf_url":null,"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:42178226","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42178226","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:13263152","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13263152/","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/btag333","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag333","pdf_url":null,"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":[{"score":0.5531015992164612,"id":"https://metadata.un.org/sdg/1","display_name":"No poverty"}],"awards":[{"id":"https://openalex.org/G2929457652","display_name":null,"funder_award_id":"2020A0505100018","funder_id":"https://openalex.org/F4320335795","funder_display_name":"Science and Technology Planning Project of Guangdong Province"},{"id":"https://openalex.org/G3095911524","display_name":null,"funder_award_id":"62372494","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5022398162","display_name":null,"funder_award_id":"62372209","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8439938051","display_name":null,"funder_award_id":"20200708112YY","funder_id":"https://openalex.org/F4320335795","funder_display_name":"Science and Technology Planning Project of Guangdong Province"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320335795","display_name":"Science and Technology Planning Project of Guangdong Province","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":27,"referenced_works":["https://openalex.org/W2073654208","https://openalex.org/W2533012945","https://openalex.org/W2616922646","https://openalex.org/W2800392236","https://openalex.org/W2996171578","https://openalex.org/W3036371598","https://openalex.org/W3108118546","https://openalex.org/W3112563877","https://openalex.org/W3126958162","https://openalex.org/W3132661792","https://openalex.org/W3134482219","https://openalex.org/W3164692211","https://openalex.org/W3165120573","https://openalex.org/W3196495189","https://openalex.org/W4226192560","https://openalex.org/W4229033508","https://openalex.org/W4285388882","https://openalex.org/W4290154117","https://openalex.org/W4306406844","https://openalex.org/W4308052489","https://openalex.org/W4322738920","https://openalex.org/W4362469659","https://openalex.org/W4388997570","https://openalex.org/W4390814844","https://openalex.org/W4406632986","https://openalex.org/W4409449054","https://openalex.org/W4417497709"],"related_works":[],"abstract_inverted_index":{"MOTIVATION:":[0],"Spatial":[1],"transcriptomics":[2],"(ST)":[3],"enables":[4],"the":[5,12,18,35],"measurement":[6],"of":[7,15,20,27,83],"gene":[8,28],"expression":[9,29],"while":[10],"preserving":[11],"spatial":[13,31,71,101],"context":[14],"tissues.":[16],"However,":[17],"sparsity":[19],"ST":[21,59,128],"data":[22,60],"leads":[23],"to":[24,66,91,126],"poor":[25],"usage":[26],"and":[30,42,103,121],"information,":[32],"resulting":[33],"in":[34,112],"embeddings":[36],"that":[37,61],"are":[38],"not":[39],"well":[40],"represented":[41],"challenging":[43],"for":[44,58],"downstream":[45],"analyses.":[46],"RESULTS:":[47],"Here,":[48],"we":[49,88],"introduced":[50],"GSG,":[51],"a":[52,63],"generative":[53],"self-supervised":[54],"representation":[55],"learning":[56],"framework":[57],"leverages":[62],"masking":[64],"mechanism":[65],"learn":[67],"informative":[68],"representations.":[69],"For":[70],"domain":[72],"identification,":[73],"GSG":[74,90],"consistently":[75],"outperformed":[76],"state-of-the-art":[77],"methods":[78],"across":[79],"benchmarking":[80],"datasets,":[81],"regardless":[82],"sequencing":[84],"platforms.":[85],"In":[86],"addition,":[87],"applied":[89],"an":[92,107],"in-house":[93],"human":[94],"fetal":[95],"heart":[96,114],"dataset,":[97],"revealing":[98],"anatomically":[99],"coherent":[100],"domains":[102],"identifying":[104],"APCDD1":[105],"as":[106],"endocardial-specific":[108],"marker":[109],"potentially":[110],"involved":[111],"congenital":[113],"disease.":[115],"Our":[116,133],"results":[117],"showcase":[118],"GSG's":[119],"superiority":[120],"underscore":[122],"its":[123],"valuable":[124],"contributions":[125],"advancing":[127],"analysis.":[129],"AVAILABILITY":[130],"AND":[131],"IMPLEMENTATION:":[132],"software":[134],"package":[135],"is":[136],"available":[137],"at":[138],"https://github.com/keaml-Guan/GSG.":[139]},"counts_by_year":[],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2026-05-26T00:00:00"}
