{"id":"https://openalex.org/W4391052015","doi":"https://doi.org/10.1093/bioinformatics/btae023","title":"Assembling spatial clustering framework for heterogeneous spatial transcriptomics data with GRAPHDeep","display_name":"Assembling spatial clustering framework for heterogeneous spatial transcriptomics data with GRAPHDeep","publication_year":2024,"publication_date":"2024-01-01","ids":{"openalex":"https://openalex.org/W4391052015","doi":"https://doi.org/10.1093/bioinformatics/btae023","pmid":"https://pubmed.ncbi.nlm.nih.gov/38243703"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae023","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae023","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae023/56254391/btae023.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/btae023/56254391/btae023.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100416715","display_name":"Teng Liu","orcid":"https://orcid.org/0000-0001-5862-0518"},"institutions":[{"id":"https://openalex.org/I158842170","display_name":"Chongqing University","ror":"https://ror.org/023rhb549","country_code":"CN","type":"education","lineage":["https://openalex.org/I158842170"]},{"id":"https://openalex.org/I50180762","display_name":"Chongqing Three Gorges University","ror":"https://ror.org/05rs3pv16","country_code":"CN","type":"education","lineage":["https://openalex.org/I50180762"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Teng Liu","raw_affiliation_strings":["Department of Chongqing Technical Innovation Center for Quality Evaluation and Identification of Authentic Medicinal Herbs , Chongqing, 400044, China","Department of Clinical Research Center (CRC), Clinical Pathology Center (CPC), Cancer Early Detection and Treatment Center (CEDTC) and Translational Medicine Research Center (TMRC), Chongqing University Three Gorges Hospital, Chongqing University , Wanzhou, Chongqing, 404000, China"],"raw_orcid":"https://orcid.org/0000-0001-5862-0518","affiliations":[{"raw_affiliation_string":"Department of Chongqing Technical Innovation Center for Quality Evaluation and Identification of Authentic Medicinal Herbs , Chongqing, 400044, China","institution_ids":[]},{"raw_affiliation_string":"Department of Clinical Research Center (CRC), Clinical Pathology Center (CPC), Cancer Early Detection and Treatment Center (CEDTC) and Translational Medicine Research Center (TMRC), Chongqing University Three Gorges Hospital, Chongqing University , Wanzhou, Chongqing, 404000, China","institution_ids":["https://openalex.org/I50180762","https://openalex.org/I158842170"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009458572","display_name":"Zhaoyu Fang","orcid":null},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhaoyu Fang","raw_affiliation_strings":["Department of Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering at Central South University , Hunan, 410083, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering at Central South University , Hunan, 410083, China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100353742","display_name":"Xin Li","orcid":"https://orcid.org/0000-0001-8140-0484"},"institutions":[{"id":"https://openalex.org/I158842170","display_name":"Chongqing University","ror":"https://ror.org/023rhb549","country_code":"CN","type":"education","lineage":["https://openalex.org/I158842170"]},{"id":"https://openalex.org/I50180762","display_name":"Chongqing Three Gorges University","ror":"https://ror.org/05rs3pv16","country_code":"CN","type":"education","lineage":["https://openalex.org/I50180762"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xin Li","raw_affiliation_strings":["Department of Chongqing Technical Innovation Center for Quality Evaluation and Identification of Authentic Medicinal Herbs , Chongqing, 400044, China","Department of Clinical Research Center (CRC), Clinical Pathology Center (CPC), Cancer Early Detection and Treatment Center (CEDTC) and Translational Medicine Research Center (TMRC), Chongqing University Three Gorges Hospital, Chongqing University , Wanzhou, Chongqing, 404000, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chongqing Technical Innovation Center for Quality Evaluation and Identification of Authentic Medicinal Herbs , Chongqing, 400044, China","institution_ids":[]},{"raw_affiliation_string":"Department of Clinical Research Center (CRC), Clinical Pathology Center (CPC), Cancer Early Detection and Treatment Center (CEDTC) and Translational Medicine Research Center (TMRC), Chongqing University Three Gorges Hospital, Chongqing University , Wanzhou, Chongqing, 404000, China","institution_ids":["https://openalex.org/I50180762","https://openalex.org/I158842170"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5105462398","display_name":"Lining Zhang","orcid":"https://orcid.org/0000-0001-7252-7168"},"institutions":[{"id":"https://openalex.org/I158842170","display_name":"Chongqing University","ror":"https://ror.org/023rhb549","country_code":"CN","type":"education","lineage":["https://openalex.org/I158842170"]},{"id":"https://openalex.org/I50180762","display_name":"Chongqing Three Gorges University","ror":"https://ror.org/05rs3pv16","country_code":"CN","type":"education","lineage":["https://openalex.org/I50180762"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lining Zhang","raw_affiliation_strings":["Department of Chongqing Technical Innovation Center for Quality Evaluation and Identification of Authentic Medicinal Herbs , Chongqing, 400044, China","Department of Clinical Research Center (CRC), Clinical Pathology Center (CPC), Cancer Early Detection and Treatment Center (CEDTC) and Translational Medicine Research Center (TMRC), Chongqing University Three Gorges Hospital, Chongqing University , Wanzhou, Chongqing, 404000, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chongqing Technical Innovation Center for Quality Evaluation and Identification of Authentic Medicinal Herbs , Chongqing, 400044, China","institution_ids":[]},{"raw_affiliation_string":"Department of Clinical Research Center (CRC), Clinical Pathology Center (CPC), Cancer Early Detection and Treatment Center (CEDTC) and Translational Medicine Research Center (TMRC), Chongqing University Three Gorges Hospital, Chongqing University , Wanzhou, Chongqing, 404000, China","institution_ids":["https://openalex.org/I50180762","https://openalex.org/I158842170"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083809384","display_name":"Dongsheng Cao","orcid":"https://orcid.org/0000-0003-3604-3785"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Dong-Sheng Cao","raw_affiliation_strings":["Department of Xiangya School of Pharmaceutical Sciences, Central South University , Changsha 410003, P.R. China"],"raw_orcid":"https://orcid.org/0000-0003-3604-3785","affiliations":[{"raw_affiliation_string":"Department of Xiangya School of Pharmaceutical Sciences, Central South University , Changsha 410003, P.R. China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100719013","display_name":"Min Li","orcid":"https://orcid.org/0000-0002-0188-1394"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Min Li","raw_affiliation_strings":["Department of Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering at Central South University , Hunan, 410083, China"],"raw_orcid":"https://orcid.org/0000-0002-0188-1394","affiliations":[{"raw_affiliation_string":"Department of Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering at Central South University , Hunan, 410083, China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5021389154","display_name":"Mingzhu Yin","orcid":"https://orcid.org/0000-0002-6964-7131"},"institutions":[{"id":"https://openalex.org/I158842170","display_name":"Chongqing University","ror":"https://ror.org/023rhb549","country_code":"CN","type":"education","lineage":["https://openalex.org/I158842170"]},{"id":"https://openalex.org/I50180762","display_name":"Chongqing Three Gorges University","ror":"https://ror.org/05rs3pv16","country_code":"CN","type":"education","lineage":["https://openalex.org/I50180762"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Mingzhu Yin","raw_affiliation_strings":["Department of Chongqing Technical Innovation Center for Quality Evaluation and Identification of Authentic Medicinal Herbs , Chongqing, 400044, China","Department of Clinical Research Center (CRC), Clinical Pathology Center (CPC), Cancer Early Detection and Treatment Center (CEDTC) and Translational Medicine Research Center (TMRC), Chongqing University Three Gorges Hospital, Chongqing University , Wanzhou, Chongqing, 404000, China"],"raw_orcid":"https://orcid.org/0000-0002-6964-7131","affiliations":[{"raw_affiliation_string":"Department of Chongqing Technical Innovation Center for Quality Evaluation and Identification of Authentic Medicinal Herbs , Chongqing, 400044, China","institution_ids":[]},{"raw_affiliation_string":"Department of Clinical Research Center (CRC), Clinical Pathology Center (CPC), Cancer Early Detection and Treatment Center (CEDTC) and Translational Medicine Research Center (TMRC), Chongqing University Three Gorges Hospital, Chongqing University , Wanzhou, Chongqing, 404000, China","institution_ids":["https://openalex.org/I50180762","https://openalex.org/I158842170"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5021389154"],"corresponding_institution_ids":["https://openalex.org/I158842170","https://openalex.org/I50180762"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.8063,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.69640897,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":98},"biblio":{"volume":"40","issue":"1","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":0.9900000095367432,"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":0.9900000095367432,"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":0.003000000026077032,"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":0.00279999990016222,"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/cluster-analysis","display_name":"Cluster analysis","score":0.7823964953422546},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6838808655738831},{"id":"https://openalex.org/keywords/spatial-analysis","display_name":"Spatial analysis","score":0.6350476145744324},{"id":"https://openalex.org/keywords/autoencoder","display_name":"Autoencoder","score":0.615114688873291},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5831173658370972},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4800361394882202},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.45402342081069946},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.4458080232143402},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3256225287914276},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.32401981949806213},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.21027922630310059},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.10549426078796387}],"concepts":[{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.7823964953422546},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6838808655738831},{"id":"https://openalex.org/C159620131","wikidata":"https://www.wikidata.org/wiki/Q1938983","display_name":"Spatial analysis","level":2,"score":0.6350476145744324},{"id":"https://openalex.org/C101738243","wikidata":"https://www.wikidata.org/wiki/Q786435","display_name":"Autoencoder","level":3,"score":0.615114688873291},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5831173658370972},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4800361394882202},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.45402342081069946},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.4458080232143402},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3256225287914276},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.32401981949806213},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.21027922630310059},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.10549426078796387},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btae023","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae023","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae023/56254391/btae023.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:38243703","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38243703","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:10832355","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10832355","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10832355/pdf/btae023.pdf","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/btae023","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae023","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae023/56254391/btae023.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/G260823480","display_name":null,"funder_award_id":"2022YFC3601800","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G5956759088","display_name":null,"funder_award_id":"KJZD-K202300105","funder_id":"https://openalex.org/F4320324805","funder_display_name":"Chongqing Municipal Education Commission"}],"funders":[{"id":"https://openalex.org/F4320324805","display_name":"Chongqing Municipal Education Commission","ror":"https://ror.org/031nm5713"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4391052015.pdf"},"referenced_works_count":27,"referenced_works":["https://openalex.org/W2800392236","https://openalex.org/W2887091285","https://openalex.org/W2897249806","https://openalex.org/W2907492528","https://openalex.org/W2923300855","https://openalex.org/W2979301772","https://openalex.org/W2999681746","https://openalex.org/W2999899884","https://openalex.org/W3093954610","https://openalex.org/W3106188259","https://openalex.org/W3108118546","https://openalex.org/W3112563877","https://openalex.org/W3147595666","https://openalex.org/W3162321577","https://openalex.org/W3165120573","https://openalex.org/W3174048442","https://openalex.org/W3181434855","https://openalex.org/W3214865687","https://openalex.org/W4210257598","https://openalex.org/W4210583065","https://openalex.org/W4221095552","https://openalex.org/W4226192560","https://openalex.org/W4281716652","https://openalex.org/W4290154117","https://openalex.org/W4306406844","https://openalex.org/W4383268677","https://openalex.org/W4390814844"],"related_works":["https://openalex.org/W3013693939","https://openalex.org/W2159052453","https://openalex.org/W2566616303","https://openalex.org/W3131327266","https://openalex.org/W2734887215","https://openalex.org/W4297051394","https://openalex.org/W2752972570","https://openalex.org/W2145836866","https://openalex.org/W2803255133","https://openalex.org/W2891286602"],"abstract_inverted_index":{"MOTIVATION:":[0],"Spatial":[1],"clustering":[2,68,99,133,145,168,181],"is":[3,91,101,128,140,183,214],"essential":[4],"and":[5,16,29,48,55,82,110,158,170],"challenging":[6],"for":[7,70,93,143,166,196,203],"spatial":[8,30,34,67,72,98,125,132,144,167,180,204,220],"transcriptomics'":[9],"data":[10,127,222],"analysis":[11],"to":[12,24,36,64,106],"unravel":[13],"tissue":[14],"microenvironment":[15],"biological":[17],"function.":[18],"Graph":[19],"neural":[20,50,85,164,175,201],"networks":[21,165],"are":[22,160,223],"promising":[23],"address":[25],"gene":[26],"expression":[27],"profiles":[28],"location":[31],"information":[32],"in":[33,131,177],"transcriptomics":[35,73],"generate":[37],"latent":[38],"representations.":[39],"However,":[40],"choosing":[41,197],"an":[42,198],"appropriate":[43,89,199],"graph":[44,49,78,84,138,149,163,174,200],"deep":[45,79,148],"learning":[46,80],"module":[47],"network":[51,176,202],"necessitates":[52],"further":[53],"exploration":[54],"investigation.":[56],"RESULTS:":[57],"In":[58],"this":[59],"article,":[60],"we":[61],"present":[62],"GRAPHDeep":[63,213],"assemble":[65],"a":[66],"framework":[69],"heterogeneous":[71],"data.":[74],"Through":[75],"integrating":[76],"2":[77],"modules":[81],"20":[83],"networks,":[86],"the":[87,118,136,161,172,178,185],"most":[88],"combination":[90],"decided":[92],"each":[94],"dataset.":[95],"The":[96,112,209,218],"constructed":[97],"method":[100],"compared":[102],"with":[103],"state-of-the-art":[104],"algorithms":[105],"demonstrate":[107],"its":[108],"effectiveness":[109],"superiority.":[111],"significant":[113],"new":[114],"findings":[115],"include:":[116],"(i)":[117],"number":[119],"of":[120,124,212],"genes":[121],"or":[122],"proteins":[123],"omics":[126,221],"quite":[129],"crucial":[130],"algorithms;":[134],"(ii)":[135],"variational":[137],"autoencoder":[139],"more":[141],"suitable":[142],"tasks":[146],"than":[147],"infomax":[150],"module;":[151],"(iii)":[152],"UniMP,":[153],"SAGE,":[154],"SuperGAT,":[155],"GATv2,":[156],"GCN,":[157],"TAG":[159],"recommended":[162],"tasks;":[169],"(iv)":[171],"used":[173],"existent":[179],"frameworks":[182],"not":[184],"best":[186],"candidate.":[187],"This":[188],"study":[189],"could":[190],"be":[191],"regarded":[192],"as":[193],"desirable":[194],"guidance":[195],"clustering.":[205],"AVAILABILITY":[206],"AND":[207],"IMPLEMENTATION:":[208],"source":[210],"code":[211],"available":[215,224],"at":[216,225],"https://github.com/narutoten520/GRAPHDeep.":[217],"studied":[219],"https://zenodo.org/record/8141084.":[226]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2}],"updated_date":"2026-06-16T07:32:37.131356","created_date":"2025-10-10T00:00:00"}
