{"id":"https://openalex.org/W4402253382","doi":"https://doi.org/10.1093/bioinformatics/btae383","title":"Predicting spatially resolved gene expression via tissue morphology using adaptive spatial GNNs","display_name":"Predicting spatially resolved gene expression via tissue morphology using adaptive spatial GNNs","publication_year":2024,"publication_date":"2024-06-19","ids":{"openalex":"https://openalex.org/W4402253382","doi":"https://doi.org/10.1093/bioinformatics/btae383","pmid":"https://pubmed.ncbi.nlm.nih.gov/39230702"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae383","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae383","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/40/Supplement_2/ii111/59017002/btae383.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/article-pdf/40/Supplement_2/ii111/59017002/btae383.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5057134657","display_name":"Tianci Song","orcid":null},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tianci Song","raw_affiliation_strings":["Department of Computer Science and Engineering, University of Minnesota , Minneapolis, MN 55455, United States","Machine Learning Department, NEC Laboratories America , Princeton, NJ 08540, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, University of Minnesota , Minneapolis, MN 55455, United States","institution_ids":["https://openalex.org/I130238516"]},{"raw_affiliation_string":"Machine Learning Department, NEC Laboratories America , Princeton, NJ 08540, United States","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012049132","display_name":"Eric Cosatto","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Eric Cosatto","raw_affiliation_strings":["Machine Learning Department, NEC Laboratories America , Princeton, NJ 08540, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Machine Learning Department, NEC Laboratories America , Princeton, NJ 08540, United States","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046849812","display_name":"Gaoyuan Wang","orcid":"https://orcid.org/0000-0003-4039-748X"},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gaoyuan Wang","raw_affiliation_strings":["Department of Molecular Biophysics and Biochemistry, Yale University , New Haven, CT 06520, United States","Program in Computational Biology and Bioinformatics, Yale University , New Haven, CT 06520, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Biophysics and Biochemistry, Yale University , New Haven, CT 06520, United States","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Program in Computational Biology and Bioinformatics, Yale University , New Haven, CT 06520, United States","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066338313","display_name":"Rui Kuang","orcid":"https://orcid.org/0000-0002-4916-903X"},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rui Kuang","raw_affiliation_strings":["Department of Computer Science and Engineering, University of Minnesota , Minneapolis, MN 55455, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, University of Minnesota , Minneapolis, MN 55455, United States","institution_ids":["https://openalex.org/I130238516"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111969129","display_name":"Mark Gerstein","orcid":null},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mark Gerstein","raw_affiliation_strings":["Department of Biomedical Informatics and Data Science, Yale University , New Haven, CT 06520, USA","Department of Computer Science, Yale University , New Haven, CT 06520, USA","Department of Molecular Biophysics and Biochemistry, Yale University , New Haven, CT 06520, United States","Department of Statistics and Data Science, Yale University , New Haven, CT 06520, USA","Program in Computational Biology and Bioinformatics, Yale University , New Haven, CT 06520, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics and Data Science, Yale University , New Haven, CT 06520, USA","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Department of Computer Science, Yale University , New Haven, CT 06520, USA","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Department of Molecular Biophysics and Biochemistry, Yale University , New Haven, CT 06520, United States","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Department of Statistics and Data Science, Yale University , New Haven, CT 06520, USA","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Program in Computational Biology and Bioinformatics, Yale University , New Haven, CT 06520, United States","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065576006","display_name":"Martin Renqiang Min","orcid":"https://orcid.org/0000-0002-8563-6133"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Martin Renqiang Min","raw_affiliation_strings":["Machine Learning Department, NEC Laboratories America , Princeton, NJ 08540, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Machine Learning Department, NEC Laboratories America , Princeton, NJ 08540, United States","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5077980658","display_name":"Jonathan Warrell","orcid":"https://orcid.org/0000-0002-1323-4602"},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jonathan Warrell","raw_affiliation_strings":["Department of Molecular Biophysics and Biochemistry, Yale University , New Haven, CT 06520, United States","Machine Learning Department, NEC Laboratories America , Princeton, NJ 08540, United States","Program in Computational Biology and Bioinformatics, Yale University , New Haven, CT 06520, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Biophysics and Biochemistry, Yale University , New Haven, CT 06520, United States","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Machine Learning Department, NEC Laboratories America , Princeton, NJ 08540, United States","institution_ids":[]},{"raw_affiliation_string":"Program in Computational Biology and Bioinformatics, Yale University , New Haven, CT 06520, United States","institution_ids":["https://openalex.org/I32971472"]}]}],"institutions":[],"countries_distinct_count":1,"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":1.4929,"has_fulltext":true,"cited_by_count":8,"citation_normalized_percentile":{"value":0.82136425,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":98},"biblio":{"volume":"40","issue":"Supplement_2","first_page":"ii111","last_page":"ii119"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.8634999990463257,"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":0.8634999990463257,"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/T10862","display_name":"AI in cancer detection","score":0.057999998331069946,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.02370000071823597,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/scalability","display_name":"Scalability","score":0.5719104409217834},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5506507754325867},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5097936987876892},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.4986915588378906},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.48318925499916077},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4176121652126312},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3523186445236206},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3312429189682007},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1485983431339264},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.07059508562088013}],"concepts":[{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.5719104409217834},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5506507754325867},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5097936987876892},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.4986915588378906},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.48318925499916077},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4176121652126312},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3523186445236206},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3312429189682007},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1485983431339264},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.07059508562088013}],"mesh":[{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":true},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":true},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":true},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":true},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":true},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","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":"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":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","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":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btae383","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae383","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/40/Supplement_2/ii111/59017002/btae383.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:39230702","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39230702","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:11373608","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11373608","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11373608/pdf/btae383.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/btae383","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae383","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/40/Supplement_2/ii111/59017002/btae383.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":[{"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure","score":0.5099999904632568}],"awards":[{"id":"https://openalex.org/G1020436016","display_name":"IIBR Informatics: Mining Spatial and Single-cell Transcriptomes to Understand Cell Locality and Heterogeneity in Tissues","funder_award_id":"2042159","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3790745846","display_name":null,"funder_award_id":"#2042159","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320330987","display_name":"Israel Institute for Biological Research","ror":"https://ror.org/05atez085"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4402253382.pdf","grobid_xml":"https://content.openalex.org/works/W4402253382.grobid-xml"},"referenced_works_count":12,"referenced_works":["https://openalex.org/W2158485828","https://openalex.org/W2165232124","https://openalex.org/W2533012945","https://openalex.org/W2898459842","https://openalex.org/W3001833132","https://openalex.org/W3021920958","https://openalex.org/W3036882247","https://openalex.org/W3203689742","https://openalex.org/W3205213119","https://openalex.org/W4220897949","https://openalex.org/W4285803722","https://openalex.org/W4324046169"],"related_works":["https://openalex.org/W2399513595","https://openalex.org/W4388386498","https://openalex.org/W2028462563","https://openalex.org/W2982720988","https://openalex.org/W3150324899","https://openalex.org/W2803323662","https://openalex.org/W3032874291","https://openalex.org/W2005057264","https://openalex.org/W2363156284","https://openalex.org/W2415025170"],"abstract_inverted_index":{"MOTIVATION:":[0],"Spatial":[1],"transcriptomics":[2],"technologies,":[3],"which":[4],"generate":[5],"a":[6,72,84],"spatial":[7,59,93,134],"map":[8],"of":[9,16,95,136],"gene":[10,60],"activity,":[11],"can":[12,128],"deepen":[13],"the":[14,28,63,92,117,122],"understanding":[15],"tissue":[17,68,78,100],"architecture":[18],"and":[19,25,48,54,124],"its":[20],"molecular":[21],"underpinnings":[22],"in":[23,37,51,67],"health":[24],"disease.":[26],"However,":[27],"high":[29],"cost":[30],"makes":[31],"these":[32],"technologies":[33],"difficult":[34],"to":[35,76,90,121,131],"use":[36],"practice.":[38],"Histological":[39],"images":[40,70],"co-registered":[41],"with":[42],"targeted":[43],"tissues":[44],"are":[45],"more":[46],"affordable":[47],"routinely":[49],"generated":[50],"many":[52],"research":[53],"clinical":[55],"studies.":[56],"Hence,":[57],"predicting":[58],"expression":[61,94],"from":[62,99],"morphological":[64],"clues":[65],"embedded":[66],"histological":[69,101],"provides":[71],"scalable":[73],"alternative":[74],"approach":[75],"decoding":[77],"complexity.":[79],"RESULTS:":[80],"Here,":[81],"we":[82],"present":[83],"graph":[85],"neural":[86],"network":[87],"based":[88],"framework":[89],"predict":[91],"highly":[96],"expressed":[97],"genes":[98],"images.":[102],"Extensive":[103],"experiments":[104],"on":[105],"two":[106],"separate":[107],"breast":[108],"cancer":[109],"data":[110],"cohorts":[111],"demonstrate":[112],"that":[113,125],"our":[114,126],"method":[115],"improves":[116],"prediction":[118],"performance":[119],"compared":[120],"state-of-the-art,":[123],"model":[127],"be":[129],"used":[130],"better":[132],"delineate":[133],"domains":[135],"biological":[137],"interest.":[138],"AVAILABILITY":[139],"AND":[140],"IMPLEMENTATION:":[141],"https://github.com/song0309/asGNN/.":[142]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":3}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}