{"id":"https://openalex.org/W4409383239","doi":"https://doi.org/10.1093/bioinformatics/btaf160","title":"GeOKG: geometry-aware knowledge graph embedding for Gene Ontology and genes","display_name":"GeOKG: geometry-aware knowledge graph embedding for Gene Ontology and genes","publication_year":2025,"publication_date":"2025-03-29","ids":{"openalex":"https://openalex.org/W4409383239","doi":"https://doi.org/10.1093/bioinformatics/btaf160","pmid":"https://pubmed.ncbi.nlm.nih.gov/40217132"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf160","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf160","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf160/62916774/btaf160.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/btaf160/62916774/btaf160.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5007184675","display_name":"Chang-Uk Jeong","orcid":null},"institutions":[{"id":"https://openalex.org/I1333153716","display_name":"University City Science Center","ror":"https://ror.org/00s5a4h94","country_code":"US","type":"facility","lineage":["https://openalex.org/I1333153716"]},{"id":"https://openalex.org/I57664883","display_name":"Ajou University","ror":"https://ror.org/03tzb2h73","country_code":"KR","type":"education","lineage":["https://openalex.org/I57664883"]},{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["KR","US"],"is_corresponding":false,"raw_author_name":"Chang-Uk Jeong","raw_affiliation_strings":["Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA 19104,","Department of Software and Computer Engineering, Ajou University , Suwon, 16499, South","Institute for Biomedical Informatics, University of Pennsylvania , Philadelphia, PA 19104,","University of Pennsylvania Department of Biostatistics, Epidemiology, and Informatics, , PA 19104,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA 19104,","institution_ids":["https://openalex.org/I79576946"]},{"raw_affiliation_string":"Department of Software and Computer Engineering, Ajou University , Suwon, 16499, South","institution_ids":["https://openalex.org/I57664883"]},{"raw_affiliation_string":"Institute for Biomedical Informatics, University of Pennsylvania , Philadelphia, PA 19104,","institution_ids":["https://openalex.org/I1333153716","https://openalex.org/I79576946"]},{"raw_affiliation_string":"University of Pennsylvania Department of Biostatistics, Epidemiology, and Informatics, , PA 19104,","institution_ids":["https://openalex.org/I79576946"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032336733","display_name":"Jaesik Kim","orcid":"https://orcid.org/0000-0003-1203-9650"},"institutions":[{"id":"https://openalex.org/I1333153716","display_name":"University City Science Center","ror":"https://ror.org/00s5a4h94","country_code":"US","type":"facility","lineage":["https://openalex.org/I1333153716"]},{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]},{"id":"https://openalex.org/I922845939","display_name":"Philadelphia University","ror":"https://ror.org/03zzmyz63","country_code":"US","type":"education","lineage":["https://openalex.org/I922845939"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jaesik Kim","raw_affiliation_strings":["Department of Bioengineering, University of Pennsylvania , Philadelphia, PA 19104,","Institute for Biomedical Informatics, University of Pennsylvania , Philadelphia, PA 19104,","University of Pennsylvania Department of Bioengineering, , PA 19104,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of Pennsylvania , Philadelphia, PA 19104,","institution_ids":["https://openalex.org/I79576946","https://openalex.org/I922845939"]},{"raw_affiliation_string":"Institute for Biomedical Informatics, University of Pennsylvania , Philadelphia, PA 19104,","institution_ids":["https://openalex.org/I1333153716","https://openalex.org/I79576946"]},{"raw_affiliation_string":"University of Pennsylvania Department of Bioengineering, , PA 19104,","institution_ids":["https://openalex.org/I79576946"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Dokyoon Kim","orcid":"https://orcid.org/0000-0002-4592-9564"},"institutions":[{"id":"https://openalex.org/I1333153716","display_name":"University City Science Center","ror":"https://ror.org/00s5a4h94","country_code":"US","type":"facility","lineage":["https://openalex.org/I1333153716"]},{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dokyoon Kim","raw_affiliation_strings":["Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA 19104,","Institute for Biomedical Informatics, University of Pennsylvania , Philadelphia, PA 19104,","University of Pennsylvania Department of Biostatistics, Epidemiology, and Informatics, , PA 19104,"],"raw_orcid":"https://orcid.org/0000-0002-4592-9564","affiliations":[{"raw_affiliation_string":"Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA 19104,","institution_ids":["https://openalex.org/I79576946"]},{"raw_affiliation_string":"Institute for Biomedical Informatics, University of Pennsylvania , Philadelphia, PA 19104,","institution_ids":["https://openalex.org/I1333153716","https://openalex.org/I79576946"]},{"raw_affiliation_string":"University of Pennsylvania Department of Biostatistics, Epidemiology, and Informatics, , PA 19104,","institution_ids":["https://openalex.org/I79576946"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5113848797","display_name":"Kyung-Ah Sohn","orcid":null},"institutions":[{"id":"https://openalex.org/I57664883","display_name":"Ajou University","ror":"https://ror.org/03tzb2h73","country_code":"KR","type":"education","lineage":["https://openalex.org/I57664883"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Kyung-Ah Sohn","raw_affiliation_strings":["Department of Artificial Intelligence, Ajou University , Suwon, 16499, South","Department of Software and Computer Engineering, Ajou University , Suwon, 16499, South","Ajou University Department of Aritificial Intelligence, , Suwon 16499, South"],"raw_orcid":"https://orcid.org/0000-0001-8941-1188","affiliations":[{"raw_affiliation_string":"Department of Artificial Intelligence, Ajou University , Suwon, 16499, South","institution_ids":["https://openalex.org/I57664883"]},{"raw_affiliation_string":"Department of Software and Computer Engineering, Ajou University , Suwon, 16499, South","institution_ids":["https://openalex.org/I57664883"]},{"raw_affiliation_string":"Ajou University Department of Aritificial Intelligence, , Suwon 16499, South","institution_ids":["https://openalex.org/I57664883"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"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":1.7279,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.83212427,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"41","issue":"4","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9129999876022339,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9129999876022339,"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/T11273","display_name":"Advanced Graph Neural Networks","score":0.0560000017285347,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.015300000086426735,"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/embedding","display_name":"Embedding","score":0.7648897171020508},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6729773879051208},{"id":"https://openalex.org/keywords/gene-ontology","display_name":"Gene ontology","score":0.6467227935791016},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.6153345704078674},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.5425179600715637},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.5167043209075928},{"id":"https://openalex.org/keywords/hierarchy","display_name":"Hierarchy","score":0.5011622905731201},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.4767207205295563},{"id":"https://openalex.org/keywords/euclidean-space","display_name":"Euclidean space","score":0.45801228284835815},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.41461899876594543},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3470003604888916},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2729901075363159},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.17316827178001404},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1060316264629364},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.09284079074859619}],"concepts":[{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.7648897171020508},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6729773879051208},{"id":"https://openalex.org/C2987395477","wikidata":"https://www.wikidata.org/wiki/Q135085","display_name":"Gene ontology","level":4,"score":0.6467227935791016},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.6153345704078674},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.5425179600715637},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.5167043209075928},{"id":"https://openalex.org/C31170391","wikidata":"https://www.wikidata.org/wiki/Q188619","display_name":"Hierarchy","level":2,"score":0.5011622905731201},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.4767207205295563},{"id":"https://openalex.org/C186450821","wikidata":"https://www.wikidata.org/wiki/Q17295","display_name":"Euclidean space","level":2,"score":0.45801228284835815},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.41461899876594543},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3470003604888916},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2729901075363159},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.17316827178001404},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1060316264629364},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.09284079074859619},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C34447519","wikidata":"https://www.wikidata.org/wiki/Q179522","display_name":"Market economy","level":1,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"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":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaf160","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf160","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf160/62916774/btaf160.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:40217132","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40217132","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:12036960","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12036960","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/btaf160","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf160","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf160/62916774/btaf160.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/4","score":0.4699999988079071,"display_name":"Quality Education"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320328359","display_name":"Ministry of Science and ICT, South Korea","ror":"https://ror.org/01wpjm123"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4409383239.pdf"},"referenced_works_count":15,"referenced_works":["https://openalex.org/W2103017472","https://openalex.org/W2786757148","https://openalex.org/W2962969117","https://openalex.org/W3035134435","https://openalex.org/W3112306601","https://openalex.org/W3136655674","https://openalex.org/W3166265964","https://openalex.org/W4210584212","https://openalex.org/W4283688275","https://openalex.org/W4308834893","https://openalex.org/W4396572199","https://openalex.org/W4396736534","https://openalex.org/W6678830454","https://openalex.org/W6762819970","https://openalex.org/W6784944647"],"related_works":["https://openalex.org/W2081900870","https://openalex.org/W2365264209","https://openalex.org/W962203960","https://openalex.org/W2026999166","https://openalex.org/W1996802783","https://openalex.org/W2509431957","https://openalex.org/W4211007821","https://openalex.org/W2802395037","https://openalex.org/W4238233526","https://openalex.org/W2794019507"],"abstract_inverted_index":{"MOTIVATION:":[0],"Leveraging":[1],"deep":[2],"learning":[3,7],"for":[4,20,101,158],"the":[5,54,88,116,125,129,152],"representation":[6],"of":[8,92,119,131,154],"Gene":[9,13],"Ontology":[10,14],"(GO)":[11],"and":[12,36,41,60,103],"Annotation":[15],"(GOA)":[16],"holds":[17],"significant":[18],"promise":[19],"enhancing":[21],"downstream":[22],"biological":[23],"tasks":[24],"such":[25],"as":[26],"protein-protein":[27,146],"interaction":[28,84,147,157],"prediction.":[29,148],"Prior":[30],"approaches":[31],"have":[32],"predominantly":[33],"used":[34],"text-":[35],"graph-based":[37],"methods,":[38],"embedding":[39,159],"GO":[40,55,102,120,126],"GOA":[42],"in":[43,145],"a":[44,58],"single":[45],"geometric":[46,83,110,134,156],"space":[47],"(e.g.":[48],"Euclidean":[49],"or":[50],"hyperbolic).":[51],"However,":[52],"since":[53],"graph":[56],"exhibits":[57],"complex":[59,117],"nonmonotonic":[61],"hierarchy,":[62],"single-space":[63],"embeddings":[64],"are":[65],"insufficient":[66],"to":[67,85],"fully":[68],"capture":[69],"its":[70],"structural":[71],"nuances.":[72],"RESULTS:":[73],"In":[74],"this":[75,79],"study,":[76],"we":[77],"address":[78],"limitation":[80],"by":[81],"exploiting":[82],"better":[86],"reflect":[87],"intricate":[89],"hierarchical":[90],"structure":[91],"GO.":[93],"Our":[94],"proposed":[95],"method,":[96],"Geometry-Aware":[97],"Knowledge":[98],"Graph":[99],"Embeddings":[100],"Genes":[104],"(GeOKG),":[105],"leverages":[106],"interactions":[107],"among":[108],"various":[109],"representations":[111],"during":[112],"training,":[113],"thereby":[114],"modeling":[115],"hierarchy":[118],"more":[121],"effectively.":[122],"Experiments":[123],"at":[124],"level":[127],"demonstrate":[128],"benefits":[130],"incorporating":[132],"these":[133],"interactions,":[135],"while":[136],"gene-level":[137],"tests":[138],"reveal":[139],"that":[140],"GeOKG":[141],"outperforms":[142],"existing":[143],"methods":[144],"These":[149],"findings":[150],"highlight":[151],"potential":[153],"using":[155],"heterogeneous":[160],"biomedical":[161],"networks.":[162],"AVAILABILITY":[163],"AND":[164],"IMPLEMENTATION:":[165],"https://github.com/ukjung21/GeOKG.":[166]},"counts_by_year":[{"year":2026,"cited_by_count":3}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
