{"id":"https://openalex.org/W7122484989","doi":"https://doi.org/10.1093/bib/bbaf712","title":"Benchmarking knowledge graph embedding models for the prediction of oligogenic combinations","display_name":"Benchmarking knowledge graph embedding models for the prediction of oligogenic combinations","publication_year":2026,"publication_date":"2026-01-01","ids":{"openalex":"https://openalex.org/W7122484989","doi":"https://doi.org/10.1093/bib/bbaf712","pmid":"https://pubmed.ncbi.nlm.nih.gov/41520226"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf712","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf712","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in 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/bib/bbaf712","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5122776521","display_name":"Inas Bosch","orcid":null},"institutions":[{"id":"https://openalex.org/I132053463","display_name":"Universit\u00e9 Libre de Bruxelles","ror":"https://ror.org/01r9htc13","country_code":"BE","type":"education","lineage":["https://openalex.org/I132053463"]},{"id":"https://openalex.org/I13469542","display_name":"Vrije Universiteit Brussel","ror":"https://ror.org/006e5kg04","country_code":"BE","type":"education","lineage":["https://openalex.org/I13469542"]}],"countries":["BE"],"is_corresponding":true,"raw_author_name":"Inas Bosch","raw_affiliation_strings":["Artificial Intelligence Laboratory, Vrije Universiteit Brussels , Pleinlaan 9, 1050 Brussels ,","FARI Institute, Universit\u00e9 Libre de Bruxelles -Vrije Universiteit Brussels , Cantersteen 16, 1000 Brussels ,","Interuniversity Institute of Bioinformatics in Brussels, Universit\u00e9 Libre de Bruxelles-Vrije Universiteit Brussel , Boulevard du Triomphe CP263, 1050 Brussels ,","Machine Learning Group, Universit\u00e9 Libre de Bruxelles , Boulevard du Triomphe CP212, 1050 Brussels ,"],"raw_orcid":"https://orcid.org/0009-0009-7776-5988","affiliations":[{"raw_affiliation_string":"Artificial Intelligence Laboratory, Vrije Universiteit Brussels , Pleinlaan 9, 1050 Brussels ,","institution_ids":["https://openalex.org/I13469542"]},{"raw_affiliation_string":"FARI Institute, Universit\u00e9 Libre de Bruxelles -Vrije Universiteit Brussels , Cantersteen 16, 1000 Brussels ,","institution_ids":["https://openalex.org/I132053463","https://openalex.org/I13469542"]},{"raw_affiliation_string":"Interuniversity Institute of Bioinformatics in Brussels, Universit\u00e9 Libre de Bruxelles-Vrije Universiteit Brussel , Boulevard du Triomphe CP263, 1050 Brussels ,","institution_ids":["https://openalex.org/I132053463","https://openalex.org/I13469542"]},{"raw_affiliation_string":"Machine Learning Group, Universit\u00e9 Libre de Bruxelles , Boulevard du Triomphe CP212, 1050 Brussels ,","institution_ids":["https://openalex.org/I132053463"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075438898","display_name":"Barbara Gravel","orcid":"https://orcid.org/0000-0002-5422-2376"},"institutions":[{"id":"https://openalex.org/I132053463","display_name":"Universit\u00e9 Libre de Bruxelles","ror":"https://ror.org/01r9htc13","country_code":"BE","type":"education","lineage":["https://openalex.org/I132053463"]},{"id":"https://openalex.org/I13469542","display_name":"Vrije Universiteit Brussel","ror":"https://ror.org/006e5kg04","country_code":"BE","type":"education","lineage":["https://openalex.org/I13469542"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Barbara Gravel","raw_affiliation_strings":["Artificial Intelligence Laboratory, Vrije Universiteit Brussels , Pleinlaan 9, 1050 Brussels ,","Interuniversity Institute of Bioinformatics in Brussels, Universit\u00e9 Libre de Bruxelles-Vrije Universiteit Brussel , Boulevard du Triomphe CP263, 1050 Brussels ,","Machine Learning Group, Universit\u00e9 Libre de Bruxelles , Boulevard du Triomphe CP212, 1050 Brussels ,"],"raw_orcid":"https://orcid.org/0000-0002-5422-2376","affiliations":[{"raw_affiliation_string":"Artificial Intelligence Laboratory, Vrije Universiteit Brussels , Pleinlaan 9, 1050 Brussels ,","institution_ids":["https://openalex.org/I13469542"]},{"raw_affiliation_string":"Interuniversity Institute of Bioinformatics in Brussels, Universit\u00e9 Libre de Bruxelles-Vrije Universiteit Brussel , Boulevard du Triomphe CP263, 1050 Brussels ,","institution_ids":["https://openalex.org/I132053463","https://openalex.org/I13469542"]},{"raw_affiliation_string":"Machine Learning Group, Universit\u00e9 Libre de Bruxelles , Boulevard du Triomphe CP212, 1050 Brussels ,","institution_ids":["https://openalex.org/I132053463"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081793262","display_name":"Alexandre Renaux","orcid":"https://orcid.org/0000-0002-4339-2791"},"institutions":[{"id":"https://openalex.org/I132053463","display_name":"Universit\u00e9 Libre de Bruxelles","ror":"https://ror.org/01r9htc13","country_code":"BE","type":"education","lineage":["https://openalex.org/I132053463"]},{"id":"https://openalex.org/I13469542","display_name":"Vrije Universiteit Brussel","ror":"https://ror.org/006e5kg04","country_code":"BE","type":"education","lineage":["https://openalex.org/I13469542"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Alexandre Renaux","raw_affiliation_strings":["Artificial Intelligence Laboratory, Vrije Universiteit Brussels , Pleinlaan 9, 1050 Brussels ,","Interuniversity Institute of Bioinformatics in Brussels, Universit\u00e9 Libre de Bruxelles-Vrije Universiteit Brussel , Boulevard du Triomphe CP263, 1050 Brussels ,","Machine Learning Group, Universit\u00e9 Libre de Bruxelles , Boulevard du Triomphe CP212, 1050 Brussels ,"],"raw_orcid":"https://orcid.org/0000-0002-4339-2791","affiliations":[{"raw_affiliation_string":"Artificial Intelligence Laboratory, Vrije Universiteit Brussels , Pleinlaan 9, 1050 Brussels ,","institution_ids":["https://openalex.org/I13469542"]},{"raw_affiliation_string":"Interuniversity Institute of Bioinformatics in Brussels, Universit\u00e9 Libre de Bruxelles-Vrije Universiteit Brussel , Boulevard du Triomphe CP263, 1050 Brussels ,","institution_ids":["https://openalex.org/I132053463","https://openalex.org/I13469542"]},{"raw_affiliation_string":"Machine Learning Group, Universit\u00e9 Libre de Bruxelles , Boulevard du Triomphe CP212, 1050 Brussels ,","institution_ids":["https://openalex.org/I132053463"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5122835188","display_name":"Ann Now\u00e9","orcid":null},"institutions":[{"id":"https://openalex.org/I132053463","display_name":"Universit\u00e9 Libre de Bruxelles","ror":"https://ror.org/01r9htc13","country_code":"BE","type":"education","lineage":["https://openalex.org/I132053463"]},{"id":"https://openalex.org/I13469542","display_name":"Vrije Universiteit Brussel","ror":"https://ror.org/006e5kg04","country_code":"BE","type":"education","lineage":["https://openalex.org/I13469542"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Ann Now\u00e9","raw_affiliation_strings":["Artificial Intelligence Laboratory, Vrije Universiteit Brussels , Pleinlaan 9, 1050 Brussels ,","FARI Institute, Universit\u00e9 Libre de Bruxelles -Vrije Universiteit Brussels , Cantersteen 16, 1000 Brussels ,","Interuniversity Institute of Bioinformatics in Brussels, Universit\u00e9 Libre de Bruxelles-Vrije Universiteit Brussel , Boulevard du Triomphe CP263, 1050 Brussels ,"],"raw_orcid":"https://orcid.org/0000-0001-6346-4564","affiliations":[{"raw_affiliation_string":"Artificial Intelligence Laboratory, Vrije Universiteit Brussels , Pleinlaan 9, 1050 Brussels ,","institution_ids":["https://openalex.org/I13469542"]},{"raw_affiliation_string":"FARI Institute, Universit\u00e9 Libre de Bruxelles -Vrije Universiteit Brussels , Cantersteen 16, 1000 Brussels ,","institution_ids":["https://openalex.org/I132053463","https://openalex.org/I13469542"]},{"raw_affiliation_string":"Interuniversity Institute of Bioinformatics in Brussels, Universit\u00e9 Libre de Bruxelles-Vrije Universiteit Brussel , Boulevard du Triomphe CP263, 1050 Brussels ,","institution_ids":["https://openalex.org/I132053463","https://openalex.org/I13469542"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033522272","display_name":"Laan Maris","orcid":null},"institutions":[{"id":"https://openalex.org/I56085075","display_name":"University of Tartu","ror":"https://ror.org/03z77qz90","country_code":"EE","type":"education","lineage":["https://openalex.org/I56085075"]}],"countries":["EE"],"is_corresponding":false,"raw_author_name":"Maris Laan","raw_affiliation_strings":["Chair of Human Genetics, Institute of Biomedicine and Translational Medicine, University of Tartu , Ravila 19, 50411 Tartu ,"],"raw_orcid":"https://orcid.org/0000-0002-8519-243X","affiliations":[{"raw_affiliation_string":"Chair of Human Genetics, Institute of Biomedicine and Translational Medicine, University of Tartu , Ravila 19, 50411 Tartu ,","institution_ids":["https://openalex.org/I56085075"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5121831080","display_name":"Tom Lenaerts","orcid":null},"institutions":[{"id":"https://openalex.org/I132053463","display_name":"Universit\u00e9 Libre de Bruxelles","ror":"https://ror.org/01r9htc13","country_code":"BE","type":"education","lineage":["https://openalex.org/I132053463"]},{"id":"https://openalex.org/I13469542","display_name":"Vrije Universiteit Brussel","ror":"https://ror.org/006e5kg04","country_code":"BE","type":"education","lineage":["https://openalex.org/I13469542"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Tom Lenaerts","raw_affiliation_strings":["Artificial Intelligence Laboratory, Vrije Universiteit Brussels , Pleinlaan 9, 1050 Brussels ,","FARI Institute, Universit\u00e9 Libre de Bruxelles -Vrije Universiteit Brussels , Cantersteen 16, 1000 Brussels ,","Interuniversity Institute of Bioinformatics in Brussels, Universit\u00e9 Libre de Bruxelles-Vrije Universiteit Brussel , Boulevard du Triomphe CP263, 1050 Brussels ,","Machine Learning Group, Universit\u00e9 Libre de Bruxelles , Boulevard du Triomphe CP212, 1050 Brussels ,"],"raw_orcid":"https://orcid.org/0000-0003-3645-1455","affiliations":[{"raw_affiliation_string":"Artificial Intelligence Laboratory, Vrije Universiteit Brussels , Pleinlaan 9, 1050 Brussels ,","institution_ids":["https://openalex.org/I13469542"]},{"raw_affiliation_string":"FARI Institute, Universit\u00e9 Libre de Bruxelles -Vrije Universiteit Brussels , Cantersteen 16, 1000 Brussels ,","institution_ids":["https://openalex.org/I132053463","https://openalex.org/I13469542"]},{"raw_affiliation_string":"Interuniversity Institute of Bioinformatics in Brussels, Universit\u00e9 Libre de Bruxelles-Vrije Universiteit Brussel , Boulevard du Triomphe CP263, 1050 Brussels ,","institution_ids":["https://openalex.org/I132053463","https://openalex.org/I13469542"]},{"raw_affiliation_string":"Machine Learning Group, Universit\u00e9 Libre de Bruxelles , Boulevard du Triomphe CP212, 1050 Brussels ,","institution_ids":["https://openalex.org/I132053463"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5122776521"],"corresponding_institution_ids":["https://openalex.org/I132053463","https://openalex.org/I13469542"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":13.3471,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.95271551,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":98},"biblio":{"volume":"27","issue":"1","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":0.571399986743927,"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":0.571399986743927,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.14959999918937683,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.12380000203847885,"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/benchmarking","display_name":"Benchmarking","score":0.7652000188827515},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.6406999826431274},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.41350001096725464},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.39879998564720154},{"id":"https://openalex.org/keywords/matching","display_name":"Matching (statistics)","score":0.3968999981880188},{"id":"https://openalex.org/keywords/domain-knowledge","display_name":"Domain knowledge","score":0.39089998602867126},{"id":"https://openalex.org/keywords/ranking","display_name":"Ranking (information retrieval)","score":0.383899986743927}],"concepts":[{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.7652000188827515},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7498999834060669},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.6406999826431274},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5159000158309937},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5062999725341797},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.41350001096725464},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.39879998564720154},{"id":"https://openalex.org/C165064840","wikidata":"https://www.wikidata.org/wiki/Q1321061","display_name":"Matching (statistics)","level":2,"score":0.3968999981880188},{"id":"https://openalex.org/C207685749","wikidata":"https://www.wikidata.org/wiki/Q2088941","display_name":"Domain knowledge","level":2,"score":0.39089998602867126},{"id":"https://openalex.org/C189430467","wikidata":"https://www.wikidata.org/wiki/Q7293293","display_name":"Ranking (information retrieval)","level":2,"score":0.383899986743927},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.36149999499320984},{"id":"https://openalex.org/C75564084","wikidata":"https://www.wikidata.org/wiki/Q5597085","display_name":"Graph embedding","level":3,"score":0.3571000099182129},{"id":"https://openalex.org/C165696696","wikidata":"https://www.wikidata.org/wiki/Q11287","display_name":"Exploit","level":2,"score":0.3416999876499176},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.33390000462532043},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.30959999561309814},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.29750001430511475},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.271699994802475},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.26809999346733093},{"id":"https://openalex.org/C136197465","wikidata":"https://www.wikidata.org/wiki/Q1729295","display_name":"Variety (cybernetics)","level":2,"score":0.2578999996185303},{"id":"https://openalex.org/C2987255567","wikidata":"https://www.wikidata.org/wiki/Q33002955","display_name":"Knowledge graph","level":2,"score":0.2538999915122986}],"mesh":[{"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":"D000465","descriptor_name":"Algorithms","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":"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D035583","descriptor_name":"Rare Diseases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D035583","descriptor_name":"Rare Diseases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D035583","descriptor_name":"Rare Diseases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D035583","descriptor_name":"Rare Diseases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bib/bbaf712","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf712","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41520226","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41520226","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:12790627","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12790627/","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"},{"id":"pmh:oai:vubissmart:VUBISSMART:2000:264197","is_oa":false,"landing_page_url":"https://biblio.vub.ac.be/vubir/benchmarking-knowledge-graph-embedding-models-for-the-prediction-of-oligogenic-combinations(d6e70dd8-81a0-4021-9994-dd4d15b7e9f8).html","pdf_url":null,"source":{"id":"https://openalex.org/S4306402573","display_name":"VUBIR (Vrije Universiteit Brussel)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I13469542","host_organization_name":"Vrije Universiteit Brussel","host_organization_lineage":["https://openalex.org/I13469542"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"}],"best_oa_location":{"id":"doi:10.1093/bib/bbaf712","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf712","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G7015110903","display_name":null,"funder_award_id":"40028692","funder_id":"https://openalex.org/F4320321090","funder_display_name":"Eesti Teadusagentuur"},{"id":"https://openalex.org/G8420048555","display_name":null,"funder_award_id":"PRG1021","funder_id":"https://openalex.org/F4320321090","funder_display_name":"Eesti Teadusagentuur"}],"funders":[{"id":"https://openalex.org/F4320321090","display_name":"Eesti Teadusagentuur","ror":"https://ror.org/00jjeja18"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":35,"referenced_works":["https://openalex.org/W1801721664","https://openalex.org/W1964426200","https://openalex.org/W1966716734","https://openalex.org/W2016753842","https://openalex.org/W2054141820","https://openalex.org/W2081459643","https://openalex.org/W2091085232","https://openalex.org/W2104549677","https://openalex.org/W2119821739","https://openalex.org/W2152565567","https://openalex.org/W2160995259","https://openalex.org/W2485576080","https://openalex.org/W2553343555","https://openalex.org/W2759136286","https://openalex.org/W2799762305","https://openalex.org/W2949598989","https://openalex.org/W2954442758","https://openalex.org/W2979669231","https://openalex.org/W3007807538","https://openalex.org/W3015409108","https://openalex.org/W3196290979","https://openalex.org/W3200057886","https://openalex.org/W3208785685","https://openalex.org/W4206627019","https://openalex.org/W4220768028","https://openalex.org/W4242401062","https://openalex.org/W4284896905","https://openalex.org/W4289794327","https://openalex.org/W4367600858","https://openalex.org/W4377245077","https://openalex.org/W4385812212","https://openalex.org/W4386254278","https://openalex.org/W4394615344","https://openalex.org/W4394711144","https://openalex.org/W4394770700"],"related_works":[],"abstract_inverted_index":{"Identifying":[0],"the":[1,12,16,58,112,120,144,177,199,229,237,278],"potential":[2],"oligogenic":[3,165,283],"causes":[4],"of":[5,22,39,60,74,114,122,147,198,211,228],"rare":[6],"diseases":[7],"remains":[8,32,47],"a":[9,20,36,82,89,96,153,202,209,262],"challenge,":[10],"notwithstanding":[11],"advancements":[13],"made":[14],"in":[15,81,164,176,187],"last":[17],"decade.":[18],"While":[19],"variety":[21],"predictive":[23,263],"and":[24,45,79,224,226,234,257],"ranking":[25],"approaches":[26,158],"have":[27],"been":[28],"proposed,":[29],"their":[30,255],"precision":[31],"limited,":[33],"as":[34,91,182,205,207,275],"only":[35],"small":[37],"number":[38],"high-quality":[40],"training":[41],"cases":[42,215],"are":[43,280],"available":[44],"it":[46,92],"difficult":[48],"to":[49,140,149,173,270,276],"know":[50],"which":[51,70],"features":[52],"may":[53],"be":[54,174,271],"most":[55],"relevant":[56,76,97,281],"for":[57,94,119,159,250,282],"design":[59],"new":[61,212,266],"predictors.":[62],"We":[63,167],"hypothesize":[64],"here":[65,108],"that":[66,132,170,217],"structured":[67],"biological":[68,77],"information,":[69],"provides":[71],"an":[72,141],"integration":[73],"various":[75,115],"networks":[78],"ontologies":[80],"single":[83],"heterogeneous":[84],"knowledge":[85],"graph,":[86],"can":[87],"make":[88],"difference":[90],"allows":[93],"learning":[95],"genetic":[98],"representation":[99],"through":[100],"KGE":[101,134,260],"methods.":[102],"An":[103],"exhaustive":[104],"benchmarking":[105],"is":[106,242],"performed":[107],"wherein":[109],"we":[110],"assess":[111],"performance":[113],"state-of-the-art":[116],"embedding":[117,188],"models":[118,221,232],"task":[121],"identifying":[123],"potentially":[124],"pathogenic":[125],"gene":[126,161,248],"pairs.":[127],"The":[128,195,240],"results":[129],"obtained":[130],"show":[131,168,216],"these":[133,251],"provide":[135,236,261],"highly":[136],"accurate":[137],"predictions,":[138],"leading":[139],"Area":[142],"Under":[143],"Precision-Recall":[145],"Curve":[146],"up":[148],"$0.93$,":[150],"representing":[151],"also":[152],"significant":[154],"advancement":[155,264],"over":[156],"previous":[157],"predicting":[160],"pairs":[162,279],"involved":[163],"diseases.":[166,284],"nonetheless":[169],"care":[171],"needs":[172],"taken":[175,272],"cross-validation":[178],"when":[179],"using":[180],"embeddings,":[181],"data":[183],"leakage":[184],"between":[185],"folds":[186],"space":[189],"will":[190,268],"reveal":[191],"overly":[192],"optimistic":[193],"results.":[194,239],"further":[196],"evaluation":[197],"methods":[200],"on":[201,208],"holdout":[203],"set":[204],"well":[206],"group":[210],"male":[213],"infertility":[214],"three":[218],"Translational":[219],"Distance":[220],"(TransE,":[222],"MurE,":[223],"RotatE)":[225],"two":[227],"Semantic":[230],"Matching":[231],"(DisMult":[233],"QuatE)":[235],"better":[238],"analysis":[241],"concluded":[243],"by":[244],"comparing":[245],"all":[246],"known":[247],"combinations":[249],"top-ranking":[252],"models,":[253],"examining":[254],"similarities":[256],"differences.":[258],"Overall,":[259],"but":[265],"steps":[267],"need":[269],"generate":[273],"explanations":[274],"why":[277]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-04-30T09:15:22.047038","created_date":"2026-01-13T00:00:00"}
