{"id":"https://openalex.org/W4395004104","doi":"https://doi.org/10.1093/bib/bbae172","title":"A comparative benchmarking and evaluation framework for heterogeneous network-based drug repositioning methods","display_name":"A comparative benchmarking and evaluation framework for heterogeneous network-based drug repositioning methods","publication_year":2024,"publication_date":"2024-03-27","ids":{"openalex":"https://openalex.org/W4395004104","doi":"https://doi.org/10.1093/bib/bbae172","pmid":"https://pubmed.ncbi.nlm.nih.gov/38647153"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbae172","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae172","pdf_url":"https://academic.oup.com/bib/article-pdf/25/3/bbae172/57295454/bbae172.pdf","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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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://academic.oup.com/bib/article-pdf/25/3/bbae172/57295454/bbae172.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5052672374","display_name":"Yinghong Li","orcid":"https://orcid.org/0000-0003-3629-519X"},"institutions":[{"id":"https://openalex.org/I10535382","display_name":"Chongqing University of Posts and Telecommunications","ror":"https://ror.org/03dgaqz26","country_code":"CN","type":"education","lineage":["https://openalex.org/I10535382"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yinghong Li","raw_affiliation_strings":["Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications , Chongqing 400065 , P. R. China"],"raw_orcid":"https://orcid.org/0000-0003-3629-519X","affiliations":[{"raw_affiliation_string":"Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications , Chongqing 400065 , P. R. China","institution_ids":["https://openalex.org/I10535382"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113017740","display_name":"Yinqi Yang","orcid":null},"institutions":[{"id":"https://openalex.org/I10535382","display_name":"Chongqing University of Posts and Telecommunications","ror":"https://ror.org/03dgaqz26","country_code":"CN","type":"education","lineage":["https://openalex.org/I10535382"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yinqi Yang","raw_affiliation_strings":["Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications , Chongqing 400065 , P. R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications , Chongqing 400065 , P. R. China","institution_ids":["https://openalex.org/I10535382"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102953899","display_name":"Zhuohao Tong","orcid":"https://orcid.org/0009-0009-5111-0449"},"institutions":[{"id":"https://openalex.org/I10535382","display_name":"Chongqing University of Posts and Telecommunications","ror":"https://ror.org/03dgaqz26","country_code":"CN","type":"education","lineage":["https://openalex.org/I10535382"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhuohao Tong","raw_affiliation_strings":["Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications , Chongqing 400065 , P. R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications , Chongqing 400065 , P. R. China","institution_ids":["https://openalex.org/I10535382"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100445368","display_name":"Yu Wang","orcid":"https://orcid.org/0000-0003-3511-0288"},"institutions":[{"id":"https://openalex.org/I10535382","display_name":"Chongqing University of Posts and Telecommunications","ror":"https://ror.org/03dgaqz26","country_code":"CN","type":"education","lineage":["https://openalex.org/I10535382"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yu Wang","raw_affiliation_strings":["Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications , Chongqing 400065 , P. R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications , Chongqing 400065 , P. R. China","institution_ids":["https://openalex.org/I10535382"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001500344","display_name":"Qin Mi","orcid":null},"institutions":[{"id":"https://openalex.org/I10535382","display_name":"Chongqing University of Posts and Telecommunications","ror":"https://ror.org/03dgaqz26","country_code":"CN","type":"education","lineage":["https://openalex.org/I10535382"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qin Mi","raw_affiliation_strings":["Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications , Chongqing 400065 , P. R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications , Chongqing 400065 , P. R. China","institution_ids":["https://openalex.org/I10535382"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048591796","display_name":"Mingze Bai","orcid":"https://orcid.org/0000-0002-9782-2056"},"institutions":[{"id":"https://openalex.org/I10535382","display_name":"Chongqing University of Posts and Telecommunications","ror":"https://ror.org/03dgaqz26","country_code":"CN","type":"education","lineage":["https://openalex.org/I10535382"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Mingze Bai","raw_affiliation_strings":["Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications , Chongqing 400065 , P. R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications , Chongqing 400065 , P. R. China","institution_ids":["https://openalex.org/I10535382"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054540808","display_name":"Guizhao Liang","orcid":"https://orcid.org/0000-0003-2293-6662"},"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/I4210123333","display_name":"Ministry of Education","ror":"https://ror.org/036nq5137","country_code":"TH","type":"government","lineage":["https://openalex.org/I4210123333"]}],"countries":["CN","TH"],"is_corresponding":false,"raw_author_name":"Guizhao Liang","raw_affiliation_strings":["Chongqing University , Ministry of Education, Bioengineering College, , Chongqing, 400044 , P. R. China","Key Laboratory of Biorheological Science and Technology , Ministry of Education, Bioengineering College, , Chongqing, 400044 , P. R. China","Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing, 400044, P. R. China"],"raw_orcid":"https://orcid.org/0000-0003-2293-6662","affiliations":[{"raw_affiliation_string":"Chongqing University , Ministry of Education, Bioengineering College, , Chongqing, 400044 , P. R. China","institution_ids":["https://openalex.org/I158842170"]},{"raw_affiliation_string":"Key Laboratory of Biorheological Science and Technology , Ministry of Education, Bioengineering College, , Chongqing, 400044 , P. R. China","institution_ids":["https://openalex.org/I4210123333"]},{"raw_affiliation_string":"Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing, 400044, P. R. China","institution_ids":["https://openalex.org/I158842170"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100374384","display_name":"Bo Li","orcid":"https://orcid.org/0000-0001-9944-0003"},"institutions":[{"id":"https://openalex.org/I126924076","display_name":"Chongqing Normal University","ror":"https://ror.org/01dcw5w74","country_code":"CN","type":"education","lineage":["https://openalex.org/I126924076"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Bo Li","raw_affiliation_strings":["College of Life Sciences, Chongqing Normal University , Chongqing 401331 , P. R. China"],"raw_orcid":"https://orcid.org/0000-0001-9944-0003","affiliations":[{"raw_affiliation_string":"College of Life Sciences, Chongqing Normal University , Chongqing 401331 , P. R. China","institution_ids":["https://openalex.org/I126924076"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5072776409","display_name":"Kunxian Shu","orcid":"https://orcid.org/0000-0003-4487-2727"},"institutions":[{"id":"https://openalex.org/I10535382","display_name":"Chongqing University of Posts and Telecommunications","ror":"https://ror.org/03dgaqz26","country_code":"CN","type":"education","lineage":["https://openalex.org/I10535382"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Kunxian Shu","raw_affiliation_strings":["Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications , Chongqing 400065 , P. R. China"],"raw_orcid":"https://orcid.org/0000-0003-4487-2727","affiliations":[{"raw_affiliation_string":"Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications , Chongqing 400065 , P. R. China","institution_ids":["https://openalex.org/I10535382"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5052672374","https://openalex.org/A5072776409","https://openalex.org/A5100374384"],"corresponding_institution_ids":["https://openalex.org/I10535382","https://openalex.org/I126924076"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":2.5104,"has_fulltext":true,"cited_by_count":8,"citation_normalized_percentile":{"value":0.89990938,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"25","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9995999932289124,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9995999932289124,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9907000064849854,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9052000045776367,"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":0.8519033193588257},{"id":"https://openalex.org/keywords/usability","display_name":"Usability","score":0.8383862376213074},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7951452732086182},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.7651665806770325},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.7340960502624512},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5378550291061401},{"id":"https://openalex.org/keywords/drug-repositioning","display_name":"Drug repositioning","score":0.4750673472881317},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.47073423862457275},{"id":"https://openalex.org/keywords/best-practice","display_name":"Best practice","score":0.4243849515914917},{"id":"https://openalex.org/keywords/service","display_name":"Service (business)","score":0.41825804114341736},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3262884020805359},{"id":"https://openalex.org/keywords/drug","display_name":"Drug","score":0.21799230575561523},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.1667073369026184},{"id":"https://openalex.org/keywords/human\u2013computer-interaction","display_name":"Human\u2013computer interaction","score":0.13503101468086243},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.07396528124809265}],"concepts":[{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.8519033193588257},{"id":"https://openalex.org/C170130773","wikidata":"https://www.wikidata.org/wiki/Q216378","display_name":"Usability","level":2,"score":0.8383862376213074},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7951452732086182},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.7651665806770325},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.7340960502624512},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5378550291061401},{"id":"https://openalex.org/C103637391","wikidata":"https://www.wikidata.org/wiki/Q5308921","display_name":"Drug repositioning","level":3,"score":0.4750673472881317},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.47073423862457275},{"id":"https://openalex.org/C184356942","wikidata":"https://www.wikidata.org/wiki/Q830382","display_name":"Best practice","level":2,"score":0.4243849515914917},{"id":"https://openalex.org/C2780378061","wikidata":"https://www.wikidata.org/wiki/Q25351891","display_name":"Service (business)","level":2,"score":0.41825804114341736},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3262884020805359},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.21799230575561523},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.1667073369026184},{"id":"https://openalex.org/C107457646","wikidata":"https://www.wikidata.org/wiki/Q207434","display_name":"Human\u2013computer interaction","level":1,"score":0.13503101468086243},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.07396528124809265},{"id":"https://openalex.org/C187736073","wikidata":"https://www.wikidata.org/wiki/Q2920921","display_name":"Management","level":1,"score":0.0},{"id":"https://openalex.org/C136264566","wikidata":"https://www.wikidata.org/wiki/Q159810","display_name":"Economy","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C118552586","wikidata":"https://www.wikidata.org/wiki/Q7867","display_name":"Psychiatry","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0}],"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":"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"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":"D058492","descriptor_name":"Drug Repositioning","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D058492","descriptor_name":"Drug Repositioning","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D058492","descriptor_name":"Drug Repositioning","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D058492","descriptor_name":"Drug Repositioning","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbae172","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae172","pdf_url":"https://academic.oup.com/bib/article-pdf/25/3/bbae172/57295454/bbae172.pdf","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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38647153","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38647153","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:11033846","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11033846","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11033846/pdf/bbae172.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbae172","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae172","pdf_url":"https://academic.oup.com/bib/article-pdf/25/3/bbae172/57295454/bbae172.pdf","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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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/G8235999723","display_name":null,"funder_award_id":"2021MD703942","funder_id":"https://openalex.org/F4320321543","funder_display_name":"China Postdoctoral Science Foundation"},{"id":"https://openalex.org/G8474453106","display_name":null,"funder_award_id":"62101087","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320321543","display_name":"China Postdoctoral Science Foundation","ror":"https://ror.org/0426zh255"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4395004104.pdf"},"referenced_works_count":62,"referenced_works":["https://openalex.org/W35816539","https://openalex.org/W1862448690","https://openalex.org/W1994658365","https://openalex.org/W1998898494","https://openalex.org/W2031954078","https://openalex.org/W2075740080","https://openalex.org/W2088632292","https://openalex.org/W2093313266","https://openalex.org/W2113072832","https://openalex.org/W2119412782","https://openalex.org/W2138715795","https://openalex.org/W2140099276","https://openalex.org/W2144267044","https://openalex.org/W2145578524","https://openalex.org/W2154654747","https://openalex.org/W2177411254","https://openalex.org/W2220358814","https://openalex.org/W2346950316","https://openalex.org/W2579434750","https://openalex.org/W2767891136","https://openalex.org/W2790385355","https://openalex.org/W2799720196","https://openalex.org/W2809156537","https://openalex.org/W2887766329","https://openalex.org/W2892573831","https://openalex.org/W2896002881","https://openalex.org/W2899915536","https://openalex.org/W2915806464","https://openalex.org/W2927507212","https://openalex.org/W2940524715","https://openalex.org/W2946099214","https://openalex.org/W2951034038","https://openalex.org/W2951624434","https://openalex.org/W2960557205","https://openalex.org/W2968848985","https://openalex.org/W2996505894","https://openalex.org/W2997323475","https://openalex.org/W3004260451","https://openalex.org/W3005533091","https://openalex.org/W3042289107","https://openalex.org/W3093030756","https://openalex.org/W3097857367","https://openalex.org/W3106972347","https://openalex.org/W3113654230","https://openalex.org/W3125008742","https://openalex.org/W3177200708","https://openalex.org/W3192134500","https://openalex.org/W4200140951","https://openalex.org/W4200253063","https://openalex.org/W4206501154","https://openalex.org/W4206547282","https://openalex.org/W4206923665","https://openalex.org/W4210641965","https://openalex.org/W4281617515","https://openalex.org/W4285024391","https://openalex.org/W4289732087","https://openalex.org/W4296777868","https://openalex.org/W4306651466","https://openalex.org/W4311508906","https://openalex.org/W4386849292","https://openalex.org/W4389131658","https://openalex.org/W6681230275"],"related_works":["https://openalex.org/W650706805","https://openalex.org/W2565660773","https://openalex.org/W2053225275","https://openalex.org/W4238897586","https://openalex.org/W2209531611","https://openalex.org/W2481035703","https://openalex.org/W2165238601","https://openalex.org/W2134852652","https://openalex.org/W1999020599","https://openalex.org/W1997916416"],"abstract_inverted_index":{"Computational":[0],"drug":[1,37,44,105,207,216],"repositioning,":[2],"which":[3],"involves":[4],"identifying":[5],"new":[6,79,241],"indications":[7],"for":[8,77,211],"existing":[9,110],"drugs,":[10],"is":[11,56],"an":[12,181,205],"increasingly":[13],"attractive":[14],"research":[15],"area":[16],"due":[17],"to":[18,50,117,187,233],"its":[19],"advantages":[20],"in":[21,190],"reducing":[22],"both":[23],"overall":[24,138],"cost":[25],"and":[26,69,122,133,151,160,169,197,236],"development":[27],"time.":[28],"As":[29],"a":[30,32,57,74,97,114,212,227],"result,":[31],"growing":[33],"number":[34],"of":[35,59,63,101,240],"computational":[36],"repositioning":[38,45,106,208],"methods":[39,46,107,128,242],"have":[40,47,84,225],"emerged.":[41],"Heterogeneous":[42],"network-based":[43,104],"been":[48],"shown":[49],"outperform":[51],"other":[52],"approaches.":[53],"However,":[54],"there":[55],"dearth":[58],"systematic":[60,98],"evaluation":[61,195],"studies":[62,83],"these":[64,177],"methods,":[65,88],"encompassing":[66],"performance,":[67,120,139,156],"scalability":[68,121],"usability,":[70,166],"as":[71,73,130,140],"well":[72],"standardized":[75],"process":[76],"evaluating":[78],"methods.":[80,222],"Additionally,":[81],"previous":[82],"only":[85],"compared":[86],"several":[87],"with":[89],"conflicting":[90],"results.":[91],"In":[92],"this":[93],"context,":[94],"we":[95,179,224],"conducted":[96],"benchmarking":[99,235],"study":[100,125],"28":[102],"heterogeneous":[103],"on":[108,143,176],"11":[109],"datasets.":[111],"We":[112],"developed":[113,180],"comprehensive":[115],"framework":[116],"evaluate":[118],"their":[119],"usability.":[123],"Our":[124],"revealed":[126],"that":[127],"such":[129],"HGIMC,":[131,167],"ITRPCA":[132,150],"BNNR":[134,170],"exhibit":[135],"the":[136,154,172,193,199,238,244],"best":[137,155],"they":[141],"rely":[142],"matrix":[144],"completion":[145],"or":[146,215],"factorization.":[147],"HINGRL,":[148],"MLMC,":[149],"HGIMC":[152],"demonstrate":[153],"while":[157],"NMFDR,":[158],"GROBMC":[159],"SCPMF":[161],"display":[162],"superior":[163],"scalability.":[164],"For":[165],"DRHGCN":[168],"are":[171],"top":[173],"performers.":[174],"Building":[175],"findings,":[178],"online":[182],"tool":[183],"called":[184],"HN-DREP":[185,202],"(http://hn-drep.lyhbio.com/)":[186],"facilitate":[188,234],"researchers":[189],"viewing":[191],"all":[192,221],"detailed":[194],"results":[196],"selecting":[198],"appropriate":[200],"method.":[201],"also":[203],"provides":[204],"external":[206],"prediction":[209],"service":[210],"specific":[213],"disease":[214],"by":[217],"integrating":[218],"predictions":[219],"from":[220],"Furthermore,":[223],"released":[226],"Snakemake":[228],"workflow":[229],"named":[230],"HN-DRES":[231],"(https://github.com/lyhbio/HN-DRES)":[232],"support":[237],"extension":[239],"into":[243],"field.":[245]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":6}],"updated_date":"2026-06-24T13:16:06.693445","created_date":"2025-10-10T00:00:00"}
