{"id":"https://openalex.org/W4401801484","doi":"https://doi.org/10.1186/s13321-024-00897-y","title":"Deep learning of multimodal networks with topological regularization for drug repositioning","display_name":"Deep learning of multimodal networks with topological regularization for drug repositioning","publication_year":2024,"publication_date":"2024-08-23","ids":{"openalex":"https://openalex.org/W4401801484","doi":"https://doi.org/10.1186/s13321-024-00897-y","pmid":"https://pubmed.ncbi.nlm.nih.gov/39180095"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-024-00897-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-024-00897-y","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-024-00897-y","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-024-00897-y","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5104226483","display_name":"Yuto Ohnuki","orcid":null},"institutions":[{"id":"https://openalex.org/I203951103","display_name":"Keio University","ror":"https://ror.org/02kn6nx58","country_code":"JP","type":"education","lineage":["https://openalex.org/I203951103"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Yuto Ohnuki","raw_affiliation_strings":["Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8522, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8522, Japan","institution_ids":["https://openalex.org/I203951103"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082419201","display_name":"Manato Akiyama","orcid":"https://orcid.org/0000-0002-5177-3199"},"institutions":[{"id":"https://openalex.org/I203951103","display_name":"Keio University","ror":"https://ror.org/02kn6nx58","country_code":"JP","type":"education","lineage":["https://openalex.org/I203951103"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Manato Akiyama","raw_affiliation_strings":["Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8522, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8522, Japan","institution_ids":["https://openalex.org/I203951103"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5105783902","display_name":"Yasubumi Sakakibara","orcid":null},"institutions":[{"id":"https://openalex.org/I203951103","display_name":"Keio University","ror":"https://ror.org/02kn6nx58","country_code":"JP","type":"education","lineage":["https://openalex.org/I203951103"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yasubumi Sakakibara","raw_affiliation_strings":["Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8522, Japan. yasu@bio.keio.ac.jp","Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8522, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8522, Japan. yasu@bio.keio.ac.jp","institution_ids":["https://openalex.org/I203951103"]},{"raw_affiliation_string":"Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8522, Japan","institution_ids":["https://openalex.org/I203951103"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5104226483"],"corresponding_institution_ids":["https://openalex.org/I203951103"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":4.1102,"has_fulltext":true,"cited_by_count":12,"citation_normalized_percentile":{"value":0.94713615,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"16","issue":"1","first_page":"103","last_page":"103"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.7785999774932861,"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":0.7785999774932861,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.1421000063419342,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.04039999842643738,"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/computer-science","display_name":"Computer science","score":0.7491846680641174},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.6359785199165344},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5047386884689331},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.46912097930908203},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.46657952666282654},{"id":"https://openalex.org/keywords/regularization","display_name":"Regularization (linguistics)","score":0.4567278027534485},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4467742443084717},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.41990649700164795},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.41522276401519775},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.34585076570510864},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.2938283681869507},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.24756351113319397},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.1910906732082367},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09203723073005676}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7491846680641174},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.6359785199165344},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5047386884689331},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.46912097930908203},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.46657952666282654},{"id":"https://openalex.org/C2776135515","wikidata":"https://www.wikidata.org/wiki/Q17143721","display_name":"Regularization (linguistics)","level":2,"score":0.4567278027534485},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4467742443084717},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.41990649700164795},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.41522276401519775},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.34585076570510864},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.2938283681869507},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.24756351113319397},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.1910906732082367},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09203723073005676},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13321-024-00897-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-024-00897-y","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-024-00897-y","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},{"id":"pmid:39180095","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39180095","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":"Journal of cheminformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11342530","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11342530","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11342530/pdf/13321_2024_Article_897.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-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Cheminform","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:d6551e4582384ec6bf08a983ed7fe1bc","is_oa":true,"landing_page_url":"https://doaj.org/article/d6551e4582384ec6bf08a983ed7fe1bc","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Cheminformatics, Vol 16, Iss 1, Pp 1-12 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s13321-024-00897-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-024-00897-y","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-024-00897-y","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3336985858","display_name":null,"funder_award_id":"23H04885","funder_id":"https://openalex.org/F4320320912","funder_display_name":"Ministry of Education, Culture, Sports, Science and Technology"},{"id":"https://openalex.org/G506916553","display_name":null,"funder_award_id":"17H06410","funder_id":"https://openalex.org/F4320320912","funder_display_name":"Ministry of Education, Culture, Sports, Science and Technology"}],"funders":[{"id":"https://openalex.org/F4320320912","display_name":"Ministry of Education, Culture, Sports, Science and Technology","ror":"https://ror.org/048rj2z13"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4401801484.pdf"},"referenced_works_count":71,"referenced_works":["https://openalex.org/W1501675811","https://openalex.org/W1539811621","https://openalex.org/W1902027874","https://openalex.org/W1971305517","https://openalex.org/W1988037271","https://openalex.org/W1994658365","https://openalex.org/W1998898494","https://openalex.org/W2033984457","https://openalex.org/W2062533676","https://openalex.org/W2070777085","https://openalex.org/W2077280419","https://openalex.org/W2085113635","https://openalex.org/W2098967508","https://openalex.org/W2113072832","https://openalex.org/W2118258530","https://openalex.org/W2141222510","https://openalex.org/W2146382443","https://openalex.org/W2158135353","https://openalex.org/W2159482845","https://openalex.org/W2161159766","https://openalex.org/W2170280345","https://openalex.org/W2276765849","https://openalex.org/W2295182096","https://openalex.org/W2341574236","https://openalex.org/W2346950316","https://openalex.org/W2462053388","https://openalex.org/W2524066112","https://openalex.org/W2568475068","https://openalex.org/W2604314403","https://openalex.org/W2610202041","https://openalex.org/W2611138580","https://openalex.org/W2767891136","https://openalex.org/W2790385355","https://openalex.org/W2799656331","https://openalex.org/W2799845593","https://openalex.org/W2826750344","https://openalex.org/W2892573831","https://openalex.org/W2922405516","https://openalex.org/W2946099214","https://openalex.org/W2946165673","https://openalex.org/W2952522777","https://openalex.org/W2960557205","https://openalex.org/W2962756421","https://openalex.org/W2983363499","https://openalex.org/W3004260451","https://openalex.org/W3005970824","https://openalex.org/W3013179442","https://openalex.org/W3015964336","https://openalex.org/W3020930839","https://openalex.org/W3042221936","https://openalex.org/W3084482269","https://openalex.org/W3093030756","https://openalex.org/W3093194543","https://openalex.org/W3107527779","https://openalex.org/W3112376646","https://openalex.org/W3116663947","https://openalex.org/W3148071990","https://openalex.org/W3157065614","https://openalex.org/W3192134500","https://openalex.org/W3204251585","https://openalex.org/W3209520664","https://openalex.org/W3209819349","https://openalex.org/W3210024567","https://openalex.org/W4206447491","https://openalex.org/W4213235856","https://openalex.org/W4226097900","https://openalex.org/W4246271082","https://openalex.org/W4294216483","https://openalex.org/W4379767398","https://openalex.org/W4381713847","https://openalex.org/W4387617009"],"related_works":["https://openalex.org/W4375867731","https://openalex.org/W2611989081","https://openalex.org/W2480711475","https://openalex.org/W4230611425","https://openalex.org/W2731899572","https://openalex.org/W4294635752","https://openalex.org/W4304166257","https://openalex.org/W4383066092","https://openalex.org/W3215138031","https://openalex.org/W2804383999"],"abstract_inverted_index":{"MOTIVATION:":[0],"Computational":[1],"techniques":[2],"for":[3,109,117,123],"drug-disease":[4,45],"prediction":[5,111],"are":[6],"essential":[7],"in":[8],"enhancing":[9],"drug":[10,98,110],"discovery":[11],"and":[12,32,55,66,93,112],"repositioning.":[13],"While":[14],"many":[15],"methods":[16,92],"utilize":[17],"multimodal":[18,49],"networks":[19,50],"from":[20],"various":[21],"biological":[22],"databases,":[23],"few":[24],"integrate":[25],"comprehensive":[26],"multi-omics":[27,64],"data,":[28],"including":[29],"transcriptomes,":[30],"proteomes,":[31],"metabolomes.":[33],"We":[34,57],"introduce":[35],"STRGNN,":[36,118],"a":[37,60,68,106],"novel":[38,97],"graph":[39],"deep":[40],"learning":[41,69],"approach":[42],"that":[43],"predicts":[44],"relationships":[46],"using":[47],"extensive":[48],"comprising":[51],"proteins,":[52],"RNAs,":[53],"metabolites,":[54],"compounds.":[56],"have":[58],"constructed":[59],"detailed":[61],"dataset":[62,122],"incorporating":[63],"data":[65],"developed":[67],"algorithm":[70,75],"with":[71,120],"topological":[72],"regularization.":[73],"This":[74],"selectively":[76],"leverages":[77],"informative":[78],"modalities":[79],"while":[80],"filtering":[81],"out":[82],"redundancies.":[83],"RESULTS:":[84],"STRGNN":[85,103],"demonstrates":[86],"superior":[87],"accuracy":[88],"compared":[89],"to":[90],"existing":[91,101],"has":[94],"identified":[95],"several":[96],"effects,":[99],"corroborating":[100],"literature.":[102],"emerges":[104],"as":[105],"powerful":[107],"tool":[108],"discovery.":[113],"The":[114],"source":[115],"code":[116],"along":[119],"the":[121],"performance":[124],"evaluation,":[125],"is":[126],"available":[127],"at":[128],"https://github.com/yuto-ohnuki/STRGNN.git":[129],".":[130]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":10}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}
