{"id":"https://openalex.org/W4415878345","doi":"https://doi.org/10.1021/acs.jcim.5c02276","title":"AGDNGDA: Unraveling Drug-Associated Genes with Adaptive Graph Diffusion Networks","display_name":"AGDNGDA: Unraveling Drug-Associated Genes with Adaptive Graph Diffusion Networks","publication_year":2025,"publication_date":"2025-11-04","ids":{"openalex":"https://openalex.org/W4415878345","doi":"https://doi.org/10.1021/acs.jcim.5c02276","pmid":"https://pubmed.ncbi.nlm.nih.gov/41186587"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.5c02276","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c02276","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Xiaowen Hu","orcid":"https://orcid.org/0009-0001-1004-5099"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaowen Hu","raw_affiliation_strings":["Central South University","School of Computer Science and Engineering"],"raw_orcid":"https://orcid.org/0009-0001-1004-5099","affiliations":[{"raw_affiliation_string":"Central South University","institution_ids":["https://openalex.org/I139660479"]},{"raw_affiliation_string":"School of Computer Science and Engineering","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045260031","display_name":"Che Zhang","orcid":"https://orcid.org/0000-0001-6757-4306"},"institutions":[{"id":"https://openalex.org/I4210157155","display_name":"Sichuan Academy of Traditional Chinese Medicine","ror":"https://ror.org/05wad7k45","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210157155"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Che Zhang","raw_affiliation_strings":["Sichuan Academy of Chinese Medicine Sciences","Sichuan Academy of Chinese Medicine Sciences, Chengdu 610041, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Sichuan Academy of Chinese Medicine Sciences","institution_ids":["https://openalex.org/I4210157155"]},{"raw_affiliation_string":"Sichuan Academy of Chinese Medicine Sciences, Chengdu 610041, China","institution_ids":["https://openalex.org/I4210157155"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032822444","display_name":"Yanhao Fan","orcid":null},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yanhao Fan","raw_affiliation_strings":["Central South University","School of Computer Science and Engineering"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Central South University","institution_ids":["https://openalex.org/I139660479"]},{"raw_affiliation_string":"School of Computer Science and Engineering","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111250627","display_name":"Kerui Wu","orcid":null},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]},{"id":"https://openalex.org/I177639307","display_name":"University of Dundee","ror":"https://ror.org/03h2bxq36","country_code":"GB","type":"education","lineage":["https://openalex.org/I177639307"]}],"countries":["CN","GB"],"is_corresponding":false,"raw_author_name":"Kerui Wu","raw_affiliation_strings":["Central South University","Dundee International Institute"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Central South University","institution_ids":["https://openalex.org/I139660479"]},{"raw_affiliation_string":"Dundee International Institute","institution_ids":["https://openalex.org/I177639307"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5113262237","display_name":"Lei Deng","orcid":null},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Lei Deng","raw_affiliation_strings":["Central South University","School of Computer Science and Engineering"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Central South University","institution_ids":["https://openalex.org/I139660479"]},{"raw_affiliation_string":"School of Computer Science and Engineering","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5113262237"],"corresponding_institution_ids":["https://openalex.org/I139660479"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.27374665,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"65","issue":"22","first_page":"12619","last_page":"12626"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.6101999878883362,"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":0.6101999878883362,"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":0.23980000615119934,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.04089999943971634,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.571399986743927},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5573999881744385},{"id":"https://openalex.org/keywords/node","display_name":"Node (physics)","score":0.43529999256134033},{"id":"https://openalex.org/keywords/kernel","display_name":"Kernel (algebra)","score":0.4083000123500824},{"id":"https://openalex.org/keywords/limit","display_name":"Limit (mathematics)","score":0.3792000114917755},{"id":"https://openalex.org/keywords/mechanism","display_name":"Mechanism (biology)","score":0.3734000027179718}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.753000020980835},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.571399986743927},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5573999881744385},{"id":"https://openalex.org/C62611344","wikidata":"https://www.wikidata.org/wiki/Q1062658","display_name":"Node (physics)","level":2,"score":0.43529999256134033},{"id":"https://openalex.org/C74193536","wikidata":"https://www.wikidata.org/wiki/Q574844","display_name":"Kernel (algebra)","level":2,"score":0.4083000123500824},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3919000029563904},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3882000148296356},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3873000144958496},{"id":"https://openalex.org/C151201525","wikidata":"https://www.wikidata.org/wiki/Q177239","display_name":"Limit (mathematics)","level":2,"score":0.3792000114917755},{"id":"https://openalex.org/C89611455","wikidata":"https://www.wikidata.org/wiki/Q6804646","display_name":"Mechanism (biology)","level":2,"score":0.3734000027179718},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.320499986410141},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.29440000653266907},{"id":"https://openalex.org/C100595998","wikidata":"https://www.wikidata.org/wiki/Q11731931","display_name":"Graph kernel","level":5,"score":0.2800999879837036},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.2766000032424927},{"id":"https://openalex.org/C13540734","wikidata":"https://www.wikidata.org/wiki/Q5318996","display_name":"Dynamic network analysis","level":2,"score":0.263700008392334},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.26109999418258667}],"mesh":[{"descriptor_ui":"D004058","descriptor_name":"Diffusion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004058","descriptor_name":"Diffusion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.5c02276","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c02276","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:41186587","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41186587","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 chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2008773563","display_name":null,"funder_award_id":"62272490","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5299854802","display_name":null,"funder_award_id":"U23A20321","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6419755262","display_name":null,"funder_award_id":"2025JJ20062","funder_id":"https://openalex.org/F4320322843","funder_display_name":"Natural Science Foundation of\u00a0Hunan Province"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320322843","display_name":"Natural Science Foundation of\u00a0Hunan Province","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":30,"referenced_works":["https://openalex.org/W1974534998","https://openalex.org/W1985270532","https://openalex.org/W2028279608","https://openalex.org/W2066201825","https://openalex.org/W2073415627","https://openalex.org/W2091439417","https://openalex.org/W2094611598","https://openalex.org/W2106417713","https://openalex.org/W2111708605","https://openalex.org/W2127553917","https://openalex.org/W2140310134","https://openalex.org/W2735272571","https://openalex.org/W2775185492","https://openalex.org/W2802314916","https://openalex.org/W2907492528","https://openalex.org/W2964321699","https://openalex.org/W3045200674","https://openalex.org/W3093030756","https://openalex.org/W3097794447","https://openalex.org/W3120280121","https://openalex.org/W3158143432","https://openalex.org/W3170286690","https://openalex.org/W3213337333","https://openalex.org/W4210607727","https://openalex.org/W4220710781","https://openalex.org/W4225402571","https://openalex.org/W4297733535","https://openalex.org/W4386316616","https://openalex.org/W4388615780","https://openalex.org/W4392523524"],"related_works":[],"abstract_inverted_index":{"Understanding":[0],"the":[1,62,127],"intricate":[2],"relationships":[3],"between":[4],"genes":[5],"and":[6,25],"drugs":[7],"is":[8],"crucial":[9],"for":[10,143],"advancing":[11],"drug":[12],"discovery.":[13],"However,":[14],"biological":[15,66],"experiments":[16],"aimed":[17],"at":[18],"identifying":[19,131],"gene-drug":[20,109,134],"associations":[21],"are":[22],"typically":[23],"time-consuming":[24],"inefficient,":[26],"leading":[27],"to":[28,60,86,92,103],"significant":[29,106],"data":[30],"sparsity.":[31],"While":[32],"Graph":[33],"Neural":[34],"Networks":[35],"(GNNs)":[36],"have":[37],"demonstrated":[38],"effectiveness":[39],"in":[40,130],"addressing":[41],"sparse":[42],"data,":[43],"existing":[44,119],"approaches":[45],"often":[46],"rely":[47],"on":[48],"uniform":[49],"node":[50],"processing":[51],"or":[52],"static":[53],"attention":[54],"mechanisms,":[55],"which":[56],"limit":[57],"their":[58],"ability":[59],"capture":[61],"dynamic":[63],"nature":[64],"of":[65],"interactions.":[67,110],"To":[68],"overcome":[69],"these":[70],"limitations,":[71],"we":[72],"propose":[73],"AGDNGDA,":[74],"an":[75],"adaptive":[76],"graph":[77],"diffusion":[78],"network":[79],"that":[80,115],"leverages":[81],"a":[82,140],"heat":[83],"kernel":[84],"mechanism":[85],"dynamically":[87],"modulate":[88],"information":[89],"aggregation":[90],"according":[91],"each":[93],"node's":[94],"specific":[95],"context.":[96],"This":[97],"innovative":[98],"approach":[99],"enables":[100],"our":[101],"model":[102],"effectively":[104],"highlight":[105],"yet":[107],"challenging":[108],"Comprehensive":[111],"experimental":[112],"results":[113],"demonstrate":[114],"AGDNGDA":[116],"consistently":[117],"surpasses":[118],"state-of-the-art":[120],"methods.":[121],"Additionally,":[122],"detailed":[123],"case":[124],"studies":[125],"illustrate":[126],"model's":[128],"capability":[129],"biologically":[132],"meaningful":[133],"associations,":[135],"highlighting":[136],"its":[137],"potential":[138],"as":[139],"powerful":[141],"tool":[142],"pharmaceutical":[144],"research.":[145]},"counts_by_year":[],"updated_date":"2025-11-25T14:43:58.451035","created_date":"2025-11-04T00:00:00"}
