{"id":"https://openalex.org/W4406238219","doi":"https://doi.org/10.1109/bibm62325.2024.10822060","title":"DDTExplainer: Mining Drug-Disease Therapeutic Mechanisms based on GNN Explainability","display_name":"DDTExplainer: Mining Drug-Disease Therapeutic Mechanisms based on GNN Explainability","publication_year":2024,"publication_date":"2024-12-03","ids":{"openalex":"https://openalex.org/W4406238219","doi":"https://doi.org/10.1109/bibm62325.2024.10822060"},"language":"en","primary_location":{"id":"doi:10.1109/bibm62325.2024.10822060","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10822060","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://pure.ulster.ac.uk/ws/files/217896996/AAM_version.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100652603","display_name":"Yidan Zhang","orcid":"https://orcid.org/0000-0002-7589-530X"},"institutions":[{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yidan Zhang","raw_affiliation_strings":["Sichuan University,School of Computer Science,Chengdu,China"],"affiliations":[{"raw_affiliation_string":"Sichuan University,School of Computer Science,Chengdu,China","institution_ids":["https://openalex.org/I24185976"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103153652","display_name":"Lei Duan","orcid":"https://orcid.org/0000-0001-7254-1832"},"institutions":[{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lei Duan","raw_affiliation_strings":["Sichuan University,School of Computer Science,Chengdu,China"],"affiliations":[{"raw_affiliation_string":"Sichuan University,School of Computer Science,Chengdu,China","institution_ids":["https://openalex.org/I24185976"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024401909","display_name":"Huiru Zheng","orcid":"https://orcid.org/0000-0001-7648-8709"},"institutions":[{"id":"https://openalex.org/I138801177","display_name":"University of Ulster","ror":"https://ror.org/01yp9g959","country_code":"GB","type":"education","lineage":["https://openalex.org/I138801177"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Huiru Zheng","raw_affiliation_strings":["Ulster University,School of Computing,Northern Ireland,United Kingdom"],"affiliations":[{"raw_affiliation_string":"Ulster University,School of Computing,Northern Ireland,United Kingdom","institution_ids":["https://openalex.org/I138801177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100379058","display_name":"Haiying Wang","orcid":"https://orcid.org/0000-0001-8358-9065"},"institutions":[{"id":"https://openalex.org/I138801177","display_name":"University of Ulster","ror":"https://ror.org/01yp9g959","country_code":"GB","type":"education","lineage":["https://openalex.org/I138801177"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Haiying Wang","raw_affiliation_strings":["Ulster University,School of Computing,Northern Ireland,United Kingdom"],"affiliations":[{"raw_affiliation_string":"Ulster University,School of Computing,Northern Ireland,United Kingdom","institution_ids":["https://openalex.org/I138801177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009571807","display_name":"Yongmei Lu","orcid":"https://orcid.org/0000-0003-1994-3458"},"institutions":[{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yongmei Lu","raw_affiliation_strings":["Sichuan University,Intensive Care Unit &amp; Chinese Evidence-based Medicine Center, West China Hospital,Sichuan,China"],"affiliations":[{"raw_affiliation_string":"Sichuan University,Intensive Care Unit &amp; Chinese Evidence-based Medicine Center, West China Hospital,Sichuan,China","institution_ids":["https://openalex.org/I24185976"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101501525","display_name":"Wen Wang","orcid":"https://orcid.org/0000-0003-4796-4790"},"institutions":[{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wen Wang","raw_affiliation_strings":["Sichuan University,Intensive Care Unit &amp; Chinese Evidence-based Medicine Center, West China Hospital,Sichuan,China"],"affiliations":[{"raw_affiliation_string":"Sichuan University,Intensive Care Unit &amp; Chinese Evidence-based Medicine Center, West China Hospital,Sichuan,China","institution_ids":["https://openalex.org/I24185976"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100950605","display_name":"Xin Sun","orcid":"https://orcid.org/0009-0003-7223-5298"},"institutions":[{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xin Sun","raw_affiliation_strings":["Sichuan University,Intensive Care Unit &amp; Chinese Evidence-based Medicine Center, West China Hospital,Sichuan,China"],"affiliations":[{"raw_affiliation_string":"Sichuan University,Intensive Care Unit &amp; Chinese Evidence-based Medicine Center, West China Hospital,Sichuan,China","institution_ids":["https://openalex.org/I24185976"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5100652603"],"corresponding_institution_ids":["https://openalex.org/I24185976"],"apc_list":null,"apc_paid":null,"fwci":0.7517,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.76872802,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":96},"biblio":{"volume":null,"issue":null,"first_page":"1350","last_page":"1355"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9761999845504761,"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":0.9761999845504761,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9266999959945679,"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/T11943","display_name":"Pharmacovigilance and Adverse Drug Reactions","score":0.9222999811172485,"subfield":{"id":"https://openalex.org/subfields/3005","display_name":"Toxicology"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/drug","display_name":"Drug","score":0.6361127495765686},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5554224848747253},{"id":"https://openalex.org/keywords/disease","display_name":"Disease","score":0.5179656744003296},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.23364657163619995},{"id":"https://openalex.org/keywords/pharmacology","display_name":"Pharmacology","score":0.16474649310112},{"id":"https://openalex.org/keywords/internal-medicine","display_name":"Internal medicine","score":0.12138873338699341}],"concepts":[{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.6361127495765686},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5554224848747253},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.5179656744003296},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.23364657163619995},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","level":1,"score":0.16474649310112},{"id":"https://openalex.org/C126322002","wikidata":"https://www.wikidata.org/wiki/Q11180","display_name":"Internal medicine","level":1,"score":0.12138873338699341}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/bibm62325.2024.10822060","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10822060","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},{"id":"pmh:oai:pure.atira.dk:openaire/a833e826-85d8-41bf-b8af-0042aedcda56","is_oa":true,"landing_page_url":"https://pure.ulster.ac.uk/en/publications/a833e826-85d8-41bf-b8af-0042aedcda56","pdf_url":"https://pure.ulster.ac.uk/ws/files/217896996/AAM_version.pdf","source":{"id":"https://openalex.org/S4306402454","display_name":"Ulster University Research Portal (Ulster University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I138801177","host_organization_name":"University of Ulster","host_organization_lineage":["https://openalex.org/I138801177"],"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":"Zhang, Y, Duan, L, Zheng, H, Wang, H, Lu, Y, Wang, W & Sun, X 2025, DDTExplainer: Mining Drug-Disease Therapeutic Mechanisms based on GNN Explainability. in 2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, pp. 1350-1355, 2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Lisbon, Portugal, 3/12/24. https://doi.org/10.1109/bibm62325.2024.10822060","raw_type":"info:eu-repo/semantics/publishedVersion"}],"best_oa_location":{"id":"pmh:oai:pure.atira.dk:openaire/a833e826-85d8-41bf-b8af-0042aedcda56","is_oa":true,"landing_page_url":"https://pure.ulster.ac.uk/en/publications/a833e826-85d8-41bf-b8af-0042aedcda56","pdf_url":"https://pure.ulster.ac.uk/ws/files/217896996/AAM_version.pdf","source":{"id":"https://openalex.org/S4306402454","display_name":"Ulster University Research Portal (Ulster University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I138801177","host_organization_name":"University of Ulster","host_organization_lineage":["https://openalex.org/I138801177"],"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":"Zhang, Y, Duan, L, Zheng, H, Wang, H, Lu, Y, Wang, W & Sun, X 2025, DDTExplainer: Mining Drug-Disease Therapeutic Mechanisms based on GNN Explainability. in 2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, pp. 1350-1355, 2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Lisbon, Portugal, 3/12/24. https://doi.org/10.1109/bibm62325.2024.10822060","raw_type":"info:eu-repo/semantics/publishedVersion"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4406238219.pdf","grobid_xml":"https://content.openalex.org/works/W4406238219.grobid-xml"},"referenced_works_count":21,"referenced_works":["https://openalex.org/W1982386486","https://openalex.org/W2032123459","https://openalex.org/W2034537627","https://openalex.org/W2052214665","https://openalex.org/W2113551867","https://openalex.org/W2304181019","https://openalex.org/W2558217333","https://openalex.org/W2604314403","https://openalex.org/W2907265097","https://openalex.org/W3116637551","https://openalex.org/W3175754231","https://openalex.org/W4206078729","https://openalex.org/W4220999455","https://openalex.org/W4221003077","https://openalex.org/W4237095724","https://openalex.org/W4294216483","https://openalex.org/W4313245377","https://openalex.org/W4367046943","https://openalex.org/W6678830454","https://openalex.org/W6767288045","https://openalex.org/W6786048916"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"For":[0],"a":[1,58,62,100,123,131,142,176],"clinical":[2],"prescription,":[3],"clarifying":[4],"the":[5,12,29,54,72,109,116,154,160,164,171,185],"molecular":[6,74],"mechanisms":[7,56,75,119],"of":[8,11,57,173,181],"actions":[9,79],"(MMOAs)":[10],"drug-disease":[13,110,117,133,186],"interaction":[14],"is":[15,68,137,150],"helpful":[16],"to":[17,52,61,107,152],"optimize":[18],"treatment,":[19],"suggest":[20],"possible":[21],"side":[22],"effects,":[23],"and":[24,41,80,139,158],"realize":[25],"individualized":[26],"treatment.":[27],"Considering":[28],"relations":[30],"among":[31],"multiple":[32],"biomedical":[33,50],"entities,":[34],"such":[35],"as":[36,199,201],"drugs,":[37],"diseases,":[38],"targets":[39],"(genes),":[40],"pathways,":[42],"what":[43],"paths":[44],"can":[45,85],"be":[46],"extracted":[47],"connecting":[48],"these":[49],"entities":[51],"resemble":[53],"real":[55],"specific":[59],"drug":[60,78],"particular":[63],"disease?":[64],"Answering":[65],"this":[66,91],"question":[67],"crucial":[69],"for":[70],"understanding":[71],"underlying":[73],"behind":[76],"complex":[77],"identifying":[81],"key":[82],"pathways":[83],"that":[84,98,179],"facilitate":[86],"effective":[87],"therapeutic":[88,111,118,134,187],"interventions.":[89],"In":[90],"paper,":[92],"we":[93,169],"propose":[94],"an":[95],"approach":[96],"DDTExplainer":[97,114,174],"constructs":[99],"path-based":[101,161],"graph":[102,144],"neural":[103],"network":[104],"(GNN)":[105],"explainer":[106],"mine":[108],"mechanisms.":[112,188],"Technically,":[113],"transforms":[115],"mining":[120],"task":[121],"into":[122],"GNN-based":[124,132],"link":[125],"prediction":[126,135],"model":[127,136],"explanation":[128],"task.":[129],"Firstly,":[130],"trained":[138],"joint-optimized":[140],"with":[141,163],"translation-based":[143],"embedding":[145],"model.":[146],"Secondly,":[147],"mask":[148],"learning":[149],"utilized":[151],"find":[153],"most":[155],"prediction-influential":[156],"edges":[157],"generate":[159],"explanations":[162],"shortest":[165],"path":[166],"algorithm.":[167],"Finally,":[168],"assess":[170],"efficacy":[172],"on":[175],"ground-truth":[177],"dataset":[178],"consists":[180],"labeled":[182],"entries":[183],"describing":[184],"These":[189],"labels":[190],"are":[191],"derived":[192],"from":[193],"well-established":[194],"drug-target":[195],"interactions,":[196,198],"disease-target":[197],"well":[200],"target-pathway":[202],"relationships,":[203],"which":[204],"were":[205],"verified":[206],"by":[207],"wet":[208],"experiments.":[209]},"counts_by_year":[{"year":2025,"cited_by_count":2}],"updated_date":"2026-03-12T08:34:05.389933","created_date":"2025-10-10T00:00:00"}
