{"id":"https://openalex.org/W4407829778","doi":"https://doi.org/10.1109/jbhi.2025.3542784","title":"DD-HGNN$^+$: Drug-Disease Association Prediction via General Hypergraph Neural Network With Hierarchical Contrastive Learning and Cross Attention Learning","display_name":"DD-HGNN$^+$: Drug-Disease Association Prediction via General Hypergraph Neural Network With Hierarchical Contrastive Learning and Cross Attention Learning","publication_year":2025,"publication_date":"2025-02-21","ids":{"openalex":"https://openalex.org/W4407829778","doi":"https://doi.org/10.1109/jbhi.2025.3542784","pmid":"https://pubmed.ncbi.nlm.nih.gov/40036538"},"language":"en","primary_location":{"id":"doi:10.1109/jbhi.2025.3542784","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2025.3542784","pdf_url":null,"source":{"id":"https://openalex.org/S2495854775","display_name":"IEEE Journal of Biomedical and Health Informatics","issn_l":"2168-2194","issn":["2168-2194","2168-2208"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Journal of Biomedical and Health Informatics","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":"Zixiao Jin","orcid":null},"institutions":[{"id":"https://openalex.org/I3124059619","display_name":"China University of Geosciences","ror":"https://ror.org/04gcegc37","country_code":"CN","type":"education","lineage":["https://openalex.org/I3124059619"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zixiao Jin","raw_affiliation_strings":["School of Computer Science, China University of Geosciences, Wuhan, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, China University of Geosciences, Wuhan, China","institution_ids":["https://openalex.org/I3124059619"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100652153","display_name":"Xiao Zheng","orcid":"https://orcid.org/0000-0002-5843-9206"},"institutions":[{"id":"https://openalex.org/I74525822","display_name":"Hubei University of Technology","ror":"https://ror.org/02d3fj342","country_code":"CN","type":"education","lineage":["https://openalex.org/I74525822"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiao Zheng","raw_affiliation_strings":["School of Computer Science, Hubei University of Technology, Wuhan, China"],"raw_orcid":"https://orcid.org/0000-0002-5843-9206","affiliations":[{"raw_affiliation_string":"School of Computer Science, Hubei University of Technology, Wuhan, China","institution_ids":["https://openalex.org/I74525822"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Hua Zhou","orcid":"https://orcid.org/0009-0009-7144-6652"},"institutions":[{"id":"https://openalex.org/I199305430","display_name":"Nantong University","ror":"https://ror.org/02afcvw97","country_code":"CN","type":"education","lineage":["https://openalex.org/I199305430"]},{"id":"https://openalex.org/I4210119554","display_name":"Yancheng First People's Hospital","ror":"https://ror.org/02rbkz523","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210119554"]},{"id":"https://openalex.org/I4210127567","display_name":"Yancheng Third People's Hospital","ror":"https://ror.org/030cwsf88","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210127567"]},{"id":"https://openalex.org/I4210132362","display_name":"Yancheng Second People's Hospital","ror":"https://ror.org/02x0x2d91","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210132362"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hua Zhou","raw_affiliation_strings":["Department of Hematology, Funing People's Hospital, Yancheng, China","Department of Hematology, Funing People&#x0027;s Hospital, Yancheng, China"],"raw_orcid":"https://orcid.org/0009-0009-7144-6652","affiliations":[{"raw_affiliation_string":"Department of Hematology, Funing People's Hospital, Yancheng, China","institution_ids":["https://openalex.org/I4210119554","https://openalex.org/I4210132362","https://openalex.org/I199305430","https://openalex.org/I4210127567"]},{"raw_affiliation_string":"Department of Hematology, Funing People&#x0027;s Hospital, Yancheng, China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085735291","display_name":"Chuanyi Ji","orcid":"https://orcid.org/0000-0001-6429-1474"},"institutions":[{"id":"https://openalex.org/I199305430","display_name":"Nantong University","ror":"https://ror.org/02afcvw97","country_code":"CN","type":"education","lineage":["https://openalex.org/I199305430"]},{"id":"https://openalex.org/I4210119554","display_name":"Yancheng First People's Hospital","ror":"https://ror.org/02rbkz523","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210119554"]},{"id":"https://openalex.org/I4210127567","display_name":"Yancheng Third People's Hospital","ror":"https://ror.org/030cwsf88","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210127567"]},{"id":"https://openalex.org/I4210132362","display_name":"Yancheng Second People's Hospital","ror":"https://ror.org/02x0x2d91","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210132362"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chengfu Ji","raw_affiliation_strings":["Department of Hematology, Funing People's Hospital, Yancheng, China","Department of Hematology, Funing People&#x0027;s Hospital, Yancheng, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Hematology, Funing People's Hospital, Yancheng, China","institution_ids":["https://openalex.org/I4210119554","https://openalex.org/I4210132362","https://openalex.org/I199305430","https://openalex.org/I4210127567"]},{"raw_affiliation_string":"Department of Hematology, Funing People&#x0027;s Hospital, Yancheng, China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009327506","display_name":"Sen Xiang","orcid":"https://orcid.org/0000-0001-5384-0730"},"institutions":[{"id":"https://openalex.org/I43922553","display_name":"Wuhan University of Science and Technology","ror":"https://ror.org/00e4hrk88","country_code":"CN","type":"education","lineage":["https://openalex.org/I43922553"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Sen Xiang","raw_affiliation_strings":["School of Information Science and Engineering, Wuhan University of Science and Technology, Wuhan, China"],"raw_orcid":"https://orcid.org/0000-0001-5384-0730","affiliations":[{"raw_affiliation_string":"School of Information Science and Engineering, Wuhan University of Science and Technology, Wuhan, China","institution_ids":["https://openalex.org/I43922553"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5033240507","display_name":"Chang Tang","orcid":"https://orcid.org/0000-0002-6515-7696"},"institutions":[{"id":"https://openalex.org/I3124059619","display_name":"China University of Geosciences","ror":"https://ror.org/04gcegc37","country_code":"CN","type":"education","lineage":["https://openalex.org/I3124059619"]},{"id":"https://openalex.org/I47720641","display_name":"Huazhong University of Science and Technology","ror":"https://ror.org/00p991c53","country_code":"CN","type":"education","lineage":["https://openalex.org/I47720641"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chang Tang","raw_affiliation_strings":["School of Software Engineering, Huazhong University of Science and Technology, Wuhan, China","School of Computer Science, China University of Geosciences, Wuhan, China"],"raw_orcid":"https://orcid.org/0000-0002-6515-7696","affiliations":[{"raw_affiliation_string":"School of Software Engineering, Huazhong University of Science and Technology, Wuhan, China","institution_ids":["https://openalex.org/I47720641"]},{"raw_affiliation_string":"School of Computer Science, China University of Geosciences, Wuhan, China","institution_ids":["https://openalex.org/I3124059619"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":5.2774,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.95497973,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":95,"max":99},"biblio":{"volume":"29","issue":"11","first_page":"7810","last_page":"7819"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9886999726295471,"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":0.9886999726295471,"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/T13702","display_name":"Machine Learning in Healthcare","score":0.9035000205039978,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6941927671432495},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.661734402179718},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.6550925970077515},{"id":"https://openalex.org/keywords/association","display_name":"Association (psychology)","score":0.5783407092094421},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5368315577507019},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.4456444978713989},{"id":"https://openalex.org/keywords/cross-validation","display_name":"Cross-validation","score":0.4308852553367615},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.4149669110774994},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3777417540550232},{"id":"https://openalex.org/keywords/psychology","display_name":"Psychology","score":0.11763590574264526}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6941927671432495},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.661734402179718},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.6550925970077515},{"id":"https://openalex.org/C142853389","wikidata":"https://www.wikidata.org/wiki/Q744778","display_name":"Association (psychology)","level":2,"score":0.5783407092094421},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5368315577507019},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.4456444978713989},{"id":"https://openalex.org/C27181475","wikidata":"https://www.wikidata.org/wiki/Q541014","display_name":"Cross-validation","level":2,"score":0.4308852553367615},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.4149669110774994},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3777417540550232},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"score":0.11763590574264526},{"id":"https://openalex.org/C542102704","wikidata":"https://www.wikidata.org/wiki/Q183257","display_name":"Psychotherapist","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"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":"D058492","descriptor_name":"Drug Repositioning","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D058492","descriptor_name":"Drug Repositioning","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D058492","descriptor_name":"Drug Repositioning","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/jbhi.2025.3542784","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2025.3542784","pdf_url":null,"source":{"id":"https://openalex.org/S2495854775","display_name":"IEEE Journal of Biomedical and Health Informatics","issn_l":"2168-2194","issn":["2168-2194","2168-2208"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Journal of Biomedical and Health Informatics","raw_type":"journal-article"},{"id":"pmid:40036538","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40036538","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":"IEEE journal of biomedical and health informatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6330077812","display_name":null,"funder_award_id":"62476258","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"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":67,"referenced_works":["https://openalex.org/W1735468488","https://openalex.org/W1791817748","https://openalex.org/W1968917372","https://openalex.org/W1971387816","https://openalex.org/W1988297989","https://openalex.org/W1999557019","https://openalex.org/W2009081245","https://openalex.org/W2009611558","https://openalex.org/W2011491015","https://openalex.org/W2037574696","https://openalex.org/W2040610660","https://openalex.org/W2042560956","https://openalex.org/W2059232449","https://openalex.org/W2082897578","https://openalex.org/W2092036091","https://openalex.org/W2103744620","https://openalex.org/W2108305936","https://openalex.org/W2113072832","https://openalex.org/W2127572022","https://openalex.org/W2163691988","https://openalex.org/W2170146596","https://openalex.org/W2170575973","https://openalex.org/W2172251832","https://openalex.org/W2181058469","https://openalex.org/W2306804766","https://openalex.org/W2339415213","https://openalex.org/W2346950316","https://openalex.org/W2482803382","https://openalex.org/W2520630506","https://openalex.org/W2526316983","https://openalex.org/W2579434750","https://openalex.org/W2733265822","https://openalex.org/W2790385355","https://openalex.org/W2809156537","https://openalex.org/W2903533144","https://openalex.org/W2946099214","https://openalex.org/W2961050676","https://openalex.org/W2967109100","https://openalex.org/W2971161508","https://openalex.org/W2995866605","https://openalex.org/W3000600836","https://openalex.org/W3004260451","https://openalex.org/W3005970824","https://openalex.org/W3037639124","https://openalex.org/W3093030756","https://openalex.org/W3106165797","https://openalex.org/W3193921017","https://openalex.org/W4206547282","https://openalex.org/W4248234957","https://openalex.org/W4282926996","https://openalex.org/W4311197760","https://openalex.org/W4367849720","https://openalex.org/W4376122068","https://openalex.org/W4376133364","https://openalex.org/W4378952262","https://openalex.org/W4385444024","https://openalex.org/W4389131658","https://openalex.org/W4389331644","https://openalex.org/W4389525220","https://openalex.org/W4389828698","https://openalex.org/W4390320384","https://openalex.org/W4390331481","https://openalex.org/W4391344850","https://openalex.org/W4391582532","https://openalex.org/W4396591964","https://openalex.org/W4400488769","https://openalex.org/W4401878948"],"related_works":["https://openalex.org/W4375867731","https://openalex.org/W816105089","https://openalex.org/W2352440174","https://openalex.org/W4309440960","https://openalex.org/W2611989081","https://openalex.org/W2062168445","https://openalex.org/W2731899572","https://openalex.org/W912456583","https://openalex.org/W4241378172","https://openalex.org/W2144801536"],"abstract_inverted_index":{"The":[0],"research":[1],"on":[2,40,104,182],"identifying":[3],"drug-disease":[4,30,42,75,100,154,174],"associations":[5,70,76,155,175],"(DDAs)":[6],"is":[7,143],"widely":[8],"used":[9],"in":[10,172],"scenarios":[11],"such":[12],"as":[13],"drug":[14,19],"development,":[15],"clinical":[16],"decision-making,":[17],"and":[18,24,108,121,126,134,159,176,184],"repurposing,":[20],"holding":[21],"significant":[22,82],"biological":[23],"medical":[25],"significance.":[26],"Existing":[27],"methods":[28,49,171],"for":[29,99],"association":[31,43,101],"prediction":[32,85,102,161],"have":[33],"achieved":[34],"decent":[35],"performance,":[36],"they":[37],"primarily":[38],"rely":[39],"simplistic":[41],"graphs":[44],"or":[45],"similarity":[46],"graphs.":[47],"These":[48],"often":[50],"struggle":[51],"to":[52,64,84,116,145,147],"capture":[53],"the":[54,66,139,148],"high-order":[55,124],"correlations":[56,125],"of":[57,68,119,152],"complex":[58],"multimodal":[59],"data,":[60],"limiting":[61],"their":[62],"ability":[63],"handle":[65],"complexity":[67],"data":[69],"effectively.":[71],"In":[72],"addition,":[73],"real":[74,153],"are":[77],"highly":[78],"sparse,":[79],"posing":[80],"a":[81,93],"challenge":[83],"accuracy.":[86],"To":[87],"tackle":[88],"these":[89],"issues,":[90],"we":[91],"propose":[92],"general":[94],"hypergraph":[95,113],"neural":[96,114],"network":[97],"framework":[98],"based":[103],"hierarchical":[105,135],"contrastive":[106,136],"learning":[107,133],"cross-attention":[109],"learning.":[110,137],"It":[111],"leverages":[112],"networks":[115],"learn":[117],"representations":[118],"drugs":[120],"diseases":[122],"carrying":[123],"strengthens":[127],"representation":[128],"quality":[129],"using":[130],"interactive":[131],"attention":[132],"Meanwhile,":[138],"$\\lambda$-weighted":[140],"loss":[141],"function":[142],"utilized":[144],"adapt":[146],"high":[149],"sparsity":[150],"property":[151],"during":[156],"model":[157],"training":[158],"improve":[160],"performance.":[162],"Extensive":[163],"experiments":[164],"demonstrate":[165],"that":[166],"DD-HGNN$^+$":[167],"surpasses":[168],"other":[169],"state-of-the-art":[170],"predicting":[173],"further":[177],"validation":[178],"through":[179],"case":[180],"studies":[181],"Leukemia":[183],"Colorectal":[185],"Neoplasms":[186],"underscores":[187],"its":[188],"reliability.":[189]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":2}],"updated_date":"2026-07-14T08:27:34.040176","created_date":"2025-10-10T00:00:00"}
