{"id":"https://openalex.org/W4408717270","doi":"https://doi.org/10.1109/tcbbio.2025.3553243","title":"PNAGMDA: A Principal Neighborhood Aggregation Based Graph Neural Network for miRNA-Disease Association Prediction","display_name":"PNAGMDA: A Principal Neighborhood Aggregation Based Graph Neural Network for miRNA-Disease Association Prediction","publication_year":2025,"publication_date":"2025-03-21","ids":{"openalex":"https://openalex.org/W4408717270","doi":"https://doi.org/10.1109/tcbbio.2025.3553243","pmid":"https://pubmed.ncbi.nlm.nih.gov/40811353"},"language":"en","primary_location":{"id":"doi:10.1109/tcbbio.2025.3553243","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3553243","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"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 Transactions on Computational Biology and Bioinformatics","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":"https://openalex.org/A5040330586","display_name":"Congzhou Chen","orcid":"https://orcid.org/0000-0001-8425-3416"},"institutions":[{"id":"https://openalex.org/I75390827","display_name":"Beijing University of Chemical Technology","ror":"https://ror.org/00df5yc52","country_code":"CN","type":"education","lineage":["https://openalex.org/I75390827"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Congzhou Chen","raw_affiliation_strings":["College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, China"],"raw_orcid":"https://orcid.org/0000-0001-8425-3416","affiliations":[{"raw_affiliation_string":"College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, China","institution_ids":["https://openalex.org/I75390827"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Mingyuan Ma","orcid":"https://orcid.org/0000-0001-8967-8894"},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Mingyuan Ma","raw_affiliation_strings":["School of Computer Science, Peking University, Beijing, China"],"raw_orcid":"https://orcid.org/0000-0001-8967-8894","affiliations":[{"raw_affiliation_string":"School of Computer Science, Peking University, Beijing, China","institution_ids":["https://openalex.org/I20231570"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055189131","display_name":"Jinyan Nie","orcid":"https://orcid.org/0000-0002-9602-8758"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210137199","display_name":"Aerospace Information Research Institute","ror":"https://ror.org/0419fj215","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210137199"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jinyan Nie","raw_affiliation_strings":["Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing, China","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210137199"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100629695","display_name":"Lingfeng Wang","orcid":"https://orcid.org/0000-0001-7198-421X"},"institutions":[{"id":"https://openalex.org/I75390827","display_name":"Beijing University of Chemical Technology","ror":"https://ror.org/00df5yc52","country_code":"CN","type":"education","lineage":["https://openalex.org/I75390827"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lingfeng Wang","raw_affiliation_strings":["College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, China","institution_ids":["https://openalex.org/I75390827"]}]},{"author_position":"last","author":{"id":null,"display_name":"Jin Xu","orcid":"https://orcid.org/0000-0002-6377-1190"},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jin Xu","raw_affiliation_strings":["School of Computer Science, Peking University, Beijing, China"],"raw_orcid":"https://orcid.org/0000-0002-6377-1190","affiliations":[{"raw_affiliation_string":"School of Computer Science, Peking University, Beijing, China","institution_ids":["https://openalex.org/I20231570"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":4.0458,"has_fulltext":false,"cited_by_count":9,"citation_normalized_percentile":{"value":0.94504124,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":95,"max":100},"biblio":{"volume":"22","issue":"3","first_page":"1189","last_page":"1200"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10062","display_name":"MicroRNA in disease regulation","score":0.9986000061035156,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T10062","display_name":"MicroRNA in disease regulation","score":0.9986000061035156,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9922999739646912,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T11482","display_name":"RNA modifications and cancer","score":0.9779000282287598,"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/association","display_name":"Association (psychology)","score":0.6272506713867188},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.5605072975158691},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.49779629707336426},{"id":"https://openalex.org/keywords/principal","display_name":"Principal (computer security)","score":0.48543745279312134},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4808652997016907},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.43310272693634033},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.32124102115631104},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2000712752342224},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.0922359824180603},{"id":"https://openalex.org/keywords/psychology","display_name":"Psychology","score":0.09047940373420715},{"id":"https://openalex.org/keywords/computer-security","display_name":"Computer security","score":0.04849863052368164}],"concepts":[{"id":"https://openalex.org/C142853389","wikidata":"https://www.wikidata.org/wiki/Q744778","display_name":"Association (psychology)","level":2,"score":0.6272506713867188},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.5605072975158691},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.49779629707336426},{"id":"https://openalex.org/C144559511","wikidata":"https://www.wikidata.org/wiki/Q2986279","display_name":"Principal (computer security)","level":2,"score":0.48543745279312134},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4808652997016907},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.43310272693634033},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.32124102115631104},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2000712752342224},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.0922359824180603},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"score":0.09047940373420715},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.04849863052368164},{"id":"https://openalex.org/C542102704","wikidata":"https://www.wikidata.org/wiki/Q183257","display_name":"Psychotherapist","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbbio.2025.3553243","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3553243","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"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 Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40811353","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40811353","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 transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2132467328","display_name":null,"funder_award_id":"buctrc202221","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G3755773796","display_name":null,"funder_award_id":"buctrc202403","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":44,"referenced_works":["https://openalex.org/W144423133","https://openalex.org/W2020187738","https://openalex.org/W2040191060","https://openalex.org/W2041509376","https://openalex.org/W2050869737","https://openalex.org/W2113209482","https://openalex.org/W2120015541","https://openalex.org/W2128768066","https://openalex.org/W2141222510","https://openalex.org/W2145361279","https://openalex.org/W2146292498","https://openalex.org/W2158135353","https://openalex.org/W2165975239","https://openalex.org/W2767061187","https://openalex.org/W2771545712","https://openalex.org/W2888216133","https://openalex.org/W2895679848","https://openalex.org/W2898440040","https://openalex.org/W2962928958","https://openalex.org/W3033736933","https://openalex.org/W3041236926","https://openalex.org/W3088932244","https://openalex.org/W3093763138","https://openalex.org/W3136834909","https://openalex.org/W3139418566","https://openalex.org/W3143789190","https://openalex.org/W3146565636","https://openalex.org/W3179572443","https://openalex.org/W3180597373","https://openalex.org/W3195247250","https://openalex.org/W4210548518","https://openalex.org/W4220859562","https://openalex.org/W4223916839","https://openalex.org/W4283209287","https://openalex.org/W4285076853","https://openalex.org/W4293476626","https://openalex.org/W4307502334","https://openalex.org/W4312084649","https://openalex.org/W4384664737","https://openalex.org/W4385442674","https://openalex.org/W4386295460","https://openalex.org/W4393380917","https://openalex.org/W4399914365","https://openalex.org/W6775947557"],"related_works":["https://openalex.org/W4405554013","https://openalex.org/W236190221","https://openalex.org/W2379779959","https://openalex.org/W2333822231","https://openalex.org/W2105505991","https://openalex.org/W2394141650","https://openalex.org/W2390200212","https://openalex.org/W2388028180","https://openalex.org/W1967372967","https://openalex.org/W1995626169"],"abstract_inverted_index":{"Increasing":[0],"research":[1],"suggests":[2],"that":[3,81,107,151],"microRNAs":[4],"(miRNAs)":[5],"serve":[6],"an":[7,131],"essential":[8],"function":[9],"as":[10],"biomarkers":[11],"in":[12,17,26],"various":[13],"diseases.":[14],"The":[15],"variations":[16],"miRNA":[18],"expression":[19,30],"can":[20],"influence":[21],"their":[22],"corresponding":[23],"mRNAs,":[24],"which,":[25],"turn,":[27],"regulate":[28],"the":[29],"of":[31,159],"target":[32],"genes.":[33],"Recently,":[34],"graph":[35,106],"neural":[36,144],"networks":[37],"(GNNs)":[38],"have":[39],"been":[40],"widely":[41],"utilized":[42],"to":[43,64,101],"predict":[44],"miRNA-disease":[45,93,179],"associations.":[46],"However,":[47],"a":[48,79,103,141],"single":[49],"GNN":[50],"model":[51],"is":[52],"insufficient":[53],"for":[54,92,146,178],"fully":[55,142],"learning":[56],"node":[57,71,114],"representations.":[58],"Furthermore,":[59],"individual":[60],"aggregation":[61],"methods":[62],"struggle":[63],"effectively":[65],"extract":[66],"diverse":[67],"structural":[68],"information":[69],"and":[70,87,126,161,166],"weights.":[72],"To":[73],"address":[74],"these":[75],"challenges,":[76],"we":[77,97],"propose":[78],"method":[80],"incorporates":[82],"Principal":[83],"Neighborhood":[84],"Aggregation":[85],"(PNA)":[86],"Graph":[88],"Attention":[89],"Networks":[90],"(GAT)":[91],"association":[94],"prediction.":[95,147,180],"First,":[96],"integrated":[98],"multiple":[99,117],"datasets":[100],"construct":[102],"weighted":[104],"heterogeneous":[105],"models":[108],"miRNA-LncRNA-disease":[109],"interactions.":[110],"Subsequently,":[111],"PNA":[112,125],"extracted":[113],"representations":[115,136],"using":[116,130],"aggregators":[118],"simultaneously.":[119],"Additionally,":[120],"features":[121],"derived":[122],"from":[123],"both":[124],"GAT":[127],"were":[128,137],"fused":[129],"attention":[132],"mechanism.":[133],"These":[134],"combined":[135],"then":[138],"fed":[139],"into":[140],"connected":[143],"network":[145],"Experimental":[148],"results":[149],"demonstrate":[150],"PNAGMDA":[152],"achieves":[153],"exceptional":[154],"performance,":[155],"with":[156,172],"AUC":[157],"values":[158],"93.82%":[160],"92.77%":[162],"on":[163],"HMDD":[164],"v2.0":[165],"v3.2,":[167],"respectively.":[168],"Case":[169],"studies,":[170],"along":[171],"supplementary":[173],"findings,":[174],"confirm":[175],"PNAGMDA's":[176],"reliability":[177]},"counts_by_year":[{"year":2026,"cited_by_count":7},{"year":2025,"cited_by_count":2}],"updated_date":"2026-08-04T08:18:43.703281","created_date":"2025-10-10T00:00:00"}
