{"id":"https://openalex.org/W4210607727","doi":"https://doi.org/10.1093/bioinformatics/btac077","title":"PDMDA: predicting deep-level miRNA\u2013disease associations with graph neural networks and sequence features","display_name":"PDMDA: predicting deep-level miRNA\u2013disease associations with graph neural networks and sequence features","publication_year":2022,"publication_date":"2022-02-05","ids":{"openalex":"https://openalex.org/W4210607727","doi":"https://doi.org/10.1093/bioinformatics/btac077","pmid":"https://pubmed.ncbi.nlm.nih.gov/35150255"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac077","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac077","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/8/2226/49009215/btac077.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/38/8/2226/49009215/btac077.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100613014","display_name":"Cheng Yan","orcid":"https://orcid.org/0000-0002-5021-6841"},"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/I14992734","display_name":"Hunan University of Traditional Chinese Medicine","ror":"https://ror.org/05qfq0x09","country_code":"CN","type":"education","lineage":["https://openalex.org/I14992734"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Cheng Yan","raw_affiliation_strings":["School of Computer Science and Engineering, Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha 410083, China","School of Information Science and Engineering, Hunan University of Chinese Medicine , Changsha 410208, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha 410083, China","institution_ids":["https://openalex.org/I139660479"]},{"raw_affiliation_string":"School of Information Science and Engineering, Hunan University of Chinese Medicine , Changsha 410208, China","institution_ids":["https://openalex.org/I14992734"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026877800","display_name":"Guihua Duan","orcid":"https://orcid.org/0000-0002-9406-6443"},"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":"Guihua Duan","raw_affiliation_strings":["School of Computer Science and Engineering, Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha 410083, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha 410083, China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100368058","display_name":"Na Li","orcid":"https://orcid.org/0000-0002-0392-6672"},"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":"Na Li","raw_affiliation_strings":["School of Computer Science and Engineering, Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha 410083, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha 410083, China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001547268","display_name":"Lishen Zhang","orcid":"https://orcid.org/0000-0002-1704-9551"},"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":"Lishen Zhang","raw_affiliation_strings":["School of Computer Science and Engineering, Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha 410083, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha 410083, China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091157395","display_name":"Fang\u2010Xiang Wu","orcid":"https://orcid.org/0000-0002-4593-9332"},"institutions":[{"id":"https://openalex.org/I32625721","display_name":"University of Saskatchewan","ror":"https://ror.org/010x8gc63","country_code":"CA","type":"education","lineage":["https://openalex.org/I32625721"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Fang-Xiang Wu","raw_affiliation_strings":["Division of Biomedical Engineering and Department of Mechanical Engineering, University of Saskatchewan , Saskatoon SK S7N5A9, Canada"],"raw_orcid":"https://orcid.org/0000-0002-4593-9332","affiliations":[{"raw_affiliation_string":"Division of Biomedical Engineering and Department of Mechanical Engineering, University of Saskatchewan , Saskatoon SK S7N5A9, Canada","institution_ids":["https://openalex.org/I32625721"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100438360","display_name":"Jianxin Wang","orcid":"https://orcid.org/0000-0003-1516-0480"},"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":"Jianxin Wang","raw_affiliation_strings":["School of Computer Science and Engineering, Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha 410083, China"],"raw_orcid":"https://orcid.org/0000-0003-1516-0480","affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha 410083, China","institution_ids":["https://openalex.org/I139660479"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5100438360"],"corresponding_institution_ids":["https://openalex.org/I139660479"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.9421,"has_fulltext":true,"cited_by_count":38,"citation_normalized_percentile":{"value":0.93154098,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"38","issue":"8","first_page":"2226","last_page":"2234"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10062","display_name":"MicroRNA in disease regulation","score":0.972599983215332,"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":0.972599983215332,"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":0.0020000000949949026,"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/T10885","display_name":"Gene expression and cancer classification","score":0.0017000000225380063,"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/softmax-function","display_name":"Softmax function","score":0.776295006275177},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5003268718719482},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.48800554871559143},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4790562391281128},{"id":"https://openalex.org/keywords/disease","display_name":"Disease","score":0.46991458535194397},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4647504687309265},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.4558164179325104},{"id":"https://openalex.org/keywords/association","display_name":"Association (psychology)","score":0.4541371464729309},{"id":"https://openalex.org/keywords/microrna","display_name":"microRNA","score":0.4423692524433136},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.34038156270980835},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.32526224851608276},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.28518763184547424},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.24535351991653442},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.12266823649406433},{"id":"https://openalex.org/keywords/pathology","display_name":"Pathology","score":0.08157742023468018}],"concepts":[{"id":"https://openalex.org/C188441871","wikidata":"https://www.wikidata.org/wiki/Q7554146","display_name":"Softmax function","level":3,"score":0.776295006275177},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5003268718719482},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.48800554871559143},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4790562391281128},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.46991458535194397},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4647504687309265},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.4558164179325104},{"id":"https://openalex.org/C142853389","wikidata":"https://www.wikidata.org/wiki/Q744778","display_name":"Association (psychology)","level":2,"score":0.4541371464729309},{"id":"https://openalex.org/C145059251","wikidata":"https://www.wikidata.org/wiki/Q310899","display_name":"microRNA","level":3,"score":0.4423692524433136},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.34038156270980835},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.32526224851608276},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.28518763184547424},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.24535351991653442},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.12266823649406433},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.08157742023468018},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","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":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btac077","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac077","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/8/2226/49009215/btac077.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:35150255","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35150255","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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btac077","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac077","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/8/2226/49009215/btac077.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4066238608","display_name":null,"funder_award_id":"B18059","funder_id":"https://openalex.org/F4320327912","funder_display_name":"Higher Education Discipline Innovation Project"},{"id":"https://openalex.org/G539260901","display_name":"\u5fae\u751f\u7269\u4e0e\u75be\u75c5\u5173\u8054\u7684\u591a\u5c42\u6b21\u5173\u7cfb\u9884\u6d4b\u7814\u7a76","funder_award_id":"61962050","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7556176861","display_name":null,"funder_award_id":"2020]1Y264","funder_id":"https://openalex.org/F4320322272","funder_display_name":"Guizhou Science and Technology Department"},{"id":"https://openalex.org/G7631435625","display_name":null,"funder_award_id":"B18059","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7923915280","display_name":null,"funder_award_id":"U1909208","funder_id":"https://openalex.org/F4320334064","funder_display_name":"National Natural Science Foundation of China-Zhejiang Joint Fund for the Integration of Industrialization and Informatization"},{"id":"https://openalex.org/G8196091623","display_name":null,"funder_award_id":"U1909208","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8450505776","display_name":null,"funder_award_id":"62072473","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"},{"id":"https://openalex.org/F4320322272","display_name":"Guizhou Science and Technology Department","ror":"https://ror.org/00kwnh405"},{"id":"https://openalex.org/F4320327912","display_name":"Higher Education Discipline Innovation Project","ror":null},{"id":"https://openalex.org/F4320334064","display_name":"National Natural Science Foundation of China-Zhejiang Joint Fund for the Integration of Industrialization and Informatization","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4210607727.pdf","grobid_xml":"https://content.openalex.org/works/W4210607727.grobid-xml"},"referenced_works_count":43,"referenced_works":["https://openalex.org/W144423133","https://openalex.org/W1991154912","https://openalex.org/W2002995168","https://openalex.org/W2026570544","https://openalex.org/W2046245088","https://openalex.org/W2046864190","https://openalex.org/W2050434028","https://openalex.org/W2053987905","https://openalex.org/W2066408068","https://openalex.org/W2070571588","https://openalex.org/W2070777085","https://openalex.org/W2074549189","https://openalex.org/W2090961656","https://openalex.org/W2103151642","https://openalex.org/W2122915854","https://openalex.org/W2128674168","https://openalex.org/W2128728535","https://openalex.org/W2128768066","https://openalex.org/W2135314242","https://openalex.org/W2135433834","https://openalex.org/W2146292498","https://openalex.org/W2155445572","https://openalex.org/W2158135353","https://openalex.org/W2162344448","https://openalex.org/W2187089797","https://openalex.org/W2609262625","https://openalex.org/W2619930203","https://openalex.org/W2766935102","https://openalex.org/W2771019114","https://openalex.org/W2781702232","https://openalex.org/W2860192827","https://openalex.org/W2923922207","https://openalex.org/W2942820662","https://openalex.org/W2952477354","https://openalex.org/W2962928958","https://openalex.org/W2971132843","https://openalex.org/W2974045261","https://openalex.org/W2999336918","https://openalex.org/W3017317719","https://openalex.org/W3093863546","https://openalex.org/W3159261411","https://openalex.org/W4246271082","https://openalex.org/W6682945643"],"related_works":["https://openalex.org/W3107204728","https://openalex.org/W4287591324","https://openalex.org/W3108503355","https://openalex.org/W4226420367","https://openalex.org/W2962876041","https://openalex.org/W3090555870","https://openalex.org/W3022820045","https://openalex.org/W3170224572","https://openalex.org/W3095506574","https://openalex.org/W3190449293"],"abstract_inverted_index":{"MOTIVATION:":[0],"Many":[1],"studies":[2],"have":[3,33],"shown":[4],"that":[5,161,235],"microRNAs":[6],"(miRNAs)":[7],"play":[8],"a":[9,69,107,130,138],"key":[10],"role":[11],"in":[12],"human":[13],"diseases.":[14,43,159],"Meanwhile,":[15],"traditional":[16],"experimental":[17],"methods":[18,32,46],"for":[19],"miRNA-disease":[20,52,60,80,147,167,242],"association":[21,61,148,168,186,195,204],"identification":[22],"are":[23,116,200,251],"extremely":[24],"costly,":[25],"time-consuming":[26],"and":[27,42,54,87,95,122,137,158,202,248],"challenging.":[28],"Therefore,":[29],"many":[30],"computational":[31],"been":[34],"developed":[35],"to":[36,77,143,172,211],"predict":[37,48,57,78,144,239],"potential":[38],"associations":[39,81],"between":[40],"miRNAs":[41,157],"However,":[44],"those":[45],"mainly":[47],"the":[49,58,93,102,119,145,152,166,174,213,221,240],"existence":[50],"of":[51,98,156,196,216],"associations,":[53],"they":[55],"cannot":[56],"deep-level":[59,79,241],"types.":[62],"RESULTS:":[63],"In":[64],"this":[65],"study,":[66],"we":[67],"propose":[68],"new":[70],"end-to-end":[71],"deep":[72],"learning":[73],"method":[74],"(called":[75],"PDMDA)":[76],"with":[82,132],"graph":[83],"neural":[84],"networks":[85],"(GNNs)":[86],"miRNA":[88,103],"sequence":[89,94],"features.":[90],"Based":[91],"on":[92,151,184],"structural":[96],"features":[97],"miRNAs,":[99],"PDMDA":[100,162,236],"extracts":[101],"feature":[104,114,154],"representations":[105,115,155],"by":[106,126],"fully":[108,134],"connected":[109,135],"network":[110,121,125],"(FCN).":[111],"The":[112,218,231],"disease":[113],"extracted":[117],"from":[118],"disease-gene":[120],"gene-gene":[123],"interaction":[124,176],"GNN":[127],"model.":[128],"Finally,":[129],"multilayer":[131],"three":[133,181],"layers":[136],"softmax":[139],"layer":[140],"is":[141,227],"designed":[142],"final":[146],"scores":[149,226],"based":[150,183],"concatenated":[153],"Note":[160],"does":[163],"not":[164],"take":[165],"matrix":[169],"as":[170,229],"input":[171],"compute":[173],"Gaussian":[175],"profile":[177],"similarity.":[178],"We":[179,206],"conduct":[180,207],"experiments":[182],"six":[185],"type":[187],"samples":[188],"(including":[189],"circulations,":[190],"epigenetics,":[191],"target,":[192],"genetics,":[193],"known":[194],"which":[197],"their":[198],"types":[199],"unknown":[201,203],"samples).":[205],"fivefold":[208],"cross-validation":[209],"validation":[210],"assess":[212],"prediction":[214],"performance":[215],"PDMDA.":[217],"area":[219],"under":[220],"receiver":[222],"operating":[223],"characteristic":[224],"curve":[225],"used":[228],"metric.":[230],"experiment":[232],"results":[233],"show":[234],"can":[237],"accurately":[238],"associations.":[243],"AVAILABILITY":[244],"AND":[245],"IMPLEMENTATION:":[246],"Data":[247],"source":[249],"codes":[250],"available":[252],"at":[253],"https://github.com/27167199/PDMDA.":[254]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":10},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":11}],"updated_date":"2026-07-16T13:24:37.021932","created_date":"2025-10-10T00:00:00"}
