{"id":"https://openalex.org/W4412985173","doi":"https://doi.org/10.1109/tcbbio.2025.3595889","title":"Predict MiRNA-Disease Associations Using a Variant of Deep Forest Model and Improving Feature Vectors by Graph Convolutional Network","display_name":"Predict MiRNA-Disease Associations Using a Variant of Deep Forest Model and Improving Feature Vectors by Graph Convolutional Network","publication_year":2025,"publication_date":"2025-08-05","ids":{"openalex":"https://openalex.org/W4412985173","doi":"https://doi.org/10.1109/tcbbio.2025.3595889","pmid":"https://pubmed.ncbi.nlm.nih.gov/40811176"},"language":"en","primary_location":{"id":"doi:10.1109/tcbbio.2025.3595889","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3595889","pdf_url":null,"source":{"id":"https://openalex.org/S5407042751","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"2998-4165","issn":["2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"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/A5103306251","display_name":"Nguyen-Phuc-Xuan Quynh","orcid":"https://orcid.org/0009-0008-9740-2562"},"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":"Nguyen-Phuc-Xuan Quynh","raw_affiliation_strings":["Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, China","Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, Hunan, China"],"affiliations":[{"raw_affiliation_string":"Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, China","institution_ids":["https://openalex.org/I139660479"]},{"raw_affiliation_string":"Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, Hunan, China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043044395","display_name":"Hoai-Nhan Tran","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":"Hoai-Nhan Tran","raw_affiliation_strings":["Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, China","Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, Hunan, China"],"affiliations":[{"raw_affiliation_string":"Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, China","institution_ids":["https://openalex.org/I139660479"]},{"raw_affiliation_string":"Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, Hunan, China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100613014","display_name":"Cheng Yan","orcid":"https://orcid.org/0000-0002-5021-6841"},"institutions":[{"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 Informatics, Hunan University of Chinese Medicine, Changsha, China","School of Informatics, Hunan University of Chinese Medicine, Changsha, Hunan, China"],"affiliations":[{"raw_affiliation_string":"School of Informatics, Hunan University of Chinese Medicine, Changsha, China","institution_ids":["https://openalex.org/I14992734"]},{"raw_affiliation_string":"School of Informatics, Hunan University of Chinese Medicine, Changsha, Hunan, China","institution_ids":["https://openalex.org/I14992734"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100438360","display_name":"Jianxin Wang","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":"Jianxin Wang","raw_affiliation_strings":["Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, China","Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, Hunan, China"],"affiliations":[{"raw_affiliation_string":"Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, China","institution_ids":["https://openalex.org/I139660479"]},{"raw_affiliation_string":"Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, Hunan, China","institution_ids":["https://openalex.org/I139660479"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5103306251"],"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":0.25052443,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"22","issue":"6","first_page":"2596","last_page":"2607"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10062","display_name":"MicroRNA in disease regulation","score":0.9952999949455261,"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":0.9952999949455261,"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":0.9919999837875366,"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/T11765","display_name":"Circular RNAs in diseases","score":0.9455999732017517,"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/graph","display_name":"Graph","score":0.594615638256073},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.591966986656189},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.5750299692153931},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.553625226020813},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.46528974175453186},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.46331074833869934},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.39211133122444153},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3469308018684387},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3354915976524353},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.20945027470588684},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.15688741207122803}],"concepts":[{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.594615638256073},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.591966986656189},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.5750299692153931},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.553625226020813},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.46528974175453186},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.46331074833869934},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.39211133122444153},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3469308018684387},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3354915976524353},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.20945027470588684},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.15688741207122803},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"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":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":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":"D020022","descriptor_name":"Genetic Predisposition to Disease","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D020022","descriptor_name":"Genetic Predisposition to Disease","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D020022","descriptor_name":"Genetic Predisposition to Disease","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"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},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbbio.2025.3595889","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3595889","pdf_url":null,"source":{"id":"https://openalex.org/S5407042751","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"2998-4165","issn":["2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"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:40811176","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40811176","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":[{"display_name":"Life in Land","score":0.5099999904632568,"id":"https://metadata.un.org/sdg/15"}],"awards":[{"id":"https://openalex.org/G3324760237","display_name":null,"funder_award_id":"62272309","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G454375334","display_name":null,"funder_award_id":"62473149","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4785461891","display_name":null,"funder_award_id":"U22A2041","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7523020803","display_name":null,"funder_award_id":"2022JJ30428","funder_id":"https://openalex.org/F4320322866","funder_display_name":"Natural Science Foundation of Hainan Province"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320322866","display_name":"Natural Science Foundation of Hainan Province","ror":"https://ror.org/01h0zpd94"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":36,"referenced_works":["https://openalex.org/W2006247279","https://openalex.org/W2096573862","https://openalex.org/W2106029302","https://openalex.org/W2128768066","https://openalex.org/W2141222510","https://openalex.org/W2155445572","https://openalex.org/W2158135353","https://openalex.org/W2180078914","https://openalex.org/W2416200080","https://openalex.org/W2592189645","https://openalex.org/W2764334123","https://openalex.org/W2770397194","https://openalex.org/W2810666617","https://openalex.org/W2909927673","https://openalex.org/W2945357511","https://openalex.org/W2962928958","https://openalex.org/W2965751992","https://openalex.org/W2970280796","https://openalex.org/W2972771793","https://openalex.org/W3003038853","https://openalex.org/W3093996932","https://openalex.org/W3157330827","https://openalex.org/W3185009863","https://openalex.org/W3188579603","https://openalex.org/W4200542843","https://openalex.org/W4206703149","https://openalex.org/W4220859562","https://openalex.org/W4232714830","https://openalex.org/W4246271082","https://openalex.org/W4281553978","https://openalex.org/W4285803631","https://openalex.org/W4311823641","https://openalex.org/W4311995275","https://openalex.org/W4367317875","https://openalex.org/W4382465307","https://openalex.org/W4390320384"],"related_works":["https://openalex.org/W4375867731","https://openalex.org/W4391621807","https://openalex.org/W2611989081","https://openalex.org/W4321487865","https://openalex.org/W4313906399","https://openalex.org/W4391621790","https://openalex.org/W4226493464","https://openalex.org/W3133861977","https://openalex.org/W2951211570","https://openalex.org/W3103566983"],"abstract_inverted_index":{"MicroRNAs":[0],"(miRNAs)":[1],"play":[2],"a":[3,37,47,51,125],"significant":[4],"role":[5],"in":[6,185],"biological":[7],"processes,":[8],"serving":[9],"as":[10],"potential":[11],"biomarkers":[12],"and":[13,19,32,73,103,116,118,146],"therapeutic":[14],"targets":[15],"for":[16,25,40,58,80,114],"disease":[17],"diagnosis":[18],"treatment.":[20],"However,":[21],"traditional":[22],"experimental":[23],"methods":[24],"identifying":[26],"miRNA-disease":[27],"associations":[28],"(MDAs)":[29],"are":[30],"costly":[31],"time-consuming.":[33],"These":[34],"challenges":[35],"prompt":[36],"critical":[38],"need":[39],"computational":[41],"approaches.":[42],"This":[43],"study":[44],"proposes":[45],"GCNDFMDA,":[46],"method":[48],"that":[49],"employs":[50,124],"variant":[52,126],"of":[53,71,127,159],"the":[54,68,128,134,156,175],"deep":[55,129],"forest":[56,130],"model":[57,131],"MDAs":[59],"prediction.":[60,136],"Unlike":[61],"simple":[62],"multi-source":[63],"integration,":[64],"GCNDFMDA":[65,160],"first":[66],"captures":[67],"interactive":[69],"features":[70],"miRNAs":[72,115,179],"diseases":[74,117,183],"by":[75,90],"extracting":[76],"diverse":[77],"information":[78],"sources":[79],"comprehensive":[81],"representation.":[82],"Next,":[83],"it":[84,123],"utilizes":[85],"graph":[86],"convolutional":[87],"networks,":[88,99],"followed":[89],"neural":[91],"projection,":[92],"to":[93,132,162,181],"derive":[94],"latent":[95],"representations":[96],"from":[97],"similarity":[98],"thereby":[100],"reducing":[101],"dimensionality":[102],"obtaining":[104],"an":[105,147],"optimal":[106],"feature":[107,120],"space.":[108],"It":[109],"then":[110],"calculates":[111],"integrated":[112],"similarities":[113],"constructs":[119],"vectors.":[121],"Finally,":[122],"obtain":[133],"final":[135],"Experimental":[137],"results":[138],"on":[139],"three":[140],"datasets":[141],"(HMDD":[142],"v2.0,":[143],"HMDD":[144],"v3.2,":[145],"independent":[148],"dataset),":[149],"along":[150],"with":[151,173],"de":[152],"novo":[153],"validation,":[154],"highlight":[155],"superior":[157],"performance":[158],"compared":[161,164],"seven":[163],"methods.":[165],"In":[166],"addition,":[167],"case":[168],"studies":[169],"confirm":[170],"its":[171],"reliability,":[172],"all":[174],"top":[176],"50":[177],"predicted":[178],"related":[180],"these":[182],"verified":[184],"real":[186],"applications.":[187]},"counts_by_year":[],"updated_date":"2026-04-09T08:11:56.329763","created_date":"2025-10-10T00:00:00"}
