{"id":"https://openalex.org/W4389076297","doi":"https://doi.org/10.1109/tcbb.2023.3335007","title":"A Multi-Relational Graph Encoder Network for Fine-Grained Prediction of MiRNA-Disease Associations","display_name":"A Multi-Relational Graph Encoder Network for Fine-Grained Prediction of MiRNA-Disease Associations","publication_year":2023,"publication_date":"2023-11-28","ids":{"openalex":"https://openalex.org/W4389076297","doi":"https://doi.org/10.1109/tcbb.2023.3335007","pmid":"https://pubmed.ncbi.nlm.nih.gov/38015672"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2023.3335007","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2023.3335007","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"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/ACM 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/A5036413795","display_name":"Shengpeng Yu","orcid":null},"institutions":[{"id":"https://openalex.org/I28006308","display_name":"Shandong Normal University","ror":"https://ror.org/01wy3h363","country_code":"CN","type":"education","lineage":["https://openalex.org/I28006308"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Shengpeng Yu","raw_affiliation_strings":["School of Information Science and Engineering, Shandong Normal University, Jinan, China"],"raw_orcid":"https://orcid.org/0000-0003-2288-5906","affiliations":[{"raw_affiliation_string":"School of Information Science and Engineering, Shandong Normal University, Jinan, China","institution_ids":["https://openalex.org/I28006308"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100370862","display_name":"Hong Wang","orcid":"https://orcid.org/0000-0001-5727-7834"},"institutions":[{"id":"https://openalex.org/I28006308","display_name":"Shandong Normal University","ror":"https://ror.org/01wy3h363","country_code":"CN","type":"education","lineage":["https://openalex.org/I28006308"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hong Wang","raw_affiliation_strings":["School of Information Science and Engineering, Shandong Normal University, Jinan, China"],"raw_orcid":"https://orcid.org/0000-0001-5727-7834","affiliations":[{"raw_affiliation_string":"School of Information Science and Engineering, Shandong Normal University, Jinan, China","institution_ids":["https://openalex.org/I28006308"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5114269727","display_name":"Jing Li","orcid":"https://orcid.org/0009-0001-9917-4080"},"institutions":[{"id":"https://openalex.org/I28006308","display_name":"Shandong Normal University","ror":"https://ror.org/01wy3h363","country_code":"CN","type":"education","lineage":["https://openalex.org/I28006308"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jing Li","raw_affiliation_strings":["School of Information Science and Engineering, Shandong Normal University, Jinan, China"],"raw_orcid":"https://orcid.org/0009-0001-9917-4080","affiliations":[{"raw_affiliation_string":"School of Information Science and Engineering, Shandong Normal University, Jinan, China","institution_ids":["https://openalex.org/I28006308"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042467880","display_name":"Jun Zhao","orcid":"https://orcid.org/0000-0003-2655-3888"},"institutions":[{"id":"https://openalex.org/I28006308","display_name":"Shandong Normal University","ror":"https://ror.org/01wy3h363","country_code":"CN","type":"education","lineage":["https://openalex.org/I28006308"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jun Zhao","raw_affiliation_strings":["School of Information Science and Engineering, Shandong Normal University, Jinan, China"],"raw_orcid":"https://orcid.org/0000-0003-2655-3888","affiliations":[{"raw_affiliation_string":"School of Information Science and Engineering, Shandong Normal University, Jinan, China","institution_ids":["https://openalex.org/I28006308"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101756728","display_name":"Cheng Liang","orcid":"https://orcid.org/0000-0003-3832-0969"},"institutions":[{"id":"https://openalex.org/I28006308","display_name":"Shandong Normal University","ror":"https://ror.org/01wy3h363","country_code":"CN","type":"education","lineage":["https://openalex.org/I28006308"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Cheng Liang","raw_affiliation_strings":["School of Information Science and Engineering, Shandong Normal University, Jinan, China"],"raw_orcid":"https://orcid.org/0000-0003-3832-0969","affiliations":[{"raw_affiliation_string":"School of Information Science and Engineering, Shandong Normal University, Jinan, China","institution_ids":["https://openalex.org/I28006308"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101844690","display_name":"Yanshen Sun","orcid":"https://orcid.org/0000-0002-4185-0066"},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yanshen Sun","raw_affiliation_strings":["Department of Computer Science, Virginia Tech, Blacksburg, VA, USA"],"raw_orcid":"https://orcid.org/0000-0002-4185-0066","affiliations":[{"raw_affiliation_string":"Department of Computer Science, Virginia Tech, Blacksburg, VA, USA","institution_ids":["https://openalex.org/I859038795"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5036413795"],"corresponding_institution_ids":["https://openalex.org/I28006308"],"apc_list":null,"apc_paid":null,"fwci":0.9319,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.7921425,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"21","issue":"1","first_page":"45","last_page":"56"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10062","display_name":"MicroRNA in disease regulation","score":1.0,"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":1.0,"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":0.9987000226974487,"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":0.9986000061035156,"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/disease","display_name":"Disease","score":0.6644930839538574},{"id":"https://openalex.org/keywords/microrna","display_name":"microRNA","score":0.6407627463340759},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5211991667747498},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4917478859424591},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3612615466117859},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.23751962184906006},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.22698736190795898},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.18951007723808289},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.11920428276062012},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.08916664123535156},{"id":"https://openalex.org/keywords/pathology","display_name":"Pathology","score":0.07939505577087402}],"concepts":[{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.6644930839538574},{"id":"https://openalex.org/C145059251","wikidata":"https://www.wikidata.org/wiki/Q310899","display_name":"microRNA","level":3,"score":0.6407627463340759},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5211991667747498},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4917478859424591},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3612615466117859},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.23751962184906006},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.22698736190795898},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.18951007723808289},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.11920428276062012},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.08916664123535156},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.07939505577087402}],"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","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/tcbb.2023.3335007","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2023.3335007","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"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/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38015672","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38015672","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/ACM transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/2","score":0.7699999809265137,"display_name":"Zero hunger"}],"awards":[{"id":"https://openalex.org/G6851897821","display_name":null,"funder_award_id":"62072290","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7921717826","display_name":null,"funder_award_id":"61672329","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":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":36,"referenced_works":["https://openalex.org/W1533230146","https://openalex.org/W1967087625","https://openalex.org/W2014946489","https://openalex.org/W2022732522","https://openalex.org/W2069370728","https://openalex.org/W2126619650","https://openalex.org/W2129158737","https://openalex.org/W2138664009","https://openalex.org/W2141222510","https://openalex.org/W2145361279","https://openalex.org/W2410390867","https://openalex.org/W2511620854","https://openalex.org/W2584926544","https://openalex.org/W2601934706","https://openalex.org/W2604314403","https://openalex.org/W2781702232","https://openalex.org/W2896010121","https://openalex.org/W2902116368","https://openalex.org/W2915154887","https://openalex.org/W2926326388","https://openalex.org/W2950834624","https://openalex.org/W2991244698","https://openalex.org/W3034974972","https://openalex.org/W3095387731","https://openalex.org/W3196533587","https://openalex.org/W3215531133","https://openalex.org/W3215660838","https://openalex.org/W4205478771","https://openalex.org/W4205923645","https://openalex.org/W4220710781","https://openalex.org/W4226276166","https://openalex.org/W4246271082","https://openalex.org/W4307498140","https://openalex.org/W4310456519","https://openalex.org/W4312195550","https://openalex.org/W6631964550"],"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/W2038886521"],"abstract_inverted_index":{"MicroRNAs":[0],"(miRNAs)":[1],"are":[2],"critical":[3],"in":[4,119],"diagnosing":[5],"and":[6,17,51,65,77,97,107,115,148],"treating":[7],"various":[8],"diseases.":[9,151],"Automatically":[10],"demystifying":[11],"the":[12,113,133],"interdependent":[13],"relationships":[14,28],"between":[15],"miRNAs":[16,64],"diseases":[18],"has":[19],"recently":[20],"made":[21],"remarkable":[22],"progress,":[23],"but":[24],"their":[25,66],"fine-grained":[26,42,140],"interactive":[27],"still":[29],"need":[30],"to":[31,54,61,144],"be":[32],"explored.":[33],"We":[34,74],"propose":[35],"a":[36,56,128,139],"multi-relational":[37,57],"graph":[38,58],"encoder":[39,59],"network":[40,60],"for":[41,90],"prediction":[43,134],"of":[44,117,135,150],"miRNA-disease":[45,83,136],"associations":[46,137],"(MRFGMDA),":[47],"which":[48,85],"uses":[49],"practical":[50],"current":[52],"datasets":[53],"construct":[55],"predict":[62],"disease-related":[63,122],"specific":[67],"relationship":[68],"types":[69],"(upregulation,":[70],"downregulation,":[71],"or":[72],"dysregulation).":[73],"evaluated":[75],"MRFGMDA":[76,118],"found":[78],"that":[79],"it":[80],"accurately":[81],"predicted":[82],"associations,":[84],"could":[86,142],"have":[87],"far-reaching":[88],"implications":[89],"clinical":[91],"medical":[92],"analysis,":[93,103,106],"early":[94],"diagnosis,":[95],"prevention,":[96],"treatment.":[98],"Case":[99],"analyses,":[100],"Kaplan-Meier":[101],"survival":[102],"expression":[104],"difference":[105],"immune":[108],"infiltration":[109],"analysis":[110],"further":[111],"demonstrated":[112],"effectiveness":[114],"feasibility":[116],"uncovering":[120],"potential":[121],"miRNAs.":[123],"Overall,":[124],"our":[125],"work":[126],"represents":[127],"significant":[129],"step":[130],"toward":[131],"improving":[132],"using":[138],"approach":[141],"lead":[143],"more":[145],"accurate":[146],"diagnosis":[147],"treatment":[149]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
