{"id":"https://openalex.org/W4413755005","doi":"https://doi.org/10.1109/tcbbio.2025.3603395","title":"A Granularity-Related Network Refinement Method Based on Module Division and Biological Information for Identifying Essential Proteins","display_name":"A Granularity-Related Network Refinement Method Based on Module Division and Biological Information for Identifying Essential Proteins","publication_year":2025,"publication_date":"2025-08-27","ids":{"openalex":"https://openalex.org/W4413755005","doi":"https://doi.org/10.1109/tcbbio.2025.3603395","pmid":"https://pubmed.ncbi.nlm.nih.gov/40864574"},"language":"en","primary_location":{"id":"doi:10.1109/tcbbio.2025.3603395","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3603395","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/A5101508365","display_name":"Li Pan","orcid":"https://orcid.org/0000-0002-9187-5544"},"institutions":[{"id":"https://openalex.org/I100286613","display_name":"Hunan Institute of Science and Technology","ror":"https://ror.org/044ysd349","country_code":"CN","type":"education","lineage":["https://openalex.org/I100286613"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Li Pan","raw_affiliation_strings":["School of Information Science and Engineering, Hunan Institute of Science and Technology, Yueyang, Hunan, China"],"raw_orcid":"https://orcid.org/0000-0002-9187-5544","affiliations":[{"raw_affiliation_string":"School of Information Science and Engineering, Hunan Institute of Science and Technology, Yueyang, Hunan, China","institution_ids":["https://openalex.org/I100286613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112812542","display_name":"Chenyang Xiao","orcid":"https://orcid.org/0009-0003-3593-4145"},"institutions":[{"id":"https://openalex.org/I100286613","display_name":"Hunan Institute of Science and Technology","ror":"https://ror.org/044ysd349","country_code":"CN","type":"education","lineage":["https://openalex.org/I100286613"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chenyang Xiao","raw_affiliation_strings":["School of Information Science and Engineering, Hunan Institute of Science and Technology, Yueyang, Hunan, China"],"raw_orcid":"https://orcid.org/0009-0003-3593-4145","affiliations":[{"raw_affiliation_string":"School of Information Science and Engineering, Hunan Institute of Science and Technology, Yueyang, Hunan, China","institution_ids":["https://openalex.org/I100286613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006569282","display_name":"Jinliang Yang","orcid":"https://orcid.org/0000-0002-0999-3518"},"institutions":[{"id":"https://openalex.org/I100286613","display_name":"Hunan Institute of Science and Technology","ror":"https://ror.org/044ysd349","country_code":"CN","type":"education","lineage":["https://openalex.org/I100286613"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jinliang Yang","raw_affiliation_strings":["School of Information Science and Engineering, Hunan Institute of Science and Technology, Yueyang, Hunan, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information Science and Engineering, Hunan Institute of Science and Technology, Yueyang, Hunan, China","institution_ids":["https://openalex.org/I100286613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109355757","display_name":"Yancheng Fang","orcid":null},"institutions":[{"id":"https://openalex.org/I100286613","display_name":"Hunan Institute of Science and Technology","ror":"https://ror.org/044ysd349","country_code":"CN","type":"education","lineage":["https://openalex.org/I100286613"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yancheng Fang","raw_affiliation_strings":["School of Information Science and Engineering, Hunan Institute of Science and Technology, Yueyang, Hunan, China"],"raw_orcid":"https://orcid.org/0009-0004-0970-9988","affiliations":[{"raw_affiliation_string":"School of Information Science and Engineering, Hunan Institute of Science and Technology, Yueyang, Hunan, China","institution_ids":["https://openalex.org/I100286613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100453376","display_name":"Bo Yang","orcid":"https://orcid.org/0000-0003-4210-8864"},"institutions":[{"id":"https://openalex.org/I100286613","display_name":"Hunan Institute of Science and Technology","ror":"https://ror.org/044ysd349","country_code":"CN","type":"education","lineage":["https://openalex.org/I100286613"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Bo Yang","raw_affiliation_strings":["School of Information Science and Engineering, Hunan Institute of Science and Technology, Yueyang, Hunan, China"],"raw_orcid":"https://orcid.org/0000-0003-4210-8864","affiliations":[{"raw_affiliation_string":"School of Information Science and Engineering, Hunan Institute of Science and Technology, Yueyang, Hunan, China","institution_ids":["https://openalex.org/I100286613"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100644285","display_name":"Wenbin Li","orcid":"https://orcid.org/0000-0002-2317-3495"},"institutions":[{"id":"https://openalex.org/I100286613","display_name":"Hunan Institute of Science and Technology","ror":"https://ror.org/044ysd349","country_code":"CN","type":"education","lineage":["https://openalex.org/I100286613"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wenbin Li","raw_affiliation_strings":["School of Information Science and Engineering, Hunan Institute of Science and Technology, Yueyang, Hunan, China"],"raw_orcid":"https://orcid.org/0000-0002-2317-3495","affiliations":[{"raw_affiliation_string":"School of Information Science and Engineering, Hunan Institute of Science and Technology, Yueyang, Hunan, China","institution_ids":["https://openalex.org/I100286613"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I100286613"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.16787725,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"22","issue":"6","first_page":"2833","last_page":"2845"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9948999881744385,"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"}},"topics":[{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9948999881744385,"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"}},{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9933000206947327,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9757999777793884,"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/granularity","display_name":"Granularity","score":0.8678885698318481},{"id":"https://openalex.org/keywords/division","display_name":"Division (mathematics)","score":0.7493473291397095},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6235141158103943},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3896252512931824},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3837236166000366},{"id":"https://openalex.org/keywords/computer-architecture","display_name":"Computer architecture","score":0.3518446087837219},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.35044050216674805},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.20435306429862976},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.15365156531333923},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1530425250530243},{"id":"https://openalex.org/keywords/arithmetic","display_name":"Arithmetic","score":0.0951799750328064}],"concepts":[{"id":"https://openalex.org/C177774035","wikidata":"https://www.wikidata.org/wiki/Q1246948","display_name":"Granularity","level":2,"score":0.8678885698318481},{"id":"https://openalex.org/C60798267","wikidata":"https://www.wikidata.org/wiki/Q1226939","display_name":"Division (mathematics)","level":2,"score":0.7493473291397095},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6235141158103943},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3896252512931824},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3837236166000366},{"id":"https://openalex.org/C118524514","wikidata":"https://www.wikidata.org/wiki/Q173212","display_name":"Computer architecture","level":1,"score":0.3518446087837219},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.35044050216674805},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.20435306429862976},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.15365156531333923},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1530425250530243},{"id":"https://openalex.org/C94375191","wikidata":"https://www.wikidata.org/wiki/Q11205","display_name":"Arithmetic","level":1,"score":0.0951799750328064}],"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D015003","descriptor_name":"Yeasts","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":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbbio.2025.3603395","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3603395","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:40864574","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40864574","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":[{"score":0.7400000095367432,"id":"https://metadata.un.org/sdg/2","display_name":"Zero hunger"}],"awards":[{"id":"https://openalex.org/G5741500157","display_name":null,"funder_award_id":"2024JJ7208","funder_id":"https://openalex.org/F4320322843","funder_display_name":"Natural Science Foundation of\u00a0Hunan Province"},{"id":"https://openalex.org/G6562874400","display_name":null,"funder_award_id":"2024JJ7207","funder_id":"https://openalex.org/F4320322843","funder_display_name":"Natural Science Foundation of\u00a0Hunan Province"},{"id":"https://openalex.org/G7444704880","display_name":null,"funder_award_id":"2024JJ7213","funder_id":"https://openalex.org/F4320322843","funder_display_name":"Natural Science Foundation of\u00a0Hunan Province"}],"funders":[{"id":"https://openalex.org/F4320322843","display_name":"Natural Science Foundation of\u00a0Hunan Province","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":56,"referenced_works":["https://openalex.org/W288163358","https://openalex.org/W1966716734","https://openalex.org/W1973758399","https://openalex.org/W1988496202","https://openalex.org/W1996612368","https://openalex.org/W2007245700","https://openalex.org/W2017975254","https://openalex.org/W2021149413","https://openalex.org/W2036799174","https://openalex.org/W2066636486","https://openalex.org/W2070582215","https://openalex.org/W2082202339","https://openalex.org/W2084619201","https://openalex.org/W2087194317","https://openalex.org/W2088590769","https://openalex.org/W2089125183","https://openalex.org/W2099636105","https://openalex.org/W2100300146","https://openalex.org/W2105089945","https://openalex.org/W2113553645","https://openalex.org/W2113654464","https://openalex.org/W2115746733","https://openalex.org/W2116117181","https://openalex.org/W2119114096","https://openalex.org/W2119571791","https://openalex.org/W2120423098","https://openalex.org/W2128366083","https://openalex.org/W2130687290","https://openalex.org/W2130790725","https://openalex.org/W2131681506","https://openalex.org/W2132253035","https://openalex.org/W2138566050","https://openalex.org/W2138582694","https://openalex.org/W2143350291","https://openalex.org/W2149119575","https://openalex.org/W2154600255","https://openalex.org/W2162891889","https://openalex.org/W2164928285","https://openalex.org/W2326727950","https://openalex.org/W2467366894","https://openalex.org/W2543582635","https://openalex.org/W2547262106","https://openalex.org/W2586452838","https://openalex.org/W2766676715","https://openalex.org/W2915108429","https://openalex.org/W2950595506","https://openalex.org/W2973129733","https://openalex.org/W3009097360","https://openalex.org/W3162389729","https://openalex.org/W3164632311","https://openalex.org/W4200365543","https://openalex.org/W4233120011","https://openalex.org/W4294167352","https://openalex.org/W4312467679","https://openalex.org/W4362593661","https://openalex.org/W4394978908"],"related_works":["https://openalex.org/W2931688134","https://openalex.org/W2377919138","https://openalex.org/W2378857091","https://openalex.org/W103652678","https://openalex.org/W4226090359","https://openalex.org/W2059697060","https://openalex.org/W936373746","https://openalex.org/W2975817033","https://openalex.org/W4256502920","https://openalex.org/W2354431794"],"abstract_inverted_index":{"Essential":[0],"proteins":[1,241],"play":[2],"a":[3,112,183],"pivotal":[4],"role":[5],"in":[6,36,64,243],"biological":[7,125,151],"systems,":[8],"and":[9,19,123,147,176,202,220,226,250],"their":[10],"identification":[11,25,41,209],"is":[12],"critical":[13],"for":[14,127],"elucidating":[15],"complex":[16],"life":[17],"mechanisms":[18],"disease":[20],"pathogenesis.":[21],"While":[22],"most":[23],"existing":[24],"methods":[26,210],"rely":[27],"on":[28,107],"protein-protein":[29],"interaction":[30],"networks":[31,198],"(PINs),":[32],"the":[33,66,100,159],"inherent":[34],"noise":[35],"raw":[37],"PINs":[38,263],"frequently":[39],"compromises":[40],"efficiency.":[42],"To":[43,187],"address":[44],"this":[45,108],"limitation,":[46],"researchers":[47],"often":[48],"employ":[49],"network":[50,115],"refinement":[51,116,258],"strategies":[52],"to":[53,162],"improve":[54,99],"PIN":[55,95,139,185],"quality,":[56],"with":[57],"modularity-based":[58],"approaches":[59],"demonstrating":[60],"particularly":[61],"strong":[62],"efficacy":[63],"enhancing":[65],"predictive":[67],"performance":[68,235],"of":[69,102,143,172],"essential":[70,103,128,207,240,267],"protein":[71,77,104,129,208,268],"identification.":[72,105],"Emerging":[73],"evidence":[74,126],"reveals":[75],"that":[76,87,118,231,255,264],"complexes":[78],"exhibit":[79],"distinct":[80],"fine-grained":[81],"modular":[82,90],"architectures.":[83],"This":[84],"observation":[85],"suggests":[86],"systematically":[88],"incorporating":[89],"granularity":[91,164],"considerations":[92],"during":[93],"refined":[94],"construction":[96,140],"could":[97],"significantly":[98],"accuracy":[101],"Building":[106],"premise,":[109],"we":[110,191],"propose":[111],"novel":[113],"granularity-aware":[114],"framework":[117],"integrates":[119],"hierarchical":[120],"module":[121,156,168],"division":[122,157],"multi-source":[124],"discovery.":[130,269],"Our":[131],"methodology":[132],"comprises":[133],"three":[134],"key":[135],"phases:":[136],"(1)":[137],"Weighted":[138],"through":[141],"integration":[142],"gene":[144],"expression":[145],"profiles":[146],"Gene":[148],"Ontology":[149],"(GO)":[150],"process":[152],"annotations;":[153],"(2)":[154],"Hierarchical":[155],"using":[158,204],"Louvain":[160],"algorithm":[161],"optimize":[163],"resolution;":[165],"(3)":[166],"Critical":[167],"detection":[169],"via":[170],"synthesis":[171],"evolutionary":[173],"conservation":[174],"scores":[175],"nuclear":[177],"localization":[178],"enrichment":[179],"metrics,":[180,238],"ultimately":[181],"generating":[182],"Granularity-Modulated":[184],"(GM-PIN).":[186],"validate":[188],"our":[189,256],"approach,":[190],"performed":[192],"comparative":[193],"evaluations":[194],"against":[195],"four":[196],"baseline":[197],"(S-PIN,":[199],"D-PIN,":[200],"RD-PIN":[201],"CM-PIN)":[203],"ten":[205],"state-of-the-art":[206],"(DC,":[211],"LAC,":[212],"NC,":[213],"EC,":[214],"BC,":[215],"CC,":[216],"SC,":[217],"PR,":[218],"PeC":[219],"WDC)":[221],"across":[222,236],"two":[223],"species":[224],"(yeast":[225],"human).":[227],"Experimental":[228],"results":[229],"demonstrate":[230],"GM-PIN":[232],"achieves":[233],"superior":[234],"multiple":[237],"including":[239],"identified":[242],"top":[244],"K,":[245],"Jackknifing,":[246],"PRAUC,":[247],"sensitivity,":[248],"F-measure":[249],"accuracy.":[251],"These":[252],"findings":[253],"confirm":[254],"granularity-modulated":[257],"method":[259],"effectively":[260],"constructs":[261],"high-quality":[262],"substantially":[265],"enhance":[266]},"counts_by_year":[],"updated_date":"2025-12-11T23:09:37.256380","created_date":"2025-10-10T00:00:00"}