{"id":"https://openalex.org/W4413557550","doi":"https://doi.org/10.1109/tcbbio.2025.3602120","title":"Nature-Inspired Meta-Heuristic Algorithms for Detecting Protein Complexes in Protein-Protein Interaction Networks: A Survey","display_name":"Nature-Inspired Meta-Heuristic Algorithms for Detecting Protein Complexes in Protein-Protein Interaction Networks: A Survey","publication_year":2025,"publication_date":"2025-08-25","ids":{"openalex":"https://openalex.org/W4413557550","doi":"https://doi.org/10.1109/tcbbio.2025.3602120","pmid":"https://pubmed.ncbi.nlm.nih.gov/40853787"},"language":"en","primary_location":{"id":"doi:10.1109/tcbbio.2025.3602120","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3602120","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/A5100763402","display_name":"Wei Zheng","orcid":"https://orcid.org/0000-0002-5471-7328"},"institutions":[{"id":"https://openalex.org/I181877577","display_name":"Shanxi University","ror":"https://ror.org/03y3e3s17","country_code":"CN","type":"education","lineage":["https://openalex.org/I181877577"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Wei Zheng","raw_affiliation_strings":["School of Computer and Information Technology, Shanxi University, Taiyuan, China"],"affiliations":[{"raw_affiliation_string":"School of Computer and Information Technology, Shanxi University, Taiyuan, China","institution_ids":["https://openalex.org/I181877577"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005474942","display_name":"Jianyong Sun","orcid":"https://orcid.org/0000-0002-9188-1856"},"institutions":[{"id":"https://openalex.org/I87445476","display_name":"Xi'an Jiaotong University","ror":"https://ror.org/017zhmm22","country_code":"CN","type":"education","lineage":["https://openalex.org/I87445476"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jianyong Sun","raw_affiliation_strings":["School of Mathematics and Statistics, Xi’an Jiaotong University, Xi’an, China","School of Mathematics and Statistics, Xi'an Jiaotong University, Xi'an, China"],"affiliations":[{"raw_affiliation_string":"School of Mathematics and Statistics, Xi’an Jiaotong University, Xi’an, China","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"School of Mathematics and Statistics, Xi'an Jiaotong University, Xi'an, China","institution_ids":["https://openalex.org/I87445476"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5060123829","display_name":"Haotian Zhang","orcid":null},"institutions":[{"id":"https://openalex.org/I87445476","display_name":"Xi'an Jiaotong University","ror":"https://ror.org/017zhmm22","country_code":"CN","type":"education","lineage":["https://openalex.org/I87445476"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Haotian Zhang","raw_affiliation_strings":["Frontier Institute of Science and Technology, Xi’an Jiaotong University, Xi’an, China","Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, China"],"affiliations":[{"raw_affiliation_string":"Frontier Institute of Science and Technology, Xi’an Jiaotong University, Xi’an, China","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, China","institution_ids":["https://openalex.org/I87445476"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5100763402"],"corresponding_institution_ids":["https://openalex.org/I181877577"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.19171927,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"22","issue":"6","first_page":"2817","last_page":"2832"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9937000274658203,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9937000274658203,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9837999939918518,"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":0.9571999907493591,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/heuristic","display_name":"Heuristic","score":0.5948581099510193},{"id":"https://openalex.org/keywords/meta-heuristic","display_name":"Meta heuristic","score":0.5490139722824097},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5466925501823425},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4860416054725647},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.37830230593681335}],"concepts":[{"id":"https://openalex.org/C173801870","wikidata":"https://www.wikidata.org/wiki/Q201413","display_name":"Heuristic","level":2,"score":0.5948581099510193},{"id":"https://openalex.org/C2988037039","wikidata":"https://www.wikidata.org/wiki/Q1385229","display_name":"Meta heuristic","level":2,"score":0.5490139722824097},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5466925501823425},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4860416054725647},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.37830230593681335}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":true},{"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":"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":"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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"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":"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":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbbio.2025.3602120","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3602120","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:40853787","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40853787","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1093286509","display_name":null,"funder_award_id":"12401672","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G1539943547","display_name":null,"funder_award_id":"2025M771731","funder_id":"https://openalex.org/F4320321543","funder_display_name":"China Postdoctoral Science Foundation"},{"id":"https://openalex.org/G3774616902","display_name":null,"funder_award_id":"ZR2022MF346","funder_id":"https://openalex.org/F4320324174","funder_display_name":"Natural Science Foundation of Shandong Province"},{"id":"https://openalex.org/G7589611490","display_name":null,"funder_award_id":"12426305","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8717214641","display_name":null,"funder_award_id":"12401670","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/F4320321543","display_name":"China Postdoctoral Science Foundation","ror":"https://ror.org/0426zh255"},{"id":"https://openalex.org/F4320324174","display_name":"Natural Science Foundation of Shandong Province","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":131,"referenced_works":["https://openalex.org/W77851419","https://openalex.org/W109709570","https://openalex.org/W122143408","https://openalex.org/W796286943","https://openalex.org/W1485582261","https://openalex.org/W1510970454","https://openalex.org/W1580954716","https://openalex.org/W1596536970","https://openalex.org/W1934405236","https://openalex.org/W1966274907","https://openalex.org/W1966546784","https://openalex.org/W1967822181","https://openalex.org/W1968842724","https://openalex.org/W1970562434","https://openalex.org/W1971013885","https://openalex.org/W1971421925","https://openalex.org/W1973508741","https://openalex.org/W1974515660","https://openalex.org/W1974613511","https://openalex.org/W1975751762","https://openalex.org/W1977186059","https://openalex.org/W1979899431","https://openalex.org/W1982732700","https://openalex.org/W1985817649","https://openalex.org/W1986214964","https://openalex.org/W2002145681","https://openalex.org/W2002850151","https://openalex.org/W2007448777","https://openalex.org/W2017117968","https://openalex.org/W2025569092","https://openalex.org/W2050721857","https://openalex.org/W2062624366","https://openalex.org/W2063508371","https://openalex.org/W2068749491","https://openalex.org/W2082565035","https://openalex.org/W2082898796","https://openalex.org/W2084619201","https://openalex.org/W2090422756","https://openalex.org/W2093083792","https://openalex.org/W2095293504","https://openalex.org/W2096173332","https://openalex.org/W2096939566","https://openalex.org/W2097706568","https://openalex.org/W2100585269","https://openalex.org/W2100628741","https://openalex.org/W2105883975","https://openalex.org/W2107067224","https://openalex.org/W2110708857","https://openalex.org/W2110711069","https://openalex.org/W2113654464","https://openalex.org/W2116117181","https://openalex.org/W2116447934","https://openalex.org/W2117412805","https://openalex.org/W2120191167","https://openalex.org/W2124112137","https://openalex.org/W2124166542","https://openalex.org/W2124354935","https://openalex.org/W2125673723","https://openalex.org/W2126105956","https://openalex.org/W2126991359","https://openalex.org/W2127048411","https://openalex.org/W2132993044","https://openalex.org/W2134695923","https://openalex.org/W2136850043","https://openalex.org/W2138003801","https://openalex.org/W2140280811","https://openalex.org/W2140462113","https://openalex.org/W2143065952","https://openalex.org/W2143381319","https://openalex.org/W2150934340","https://openalex.org/W2151176490","https://openalex.org/W2152195021","https://openalex.org/W2152336513","https://openalex.org/W2152495216","https://openalex.org/W2153161570","https://openalex.org/W2155320925","https://openalex.org/W2156070536","https://openalex.org/W2156194072","https://openalex.org/W2160313295","https://openalex.org/W2162891889","https://openalex.org/W2163485494","https://openalex.org/W2165232124","https://openalex.org/W2165533101","https://openalex.org/W2254563062","https://openalex.org/W2294708468","https://openalex.org/W2497472168","https://openalex.org/W2504708064","https://openalex.org/W2531496612","https://openalex.org/W2563515532","https://openalex.org/W2581439210","https://openalex.org/W2606309320","https://openalex.org/W2750490914","https://openalex.org/W2797989094","https://openalex.org/W2806781084","https://openalex.org/W2896901786","https://openalex.org/W2905614462","https://openalex.org/W2911363402","https://openalex.org/W2912312581","https://openalex.org/W2966453304","https://openalex.org/W2966787003","https://openalex.org/W2973129733","https://openalex.org/W2981958531","https://openalex.org/W2994575157","https://openalex.org/W3008459824","https://openalex.org/W3126600466","https://openalex.org/W3126625348","https://openalex.org/W3136933010","https://openalex.org/W3182563698","https://openalex.org/W3196854072","https://openalex.org/W3198527636","https://openalex.org/W3203791359","https://openalex.org/W4200350015","https://openalex.org/W4200555891","https://openalex.org/W4206646274","https://openalex.org/W4210705151","https://openalex.org/W4220981648","https://openalex.org/W4281676089","https://openalex.org/W4292083457","https://openalex.org/W4293183328","https://openalex.org/W4294216483","https://openalex.org/W4303411653","https://openalex.org/W4311772362","https://openalex.org/W4312431055","https://openalex.org/W4365459335","https://openalex.org/W4385514835","https://openalex.org/W4386215940","https://openalex.org/W4391958977","https://openalex.org/W4396768269","https://openalex.org/W4404202766","https://openalex.org/W4405907205","https://openalex.org/W4411054984"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2051487156","https://openalex.org/W2073681303","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W4310120240"],"abstract_inverted_index":{"In":[0,39],"cells,":[1],"various":[2],"proteins":[3],"interact":[4],"to":[5,110],"form":[6],"protein-protein":[7,29],"interaction":[8,30],"networks.":[9,55],"Protein":[10],"complexes":[11,27,52],"serve":[12],"as":[13],"the":[14,61,63,119],"fundamental":[15],"units":[16],"that":[17],"enable":[18],"essential":[19],"functions":[20],"in":[21,28,82,133],"biological":[22],"organisms.":[23],"Directly":[24],"detecting":[25],"protein":[26,51],"networks":[31],"using":[32],"biology-based":[33],"methods":[34,44,69,97],"is":[35],"costly":[36],"and":[37,101,105,113,127,136],"time-consuming.":[38],"recent":[40],"years,":[41],"different":[42],"computational":[43],"have":[45,129],"emerged":[46],"for":[47,74,140],"identifying":[48],"or":[49],"predicting":[50],"within":[53],"these":[54],"Following":[56],"a":[57,87],"comprehensive":[58],"analysis":[59],"of":[60,78,90,122],"issue,":[62],"optimization":[64,115],"algorithm":[65],"based":[66],"on":[67,108],"meta-heuristic":[68,92],"has":[70],"been":[71],"completely":[72],"executed":[73],"this":[75,123],"specific":[76],"type":[77],"challenge,":[79],"which":[80,117],"started":[81],"2004.":[83],"This":[84],"paper":[85],"provides":[86],"systematic":[88],"survey":[89],"such":[91],"algorithms.":[93],"Specifically,":[94],"34":[95],"related":[96],"published":[98],"between":[99],"2004":[100],"2024":[102],"are":[103,118],"collected":[104],"summarized,":[106],"focusing":[107],"how":[109],"model":[111],"problems":[112],"design":[114],"algorithms,":[116],"key":[120],"components":[121],"survey.":[124],"Our":[125],"observations":[126],"analyses":[128],"revealed":[130],"several":[131],"limitations":[132],"existing":[134],"studies":[135],"suggested":[137],"potential":[138],"avenues":[139],"future":[141],"research.":[142]},"counts_by_year":[],"updated_date":"2026-04-09T08:11:56.329763","created_date":"2025-10-10T00:00:00"}