{"id":"https://openalex.org/W4389702430","doi":"https://doi.org/10.1515/jib-2023-0006","title":"SAMNA: accurate alignment of multiple biological networks based on simulated annealing","display_name":"SAMNA: accurate alignment of multiple biological networks based on simulated annealing","publication_year":2023,"publication_date":"2023-12-01","ids":{"openalex":"https://openalex.org/W4389702430","doi":"https://doi.org/10.1515/jib-2023-0006","pmid":"https://pubmed.ncbi.nlm.nih.gov/38097366"},"language":"en","primary_location":{"id":"doi:10.1515/jib-2023-0006","is_oa":true,"landing_page_url":"http://dx.doi.org/10.1515/jib-2023-0006","pdf_url":"https://www.degruyterbrill.com/document/doi/10.1515/jib-2023-0006/pdf","source":{"id":"https://openalex.org/S4393917359","display_name":"Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics","issn_l":"1432-4385","issn":["1432-4385","1613-4516"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Integrative Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://www.degruyterbrill.com/document/doi/10.1515/jib-2023-0006/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5065653013","display_name":"Jing Chen","orcid":"https://orcid.org/0000-0003-1673-9734"},"institutions":[{"id":"https://openalex.org/I111599522","display_name":"Jiangnan University","ror":"https://ror.org/04mkzax54","country_code":"CN","type":"education","lineage":["https://openalex.org/I111599522"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Jing Chen","raw_affiliation_strings":["Jiangsu Provincial Engineering Laboratory of Pattern Recognition and Computational Intelligence, Jiangnan University , Wuxi , China","School of Artificial Intelligence and Computer Science, Jiangnan University , Wuxi , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Jiangsu Provincial Engineering Laboratory of Pattern Recognition and Computational Intelligence, Jiangnan University , Wuxi , China","institution_ids":["https://openalex.org/I111599522"]},{"raw_affiliation_string":"School of Artificial Intelligence and Computer Science, Jiangnan University , Wuxi , China","institution_ids":["https://openalex.org/I111599522"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101877374","display_name":"Zixiang Wang","orcid":"https://orcid.org/0009-0005-8783-7755"},"institutions":[{"id":"https://openalex.org/I111599522","display_name":"Jiangnan University","ror":"https://ror.org/04mkzax54","country_code":"CN","type":"education","lineage":["https://openalex.org/I111599522"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zixiang Wang","raw_affiliation_strings":["School of Artificial Intelligence and Computer Science, Jiangnan University , Wuxi , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Artificial Intelligence and Computer Science, Jiangnan University , Wuxi , China","institution_ids":["https://openalex.org/I111599522"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5091235672","display_name":"Jia Huang","orcid":"https://orcid.org/0000-0002-0976-9882"},"institutions":[{"id":"https://openalex.org/I111599522","display_name":"Jiangnan University","ror":"https://ror.org/04mkzax54","country_code":"CN","type":"education","lineage":["https://openalex.org/I111599522"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jia Huang","raw_affiliation_strings":["School of Artificial Intelligence and Computer Science, Jiangnan University , Wuxi , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Artificial Intelligence and Computer Science, Jiangnan University , Wuxi , China","institution_ids":["https://openalex.org/I111599522"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5065653013"],"corresponding_institution_ids":["https://openalex.org/I111599522"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.10902789,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"20","issue":"4","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998000264167786,"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":0.9998000264167786,"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":0.983299970626831,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9811999797821045,"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/computer-science","display_name":"Computer science","score":0.7060293555259705},{"id":"https://openalex.org/keywords/simulated-annealing","display_name":"Simulated annealing","score":0.678048849105835},{"id":"https://openalex.org/keywords/encode","display_name":"ENCODE","score":0.6676375269889832},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.5953845977783203},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.5515878796577454},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.5483322143554688},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.48387396335601807},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.47758248448371887},{"id":"https://openalex.org/keywords/alignment-free-sequence-analysis","display_name":"Alignment-free sequence analysis","score":0.46322372555732727},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4474935531616211},{"id":"https://openalex.org/keywords/network-topology","display_name":"Network topology","score":0.42837631702423096},{"id":"https://openalex.org/keywords/structural-alignment","display_name":"Structural alignment","score":0.41578930616378784},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.3678775131702423},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3463256061077118},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.340302973985672},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.29694864153862},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.2198987901210785},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.10069140791893005},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.08054384589195251}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7060293555259705},{"id":"https://openalex.org/C126980161","wikidata":"https://www.wikidata.org/wiki/Q863783","display_name":"Simulated annealing","level":2,"score":0.678048849105835},{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.6676375269889832},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.5953845977783203},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.5515878796577454},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.5483322143554688},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.48387396335601807},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.47758248448371887},{"id":"https://openalex.org/C180384323","wikidata":"https://www.wikidata.org/wiki/Q16335137","display_name":"Alignment-free sequence analysis","level":5,"score":0.46322372555732727},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4474935531616211},{"id":"https://openalex.org/C199845137","wikidata":"https://www.wikidata.org/wiki/Q145490","display_name":"Network topology","level":2,"score":0.42837631702423096},{"id":"https://openalex.org/C4668613","wikidata":"https://www.wikidata.org/wiki/Q4116110","display_name":"Structural alignment","level":5,"score":0.41578930616378784},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.3678775131702423},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3463256061077118},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.340302973985672},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.29694864153862},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.2198987901210785},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.10069140791893005},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.08054384589195251},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0}],"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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","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":null,"qualifier_name":null,"is_major_topic":true},{"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":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1515/jib-2023-0006","is_oa":true,"landing_page_url":"http://dx.doi.org/10.1515/jib-2023-0006","pdf_url":"https://www.degruyterbrill.com/document/doi/10.1515/jib-2023-0006/pdf","source":{"id":"https://openalex.org/S4393917359","display_name":"Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics","issn_l":"1432-4385","issn":["1432-4385","1613-4516"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Integrative Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38097366","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38097366","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":"Journal of integrative bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10777366","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10777366","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10777366/pdf/jib-20-4-jib-2023-0006.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Integr Bioinform","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:11aa6bcc828e444bb6d6039c7d05818f","is_oa":true,"landing_page_url":"https://doaj.org/article/11aa6bcc828e444bb6d6039c7d05818f","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"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":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Integrative Bioinformatics, Vol 20, Iss 4, Pp 155-71 (2023)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1515/jib-2023-0006","is_oa":true,"landing_page_url":"http://dx.doi.org/10.1515/jib-2023-0006","pdf_url":"https://www.degruyterbrill.com/document/doi/10.1515/jib-2023-0006/pdf","source":{"id":"https://openalex.org/S4393917359","display_name":"Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics","issn_l":"1432-4385","issn":["1432-4385","1613-4516"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Integrative Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land","score":0.6200000047683716}],"awards":[],"funders":[{"id":"https://openalex.org/F4320321605","display_name":"Government of Jiangsu Province","ror":"https://ror.org/004svx814"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4389702430.pdf","grobid_xml":"https://content.openalex.org/works/W4389702430.grobid-xml"},"referenced_works_count":38,"referenced_works":["https://openalex.org/W1538574688","https://openalex.org/W2012139697","https://openalex.org/W2056124433","https://openalex.org/W2127957894","https://openalex.org/W2128408632","https://openalex.org/W2139361324","https://openalex.org/W2140084895","https://openalex.org/W2142678478","https://openalex.org/W2153929049","https://openalex.org/W2168926448","https://openalex.org/W2171053395","https://openalex.org/W2171255489","https://openalex.org/W2409564679","https://openalex.org/W2569705007","https://openalex.org/W2587997094","https://openalex.org/W2738984681","https://openalex.org/W2798819943","https://openalex.org/W2899498748","https://openalex.org/W2964024205","https://openalex.org/W2971248389","https://openalex.org/W2996905365","https://openalex.org/W2997654457","https://openalex.org/W3002335812","https://openalex.org/W3007888226","https://openalex.org/W3017223498","https://openalex.org/W3030734823","https://openalex.org/W3087069438","https://openalex.org/W3098951026","https://openalex.org/W3100057034","https://openalex.org/W3103118351","https://openalex.org/W3126817587","https://openalex.org/W3149236675","https://openalex.org/W3157049006","https://openalex.org/W3194156258","https://openalex.org/W4205565320","https://openalex.org/W4206353653","https://openalex.org/W4211085285","https://openalex.org/W4386195729"],"related_works":["https://openalex.org/W2051969447","https://openalex.org/W2111937814","https://openalex.org/W2029514038","https://openalex.org/W2141411672","https://openalex.org/W2133116680","https://openalex.org/W1482324242","https://openalex.org/W2468116983","https://openalex.org/W2088487249","https://openalex.org/W187239587","https://openalex.org/W2158700816"],"abstract_inverted_index":{"Abstract":[0],"Proteins":[1],"are":[2],"important":[3],"parts":[4],"of":[5,13,64],"the":[6,44,55,61,106,148,160,166],"biological":[7,14,170],"structures":[8],"and":[9,33,74,100,129,138,155,159],"encode":[10],"a":[11,21,77,83,115,119],"lot":[12],"information.":[15,103],"Protein\u2013protein":[16],"interaction":[17],"network":[18,49,70,86,98,157],"alignment":[19,40,71,87,136],"is":[20,76],"model":[22],"for":[23],"analyzing":[24],"proteins":[25],"that":[26,163],"helps":[27],"discover":[28],"conserved":[29],"functions":[30],"between":[31],"organisms":[32],"predict":[34],"unknown":[35],"functions.":[36],"In":[37],"particular,":[38],"multi-network":[39],"aims":[41],"at":[42],"finding":[43],"mapping":[45],"relationship":[46],"among":[47],"multiple":[48],"nodes,":[50],"so":[51],"as":[52,135],"to":[53,68],"transfer":[54],"knowledge":[56],"across":[57],"species.":[58],"However,":[59],"with":[60,125],"increasing":[62],"complexity":[63],"PPI":[65],"networks,":[66],"how":[67],"perform":[69],"more":[72],"accurately":[73],"efficiently":[75],"new":[78,84],"challenge.":[79],"This":[80],"paper":[81],"proposes":[82],"global":[85],"algorithm":[88,117,150,168],"called":[89],"Simulated":[90],"Annealing":[91],"Multiple":[92],"Network":[93],"Alignment":[94],"(SAMNA),":[95],"using":[96,141],"both":[97],"topology":[99],"sequence":[101,126],"homology":[102],"To":[104],"generate":[105],"alignment,":[107],"SAMNA":[108,149,164],"first":[109],"generates":[110],"cross-network":[111],"candidate":[112,132],"clusters":[113],"by":[114],"clustering":[116],"on":[118,153],"k":[120],"-partite":[121],"similarity":[122,127],"graph":[123],"constructed":[124],"information,":[128],"then":[130],"selects":[131],"cluster":[133],"nodes":[134],"results":[137,161],"optimizes":[139],"them":[140],"an":[142],"improved":[143],"simulated":[144],"annealing":[145],"algorithm.":[146],"Finally,":[147],"was":[151],"experimented":[152],"synthetic":[154],"real-world":[156],"datasets,":[158],"showed":[162],"outperformed":[165],"state-of-the-art":[167],"in":[169],"performance.":[171]},"counts_by_year":[],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}