{"id":"https://openalex.org/W2944373801","doi":"https://doi.org/10.1142/s0219720019500239","title":"A sparse and decomposed particle swarm optimization for inferring gene regulatory networks based on fuzzy cognitive maps","display_name":"A sparse and decomposed particle swarm optimization for inferring gene regulatory networks based on fuzzy cognitive maps","publication_year":2019,"publication_date":"2019-05-10","ids":{"openalex":"https://openalex.org/W2944373801","doi":"https://doi.org/10.1142/s0219720019500239","mag":"2944373801","pmid":"https://pubmed.ncbi.nlm.nih.gov/31617458"},"language":"en","primary_location":{"id":"doi:10.1142/s0219720019500239","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720019500239","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","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/A5010157183","display_name":"Luowen Liu","orcid":"https://orcid.org/0000-0002-0698-1423"},"institutions":[{"id":"https://openalex.org/I149594827","display_name":"Xidian University","ror":"https://ror.org/05s92vm98","country_code":"CN","type":"education","lineage":["https://openalex.org/I149594827"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Luowen Liu","raw_affiliation_strings":["Key Laboratory of Intelligent Perception and Image Understanding of Ministry of Education, Xidian University, Xi\u2019an 710071, P.\u00a0R.\u00a0China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory of Intelligent Perception and Image Understanding of Ministry of Education, Xidian University, Xi\u2019an 710071, P.\u00a0R.\u00a0China","institution_ids":["https://openalex.org/I149594827"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100375038","display_name":"Jing Liu","orcid":"https://orcid.org/0000-0002-6834-5350"},"institutions":[{"id":"https://openalex.org/I149594827","display_name":"Xidian University","ror":"https://ror.org/05s92vm98","country_code":"CN","type":"education","lineage":["https://openalex.org/I149594827"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jing Liu","raw_affiliation_strings":["Key Laboratory of Intelligent Perception and Image Understanding of Ministry of Education, Xidian University, Xi\u2019an 710071, P.\u00a0R.\u00a0China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory of Intelligent Perception and Image Understanding of Ministry of Education, Xidian University, Xi\u2019an 710071, P.\u00a0R.\u00a0China","institution_ids":["https://openalex.org/I149594827"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5010157183"],"corresponding_institution_ids":["https://openalex.org/I149594827"],"apc_list":null,"apc_paid":null,"fwci":0.1451,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.56077259,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"17","issue":"04","first_page":"1950023","last_page":"1950023"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12805","display_name":"Cognitive Science and Mapping","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T12805","display_name":"Cognitive Science and Mapping","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"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/fuzzy-cognitive-map","display_name":"Fuzzy cognitive map","score":0.7732982635498047},{"id":"https://openalex.org/keywords/particle-swarm-optimization","display_name":"Particle swarm optimization","score":0.6920872330665588},{"id":"https://openalex.org/keywords/fuzzy-logic","display_name":"Fuzzy logic","score":0.558601438999176},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5373173952102661},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.45761460065841675},{"id":"https://openalex.org/keywords/cognition","display_name":"Cognition","score":0.42474284768104553},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3708626627922058},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3579748868942261},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2999994456768036},{"id":"https://openalex.org/keywords/neuro-fuzzy","display_name":"Neuro-fuzzy","score":0.24125328660011292},{"id":"https://openalex.org/keywords/fuzzy-control-system","display_name":"Fuzzy control system","score":0.208831787109375},{"id":"https://openalex.org/keywords/neuroscience","display_name":"Neuroscience","score":0.08162429928779602}],"concepts":[{"id":"https://openalex.org/C5041914","wikidata":"https://www.wikidata.org/wiki/Q5511107","display_name":"Fuzzy cognitive map","level":5,"score":0.7732982635498047},{"id":"https://openalex.org/C85617194","wikidata":"https://www.wikidata.org/wiki/Q2072794","display_name":"Particle swarm optimization","level":2,"score":0.6920872330665588},{"id":"https://openalex.org/C58166","wikidata":"https://www.wikidata.org/wiki/Q224821","display_name":"Fuzzy logic","level":2,"score":0.558601438999176},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5373173952102661},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.45761460065841675},{"id":"https://openalex.org/C169900460","wikidata":"https://www.wikidata.org/wiki/Q2200417","display_name":"Cognition","level":2,"score":0.42474284768104553},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3708626627922058},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3579748868942261},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2999994456768036},{"id":"https://openalex.org/C29470771","wikidata":"https://www.wikidata.org/wiki/Q4165150","display_name":"Neuro-fuzzy","level":4,"score":0.24125328660011292},{"id":"https://openalex.org/C195975749","wikidata":"https://www.wikidata.org/wiki/Q1475705","display_name":"Fuzzy control system","level":3,"score":0.208831787109375},{"id":"https://openalex.org/C169760540","wikidata":"https://www.wikidata.org/wiki/Q207011","display_name":"Neuroscience","level":1,"score":0.08162429928779602}],"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":"D017143","descriptor_name":"Fuzzy Logic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017143","descriptor_name":"Fuzzy Logic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017143","descriptor_name":"Fuzzy Logic","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":"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":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1142/s0219720019500239","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720019500239","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},{"id":"pmid:31617458","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31617458","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 bioinformatics and computational biology","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals","score":0.4000000059604645}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":43,"referenced_works":["https://openalex.org/W338388561","https://openalex.org/W927564712","https://openalex.org/W1459085915","https://openalex.org/W1514247755","https://openalex.org/W1578549529","https://openalex.org/W1965739610","https://openalex.org/W1966250206","https://openalex.org/W1986688807","https://openalex.org/W1989652873","https://openalex.org/W2017731388","https://openalex.org/W2023348596","https://openalex.org/W2031535420","https://openalex.org/W2033385355","https://openalex.org/W2034669994","https://openalex.org/W2035793819","https://openalex.org/W2057867492","https://openalex.org/W2066031679","https://openalex.org/W2072934801","https://openalex.org/W2081232506","https://openalex.org/W2092394555","https://openalex.org/W2095224843","https://openalex.org/W2095622082","https://openalex.org/W2115664087","https://openalex.org/W2115845871","https://openalex.org/W2135046866","https://openalex.org/W2137947700","https://openalex.org/W2141239733","https://openalex.org/W2145590522","https://openalex.org/W2148605346","https://openalex.org/W2152195021","https://openalex.org/W2157121418","https://openalex.org/W2157984621","https://openalex.org/W2159055726","https://openalex.org/W2160533336","https://openalex.org/W2161409973","https://openalex.org/W2165299997","https://openalex.org/W2306180594","https://openalex.org/W2312599005","https://openalex.org/W2520865593","https://openalex.org/W2550255991","https://openalex.org/W2606301575","https://openalex.org/W2612413108","https://openalex.org/W2765806132"],"related_works":["https://openalex.org/W2063798559","https://openalex.org/W2991207020","https://openalex.org/W1661487699","https://openalex.org/W2372922208","https://openalex.org/W1491151750","https://openalex.org/W2145925682","https://openalex.org/W2777396095","https://openalex.org/W2617561368","https://openalex.org/W1982418457","https://openalex.org/W2365224437"],"abstract_inverted_index":{"Inferring":[0],"gene":[1],"regulatory":[2,16],"networks":[3],"(GRNs)":[4],"is":[5,75,108],"vital":[6],"to":[7,38,77,90],"understand":[8],"the":[9,15,32,82,92,100,102,114,130],"complex":[10],"cellular":[11],"processes":[12],"and":[13,52,65,86,113,118,134,141],"reveal":[14],"mechanisms":[17],"among":[18],"genes.":[19],"Although":[20],"various":[21],"methods":[22],"have":[23],"been":[24],"developed,":[25],"more":[26],"accurate":[27],"algorithms":[28],"which":[29,80],"can":[30,127],"control":[31,91,129],"sparseness":[33,94,131],"of":[34,104,132],"GRNs":[35,46,137],"still":[36],"need":[37],"be":[39],"developed.":[40],"In":[41,99],"this":[42],"work,":[43],"we":[44],"model":[45],"by":[47],"fuzzy":[48],"cognitive":[49],"maps":[50],"(FCMs),":[51],"a":[53,59,62,96],"node":[54],"in":[55],"an":[56],"FCM":[57,73,106,125],"means":[58],"gene.":[60],"Then,":[61],"new":[63],"sparse":[64],"decomposed":[66,97],"particle":[67],"swarm":[68],"optimization,":[69],"termed":[70],"as":[71],"SDPSO":[72,105,124],"-GRN,":[74],"proposed":[76],"train":[78],"FCMs,":[79],"employs":[81],"least":[83],"absolute":[84],"shrinkage":[85],"selection":[87],"operator":[88],"(Lasso)":[89],"network":[93],"with":[95,138],"strategy.":[98],"experiments,":[101],"performance":[103],"-GRN":[107,126],"validated":[109],"on":[110],"synthetic":[111],"data":[112],"well-known":[115],"benchmark":[116],"DREAM3":[117],"DREAM4.":[119],"The":[120],"results":[121],"show":[122],"that":[123],"well":[128],"GRNs,":[133],"infer":[135],"directed":[136],"high":[139],"accuracy":[140],"efficiency.":[142]},"counts_by_year":[{"year":2019,"cited_by_count":1}],"updated_date":"2026-05-16T08:24:45.110214","created_date":"2025-10-10T00:00:00"}
