{"id":"https://openalex.org/W2065767832","doi":"https://doi.org/10.1142/s0219720013500091","title":"A HEURISTIC CLUSTER-BASED EM ALGORITHM FOR THE PLANTED (l, d) PROBLEM","display_name":"A HEURISTIC CLUSTER-BASED EM ALGORITHM FOR THE PLANTED (l, d) PROBLEM","publication_year":2013,"publication_date":"2013-05-12","ids":{"openalex":"https://openalex.org/W2065767832","doi":"https://doi.org/10.1142/s0219720013500091","mag":"2065767832","pmid":"https://pubmed.ncbi.nlm.nih.gov/23859273"},"language":"en","primary_location":{"id":"doi:10.1142/s0219720013500091","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720013500091","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/A5101401833","display_name":"Yipu Zhang","orcid":"https://orcid.org/0000-0001-5669-5292"},"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":"YIPU ZHANG","raw_affiliation_strings":["Department of Computer Science, Xidian University, Xi'an, 710071, Shaanxi, P. R. China"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Xidian University, Xi'an, 710071, Shaanxi, P. R. China","institution_ids":["https://openalex.org/I149594827"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072102175","display_name":"Hongwei Huo","orcid":"https://orcid.org/0000-0002-5436-1851"},"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":"HONGWEI HUO","raw_affiliation_strings":["Department of Computer Science, Xidian University, Xi'an, 710071, Shaanxi, P. R. China"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Xidian University, Xi'an, 710071, Shaanxi, P. R. China","institution_ids":["https://openalex.org/I149594827"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100665870","display_name":"Qiang Yu","orcid":"https://orcid.org/0000-0002-8725-6687"},"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":"QIANG YU","raw_affiliation_strings":["Department of Computer Science, Xidian University, Xi'an, 710071, Shaanxi, P. R. China"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Xidian University, Xi'an, 710071, Shaanxi, P. R. China","institution_ids":["https://openalex.org/I149594827"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5101401833"],"corresponding_institution_ids":["https://openalex.org/I149594827"],"apc_list":null,"apc_paid":null,"fwci":0.5849,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.68205963,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"11","issue":"04","first_page":"1350009","last_page":"1350009"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9994999766349792,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9994999766349792,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9894000291824341,"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/T10885","display_name":"Gene expression and cancer classification","score":0.989300012588501,"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/local-optimum","display_name":"Local optimum","score":0.7570189833641052},{"id":"https://openalex.org/keywords/motif","display_name":"Motif (music)","score":0.6331369280815125},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.58210688829422},{"id":"https://openalex.org/keywords/heuristic","display_name":"Heuristic","score":0.5288447141647339},{"id":"https://openalex.org/keywords/maximization","display_name":"Maximization","score":0.47775664925575256},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.45804092288017273},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4439719021320343},{"id":"https://openalex.org/keywords/mathematical-optimization","display_name":"Mathematical optimization","score":0.38884443044662476},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.35917556285858154},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3252905011177063},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2536957561969757}],"concepts":[{"id":"https://openalex.org/C141934464","wikidata":"https://www.wikidata.org/wiki/Q3305386","display_name":"Local optimum","level":2,"score":0.7570189833641052},{"id":"https://openalex.org/C32276052","wikidata":"https://www.wikidata.org/wiki/Q908349","display_name":"Motif (music)","level":2,"score":0.6331369280815125},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.58210688829422},{"id":"https://openalex.org/C173801870","wikidata":"https://www.wikidata.org/wiki/Q201413","display_name":"Heuristic","level":2,"score":0.5288447141647339},{"id":"https://openalex.org/C2776330181","wikidata":"https://www.wikidata.org/wiki/Q18358244","display_name":"Maximization","level":2,"score":0.47775664925575256},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.45804092288017273},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4439719021320343},{"id":"https://openalex.org/C126255220","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Mathematical optimization","level":1,"score":0.38884443044662476},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.35917556285858154},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3252905011177063},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2536957561969757},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"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":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","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}],"locations_count":2,"locations":[{"id":"doi:10.1142/s0219720013500091","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720013500091","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:23859273","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23859273","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":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":33,"referenced_works":["https://openalex.org/W1571755427","https://openalex.org/W1580213736","https://openalex.org/W1592870802","https://openalex.org/W1975924111","https://openalex.org/W1998300401","https://openalex.org/W2002586473","https://openalex.org/W2003967338","https://openalex.org/W2023863508","https://openalex.org/W2028904582","https://openalex.org/W2034206030","https://openalex.org/W2047386086","https://openalex.org/W2048869777","https://openalex.org/W2049114051","https://openalex.org/W2062088872","https://openalex.org/W2069611131","https://openalex.org/W2073850887","https://openalex.org/W2081277704","https://openalex.org/W2084908610","https://openalex.org/W2098058554","https://openalex.org/W2099316694","https://openalex.org/W2105502604","https://openalex.org/W2111359483","https://openalex.org/W2115603438","https://openalex.org/W2115979107","https://openalex.org/W2118393799","https://openalex.org/W2128091972","https://openalex.org/W2138247964","https://openalex.org/W2141408320","https://openalex.org/W2149769193","https://openalex.org/W2163133632","https://openalex.org/W2163713628","https://openalex.org/W2185072563","https://openalex.org/W2610493035"],"related_works":["https://openalex.org/W3170299350","https://openalex.org/W2368410102","https://openalex.org/W2368037387","https://openalex.org/W190186656","https://openalex.org/W2377079823","https://openalex.org/W2902352756","https://openalex.org/W2605676258","https://openalex.org/W2599962286","https://openalex.org/W2319582300","https://openalex.org/W2890847211"],"abstract_inverted_index":{"The":[0],"planted":[1,117],"motif":[2,103,118],"search":[3],"problem":[4],"arises":[5],"from":[6],"locating":[7],"the":[8,19,43,55,73,81,102,126,134],"transcription":[9],"factor":[10],"binding":[11],"sites":[12],"(TFBSs)":[13],"which":[14,71,121],"are":[15,32,48],"crucial":[16],"for":[17,29],"understanding":[18],"gene":[20],"regulatory":[21],"relationship.":[22],"Many":[23],"attempts":[24],"in":[25,34,76,100],"using":[26,89],"expectation":[27],"maximization":[28],"TFBSs":[30],"discovery":[31],"successful":[33],"past.":[35],"However,":[36],"identifying":[37,101],"highly":[38],"degenerate":[39],"motifs":[40],"and":[41,92,105,129],"reducing":[42],"effect":[44],"of":[45,57,136],"local":[46,60,83],"optima":[47,61],"still":[49],"an":[50],"arduous":[51],"task.":[52],"To":[53],"alleviate":[54],"vulnerability":[56],"EM":[58,68,77],"to":[59,79,124,131],"trapping,":[62],"we":[63],"present":[64],"a":[65,115],"heuristic":[66],"cluster-based":[67],"algorithm,":[69,120],"CEM,":[70],"refines":[72],"cluster":[74,139],"subsets":[75],"method":[78],"explore":[80],"best":[82],"optimal":[84],"solution.":[85],"Based":[86],"on":[87],"experiments":[88],"both":[90],"synthetic":[91],"real":[93],"datasets,":[94],"our":[95],"algorithm":[96],"demonstrates":[97],"significant":[98],"improvements":[99],"instances":[104,128],"performs":[106],"better":[107],"than":[108],"current":[109],"widely":[110],"used":[111],"algorithms.":[112],"CEM":[113],"is":[114,122,141],"novel":[116],"finding":[119],"able":[123],"solve":[125],"challenging":[127],"easy":[130],"parallel":[132],"since":[133],"process":[135],"solving":[137],"each":[138],"subset":[140],"independent.":[142]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
