{"id":"https://openalex.org/W4409986743","doi":"https://doi.org/10.1021/acs.jcim.4c02341","title":"Extended Quality (eQual): Radial Threshold Clustering Based on <i>n</i> -ary Similarity","display_name":"Extended Quality (eQual): Radial Threshold Clustering Based on <i>n</i> -ary Similarity","publication_year":2025,"publication_date":"2025-05-01","ids":{"openalex":"https://openalex.org/W4409986743","doi":"https://doi.org/10.1021/acs.jcim.4c02341","pmid":"https://pubmed.ncbi.nlm.nih.gov/40309753"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.4c02341","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c02341","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12148646","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5046415026","display_name":"Lexin Chen","orcid":"https://orcid.org/0000-0002-9528-942X"},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lexin Chen","raw_affiliation_strings":["Department of Chemistry","Quantum Theory Project","University of Florida"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry","institution_ids":[]},{"raw_affiliation_string":"Quantum Theory Project","institution_ids":[]},{"raw_affiliation_string":"University of Florida","institution_ids":["https://openalex.org/I33213144"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103970214","display_name":"Micah J. Smith","orcid":null},"institutions":[{"id":"https://openalex.org/I1321296531","display_name":"National Institute of Standards and Technology","ror":"https://ror.org/05xpvk416","country_code":"US","type":"funder","lineage":["https://openalex.org/I1321296531","https://openalex.org/I1343035065"]},{"id":"https://openalex.org/I4210138998","display_name":"Research Institute for Bioscience and Biotechnology","ror":"https://ror.org/045hp3b72","country_code":"NP","type":"nonprofit","lineage":["https://openalex.org/I4210138998"]},{"id":"https://openalex.org/I4389425230","display_name":"Institute for Bioscience and Biotechnology Research","ror":"https://ror.org/02zs3hb12","country_code":null,"type":"facility","lineage":["https://openalex.org/I126744593","https://openalex.org/I1321296531","https://openalex.org/I1343035065","https://openalex.org/I4389425230","https://openalex.org/I66946132"]}],"countries":["NP","US"],"is_corresponding":false,"raw_author_name":"Micah Smith","raw_affiliation_strings":["Institute for Bioscience and Biotechnology Research","National Institute of Standards and Technology and the University of Maryland"],"affiliations":[{"raw_affiliation_string":"Institute for Bioscience and Biotechnology Research","institution_ids":["https://openalex.org/I4210138998","https://openalex.org/I4389425230"]},{"raw_affiliation_string":"National Institute of Standards and Technology and the University of Maryland","institution_ids":["https://openalex.org/I1321296531"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062098434","display_name":"Daniel R. Roe","orcid":"https://orcid.org/0000-0002-5834-2447"},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210106489","display_name":"National Heart Lung and Blood Institute","ror":"https://ror.org/012pb6c26","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210106489"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Daniel R. Roe","raw_affiliation_strings":["Laboratory of Computational Biology, National Heart, Lung, and Blood Institute","National Institutes of Health"],"affiliations":[{"raw_affiliation_string":"Laboratory of Computational Biology, National Heart, Lung, and Blood Institute","institution_ids":["https://openalex.org/I4210106489"]},{"raw_affiliation_string":"National Institutes of Health","institution_ids":["https://openalex.org/I1299303238"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5039322037","display_name":"Ram\u00f3n Alain Miranda\u2010Quintana","orcid":"https://orcid.org/0000-0003-2121-4449"},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ram\u00f3n Alain Miranda-Quintana","raw_affiliation_strings":["Department of Chemistry","Quantum Theory Project","University of Florida"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry","institution_ids":[]},{"raw_affiliation_string":"Quantum Theory Project","institution_ids":[]},{"raw_affiliation_string":"University of Florida","institution_ids":["https://openalex.org/I33213144"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5039322037"],"corresponding_institution_ids":["https://openalex.org/I33213144"],"apc_list":null,"apc_paid":null,"fwci":9.9395,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.97608144,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":98},"biblio":{"volume":"65","issue":"10","first_page":"5062","last_page":"5070"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10637","display_name":"Advanced Clustering Algorithms Research","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/T10637","display_name":"Advanced Clustering Algorithms Research","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"}},{"id":"https://openalex.org/T10057","display_name":"Face and Expression Recognition","score":0.9983999729156494,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"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/T10824","display_name":"Image Retrieval and Classification Techniques","score":0.9909999966621399,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"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/cluster-analysis","display_name":"Cluster analysis","score":0.7123007774353027},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.639090895652771},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.4761386215686798},{"id":"https://openalex.org/keywords/quality","display_name":"Quality (philosophy)","score":0.45992618799209595},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4215430021286011},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.396179735660553},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.379936546087265},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.20691296458244324}],"concepts":[{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.7123007774353027},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.639090895652771},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.4761386215686798},{"id":"https://openalex.org/C2779530757","wikidata":"https://www.wikidata.org/wiki/Q1207505","display_name":"Quality (philosophy)","level":2,"score":0.45992618799209595},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4215430021286011},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.396179735660553},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.379936546087265},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.20691296458244324},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"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":"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":3,"locations":[{"id":"doi:10.1021/acs.jcim.4c02341","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c02341","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:40309753","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40309753","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 chemical information and modeling","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:12148646","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12148646","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Chem Inf Model","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:12148646","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12148646","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Chem Inf Model","raw_type":"Text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3926417061","display_name":null,"funder_award_id":"R35GM150620","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":42,"referenced_works":["https://openalex.org/W1493454437","https://openalex.org/W1973858832","https://openalex.org/W1984994707","https://openalex.org/W2013638340","https://openalex.org/W2013792107","https://openalex.org/W2051224630","https://openalex.org/W2053348581","https://openalex.org/W2085487226","https://openalex.org/W2095897464","https://openalex.org/W2112878090","https://openalex.org/W2118571345","https://openalex.org/W2131793079","https://openalex.org/W2145361639","https://openalex.org/W2147988069","https://openalex.org/W2163915395","https://openalex.org/W2165779834","https://openalex.org/W2165835468","https://openalex.org/W2271736303","https://openalex.org/W2548503138","https://openalex.org/W2783073729","https://openalex.org/W2791653366","https://openalex.org/W2953016572","https://openalex.org/W2968426314","https://openalex.org/W2974711963","https://openalex.org/W3153640839","https://openalex.org/W3156755596","https://openalex.org/W3159156584","https://openalex.org/W3162048346","https://openalex.org/W3189345586","https://openalex.org/W3189465577","https://openalex.org/W3209805961","https://openalex.org/W3216238908","https://openalex.org/W4220835489","https://openalex.org/W4285387825","https://openalex.org/W4297779812","https://openalex.org/W4306897068","https://openalex.org/W4393240342","https://openalex.org/W4396712309","https://openalex.org/W4399879257","https://openalex.org/W4400466484","https://openalex.org/W4401496991","https://openalex.org/W4402082179"],"related_works":["https://openalex.org/W4298130764","https://openalex.org/W2804364458","https://openalex.org/W2132641928","https://openalex.org/W4310225030","https://openalex.org/W2090259340","https://openalex.org/W1926736923","https://openalex.org/W2158836806","https://openalex.org/W2393816671","https://openalex.org/W2033914206","https://openalex.org/W2042327336"],"abstract_inverted_index":{"We":[0],"are":[1],"transforming":[2],"Radial":[3],"Threshold":[4],"Clustering":[5,13],"(RTC),":[6],"an":[7,15],"<i>O</i>(<i>N</i><sup>2</sup>)":[8],"algorithm,":[9],"into":[10],"Extended":[11],"Quality":[12],"(eQual),":[14],"<i>O</i>(<i>N</i>)":[16],"algorithm":[17,26,31,137],"with":[18,117],"several":[19],"novel":[20],"features.":[21],"Daura":[22],"et":[23],"al.'s":[24],"RTC":[25,45],"is":[27,74,128,138],"a":[28,75],"partitioning":[29],"clustering":[30,63],"that":[32],"groups":[33],"similar":[34],"frames":[35,71],"together":[36],"based":[37],"on":[38,66],"their":[39],"similarity":[40,133],"to":[41,99,119,140],"the":[42,67,78,84,90,93,101,104,109,114,122,131],"seed":[43,94],"configuration.":[44],"has":[46],"two":[47],"main":[48],"issues:":[49],"it":[50,55],"scales":[51],"as":[52],"<i>O</i>(<i>N</i><sup>2</sup>),":[53],"making":[54],"inefficient":[56],"for":[57],"large":[58],"frame":[59,120],"counts,":[60],"and":[61,112,124,145,149],"its":[62],"results":[64,115],"depend":[65],"order":[68],"of":[69,92,103],"input":[70],"whenever":[72],"there":[73],"tie":[76],"in":[77,142],"most":[79,125],"populated":[80],"cluster.":[81],"To":[82,107],"address":[83,108],"first":[85],"issue,":[86],"we":[87],"have":[88],"increased":[89],"speed":[91],"selection":[95],"by":[96],"using":[97,130],"<i>k</i>-means++":[98],"select":[100],"seeds":[102],"available":[105],"frames.":[106],"second":[110],"issue":[111],"make":[113],"invariant":[116],"respect":[118],"order,":[121],"densest":[123],"compact":[126,148],"cluster":[127,141],"chosen":[129],"extended":[132],"indices.":[134],"The":[135],"new":[136],"able":[139],"linear":[143],"time":[144],"produce":[146],"more":[147],"separate":[150],"clusters.":[151]},"counts_by_year":[{"year":2025,"cited_by_count":4}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-05-01T00:00:00"}
