{"id":"https://openalex.org/W2132966888","doi":"https://doi.org/10.1109/hpcsim.2011.5999896","title":"Optimisation and parallelisation of the partitioning around medoids function in R","display_name":"Optimisation and parallelisation of the partitioning around medoids function in R","publication_year":2011,"publication_date":"2011-07-01","ids":{"openalex":"https://openalex.org/W2132966888","doi":"https://doi.org/10.1109/hpcsim.2011.5999896","mag":"2132966888"},"language":"en","primary_location":{"id":"doi:10.1109/hpcsim.2011.5999896","is_oa":false,"landing_page_url":"https://doi.org/10.1109/hpcsim.2011.5999896","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2011 International Conference on High Performance Computing &amp; Simulation","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5103114310","display_name":"Micha\u0142 Piotrowski","orcid":"https://orcid.org/0009-0002-6939-782X"},"institutions":[{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]},{"id":"https://openalex.org/I1299528221","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842","country_code":"GB","type":"government","lineage":["https://openalex.org/I1299528221","https://openalex.org/I4210087105"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Michal Piotrowski","raw_affiliation_strings":["EPCC, JCMB, University of Edinburgh, UK","[EPCC, JCMB, King's, Buildings, University of Edinburgh, EH93JZ, UK]"],"affiliations":[{"raw_affiliation_string":"EPCC, JCMB, University of Edinburgh, UK","institution_ids":["https://openalex.org/I1299528221","https://openalex.org/I98677209"]},{"raw_affiliation_string":"[EPCC, JCMB, King's, Buildings, University of Edinburgh, EH93JZ, UK]","institution_ids":["https://openalex.org/I98677209"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064045642","display_name":"Thorsten Forster","orcid":"https://orcid.org/0000-0002-4483-3069"},"institutions":[{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]},{"id":"https://openalex.org/I1299528221","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842","country_code":"GB","type":"government","lineage":["https://openalex.org/I1299528221","https://openalex.org/I4210087105"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Thorsten Forster","raw_affiliation_strings":["EPCC, JCMB, University of Edinburgh, UK","Division of Pathway Medicine, University of Edinburgh, EH16 4SB, UK"],"affiliations":[{"raw_affiliation_string":"EPCC, JCMB, University of Edinburgh, UK","institution_ids":["https://openalex.org/I1299528221","https://openalex.org/I98677209"]},{"raw_affiliation_string":"Division of Pathway Medicine, University of Edinburgh, EH16 4SB, UK","institution_ids":["https://openalex.org/I98677209"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049760931","display_name":"Bartosz Dobrezelecki","orcid":null},"institutions":[{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Bartosz Dobrezelecki","raw_affiliation_strings":["Division of Pathway Medicine, University of Edinburgh, UK","EPCC, JCMB, King's, Buildings, University of Edinburgh, EH9 3JZ UK"],"affiliations":[{"raw_affiliation_string":"Division of Pathway Medicine, University of Edinburgh, UK","institution_ids":["https://openalex.org/I98677209"]},{"raw_affiliation_string":"EPCC, JCMB, King's, Buildings, University of Edinburgh, EH9 3JZ UK","institution_ids":["https://openalex.org/I98677209"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055159868","display_name":"Terence Sloan","orcid":null},"institutions":[{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Terence M. Sloan","raw_affiliation_strings":["Division of Pathway Medicine, University of Edinburgh, UK","EPCC, JCMB, King's, Builindgs University of Edinburgh, EH93JZ, UK"],"affiliations":[{"raw_affiliation_string":"Division of Pathway Medicine, University of Edinburgh, UK","institution_ids":["https://openalex.org/I98677209"]},{"raw_affiliation_string":"EPCC, JCMB, King's, Builindgs University of Edinburgh, EH93JZ, UK","institution_ids":["https://openalex.org/I98677209"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075683889","display_name":"Lawrence Mitchell","orcid":"https://orcid.org/0000-0001-8062-1453"},"institutions":[{"id":"https://openalex.org/I1299528221","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842","country_code":"GB","type":"government","lineage":["https://openalex.org/I1299528221","https://openalex.org/I4210087105"]},{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Lawrence Mitchell","raw_affiliation_strings":["EPCC, JCMB, University of Edinburgh, UK","EPCC, JCMB, King's, Buildings, University of Edinburgh, UK"],"affiliations":[{"raw_affiliation_string":"EPCC, JCMB, University of Edinburgh, UK","institution_ids":["https://openalex.org/I1299528221","https://openalex.org/I98677209"]},{"raw_affiliation_string":"EPCC, JCMB, King's, Buildings, University of Edinburgh, UK","institution_ids":["https://openalex.org/I98677209"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065696246","display_name":"Peter Ghazal","orcid":"https://orcid.org/0000-0003-0035-2228"},"institutions":[{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]},{"id":"https://openalex.org/I1299528221","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842","country_code":"GB","type":"government","lineage":["https://openalex.org/I1299528221","https://openalex.org/I4210087105"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Peter Ghazal","raw_affiliation_strings":["EPCC, JCMB, University of Edinburgh, UK","Division of Pathway Medicine, University of Edinburgh, EH16 4SB, UK"],"affiliations":[{"raw_affiliation_string":"EPCC, JCMB, University of Edinburgh, UK","institution_ids":["https://openalex.org/I1299528221","https://openalex.org/I98677209"]},{"raw_affiliation_string":"Division of Pathway Medicine, University of Edinburgh, EH16 4SB, UK","institution_ids":["https://openalex.org/I98677209"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091783537","display_name":"Muriel Mewsissen","orcid":null},"institutions":[{"id":"https://openalex.org/I1299528221","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842","country_code":"GB","type":"government","lineage":["https://openalex.org/I1299528221","https://openalex.org/I4210087105"]},{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Muriel Mewsissen","raw_affiliation_strings":["EPCC, JCMB, University of Edinburgh, UK","Division of Pathway Medicine, University of Edinburgh, EH16 4SB, UK"],"affiliations":[{"raw_affiliation_string":"EPCC, JCMB, University of Edinburgh, UK","institution_ids":["https://openalex.org/I1299528221","https://openalex.org/I98677209"]},{"raw_affiliation_string":"Division of Pathway Medicine, University of Edinburgh, EH16 4SB, UK","institution_ids":["https://openalex.org/I98677209"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089397522","display_name":"Savvas Petrou","orcid":null},"institutions":[{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Savvas Petrou","raw_affiliation_strings":["Division of Pathway Medicine, University of Edinburgh, UK","[EPCC, JCMB, King's Buidings, University of Edinburgh, UK]"],"affiliations":[{"raw_affiliation_string":"Division of Pathway Medicine, University of Edinburgh, UK","institution_ids":["https://openalex.org/I98677209"]},{"raw_affiliation_string":"[EPCC, JCMB, King's Buidings, University of Edinburgh, UK]","institution_ids":["https://openalex.org/I98677209"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040847245","display_name":"Arthur Trew","orcid":null},"institutions":[{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]},{"id":"https://openalex.org/I1299528221","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842","country_code":"GB","type":"government","lineage":["https://openalex.org/I1299528221","https://openalex.org/I4210087105"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Arthur Trew","raw_affiliation_strings":["EPCC, JCMB, University of Edinburgh, UK","[EPCC, JCMB, King's, Buildings, The University of Edinburgh, EH9 3JZ UK]"],"affiliations":[{"raw_affiliation_string":"EPCC, JCMB, University of Edinburgh, UK","institution_ids":["https://openalex.org/I1299528221","https://openalex.org/I98677209"]},{"raw_affiliation_string":"[EPCC, JCMB, King's, Buildings, The University of Edinburgh, EH9 3JZ UK]","institution_ids":["https://openalex.org/I98677209"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5079776964","display_name":"Jon Hill","orcid":"https://orcid.org/0000-0003-1340-4373"},"institutions":[{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]},{"id":"https://openalex.org/I124357947","display_name":"University of London","ror":"https://ror.org/04cw6st05","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Jon Hill","raw_affiliation_strings":["Department of Earth Sciences & Engineering, Imperial College, University of London, UK","[Dept. of Earth Sciences & Engineering, Imperial College, University of London, UK]"],"affiliations":[{"raw_affiliation_string":"Department of Earth Sciences & Engineering, Imperial College, University of London, UK","institution_ids":["https://openalex.org/I47508984","https://openalex.org/I124357947"]},{"raw_affiliation_string":"[Dept. of Earth Sciences & Engineering, Imperial College, University of London, UK]","institution_ids":["https://openalex.org/I124357947"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":10,"corresponding_author_ids":["https://openalex.org/A5103114310"],"corresponding_institution_ids":["https://openalex.org/I1299528221","https://openalex.org/I98677209"],"apc_list":null,"apc_paid":null,"fwci":0.1303,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.532094,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"31","issue":null,"first_page":"707","last_page":"713"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9988999962806702,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9988999962806702,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9955999851226807,"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/T11468","display_name":"Genetic Mapping and Diversity in Plants and Animals","score":0.9824000000953674,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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":0.8466695547103882},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.6908040046691895},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.6553560495376587},{"id":"https://openalex.org/keywords/medoid","display_name":"Medoid","score":0.6318929195404053},{"id":"https://openalex.org/keywords/exploit","display_name":"Exploit","score":0.5464507341384888},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.42749732732772827},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.33830487728118896},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.19085654616355896},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.14611226320266724}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8466695547103882},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.6908040046691895},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.6553560495376587},{"id":"https://openalex.org/C63085389","wikidata":"https://www.wikidata.org/wiki/Q4287912","display_name":"Medoid","level":3,"score":0.6318929195404053},{"id":"https://openalex.org/C165696696","wikidata":"https://www.wikidata.org/wiki/Q11287","display_name":"Exploit","level":2,"score":0.5464507341384888},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.42749732732772827},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.33830487728118896},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.19085654616355896},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.14611226320266724},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/hpcsim.2011.5999896","is_oa":false,"landing_page_url":"https://doi.org/10.1109/hpcsim.2011.5999896","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2011 International Conference on High Performance Computing &amp; Simulation","raw_type":"proceedings-article"},{"id":"pmh:oai:https://orca.cardiff.ac.uk:112591","is_oa":false,"landing_page_url":"https://orca.cardiff.ac.uk/id/eprint/112591/","pdf_url":null,"source":{"id":"https://openalex.org/S4306401195","display_name":"ORCA Online Research @Cardiff (Cardiff University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I79510175","host_organization_name":"Cardiff University","host_organization_lineage":["https://openalex.org/I79510175"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Conference or Workshop Item"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G314031883","display_name":null,"funder_award_id":"ES/H021787/1","funder_id":"https://openalex.org/F4320334630","funder_display_name":"Economic and Social Research Council"},{"id":"https://openalex.org/G5406021675","display_name":null,"funder_award_id":"EP/H006753/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320311904","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08"},{"id":"https://openalex.org/F4320320064","display_name":"Scottish Funding Council","ror":"https://ror.org/056bwcz71"},{"id":"https://openalex.org/F4320334627","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842"},{"id":"https://openalex.org/F4320334630","display_name":"Economic and Social Research Council","ror":"https://ror.org/03n0ht308"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":15,"referenced_works":["https://openalex.org/W31923072","https://openalex.org/W1585576391","https://openalex.org/W1966420492","https://openalex.org/W1982113214","https://openalex.org/W2029018990","https://openalex.org/W2040588881","https://openalex.org/W2068858902","https://openalex.org/W2075715210","https://openalex.org/W2083620785","https://openalex.org/W2096842432","https://openalex.org/W2127156690","https://openalex.org/W2139282709","https://openalex.org/W2156995578","https://openalex.org/W2158042082","https://openalex.org/W2166925272"],"related_works":["https://openalex.org/W17155033","https://openalex.org/W3207760230","https://openalex.org/W1496222301","https://openalex.org/W4312814274","https://openalex.org/W1590307681","https://openalex.org/W2536018345","https://openalex.org/W2587710587","https://openalex.org/W2100425112","https://openalex.org/W3037673319","https://openalex.org/W2742735109"],"abstract_inverted_index":{"R":[0,33,114,119],"is":[1,19],"a":[2,102,137,145],"free":[3],"statistical":[4],"programming":[5],"language":[6],"commonly":[7],"used":[8],"for":[9,110],"the":[10,97,111,141,153,160,169],"analysis":[11],"of":[12,40,101,130,140,155],"high-throughput":[13],"microarray":[14],"and":[15,47,61,89,99,144,164],"other":[16],"data.":[17],"It":[18],"currently":[20],"unable":[21],"to":[22,31,44,72,121],"easily":[23],"utilise":[24],"multi":[25],"processor":[26],"architectures":[27],"without":[28,127],"substantial":[29],"changes":[30],"existing":[32],"scripts.":[34],"Further,":[35],"working":[36],"with":[37],"large":[38],"volumes":[39],"data":[41,62,67,156,170],"often":[42],"leads":[43],"slow":[45],"processing":[46,154],"even":[48],"memory":[49,163],"allocation":[50],"faults.":[51],"A":[52],"recent":[53],"survey":[54],"highlighted":[55],"clustering":[56,104],"algorithms":[57,70],"as":[58,77],"both":[59],"computation":[60],"intensive":[63],"bottlenecks":[64],"in":[65,175],"post-genomic":[66],"analyses.":[68],"These":[69],"aim":[71],"sort":[73],"numeric":[74],"vectors":[75],"(such":[76],"gene":[78],"expression":[79],"profiles)":[80],"into":[81],"groups":[82,88],"by":[83],"minimising":[84],"vector":[85],"distances":[86],"within":[87],"maximising":[90],"them":[91],"between":[92],"groups.":[93],"This":[94,133],"paper":[95,134],"describes":[96],"optimisation":[98,139],"parallelisation":[100],"popular":[103],"algorithm,":[105],"partitioning":[106],"around":[107],"medoids":[108],"(PAM),":[109],"Simple":[112],"Parallel":[113],"INTerface":[115],"(SPRINT).":[116],"SPRINT":[117],"allows":[118],"users":[120],"exploit":[122],"high":[123],"performance":[124],"computing":[125],"systems":[126],"expert":[128],"knowledge":[129],"such":[131],"systems.":[132],"reports":[135],"on":[136,168],"serial":[138],"original":[142],"code":[143],"subsequent":[146],"parallel":[147,150],"implementation.":[148],"The":[149],"implementation":[151],"enables":[152],"sets":[157],"that":[158],"exceed":[159],"available":[161],"physical":[162],"can":[165],"yield,":[166],"depending":[167],"set,":[171],"over":[172],"100-fold":[173],"increase":[174],"performance.":[176]},"counts_by_year":[{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
