{"id":"https://openalex.org/W2947625469","doi":"https://doi.org/10.1177/1094342019852128","title":"Fast search of third-order epistatic interactions on CPU and GPU clusters","display_name":"Fast search of third-order epistatic interactions on CPU and GPU clusters","publication_year":2019,"publication_date":"2019-05-27","ids":{"openalex":"https://openalex.org/W2947625469","doi":"https://doi.org/10.1177/1094342019852128","mag":"2947625469"},"language":"en","primary_location":{"id":"doi:10.1177/1094342019852128","is_oa":false,"landing_page_url":"https://doi.org/10.1177/1094342019852128","pdf_url":null,"source":{"id":"https://openalex.org/S60606485","display_name":"The International Journal of High Performance Computing Applications","issn_l":"1094-3420","issn":["1094-3420","1741-2846"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320017","host_organization_name":"SAGE Publishing","host_organization_lineage":["https://openalex.org/P4310320017"],"host_organization_lineage_names":["SAGE Publishing"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The International Journal of High Performance Computing Applications","raw_type":"journal-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/A5050214921","display_name":"Christian Ponte-Fern\u00e1ndez","orcid":"https://orcid.org/0000-0002-4728-6398"},"institutions":[{"id":"https://openalex.org/I11019714","display_name":"Universidade da Coru\u00f1a","ror":"https://ror.org/01qckj285","country_code":"ES","type":"education","lineage":["https://openalex.org/I11019714"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Christian Ponte-Fern\u00e1ndez","raw_affiliation_strings":["Departamento de Ingenier\u00eda de Computadores, CITIC, Grupo de Arquitectura de Computadores, Universidade da Coru\u00f1a, A Coru\u00f1a, Spain"],"affiliations":[{"raw_affiliation_string":"Departamento de Ingenier\u00eda de Computadores, CITIC, Grupo de Arquitectura de Computadores, Universidade da Coru\u00f1a, A Coru\u00f1a, Spain","institution_ids":["https://openalex.org/I11019714"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008112601","display_name":"Jorge Gonz\u00e1lez\u2010Dom\u00ednguez","orcid":"https://orcid.org/0000-0002-2602-4874"},"institutions":[{"id":"https://openalex.org/I11019714","display_name":"Universidade da Coru\u00f1a","ror":"https://ror.org/01qckj285","country_code":"ES","type":"education","lineage":["https://openalex.org/I11019714"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Jorge Gonz\u00e1lez-Dom\u00ednguez","raw_affiliation_strings":["Departamento de Ingenier\u00eda de Computadores, CITIC, Grupo de Arquitectura de Computadores, Universidade da Coru\u00f1a, A Coru\u00f1a, Spain"],"affiliations":[{"raw_affiliation_string":"Departamento de Ingenier\u00eda de Computadores, CITIC, Grupo de Arquitectura de Computadores, Universidade da Coru\u00f1a, A Coru\u00f1a, Spain","institution_ids":["https://openalex.org/I11019714"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5021488012","display_name":"Mar\u00eda J. Mart\u00edn","orcid":"https://orcid.org/0000-0002-9153-0909"},"institutions":[{"id":"https://openalex.org/I11019714","display_name":"Universidade da Coru\u00f1a","ror":"https://ror.org/01qckj285","country_code":"ES","type":"education","lineage":["https://openalex.org/I11019714"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Mar\u00eda J Mart\u00edn","raw_affiliation_strings":["Departamento de Ingenier\u00eda de Computadores, CITIC, Grupo de Arquitectura de Computadores, Universidade da Coru\u00f1a, A Coru\u00f1a, Spain"],"affiliations":[{"raw_affiliation_string":"Departamento de Ingenier\u00eda de Computadores, CITIC, Grupo de Arquitectura de Computadores, Universidade da Coru\u00f1a, A Coru\u00f1a, Spain","institution_ids":["https://openalex.org/I11019714"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5050214921"],"corresponding_institution_ids":["https://openalex.org/I11019714"],"apc_list":null,"apc_paid":null,"fwci":1.3701,"has_fulltext":false,"cited_by_count":24,"citation_normalized_percentile":{"value":0.8102304,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"34","issue":"1","first_page":"20","last_page":"29"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9958000183105469,"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":0.9958000183105469,"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":0.9861000180244446,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9767000079154968,"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/epistasis","display_name":"Epistasis","score":0.8012717962265015},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7835142612457275},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.5167548060417175},{"id":"https://openalex.org/keywords/implementation","display_name":"Implementation","score":0.47573256492614746},{"id":"https://openalex.org/keywords/heuristic","display_name":"Heuristic","score":0.42781081795692444},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1740647554397583},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1500561535358429},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.14365318417549133},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.13845118880271912},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.10406014323234558}],"concepts":[{"id":"https://openalex.org/C61727976","wikidata":"https://www.wikidata.org/wiki/Q751748","display_name":"Epistasis","level":3,"score":0.8012717962265015},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7835142612457275},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.5167548060417175},{"id":"https://openalex.org/C26713055","wikidata":"https://www.wikidata.org/wiki/Q245962","display_name":"Implementation","level":2,"score":0.47573256492614746},{"id":"https://openalex.org/C173801870","wikidata":"https://www.wikidata.org/wiki/Q201413","display_name":"Heuristic","level":2,"score":0.42781081795692444},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1740647554397583},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1500561535358429},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.14365318417549133},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.13845118880271912},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.10406014323234558}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1177/1094342019852128","is_oa":false,"landing_page_url":"https://doi.org/10.1177/1094342019852128","pdf_url":null,"source":{"id":"https://openalex.org/S60606485","display_name":"The International Journal of High Performance Computing Applications","issn_l":"1094-3420","issn":["1094-3420","1741-2846"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320017","host_organization_name":"SAGE Publishing","host_organization_lineage":["https://openalex.org/P4310320017"],"host_organization_lineage_names":["SAGE Publishing"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The International Journal of High Performance Computing Applications","raw_type":"journal-article"},{"id":"pmh:oai:ruc.udc.es:2183/27614","is_oa":false,"landing_page_url":"http://hdl.handle.net/2183/27614","pdf_url":null,"source":{"id":"https://openalex.org/S4306402204","display_name":"RUC (Universidade Da Coru\u00f1a)","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321837","display_name":"Ministerio de Econom\u00eda y Competitividad","ror":"https://ror.org/034900433"},{"id":"https://openalex.org/F4320326655","display_name":"Xunta de Galicia","ror":"https://ror.org/0181xnw06"},{"id":"https://openalex.org/F4320328802","display_name":"Universidade de Santiago de Compostela","ror":"https://ror.org/030eybx10"},{"id":"https://openalex.org/F4320330134","display_name":"Centro Singular de Investigaci\u00f3n de Galicia","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":35,"referenced_works":["https://openalex.org/W116308793","https://openalex.org/W1501108249","https://openalex.org/W1964525882","https://openalex.org/W1981723690","https://openalex.org/W1985288864","https://openalex.org/W2003631473","https://openalex.org/W2006880437","https://openalex.org/W2015523078","https://openalex.org/W2041170649","https://openalex.org/W2042680665","https://openalex.org/W2046316315","https://openalex.org/W2048993554","https://openalex.org/W2063575312","https://openalex.org/W2068966425","https://openalex.org/W2070082005","https://openalex.org/W2070644791","https://openalex.org/W2073835783","https://openalex.org/W2087121965","https://openalex.org/W2091518215","https://openalex.org/W2094170482","https://openalex.org/W2112966225","https://openalex.org/W2117138514","https://openalex.org/W2120888506","https://openalex.org/W2130856032","https://openalex.org/W2137655966","https://openalex.org/W2145022912","https://openalex.org/W2152905639","https://openalex.org/W2154572047","https://openalex.org/W2155078868","https://openalex.org/W2155781289","https://openalex.org/W2156064982","https://openalex.org/W2156429378","https://openalex.org/W2156995578","https://openalex.org/W2265889397","https://openalex.org/W2617467681"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W1547817677","https://openalex.org/W2023460495","https://openalex.org/W2615678788","https://openalex.org/W2109954095","https://openalex.org/W1967902778","https://openalex.org/W3083099115","https://openalex.org/W1981509636","https://openalex.org/W4235217192","https://openalex.org/W3139253026"],"abstract_inverted_index":{"Genome-Wide":[0],"Association":[1],"Studies":[2],"(GWASs),":[3],"analyses":[4],"that":[5,124],"try":[6],"to":[7,39,64,72,89,168],"find":[8],"a":[9,12,17,47,55,91,122,126],"link":[10],"between":[11,32,52],"given":[13],"phenotype":[14],"(such":[15],"as":[16,41,58,96],"disease)":[18],"and":[19,34,67,157,176],"genetic":[20,101,174],"markers,":[21],"have":[22,62],"been":[23],"growing":[24],"in":[25,27,70,87,104,113,179],"popularity":[26],"the":[28,44,50,74,79,98,105,134,138,142,162],"recent":[29],"years.":[30],"Relations":[31],"phenotypes":[33,45],"genotypes":[35],"are":[36,46],"not":[37],"easy":[38],"identify,":[40],"most":[42],"of":[43,49,78,100,110,136,141,172],"product":[48],"interaction":[51],"multiple":[53],"genes,":[54],"phenomenon":[56],"known":[57],"epistasis.":[59],"Many":[60],"authors":[61],"resorted":[63],"different":[65],"approaches":[66],"hardware":[68],"architectures":[69,132],"order":[71,88],"mitigate":[73],"exponential":[75,139],"time":[76],"complexity":[77],"problem.":[80],"However,":[81],"these":[82,111],"studies":[83],"make":[84],"some":[85,109],"compromises":[86],"keep":[90],"reasonable":[92],"execution":[93],"time,":[94],"such":[95],"limiting":[97],"number":[99],"markers":[102,112,175],"involved":[103],"interaction,":[106],"or":[107,188],"discarding":[108],"an":[114,170],"initial":[115],"filtering":[116],"stage.":[117],"This":[118],"work":[119],"presents":[120],"MPI3SNP,":[121],"tool":[123],"implements":[125],"three-way":[127],"exhaustive":[128],"search":[129],"for":[130,154],"cluster":[131,145],"with":[133],"aim":[135],"mitigating":[137],"growth":[140],"run-time.":[143],"Modern":[144],"solutions":[146],"usually":[147],"incorporate":[148],"GPUs.":[149,195],"Thus,":[150],"MPI3SNP":[151,165],"includes":[152],"implementations":[153],"both":[155],"multi-CPU":[156],"multi-GPU":[158],"clusters.":[159],"To":[160],"contextualize":[161],"performance":[163],"achieved,":[164],"is":[166,199],"able":[167],"analyze":[169],"input":[171],"6300":[173],"3200":[177],"samples":[178],"less":[180],"than":[181],"6":[182],"min":[183,190],"using":[184,191],"768":[185],"CPU":[186],"cores":[187],"4":[189],"8":[192],"NVIDIA":[193],"K80":[194],"The":[196],"source":[197],"code":[198],"available":[200],"at":[201],"https://github.com/chponte/mpi3snp":[202],".":[203]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":7},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
