{"id":"https://openalex.org/W3153992345","doi":"https://doi.org/10.1145/3437359.3465562","title":"Accelerating Key Bioinformatics Tasks 100-fold by Improving Memory Access","display_name":"Accelerating Key Bioinformatics Tasks 100-fold by Improving Memory Access","publication_year":2021,"publication_date":"2021-07-17","ids":{"openalex":"https://openalex.org/W3153992345","doi":"https://doi.org/10.1145/3437359.3465562","mag":"3153992345"},"language":"en","primary_location":{"id":"doi:10.1145/3437359.3465562","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3437359.3465562","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3437359.3465562","source":{"id":"https://openalex.org/S4306523034","display_name":"Practice and Experience in Advanced Research Computing","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Practice and Experience in Advanced Research Computing","raw_type":"proceedings-article"},"type":"preprint","indexed_in":["arxiv","crossref"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://dl.acm.org/doi/pdf/10.1145/3437359.3465562","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5002738602","display_name":"I. Sfiligoi","orcid":"https://orcid.org/0000-0002-9308-5327"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Igor Sfiligoi","raw_affiliation_strings":["University of California San Diego, USA"],"affiliations":[{"raw_affiliation_string":"University of California San Diego, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022461817","display_name":"Daniel McDonald","orcid":"https://orcid.org/0000-0003-0876-9060"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Daniel McDonald","raw_affiliation_strings":["University of California San Diego, USA"],"affiliations":[{"raw_affiliation_string":"University of California San Diego, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5033881627","display_name":"Rob Knight","orcid":"https://orcid.org/0000-0002-0975-9019"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rob Knight","raw_affiliation_strings":["University of California San Diego, USA"],"affiliations":[{"raw_affiliation_string":"University of California San Diego, USA","institution_ids":["https://openalex.org/I36258959"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5002738602"],"corresponding_institution_ids":["https://openalex.org/I36258959"],"apc_list":null,"apc_paid":null,"fwci":0.0813,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.42565963,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"5"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9922999739646912,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9922999739646912,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9848999977111816,"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":0.9812999963760376,"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/computer-science","display_name":"Computer science","score":0.8508894443511963},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.7517117261886597},{"id":"https://openalex.org/keywords/memory-footprint","display_name":"Memory footprint","score":0.7011110782623291},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.588529109954834},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.5601276755332947},{"id":"https://openalex.org/keywords/supercomputer","display_name":"Supercomputer","score":0.5176899433135986},{"id":"https://openalex.org/keywords/central-processing-unit","display_name":"Central processing unit","score":0.5139029026031494},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.4408300817012787},{"id":"https://openalex.org/keywords/principal","display_name":"Principal (computer security)","score":0.4272485375404358},{"id":"https://openalex.org/keywords/computer-architecture","display_name":"Computer architecture","score":0.39857515692710876},{"id":"https://openalex.org/keywords/computer-engineering","display_name":"Computer engineering","score":0.3534456491470337},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.337765634059906},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.2598419785499573},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1762980818748474}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8508894443511963},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.7517117261886597},{"id":"https://openalex.org/C74912251","wikidata":"https://www.wikidata.org/wiki/Q6815727","display_name":"Memory footprint","level":2,"score":0.7011110782623291},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.588529109954834},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.5601276755332947},{"id":"https://openalex.org/C83283714","wikidata":"https://www.wikidata.org/wiki/Q121117","display_name":"Supercomputer","level":2,"score":0.5176899433135986},{"id":"https://openalex.org/C49154492","wikidata":"https://www.wikidata.org/wiki/Q5300","display_name":"Central processing unit","level":2,"score":0.5139029026031494},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.4408300817012787},{"id":"https://openalex.org/C144559511","wikidata":"https://www.wikidata.org/wiki/Q2986279","display_name":"Principal (computer security)","level":2,"score":0.4272485375404358},{"id":"https://openalex.org/C118524514","wikidata":"https://www.wikidata.org/wiki/Q173212","display_name":"Computer architecture","level":1,"score":0.39857515692710876},{"id":"https://openalex.org/C113775141","wikidata":"https://www.wikidata.org/wiki/Q428691","display_name":"Computer engineering","level":1,"score":0.3534456491470337},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.337765634059906},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.2598419785499573},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1762980818748474}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1145/3437359.3465562","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3437359.3465562","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3437359.3465562","source":{"id":"https://openalex.org/S4306523034","display_name":"Practice and Experience in Advanced Research Computing","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Practice and Experience in Advanced Research Computing","raw_type":"proceedings-article"},{"id":"pmh:oai:arXiv.org:2104.09565","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2104.09565","pdf_url":"https://arxiv.org/pdf/2104.09565","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"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":"text"}],"best_oa_location":{"id":"doi:10.1145/3437359.3465562","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3437359.3465562","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3437359.3465562","source":{"id":"https://openalex.org/S4306523034","display_name":"Practice and Experience in Advanced Research Computing","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Practice and Experience in Advanced Research Computing","raw_type":"proceedings-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3176115892","display_name":null,"funder_award_id":"OAC-1541349","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G502606643","display_name":null,"funder_award_id":"1826967","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7278722489","display_name":null,"funder_award_id":"1541349","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8131056805","display_name":null,"funder_award_id":"DBI-2038509,OAC-1541349,OAC-1826967","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G953843664","display_name":null,"funder_award_id":"2038509","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320320671","display_name":"National Research Foundation","ror":"https://ror.org/05s0g1g46"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3153992345.pdf","grobid_xml":"https://content.openalex.org/works/W3153992345.grobid-xml"},"referenced_works_count":13,"referenced_works":["https://openalex.org/W1502340801","https://openalex.org/W1505090736","https://openalex.org/W2158158791","https://openalex.org/W2766358903","https://openalex.org/W2963276645","https://openalex.org/W3003257820","https://openalex.org/W3025629042","https://openalex.org/W3035965352","https://openalex.org/W3099878876","https://openalex.org/W3103145119","https://openalex.org/W4242982359","https://openalex.org/W4245312332","https://openalex.org/W4252536501"],"related_works":["https://openalex.org/W2384867379","https://openalex.org/W4400094300","https://openalex.org/W2329539859","https://openalex.org/W2227905990","https://openalex.org/W2765823764","https://openalex.org/W3214280620","https://openalex.org/W3191490922","https://openalex.org/W2929170389","https://openalex.org/W4300097863","https://openalex.org/W2950268673"],"abstract_inverted_index":{"Most":[0],"experimental":[1],"sciences":[2,9],"now":[3],"rely":[4],"on":[5,43,145],"computing,":[6],"and":[7,53,130,159],"biological":[8],"are":[10,41,88],"no":[11],"exception.":[12],"As":[13],"datasets":[14],"get":[15],"bigger,":[16],"so":[17],"do":[18],"the":[19,26,35,44,69,82,94,103,110,119,125,153,160],"computing":[20],"costs,":[21],"making":[22,75],"proper":[23],"optimization":[24],"of":[25,34,51,60,72,90],"codes":[27,36],"used":[28],"by":[29,81],"scientists":[30],"increasingly":[31],"important.":[32],"Many":[33],"developed":[37],"in":[38,118,152,165,170],"recent":[39],"years":[40],"based":[42,144],"Python-based":[45],"NumPy,":[46,61],"due":[47],"to":[48,100,116,148],"its":[49],"ease":[50],"use":[52],"good":[54],"performance":[55],"characteristics.":[56],"The":[57],"composable":[58],"nature":[59,71],"however,":[62],"does":[63],"not":[64],"generally":[65],"play":[66],"well":[67],"with":[68],"multi-tier":[70],"modern":[73],"CPUs,":[74],"any":[76],"non-trivial":[77],"multi-step":[78],"algorithm":[79],"limited":[80],"external":[83],"memory":[84,112],"access":[85],"speeds,":[86],"which":[87,122],"hundreds":[89],"times":[91],"slower":[92],"than":[93],"CPU's":[95],"compute":[96,105],"capabilities.":[97],"In":[98,138],"order":[99],"fully":[101],"utilize":[102],"CPU":[104,120],"capabilities,":[106],"one":[107],"must":[108],"keep":[109],"working":[111],"footprint":[113],"small":[114],"enough":[115],"fit":[117],"caches,":[121],"requires":[123],"splitting":[124],"problem":[126],"into":[127],"smaller":[128],"portions":[129],"fusing":[131],"together":[132],"as":[133,136],"many":[134],"steps":[135],"possible.":[137],"this":[139],"paper,":[140],"we":[141],"present":[142],"changes":[143],"these":[146,171],"principles":[147],"two":[149],"important":[150],"functions":[151],"scikit-bio":[154],"library,":[155],"principal":[156],"coordinates":[157],"analysis":[158],"Mantel":[161],"test,":[162],"that":[163],"resulted":[164],"over":[166],"100x":[167],"speed":[168],"improvement":[169],"widely":[172],"used,":[173],"general-purpose":[174],"tools.":[175]},"counts_by_year":[{"year":2021,"cited_by_count":1}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}