{"id":"https://openalex.org/W4402673836","doi":"https://doi.org/10.1109/e-science62913.2024.10678707","title":"Mitigating memory latency in FM Index search","display_name":"Mitigating memory latency in FM Index search","publication_year":2024,"publication_date":"2024-09-16","ids":{"openalex":"https://openalex.org/W4402673836","doi":"https://doi.org/10.1109/e-science62913.2024.10678707"},"language":"en","primary_location":{"id":"doi:10.1109/e-science62913.2024.10678707","is_oa":false,"landing_page_url":"http://dx.doi.org/10.1109/e-science62913.2024.10678707","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE 20th International Conference on e-Science (e-Science)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://escholarship.org/content/qt4nt0s6gj/qt4nt0s6gj.pdf","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,La Jolla,CA,USA"],"affiliations":[{"raw_affiliation_string":"University of California San Diego,La Jolla,CA,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,La Jolla,CA,USA"],"affiliations":[{"raw_affiliation_string":"University of California San Diego,La Jolla,CA,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,La Jolla,CA,USA"],"affiliations":[{"raw_affiliation_string":"University of California San Diego,La Jolla,CA,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":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.24608355,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"2"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10286","display_name":"Information Retrieval and Search Behavior","score":0.9538999795913696,"subfield":{"id":"https://openalex.org/subfields/1710","display_name":"Information Systems"},"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/T10286","display_name":"Information Retrieval and Search Behavior","score":0.9538999795913696,"subfield":{"id":"https://openalex.org/subfields/1710","display_name":"Information Systems"},"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":0.9218000173568726,"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/T10627","display_name":"Advanced Image and Video Retrieval Techniques","score":0.9204999804496765,"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/computer-science","display_name":"Computer science","score":0.6709791421890259},{"id":"https://openalex.org/keywords/latency","display_name":"Latency (audio)","score":0.5648461580276489},{"id":"https://openalex.org/keywords/index","display_name":"Index (typography)","score":0.5341837406158447},{"id":"https://openalex.org/keywords/telecommunications","display_name":"Telecommunications","score":0.19074037671089172},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.10991927981376648}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6709791421890259},{"id":"https://openalex.org/C82876162","wikidata":"https://www.wikidata.org/wiki/Q17096504","display_name":"Latency (audio)","level":2,"score":0.5648461580276489},{"id":"https://openalex.org/C2777382242","wikidata":"https://www.wikidata.org/wiki/Q6017816","display_name":"Index (typography)","level":2,"score":0.5341837406158447},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.19074037671089172},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.10991927981376648}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1109/e-science62913.2024.10678707","is_oa":false,"landing_page_url":"http://dx.doi.org/10.1109/e-science62913.2024.10678707","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE 20th International Conference on e-Science (e-Science)","raw_type":"proceedings-article"},{"id":"pmh:oai:escholarship.org:ark:/13030/qt4nt0s6gj","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/4nt0s6gj","pdf_url":"https://escholarship.org/content/qt4nt0s6gj/qt4nt0s6gj.pdf","source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:ark:/13030/qt4nt0s6gj","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":{"id":"pmh:oai:escholarship.org:ark:/13030/qt4nt0s6gj","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/4nt0s6gj","pdf_url":"https://escholarship.org/content/qt4nt0s6gj/qt4nt0s6gj.pdf","source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4402673836.pdf","grobid_xml":"https://content.openalex.org/works/W4402673836.grobid-xml"},"referenced_works_count":4,"referenced_works":["https://openalex.org/W2158322625","https://openalex.org/W2170551349","https://openalex.org/W2892206041","https://openalex.org/W2951076599"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052","https://openalex.org/W2382290278","https://openalex.org/W4395014643"],"abstract_inverted_index":{"Bowtie":[0],"2":[1],"is":[2,31],"a":[3,64],"popular":[4],"short":[5],"sequence":[6],"aligner":[7],"used":[8,75],"by":[9,81],"many":[10],"bioinformatics":[11],"groups,":[12],"often":[13],"as":[14,58],"part":[15],"of":[16,24,34,46],"the":[17,25,32,37,44,47,59,72,77,83],"Qiita":[18],"microbial":[19],"study":[20],"management":[21],"platform.":[22],"One":[23],"key":[26],"computational":[27],"steps":[28],"during":[29],"alignment":[30],"extraction":[33],"seeds":[35],"from":[36],"read":[38],"sequences":[39],"and":[40,76],"aligning":[41],"them":[42],"with":[43,55,88],"help":[45],"FM":[48],"Index.":[49],"This":[50],"step":[51],"was":[52],"memory":[53,89],"access-bound,":[54],"access":[56],"latency":[57],"primary":[60],"limitation":[61],"due":[62],"to":[63,85],"pseudo-random-access":[65],"pattern.":[66],"In":[67],"this":[68],"paper":[69],"we":[70],"present":[71],"algorithmic":[73],"changes":[74],"performance":[78],"improvements":[79],"obtained":[80],"re-factoring":[82],"code":[84],"overlap":[86],"compute":[87],"pre-fetching.":[90]},"counts_by_year":[],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}
