{"id":"https://openalex.org/W3171151152","doi":"https://doi.org/10.1145/3472456.3472460","title":"MetaCache-GPU: Ultra-Fast Metagenomic Classification","display_name":"MetaCache-GPU: Ultra-Fast Metagenomic Classification","publication_year":2021,"publication_date":"2021-08-09","ids":{"openalex":"https://openalex.org/W3171151152","doi":"https://doi.org/10.1145/3472456.3472460","mag":"3171151152"},"language":"en","primary_location":{"id":"doi:10.1145/3472456.3472460","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3472456.3472460","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"50th International Conference on Parallel Processing","raw_type":"proceedings-article"},"type":"preprint","indexed_in":["arxiv","crossref","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2106.08150","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5043372390","display_name":"Robin Kobus","orcid":"https://orcid.org/0000-0003-2726-1908"},"institutions":[{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Robin Kobus","raw_affiliation_strings":["Johannes Gutenberg University Mainz, Germany","Johannes Gutenberg-University, Mainz, Germany"],"affiliations":[{"raw_affiliation_string":"Johannes Gutenberg University Mainz, Germany","institution_ids":["https://openalex.org/I197323543"]},{"raw_affiliation_string":"Johannes Gutenberg-University, Mainz, Germany","institution_ids":["https://openalex.org/I197323543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5107834032","display_name":"Andr\u00e9 C. M\u00fcller","orcid":"https://orcid.org/0000-0002-8312-5786"},"institutions":[{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Andr\u00e9 M\u00fcller","raw_affiliation_strings":["Johannes Gutenberg University Mainz, Germany","Johannes Gutenberg-University, Mainz, Germany"],"affiliations":[{"raw_affiliation_string":"Johannes Gutenberg University Mainz, Germany","institution_ids":["https://openalex.org/I197323543"]},{"raw_affiliation_string":"Johannes Gutenberg-University, Mainz, Germany","institution_ids":["https://openalex.org/I197323543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084101957","display_name":"Daniel J\u00fcnger","orcid":"https://orcid.org/0000-0002-6899-9311"},"institutions":[{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Daniel J\u00fcnger","raw_affiliation_strings":["Johannes Gutenberg University Mainz, Germany","Johannes Gutenberg-University, Mainz, Germany"],"affiliations":[{"raw_affiliation_string":"Johannes Gutenberg University Mainz, Germany","institution_ids":["https://openalex.org/I197323543"]},{"raw_affiliation_string":"Johannes Gutenberg-University, Mainz, Germany","institution_ids":["https://openalex.org/I197323543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027561629","display_name":"Christian Hundt","orcid":"https://orcid.org/0000-0002-7995-1858"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Christian Hundt","raw_affiliation_strings":["NVIDIA AI Technology Center Luxembourg, Luxembourg","NVIDIA AI Technology Center Luxembourg"],"affiliations":[{"raw_affiliation_string":"NVIDIA AI Technology Center Luxembourg, Luxembourg","institution_ids":[]},{"raw_affiliation_string":"NVIDIA AI Technology Center Luxembourg","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5020388832","display_name":"Bertil Schmidt","orcid":"https://orcid.org/0000-0003-2597-8331"},"institutions":[{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Bertil Schmidt","raw_affiliation_strings":["Johannes Gutenberg University Mainz, Germany","Johannes Gutenberg-University, Mainz, Germany"],"affiliations":[{"raw_affiliation_string":"Johannes Gutenberg University Mainz, Germany","institution_ids":["https://openalex.org/I197323543"]},{"raw_affiliation_string":"Johannes Gutenberg-University, Mainz, Germany","institution_ids":["https://openalex.org/I197323543"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5043372390"],"corresponding_institution_ids":["https://openalex.org/I197323543"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.05076029,"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":"11"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9983999729156494,"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":0.9983999729156494,"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/T11269","display_name":"Algorithms and Data Compression","score":0.9954000115394592,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9690999984741211,"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":0.8085873126983643},{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.6504086852073669},{"id":"https://openalex.org/keywords/hash-function","display_name":"Hash function","score":0.5926988124847412},{"id":"https://openalex.org/keywords/preprocessor","display_name":"Preprocessor","score":0.5560203194618225},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5440477728843689},{"id":"https://openalex.org/keywords/reference-genome","display_name":"Reference genome","score":0.5048285126686096},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.46040403842926025},{"id":"https://openalex.org/keywords/terabyte","display_name":"Terabyte","score":0.45690667629241943},{"id":"https://openalex.org/keywords/cuda","display_name":"CUDA","score":0.44759753346443176},{"id":"https://openalex.org/keywords/hash-table","display_name":"Hash table","score":0.42228758335113525},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.25073933601379395},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.20388472080230713},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11466670036315918}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8085873126983643},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.6504086852073669},{"id":"https://openalex.org/C99138194","wikidata":"https://www.wikidata.org/wiki/Q183427","display_name":"Hash function","level":2,"score":0.5926988124847412},{"id":"https://openalex.org/C34736171","wikidata":"https://www.wikidata.org/wiki/Q918333","display_name":"Preprocessor","level":2,"score":0.5560203194618225},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5440477728843689},{"id":"https://openalex.org/C192953774","wikidata":"https://www.wikidata.org/wiki/Q7307127","display_name":"Reference genome","level":4,"score":0.5048285126686096},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.46040403842926025},{"id":"https://openalex.org/C199683683","wikidata":"https://www.wikidata.org/wiki/Q8799","display_name":"Terabyte","level":2,"score":0.45690667629241943},{"id":"https://openalex.org/C2778119891","wikidata":"https://www.wikidata.org/wiki/Q477690","display_name":"CUDA","level":2,"score":0.44759753346443176},{"id":"https://openalex.org/C67388219","wikidata":"https://www.wikidata.org/wiki/Q207440","display_name":"Hash table","level":3,"score":0.42228758335113525},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.25073933601379395},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.20388472080230713},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11466670036315918},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1145/3472456.3472460","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3472456.3472460","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"50th International Conference on Parallel Processing","raw_type":"proceedings-article"},{"id":"pmh:oai:arXiv.org:2106.08150","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2106.08150","pdf_url":"https://arxiv.org/pdf/2106.08150","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":"","raw_type":"text"},{"id":"mag:3171151152","is_oa":true,"landing_page_url":"http://export.arxiv.org/pdf/2106.08150v1","pdf_url":null,"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":"arXiv (Cornell University)","raw_type":null},{"id":"doi:10.48550/arxiv.2106.08150","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2106.08150","pdf_url":null,"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":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2106.08150","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2106.08150","pdf_url":"https://arxiv.org/pdf/2106.08150","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":"","raw_type":"text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6753246005","display_name":null,"funder_award_id":"HySim","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3171151152.pdf","grobid_xml":"https://content.openalex.org/works/W3171151152.grobid-xml"},"referenced_works_count":36,"referenced_works":["https://openalex.org/W1982088757","https://openalex.org/W1996717081","https://openalex.org/W2003347102","https://openalex.org/W2104846587","https://openalex.org/W2128964206","https://openalex.org/W2148885851","https://openalex.org/W2154468535","https://openalex.org/W2159954944","https://openalex.org/W2173732482","https://openalex.org/W2218392081","https://openalex.org/W2256665843","https://openalex.org/W2265709988","https://openalex.org/W2562227272","https://openalex.org/W2597444305","https://openalex.org/W2620106252","https://openalex.org/W2745994342","https://openalex.org/W2797956284","https://openalex.org/W2802282671","https://openalex.org/W2887155473","https://openalex.org/W2888502390","https://openalex.org/W2889313110","https://openalex.org/W2902483623","https://openalex.org/W2951176108","https://openalex.org/W2962703427","https://openalex.org/W2962896111","https://openalex.org/W2963173114","https://openalex.org/W2963585318","https://openalex.org/W2964064024","https://openalex.org/W2964104075","https://openalex.org/W2990618091","https://openalex.org/W2994050678","https://openalex.org/W3011893537","https://openalex.org/W3016441544","https://openalex.org/W3038374326","https://openalex.org/W3158242983","https://openalex.org/W4205568063"],"related_works":["https://openalex.org/W3204919386","https://openalex.org/W1964977363","https://openalex.org/W2576249239","https://openalex.org/W2801626568","https://openalex.org/W2283787433","https://openalex.org/W3184371027","https://openalex.org/W2111367247","https://openalex.org/W2918605816","https://openalex.org/W2596935532","https://openalex.org/W1979994831","https://openalex.org/W1978049818","https://openalex.org/W3174903146","https://openalex.org/W2535722386","https://openalex.org/W2121383574","https://openalex.org/W1986681515","https://openalex.org/W3046364546","https://openalex.org/W359997929","https://openalex.org/W2953008890","https://openalex.org/W2745274425","https://openalex.org/W1880759167"],"abstract_inverted_index":{"The":[0,229],"cost":[1,85],"of":[2,20,25,47,86,100,134,149,177,203,207,223],"DNA":[3,27],"sequencing":[4],"has":[5],"dropped":[6],"exponentially":[7],"over":[8,190],"the":[9,82,96,105,132,197,201,212],"past":[10],"decade,":[11],"making":[12],"genomic":[13,32],"data":[14,40,89],"accessible":[15],"to":[16,65,81,130,169],"a":[17,66,77,140,175],"growing":[18,98],"number":[19,206],"scientists.":[21],"In":[22,115,200],"bioinformatics,":[23],"localization":[24],"short":[26,125],"sequences":[28,33],"(reads)":[29],"within":[30],"large":[31,171],"is":[34,73,167,211,232],"commonly":[35],"facilitated":[36],"by":[37,58],"constructing":[38],"index":[39,71,108,194],"structures":[41,90],"which":[42],"allow":[43],"for":[44,107,151,193],"efficient":[45,146],"querying":[46,111],"substrings.":[48],"Recent":[49],"metagenomic":[50,124,214],"classification":[51],"pipelines":[52,219],"annotate":[53],"reads":[54,150],"with":[55,63,220],"taxonomic":[56],"labels":[57],"analyzing":[59],"their":[60,155],"k-mer":[61],"histograms":[62],"respect":[64],"reference":[67,102,172,208,225],"genome":[68,226],"database.":[69],"CPU-based":[70,184],"construction":[72,109,195],"often":[74],"performed":[75],"in":[76,174],"preprocessing":[78],"phase":[79],"due":[80],"relatively":[83],"high":[84],"building":[87],"irregular":[88],"such":[91,186],"as":[92,187],"hash":[93,142],"maps.":[94],"However,":[95],"rapidly":[97],"amount":[99],"available":[101,234],"genomes":[103],"establishes":[104],"need":[106],"and":[110,154],"at":[112,235],"interactive":[113],"speeds.":[114],"this":[116],"paper,":[117],"we":[118],"introduce":[119],"MetaCache-GPU":[120,166,210],"\u2013":[121],"an":[122,191,204],"ultra-fast":[123],"read":[126],"classifier":[127,215],"specifically":[128],"tailored":[129],"fit":[131],"characteristics":[133],"CUDA-enabled":[135],"accelerators.":[136],"Our":[137,161],"approach":[138],"employs":[139],"novel":[141],"table":[143],"variant":[144],"featuring":[145],"minhash":[147],"fingerprinting":[148],"locality-sensitive":[152],"hashing":[153],"rapid":[156],"insertion":[157],"using":[158],"warp-aggregated":[159],"operations.":[160],"performance":[162],"evaluation":[163],"shows":[164],"that":[165,216],"able":[168],"build":[170],"databases":[173],"matter":[176],"seconds,":[178],"enabling":[179],"instantaneous":[180],"operability,":[181],"while":[182],"popular":[183],"tools":[185],"Kraken2":[188],"require":[189],"hour":[192],"on":[196],"same":[198],"data.":[199],"context":[202],"ever-growing":[205],"genomes,":[209],"first":[213],"makes":[217],"analysis":[218],"on-demand":[221],"composition":[222],"large-scale":[224],"sets":[227],"practical.":[228],"source":[230],"code":[231],"publicly":[233],"https://github.com/muellan/metacache.":[236]},"counts_by_year":[],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
