{"id":"https://openalex.org/W4283021319","doi":"https://doi.org/10.1145/3524059.3532367","title":"KrakenOnMem","display_name":"KrakenOnMem","publication_year":2022,"publication_date":"2022-06-16","ids":{"openalex":"https://openalex.org/W4283021319","doi":"https://doi.org/10.1145/3524059.3532367"},"language":"en","primary_location":{"id":"doi:10.1145/3524059.3532367","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3524059.3532367","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3524059.3532367","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 36th ACM International Conference on Supercomputing","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://dl.acm.org/doi/pdf/10.1145/3524059.3532367","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5045031453","display_name":"Taha Shahroodi","orcid":"https://orcid.org/0000-0003-4576-0030"},"institutions":[{"id":"https://openalex.org/I98358874","display_name":"Delft University of Technology","ror":"https://ror.org/02e2c7k09","country_code":"NL","type":"education","lineage":["https://openalex.org/I98358874"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Taha Shahroodi","raw_affiliation_strings":["TU Delft, Delft, Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"TU Delft, Delft, Netherlands","institution_ids":["https://openalex.org/I98358874"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055616595","display_name":"Mahdi Zahedi","orcid":"https://orcid.org/0000-0002-7602-5066"},"institutions":[{"id":"https://openalex.org/I98358874","display_name":"Delft University of Technology","ror":"https://ror.org/02e2c7k09","country_code":"NL","type":"education","lineage":["https://openalex.org/I98358874"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Mahdi Zahedi","raw_affiliation_strings":["TU Delft, Delft, Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"TU Delft, Delft, Netherlands","institution_ids":["https://openalex.org/I98358874"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056263300","display_name":"Abhairaj Singh","orcid":"https://orcid.org/0000-0002-2729-7057"},"institutions":[{"id":"https://openalex.org/I98358874","display_name":"Delft University of Technology","ror":"https://ror.org/02e2c7k09","country_code":"NL","type":"education","lineage":["https://openalex.org/I98358874"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Abhairaj Singh","raw_affiliation_strings":["TU Delft, Delft, Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"TU Delft, Delft, Netherlands","institution_ids":["https://openalex.org/I98358874"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036463224","display_name":"Stephan Wong","orcid":"https://orcid.org/0000-0003-3521-2612"},"institutions":[{"id":"https://openalex.org/I98358874","display_name":"Delft University of Technology","ror":"https://ror.org/02e2c7k09","country_code":"NL","type":"education","lineage":["https://openalex.org/I98358874"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Stephan Wong","raw_affiliation_strings":["TU Delft, Delft, Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"TU Delft, Delft, Netherlands","institution_ids":["https://openalex.org/I98358874"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5005739146","display_name":"Said Hamdioui","orcid":"https://orcid.org/0000-0002-8961-0387"},"institutions":[{"id":"https://openalex.org/I98358874","display_name":"Delft University of Technology","ror":"https://ror.org/02e2c7k09","country_code":"NL","type":"education","lineage":["https://openalex.org/I98358874"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Said Hamdioui","raw_affiliation_strings":["TU Delft, Delft, Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"TU Delft, Delft, Netherlands","institution_ids":["https://openalex.org/I98358874"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I98358874"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":17,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"14"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9979000091552734,"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":0.9979000091552734,"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/T11986","display_name":"Scientific Computing and Data Management","score":0.9887999892234802,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9751999974250793,"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":0.7952195405960083},{"id":"https://openalex.org/keywords/bottleneck","display_name":"Bottleneck","score":0.7405444979667664},{"id":"https://openalex.org/keywords/lookup-table","display_name":"Lookup table","score":0.6562820672988892},{"id":"https://openalex.org/keywords/profiling","display_name":"Profiling (computer programming)","score":0.609351396560669},{"id":"https://openalex.org/keywords/energy-consumption","display_name":"Energy consumption","score":0.5539568066596985},{"id":"https://openalex.org/keywords/table","display_name":"Table (database)","score":0.537241518497467},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.5246543884277344},{"id":"https://openalex.org/keywords/latency","display_name":"Latency (audio)","score":0.4743327498435974},{"id":"https://openalex.org/keywords/computer-architecture","display_name":"Computer architecture","score":0.45751067996025085},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.44679805636405945},{"id":"https://openalex.org/keywords/embedded-system","display_name":"Embedded system","score":0.4434834420681},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.3432452082633972},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.2902129292488098},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.13764235377311707},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.08487707376480103}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7952195405960083},{"id":"https://openalex.org/C2780513914","wikidata":"https://www.wikidata.org/wiki/Q18210350","display_name":"Bottleneck","level":2,"score":0.7405444979667664},{"id":"https://openalex.org/C134835016","wikidata":"https://www.wikidata.org/wiki/Q690265","display_name":"Lookup table","level":2,"score":0.6562820672988892},{"id":"https://openalex.org/C187191949","wikidata":"https://www.wikidata.org/wiki/Q1138496","display_name":"Profiling (computer programming)","level":2,"score":0.609351396560669},{"id":"https://openalex.org/C2780165032","wikidata":"https://www.wikidata.org/wiki/Q16869822","display_name":"Energy consumption","level":2,"score":0.5539568066596985},{"id":"https://openalex.org/C45235069","wikidata":"https://www.wikidata.org/wiki/Q278425","display_name":"Table (database)","level":2,"score":0.537241518497467},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.5246543884277344},{"id":"https://openalex.org/C82876162","wikidata":"https://www.wikidata.org/wiki/Q17096504","display_name":"Latency (audio)","level":2,"score":0.4743327498435974},{"id":"https://openalex.org/C118524514","wikidata":"https://www.wikidata.org/wiki/Q173212","display_name":"Computer architecture","level":1,"score":0.45751067996025085},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.44679805636405945},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.4434834420681},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.3432452082633972},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.2902129292488098},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.13764235377311707},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.08487707376480103},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1145/3524059.3532367","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3524059.3532367","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3524059.3532367","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 36th ACM International Conference on Supercomputing","raw_type":"proceedings-article"},{"id":"pmh:oai:tudelft.nl:uuid:ae58263f-8732-48dc-91d4-48898852c710","is_oa":false,"landing_page_url":"http://resolver.tudelft.nl/uuid:ae58263f-8732-48dc-91d4-48898852c710","pdf_url":null,"source":{"id":"https://openalex.org/S4306400906","display_name":"Research Repository (Delft University of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I98358874","host_organization_name":"Delft University of Technology","host_organization_lineage":["https://openalex.org/I98358874"],"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 paper"}],"best_oa_location":{"id":"doi:10.1145/3524059.3532367","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3524059.3532367","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3524059.3532367","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 36th ACM International Conference on Supercomputing","raw_type":"proceedings-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/7","score":0.8999999761581421,"display_name":"Affordable and clean energy"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320321012","display_name":"Technische Universiteit Delft","ror":"https://ror.org/02e2c7k09"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4283021319.pdf","grobid_xml":"https://content.openalex.org/works/W4283021319.grobid-xml"},"referenced_works_count":78,"referenced_works":["https://openalex.org/W1703384511","https://openalex.org/W1850429294","https://openalex.org/W1977721562","https://openalex.org/W2000589358","https://openalex.org/W2003347102","https://openalex.org/W2040486579","https://openalex.org/W2065461987","https://openalex.org/W2074357625","https://openalex.org/W2075716829","https://openalex.org/W2083544890","https://openalex.org/W2090413838","https://openalex.org/W2105827747","https://openalex.org/W2118870365","https://openalex.org/W2128524432","https://openalex.org/W2131026689","https://openalex.org/W2141929300","https://openalex.org/W2144560237","https://openalex.org/W2155263300","https://openalex.org/W2159954944","https://openalex.org/W2218392081","https://openalex.org/W2260037449","https://openalex.org/W2310259903","https://openalex.org/W2345658906","https://openalex.org/W2396622873","https://openalex.org/W2465681871","https://openalex.org/W2554162996","https://openalex.org/W2562227272","https://openalex.org/W2588191434","https://openalex.org/W2606268188","https://openalex.org/W2728203316","https://openalex.org/W2738894409","https://openalex.org/W2756568087","https://openalex.org/W2758005814","https://openalex.org/W2760000637","https://openalex.org/W2765188474","https://openalex.org/W2765234579","https://openalex.org/W2766489088","https://openalex.org/W2773939681","https://openalex.org/W2786547608","https://openalex.org/W2801000640","https://openalex.org/W2870561134","https://openalex.org/W2900664819","https://openalex.org/W2906821879","https://openalex.org/W2923010225","https://openalex.org/W2949192478","https://openalex.org/W2952946307","https://openalex.org/W2965566614","https://openalex.org/W2976918410","https://openalex.org/W2979823675","https://openalex.org/W2980639821","https://openalex.org/W3000695118","https://openalex.org/W3009643182","https://openalex.org/W3011893537","https://openalex.org/W3045315617","https://openalex.org/W3046936379","https://openalex.org/W3086574032","https://openalex.org/W3091333637","https://openalex.org/W3110777056","https://openalex.org/W3111918943","https://openalex.org/W3153645570","https://openalex.org/W3179854101","https://openalex.org/W3191503410","https://openalex.org/W3194918228","https://openalex.org/W3198539992","https://openalex.org/W4243519499","https://openalex.org/W4254672563","https://openalex.org/W6632132314","https://openalex.org/W6638564077","https://openalex.org/W6652137313","https://openalex.org/W6671249417","https://openalex.org/W6679889825","https://openalex.org/W6737786906","https://openalex.org/W6745494716","https://openalex.org/W6763693663","https://openalex.org/W6763696390","https://openalex.org/W6764246600","https://openalex.org/W6767601804","https://openalex.org/W6891762763"],"related_works":["https://openalex.org/W2058965144","https://openalex.org/W2164382479","https://openalex.org/W98480971","https://openalex.org/W2150291671","https://openalex.org/W2027972911","https://openalex.org/W2146343568","https://openalex.org/W2013643406","https://openalex.org/W2157978810","https://openalex.org/W1657880117","https://openalex.org/W2891987081"],"abstract_inverted_index":{"State-of-the-art":[0],"taxonomic":[1],"profilers":[2],"that":[3,119],"comprise":[4],"the":[5,24,54,64,105,139,148],"first":[6,46],"step":[7],"in":[8],"larger-context":[9],"metagenomic":[10,85],"studies":[11],"have":[12],"proven":[13],"to":[14,58,129,147],"be":[15],"computationally":[16],"intensive,":[17],"i.e.,":[18],"while":[19,151],"accurate,":[20],"they":[21],"come":[22],"at":[23],"cost":[25],"of":[26,39,68,100,125,144],"high":[27],"latency":[28],"and":[29,87,107],"energy":[30,140],"consumption.":[31],"Table":[32,60],"Lookup":[33],"operation":[34],"is":[35],"a":[36,49,83,97,111,153],"primary":[37],"bottleneck":[38],"today's":[40],"profilers.":[41],"In":[42],"this":[43],"paper,":[44],"we":[45,78],"propose":[47],"TL-PIM,":[48],"hardware":[50],"accelerator":[51],"based":[52],"on":[53,110],"processing-in-memory":[55],"(PIM)":[56],"paradigm":[57],"accelerate":[59],"Lookup.":[61],"TL-PIM":[62,80],"leverages":[63],"in-memory":[65],"compute":[66],"capability":[67],"emerging":[69,102],"memory":[70,103],"technologies":[71],"along":[72],"with":[73],"intelligent":[74],"data":[75],"mapping.":[76],"Then,":[77],"integrate":[79],"into":[81],"Kraken2,":[82],"state-of-the-art":[84],"profiler,":[86,92],"build":[88],"an":[89,123],"HW/SW":[90],"co-designed":[91],"called":[93],"KrakenOnMem.":[94],"Results":[95],"from":[96],"silicon-based":[98],"prototype":[99],"our":[101,136],"validate":[104],"design":[106,137],"required":[108],"operations":[109],"smaller":[112],"scale.":[113],"Our":[114],"large-scale":[115],"calibrated":[116],"simulations":[117],"show":[118],"KrakenOnMem":[120],"can":[121],"provide":[122],"average":[124],"61.3%":[126],"speedup":[127],"compared":[128,146],"original":[130,149],"Kraken2":[131,150],"for":[132],"end-to-end":[133],"profiling.":[134],"Additionally,":[135],"improves":[138],"consumption":[141],"by":[142],"orders":[143],"magnitude":[145],"incurring":[152],"negligible":[154],"area":[155],"overhead.":[156]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":1}],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2022-06-18T00:00:00"}