{"id":"https://openalex.org/W4388927910","doi":"https://doi.org/10.48550/arxiv.2311.12527","title":"MetaStore: High-Performance Metagenomic Analysis via In-Storage Computing","display_name":"MetaStore: High-Performance Metagenomic Analysis via In-Storage Computing","publication_year":2023,"publication_date":"2023-01-01","ids":{"openalex":"https://openalex.org/W4388927910","doi":"https://doi.org/10.48550/arxiv.2311.12527"},"language":"en","primary_location":{"is_oa":true,"landing_page_url":"https://arxiv.org/abs/2311.12527","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":["Cornell University"],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false},"type":"preprint","type_crossref":"posted-content","indexed_in":["arxiv","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/abs/2311.12527","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5048764555","display_name":"Nika Mansouri Ghiasi","orcid":"https://orcid.org/0000-0002-0833-0042"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ghiasi, Nika Mansouri","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008240365","display_name":"Mohammad Sadrosadati","orcid":"https://orcid.org/0000-0002-4029-0175"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Sadrosadati, Mohammad","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033347097","display_name":"Harun Mustafa","orcid":"https://orcid.org/0000-0002-2125-6086"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Mustafa, Harun","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052807455","display_name":"Arvid Gollwitzer","orcid":"https://orcid.org/0009-0001-2170-8089"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Gollwitzer, Arvid","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066286509","display_name":"Can F\u0131rt\u0131na","orcid":"https://orcid.org/0000-0002-6548-7863"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Firtina, Can","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007205853","display_name":"Julien Eudine","orcid":"https://orcid.org/0000-0001-6482-0110"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Eudine, Julien","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102647871","display_name":"Haiyu Ma","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ma, Haiyu","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042072020","display_name":"Jo\u00ebl Lindegger","orcid":"https://orcid.org/0000-0003-2581-8637"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Lindegger, Jo\u00ebl","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060363985","display_name":"Meryem Banu Cavlak","orcid":"https://orcid.org/0000-0003-4475-6945"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Cavlak, Meryem Banu","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081055664","display_name":"Mohammed Alser","orcid":"https://orcid.org/0000-0002-6117-3701"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Alser, Mohammed","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010929521","display_name":"Jisung Park","orcid":"https://orcid.org/0000-0002-1826-9003"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Park, Jisung","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5050695684","display_name":"Onur Mutlu","orcid":"https://orcid.org/0000-0002-0075-2312"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Mutlu, Onur","raw_affiliation_strings":[],"affiliations":[]}],"institution_assertions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.0,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":0,"max":67},"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"primary_topic":{"id":"https://openalex.org/T11181","display_name":"Advanced Data Storage Technologies","score":0.9972,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"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/T11181","display_name":"Advanced Data Storage Technologies","score":0.9972,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"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/T10715","display_name":"Distributed and Parallel Computing Systems","score":0.984,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"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/T10101","display_name":"Cloud Computing and Resource Management","score":0.974,"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"}}],"keywords":[],"concepts":[{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.8671992},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7132065},{"id":"https://openalex.org/C2779960059","wikidata":"https://www.wikidata.org/wiki/Q7113681","display_name":"Overhead (engineering)","level":2,"score":0.6072143},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.56027967},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.50942975},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.4110684},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.34230548},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.32585466},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.12842572},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.08619875},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","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}],"mesh":[],"locations_count":3,"locations":[{"is_oa":true,"landing_page_url":"https://arxiv.org/abs/2311.12527","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":["Cornell University"],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false},{"is_oa":true,"landing_page_url":"http://arxiv.org/abs/2311.12527","pdf_url":"http://arxiv.org/pdf/2311.12527","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":["Cornell University"],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false},{"is_oa":false,"landing_page_url":"https://api.datacite.org/dois/10.48550/arxiv.2311.12527","pdf_url":null,"source":{"id":"https://openalex.org/S4393179698","display_name":"DataCite API","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210145204","host_organization_name":"DataCite","host_organization_lineage":["https://openalex.org/I4210145204"],"host_organization_lineage_names":["DataCite"],"type":"metadata"},"license":null,"license_id":null,"version":null}],"best_oa_location":{"is_oa":true,"landing_page_url":"https://arxiv.org/abs/2311.12527","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":["Cornell University"],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false},"sustainable_development_goals":[],"grants":[],"datasets":[],"versions":[],"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W638577851","https://openalex.org/W4388282505","https://openalex.org/W4255657129","https://openalex.org/W4242417330","https://openalex.org/W3198631238","https://openalex.org/W3135997498","https://openalex.org/W3013372948","https://openalex.org/W2968354375","https://openalex.org/W2889550857","https://openalex.org/W2359440920"],"abstract_inverted_index":{"Metagenomics":[0],"has":[1],"led":[2],"to":[3,50,61,103,119,228],"significant":[4,45],"advancements":[5],"in":[6,21,99],"many":[7],"fields.":[8],"Metagenomic":[9,41],"analysis":[10,42,154,159],"commonly":[11],"involves":[12],"the":[13,18,58,62,65,92,104,113,122,148,156,202,217,220,229],"key":[14],"tasks":[15,29],"of":[16,54,64,91,107,126,155,219],"determining":[17],"species":[19],"present":[20],"a":[22,71],"sample":[23],"and":[24,136,142,146,161,174,192,205,212],"their":[25],"relative":[26],"abundances.":[27],"These":[28],"require":[30],"searching":[31],"large":[32,52],"metagenomic":[33,128,158,208,231],"databases":[34],"containing":[35],"information":[36],"on":[37],"different":[38],"species'":[39],"genomes.":[40],"suffers":[43],"from":[44,57],"data":[46,56,76,123,194],"movement":[47,77,124],"overhead":[48,125],"due":[49,102],"moving":[51],"amounts":[53],"low-reuse":[55],"storage":[59,100,149,184],"system":[60,84,117],"rest":[63],"system.":[66,150],"In-storage":[67],"processing":[68,83,116,144,168],"can":[69,95],"be":[70,96],"fundamental":[72],"solution":[73],"for":[74,85,170],"reducing":[75],"overhead.":[78],"However,":[79],"designing":[80],"an":[81],"in-storage":[82,115,167,190],"metagenomics":[86,171],"is":[87,131],"challenging":[88],"because":[89],"none":[90],"existing":[93],"approaches":[94],"directly":[97],"implemented":[98],"effectively":[101,140],"hardware":[105],"limitations":[106],"modern":[108],"SSDs.":[109],"We":[110],"propose":[111],"MetaStore,":[112],"first":[114],"designed":[118],"significantly":[120,236],"reduce":[121],"end-to-end":[127,157],"analysis.":[129],"MetaStore":[130,200,223],"enabled":[132],"by":[133,210],"our":[134,152],"lightweight":[135],"cooperative":[137],"design":[138],"that":[139,199],"leverages":[141],"orchestrates":[143],"inside":[145],"outside":[147],"Through":[151],"detailed":[153],"pipeline":[160],"careful":[162],"hardware/software":[163],"co-design,":[164],"we":[165],"address":[166],"challenges":[169],"via":[172],"specialized":[173],"efficient":[175],"1)":[176],"task":[177],"partitioning,":[178],"2)":[179],"data/computation":[180],"flow":[181],"coordination,":[182],"3)":[183],"technology-aware":[185],"algorithmic":[186],"optimizations,":[187],"4)":[188],"light-weight":[189],"accelerators,":[191],"5)":[193],"mapping.":[195],"Our":[196],"evaluation":[197],"shows":[198],"outperforms":[201],"state-of-the-art":[203,230],"performance-":[204],"accuracy-optimized":[206,221],"software":[207],"tools":[209],"2.7-37.2$\\times$":[211],"6.9-100.2$\\times$,":[213],"respectively,":[214],"while":[215,234],"matching":[216],"accuracy":[218],"tool.":[222],"achieves":[224],"1.5-5.1$\\times$":[225],"speedup":[226],"compared":[227],"hardware-accelerated":[232],"tool,":[233],"achieving":[235],"higher":[237],"accuracy.":[238]},"cited_by_api_url":"https://api.openalex.org/works?filter=cites:W4388927910","counts_by_year":[],"updated_date":"2024-12-31T09:35:42.247076","created_date":"2023-11-23"}