{"id":"https://openalex.org/W7166081154","doi":"https://doi.org/10.48550/arxiv.2606.26468","title":"GRAINS: Storage-Aware Algorithm-Architecture Co-Design Enabling High-Performance and Low-Cost Graph-Based Genome Analysis","display_name":"GRAINS: Storage-Aware Algorithm-Architecture Co-Design Enabling High-Performance and Low-Cost Graph-Based Genome Analysis","publication_year":2026,"publication_date":"2026-06-25","ids":{"openalex":"https://openalex.org/W7166081154","doi":"https://doi.org/10.48550/arxiv.2606.26468"},"language":null,"primary_location":{"id":"doi:10.48550/arxiv.2606.26468","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2606.26468","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Preprint"},"type":"preprint","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.48550/arxiv.2606.26468","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":[],"raw_orcid":null,"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":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5120323378","display_name":"Talu G\u00fcloglu","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"G\u00fcloglu, Talu","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044716557","display_name":"Rakesh Nadig","orcid":"https://orcid.org/0000-0002-4709-2323"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Nadig, Rakesh","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024565360","display_name":"Konstantina Koliogeorgi","orcid":"https://orcid.org/0000-0003-0064-7616"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Koliogeorgi, Konstantina","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5099097658","display_name":"Susana Rebolledo Ruiz","orcid":"https://orcid.org/0000-0002-1797-4202"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ruiz, Susana Rebolledo","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5139416362","display_name":"Marc Rautmann","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Rautmann, Marc","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5139409660","display_name":"Furkan Eris","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Eris, Furkan","raw_affiliation_strings":[],"raw_orcid":null,"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":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5139394479","display_name":"Jisung Park","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Park, Jisung","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5139463167","display_name":"Onur Mutlu","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Mutlu, Onur","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"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":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12292","display_name":"Graph Theory and Algorithms","score":0.36820000410079956,"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"}},"topics":[{"id":"https://openalex.org/T12292","display_name":"Graph Theory and Algorithms","score":0.36820000410079956,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.3605000078678131,"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":0.08079999685287476,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.7222999930381775},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.7019000053405762},{"id":"https://openalex.org/keywords/leverage","display_name":"Leverage (statistics)","score":0.573199987411499},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.46219998598098755},{"id":"https://openalex.org/keywords/pipeline-transport","display_name":"Pipeline transport","score":0.3878999948501587},{"id":"https://openalex.org/keywords/scheduling","display_name":"Scheduling (production processes)","score":0.3862000107765198},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.3625999987125397},{"id":"https://openalex.org/keywords/overhead","display_name":"Overhead (engineering)","score":0.3621000051498413}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7483999729156494},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.7222999930381775},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.7019000053405762},{"id":"https://openalex.org/C153083717","wikidata":"https://www.wikidata.org/wiki/Q6535263","display_name":"Leverage (statistics)","level":2,"score":0.573199987411499},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.46219998598098755},{"id":"https://openalex.org/C175309249","wikidata":"https://www.wikidata.org/wiki/Q725864","display_name":"Pipeline transport","level":2,"score":0.3878999948501587},{"id":"https://openalex.org/C206729178","wikidata":"https://www.wikidata.org/wiki/Q2271896","display_name":"Scheduling (production processes)","level":2,"score":0.3862000107765198},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.3625999987125397},{"id":"https://openalex.org/C2779960059","wikidata":"https://www.wikidata.org/wiki/Q7113681","display_name":"Overhead (engineering)","level":2,"score":0.3621000051498413},{"id":"https://openalex.org/C192953774","wikidata":"https://www.wikidata.org/wiki/Q7307127","display_name":"Reference genome","level":4,"score":0.3546000123023987},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.34790000319480896},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.34439998865127563},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.334199994802475},{"id":"https://openalex.org/C162319229","wikidata":"https://www.wikidata.org/wiki/Q175263","display_name":"Data structure","level":2,"score":0.32350000739097595},{"id":"https://openalex.org/C89566754","wikidata":"https://www.wikidata.org/wiki/Q2273828","display_name":"Genome project","level":4,"score":0.3179999887943268},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.3131999969482422},{"id":"https://openalex.org/C113425843","wikidata":"https://www.wikidata.org/wiki/Q5953213","display_name":"Hybrid genome assembly","level":5,"score":0.3019999861717224},{"id":"https://openalex.org/C2742236","wikidata":"https://www.wikidata.org/wiki/Q924713","display_name":"Efficient energy use","level":2,"score":0.2870999872684479},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.26350000500679016},{"id":"https://openalex.org/C194739806","wikidata":"https://www.wikidata.org/wiki/Q66221","display_name":"Computer data storage","level":2,"score":0.2597000002861023},{"id":"https://openalex.org/C2780165032","wikidata":"https://www.wikidata.org/wiki/Q16869822","display_name":"Energy consumption","level":2,"score":0.2540000081062317},{"id":"https://openalex.org/C197077220","wikidata":"https://www.wikidata.org/wiki/Q720988","display_name":"Human genome","level":4,"score":0.2529999911785126},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.25130000710487366}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.48550/arxiv.2606.26468","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2606.26468","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"Preprint"}],"best_oa_location":{"id":"doi:10.48550/arxiv.2606.26468","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2606.26468","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Preprint"},"sustainable_development_goals":[{"score":0.8780860304832458,"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Graph-based":[0],"representations":[1],"of":[2,44,65,123,145,200,221],"genome":[3,28,71,104,125,137,152,201],"sequences":[4],"have":[5],"emerged":[6],"as":[7],"a":[8,56,190,258],"powerful":[9],"approach":[10],"for":[11,59,69,99,115,133],"representing":[12],"massive":[13],"genomic":[14],"databases":[15],"in":[16,88,139],"an":[17,226],"expressive":[18],"and":[19,120,166,172,176,193,206,251],"efficient":[20],"way.":[21],"Despite":[22],"their":[23],"benefits,":[24],"analysis":[25,72,105,111,134,147],"on":[26,151,183,197],"large-scale":[27,136],"graphs":[29,138],"incurs":[30],"significant":[31],"data":[32,48,118],"movement":[33],"overhead":[34],"from":[35],"the":[36,51,66,78,83,92,116,130,218,235,247],"storage":[37,52,79],"system":[38,80,132],"due":[39,81],"to":[40,82,159,216],"accessing":[41],"large":[42],"amounts":[43],"low-reuse":[45],"data.":[46],"Processing":[47],"directly":[49],"inside":[50,77],"device":[53],"can":[54,73],"be":[55,74],"fundamental":[57],"solution":[58],"mitigating":[60],"this":[61],"overhead.":[62],"However,":[63],"none":[64],"existing":[67,236],"tools":[68],"graph-based":[70,124],"efficiently":[75],"used":[76],"limited":[84],"internal":[85],"hardware":[86],"resources":[87],"modern":[89],"SSDs.":[90],"At":[91],"same":[93],"time,":[94],"prior":[95],"storage-centric":[96],"systems":[97],"developed":[98],"(i)":[100,160],"traditional,":[101],"linear":[102],"non-graph-based":[103],"or":[106],"(ii)":[107,167],"conventional,":[108],"non-genomic":[109],"graph":[110],"are":[112],"not":[113],"suitable":[114],"unique":[117,198],"structures":[119],"access":[121],"patterns":[122],"analysis.":[126],"We":[127],"propose":[128,189],"GRAINS,":[129],"first":[131],"with":[135],"storage.":[140],"Through":[141],"our":[142],"detailed":[143],"examination":[144],"typical":[146],"pipelines":[148,163],"that":[149],"operate":[150],"graphs,":[153],"we":[154,188,209,224],"perform":[155],"storage-aware":[156],"algorithm-architecture":[157],"co-design":[158,180],"make":[161],"these":[162],"more":[164],"storage-friendly":[165],"further":[168],"improve":[169],"performance,":[170],"energy-efficiency,":[171],"cost":[173],"via":[174,204],"in-storage":[175,207],"in-flash":[177,205],"processing.":[178],"GRAINS's":[179],"is":[181],"based":[182,196],"three":[184],"key":[185],"aspects.":[186],"First,":[187],"new":[191],"batching":[192],"execution":[194],"flow,":[195],"features":[199],"graphs.":[202],"Second,":[203],"processing,":[208],"avoid":[210],"transferring":[211],"low-reused":[212],"flash":[213,222],"pages.":[214],"Third,":[215],"leverage":[217],"full":[219],"parallelism":[220],"dies,":[223],"design":[225],"effective,":[227],"yet":[228],"lightweight,":[229],"scheduling":[230],"technique,":[231],"enabled":[232],"by":[233],"re-purposing":[234],"SSD":[237],"structures.":[238],"GRAINS":[239],"provides":[240],"2.7x-47.8x":[241],"speedup":[242,253],"(4.4x-31.6x":[243],"energy":[244,255],"reduction)":[245,256],"over":[246,257],"state-of-the-art":[248],"software":[249],"baselines,":[250],"1.5x-17.0x":[252],"(3.1x-20.7x":[254],"hardware-accelerated":[259],"baseline.":[260]},"counts_by_year":[],"updated_date":"2026-07-01T06:00:48.157686","created_date":"2026-06-27T00:00:00"}
