{"id":"https://openalex.org/W4415285482","doi":"https://doi.org/10.1145/3725843.3756018","title":"SMX: Heterogeneous Architecture for Universal Sequence Alignment Acceleration","display_name":"SMX: Heterogeneous Architecture for Universal Sequence Alignment Acceleration","publication_year":2025,"publication_date":"2025-10-17","ids":{"openalex":"https://openalex.org/W4415285482","doi":"https://doi.org/10.1145/3725843.3756018"},"language":"en","primary_location":{"id":"doi:10.1145/3725843.3756018","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3725843.3756018","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 58th IEEE/ACM International Symposium on Microarchitecture","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://hdl.handle.net/2117/454001","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5029739066","display_name":"Max Doblas","orcid":"https://orcid.org/0000-0002-8909-3033"},"institutions":[{"id":"https://openalex.org/I2799803557","display_name":"Barcelona Supercomputing Center","ror":"https://ror.org/05sd8tv96","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2799803557","https://openalex.org/I9617848"]},{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Max Doblas","raw_affiliation_strings":["Barcelona Supercomputing Center (BSC), Barcelona, Barcelona, Spain and Universitat Polit\u00e8cnica de Catalunya (UPC), Barcelona, Barcelona, Spain"],"raw_orcid":"https://orcid.org/0000-0002-8909-3033","affiliations":[{"raw_affiliation_string":"Barcelona Supercomputing Center (BSC), Barcelona, Barcelona, Spain and Universitat Polit\u00e8cnica de Catalunya (UPC), Barcelona, Barcelona, Spain","institution_ids":["https://openalex.org/I2799803557","https://openalex.org/I9617848"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060268316","display_name":"Po Jui Shih","orcid":"https://orcid.org/0000-0001-9088-4409"},"institutions":[{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Po Jui Shih","raw_affiliation_strings":["Cornell University, Ithaca, NY, USA"],"raw_orcid":"https://orcid.org/0000-0001-9088-4409","affiliations":[{"raw_affiliation_string":"Cornell University, Ithaca, NY, USA","institution_ids":["https://openalex.org/I205783295"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5093446911","display_name":"Oscar Lostes-Cazorla","orcid":"https://orcid.org/0000-0001-5166-3806"},"institutions":[{"id":"https://openalex.org/I2799803557","display_name":"Barcelona Supercomputing Center","ror":"https://ror.org/05sd8tv96","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2799803557","https://openalex.org/I9617848"]},{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Oscar Lostes-Cazorla","raw_affiliation_strings":["Universitat Polit\u00e8cnica de Catalunya (UPC), Barcelona, Barcelona, Spain and Barcelona Supercomputing Center (BSC), Barcelona, Barcelona, Spain"],"raw_orcid":"https://orcid.org/0000-0001-5166-3806","affiliations":[{"raw_affiliation_string":"Universitat Polit\u00e8cnica de Catalunya (UPC), Barcelona, Barcelona, Spain and Barcelona Supercomputing Center (BSC), Barcelona, Barcelona, Spain","institution_ids":["https://openalex.org/I2799803557","https://openalex.org/I9617848"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088729105","display_name":"Miquel Moret\u00f3","orcid":"https://orcid.org/0000-0002-9848-8758"},"institutions":[{"id":"https://openalex.org/I2799803557","display_name":"Barcelona Supercomputing Center","ror":"https://ror.org/05sd8tv96","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2799803557","https://openalex.org/I9617848"]},{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Miquel Moreto","raw_affiliation_strings":["Universitat Polit\u00e8cnica de Catalunya (UPC), Barcelona, Barcelona, Spain and Barcelona Supercomputing Center (BSC), Barcelona, Barcelona, Spain"],"raw_orcid":"https://orcid.org/0000-0002-9848-8758","affiliations":[{"raw_affiliation_string":"Universitat Polit\u00e8cnica de Catalunya (UPC), Barcelona, Barcelona, Spain and Barcelona Supercomputing Center (BSC), Barcelona, Barcelona, Spain","institution_ids":["https://openalex.org/I2799803557","https://openalex.org/I9617848"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091660287","display_name":"Christopher Batten","orcid":"https://orcid.org/0000-0002-2835-667X"},"institutions":[{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Christopher Batten","raw_affiliation_strings":["Cornell University, Ithaca, NY, USA"],"raw_orcid":"https://orcid.org/0000-0002-2835-667X","affiliations":[{"raw_affiliation_string":"Cornell University, Ithaca, NY, USA","institution_ids":["https://openalex.org/I205783295"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5052502603","display_name":"Santiago Marco\u2010Sola","orcid":"https://orcid.org/0000-0001-7951-3914"},"institutions":[{"id":"https://openalex.org/I2799803557","display_name":"Barcelona Supercomputing Center","ror":"https://ror.org/05sd8tv96","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2799803557","https://openalex.org/I9617848"]},{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Santiago Marco-Sola","raw_affiliation_strings":["Universitat Polit\u00e8cnica de Catalunya (UPC), Barcelona, Barcelona, Spain and Barcelona Supercomputing Center (BSC), Barcelona, Barcelona, Spain"],"raw_orcid":"https://orcid.org/0000-0001-7951-3914","affiliations":[{"raw_affiliation_string":"Universitat Polit\u00e8cnica de Catalunya (UPC), Barcelona, Barcelona, Spain and Barcelona Supercomputing Center (BSC), Barcelona, Barcelona, Spain","institution_ids":["https://openalex.org/I2799803557","https://openalex.org/I9617848"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1656","last_page":"1671"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9976999759674072,"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"}},"topics":[{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9976999759674072,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9972000122070312,"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/T11181","display_name":"Advanced Data Storage Technologies","score":0.9829000234603882,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.621999979019165},{"id":"https://openalex.org/keywords/flexibility","display_name":"Flexibility (engineering)","score":0.5777000188827515},{"id":"https://openalex.org/keywords/block","display_name":"Block (permutation group theory)","score":0.5059000253677368},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.45890000462532043},{"id":"https://openalex.org/keywords/variety","display_name":"Variety (cybernetics)","score":0.44589999318122864},{"id":"https://openalex.org/keywords/alignment-free-sequence-analysis","display_name":"Alignment-free sequence analysis","score":0.41260001063346863},{"id":"https://openalex.org/keywords/node","display_name":"Node (physics)","score":0.40790000557899475},{"id":"https://openalex.org/keywords/architecture","display_name":"Architecture","score":0.40529999136924744}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6833000183105469},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.621999979019165},{"id":"https://openalex.org/C2780598303","wikidata":"https://www.wikidata.org/wiki/Q65921492","display_name":"Flexibility (engineering)","level":2,"score":0.5777000188827515},{"id":"https://openalex.org/C2777210771","wikidata":"https://www.wikidata.org/wiki/Q4927124","display_name":"Block (permutation group theory)","level":2,"score":0.5059000253677368},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.45890000462532043},{"id":"https://openalex.org/C136197465","wikidata":"https://www.wikidata.org/wiki/Q1729295","display_name":"Variety (cybernetics)","level":2,"score":0.44589999318122864},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.4219000041484833},{"id":"https://openalex.org/C180384323","wikidata":"https://www.wikidata.org/wiki/Q16335137","display_name":"Alignment-free sequence analysis","level":5,"score":0.41260001063346863},{"id":"https://openalex.org/C62611344","wikidata":"https://www.wikidata.org/wiki/Q1062658","display_name":"Node (physics)","level":2,"score":0.40790000557899475},{"id":"https://openalex.org/C123657996","wikidata":"https://www.wikidata.org/wiki/Q12271","display_name":"Architecture","level":2,"score":0.40529999136924744},{"id":"https://openalex.org/C26713055","wikidata":"https://www.wikidata.org/wiki/Q245962","display_name":"Implementation","level":2,"score":0.39640000462532043},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.38749998807907104},{"id":"https://openalex.org/C117896860","wikidata":"https://www.wikidata.org/wiki/Q11376","display_name":"Acceleration","level":2,"score":0.33719998598098755},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.30730000138282776},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.2985999882221222},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.29190000891685486},{"id":"https://openalex.org/C113775141","wikidata":"https://www.wikidata.org/wiki/Q428691","display_name":"Computer engineering","level":1,"score":0.28209999203681946},{"id":"https://openalex.org/C118524514","wikidata":"https://www.wikidata.org/wiki/Q173212","display_name":"Computer architecture","level":1,"score":0.28200000524520874},{"id":"https://openalex.org/C172430144","wikidata":"https://www.wikidata.org/wiki/Q17111997","display_name":"Symmetric multiprocessor system","level":2,"score":0.2784999907016754},{"id":"https://openalex.org/C21442007","wikidata":"https://www.wikidata.org/wiki/Q1027879","display_name":"Graphics","level":2,"score":0.2761000096797943},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.2754000127315521},{"id":"https://openalex.org/C86111242","wikidata":"https://www.wikidata.org/wiki/Q859595","display_name":"Coprocessor","level":2,"score":0.2703999876976013},{"id":"https://openalex.org/C13164978","wikidata":"https://www.wikidata.org/wiki/Q600158","display_name":"Hardware acceleration","level":3,"score":0.27000001072883606},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.26330000162124634},{"id":"https://openalex.org/C101468663","wikidata":"https://www.wikidata.org/wiki/Q1620158","display_name":"Modular design","level":2,"score":0.2502000033855438}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1145/3725843.3756018","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3725843.3756018","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 58th IEEE/ACM International Symposium on Microarchitecture","raw_type":"proceedings-article"},{"id":"pmh:oai:upcommons.upc.edu:2117/454001","is_oa":true,"landing_page_url":"https://hdl.handle.net/2117/454001","pdf_url":null,"source":{"id":"https://openalex.org/S4377196262","display_name":"UPCommons institutional repository (Universitat Polit\u00e8cnica de Catalunya)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I9617848","host_organization_name":"Universitat Polit\u00e8cnica de Catalunya","host_organization_lineage":["https://openalex.org/I9617848"],"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":"Conference report"}],"best_oa_location":{"id":"pmh:oai:upcommons.upc.edu:2117/454001","is_oa":true,"landing_page_url":"https://hdl.handle.net/2117/454001","pdf_url":null,"source":{"id":"https://openalex.org/S4377196262","display_name":"UPCommons institutional repository (Universitat Polit\u00e8cnica de Catalunya)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I9617848","host_organization_name":"Universitat Polit\u00e8cnica de Catalunya","host_organization_lineage":["https://openalex.org/I9617848"],"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":"Conference report"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3606881617","display_name":null,"funder_award_id":"CSSI Award #2311890, PPoSS Award #2118709","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4142175894","display_name":null,"funder_award_id":"PID2019-107255GB-C21, PID2020-113614RB-C21, TED2021-132634A-I00, PID2023-146511NB-I00, FPU20-04076","funder_id":"https://openalex.org/F4320315062","funder_display_name":"Ministerio de Ciencia, Innovaci\u00f3n y Universidades"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320315062","display_name":"Ministerio de Ciencia, Innovaci\u00f3n y Universidades","ror":null},{"id":"https://openalex.org/F4320331084","display_name":"Lenovo Group","ror":"https://ror.org/04srd9d93"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":98,"referenced_works":["https://openalex.org/W1566539040","https://openalex.org/W2001496424","https://openalex.org/W2010595692","https://openalex.org/W2011218124","https://openalex.org/W2011632873","https://openalex.org/W2015292449","https://openalex.org/W2016219933","https://openalex.org/W2016871293","https://openalex.org/W2028431438","https://openalex.org/W2030966511","https://openalex.org/W2039001182","https://openalex.org/W2042210471","https://openalex.org/W2045204781","https://openalex.org/W2055043387","https://openalex.org/W2074231493","https://openalex.org/W2082346787","https://openalex.org/W2087064593","https://openalex.org/W2088749788","https://openalex.org/W2100751585","https://openalex.org/W2106882534","https://openalex.org/W2124985265","https://openalex.org/W2127774996","https://openalex.org/W2132926880","https://openalex.org/W2132967231","https://openalex.org/W2133098231","https://openalex.org/W2142678478","https://openalex.org/W2143210482","https://openalex.org/W2146379626","https://openalex.org/W2146696273","https://openalex.org/W2147657366","https://openalex.org/W2158714788","https://openalex.org/W2165654401","https://openalex.org/W2169456326","https://openalex.org/W2293727009","https://openalex.org/W2513408092","https://openalex.org/W2563844719","https://openalex.org/W2575750030","https://openalex.org/W2588191434","https://openalex.org/W2594560662","https://openalex.org/W2604799547","https://openalex.org/W2607669908","https://openalex.org/W2609131492","https://openalex.org/W2762638728","https://openalex.org/W2788876413","https://openalex.org/W2789843538","https://openalex.org/W2799394118","https://openalex.org/W2801006204","https://openalex.org/W2801264239","https://openalex.org/W2883847355","https://openalex.org/W2889019034","https://openalex.org/W2941052365","https://openalex.org/W2953174564","https://openalex.org/W2970325945","https://openalex.org/W2971801673","https://openalex.org/W2979449748","https://openalex.org/W2981619930","https://openalex.org/W2991998747","https://openalex.org/W3006629507","https://openalex.org/W3013788148","https://openalex.org/W3032041425","https://openalex.org/W3043148535","https://openalex.org/W3086678357","https://openalex.org/W3099458570","https://openalex.org/W3105003914","https://openalex.org/W3111187134","https://openalex.org/W3143063265","https://openalex.org/W3172556138","https://openalex.org/W3206914323","https://openalex.org/W4205946424","https://openalex.org/W4210951666","https://openalex.org/W4212881197","https://openalex.org/W4214546858","https://openalex.org/W4220739086","https://openalex.org/W4224278121","https://openalex.org/W4254502766","https://openalex.org/W4281647104","https://openalex.org/W4285109286","https://openalex.org/W4289827499","https://openalex.org/W4292240213","https://openalex.org/W4295500606","https://openalex.org/W4308083600","https://openalex.org/W4309506674","https://openalex.org/W4319334382","https://openalex.org/W4360806537","https://openalex.org/W4362204511","https://openalex.org/W4376133202","https://openalex.org/W4380730560","https://openalex.org/W4382918133","https://openalex.org/W4385563365","https://openalex.org/W4388754285","https://openalex.org/W4388801332","https://openalex.org/W4389476160","https://openalex.org/W4390280285","https://openalex.org/W4391174133","https://openalex.org/W4393406995","https://openalex.org/W4402626026","https://openalex.org/W4403998417","https://openalex.org/W6891741504"],"related_works":[],"abstract_inverted_index":{"Sequence":[0],"alignment":[1,51,99,122,135,150,193,205,280],"is":[2,260],"a":[3,43,104,128,170,250,264,270,283],"fundamental":[4],"building":[5],"block":[6],"for":[7,46,132,140,164,276],"critical":[8],"applications":[9],"across":[10],"multiple":[11],"fields,":[12],"such":[13],"as":[14],"computational":[15],"biology":[16],"and":[17,27,48,68,74,83,114,146,149,155,166,169,177,272,285,307,312],"information":[18],"retrieval.":[19],"The":[20],"rapid":[21],"advancement":[22],"of":[23,91,120,263,293],"genome":[24],"sequencing":[25],"technologies":[26],"breakthrough":[28],"generative":[29],"AI":[30],"tools,":[31],"like":[32],"AlphaFold,":[33],"has":[34],"driven":[35],"an":[36,108,160,298],"exponential":[37],"increase":[38],"in":[39,309],"sequence-data":[40],"production,":[41],"creating":[42],"pressing":[44],"need":[45],"fast":[47],"efficient":[49,78,273],"sequence":[50,57,98,134,142,192,204,279],"tools":[52],"to":[53,70,85,87,106,116,174,186,212,221,228,241,289],"analyze":[54],"ever-growing":[55],"biological":[56],"databases.":[58],"Notwithstanding":[59],"the":[60,76,88,118,183,291,303],"numerous":[61],"accelerators":[62],"proposed,":[63],"from":[64,81],"general-purpose":[65,184],"architectures":[66,311],"(CPUs":[67],"GPUs)":[69],"domain-specific":[71,310],"designs":[72],"(FPGAs":[73],"ASICs),":[75],"most":[77],"solutions":[79],"suffer":[80],"over-specialization":[82],"fail":[84],"adapt":[86],"wide":[89],"variety":[90],"irregular":[92,165],"use":[93,206,244],"cases":[94,207],"demanded":[95],"by":[96,182,208],"practical":[97,278],"applications.":[100,123],"Thus,":[101],"it":[102],"remains":[103],"challenge":[105],"design":[107,247],"architecture":[109,130,201,275],"that":[110,136,198],"can":[111],"balance":[112],"efficiency":[113,308],"flexibility":[115,240,306],"meet":[117,290],"demands":[119],"real-world":[121],"This":[124],"work":[125],"introduces":[126],"SMX,":[127],"heterogeneous":[129,200,274],"designed":[131],"high-performance":[133,271],"supports":[137],"various":[138],"configurations":[139],"different":[141,203,243],"types":[143],"(DNA,":[144],"protein,":[145],"ASCII":[147],"text)":[148],"models":[151],"(including":[152],"weighted":[153],"gaps":[154],"substitution":[156],"matrices).":[157],"SMX":[158,225,268,299],"integrates":[159],"ISA":[161],"extension":[162],"(SMX-1D)":[163],"sequential":[167],"tasks":[168],"specialized":[171,222],"coprocessor":[172],"(SMX-2D)":[173],"accelerate":[175,242],"regular":[176],"parallel":[178],"tasks,":[179],"both":[180],"orchestrated":[181],"core":[185],"enable":[187],"seamless":[188],"integration":[189],"with":[190],"state-of-the-art":[191,213],"algorithms.":[194],"Our":[195],"results":[196,248],"demonstrate":[197],"SMX\u2019s":[199,255],"accelerates":[202],"256\u2013744":[209],"\u00d7":[210,230],"compared":[211],"software":[214],"implementations":[215],"when":[216],"aligning":[217],"real":[218],"datasets.":[219],"Compared":[220],"hardware":[223],"accelerators,":[224],"delivers":[226],"up":[227],"18.5":[229],"more":[231],"peak":[232],"performance":[233],"per":[234],"area":[235,256],"added":[236],"while":[237],"providing":[238,282],"greater":[239],"cases.":[245],"Physical":[246],"targeting":[249],"22nm":[251],"technology":[252],"node":[253],"estimate":[254],"at":[257],"0.34mm2,":[258],"which":[259],"only":[261],"30%":[262],"single-issue":[265],"in-order":[266],"CPU.":[267],"offers":[269],"accelerating":[277],"algorithms,":[281],"scalable":[284],"flexible":[286],"solution":[287],"tailored":[288],"needs":[292],"modern":[294],"sequence-analysis":[295],"tools.":[296],"Furthermore,":[297],"case":[300],"study":[301],"explores":[302],"frontier":[304],"between":[305],"accelerators.":[313]},"counts_by_year":[{"year":2026,"cited_by_count":4}],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-17T00:00:00"}
