{"id":"https://openalex.org/W4281961012","doi":"https://doi.org/10.1145/3470496.3527422","title":"BioHD","display_name":"BioHD","publication_year":2022,"publication_date":"2022-05-31","ids":{"openalex":"https://openalex.org/W4281961012","doi":"https://doi.org/10.1145/3470496.3527422"},"language":"en","primary_location":{"id":"doi:10.1145/3470496.3527422","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3470496.3527422","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3470496.3527422","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 49th Annual International Symposium on Computer Architecture","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://dl.acm.org/doi/pdf/10.1145/3470496.3527422","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5035947458","display_name":"Zhuowen Zou","orcid":"https://orcid.org/0000-0001-9057-8815"},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Zhuowen Zou","raw_affiliation_strings":["University of California Irvine"],"affiliations":[{"raw_affiliation_string":"University of California Irvine","institution_ids":["https://openalex.org/I204250578"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040624202","display_name":"Hanning Chen","orcid":"https://orcid.org/0000-0003-3568-8039"},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hanning Chen","raw_affiliation_strings":["University of California Irvine"],"affiliations":[{"raw_affiliation_string":"University of California Irvine","institution_ids":["https://openalex.org/I204250578"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057919875","display_name":"Prathyush Poduval","orcid":"https://orcid.org/0009-0009-8031-0167"},"institutions":[{"id":"https://openalex.org/I59270414","display_name":"Indian Institute of Science Bangalore","ror":"https://ror.org/04dese585","country_code":"IN","type":"education","lineage":["https://openalex.org/I59270414"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Prathyush Poduval","raw_affiliation_strings":["Indian Institute of Science"],"affiliations":[{"raw_affiliation_string":"Indian Institute of Science","institution_ids":["https://openalex.org/I59270414"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067380102","display_name":"Yeseong Kim","orcid":"https://orcid.org/0000-0001-5947-9632"},"institutions":[{"id":"https://openalex.org/I193352282","display_name":"Daegu Gyeongbuk Institute of Science and Technology","ror":"https://ror.org/03frjya69","country_code":"KR","type":"education","lineage":["https://openalex.org/I193352282"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Yeseong Kim","raw_affiliation_strings":["Daegu Gyeongbuk Institute of Science and Technology"],"affiliations":[{"raw_affiliation_string":"Daegu Gyeongbuk Institute of Science and Technology","institution_ids":["https://openalex.org/I193352282"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002579260","display_name":"Mahdi Imani","orcid":null},"institutions":[{"id":"https://openalex.org/I87182695","display_name":"Universidad del Noreste","ror":"https://ror.org/02ahky613","country_code":"MX","type":"education","lineage":["https://openalex.org/I87182695"]}],"countries":["MX"],"is_corresponding":false,"raw_author_name":"Mahdi Imani","raw_affiliation_strings":["Northeastern University"],"affiliations":[{"raw_affiliation_string":"Northeastern University","institution_ids":["https://openalex.org/I87182695"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014717235","display_name":"Elaheh Sadredini","orcid":"https://orcid.org/0000-0002-5834-4346"},"institutions":[{"id":"https://openalex.org/I103635307","display_name":"University of California, Riverside","ror":"https://ror.org/03nawhv43","country_code":"US","type":"education","lineage":["https://openalex.org/I103635307"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Elaheh Sadredini","raw_affiliation_strings":["University of California Riverside"],"affiliations":[{"raw_affiliation_string":"University of California Riverside","institution_ids":["https://openalex.org/I103635307"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085883266","display_name":"Rosario Cammarota","orcid":"https://orcid.org/0000-0002-2965-8987"},"institutions":[{"id":"https://openalex.org/I1343180700","display_name":"Intel (United States)","ror":"https://ror.org/01ek73717","country_code":"US","type":"company","lineage":["https://openalex.org/I1343180700"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rosario Cammarota","raw_affiliation_strings":["Intel Labs"],"affiliations":[{"raw_affiliation_string":"Intel Labs","institution_ids":["https://openalex.org/I1343180700"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5033221192","display_name":"Mohsen Imani","orcid":"https://orcid.org/0000-0002-5761-0622"},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mohsen Imani","raw_affiliation_strings":["University of California Irvine"],"affiliations":[{"raw_affiliation_string":"University of California Irvine","institution_ids":["https://openalex.org/I204250578"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5035947458"],"corresponding_institution_ids":["https://openalex.org/I204250578"],"apc_list":null,"apc_paid":null,"fwci":5.2942,"has_fulltext":true,"cited_by_count":64,"citation_normalized_percentile":{"value":0.9697695,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":null,"issue":null,"first_page":"656","last_page":"669"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9988999962806702,"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":0.9988999962806702,"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/T11975","display_name":"Evolutionary Algorithms and Applications","score":0.9685999751091003,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9588000178337097,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8251707553863525},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.7653329372406006},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.6559634208679199},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.5158802270889282},{"id":"https://openalex.org/keywords/simd","display_name":"SIMD","score":0.505490779876709},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.46156564354896545},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3299190104007721},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.22161182761192322}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8251707553863525},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.7653329372406006},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.6559634208679199},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.5158802270889282},{"id":"https://openalex.org/C150552126","wikidata":"https://www.wikidata.org/wiki/Q339387","display_name":"SIMD","level":2,"score":0.505490779876709},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.46156564354896545},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3299190104007721},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.22161182761192322},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"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/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3470496.3527422","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3470496.3527422","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3470496.3527422","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 49th Annual International Symposium on Computer Architecture","raw_type":"proceedings-article"}],"best_oa_location":{"id":"doi:10.1145/3470496.3527422","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3470496.3527422","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3470496.3527422","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 49th Annual International Symposium on Computer Architecture","raw_type":"proceedings-article"},"sustainable_development_goals":[{"display_name":"Affordable and clean energy","score":0.8899999856948853,"id":"https://metadata.un.org/sdg/7"}],"awards":[{"id":"https://openalex.org/G3019876348","display_name":null,"funder_award_id":"#N00014-21-1-2225","funder_id":"https://openalex.org/F4320337345","funder_display_name":"Office of Naval Research"},{"id":"https://openalex.org/G4264929259","display_name":null,"funder_award_id":"N00014-21-1-2225 and N00014-22-1-2067","funder_id":"https://openalex.org/F4320337345","funder_display_name":"Office of Naval Research"},{"id":"https://openalex.org/G4422425012","display_name":null,"funder_award_id":"2988.001","funder_id":"https://openalex.org/F4320306087","funder_display_name":"Semiconductor Research Corporation"},{"id":"https://openalex.org/G4925361597","display_name":null,"funder_award_id":"#2988.001","funder_id":"https://openalex.org/F4320306087","funder_display_name":"Semiconductor Research Corporation"},{"id":"https://openalex.org/G8017170229","display_name":null,"funder_award_id":"N00014-21-1-2225","funder_id":"https://openalex.org/F4320306087","funder_display_name":"Semiconductor Research Corporation"},{"id":"https://openalex.org/G8562790839","display_name":null,"funder_award_id":"#2127780","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8862787963","display_name":null,"funder_award_id":"2127780","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8876996369","display_name":null,"funder_award_id":"N00014","funder_id":"https://openalex.org/F4320337345","funder_display_name":"Office of Naval Research"},{"id":"https://openalex.org/G8915565379","display_name":null,"funder_award_id":"N00014-21-1-2225","funder_id":"https://openalex.org/F4320337345","funder_display_name":"Office of Naval Research"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306087","display_name":"Semiconductor Research Corporation","ror":"https://ror.org/047z4n946"},{"id":"https://openalex.org/F4320307791","display_name":"Cisco Systems","ror":"https://ror.org/03yt1ez60"},{"id":"https://openalex.org/F4320332923","display_name":"U.S. Navy","ror":"https://ror.org/03ar0mv07"},{"id":"https://openalex.org/F4320337345","display_name":"Office of Naval Research","ror":"https://ror.org/00rk2pe57"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4281961012.pdf","grobid_xml":"https://content.openalex.org/works/W4281961012.grobid-xml"},"referenced_works_count":75,"referenced_works":["https://openalex.org/W1527632333","https://openalex.org/W1578783943","https://openalex.org/W1584739173","https://openalex.org/W1984209790","https://openalex.org/W1984504232","https://openalex.org/W1993533483","https://openalex.org/W2013028205","https://openalex.org/W2025674646","https://openalex.org/W2061071837","https://openalex.org/W2062143991","https://openalex.org/W2066280488","https://openalex.org/W2070862086","https://openalex.org/W2081729575","https://openalex.org/W2096041635","https://openalex.org/W2112547256","https://openalex.org/W2154478075","https://openalex.org/W2170551349","https://openalex.org/W2271840356","https://openalex.org/W2331911190","https://openalex.org/W2407339173","https://openalex.org/W2476008461","https://openalex.org/W2505929033","https://openalex.org/W2560228154","https://openalex.org/W2560329562","https://openalex.org/W2599597882","https://openalex.org/W2613989746","https://openalex.org/W2789843538","https://openalex.org/W2794757234","https://openalex.org/W2935576241","https://openalex.org/W2946512196","https://openalex.org/W2950629094","https://openalex.org/W2963027573","https://openalex.org/W2966470162","https://openalex.org/W2970402754","https://openalex.org/W2971801673","https://openalex.org/W2988640543","https://openalex.org/W2990618091","https://openalex.org/W2999932424","https://openalex.org/W3003668884","https://openalex.org/W3005783121","https://openalex.org/W3008827533","https://openalex.org/W3010223921","https://openalex.org/W3013630838","https://openalex.org/W3016919608","https://openalex.org/W3019791076","https://openalex.org/W3021673562","https://openalex.org/W3036029011","https://openalex.org/W3036478084","https://openalex.org/W3103187010","https://openalex.org/W3105003914","https://openalex.org/W3105115497","https://openalex.org/W3134195144","https://openalex.org/W3136117125","https://openalex.org/W3168260338","https://openalex.org/W3171487449","https://openalex.org/W3174581039","https://openalex.org/W3196482074","https://openalex.org/W3202318245","https://openalex.org/W3208591904","https://openalex.org/W3212827699","https://openalex.org/W3212965658","https://openalex.org/W3213820542","https://openalex.org/W4210566186","https://openalex.org/W4214820583","https://openalex.org/W4229976825","https://openalex.org/W4243519499","https://openalex.org/W4247082477","https://openalex.org/W4254672563","https://openalex.org/W6638564077","https://openalex.org/W6679354330","https://openalex.org/W6737476433","https://openalex.org/W6743970594","https://openalex.org/W6749667714","https://openalex.org/W6788939328","https://openalex.org/W7018628422"],"related_works":["https://openalex.org/W2317245370","https://openalex.org/W2099629705","https://openalex.org/W4249323025","https://openalex.org/W198851386","https://openalex.org/W1980160788","https://openalex.org/W2030310580","https://openalex.org/W947442053","https://openalex.org/W2148915962","https://openalex.org/W2283866686","https://openalex.org/W2948365806"],"abstract_inverted_index":{"In":[0],"this":[1],"paper,":[2],"we":[3,106],"propose":[4],"BioHD,":[5],"a":[6,88,108,147],"novel":[7],"genomic":[8],"sequence":[9,60,83],"searching":[10],"platform":[11],"based":[12],"on":[13,137,146,180],"Hyper-Dimensional":[14],"Computing":[15],"(HDC)":[16],"for":[17],"hardware-friendly":[18],"computation.":[19],"BioHD":[20,62,101,129,142],"transforms":[21],"inherent":[22,102],"sequential":[23],"processes":[24],"of":[25,69,150],"genome":[26,41,50],"matching":[27,84,177],"to":[28,36,52,91,173],"highly-parallelizable":[29],"computation":[30],"tasks.":[31],"We":[32,140],"exploit":[33],"HDC":[34,55,75],"memorization":[35],"encode":[37],"and":[38,104,116,144,163,166,169],"represent":[39],"the":[40,49,59,74,81,93,119,138,174],"sequences":[42,51],"using":[43],"high-dimensional":[44],"vectors.":[45],"Then,":[46],"it":[47],"combines":[48],"generate":[53],"an":[54,70],"reference":[56,76],"library.":[57,77],"During":[58],"searching,":[61],"performs":[63],"exact":[64],"or":[65],"approximate":[66],"similarity":[67],"check":[68],"encoded":[71],"query":[72],"with":[73,113,118,134],"Our":[78,123,156],"framework":[79],"simplifies":[80],"required":[82],"operations":[85,130],"while":[86],"introducing":[87],"statistical":[89],"model":[90],"control":[92],"alignment":[94],"quality.":[95],"To":[96],"get":[97],"actual":[98],"advantage":[99],"from":[100],"robustness":[103],"parallelism,":[105],"design":[107],"processing":[109],"in-memory":[110],"(PIM)":[111],"architecture":[112,125],"massive":[114],"parallelism":[115],"compatible":[117],"existing":[120],"crossbar":[121],"memory.":[122],"PIM":[124,160,187],"supports":[126],"all":[127],"essential":[128],"natively":[131],"in":[132],"memory":[133],"minimal":[135],"modification":[136],"array.":[139],"evaluate":[141],"accuracy":[143],"efficiency":[145,171],"wide":[148],"range":[149],"genomics":[151],"data,":[152],"including":[153],"COVID-19":[154],"databases.":[155],"results":[157],"indicate":[158],"that":[159],"provides":[161],"102.8\u00d7":[162],"116.1\u00d7":[164],"(9.3\u00d7":[165],"13.2\u00d7)":[167],"speedup":[168],"energy":[170],"compared":[172],"state-of-the-art":[175],"pattern":[176],"algorithm":[178],"running":[179],"GeForce":[181],"RTX":[182],"3060":[183],"Ti":[184],"GPU":[185],"(state-of-the-art":[186],"accelerator).":[188]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":20},{"year":2024,"cited_by_count":19},{"year":2023,"cited_by_count":18},{"year":2022,"cited_by_count":4}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2022-06-13T00:00:00"}
