{"id":"https://openalex.org/W2006595279","doi":"https://doi.org/10.1587/transinf.2014pap0011","title":"An Optimal Implementation of the Approximate String Matching on the Hierarchical Memory Machine, with Performance Evaluation on the GPU","display_name":"An Optimal Implementation of the Approximate String Matching on the Hierarchical Memory Machine, with Performance Evaluation on the GPU","publication_year":2014,"publication_date":"2014-01-01","ids":{"openalex":"https://openalex.org/W2006595279","doi":"https://doi.org/10.1587/transinf.2014pap0011","mag":"2006595279"},"language":"en","primary_location":{"id":"doi:10.1587/transinf.2014pap0011","is_oa":true,"landing_page_url":"https://doi.org/10.1587/transinf.2014pap0011","pdf_url":"https://www.jstage.jst.go.jp/article/transinf/E97.D/12/E97.D_2014PAP0011/_pdf","source":{"id":"https://openalex.org/S2486202937","display_name":"IEICE Transactions on Information and Systems","issn_l":"0916-8532","issn":["0916-8532","1745-1361"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4320800604","host_organization_name":"Institute of Electronics, Information and Communication Engineers","host_organization_lineage":["https://openalex.org/P4320800604"],"host_organization_lineage_names":["Institute of Electronics, Information and Communication Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEICE Transactions on Information and Systems","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://www.jstage.jst.go.jp/article/transinf/E97.D/12/E97.D_2014PAP0011/_pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5025505582","display_name":"Duhu Man","orcid":null},"institutions":[{"id":"https://openalex.org/I113306721","display_name":"Hiroshima University","ror":"https://ror.org/03t78wx29","country_code":"JP","type":"education","lineage":["https://openalex.org/I113306721"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Duhu MAN","raw_affiliation_strings":["Department of Information Engineering, Hiroshima University"],"affiliations":[{"raw_affiliation_string":"Department of Information Engineering, Hiroshima University","institution_ids":["https://openalex.org/I113306721"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086055038","display_name":"Koji Nakano","orcid":"https://orcid.org/0000-0002-2040-4032"},"institutions":[{"id":"https://openalex.org/I113306721","display_name":"Hiroshima University","ror":"https://ror.org/03t78wx29","country_code":"JP","type":"education","lineage":["https://openalex.org/I113306721"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Koji NAKANO","raw_affiliation_strings":["Department of Information Engineering, Hiroshima University"],"affiliations":[{"raw_affiliation_string":"Department of Information Engineering, Hiroshima University","institution_ids":["https://openalex.org/I113306721"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5009547258","display_name":"Yasuaki Ito","orcid":"https://orcid.org/0000-0003-0593-231X"},"institutions":[{"id":"https://openalex.org/I113306721","display_name":"Hiroshima University","ror":"https://ror.org/03t78wx29","country_code":"JP","type":"education","lineage":["https://openalex.org/I113306721"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yasuaki ITO","raw_affiliation_strings":["Department of Information Engineering, Hiroshima University"],"affiliations":[{"raw_affiliation_string":"Department of Information Engineering, Hiroshima University","institution_ids":["https://openalex.org/I113306721"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5025505582"],"corresponding_institution_ids":["https://openalex.org/I113306721"],"apc_list":null,"apc_paid":null,"fwci":1.227,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.84125115,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"E97.D","issue":"12","first_page":"3063","last_page":"3071"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":1.0,"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":1.0,"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/T12326","display_name":"Network Packet Processing and Optimization","score":0.9984999895095825,"subfield":{"id":"https://openalex.org/subfields/1708","display_name":"Hardware and Architecture"},"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/T12029","display_name":"DNA and Biological Computing","score":0.9889000058174133,"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":0.8591646552085876},{"id":"https://openalex.org/keywords/cuda","display_name":"CUDA","score":0.8092948198318481},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.7528070211410522},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.741790771484375},{"id":"https://openalex.org/keywords/string-searching-algorithm","display_name":"String searching algorithm","score":0.7301416397094727},{"id":"https://openalex.org/keywords/substring","display_name":"Substring","score":0.6683735847473145},{"id":"https://openalex.org/keywords/string","display_name":"String (physics)","score":0.5788134336471558},{"id":"https://openalex.org/keywords/latency","display_name":"Latency (audio)","score":0.5272520780563354},{"id":"https://openalex.org/keywords/approximate-string-matching","display_name":"Approximate string matching","score":0.4932023882865906},{"id":"https://openalex.org/keywords/pattern-matching","display_name":"Pattern matching","score":0.4864203929901123},{"id":"https://openalex.org/keywords/matching","display_name":"Matching (statistics)","score":0.4765756130218506},{"id":"https://openalex.org/keywords/general-purpose-computing-on-graphics-processing-units","display_name":"General-purpose computing on graphics processing units","score":0.42140254378318787},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.38983073830604553},{"id":"https://openalex.org/keywords/graphics","display_name":"Graphics","score":0.11937159299850464},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.11140969395637512},{"id":"https://openalex.org/keywords/data-structure","display_name":"Data structure","score":0.09684184193611145},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.09336593747138977},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.08782774209976196}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8591646552085876},{"id":"https://openalex.org/C2778119891","wikidata":"https://www.wikidata.org/wiki/Q477690","display_name":"CUDA","level":2,"score":0.8092948198318481},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.7528070211410522},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.741790771484375},{"id":"https://openalex.org/C7757238","wikidata":"https://www.wikidata.org/wiki/Q374040","display_name":"String searching algorithm","level":3,"score":0.7301416397094727},{"id":"https://openalex.org/C182407805","wikidata":"https://www.wikidata.org/wiki/Q2626534","display_name":"Substring","level":3,"score":0.6683735847473145},{"id":"https://openalex.org/C157486923","wikidata":"https://www.wikidata.org/wiki/Q1376436","display_name":"String (physics)","level":2,"score":0.5788134336471558},{"id":"https://openalex.org/C82876162","wikidata":"https://www.wikidata.org/wiki/Q17096504","display_name":"Latency (audio)","level":2,"score":0.5272520780563354},{"id":"https://openalex.org/C32610155","wikidata":"https://www.wikidata.org/wiki/Q1798621","display_name":"Approximate string matching","level":3,"score":0.4932023882865906},{"id":"https://openalex.org/C68859911","wikidata":"https://www.wikidata.org/wiki/Q1503724","display_name":"Pattern matching","level":2,"score":0.4864203929901123},{"id":"https://openalex.org/C165064840","wikidata":"https://www.wikidata.org/wiki/Q1321061","display_name":"Matching (statistics)","level":2,"score":0.4765756130218506},{"id":"https://openalex.org/C50630238","wikidata":"https://www.wikidata.org/wiki/Q971505","display_name":"General-purpose computing on graphics processing units","level":3,"score":0.42140254378318787},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.38983073830604553},{"id":"https://openalex.org/C21442007","wikidata":"https://www.wikidata.org/wiki/Q1027879","display_name":"Graphics","level":2,"score":0.11937159299850464},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.11140969395637512},{"id":"https://openalex.org/C162319229","wikidata":"https://www.wikidata.org/wiki/Q175263","display_name":"Data structure","level":2,"score":0.09684184193611145},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.09336593747138977},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.08782774209976196},{"id":"https://openalex.org/C37914503","wikidata":"https://www.wikidata.org/wiki/Q156495","display_name":"Mathematical physics","level":1,"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/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1587/transinf.2014pap0011","is_oa":true,"landing_page_url":"https://doi.org/10.1587/transinf.2014pap0011","pdf_url":"https://www.jstage.jst.go.jp/article/transinf/E97.D/12/E97.D_2014PAP0011/_pdf","source":{"id":"https://openalex.org/S2486202937","display_name":"IEICE Transactions on Information and Systems","issn_l":"0916-8532","issn":["0916-8532","1745-1361"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4320800604","host_organization_name":"Institute of Electronics, Information and Communication Engineers","host_organization_lineage":["https://openalex.org/P4320800604"],"host_organization_lineage_names":["Institute of Electronics, Information and Communication Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEICE Transactions on Information and Systems","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.1587/transinf.2014pap0011","is_oa":true,"landing_page_url":"https://doi.org/10.1587/transinf.2014pap0011","pdf_url":"https://www.jstage.jst.go.jp/article/transinf/E97.D/12/E97.D_2014PAP0011/_pdf","source":{"id":"https://openalex.org/S2486202937","display_name":"IEICE Transactions on Information and Systems","issn_l":"0916-8532","issn":["0916-8532","1745-1361"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4320800604","host_organization_name":"Institute of Electronics, Information and Communication Engineers","host_organization_lineage":["https://openalex.org/P4320800604"],"host_organization_lineage_names":["Institute of Electronics, Information and Communication Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEICE Transactions on Information and Systems","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.5199999809265137,"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy"}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2006595279.pdf","grobid_xml":"https://content.openalex.org/works/W2006595279.grobid-xml"},"referenced_works_count":24,"referenced_works":["https://openalex.org/W48891771","https://openalex.org/W1675130169","https://openalex.org/W1950131209","https://openalex.org/W1977618577","https://openalex.org/W1983929828","https://openalex.org/W1990413869","https://openalex.org/W1997123360","https://openalex.org/W1998039805","https://openalex.org/W2011632873","https://openalex.org/W2041720388","https://openalex.org/W2070865675","https://openalex.org/W2094969361","https://openalex.org/W2100751585","https://openalex.org/W2102877737","https://openalex.org/W2162760245","https://openalex.org/W2259192088","https://openalex.org/W2533058927","https://openalex.org/W2533433706","https://openalex.org/W2540221139","https://openalex.org/W2540645700","https://openalex.org/W2542099479","https://openalex.org/W2752885492","https://openalex.org/W2753176400","https://openalex.org/W2953580869"],"related_works":["https://openalex.org/W52396946","https://openalex.org/W2298204719","https://openalex.org/W1564013439","https://openalex.org/W2395807140","https://openalex.org/W2351800092","https://openalex.org/W2902482624","https://openalex.org/W3112977702","https://openalex.org/W2376315482","https://openalex.org/W2366227422","https://openalex.org/W2218650848"],"abstract_inverted_index":{"The":[0,20,49,157],"Hierarchical":[1],"Memory":[2],"Machine":[3],"(HMM)":[4],"is":[5,36,55,124,140],"a":[6,37,41,194],"theoretical":[7],"parallel":[8,60],"computing":[9,16,122],"model":[10],"that":[11,116,161],"captures":[12],"the":[13,63,68,90,117,121,136,155,162,179,191,200],"essence":[14],"of":[15,31,43,52,120,164,167,197],"on":[17,67,73,89,148,190],"CUDA-enabled":[18],"GPUs.":[19],"approximate":[21,64,137],"string":[22,65,138],"matching":[23,66,139],"(ASM)":[24],"for":[25,62,135],"two":[26,165],"strings":[27,166],"X":[28],"and":[29,34,70,107,153,169],"Y":[30,44],"length":[32],"m":[33],"n":[35],"task":[38],"to":[39,47,56],"find":[40],"substring":[42],"most":[45],"similar":[46],"X.":[48],"main":[50],"contribution":[51],"this":[53],"paper":[54],"show":[57,115,160],"an":[58],"optimal":[59],"algorithm":[61,79,134,147,181],"HMM":[69,91],"implement":[71],"it":[72,184],"GeForce":[74,149],"GTX":[75,150],"580":[76,151],"GPU.":[77],"Our":[78],"runs":[80],"in":[81,176,185],"$O({n\\over":[82],"w}+{mn\\over":[83,126],"dw}+{nL\\over":[84,127],"p}+{mnl\\over":[85,128],"p})$":[86,129],"time":[87,123,130,141],"units":[88],"with":[92],"p":[93],"threads,":[94],"d":[95],"streaming":[96],"processors,":[97],"memory":[98,103,109],"band":[99],"width":[100],"w,":[101],"global":[102],"access":[104,110],"latency":[105,111],"L,":[106],"shared":[108],"l.":[112],"We":[113],"also":[114],"lower":[118],"bound":[119],"$\\Omega({n\\over":[125],"units.":[131],"Thus,":[132,187],"our":[133,146,188],"optimal.":[142],"Further,":[143],"we":[144],"implemented":[145],"GPU":[152,192],"evaluated":[154],"performance.":[156],"experimental":[158],"results":[159],"ASM":[163],"1024":[168],"4M":[170],"(=222)":[171],"characters":[172],"can":[173,182],"be":[174],"done":[175],"419.6ms,":[177],"while":[178],"sequential":[180],"compute":[183],"27720ms.":[186],"implementation":[189],"attains":[193],"speedup":[195],"factor":[196],"66.1":[198],"over":[199],"single":[201],"CPU":[202],"implementation.":[203]},"counts_by_year":[{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
