{"id":"https://openalex.org/W2395972402","doi":"https://doi.org/10.2390/biecoll-jib-2014-253","title":"High Performance Pattern Matching on Heterogeneous Platform","display_name":"High Performance Pattern Matching on Heterogeneous Platform","publication_year":2014,"publication_date":"2014-01-01","ids":{"openalex":"https://openalex.org/W2395972402","doi":"https://doi.org/10.2390/biecoll-jib-2014-253","mag":"2395972402","pmid":"https://pubmed.ncbi.nlm.nih.gov/25339087"},"language":"en","primary_location":{"id":"pmid:25339087","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25339087","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of integrative bioinformatics","raw_type":null},"type":"article","indexed_in":["datacite","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.2390/biecoll-jib-2014-253","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5016921968","display_name":"Shima Soroushnia","orcid":null},"institutions":[{"id":"https://openalex.org/I155660961","display_name":"University of Turku","ror":"https://ror.org/05vghhr25","country_code":"FI","type":"education","lineage":["https://openalex.org/I155660961"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Soroushnia, Shima","raw_affiliation_strings":["Department of Information Technology, University of Turku, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Information Technology, University of Turku, Finland","institution_ids":["https://openalex.org/I155660961"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063193249","display_name":"Masoud Daneshtalab","orcid":"https://orcid.org/0000-0001-6289-1521"},"institutions":[{"id":"https://openalex.org/I155660961","display_name":"University of Turku","ror":"https://ror.org/05vghhr25","country_code":"FI","type":"education","lineage":["https://openalex.org/I155660961"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Daneshtalab, Masoud","raw_affiliation_strings":["Department of Information Technology, University of Turku, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Information Technology, University of Turku, Finland","institution_ids":["https://openalex.org/I155660961"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075314597","display_name":"Juha Plosila","orcid":"https://orcid.org/0000-0003-4018-5495"},"institutions":[{"id":"https://openalex.org/I155660961","display_name":"University of Turku","ror":"https://ror.org/05vghhr25","country_code":"FI","type":"education","lineage":["https://openalex.org/I155660961"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Plosila, Juha","raw_affiliation_strings":["Department of Information Technology, University of Turku, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Information Technology, University of Turku, Finland","institution_ids":["https://openalex.org/I155660961"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021993986","display_name":"Tapio Pahikkala","orcid":"https://orcid.org/0000-0003-4183-2455"},"institutions":[{"id":"https://openalex.org/I155660961","display_name":"University of Turku","ror":"https://ror.org/05vghhr25","country_code":"FI","type":"education","lineage":["https://openalex.org/I155660961"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Pahikkala, Tapio","raw_affiliation_strings":["Department of Information Technology, University of Turku, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Information Technology, University of Turku, Finland","institution_ids":["https://openalex.org/I155660961"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5019546150","display_name":"Pasi Liljeberg","orcid":"https://orcid.org/0000-0002-9392-3589"},"institutions":[{"id":"https://openalex.org/I155660961","display_name":"University of Turku","ror":"https://ror.org/05vghhr25","country_code":"FI","type":"education","lineage":["https://openalex.org/I155660961"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Liljeberg, Pasi","raw_affiliation_strings":["Department of Information Technology, University of Turku, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Information Technology, University of Turku, Finland","institution_ids":["https://openalex.org/I155660961"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I155660961"],"apc_list":null,"apc_paid":null,"fwci":0.9768,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.86000847,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"11","issue":"3","first_page":"253","last_page":"253"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9980000257492065,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9932000041007996,"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":0.8262186050415039},{"id":"https://openalex.org/keywords/massively-parallel","display_name":"Massively parallel","score":0.6216250061988831},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.6103740930557251},{"id":"https://openalex.org/keywords/matching","display_name":"Matching (statistics)","score":0.6026586890220642},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.5370503664016724},{"id":"https://openalex.org/keywords/architecture","display_name":"Architecture","score":0.47581416368484497},{"id":"https://openalex.org/keywords/pattern-matching","display_name":"Pattern matching","score":0.46819576621055603},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.46188563108444214},{"id":"https://openalex.org/keywords/supercomputer","display_name":"Supercomputer","score":0.44596871733665466},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.12372365593910217},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.0790468156337738}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8262186050415039},{"id":"https://openalex.org/C190475519","wikidata":"https://www.wikidata.org/wiki/Q544384","display_name":"Massively parallel","level":2,"score":0.6216250061988831},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.6103740930557251},{"id":"https://openalex.org/C165064840","wikidata":"https://www.wikidata.org/wiki/Q1321061","display_name":"Matching (statistics)","level":2,"score":0.6026586890220642},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.5370503664016724},{"id":"https://openalex.org/C123657996","wikidata":"https://www.wikidata.org/wiki/Q12271","display_name":"Architecture","level":2,"score":0.47581416368484497},{"id":"https://openalex.org/C68859911","wikidata":"https://www.wikidata.org/wiki/Q1503724","display_name":"Pattern matching","level":2,"score":0.46819576621055603},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.46188563108444214},{"id":"https://openalex.org/C83283714","wikidata":"https://www.wikidata.org/wiki/Q121117","display_name":"Supercomputer","level":2,"score":0.44596871733665466},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.12372365593910217},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0790468156337738},{"id":"https://openalex.org/C153349607","wikidata":"https://www.wikidata.org/wiki/Q36649","display_name":"Visual arts","level":1,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C142362112","wikidata":"https://www.wikidata.org/wiki/Q735","display_name":"Art","level":0,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"pmid:25339087","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25339087","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of integrative bioinformatics","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.665.9323","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.665.9323","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://journal.imbio.de/articles/pdf/jib-253.pdf","raw_type":"text"},{"id":"pmh:oai:biecoll.ub.uni-bielefeld.de:5345","is_oa":false,"landing_page_url":"http://biecoll.ub.uni-bielefeld.de/volltexte/2014/5345/","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://journal.imbio.de/article.php?aid=253","raw_type":"Journal Article"},{"id":"doi:10.2390/biecoll-jib-2014-253","is_oa":true,"landing_page_url":"https://doi.org/10.2390/biecoll-jib-2014-253","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"doi:10.2390/biecoll-jib-2014-253","is_oa":true,"landing_page_url":"https://doi.org/10.2390/biecoll-jib-2014-253","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article-journal"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/7","score":0.8999999761581421,"display_name":"Affordable and clean energy"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":12,"referenced_works":["https://openalex.org/W103634144","https://openalex.org/W1981956359","https://openalex.org/W2074373096","https://openalex.org/W2099964107","https://openalex.org/W2116052408","https://openalex.org/W2116079772","https://openalex.org/W2122840982","https://openalex.org/W2133325495","https://openalex.org/W2134826720","https://openalex.org/W2150210843","https://openalex.org/W2165766588","https://openalex.org/W2167575427"],"related_works":["https://openalex.org/W1542309263","https://openalex.org/W2000045872","https://openalex.org/W4255194554","https://openalex.org/W3123369682","https://openalex.org/W2101288321","https://openalex.org/W2123466504","https://openalex.org/W2002942683","https://openalex.org/W1592820899","https://openalex.org/W2374098690","https://openalex.org/W3027688390"],"abstract_inverted_index":{"Pattern":[0],"discovery":[1],"is":[2,13,98,116],"one":[3],"of":[4,50,62,94,121,168],"the":[5,22,44,48,56,60,117,135,143,156,165,169],"fundamental":[6],"tasks":[7],"in":[8,21,34,37,47],"bioinformatics":[9,38],"and":[10,27,39,52,83,109,137],"pattern":[11,63,103],"recognition":[12],"a":[14,73,99,128],"powerful":[15],"technique":[16],"for":[17,58,80],"searching":[18],"sequence":[19,24,151],"patterns":[20],"biological":[23],"databases.":[25],"Fast":[26],"high":[28,81],"performance":[29,61,82],"algorithms":[30,136],"are":[31],"highly":[32],"demanded":[33],"many":[35],"applications":[36],"computational":[40],"molecular":[41],"biology":[42],"since":[43],"significant":[45],"increase":[46],"number":[49],"DNA":[51],"protein":[53,150],"sequences":[54],"expand":[55],"need":[57],"raising":[59],"matching":[64,104],"algorithms.":[65],"For":[66],"this":[67,87],"purpose,":[68],"heterogeneous":[69,129],"architectures":[70],"can":[71],"be":[72],"good":[74],"choice":[75],"due":[76],"to":[77,140,164],"their":[78],"potential":[79],"energy":[84],"efficiency.":[85],"In":[86],"paper":[88],"we":[89],"present":[90],"an":[91],"efficient":[92],"implementation":[93,158,167],"Aho-Corasick":[95,112],"(AC)":[96],"which":[97,115],"well":[100],"known":[101],"exact":[102],"algorithm":[105,114,123],"with":[106],"linear":[107],"complexity,":[108],"Parallel":[110],"Failureless":[111],"(PFAC)":[113],"massively":[118],"parallelized":[119],"version":[120],"AC":[122],"without":[124],"failure":[125],"transitions,":[126],"on":[127,142,148],"CPU/GPU":[130],"architecture.":[131,145],"We":[132],"progressively":[133],"redesigned":[134],"data":[138,152],"structures":[139],"fit":[141],"GPU":[144],"Our":[146],"results":[147],"different":[149],"sets":[153],"show":[154],"that":[155],"new":[157],"runs":[159],"15":[160],"times":[161],"faster":[162],"compared":[163],"original":[166],"PFAC":[170],"algorithm.":[171]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":2}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
