{"id":"https://openalex.org/W2967071141","doi":"https://doi.org/10.1109/tcbb.2019.2935061","title":"Parallel Methods for Finding k-Mismatch Shortest Unique Substrings Using GPU","display_name":"Parallel Methods for Finding k-Mismatch Shortest Unique Substrings Using GPU","publication_year":2019,"publication_date":"2019-08-14","ids":{"openalex":"https://openalex.org/W2967071141","doi":"https://doi.org/10.1109/tcbb.2019.2935061","mag":"2967071141","pmid":"https://pubmed.ncbi.nlm.nih.gov/31425048"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2019.2935061","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2019.2935061","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5071834176","display_name":"Daniel Schultz","orcid":"https://orcid.org/0000-0003-3912-2841"},"institutions":[{"id":"https://openalex.org/I75027704","display_name":"University of Tennessee at Knoxville","ror":"https://ror.org/020f3ap87","country_code":"US","type":"education","lineage":["https://openalex.org/I75027704"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Daniel W. Schultz","raw_affiliation_strings":["Department of Electrical Engineering and Computer Science, The University of Tennessee, Knoxville, TN, USA"],"raw_orcid":"https://orcid.org/0000-0003-3912-2841","affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering and Computer Science, The University of Tennessee, Knoxville, TN, USA","institution_ids":["https://openalex.org/I75027704"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5058084642","display_name":"Bojian Xu","orcid":"https://orcid.org/0000-0001-5642-6826"},"institutions":[{"id":"https://openalex.org/I159107703","display_name":"Eastern Washington University","ror":"https://ror.org/002g57a93","country_code":"US","type":"education","lineage":["https://openalex.org/I159107703"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bojian Xu","raw_affiliation_strings":["Department of Computer Science, Eastern Washington University, Cheney, WA, USA"],"raw_orcid":"https://orcid.org/0000-0001-5642-6826","affiliations":[{"raw_affiliation_string":"Department of Computer Science, Eastern Washington University, Cheney, WA, USA","institution_ids":["https://openalex.org/I159107703"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5071834176"],"corresponding_institution_ids":["https://openalex.org/I75027704"],"apc_list":null,"apc_paid":null,"fwci":0.7225,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.78736236,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"18","issue":"1","first_page":"386","last_page":"395"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9997000098228455,"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":0.9997000098228455,"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/T12029","display_name":"DNA and Biological Computing","score":0.9958000183105469,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9952999949455261,"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/substring","display_name":"Substring","score":0.8632243871688843},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8092159032821655},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.678242027759552},{"id":"https://openalex.org/keywords/massively-parallel","display_name":"Massively parallel","score":0.6129216551780701},{"id":"https://openalex.org/keywords/string","display_name":"String (physics)","score":0.5989546775817871},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.547353982925415},{"id":"https://openalex.org/keywords/cuda","display_name":"CUDA","score":0.4895961880683899},{"id":"https://openalex.org/keywords/central-processing-unit","display_name":"Central processing unit","score":0.47022151947021484},{"id":"https://openalex.org/keywords/hamming-distance","display_name":"Hamming distance","score":0.44343188405036926},{"id":"https://openalex.org/keywords/graphics-processing-unit","display_name":"Graphics processing unit","score":0.44158342480659485},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.4206704795360565},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.33887192606925964},{"id":"https://openalex.org/keywords/data-structure","display_name":"Data structure","score":0.3170185387134552},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.15000036358833313}],"concepts":[{"id":"https://openalex.org/C182407805","wikidata":"https://www.wikidata.org/wiki/Q2626534","display_name":"Substring","level":3,"score":0.8632243871688843},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8092159032821655},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.678242027759552},{"id":"https://openalex.org/C190475519","wikidata":"https://www.wikidata.org/wiki/Q544384","display_name":"Massively parallel","level":2,"score":0.6129216551780701},{"id":"https://openalex.org/C157486923","wikidata":"https://www.wikidata.org/wiki/Q1376436","display_name":"String (physics)","level":2,"score":0.5989546775817871},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.547353982925415},{"id":"https://openalex.org/C2778119891","wikidata":"https://www.wikidata.org/wiki/Q477690","display_name":"CUDA","level":2,"score":0.4895961880683899},{"id":"https://openalex.org/C49154492","wikidata":"https://www.wikidata.org/wiki/Q5300","display_name":"Central processing unit","level":2,"score":0.47022151947021484},{"id":"https://openalex.org/C193319292","wikidata":"https://www.wikidata.org/wiki/Q272172","display_name":"Hamming distance","level":2,"score":0.44343188405036926},{"id":"https://openalex.org/C2779851693","wikidata":"https://www.wikidata.org/wiki/Q183484","display_name":"Graphics processing unit","level":2,"score":0.44158342480659485},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4206704795360565},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.33887192606925964},{"id":"https://openalex.org/C162319229","wikidata":"https://www.wikidata.org/wiki/Q175263","display_name":"Data structure","level":2,"score":0.3170185387134552},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.15000036358833313},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C37914503","wikidata":"https://www.wikidata.org/wiki/Q156495","display_name":"Mathematical physics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2019.2935061","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2019.2935061","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31425048","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31425048","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":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":18,"referenced_works":["https://openalex.org/W212038867","https://openalex.org/W263816278","https://openalex.org/W1489909987","https://openalex.org/W1614203862","https://openalex.org/W1751724878","https://openalex.org/W1778337628","https://openalex.org/W2002204859","https://openalex.org/W2040322457","https://openalex.org/W2133732112","https://openalex.org/W2259120662","https://openalex.org/W2524597039","https://openalex.org/W2533951358","https://openalex.org/W2621569787","https://openalex.org/W2844403901","https://openalex.org/W2950025489","https://openalex.org/W6650585354","https://openalex.org/W6727341658","https://openalex.org/W6728921054"],"related_works":["https://openalex.org/W1674453943","https://openalex.org/W1540916738","https://openalex.org/W3127593639","https://openalex.org/W2062696773","https://openalex.org/W2122887143","https://openalex.org/W4287814113","https://openalex.org/W3016364484","https://openalex.org/W2999485669","https://openalex.org/W2020935936","https://openalex.org/W2064153048"],"abstract_inverted_index":{"k-mismatch":[0,25,122],"shortest":[1,38],"unique":[2],"substring":[3,39],"(SUS)":[4],"queries":[5,172,182,243],"have":[6,48,92],"been":[7,93],"proposed":[8],"and":[9,45,84,90,97,101,175,217],"studied":[10],"very":[11],"recently":[12],"due":[13],"to":[14,67,249],"its":[15],"useful":[16],"applications":[17],"in":[18,58,63,80,107],"the":[19,42,59,70,99,108,117,128,133,158,191,197,220,229,235],"subfield":[20],"of":[21,32,55,75,104,132,165,234],"computational":[22],"biology.":[23],"The":[24,61],"SUS":[26,64,71,105,123,171,181,211,226,242],"query":[27,65],"over":[28,183],"one":[29],"given":[30,43],"position":[31,44,74],"a":[33,37,49,52,76,81,143,163,207],"string":[34,79],"asks":[35],"for":[36,72,121,169,179,210,224,240],"that":[40,151],"covers":[41],"does":[46,244],"not":[47,245],"duplicate":[50],"(within":[51],"Hamming":[53],"distance":[54],"k)":[56],"elsewhere":[57],"string.":[60],"challenge":[62],"is":[66,154],"collectively":[68],"find":[69],"every":[73],"massively":[77,214],"long":[78,215,251],"both":[82],"time-":[83],"space-efficient":[85],"manner.":[86],"All":[87],"known":[88],"efforts":[89],"results":[91],"focused":[94],"on":[95,127,142,213],"improving":[96],"optimizing":[98],"time":[100,232],"space":[102],"efficiency":[103],"computation":[106],"sequential":[109,200,237],"CPU":[110,160,201,238],"model.":[111],"In":[112],"this":[113],"work,":[114],"we":[115],"propose":[116],"first":[118,221],"parallel":[119],"approach":[120],"queries,":[124],"particularly":[125],"leveraging":[126],"massive":[129],"multi-threading":[130],"architecture":[131],"graphic":[134],"processing":[135],"unit":[136],"(GPU)":[137],"technology.":[138],"Experimental":[139],"study":[140],"performed":[141],"mid-end":[144],"GPU":[145],"using":[146],"real-world":[147],"biological":[148],"data":[149],"shows":[150],"our":[152],"proposal":[153],"consistently":[155],"faster":[156,208],"than":[157],"fastest":[159],"solution":[161],"by":[162],"factor":[164],"at":[166,176],"least":[167,177],"6":[168],"exact":[170],"(":[173,186],"k=0)":[174],"23":[178],"approximate":[180,225,241],"DNA":[184],"sequences":[185],"),":[187],"while":[188],"maintaining":[189],"nearly":[190],"same":[192],"peak":[193],"memory":[194],"usage":[195],"as":[196],"most":[198],"memory-efficient":[199],"proposal.":[202],"Our":[203],"work":[204],"provides":[205,219],"practitioners":[206],"tool":[209,223],"finding":[212],"strings,":[216],"indeed":[218],"practical":[222],"computation,":[227],"because":[228],"any-case":[230],"quadratical":[231],"cost":[233],"state-of-the-art":[236],"method":[239],"scale":[246],"well":[247],"even":[248],"modestly":[250],"strings.":[252]},"counts_by_year":[{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
