{"id":"https://openalex.org/W2087835429","doi":"https://doi.org/10.1109/iccabs.2014.6863917","title":"SAIS-OPT: On the characterization and optimization of the SA-IS algorithm for suffix array construction","display_name":"SAIS-OPT: On the characterization and optimization of the SA-IS algorithm for suffix array construction","publication_year":2014,"publication_date":"2014-06-01","ids":{"openalex":"https://openalex.org/W2087835429","doi":"https://doi.org/10.1109/iccabs.2014.6863917","mag":"2087835429"},"language":"en","primary_location":{"id":"doi:10.1109/iccabs.2014.6863917","is_oa":false,"landing_page_url":"https://doi.org/10.1109/iccabs.2014.6863917","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2014 IEEE 4th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5045012422","display_name":"Nataliya Timoshevskaya","orcid":"https://orcid.org/0000-0002-9775-5877"},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Nataliya Timoshevskaya","raw_affiliation_strings":["Department of Computer Science, Virginia Tech Blacksburg, Virginia, USA","Department of Computer Science Virginia Tech Blacksburg, USA#TAB#"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Virginia Tech Blacksburg, Virginia, USA","institution_ids":["https://openalex.org/I859038795"]},{"raw_affiliation_string":"Department of Computer Science Virginia Tech Blacksburg, USA#TAB#","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5058539554","display_name":"Wu-chun Feng","orcid":"https://orcid.org/0000-0002-6015-0727"},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wu-chun Feng","raw_affiliation_strings":["Department of Computer Science, Virginia Tech Blacksburg, Virginia, USA","Department of Computer Science Virginia Tech Blacksburg, USA#TAB#"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Virginia Tech Blacksburg, Virginia, USA","institution_ids":["https://openalex.org/I859038795"]},{"raw_affiliation_string":"Department of Computer Science Virginia Tech Blacksburg, USA#TAB#","institution_ids":["https://openalex.org/I859038795"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5045012422"],"corresponding_institution_ids":["https://openalex.org/I859038795"],"apc_list":null,"apc_paid":null,"fwci":0.8457,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.81889595,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"31","issue":null,"first_page":"1","last_page":"6"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9929999709129333,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9779000282287598,"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/characterization","display_name":"Characterization (materials science)","score":0.7713374495506287},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6404480934143066},{"id":"https://openalex.org/keywords/suffix","display_name":"Suffix","score":0.6002086997032166},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.551983654499054},{"id":"https://openalex.org/keywords/suffix-array","display_name":"Suffix array","score":0.5497218370437622},{"id":"https://openalex.org/keywords/compressed-suffix-array","display_name":"Compressed suffix array","score":0.5190723538398743},{"id":"https://openalex.org/keywords/data-structure","display_name":"Data structure","score":0.21492207050323486},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.16115671396255493},{"id":"https://openalex.org/keywords/suffix-tree","display_name":"Suffix tree","score":0.08493036031723022},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.07121360301971436},{"id":"https://openalex.org/keywords/linguistics","display_name":"Linguistics","score":0.06447142362594604},{"id":"https://openalex.org/keywords/nanotechnology","display_name":"Nanotechnology","score":0.0584770143032074}],"concepts":[{"id":"https://openalex.org/C2780841128","wikidata":"https://www.wikidata.org/wiki/Q5073781","display_name":"Characterization (materials science)","level":2,"score":0.7713374495506287},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6404480934143066},{"id":"https://openalex.org/C2779804580","wikidata":"https://www.wikidata.org/wiki/Q102047","display_name":"Suffix","level":2,"score":0.6002086997032166},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.551983654499054},{"id":"https://openalex.org/C2779259728","wikidata":"https://www.wikidata.org/wiki/Q281472","display_name":"Suffix array","level":3,"score":0.5497218370437622},{"id":"https://openalex.org/C100903775","wikidata":"https://www.wikidata.org/wiki/Q5157028","display_name":"Compressed suffix array","level":4,"score":0.5190723538398743},{"id":"https://openalex.org/C162319229","wikidata":"https://www.wikidata.org/wiki/Q175263","display_name":"Data structure","level":2,"score":0.21492207050323486},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.16115671396255493},{"id":"https://openalex.org/C2781166958","wikidata":"https://www.wikidata.org/wiki/Q1426863","display_name":"Suffix tree","level":3,"score":0.08493036031723022},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.07121360301971436},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.06447142362594604},{"id":"https://openalex.org/C171250308","wikidata":"https://www.wikidata.org/wiki/Q11468","display_name":"Nanotechnology","level":1,"score":0.0584770143032074},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/iccabs.2014.6863917","is_oa":false,"landing_page_url":"https://doi.org/10.1109/iccabs.2014.6863917","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2014 IEEE 4th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS)","raw_type":"proceedings-article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.648.3582","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.648.3582","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://synergy.cs.vt.edu/pubs/papers/timoshevskaya-saisopt-iccabs14.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":20,"referenced_works":["https://openalex.org/W117230746","https://openalex.org/W1485847476","https://openalex.org/W1976682045","https://openalex.org/W1977174119","https://openalex.org/W2017808314","https://openalex.org/W2030178036","https://openalex.org/W2067974452","https://openalex.org/W2087262967","https://openalex.org/W2091273836","https://openalex.org/W2093516854","https://openalex.org/W2103441770","https://openalex.org/W2115501618","https://openalex.org/W2118703123","https://openalex.org/W2122910323","https://openalex.org/W2136043658","https://openalex.org/W2150749717","https://openalex.org/W2152073175","https://openalex.org/W2157546065","https://openalex.org/W2158585409","https://openalex.org/W2326099363"],"related_works":["https://openalex.org/W2576782855","https://openalex.org/W2359436045","https://openalex.org/W153119118","https://openalex.org/W2143531254","https://openalex.org/W2608759984","https://openalex.org/W363060408","https://openalex.org/W2003608043","https://openalex.org/W2055795184","https://openalex.org/W2123393931","https://openalex.org/W2295072202"],"abstract_inverted_index":{"The":[0,15,65],"suffix":[1],"array":[2],"and":[3],"Burrows-Wheeler":[4],"Transform":[5],"are":[6],"critical":[7],"index":[8,19],"structures":[9,20],"in":[10,59,84],"next":[11],"generation":[12],"sequence":[13],"analysis.":[14],"construction":[16,34],"of":[17,27,31,55,78],"such":[18],"for":[21],"mammalian-sized":[22],"genomes":[23],"can":[24],"take":[25],"thousands":[26],"seconds":[28],"(i.e.":[29],"tens":[30],"minutes).":[32],"Its":[33],"is":[35],"complicated":[36],"by":[37],"computational":[38],"overheads":[39],"that":[40],"coming":[41],"from":[42],"irregular":[43],"or":[44],"complex":[45],"memory-access":[46],"patterns.":[47],"This":[48],"paper":[49],"rigorously":[50],"characterizes":[51],"the":[52,56],"execution":[53],"profile":[54],"SA-IS":[57,79],"algorithm":[58],"order":[60],"to":[61,72,89],"guide":[62],"its":[63],"optimization.":[64],"resulting":[66],"optimized":[67],"SA-IS,":[68],"which":[69],"we":[70],"refer":[71],"as":[73,80,82],"sais-opt,":[74],"outperforms":[75],"previous":[76],"implementations":[77],"well":[81],"\u201cbest":[83],"practice\u201d":[85],"algorithms,":[86],"when":[87],"applied":[88],"large":[90],"DNA":[91],"strings.":[92]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2015,"cited_by_count":1}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}