{"id":"https://openalex.org/W2889833303","doi":"https://doi.org/10.1145/3375890","title":"Fully Functional Suffix Trees and Optimal Text Searching in BWT-Runs Bounded Space","display_name":"Fully Functional Suffix Trees and Optimal Text Searching in BWT-Runs Bounded Space","publication_year":2020,"publication_date":"2020-01-15","ids":{"openalex":"https://openalex.org/W2889833303","doi":"https://doi.org/10.1145/3375890","mag":"2889833303"},"language":"en","primary_location":{"id":"doi:10.1145/3375890","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3375890","pdf_url":null,"source":{"id":"https://openalex.org/S118992489","display_name":"Journal of the ACM","issn_l":"0004-5411","issn":["0004-5411","1557-735X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319798","host_organization_name":"Association for Computing Machinery","host_organization_lineage":["https://openalex.org/P4310319798"],"host_organization_lineage_names":["Association for Computing Machinery"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of the ACM","raw_type":"journal-article"},"type":"article","indexed_in":["arxiv","crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/1809.02792","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Travis Gagie","orcid":null},"institutions":[{"id":"https://openalex.org/I129902397","display_name":"Dalhousie University","ror":"https://ror.org/01e6qks80","country_code":"CA","type":"education","lineage":["https://openalex.org/I129902397"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Travis Gagie","raw_affiliation_strings":["Dalhousie University, Halifax, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dalhousie University, Halifax, Canada","institution_ids":["https://openalex.org/I129902397"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Gonzalo Navarro","orcid":null},"institutions":[{"id":"https://openalex.org/I69737025","display_name":"University of Chile","ror":"https://ror.org/047gc3g35","country_code":"CL","type":"education","lineage":["https://openalex.org/I69737025"]}],"countries":["CL"],"is_corresponding":false,"raw_author_name":"Gonzalo Navarro","raw_affiliation_strings":["University of Chile, Santiago, Chile"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Chile, Santiago, Chile","institution_ids":["https://openalex.org/I69737025"]}]},{"author_position":"last","author":{"id":null,"display_name":"Nicola Prezza","orcid":null},"institutions":[{"id":"https://openalex.org/I108290504","display_name":"University of Pisa","ror":"https://ror.org/03ad39j10","country_code":"IT","type":"education","lineage":["https://openalex.org/I108290504"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Nicola Prezza","raw_affiliation_strings":["University of Pisa, Pisa, Rome, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Pisa, Pisa, Rome, Italy","institution_ids":["https://openalex.org/I108290504"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":10.0501,"has_fulltext":false,"cited_by_count":141,"citation_normalized_percentile":{"value":0.98512488,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"67","issue":"1","first_page":"1","last_page":"54"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9546999931335449,"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":0.9546999931335449,"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/T11106","display_name":"Data Management and Algorithms","score":0.006200000178068876,"subfield":{"id":"https://openalex.org/subfields/1711","display_name":"Signal Processing"},"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/T10720","display_name":"Complexity and Algorithms in Graphs","score":0.005900000222027302,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/log-log-plot","display_name":"Log-log plot","score":0.7179999947547913},{"id":"https://openalex.org/keywords/binary-logarithm","display_name":"Binary logarithm","score":0.6841999888420105},{"id":"https://openalex.org/keywords/bounded-function","display_name":"Bounded function","score":0.6690999865531921},{"id":"https://openalex.org/keywords/search-engine-indexing","display_name":"Search engine indexing","score":0.6272000074386597},{"id":"https://openalex.org/keywords/space","display_name":"Space (punctuation)","score":0.5627999901771545},{"id":"https://openalex.org/keywords/suffix","display_name":"Suffix","score":0.5375000238418579},{"id":"https://openalex.org/keywords/generalized-suffix-tree","display_name":"Generalized suffix tree","score":0.515999972820282},{"id":"https://openalex.org/keywords/suffix-tree","display_name":"Suffix tree","score":0.5113999843597412},{"id":"https://openalex.org/keywords/suffix-array","display_name":"Suffix array","score":0.4943999946117401}],"concepts":[{"id":"https://openalex.org/C195292467","wikidata":"https://www.wikidata.org/wiki/Q2091879","display_name":"Log-log plot","level":3,"score":0.7179999947547913},{"id":"https://openalex.org/C63553672","wikidata":"https://www.wikidata.org/wiki/Q581168","display_name":"Binary logarithm","level":2,"score":0.6841999888420105},{"id":"https://openalex.org/C34388435","wikidata":"https://www.wikidata.org/wiki/Q2267362","display_name":"Bounded function","level":2,"score":0.6690999865531921},{"id":"https://openalex.org/C75165309","wikidata":"https://www.wikidata.org/wiki/Q2258979","display_name":"Search engine indexing","level":2,"score":0.6272000074386597},{"id":"https://openalex.org/C2778572836","wikidata":"https://www.wikidata.org/wiki/Q380933","display_name":"Space (punctuation)","level":2,"score":0.5627999901771545},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.5529000163078308},{"id":"https://openalex.org/C2779804580","wikidata":"https://www.wikidata.org/wiki/Q102047","display_name":"Suffix","level":2,"score":0.5375000238418579},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.5224000215530396},{"id":"https://openalex.org/C118146561","wikidata":"https://www.wikidata.org/wiki/Q5532514","display_name":"Generalized suffix tree","level":4,"score":0.515999972820282},{"id":"https://openalex.org/C2781166958","wikidata":"https://www.wikidata.org/wiki/Q1426863","display_name":"Suffix tree","level":3,"score":0.5113999843597412},{"id":"https://openalex.org/C2779259728","wikidata":"https://www.wikidata.org/wiki/Q281472","display_name":"Suffix array","level":3,"score":0.4943999946117401},{"id":"https://openalex.org/C112876837","wikidata":"https://www.wikidata.org/wiki/Q837518","display_name":"Alphabet","level":2,"score":0.4702000021934509},{"id":"https://openalex.org/C100903775","wikidata":"https://www.wikidata.org/wiki/Q5157028","display_name":"Compressed suffix array","level":4,"score":0.45980000495910645},{"id":"https://openalex.org/C90805587","wikidata":"https://www.wikidata.org/wiki/Q10944557","display_name":"Word (group theory)","level":2,"score":0.4171000123023987},{"id":"https://openalex.org/C2780009758","wikidata":"https://www.wikidata.org/wiki/Q6804172","display_name":"Measure (data warehouse)","level":2,"score":0.40799999237060547},{"id":"https://openalex.org/C118615104","wikidata":"https://www.wikidata.org/wiki/Q121416","display_name":"Discrete mathematics","level":1,"score":0.3865000009536743},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3668999969959259},{"id":"https://openalex.org/C77553402","wikidata":"https://www.wikidata.org/wiki/Q13222579","display_name":"Upper and lower bounds","level":2,"score":0.3513000011444092},{"id":"https://openalex.org/C182407805","wikidata":"https://www.wikidata.org/wiki/Q2626534","display_name":"Substring","level":3,"score":0.3449000120162964},{"id":"https://openalex.org/C162319229","wikidata":"https://www.wikidata.org/wiki/Q175263","display_name":"Data structure","level":2,"score":0.34450000524520874},{"id":"https://openalex.org/C97137487","wikidata":"https://www.wikidata.org/wiki/Q729138","display_name":"Integer (computer science)","level":2,"score":0.3336000144481659},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.32850000262260437},{"id":"https://openalex.org/C148043351","wikidata":"https://www.wikidata.org/wiki/Q4456944","display_name":"Current (fluid)","level":2,"score":0.301800012588501},{"id":"https://openalex.org/C164226766","wikidata":"https://www.wikidata.org/wiki/Q7293202","display_name":"Rank (graph theory)","level":2,"score":0.2754000127315521},{"id":"https://openalex.org/C204241405","wikidata":"https://www.wikidata.org/wiki/Q461499","display_name":"Transformation (genetics)","level":3,"score":0.27000001072883606},{"id":"https://openalex.org/C190290938","wikidata":"https://www.wikidata.org/wiki/Q387015","display_name":"Trie","level":3,"score":0.2687000036239624},{"id":"https://openalex.org/C311688","wikidata":"https://www.wikidata.org/wiki/Q2393193","display_name":"Time complexity","level":2,"score":0.25589999556541443},{"id":"https://openalex.org/C2780589192","wikidata":"https://www.wikidata.org/wiki/Q7285140","display_name":"Raising (metalworking)","level":2,"score":0.2515000104904175}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1145/3375890","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3375890","pdf_url":null,"source":{"id":"https://openalex.org/S118992489","display_name":"Journal of the ACM","issn_l":"0004-5411","issn":["0004-5411","1557-735X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319798","host_organization_name":"Association for Computing Machinery","host_organization_lineage":["https://openalex.org/P4310319798"],"host_organization_lineage_names":["Association for Computing Machinery"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of the ACM","raw_type":"journal-article"},{"id":"pmh:oai:arXiv.org:1809.02792","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1809.02792","pdf_url":"https://arxiv.org/pdf/1809.02792","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"pmh:oai:iris.luiss.it:11385/192324","is_oa":true,"landing_page_url":"https://dl.acm.org/doi/10.1145/3375890#d10052772e1","pdf_url":null,"source":{"id":"https://openalex.org/S4377196446","display_name":"IRIS - Institutional Research Information System (Libera Universit\u00e0 Internazionale degli Studi Sociali Guido Carli)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I56441308","host_organization_name":"Libera Universit\u00e0 Internazionale degli Studi Sociali Guido Carli","host_organization_lineage":["https://openalex.org/I56441308"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:iris.unive.it:10278/3729797","is_oa":false,"landing_page_url":"https://hdl.handle.net/10278/3729797","pdf_url":null,"source":{"id":"https://openalex.org/S4306402336","display_name":"ARCA (Universit\u00e0 Ca' Foscari Venezia)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I149461666","host_organization_name":"Ca' Foscari University of Venice","host_organization_lineage":["https://openalex.org/I149461666"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:repositorio.uchile.cl:2250/178684","is_oa":true,"landing_page_url":"https://repositorio.uchile.cl/handle/2250/178684","pdf_url":null,"source":{"id":"https://openalex.org/S4306481413","display_name":"Universidad de Chile","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of the ACM","raw_type":"Art\u00edculo de revista"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:1809.02792","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1809.02792","pdf_url":"https://arxiv.org/pdf/1809.02792","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":67,"referenced_works":["https://openalex.org/W1532033082","https://openalex.org/W1965853364","https://openalex.org/W1969884330","https://openalex.org/W1973608346","https://openalex.org/W1974033543","https://openalex.org/W1976918780","https://openalex.org/W2000788935","https://openalex.org/W2007791040","https://openalex.org/W2022126655","https://openalex.org/W2024147613","https://openalex.org/W2030839740","https://openalex.org/W2033005962","https://openalex.org/W2059029449","https://openalex.org/W2059513841","https://openalex.org/W2064184672","https://openalex.org/W2067974452","https://openalex.org/W2072021854","https://openalex.org/W2073921136","https://openalex.org/W2074229180","https://openalex.org/W2074286662","https://openalex.org/W2077770566","https://openalex.org/W2088386938","https://openalex.org/W2088521838","https://openalex.org/W2101881908","https://openalex.org/W2103850023","https://openalex.org/W2104846587","https://openalex.org/W2107082304","https://openalex.org/W2113004376","https://openalex.org/W2118703123","https://openalex.org/W2119924552","https://openalex.org/W2121252285","https://openalex.org/W2124985265","https://openalex.org/W2130956967","https://openalex.org/W2135208303","https://openalex.org/W2147935317","https://openalex.org/W2148294372","https://openalex.org/W2154803978","https://openalex.org/W2157793907","https://openalex.org/W2158874082","https://openalex.org/W2159084616","https://openalex.org/W2159647614","https://openalex.org/W2164107415","https://openalex.org/W2165446840","https://openalex.org/W2165621523","https://openalex.org/W2170551349","https://openalex.org/W2170899819","https://openalex.org/W2171532727","https://openalex.org/W2299901589","https://openalex.org/W2343474118","https://openalex.org/W2406547600","https://openalex.org/W2533248932","https://openalex.org/W2587741488","https://openalex.org/W2602771387","https://openalex.org/W2617428261","https://openalex.org/W2724271711","https://openalex.org/W2736180370","https://openalex.org/W2786835988","https://openalex.org/W2794300029","https://openalex.org/W2794898040","https://openalex.org/W2901237963","https://openalex.org/W2901851084","https://openalex.org/W2911967969","https://openalex.org/W2952899751","https://openalex.org/W2963210383","https://openalex.org/W2964108621","https://openalex.org/W3161673966","https://openalex.org/W6601972278"],"related_works":[],"abstract_inverted_index":{"Indexing":[0],"highly":[1],"repetitive":[2,28,48],"texts\u2014such":[3],"as":[4,183],"genomic":[5],"databases,":[6],"software":[7],"repositories":[8],"and":[9,59,177,211,228,238,257,286,323,338],"versioned":[10],"text":[11,77,285,289],"collections\u2014has":[12],"become":[13],"an":[14,197],"important":[15],"problem":[16],"since":[17],"the":[18,21,33,44,50,65,99,126,134,155,168,194,208,219,254,284,295,370,383],"turn":[19],"of":[20,35,43,67,69,72,78,101,111,291,376,382,391],"millennium.":[22],"A":[23],"relevant":[24],"compressibility":[25],"measure":[26],"for":[27,47],"texts":[29],"is":[30,207,218,251],"r":[31,56,112,150,160,274,279,303,336,354,366],",":[32],"number":[34,66],"runs":[36],"in":[37,75,109,170,180,223,230,253,263,294,329,348,378,393,397],"their":[38],"Burrows-Wheeler":[39],"Transforms":[40],"(BWTs).":[41],"One":[42],"earliest":[45],"indexes":[46],"collections,":[49],"Run-Length":[51,127],"FM-index,":[52],"used":[53],"O":[54,82,139,148,158,173,185,198,231,239,272,298,331,349,364],"(":[55,83,140,149,159,174,186,199,273,276,300,333,351,365],")":[57,88,145,151,217,248],"space":[58,107,156,195,281,394],"was":[60,95],"able":[61],"to":[62,97,124,157,316,342],"efficiently":[63,104,137],"count":[64,227],"occurrences":[68,103,136,169],"a":[70,76,106,269],"pattern":[71],"length":[73,79,292],"m":[74,84,175,187,233,241],"n":[80,87,144,163,216,277,301,334,352],"(in":[81,138],"log":[85,86,142,143,161,162,202,234,242,275,305],"time,":[89,172,249],"with":[90],"current":[91],"techniques).":[92],"However,":[93],"it":[94,131],"unable":[96],"locate":[98,133,229],"positions":[100],"those":[102],"within":[105,147],"bounded":[108],"terms":[110],".":[113],"In":[114],"this":[115,119],"article,":[116],"we":[117,225,312],"close":[118],"long-standing":[120],"problem,":[121],"showing":[122],"how":[123],"extend":[125,339],"FM-index":[128,385],"so":[129],"that":[130,282,310,362],"can":[132],"occ":[135,141,189,247],"time)":[146],"space.":[152,265],"By":[153,191],"raising":[154,193],"),":[164,176],"our":[165,363],"index":[166,368],"counts":[167],"optimal":[171,181,252],"locates":[178],"them":[179],"time":[182,297,330,356],"well,":[184],"+":[188,246],").":[190,308],"further":[192],"by":[196,373,388],"w":[200,212,236,244,307],"/":[201,278,302,335,353],"\u03c3)":[203],"factor,":[204],"where":[205],"\u03c3":[206],"alphabet":[209],"size":[210,222],"=":[213],"\u03a9":[214],"(log":[215,299,332,350],"RAM":[220],"machine":[221],"bits,":[224],"support":[226],"(\u2308":[232,240],"(\u03c3)/":[235,243,306],"\u2309)":[237],"\u2309":[245],"which":[250],"packed":[255],"setting":[256],"had":[258],"not":[259],"been":[260],"obtained":[261],"before":[262],"compressed":[264],"We":[266],"also":[267],"describe":[268],"structure":[270],"using":[271],"))":[280,355],"replaces":[283],"extracts":[287],"any":[288],"substring":[290],"\u2113":[293],"almost-optimal":[296],")+\u2113":[304],"Within":[309],"space,":[311],"similarly":[313],"provide":[314],"access":[315],"arbitrary":[317],"suffix":[318,321,344],"array,":[319,322],"inverse":[320],"longest":[324],"common":[325],"prefix":[326],"array":[327],"cells":[328],")),":[337],"these":[340],"capabilities":[341],"full":[343],"tree":[345],"functionality,":[346],"typically":[347],"per":[357],"operation.":[358],"Our":[359],"experiments":[360],"show":[361],")-space":[367],"outperforms":[369],"space-competitive":[371],"alternatives":[372],"1--2":[374,389],"orders":[375,390],"magnitude":[377,392],"time.":[379,398],"Competitive":[380],"implementations":[381],"original":[384],"are":[386],"outperformed":[387],"and/or":[395],"2--3":[396]},"counts_by_year":[{"year":2026,"cited_by_count":10},{"year":2025,"cited_by_count":31},{"year":2024,"cited_by_count":24},{"year":2023,"cited_by_count":25},{"year":2022,"cited_by_count":21},{"year":2021,"cited_by_count":16},{"year":2020,"cited_by_count":13},{"year":2012,"cited_by_count":1}],"updated_date":"2026-08-05T07:39:15.569665","created_date":"2018-09-27T00:00:00"}
