{"id":"https://openalex.org/W4416343280","doi":"https://doi.org/10.4230/lipics.cpm.2026.10","title":"R-Enum Revisited: Speedup and Extension for Context-Sensitive Repeats and Net Frequencies","display_name":"R-Enum Revisited: Speedup and Extension for Context-Sensitive Repeats and Net Frequencies","publication_year":2025,"publication_date":"2025-11-14","ids":{"openalex":"https://openalex.org/W4416343280","doi":"https://doi.org/10.4230/lipics.cpm.2026.10"},"language":"en","primary_location":{"id":"pmh:oai:arXiv.org:2511.11057","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2511.11057","pdf_url":"https://arxiv.org/pdf/2511.11057","source":{"id":"https://openalex.org/S4393918464","display_name":"ArXiv.org","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"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"},"type":"article","indexed_in":["arxiv","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2511.11057","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5052235269","display_name":"Kotaro Kimura","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Kimura, Kotaro","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5074343416","display_name":"I Tomohiro","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"I, Tomohiro","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.1680489,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9491999745368958,"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":0.9491999745368958,"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":0.004800000227987766,"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/T10317","display_name":"Advanced Database Systems and Queries","score":0.004399999976158142,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"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/net","display_name":"Net (polyhedron)","score":0.7325000166893005},{"id":"https://openalex.org/keywords/extension","display_name":"Extension (predicate logic)","score":0.6035000085830688},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5856999754905701},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5468999743461609},{"id":"https://openalex.org/keywords/string","display_name":"String (physics)","score":0.5378999710083008},{"id":"https://openalex.org/keywords/word","display_name":"Word (group theory)","score":0.5350000262260437},{"id":"https://openalex.org/keywords/space","display_name":"Space (punctuation)","score":0.3894999921321869},{"id":"https://openalex.org/keywords/term","display_name":"Term (time)","score":0.36739999055862427}],"concepts":[{"id":"https://openalex.org/C14166107","wikidata":"https://www.wikidata.org/wiki/Q253829","display_name":"Net (polyhedron)","level":2,"score":0.7325000166893005},{"id":"https://openalex.org/C2778029271","wikidata":"https://www.wikidata.org/wiki/Q5421931","display_name":"Extension (predicate logic)","level":2,"score":0.6035000085830688},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5856999754905701},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5468999743461609},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.545799970626831},{"id":"https://openalex.org/C157486923","wikidata":"https://www.wikidata.org/wiki/Q1376436","display_name":"String (physics)","level":2,"score":0.5378999710083008},{"id":"https://openalex.org/C90805587","wikidata":"https://www.wikidata.org/wiki/Q10944557","display_name":"Word (group theory)","level":2,"score":0.5350000262260437},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.5307000279426575},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.44290000200271606},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3910999894142151},{"id":"https://openalex.org/C2778572836","wikidata":"https://www.wikidata.org/wiki/Q380933","display_name":"Space (punctuation)","level":2,"score":0.3894999921321869},{"id":"https://openalex.org/C61797465","wikidata":"https://www.wikidata.org/wiki/Q1188986","display_name":"Term (time)","level":2,"score":0.36739999055862427},{"id":"https://openalex.org/C162319229","wikidata":"https://www.wikidata.org/wiki/Q175263","display_name":"Data structure","level":2,"score":0.3650999963283539},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.3605000078678131},{"id":"https://openalex.org/C118615104","wikidata":"https://www.wikidata.org/wiki/Q121416","display_name":"Discrete mathematics","level":1,"score":0.3467999994754791},{"id":"https://openalex.org/C311688","wikidata":"https://www.wikidata.org/wiki/Q2393193","display_name":"Time complexity","level":2,"score":0.3441999852657318},{"id":"https://openalex.org/C2777027219","wikidata":"https://www.wikidata.org/wiki/Q1284190","display_name":"Constant (computer programming)","level":2,"score":0.29899999499320984},{"id":"https://openalex.org/C78548338","wikidata":"https://www.wikidata.org/wiki/Q2493","display_name":"Data compression","level":2,"score":0.28349998593330383},{"id":"https://openalex.org/C188521023","wikidata":"https://www.wikidata.org/wiki/Q6795644","display_name":"Maximal set","level":3,"score":0.26930001378059387},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.2630999982357025},{"id":"https://openalex.org/C27149982","wikidata":"https://www.wikidata.org/wiki/Q3456514","display_name":"Tandem repeat","level":4,"score":0.26159998774528503},{"id":"https://openalex.org/C2776291640","wikidata":"https://www.wikidata.org/wiki/Q2912517","display_name":"Value (mathematics)","level":2,"score":0.2515999972820282}],"mesh":[],"locations_count":4,"locations":[{"id":"pmh:oai:arXiv.org:2511.11057","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2511.11057","pdf_url":"https://arxiv.org/pdf/2511.11057","source":{"id":"https://openalex.org/S4393918464","display_name":"ArXiv.org","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"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:drops-oai.dagstuhl.de:25936","is_oa":true,"landing_page_url":"https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2026.10","pdf_url":"https://drops.dagstuhl.de/storage/00lipics/lipics-vol369-cpm2026/LIPIcs.CPM.2026.10/LIPIcs.CPM.2026.10.pdf","source":{"id":"https://openalex.org/S4377196569","display_name":"DROPS (Schloss Dagstuhl \u2013 Leibniz Center for Informatics)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2799853480","host_organization_name":"Schloss Dagstuhl \u2013 Leibniz Center for Informatics","host_organization_lineage":["https://openalex.org/I2799853480"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"publishedVersion"},{"id":"doi:10.48550/arxiv.2511.11057","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2511.11057","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article"},{"id":"doi:10.4230/lipics.cpm.2026.10","is_oa":true,"landing_page_url":"https://doi.org/10.4230/lipics.cpm.2026.10","pdf_url":null,"source":{"id":"https://openalex.org/S7407052059","display_name":"Dagstuhl Research Online Publication Server","issn_l":null,"issn":[],"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","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":""}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2511.11057","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2511.11057","pdf_url":"https://arxiv.org/pdf/2511.11057","source":{"id":"https://openalex.org/S4393918464","display_name":"ArXiv.org","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"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":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"A":[0],"repeat":[1,18,153,167,187,202],"is":[2,14,64,109,168,175,188,200,265,291,309],"a":[3,11,16,47,166,170,186,201,204,326],"substring":[4],"that":[5,240,302],"occurs":[6],"at":[7],"least":[8],"twice":[9],"in":[10,46,53,69,86,92,154,224,231,259,267,271,336],"string,":[12],"and":[13,30,141,181,234,270,319],"called":[15,169],"maximal":[17,44,152],"if":[19,173],"it":[20,174],"cannot":[21],"be":[22,246,340],"extended":[23],"outwards":[24],"without":[25],"reducing":[26],"its":[27,192],"frequency.":[28,207],"Nishimoto":[29],"Tabei":[31],"[CPM,":[32],"2021]":[33],"proposed":[34],"r-enum,":[35],"an":[36,198,241],"algorithm":[37],"to":[38,94,98,125,131,216,251],"enumerate":[39],"various":[40],"characteristic":[41],"substrings,":[42],"including":[43],"repeats,":[45,143],"string":[48],"T":[49,225],"of":[50,56,67,74,82,101,165,185,191,211,221,256,295,306,331,334,341],"length":[51],"n":[52,63],"O(r)":[54,235,268],"words":[55],"compressed":[57],"working":[58],"space,":[59],"where":[60,104,287],"r":[61,290],"\u2264":[62,289],"the":[65,70,77,95,99,110,119,147,155,182,189,209,218,249,253,292,303,314,332],"number":[66,100,190,305,333],"runs":[68,85],"Burrows-Wheeler":[71],"transform":[72],"(BWT)":[73],"T.":[75,296],"Given":[76,208],"run-length":[78],"encoded":[79],"BWT":[80],"(RLBWT)":[81],"T,":[83,212,337],"r-enum":[84,130],"O(n":[87,120,279],"log":[88,121,282,283],"log_w":[89,122],"(n/r))":[90,123],"time":[91,96,233,273],"addition":[93],"linear":[97],"output":[102],"strings,":[103],"w":[105],"=":[106],"\u0398(log":[107],"n)":[108],"word":[111],"size.":[112],"In":[113],"this":[114,196],"paper,":[115],"we":[116,159,213,300,324],"first":[117],"improve":[118],"term":[124],"O(n).":[126],"We":[127,237],"next":[128],"extend":[129],"compute":[132,217,252],"other":[133],"context-sensitive":[134],"repeats":[135,139],"such":[136],"as":[137,144,146],"near-supermaximal":[138],"(NSMRs)":[140],"supermaximal":[142],"well":[145],"context":[148],"diversity":[149],"for":[150],"every":[151],"same":[156],"complexities.":[157],"Furthermore,":[158],"study":[160],"net":[161,171,183,193,206,229,254,307,317],"occurrences:":[162],"An":[163],"occurrence":[164,172],"not":[176],"covered":[177],"by":[178],"another":[179],"repeat,":[180],"frequency":[184],"occurrences.":[194],"With":[195,313],"terminology,":[197],"NSMR":[199],"with":[203,227,274],"positive":[205],"RLBWT":[210,250],"show":[214,239],"how":[215],"set":[219],"\ud835\udcae^{nsmr}":[220],"all":[222],"NSMRs":[223],"together":[226],"their":[228],"frequency/occurrences":[230,255],"O(n)":[232,272],"space.":[236],"also":[238],"O(r)-space":[242],"data":[243,263],"structure":[244,264],"can":[245],"built":[247,266],"from":[248],"any":[257],"pattern":[258],"optimal":[260],"time.":[261],"The":[262],"space":[269],"high":[275],"probability":[276],"or":[277],"deterministic":[278],"+":[280],"|\ud835\udcae^{nsmr}|":[281],"min(\u03c3,":[284],"|\ud835\udcae^{nsmr}|))":[285],"time,":[286],"\u03c3":[288],"alphabet":[293],"size":[294],"To":[297],"achieve":[298],"this,":[299],"prove":[301],"total":[304],"occurrences":[308,318],"less":[310],"than":[311],"2r.":[312],"duality":[315],"between":[316],"minimal":[320],"unique":[321],"substrings":[322],"(MUSs),":[323],"get":[325],"new":[327],"upper":[328],"bound":[329],"2r":[330],"MUSs":[335],"which":[338],"may":[339],"independent":[342],"interest.":[343]},"counts_by_year":[],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-11-18T00:00:00"}
