{"id":"https://openalex.org/W4323927105","doi":"https://doi.org/10.48550/arxiv.2303.05336","title":"Elastic Founder Graphs Improved and Enhanced","display_name":"Elastic Founder Graphs Improved and Enhanced","publication_year":2023,"publication_date":"2023-03-09","ids":{"openalex":"https://openalex.org/W4323927105","doi":"https://doi.org/10.48550/arxiv.2303.05336"},"language":"en","primary_location":{"id":"pmh:oai:arXiv.org:2303.05336","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2303.05336","pdf_url":"https://arxiv.org/pdf/2303.05336","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"text"},"type":"preprint","indexed_in":["arxiv","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2303.05336","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101764985","display_name":"Nicola Rizzo","orcid":"https://orcid.org/0000-0002-2035-6309"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Rizzo, Nicola","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053359236","display_name":"Massimo Equi","orcid":"https://orcid.org/0000-0001-8609-0040"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Equi, Massimo","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025780344","display_name":"Tuukka Norri","orcid":"https://orcid.org/0000-0002-8276-0585"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Norri, Tuukka","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5043558409","display_name":"Veli M\u00e4kinen","orcid":"https://orcid.org/0000-0003-4454-1493"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"M\u00e4kinen, Veli","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5101764985"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":null,"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":0.9988999962806702,"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":0.9988999962806702,"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/T10181","display_name":"Natural Language Processing Techniques","score":0.9940999746322632,"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":0.975600004196167,"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":0.735711932182312},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.6596428751945496},{"id":"https://openalex.org/keywords/time-complexity","display_name":"Time complexity","score":0.5288181304931641},{"id":"https://openalex.org/keywords/linear-space","display_name":"Linear space","score":0.4984548091888428},{"id":"https://openalex.org/keywords/search-engine-indexing","display_name":"Search engine indexing","score":0.4829239547252655},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.4420646131038666},{"id":"https://openalex.org/keywords/pattern-matching","display_name":"Pattern matching","score":0.42068976163864136},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4179782271385193},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4032813310623169},{"id":"https://openalex.org/keywords/discrete-mathematics","display_name":"Discrete mathematics","score":0.38899582624435425},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.3476284146308899}],"concepts":[{"id":"https://openalex.org/C182407805","wikidata":"https://www.wikidata.org/wiki/Q2626534","display_name":"Substring","level":3,"score":0.735711932182312},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.6596428751945496},{"id":"https://openalex.org/C311688","wikidata":"https://www.wikidata.org/wiki/Q2393193","display_name":"Time complexity","level":2,"score":0.5288181304931641},{"id":"https://openalex.org/C176370821","wikidata":"https://www.wikidata.org/wiki/Q1826459","display_name":"Linear space","level":2,"score":0.4984548091888428},{"id":"https://openalex.org/C75165309","wikidata":"https://www.wikidata.org/wiki/Q2258979","display_name":"Search engine indexing","level":2,"score":0.4829239547252655},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.4420646131038666},{"id":"https://openalex.org/C68859911","wikidata":"https://www.wikidata.org/wiki/Q1503724","display_name":"Pattern matching","level":2,"score":0.42068976163864136},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4179782271385193},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4032813310623169},{"id":"https://openalex.org/C118615104","wikidata":"https://www.wikidata.org/wiki/Q121416","display_name":"Discrete mathematics","level":1,"score":0.38899582624435425},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.3476284146308899},{"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/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:arXiv.org:2303.05336","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2303.05336","pdf_url":"https://arxiv.org/pdf/2303.05336","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"text"},{"id":"doi:10.48550/arxiv.2303.05336","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2303.05336","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":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2303.05336","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2303.05336","pdf_url":"https://arxiv.org/pdf/2303.05336","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2689612763","display_name":null,"funder_award_id":"Marie","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G6224492464","display_name":"Safe and Complete Algorithms for Bioinformatics","funder_award_id":"851093","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G7440903218","display_name":null,"funder_award_id":"956229","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G8318064016","display_name":null,"funder_award_id":"Horizon","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4323927105.pdf","grobid_xml":"https://content.openalex.org/works/W4323927105.grobid-xml"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2902555313","https://openalex.org/W2731201547","https://openalex.org/W2135574162","https://openalex.org/W2890359459","https://openalex.org/W4249054680","https://openalex.org/W2055497872","https://openalex.org/W2902482624","https://openalex.org/W2218650848","https://openalex.org/W2091929432","https://openalex.org/W3112977702"],"abstract_inverted_index":{"Indexing":[0],"labeled":[1,73],"graphs":[2,74],"for":[3,61,128,152,231],"pattern":[4,63,92,213],"matching":[5,93],"is":[6],"a":[7,58,185,200,211,215],"central":[8],"challenge":[9],"of":[10,26,29,87,103,117,180,202,204,228,249],"pangenomics.":[11],"Equi":[12],"et":[13,76],"al.":[14],"(Algorithmica,":[15],"2022)":[16],"developed":[17],"the":[18,37,41,44,52,55,67,85,88,101,115,118,133,142,153,161,178,181,205,219,229,232,247],"Elastic":[19],"Founder":[20],"Graph":[21],"($\\mathsf{EFG}$)":[22],"representing":[23],"an":[24,157,223],"alignment":[25],"$m$":[27],"sequences":[28,46],"length":[30,102],"$n$,":[31],"drawn":[32],"from":[33,98],"alphabet":[34],"$\u03a3$":[35],"plus":[36],"special":[38],"gap":[39],"character:":[40],"paths":[42,203,209],"spell":[43],"original":[45],"or":[47],"their":[48],"recombination.":[49],"By":[50],"enforcing":[51],"semi-repeat-free":[53],"property,":[54],"$\\mathsf{EFG}$":[56,89,187,220],"admits":[57],"polynomial-space":[59],"index":[60,90,188],"linear-time":[62,124],"matching,":[64],"breaking":[65],"through":[66],"conditional":[68],"lower":[69],"bounds":[70],"on":[71,148,199],"indexing":[72],"(Equi":[75],"al.,":[77],"SOFSEM":[78],"2021).":[79],"In":[80],"this":[81],"work":[82],"we":[83,122,131,150,166,183],"improve":[84,132],"space":[86],"answering":[91],"queries":[94,198],"in":[95,100,114,242],"linear":[96,99,113],"time,":[97],"all":[104],"strings":[105],"spelled":[106],"by":[107,140,168],"three":[108],"consecutive":[109],"node":[110],"labels,":[111],"to":[112,138,176,192],"size":[116],"edge":[119],"labels.":[120],"Then,":[121],"develop":[123,184],"construction":[125,136,237],"algorithms":[126,137],"optimizing":[127],"different":[129],"metrics:":[130],"existing":[134],"linearithmic":[135],"$O(mn)$,":[139],"solving":[141],"novel":[143],"exclusive":[144],"ancestor":[145],"set":[146,201],"problem":[147],"trees;":[149],"propose,":[151],"simplified":[154],"gapless":[155,233],"setting,":[156,234],"$O(mn)$-time":[158],"solution":[159],"minimizing":[160],"maximum":[162],"block":[163,170],"height,":[164],"that":[165,239],"generalize":[167],"substituting":[169],"height":[171],"with":[172,236,246],"prefix-aware":[173],"height.":[174],"Finally,":[175],"show":[177],"versatility":[179],"framework,":[182],"BWT-based":[186],"and":[189,194,225],"study":[190],"how":[191],"encode":[193],"perform":[195],"document":[196],"listing":[197],"graphs,":[206],"reporting":[207],"which":[208],"present":[210],"given":[212],"as":[214,222],"substring.":[216],"We":[217],"propose":[218],"framework":[221,230],"improved":[224],"enhanced":[226],"version":[227],"along":[235],"methods":[238],"are":[240],"valid":[241],"any":[243],"setting":[244],"concerned":[245],"segmentation":[248],"aligned":[250],"sequences.":[251]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-04-13T07:58:08.660418","created_date":"2025-10-10T00:00:00"}
