{"id":"https://openalex.org/W4410316161","doi":"https://doi.org/10.1287/ijoc.2023.0373","title":"Sempervirens: A Fast Reconstruction Algorithm for Noisy and Incomplete Binary Matrix Representations of Trees","display_name":"Sempervirens: A Fast Reconstruction Algorithm for Noisy and Incomplete Binary Matrix Representations of Trees","publication_year":2025,"publication_date":"2025-05-13","ids":{"openalex":"https://openalex.org/W4410316161","doi":"https://doi.org/10.1287/ijoc.2023.0373"},"language":"en","primary_location":{"id":"doi:10.1287/ijoc.2023.0373","is_oa":false,"landing_page_url":"https://doi.org/10.1287/ijoc.2023.0373","pdf_url":null,"source":{"id":"https://openalex.org/S165318533","display_name":"INFORMS journal on computing","issn_l":"0899-1499","issn":["0899-1499","1091-9856","1526-5528","2326-3245"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310315699","host_organization_name":"Institute for Operations Research and the Management Sciences","host_organization_lineage":["https://openalex.org/P4310315699"],"host_organization_lineage_names":["Institute for Operations Research and the Management Sciences"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"INFORMS Journal on Computing","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://escholarship.org/content/qt48t9n6j5/qt48t9n6j5.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5018502826","display_name":"Neelay Junnarkar","orcid":"https://orcid.org/0000-0002-2644-9856"},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Neelay Junnarkar","raw_affiliation_strings":["Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, California 94720"],"raw_orcid":"https://orcid.org/0000-0002-2644-9856","affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, California 94720","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017364251","display_name":"Can K\u0131z\u0131lkale","orcid":"https://orcid.org/0009-0007-3444-4389"},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Can K\u0131z\u0131lkale","raw_affiliation_strings":["Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, California 94720; and Applied Mathematics and Computational Research Division, Berkeley, California 94720"],"raw_orcid":"https://orcid.org/0009-0007-3444-4389","affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, California 94720; and Applied Mathematics and Computational Research Division, Berkeley, California 94720","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5117084778","display_name":"Nevena Golubovic","orcid":null},"institutions":[{"id":"https://openalex.org/I154570441","display_name":"University of California, Santa Barbara","ror":"https://ror.org/02t274463","country_code":"US","type":"education","lineage":["https://openalex.org/I154570441"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nevena Golubovic","raw_affiliation_strings":["Department of Computer Science, University of California, Santa Barbara, Santa Barbara, California 93106"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of California, Santa Barbara, Santa Barbara, California 93106","institution_ids":["https://openalex.org/I154570441"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025743742","display_name":"Murat Arcak","orcid":"https://orcid.org/0000-0001-9060-4032"},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Murat Arcak","raw_affiliation_strings":["Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, California 94720"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, California 94720","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5035719914","display_name":"Ayd\u0131n Bulu\u00e7","orcid":"https://orcid.org/0000-0001-7253-9038"},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ayd\u0131n Bulu\u00e7","raw_affiliation_strings":["Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, California 94720; and Applied Mathematics and Computational Research Division, Berkeley, California 94720"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, California 94720; and Applied Mathematics and Computational Research Division, Berkeley, California 94720","institution_ids":["https://openalex.org/I95457486"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5017364251"],"corresponding_institution_ids":["https://openalex.org/I95457486"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.0969264,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"38","issue":"2","first_page":"590","last_page":"604"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11321","display_name":"Error Correcting Code Techniques","score":0.9955000281333923,"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"}},"topics":[{"id":"https://openalex.org/T11321","display_name":"Error Correcting Code Techniques","score":0.9955000281333923,"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"}},{"id":"https://openalex.org/T12292","display_name":"Graph Theory and Algorithms","score":0.9943000078201294,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"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":0.9857000112533569,"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/binary-number","display_name":"Binary number","score":0.554783284664154},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5389424562454224},{"id":"https://openalex.org/keywords/matrix","display_name":"Matrix (chemical analysis)","score":0.52442467212677},{"id":"https://openalex.org/keywords/binary-tree","display_name":"Binary tree","score":0.4633740484714508},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.4531756043434143},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4376702308654785},{"id":"https://openalex.org/keywords/binary-search-tree","display_name":"Binary search tree","score":0.41721975803375244},{"id":"https://openalex.org/keywords/arithmetic","display_name":"Arithmetic","score":0.2075103521347046}],"concepts":[{"id":"https://openalex.org/C48372109","wikidata":"https://www.wikidata.org/wiki/Q3913","display_name":"Binary number","level":2,"score":0.554783284664154},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5389424562454224},{"id":"https://openalex.org/C106487976","wikidata":"https://www.wikidata.org/wiki/Q685816","display_name":"Matrix (chemical analysis)","level":2,"score":0.52442467212677},{"id":"https://openalex.org/C197855036","wikidata":"https://www.wikidata.org/wiki/Q380172","display_name":"Binary tree","level":2,"score":0.4633740484714508},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.4531756043434143},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4376702308654785},{"id":"https://openalex.org/C91154448","wikidata":"https://www.wikidata.org/wiki/Q623818","display_name":"Binary search tree","level":3,"score":0.41721975803375244},{"id":"https://openalex.org/C94375191","wikidata":"https://www.wikidata.org/wiki/Q11205","display_name":"Arithmetic","level":1,"score":0.2075103521347046},{"id":"https://openalex.org/C159985019","wikidata":"https://www.wikidata.org/wiki/Q181790","display_name":"Composite material","level":1,"score":0.0},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1287/ijoc.2023.0373","is_oa":false,"landing_page_url":"https://doi.org/10.1287/ijoc.2023.0373","pdf_url":null,"source":{"id":"https://openalex.org/S165318533","display_name":"INFORMS journal on computing","issn_l":"0899-1499","issn":["0899-1499","1091-9856","1526-5528","2326-3245"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310315699","host_organization_name":"Institute for Operations Research and the Management Sciences","host_organization_lineage":["https://openalex.org/P4310315699"],"host_organization_lineage_names":["Institute for Operations Research and the Management Sciences"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"INFORMS Journal on Computing","raw_type":"journal-article"},{"id":"pmh:oai:escholarship.org:ark:/13030/qt48t9n6j5","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/48t9n6j5","pdf_url":"https://escholarship.org/content/qt48t9n6j5/qt48t9n6j5.pdf","source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"INFORMS Journal on Computing, vol 38, iss 2","raw_type":"article"},{"id":"pmh:ark:/13030/qt48t9n6j5","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":{"id":"pmh:oai:escholarship.org:ark:/13030/qt48t9n6j5","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/48t9n6j5","pdf_url":"https://escholarship.org/content/qt48t9n6j5/qt48t9n6j5.pdf","source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"INFORMS Journal on Computing, vol 38, iss 2","raw_type":"article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4410316161.pdf","grobid_xml":"https://content.openalex.org/works/W4410316161.grobid-xml"},"referenced_works_count":9,"referenced_works":["https://openalex.org/W1571134196","https://openalex.org/W2074507113","https://openalex.org/W2154068087","https://openalex.org/W2346273585","https://openalex.org/W2890035501","https://openalex.org/W2949688529","https://openalex.org/W2970840218","https://openalex.org/W3042807857","https://openalex.org/W4294993177"],"related_works":["https://openalex.org/W4399803855","https://openalex.org/W2056975861","https://openalex.org/W2363556447","https://openalex.org/W2089900921","https://openalex.org/W2501849745","https://openalex.org/W2011933350","https://openalex.org/W1510719821","https://openalex.org/W2539085113","https://openalex.org/W2093708041","https://openalex.org/W2041182800"],"abstract_inverted_index":{"Applications":[0,148],"such":[1],"as":[2,8,194,196],"reconstructing":[3,16,112],"cell":[4],"lineage":[5],"trees":[6],"(represented":[7],"phylogenetic":[9,44],"trees)":[10],"from":[11,197],"single-cell":[12],"sequencing":[13],"data":[14],"require":[15],"a":[17,31,133],"[Formula:":[18],"see":[19],"text]-matrix":[20],"that":[21,64,93,118,175],"has":[22],"many":[23],"errors":[24],"and":[25,39,187,210],"missing":[26],"entries.":[27],"We":[28,62,90],"introduce":[29],"Sempervirens,":[30],"very":[32],"fast":[33],"matrix":[34,41],"reconstruction":[35,99],"algorithm":[36,131],"for":[37,147],"noisy":[38],"incomplete":[40],"representations":[42],"of":[43,71,103,136,162,164,167,179],"trees.":[45],"Sempervirens":[46,65,94,104],"uses":[47],"an":[48],"iterative":[49],"maximum-likelihood":[50],"approach":[51],"to":[52,107,111,125],"determine":[53],"the":[54,59,83,130,160,165,177,185,198],"topology":[55],"tree":[56],"represented":[57],"by":[58,79,141,159],"corrupted":[60],"data.":[61],"show":[63,92],"is":[66,182,213],"at":[67,215],"least":[68],"three":[69],"orders":[70],"magnitude":[72],"faster":[73],"than":[74,116],"other":[75,119],"methods":[76,97,120],"on":[77],"thousand":[78,80],"matrices,":[81],"with":[82,87,132],"speed":[84,102],"gap":[85],"widening":[86],"larger":[88,114],"matrices.":[89],"also":[91],"matches":[95],"state-of-the-art":[96],"in":[98,149],"accuracy.":[100],"The":[101,173,206],"enables":[105],"it":[106],"be":[108],"tractably":[109],"applied":[110],"much":[113],"matrices":[115],"those":[117],"can":[121],"reconstruct.":[122],"In":[123],"addition":[124],"experimental":[126],"results,":[127],"we":[128],"justify":[129],"mathematical":[134],"treatment":[135],"its":[137,188],"subprocedures.":[138],"History:":[139],"Accepted":[140],"J.":[142],"Paul":[143],"Brooks,":[144],"Area":[145],"Editor":[146],"Biology,":[150],"Medicine,":[151],"&amp;":[152],"Healthcare.":[153],"Funding:":[154],"This":[155],"work":[156],"was":[157],"supported":[158],"Office":[161],"Science":[163],"Department":[166],"Energy":[168],"[Contract":[169],"DE-AC02-05CH11231].":[170],"Supplemental":[171,189],"Material:":[172],"software":[174,201],"supports":[176],"findings":[178],"this":[180],"study":[181],"available":[183,214],"within":[184],"paper":[186],"Information":[190],"(":[191,203],"https://pubsonline.informs.org/doi/suppl/10.1287/ijoc.2023.0373":[192],")":[193],"well":[195],"IJOC":[199,208],"GitHub":[200],"repository":[202],"https://github.com/INFORMSJoC/2023.0373":[204],").":[205],"complete":[207],"Software":[209],"Data":[211],"Repository":[212],"https://informsjoc.github.io/":[216],".":[217]},"counts_by_year":[],"updated_date":"2026-07-31T08:31:51.225901","created_date":"2025-10-10T00:00:00"}
