{"id":"https://openalex.org/W4410227271","doi":"https://doi.org/10.1109/tcbbio.2025.3568630","title":"A Kernelization Algorithm for Finding a Perfect Phylogeny From Mixed Tumor Samples","display_name":"A Kernelization Algorithm for Finding a Perfect Phylogeny From Mixed Tumor Samples","publication_year":2025,"publication_date":"2025-05-09","ids":{"openalex":"https://openalex.org/W4410227271","doi":"https://doi.org/10.1109/tcbbio.2025.3568630","pmid":"https://pubmed.ncbi.nlm.nih.gov/40811259"},"language":"en","primary_location":{"id":"doi:10.1109/tcbbio.2025.3568630","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3568630","pdf_url":null,"source":{"id":"https://openalex.org/S5407042751","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"2998-4165","issn":["2998-4165"],"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":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"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/A5092873257","display_name":"Wen-Horng Sheu","orcid":"https://orcid.org/0000-0002-2707-8612"},"institutions":[{"id":"https://openalex.org/I84218800","display_name":"University of California, Davis","ror":"https://ror.org/05rrcem69","country_code":"US","type":"education","lineage":["https://openalex.org/I84218800"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Wen-Horng Sheu","raw_affiliation_strings":["Department of Computer Science, University of California, Davis Davis, CA, USA","Department of Computer Science, University of California, Davis, CA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of California, Davis Davis, CA, USA","institution_ids":["https://openalex.org/I84218800"]},{"raw_affiliation_string":"Department of Computer Science, University of California, Davis, CA, USA","institution_ids":["https://openalex.org/I84218800"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5001316179","display_name":"Biing-Feng Wang","orcid":"https://orcid.org/0000-0002-8109-1914"},"institutions":[{"id":"https://openalex.org/I25846049","display_name":"National Tsing Hua University","ror":"https://ror.org/00zdnkx70","country_code":"TW","type":"education","lineage":["https://openalex.org/I25846049"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Biing-Feng Wang","raw_affiliation_strings":["Department of Computer Science, National Tsing Hua University Hsinchu, Hsinchu, Taiwan","Department of Computer Science, National Tsing Hua University Hsinchu, Taiwan, Republic of China"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, National Tsing Hua University Hsinchu, Hsinchu, Taiwan","institution_ids":["https://openalex.org/I25846049"]},{"raw_affiliation_string":"Department of Computer Science, National Tsing Hua University Hsinchu, Taiwan, Republic of China","institution_ids":["https://openalex.org/I25846049"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5092873257"],"corresponding_institution_ids":["https://openalex.org/I84218800"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.10810317,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"22","issue":"5","first_page":"2280","last_page":"2292"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9258999824523926,"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"}},"topics":[{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9258999824523926,"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/kernelization","display_name":"Kernelization","score":0.9617904424667358},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.6508281826972961},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.44605332612991333},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4249059557914734},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.39848577976226807},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2745720148086548},{"id":"https://openalex.org/keywords/parameterized-complexity","display_name":"Parameterized complexity","score":0.17396456003189087},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.10889256000518799}],"concepts":[{"id":"https://openalex.org/C207225210","wikidata":"https://www.wikidata.org/wiki/Q1759539","display_name":"Kernelization","level":3,"score":0.9617904424667358},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.6508281826972961},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.44605332612991333},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4249059557914734},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.39848577976226807},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2745720148086548},{"id":"https://openalex.org/C165464430","wikidata":"https://www.wikidata.org/wiki/Q1570441","display_name":"Parameterized complexity","level":2,"score":0.17396456003189087},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.10889256000518799},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbbio.2025.3568630","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3568630","pdf_url":null,"source":{"id":"https://openalex.org/S5407042751","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"2998-4165","issn":["2998-4165"],"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":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40811259","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40811259","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":27,"referenced_works":["https://openalex.org/W160062585","https://openalex.org/W938539187","https://openalex.org/W1986888627","https://openalex.org/W2002295829","https://openalex.org/W2049451257","https://openalex.org/W2074507113","https://openalex.org/W2075495614","https://openalex.org/W2109991075","https://openalex.org/W2110920860","https://openalex.org/W2112997276","https://openalex.org/W2114095872","https://openalex.org/W2120248756","https://openalex.org/W2122392334","https://openalex.org/W2144847592","https://openalex.org/W2155316689","https://openalex.org/W2157751858","https://openalex.org/W2166815431","https://openalex.org/W2168156874","https://openalex.org/W2192492580","https://openalex.org/W2757107770","https://openalex.org/W2785754681","https://openalex.org/W2887247095","https://openalex.org/W2914414140","https://openalex.org/W2962973261","https://openalex.org/W2992605988","https://openalex.org/W3031062390","https://openalex.org/W4386749297"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W3020640542","https://openalex.org/W4245720151","https://openalex.org/W2128252278","https://openalex.org/W1923231248","https://openalex.org/W2383763250","https://openalex.org/W248275141","https://openalex.org/W2518331723"],"abstract_inverted_index":{"The":[0,60,77],"split-row":[1,37],"problem":[2],"(SR),":[3],"introduced":[4],"by":[5,48],"Hajirasouliha":[6],"and":[7,97,144],"Raphael":[8],"[WABI":[9],"2014],":[10],"models":[11],"an":[12,27],"effective":[13],"method":[14],"for":[15,186],"reconstructing":[16],"a":[17,45,82,90,94,131,176],"perfect":[18,95],"phylogeny":[19,96],"from":[20],"mixed":[21],"tumor":[22],"samples.":[23],"In":[24,123],"this":[25,124],"problem,":[26],"$m":[28],"\\times":[29],"n$":[30],"binary":[31],"matrix":[32,91],"$M$":[33,40,88],"is":[34,41,56,65,79,101,169],"given.":[35],"A":[36],"operation":[38,64],"on":[39],"defined":[42],"as":[43,175],"replacing":[44],"row":[46],"$r$":[47],"$k":[49,74],">":[50],"1$":[51,150],"rows":[52,70,143],"whose":[53],"bitwise":[54],"OR":[55],"equal":[57],"to":[58,80,93,179],"$r$.":[59],"cost":[61,100],"of":[62,68,84,111],"the":[63,66,98,109,119],"number":[67],"additional":[69],"induced,":[71],"that":[72,86,128],"is,":[73],"-":[75,149],"1$.":[76],"objective":[78],"find":[81],"sequence":[83],"operations":[85],"transforms":[87],"into":[89],"corresponding":[92],"total":[99,121],"minimized.":[102],"Hujdurovi\u0107":[103],"et":[104],"al.":[105],"[TCBB":[106],"2018]":[107],"proved":[108],"NP-hardness":[110],"SR.":[112,187],"Let":[113],"${\\rm{\\varepsilon":[114],"}}(":[115,140,146],"M":[116,141,147,167],")$":[117,142,162,168],"denote":[118],"minimum":[120],"cost.":[122],"paper,":[125],"we":[126],"show":[127],"SR":[129],"admits":[130],"polynomial":[132],"size":[133],"kernel,":[134],"which":[135],"has":[136],"at":[137],"most":[138],"$3{\\rm{\\varepsilon":[139],"$4{\\rm{\\varepsilon":[145],")":[148],"columns.":[151],"Our":[152],"kernelization":[153],"algorithm":[154],"requires":[155],"$O(":[156],"{\\max":[157],"(":[158,166],"{{{m}^{0.373}}{{n}^2},":[159],"m{{n}^{1.373}}}":[160],")}":[161],"time.":[163],"When":[164],"$\\varepsilon":[165],"small,":[170],"it":[171],"can":[172],"be":[173],"used":[174],"preprocessing":[177],"procedure":[178],"speed":[180],"up":[181],"all":[182],"previous":[183],"exact":[184],"algorithms":[185]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}