{"id":"https://openalex.org/W7125380902","doi":"https://doi.org/10.48550/arxiv.2601.14285","title":"A Comparison of Polynomial-Based Tree Clustering Methods","display_name":"A Comparison of Polynomial-Based Tree Clustering Methods","publication_year":2026,"publication_date":"2026-01-13","ids":{"openalex":"https://openalex.org/W7125380902","doi":"https://doi.org/10.48550/arxiv.2601.14285"},"language":null,"primary_location":{"id":"doi:10.48550/arxiv.2601.14285","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2601.14285","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":false,"raw_source_name":null,"raw_type":"article"},"type":"preprint","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.48550/arxiv.2601.14285","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5123560205","display_name":"Pengyu Liu","orcid":null},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Liu, Pengyu","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5123541162","display_name":"Mariel V\u00e1zquez","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"V\u00e1zquez, Mariel","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5123596580","display_name":"Nata\u0161a Jonoska","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jonoska, Nata\u0161a","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5123560205"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.4131999909877777,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.4131999909877777,"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/T12946","display_name":"Fractal and DNA sequence analysis","score":0.07460000365972519,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.07370000332593918,"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/cluster-analysis","display_name":"Cluster analysis","score":0.6922000050544739},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.6722999811172485},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.4350999891757965},{"id":"https://openalex.org/keywords/tree-structure","display_name":"Tree structure","score":0.4293999969959259},{"id":"https://openalex.org/keywords/autoencoder","display_name":"Autoencoder","score":0.4156999886035919},{"id":"https://openalex.org/keywords/hierarchical-clustering","display_name":"Hierarchical clustering","score":0.387800008058548},{"id":"https://openalex.org/keywords/fractal-tree-index","display_name":"Fractal tree index","score":0.3264999985694885}],"concepts":[{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.6922000050544739},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.6722999811172485},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.555400013923645},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5254999995231628},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.4350999891757965},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.43059998750686646},{"id":"https://openalex.org/C163797641","wikidata":"https://www.wikidata.org/wiki/Q2067937","display_name":"Tree structure","level":3,"score":0.4293999969959259},{"id":"https://openalex.org/C101738243","wikidata":"https://www.wikidata.org/wiki/Q786435","display_name":"Autoencoder","level":3,"score":0.4156999886035919},{"id":"https://openalex.org/C92835128","wikidata":"https://www.wikidata.org/wiki/Q1277447","display_name":"Hierarchical clustering","level":3,"score":0.387800008058548},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.35899999737739563},{"id":"https://openalex.org/C163736687","wikidata":"https://www.wikidata.org/wiki/Q17014592","display_name":"Fractal tree index","level":5,"score":0.3264999985694885},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.3255999982357025},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.32510000467300415},{"id":"https://openalex.org/C39235581","wikidata":"https://www.wikidata.org/wiki/Q5158434","display_name":"Conceptual clustering","level":5,"score":0.3125999867916107},{"id":"https://openalex.org/C111442797","wikidata":"https://www.wikidata.org/wiki/Q7291446","display_name":"Rand index","level":3,"score":0.30550000071525574},{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.3037000000476837},{"id":"https://openalex.org/C184509293","wikidata":"https://www.wikidata.org/wiki/Q5136711","display_name":"Clustering high-dimensional data","level":3,"score":0.2678000032901764},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.2637999951839447},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.26019999384880066},{"id":"https://openalex.org/C124388736","wikidata":"https://www.wikidata.org/wiki/Q3247497","display_name":"Tree of life (biology)","level":4,"score":0.2529999911785126}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.48550/arxiv.2601.14285","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2601.14285","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":"doi:10.48550/arxiv.2601.14285","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2601.14285","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":false,"raw_source_name":null,"raw_type":"article"},"sustainable_development_goals":[{"display_name":"Responsible consumption and production","id":"https://metadata.un.org/sdg/12","score":0.4653782248497009}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Tree":[0,65],"structures":[1,78],"appear":[2],"in":[3,38,120],"many":[4],"fields":[5],"of":[6,33,117],"the":[7,31,94,115,141,146,155,160],"life":[8],"sciences,":[9],"including":[10],"phylogenetics,":[11],"developmental":[12],"biology":[13],"and":[14,41,72,106],"nucleic":[15,107],"acid":[16,108],"structures.":[17,55,109],"Trees":[18],"can":[19,50],"be":[20,51],"used":[21],"to":[22,30,75,103],"represent":[23],"RNA":[24],"secondary":[25],"structures,":[26],"which":[27,81],"directly":[28],"relate":[29],"function":[32],"non-coding":[34],"RNAs.":[35],"Recent":[36],"developments":[37],"sequencing":[39],"technology":[40],"artificial":[42],"intelligence":[43],"have":[44,100,154],"yielded":[45],"numerous":[46],"biological":[47],"data":[48,63,86],"that":[49,145],"represented":[52],"with":[53,84,150],"tree":[54,61,77,98,121,127],"This":[56],"requires":[57],"novel":[58],"methods":[59,91,123,149],"for":[60,137],"structure":[62],"analytics.":[64],"polynomials":[66,99],"provide":[67],"a":[68,126],"computationally":[69],"efficient,":[70],"interpretable":[71],"comprehensive":[73],"way":[74],"encode":[76],"as":[79],"matrices,":[80],"are":[82],"compatible":[83],"most":[85],"analytics":[87],"tools.":[88],"Machine":[89],"learning":[90],"based":[92,124,148],"on":[93,125],"Canberra":[95],"distance":[96,147],"between":[97],"been":[101],"introduced":[102],"analyze":[104],"phylogenies":[105],"In":[110],"this":[111],"paper,":[112],"we":[113],"compare":[114],"performance":[116],"different":[118],"distances":[119,153],"clustering":[122,138,157],"distinguishing":[128],"polynomial.":[129,142],"We":[130,143],"also":[131],"implement":[132],"two":[133],"basic":[134],"autoencoder":[135],"models":[136],"trees":[139],"using":[140],"find":[144],"entry-level":[151],"normalized":[152],"highest":[156],"accuracy":[158],"among":[159],"compared":[161],"methods.":[162]},"counts_by_year":[],"updated_date":"2026-01-23T23:24:52.574035","created_date":"2026-01-23T00:00:00"}