{"id":"https://openalex.org/W2120158609","doi":"https://doi.org/10.1109/ssdm.2003.1214978","title":"TreeRank: a similarity measure for nearest neighbor searching in phylogenetic databases","display_name":"TreeRank: a similarity measure for nearest neighbor searching in phylogenetic databases","publication_year":2004,"publication_date":"2004-01-24","ids":{"openalex":"https://openalex.org/W2120158609","doi":"https://doi.org/10.1109/ssdm.2003.1214978","mag":"2120158609"},"language":"en","primary_location":{"id":"doi:10.1109/ssdm.2003.1214978","is_oa":false,"landing_page_url":"https://doi.org/10.1109/ssdm.2003.1214978","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"15th International Conference on Scientific and Statistical Database Management, 2003.","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5110106915","display_name":"J.T.L. Wang","orcid":"https://orcid.org/0009-0007-9928-980X"},"institutions":[{"id":"https://openalex.org/I118118575","display_name":"New Jersey Institute of Technology","ror":"https://ror.org/05e74xb87","country_code":"US","type":"education","lineage":["https://openalex.org/I118118575"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"J.T.L. Wang","raw_affiliation_strings":["College of Computing Sciences, New Jersey Institute of Technology, Newark, NJ, USA","Coll. of Comput. Sci., New Jersey Inst. of Technol., Newark, NJ, USA"],"affiliations":[{"raw_affiliation_string":"College of Computing Sciences, New Jersey Institute of Technology, Newark, NJ, USA","institution_ids":["https://openalex.org/I118118575"]},{"raw_affiliation_string":"Coll. of Comput. Sci., New Jersey Inst. of Technol., Newark, NJ, USA","institution_ids":["https://openalex.org/I118118575"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025086626","display_name":"Huiyuan Shan","orcid":null},"institutions":[{"id":"https://openalex.org/I118118575","display_name":"New Jersey Institute of Technology","ror":"https://ror.org/05e74xb87","country_code":"US","type":"education","lineage":["https://openalex.org/I118118575"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Huiyuan Shan","raw_affiliation_strings":["Department of Computer Science, New Jersey Institute of Technology, Newark, NJ, USA","New Jersey Institute of Technology"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, New Jersey Institute of Technology, Newark, NJ, USA","institution_ids":["https://openalex.org/I118118575"]},{"raw_affiliation_string":"New Jersey Institute of Technology","institution_ids":["https://openalex.org/I118118575"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055576104","display_name":"Dennis Shasha","orcid":"https://orcid.org/0000-0002-7036-3312"},"institutions":[{"id":"https://openalex.org/I36672615","display_name":"Courant Institute of Mathematical Sciences","ror":"https://ror.org/037tm7f56","country_code":"US","type":"education","lineage":["https://openalex.org/I36672615","https://openalex.org/I57206974"]},{"id":"https://openalex.org/I57206974","display_name":"New York University","ror":"https://ror.org/0190ak572","country_code":"US","type":"education","lineage":["https://openalex.org/I57206974"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"D. Shasha","raw_affiliation_strings":["Courant Institute of Mathematical Sciences, New York University, New York, NY, USA","New York University"],"affiliations":[{"raw_affiliation_string":"Courant Institute of Mathematical Sciences, New York University, New York, NY, USA","institution_ids":["https://openalex.org/I36672615","https://openalex.org/I57206974"]},{"raw_affiliation_string":"New York University","institution_ids":["https://openalex.org/I57206974"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5068494351","display_name":"William H. Piel","orcid":"https://orcid.org/0000-0002-0429-9797"},"institutions":[{"id":"https://openalex.org/I63190737","display_name":"University at Buffalo, State University of New York","ror":"https://ror.org/01y64my43","country_code":"US","type":"education","lineage":["https://openalex.org/I63190737"]},{"id":"https://openalex.org/I57206974","display_name":"New York University","ror":"https://ror.org/0190ak572","country_code":"US","type":"education","lineage":["https://openalex.org/I57206974"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"W.H. Piel","raw_affiliation_strings":["Department of Biological Sciences, State University of New York, University at Buffalo, Buffalo, NY, USA","University at buffalo"],"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, State University of New York, University at Buffalo, Buffalo, NY, USA","institution_ids":["https://openalex.org/I63190737","https://openalex.org/I57206974"]},{"raw_affiliation_string":"University at buffalo","institution_ids":["https://openalex.org/I63190737"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5110106915"],"corresponding_institution_ids":["https://openalex.org/I118118575"],"apc_list":null,"apc_paid":null,"fwci":2.05,"has_fulltext":false,"cited_by_count":32,"citation_normalized_percentile":{"value":0.86154727,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":null,"issue":null,"first_page":"171","last_page":"180"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9991000294685364,"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":0.9991000294685364,"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/T10012","display_name":"Genetic diversity and population structure","score":0.9763000011444092,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T11354","display_name":"Evolution and Paleontology Studies","score":0.9692999720573425,"subfield":{"id":"https://openalex.org/subfields/1911","display_name":"Paleontology"},"field":{"id":"https://openalex.org/fields/19","display_name":"Earth and Planetary Sciences"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.7345162034034729},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.7138490676879883},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.6468663811683655},{"id":"https://openalex.org/keywords/measure","display_name":"Measure (data warehouse)","score":0.5989455580711365},{"id":"https://openalex.org/keywords/nearest-neighbor-search","display_name":"Nearest neighbor search","score":0.5675967931747437},{"id":"https://openalex.org/keywords/similarity-measure","display_name":"Similarity measure","score":0.524133026599884},{"id":"https://openalex.org/keywords/k-nearest-neighbors-algorithm","display_name":"k-nearest neighbors algorithm","score":0.5005240440368652},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4997725486755371},{"id":"https://openalex.org/keywords/node","display_name":"Node (physics)","score":0.4893597960472107},{"id":"https://openalex.org/keywords/phylogenetic-network","display_name":"Phylogenetic network","score":0.4341173470020294},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.43213874101638794},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.42678558826446533},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.41309213638305664},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.38688740134239197},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.37901896238327026},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2839440405368805},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.08675232529640198},{"id":"https://openalex.org/keywords/image","display_name":"Image (mathematics)","score":0.06765753030776978},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.06592190265655518}],"concepts":[{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.7345162034034729},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.7138490676879883},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.6468663811683655},{"id":"https://openalex.org/C2780009758","wikidata":"https://www.wikidata.org/wiki/Q6804172","display_name":"Measure (data warehouse)","level":2,"score":0.5989455580711365},{"id":"https://openalex.org/C116738811","wikidata":"https://www.wikidata.org/wiki/Q608751","display_name":"Nearest neighbor search","level":2,"score":0.5675967931747437},{"id":"https://openalex.org/C2776517306","wikidata":"https://www.wikidata.org/wiki/Q29017317","display_name":"Similarity measure","level":2,"score":0.524133026599884},{"id":"https://openalex.org/C113238511","wikidata":"https://www.wikidata.org/wiki/Q1071612","display_name":"k-nearest neighbors algorithm","level":2,"score":0.5005240440368652},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4997725486755371},{"id":"https://openalex.org/C62611344","wikidata":"https://www.wikidata.org/wiki/Q1062658","display_name":"Node (physics)","level":2,"score":0.4893597960472107},{"id":"https://openalex.org/C26619641","wikidata":"https://www.wikidata.org/wiki/Q3142246","display_name":"Phylogenetic network","level":4,"score":0.4341173470020294},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.43213874101638794},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.42678558826446533},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.41309213638305664},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.38688740134239197},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.37901896238327026},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2839440405368805},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.08675232529640198},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.06765753030776978},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.06592190265655518},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1109/ssdm.2003.1214978","is_oa":false,"landing_page_url":"https://doi.org/10.1109/ssdm.2003.1214978","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"15th International Conference on Scientific and Statistical Database Management, 2003.","raw_type":"proceedings-article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.118.1840","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.118.1840","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.treebase.org/~piel/pdfs/wang03.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.74.687","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.74.687","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://web.njit.edu/~wangj/publications/ARTICLES/ssdbm2003.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":45,"referenced_works":["https://openalex.org/W1849794777","https://openalex.org/W1941736675","https://openalex.org/W1968300516","https://openalex.org/W1970802957","https://openalex.org/W1978384785","https://openalex.org/W1996437477","https://openalex.org/W2003554135","https://openalex.org/W2004555680","https://openalex.org/W2017719595","https://openalex.org/W2019026763","https://openalex.org/W2019736214","https://openalex.org/W2034145232","https://openalex.org/W2047715328","https://openalex.org/W2050137450","https://openalex.org/W2050297726","https://openalex.org/W2052471587","https://openalex.org/W2053794772","https://openalex.org/W2055568252","https://openalex.org/W2057294899","https://openalex.org/W2065067768","https://openalex.org/W2070976434","https://openalex.org/W2078481763","https://openalex.org/W2080541436","https://openalex.org/W2120130627","https://openalex.org/W2120653759","https://openalex.org/W2144898181","https://openalex.org/W2145805921","https://openalex.org/W2146245219","https://openalex.org/W2146258444","https://openalex.org/W2153546136","https://openalex.org/W2160350701","https://openalex.org/W2160517437","https://openalex.org/W2160983082","https://openalex.org/W2163509192","https://openalex.org/W2166838615","https://openalex.org/W4236824548","https://openalex.org/W4241418020","https://openalex.org/W6638893695","https://openalex.org/W6642211629","https://openalex.org/W6642362701","https://openalex.org/W6644727703","https://openalex.org/W6654813271","https://openalex.org/W6664047960","https://openalex.org/W6668243896","https://openalex.org/W6684422132"],"related_works":["https://openalex.org/W2148008870","https://openalex.org/W2381195555","https://openalex.org/W2368606575","https://openalex.org/W4246757943","https://openalex.org/W2085998272","https://openalex.org/W2132753198","https://openalex.org/W2369874856","https://openalex.org/W2182477562","https://openalex.org/W2792185758","https://openalex.org/W2787484455"],"abstract_inverted_index":{"Phylogenetic":[0],"trees":[1,5,34,135],"are":[2,72],"unordered":[3],"labeled":[4],"in":[6,69,80,89,103,115,145],"which":[7],"each":[8],"leaf":[9],"node":[10],"has":[11],"a":[12,26,44,51,63,120,125,132],"label":[13],"and":[14,35,50,106,108,131,138,164],"the":[15,55,66,76,86,98,111,140,148,153,168],"order":[16],"among":[17],"siblings":[18],"is":[19,62,97,110,150,161,165],"unimportant.":[20],"In":[21],"this":[22],"paper":[23],"we":[24],"propose":[25],"new":[27],"similarity":[28,155],"measure,":[29],"called":[30],"TreeRank,":[31],"for":[32,39],"phylogenetic":[33],"present":[36],"an":[37],"algorithm":[38,84],"computing":[40],"TreeRank":[41,56,87],"scores.":[42],"Given":[43],"query":[45,126],"or":[46,78,127],"pattern":[47,128],"tree":[48,53,129],"P":[49,59,70,105,130,144],"data":[52],"D,":[54,107,136],"score":[57,88],"from":[58],"to":[60,74],"D":[61,146],"measure":[64],"of":[65,100,113,134,143],"topological":[67],"relationships":[68],"that":[71],"found":[73],"be":[75],"same":[77],"similar":[79],"D.":[81,116],"The":[82],"proposed":[83,154],"calculates":[85],"O(M/sup":[90],"2/":[91],"+":[92],"N)":[93],"time":[94],"where":[95,147],"M":[96],"number":[99,112],"nodes":[101,114],"appearing":[102],"both":[104],"N":[109],"We":[117],"then":[118],"develop":[119],"search":[121,159],"engine":[122,160],"that,":[123],"given":[124],"database":[133],"finds":[137],"ranks":[139],"nearest":[141],"neighbors":[142],"\"nearness\"":[149],"measured":[151],"by":[152],"function.":[156],"This":[157],"structure-based":[158],"fully":[162],"operational":[163],"available":[166],"on":[167],"World":[169],"Wide":[170],"Web.":[171]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2012,"cited_by_count":2}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}
