{"id":"https://openalex.org/W2124515224","doi":"https://doi.org/10.1109/cdc.2007.4434352","title":"Solving the contact map overlap problem via tree decomposition and a DEE-like pruning strategy","display_name":"Solving the contact map overlap problem via tree decomposition and a DEE-like pruning strategy","publication_year":2007,"publication_date":"2007-01-01","ids":{"openalex":"https://openalex.org/W2124515224","doi":"https://doi.org/10.1109/cdc.2007.4434352","mag":"2124515224"},"language":"en","primary_location":{"id":"doi:10.1109/cdc.2007.4434352","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cdc.2007.4434352","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2007 46th IEEE Conference on Decision and Control","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/A5019398608","display_name":"Jinbo Xu","orcid":"https://orcid.org/0000-0001-7111-4839"},"institutions":[{"id":"https://openalex.org/I1293612202","display_name":"Toyota Motor Corporation (Switzerland)","ror":"https://ror.org/05p0pbv75","country_code":"CH","type":"company","lineage":["https://openalex.org/I1293612202","https://openalex.org/I4210125472","https://openalex.org/I4210137853"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Jinbo Xu","raw_affiliation_strings":["Institute at Chicago, USA","Toyota Technol. Inst., Chicago"],"affiliations":[{"raw_affiliation_string":"Institute at Chicago, USA","institution_ids":[]},{"raw_affiliation_string":"Toyota Technol. Inst., Chicago","institution_ids":["https://openalex.org/I1293612202"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5019398608"],"corresponding_institution_ids":["https://openalex.org/I1293612202"],"apc_list":null,"apc_paid":null,"fwci":0.1309,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.53248372,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"1","issue":null,"first_page":"4531","last_page":"4538"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9983999729156494,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9983999729156494,"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/T11269","display_name":"Algorithms and Data Compression","score":0.9957000017166138,"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":0.9941999912261963,"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/tree-decomposition","display_name":"Tree decomposition","score":0.6489051580429077},{"id":"https://openalex.org/keywords/pruning","display_name":"Pruning","score":0.6257957220077515},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5602086782455444},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5430667996406555},{"id":"https://openalex.org/keywords/search-tree","display_name":"Search tree","score":0.5244384407997131},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5048914551734924},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.4736786186695099},{"id":"https://openalex.org/keywords/data-structure","display_name":"Data structure","score":0.43312519788742065},{"id":"https://openalex.org/keywords/computational-complexity-theory","display_name":"Computational complexity theory","score":0.4298184812068939},{"id":"https://openalex.org/keywords/constraint","display_name":"Constraint (computer-aided design)","score":0.41946983337402344},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3322945237159729},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3103770911693573},{"id":"https://openalex.org/keywords/search-algorithm","display_name":"Search algorithm","score":0.30524349212646484},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.2808229923248291}],"concepts":[{"id":"https://openalex.org/C70501317","wikidata":"https://www.wikidata.org/wiki/Q462095","display_name":"Tree decomposition","level":5,"score":0.6489051580429077},{"id":"https://openalex.org/C108010975","wikidata":"https://www.wikidata.org/wiki/Q500094","display_name":"Pruning","level":2,"score":0.6257957220077515},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5602086782455444},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5430667996406555},{"id":"https://openalex.org/C207024777","wikidata":"https://www.wikidata.org/wiki/Q621673","display_name":"Search tree","level":3,"score":0.5244384407997131},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5048914551734924},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.4736786186695099},{"id":"https://openalex.org/C162319229","wikidata":"https://www.wikidata.org/wiki/Q175263","display_name":"Data structure","level":2,"score":0.43312519788742065},{"id":"https://openalex.org/C179799912","wikidata":"https://www.wikidata.org/wiki/Q205084","display_name":"Computational complexity theory","level":2,"score":0.4298184812068939},{"id":"https://openalex.org/C2776036281","wikidata":"https://www.wikidata.org/wiki/Q48769818","display_name":"Constraint (computer-aided design)","level":2,"score":0.41946983337402344},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3322945237159729},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3103770911693573},{"id":"https://openalex.org/C125583679","wikidata":"https://www.wikidata.org/wiki/Q755673","display_name":"Search algorithm","level":2,"score":0.30524349212646484},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.2808229923248291},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C43517604","wikidata":"https://www.wikidata.org/wiki/Q7144893","display_name":"Pathwidth","level":4,"score":0.0},{"id":"https://openalex.org/C6557445","wikidata":"https://www.wikidata.org/wiki/Q173113","display_name":"Agronomy","level":1,"score":0.0},{"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/C203776342","wikidata":"https://www.wikidata.org/wiki/Q1378376","display_name":"Line graph","level":3,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/cdc.2007.4434352","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cdc.2007.4434352","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2007 46th IEEE Conference on Decision and Control","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":28,"referenced_works":["https://openalex.org/W1502360391","https://openalex.org/W1520321564","https://openalex.org/W1554450286","https://openalex.org/W1573344978","https://openalex.org/W1575639801","https://openalex.org/W1582136936","https://openalex.org/W1757046366","https://openalex.org/W1916412816","https://openalex.org/W1965910641","https://openalex.org/W1969740180","https://openalex.org/W1972728295","https://openalex.org/W1973503184","https://openalex.org/W1975168057","https://openalex.org/W1978273076","https://openalex.org/W1988874269","https://openalex.org/W2022058405","https://openalex.org/W2064651547","https://openalex.org/W2115177539","https://openalex.org/W2120000589","https://openalex.org/W2122451172","https://openalex.org/W2127054268","https://openalex.org/W2130479394","https://openalex.org/W2137796207","https://openalex.org/W2148101168","https://openalex.org/W2152326664","https://openalex.org/W2465097926","https://openalex.org/W6631239882","https://openalex.org/W6678966363"],"related_works":["https://openalex.org/W1591786641","https://openalex.org/W1017753691","https://openalex.org/W2390746690","https://openalex.org/W2288580478","https://openalex.org/W2088116875","https://openalex.org/W2985498454","https://openalex.org/W2609269940","https://openalex.org/W49964765","https://openalex.org/W2349743712","https://openalex.org/W2789480285"],"abstract_inverted_index":{"This":[0,86],"paper":[1],"proposes":[2],"a":[3,14,20,58,72,95,107,132,144,168],"new":[4],"algorithm":[5,41,87],"for":[6],"protein":[7,15,74,108],"structure":[8,16,109,145],"alignment":[9,146],"in":[10,33,44,51,71,77],"the":[11,25,34,40,47,55,67,78,103,122,151,156],"case":[12],"where":[13],"is":[17,30,42,83],"represented":[18,76],"by":[19],"contact":[21,59,62,157],"map":[22,158],"graph":[23],"and":[24,54,66,94,110,125,182],"sequential":[26,123],"order":[27],"of":[28,39,46,49,57,89,106,155],"residues":[29,50],"strictly":[31],"enforced":[32],"alignment.":[35],"The":[36,61,80,99,117,161],"time":[37,81],"complexity":[38,82],"given":[43],"terms":[45],"number":[48],"two":[52,90,139,177,183],"proteins":[53,179,185],"treewidth":[56],"graph.":[60],"distance":[63,70],"cut":[64],"off":[65],"minimum":[68],"inter-residue":[69],"typical":[73],"are":[75],"algorithm.":[79],"also":[84],"discussed.":[85],"consists":[88],"major":[91],"components:":[92],"tree-decomposition":[93,100],"DEE-like":[96,118],"pruning":[97,119],"strategy.":[98],"method":[101],"exploits":[102,121],"geometric":[104],"feature":[105],"guarantees":[111],"to":[112,149],"terminate":[113],"within":[114,180,186],"subexponential":[115],"time.":[116],"strategy":[120],"constraint":[124],"can":[126,175],"quickly":[127],"eliminate":[128],"non-optimal":[129],"alignments":[130],"from":[131],"large":[133],"search":[134],"space.":[135],"Based":[136],"on":[137,167],"these":[138],"techniques,":[140],"we":[141],"have":[142],"developed":[143],"program":[147],"TreeAlign":[148,174],"find":[150],"globally":[152],"optimal":[153],"solution":[154],"overlap":[159],"problem.":[160],"preliminary":[162],"experimental":[163],"results":[164],"indicate":[165],"that":[166],"Linux":[169],"PC":[170],"with":[171],"2.5GHz":[172],"CPU,":[173],"align":[176],"similar":[178],"seconds":[181],"dissimilar":[184],"minutes.":[187]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}