{"id":"https://openalex.org/W2035594133","doi":"https://doi.org/10.1145/2649387.2649448","title":"Learning parameter sets for alignment advising","display_name":"Learning parameter sets for alignment advising","publication_year":2014,"publication_date":"2014-09-20","ids":{"openalex":"https://openalex.org/W2035594133","doi":"https://doi.org/10.1145/2649387.2649448","mag":"2035594133"},"language":"en","primary_location":{"id":"doi:10.1145/2649387.2649448","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2649387.2649448","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics","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/A5014004628","display_name":"Dan DeBlasio","orcid":"https://orcid.org/0000-0003-4110-4431"},"institutions":[{"id":"https://openalex.org/I138006243","display_name":"University of Arizona","ror":"https://ror.org/03m2x1q45","country_code":"US","type":"education","lineage":["https://openalex.org/I138006243"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dan DeBlasio","raw_affiliation_strings":["The University of Arizona, Tucson AZ","The University of Arizona, Tucson -- AZ"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The University of Arizona, Tucson AZ","institution_ids":["https://openalex.org/I138006243"]},{"raw_affiliation_string":"The University of Arizona, Tucson -- AZ","institution_ids":["https://openalex.org/I138006243"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5083998316","display_name":"John Kececioglu","orcid":"https://orcid.org/0000-0003-1204-6535"},"institutions":[{"id":"https://openalex.org/I138006243","display_name":"University of Arizona","ror":"https://ror.org/03m2x1q45","country_code":"US","type":"education","lineage":["https://openalex.org/I138006243"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"John Kececioglu","raw_affiliation_strings":["The University of Arizona, Tucson AZ","The University of Arizona, Tucson -- AZ"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The University of Arizona, Tucson AZ","institution_ids":["https://openalex.org/I138006243"]},{"raw_affiliation_string":"The University of Arizona, Tucson -- AZ","institution_ids":["https://openalex.org/I138006243"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":1.4233,"has_fulltext":false,"cited_by_count":11,"citation_normalized_percentile":{"value":0.8081501,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":null,"issue":null,"first_page":"230","last_page":"239"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9968000054359436,"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":0.9968000054359436,"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/T11482","display_name":"RNA modifications and cancer","score":0.9878000020980835,"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":0.9797000288963318,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.6684149503707886},{"id":"https://openalex.org/keywords/estimator","display_name":"Estimator","score":0.6625073552131653},{"id":"https://openalex.org/keywords/estimation-theory","display_name":"Estimation theory","score":0.6272934675216675},{"id":"https://openalex.org/keywords/shape-parameter","display_name":"Shape parameter","score":0.6114916205406189},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.5674837231636047},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5660839080810547},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.566052258014679},{"id":"https://openalex.org/keywords/parameter-space","display_name":"Parameter space","score":0.5443668961524963},{"id":"https://openalex.org/keywords/quality","display_name":"Quality (philosophy)","score":0.4641512632369995},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3826757073402405},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3327248692512512},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3288099765777588},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.25716450810432434}],"concepts":[{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.6684149503707886},{"id":"https://openalex.org/C185429906","wikidata":"https://www.wikidata.org/wiki/Q1130160","display_name":"Estimator","level":2,"score":0.6625073552131653},{"id":"https://openalex.org/C167928553","wikidata":"https://www.wikidata.org/wiki/Q1376021","display_name":"Estimation theory","level":2,"score":0.6272934675216675},{"id":"https://openalex.org/C199435849","wikidata":"https://www.wikidata.org/wiki/Q3179293","display_name":"Shape parameter","level":2,"score":0.6114916205406189},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.5674837231636047},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5660839080810547},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.566052258014679},{"id":"https://openalex.org/C73586568","wikidata":"https://www.wikidata.org/wiki/Q2600211","display_name":"Parameter space","level":2,"score":0.5443668961524963},{"id":"https://openalex.org/C2779530757","wikidata":"https://www.wikidata.org/wiki/Q1207505","display_name":"Quality (philosophy)","level":2,"score":0.4641512632369995},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3826757073402405},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3327248692512512},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3288099765777588},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.25716450810432434},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"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/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1145/2649387.2649448","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2649387.2649448","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics","raw_type":"proceedings-article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.431.2736","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.431.2736","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.cs.arizona.edu/~deblasio/papers/DK14.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.696.1069","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.696.1069","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.cs.arizona.edu/%7Ekece/Research/papers/DK14.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/16","display_name":"Peace, Justice and strong institutions","score":0.6700000166893005}],"awards":[{"id":"https://openalex.org/G7434694044","display_name":null,"funder_award_id":"IIS-1217886, DGE-0654435","funder_id":"https://openalex.org/F4320337368","funder_display_name":"Division of Graduate Education"},{"id":"https://openalex.org/G806652085","display_name":null,"funder_award_id":"IIS-1217886, DGE-0654435","funder_id":"https://openalex.org/F4320337389","funder_display_name":"Division of Information and Intelligent Systems"}],"funders":[{"id":"https://openalex.org/F4320337368","display_name":"Division of Graduate Education","ror":"https://ror.org/00whkrf32"},{"id":"https://openalex.org/F4320337389","display_name":"Division of Information and Intelligent Systems","ror":"https://ror.org/053a2cp42"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":21,"referenced_works":["https://openalex.org/W171034855","https://openalex.org/W2007924998","https://openalex.org/W2011039300","https://openalex.org/W2030750720","https://openalex.org/W2060791849","https://openalex.org/W2075451741","https://openalex.org/W2097059553","https://openalex.org/W2097818324","https://openalex.org/W2101969356","https://openalex.org/W2110919845","https://openalex.org/W2111551123","https://openalex.org/W2125670145","https://openalex.org/W2130625618","https://openalex.org/W2130909239","https://openalex.org/W2140890018","https://openalex.org/W2143210482","https://openalex.org/W2143292980","https://openalex.org/W2148311769","https://openalex.org/W2153187042","https://openalex.org/W2155320525","https://openalex.org/W2476096155"],"related_works":["https://openalex.org/W2077038896","https://openalex.org/W1998254728","https://openalex.org/W2069805373","https://openalex.org/W2810607982","https://openalex.org/W1987771408","https://openalex.org/W2042934151","https://openalex.org/W2905630886","https://openalex.org/W2472237270","https://openalex.org/W2612639608","https://openalex.org/W2023661646"],"abstract_inverted_index":{"While":[0],"the":[1,12,17,23,35,42,56,104,107,111,121,125],"multiple":[2],"sequence":[3],"alignment":[4,18,54,108,129],"output":[5],"by":[6,41,110],"an":[7,97,101],"aligner":[8,112],"strongly":[9],"depends":[10],"on":[11,34],"parameter":[13,38,46,70,78,81,90,115,118,122],"values":[14,71],"used":[15],"for":[16,55,72],"scoring":[19],"function":[20],"(such":[21],"as":[22],"choice":[24,68,123],"of":[25,59,64,69,89,103,106],"gap":[26],"penalties":[27],"and":[28,95],"substitution":[29],"scores),":[30],"most":[31],"users":[32],"rely":[33],"single":[36],"default":[37],"setting":[39],"provided":[40],"aligner.":[43],"A":[44,80],"different":[45],"setting,":[47],"however,":[48],"might":[49],"yield":[50],"a":[51,66,87,114],"much":[52],"higher-quality":[53],"specific":[57,73],"set":[58,88,126],"input":[60,74],"sequences.":[61],"The":[62,117],"problem":[63],"picking":[65],"good":[67],"sequences":[75],"is":[76],"called":[77],"advising.":[79],"advisor":[82,119],"has":[83,130],"two":[84],"ingredients:":[85],"(i)":[86],"choices":[91],"to":[92],"select":[93],"from,":[94],"(ii)":[96],"estimator":[98],"that":[99],"provides":[100],"estimate":[102],"accuracy":[105],"computed":[109],"using":[113],"choice.":[116],"picks":[120],"from":[124],"whose":[127],"resulting":[128],"highest":[131],"estimated":[132],"accuracy.":[133]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":3}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}