{"id":"https://openalex.org/W2345234399","doi":"https://doi.org/10.1109/tcbb.2015.2495186","title":"A Guaranteed Similarity Metric Learning Framework for Biological Sequence Comparison","display_name":"A Guaranteed Similarity Metric Learning Framework for Biological Sequence Comparison","publication_year":2015,"publication_date":"2015-10-26","ids":{"openalex":"https://openalex.org/W2345234399","doi":"https://doi.org/10.1109/tcbb.2015.2495186","mag":"2345234399","pmid":"https://pubmed.ncbi.nlm.nih.gov/26529778"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2015.2495186","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2015.2495186","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM 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/A5037212212","display_name":"Keru Hua","orcid":null},"institutions":[{"id":"https://openalex.org/I89652312","display_name":"Northwest A&F University","ror":"https://ror.org/0051rme32","country_code":"CN","type":"education","lineage":["https://openalex.org/I89652312"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Keru Hua","raw_affiliation_strings":["College of Science, Northwest A&F University, Yangling, Shaanxi, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Science, Northwest A&F University, Yangling, Shaanxi, China","institution_ids":["https://openalex.org/I89652312"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102782699","display_name":"Qin Yu","orcid":"https://orcid.org/0000-0002-4652-0795"},"institutions":[{"id":"https://openalex.org/I89652312","display_name":"Northwest A&F University","ror":"https://ror.org/0051rme32","country_code":"CN","type":"education","lineage":["https://openalex.org/I89652312"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qin Yu","raw_affiliation_strings":["College of Science, Northwest A&F University, Yangling, Shaanxi, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Science, Northwest A&F University, Yangling, Shaanxi, China","institution_ids":["https://openalex.org/I89652312"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101738004","display_name":"Ruiming Zhang","orcid":"https://orcid.org/0000-0002-6310-7468"},"institutions":[{"id":"https://openalex.org/I89652312","display_name":"Northwest A&F University","ror":"https://ror.org/0051rme32","country_code":"CN","type":"education","lineage":["https://openalex.org/I89652312"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ruiming Zhang","raw_affiliation_strings":["College of Science, Northwest A&F University, Yangling, Shaanxi, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Science, Northwest A&F University, Yangling, Shaanxi, China","institution_ids":["https://openalex.org/I89652312"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I89652312"],"apc_list":null,"apc_paid":null,"fwci":0.4434,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.66675225,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"13","issue":"5","first_page":"868","last_page":"877"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","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/T12254","display_name":"Machine Learning in Bioinformatics","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/T12946","display_name":"Fractal and DNA sequence analysis","score":0.998199999332428,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.996399998664856,"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/similarity","display_name":"Similarity (geometry)","score":0.7627060413360596},{"id":"https://openalex.org/keywords/metric","display_name":"Metric (unit)","score":0.6896737217903137},{"id":"https://openalex.org/keywords/mahalanobis-distance","display_name":"Mahalanobis distance","score":0.6149042844772339},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5652350187301636},{"id":"https://openalex.org/keywords/similarity-learning","display_name":"Similarity learning","score":0.5118328928947449},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.5070106983184814},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.49568092823028564},{"id":"https://openalex.org/keywords/feature-vector","display_name":"Feature vector","score":0.49046656489372253},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4496786594390869},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4244956374168396},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3644278347492218},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3247024118900299},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.32457566261291504},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.08761197328567505}],"concepts":[{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.7627060413360596},{"id":"https://openalex.org/C176217482","wikidata":"https://www.wikidata.org/wiki/Q860554","display_name":"Metric (unit)","level":2,"score":0.6896737217903137},{"id":"https://openalex.org/C1921717","wikidata":"https://www.wikidata.org/wiki/Q1334846","display_name":"Mahalanobis distance","level":2,"score":0.6149042844772339},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5652350187301636},{"id":"https://openalex.org/C2779597229","wikidata":"https://www.wikidata.org/wiki/Q17146505","display_name":"Similarity learning","level":3,"score":0.5118328928947449},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.5070106983184814},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.49568092823028564},{"id":"https://openalex.org/C83665646","wikidata":"https://www.wikidata.org/wiki/Q42139305","display_name":"Feature vector","level":2,"score":0.49046656489372253},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4496786594390869},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4244956374168396},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3644278347492218},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3247024118900299},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.32457566261291504},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.08761197328567505},{"id":"https://openalex.org/C21547014","wikidata":"https://www.wikidata.org/wiki/Q1423657","display_name":"Operations management","level":1,"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/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","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":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017421","descriptor_name":"Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017421","descriptor_name":"Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017421","descriptor_name":"Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2015.2495186","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2015.2495186","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:26529778","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26529778","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/ACM transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1424762317","display_name":"\u4e00\u4e9bq-\u7279\u6b8a\u51fd\u6570\u7684\u7814\u7a76","funder_award_id":"11371294","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":71,"referenced_works":["https://openalex.org/W127798343","https://openalex.org/W158216348","https://openalex.org/W203437397","https://openalex.org/W1414199774","https://openalex.org/W1453264805","https://openalex.org/W1499991161","https://openalex.org/W1523154159","https://openalex.org/W1523223774","https://openalex.org/W1539117683","https://openalex.org/W1540596182","https://openalex.org/W1546430343","https://openalex.org/W1560724230","https://openalex.org/W1596429464","https://openalex.org/W1620759536","https://openalex.org/W1781954958","https://openalex.org/W1800919879","https://openalex.org/W1973309569","https://openalex.org/W1979191353","https://openalex.org/W1987091651","https://openalex.org/W1992502250","https://openalex.org/W2002956097","https://openalex.org/W2003677307","https://openalex.org/W2014987111","https://openalex.org/W2017093281","https://openalex.org/W2030774451","https://openalex.org/W2032870665","https://openalex.org/W2041624900","https://openalex.org/W2044153604","https://openalex.org/W2079809266","https://openalex.org/W2083395367","https://openalex.org/W2085498221","https://openalex.org/W2088779313","https://openalex.org/W2089453789","https://openalex.org/W2091632079","https://openalex.org/W2104752854","https://openalex.org/W2106053110","https://openalex.org/W2107034620","https://openalex.org/W2112072385","https://openalex.org/W2116731705","https://openalex.org/W2117154949","https://openalex.org/W2118393783","https://openalex.org/W2118840614","https://openalex.org/W2118979615","https://openalex.org/W2121811815","https://openalex.org/W2123170127","https://openalex.org/W2125229658","https://openalex.org/W2128124531","https://openalex.org/W2130556178","https://openalex.org/W2133637723","https://openalex.org/W2143772141","https://openalex.org/W2144935315","https://openalex.org/W2145773134","https://openalex.org/W2151483828","https://openalex.org/W2152010828","https://openalex.org/W2153990926","https://openalex.org/W2158139921","https://openalex.org/W2159364980","https://openalex.org/W2159583439","https://openalex.org/W2159954944","https://openalex.org/W2169495281","https://openalex.org/W2536305071","https://openalex.org/W2950945979","https://openalex.org/W6628424692","https://openalex.org/W6632543029","https://openalex.org/W6635548393","https://openalex.org/W6637787236","https://openalex.org/W6648359283","https://openalex.org/W6681440187","https://openalex.org/W6682470622","https://openalex.org/W6684704328","https://openalex.org/W7027956375"],"related_works":["https://openalex.org/W2589345682","https://openalex.org/W2063417830","https://openalex.org/W1544103676","https://openalex.org/W2136550263","https://openalex.org/W3139362840","https://openalex.org/W1995655823","https://openalex.org/W199855617","https://openalex.org/W2123191275","https://openalex.org/W2246460439","https://openalex.org/W1978697738","https://openalex.org/W2051916637","https://openalex.org/W1543391926","https://openalex.org/W1600909276","https://openalex.org/W2045127637","https://openalex.org/W3105695320","https://openalex.org/W3175023467","https://openalex.org/W1978917728","https://openalex.org/W2026498605","https://openalex.org/W2064342721","https://openalex.org/W1580275191"],"abstract_inverted_index":{"Similarity":[0],"of":[1,37,41,77,86],"sequences":[2,88,142],"is":[3,35,55],"a":[4,74,107],"key":[5],"mathematical":[6],"notion":[7],"for":[8],"Classification":[9],"and":[10,17,25,125,145,154],"Phylogenetic":[11],"studies":[12],"in":[13,50,89,123,151],"Biology.":[14],"The":[15],"distance":[16],"similarity":[18,64,79,100,110,119,147],"between":[19],"two":[20],"sequence":[21],"are":[22],"very":[23],"important":[24],"widely":[26],"studied.":[27],"During":[28],"the":[29,38,51,96,117,130,139],"last":[30],"decades,":[31],"Similarity(distance)":[32],"metric":[33,65,80,104,111,148],"learning":[34,60,81,112,149],"one":[36],"hottest":[39],"topics":[40],"machine":[42,59],"learning/data":[43],"mining":[44],"as":[45,47],"well":[46,122],"their":[48],"applications":[49],"bioinformatics":[52],"field.":[53],"It":[54,94],"feasible":[56],"to":[57,62,83,102],"introduce":[58],"technology":[61],"learn":[63],"from":[66],"biological":[67,141],"data.":[68],"In":[69],"this":[70],"paper,":[71],"we":[72],"propose":[73],"novel":[75],"framework":[76],"guaranteed":[78,109],"(GMSL)":[82],"perform":[84],"alignment":[85,143],"biology":[87],"any":[90],"feature":[91],"vector":[92],"space.":[93],"introduces":[95],"(\u03f5,":[97],"\u03b3,":[98],"\u03c4)-goodness":[99],"theory":[101],"Mahalanobis":[103],"learning.":[105],"As":[106],"theoretical":[108],"approach,":[113],"GMSL":[114],"guarantees":[115],"that":[116,135],"learned":[118],"function":[120],"performs":[121],"classification":[124],"clustering.":[126],"Our":[127],"experiments":[128],"on":[129],"most":[131],"used":[132],"datasets":[133],"demonstrate":[134],"our":[136],"approach":[137],"outperforms":[138],"state-of-the-art":[140],"methods":[144],"other":[146],"algorithms":[150],"both":[152],"accuracy":[153],"stability.":[155]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}