{"id":"https://openalex.org/W2940926484","doi":"https://doi.org/10.4230/lipics.wabi.2026.17","title":"Discriminative Learning of Substitution Matrices and Gap Penalties for Pairwise Alignment of Biological Sequences","display_name":"Discriminative Learning of Substitution Matrices and Gap Penalties for Pairwise Alignment of Biological Sequences","publication_year":2019,"publication_date":"2019-04-29","ids":{"openalex":"https://openalex.org/W2940926484","doi":"https://doi.org/10.4230/lipics.wabi.2026.17","mag":"2940926484"},"language":"en","primary_location":{"id":"pmh:oai:arXiv.org:1904.12562","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1904.12562","pdf_url":"https://arxiv.org/pdf/1904.12562","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"type":"preprint","indexed_in":["arxiv","datacite","doaj"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/1904.12562","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5090165257","display_name":"Micha\u0142 Aleksander Ciach","orcid":"https://orcid.org/0000-0003-4961-7071"},"institutions":[{"id":"https://openalex.org/I197854408","display_name":"University of Malta","ror":"https://ror.org/03a62bv60","country_code":"MT","type":"education","lineage":["https://openalex.org/I197854408"]}],"countries":["MT"],"is_corresponding":false,"raw_author_name":"Ciach, Micha\u0142 Aleksander","raw_affiliation_strings":["Department of Applied Biomedical Science, Faculty of Health Sciences, University of Malta, Msida, Malta"],"raw_orcid":"https://orcid.org/0000-0003-4961-7071","affiliations":[{"raw_affiliation_string":"Department of Applied Biomedical Science, Faculty of Health Sciences, University of Malta, Msida, Malta","institution_ids":["https://openalex.org/I197854408"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061676840","display_name":"\u0412. \u042f. \u0426\u0432\u0435\u0442\u043a\u043e\u0432","orcid":null},"institutions":[{"id":"https://openalex.org/I197854408","display_name":"University of Malta","ror":"https://ror.org/03a62bv60","country_code":"MT","type":"education","lineage":["https://openalex.org/I197854408"]}],"countries":["MT"],"is_corresponding":false,"raw_author_name":"Zacharopoulou, Elissavet","raw_affiliation_strings":["Department of Applied Biomedical Science, Faculty of Health Sciences, University of Malta, Msida, Malta"],"raw_orcid":"https://orcid.org/0009-0008-3566-7135","affiliations":[{"raw_affiliation_string":"Department of Applied Biomedical Science, Faculty of Health Sciences, University of Malta, Msida, Malta","institution_ids":["https://openalex.org/I197854408"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084036949","display_name":"Micha\u0142 Startek","orcid":"https://orcid.org/0000-0001-5227-3447"},"institutions":[{"id":"https://openalex.org/I4654613","display_name":"University of Warsaw","ror":"https://ror.org/039bjqg32","country_code":"PL","type":"education","lineage":["https://openalex.org/I4654613"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Startek, Micha\u0142 Piotr","raw_affiliation_strings":["Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Poland"],"raw_orcid":"https://orcid.org/0000-0001-5227-3447","affiliations":[{"raw_affiliation_string":"Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Poland","institution_ids":["https://openalex.org/I4654613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028611632","display_name":"B\u0142a\u017cej Miasojedow","orcid":"https://orcid.org/0000-0002-3691-9372"},"institutions":[{"id":"https://openalex.org/I4654613","display_name":"University of Warsaw","ror":"https://ror.org/039bjqg32","country_code":"PL","type":"education","lineage":["https://openalex.org/I4654613"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Miasojedow, B\u0142a\u017cej","raw_affiliation_strings":["Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Poland"],"raw_orcid":"https://orcid.org/0000-0002-3691-9372","affiliations":[{"raw_affiliation_string":"Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Poland","institution_ids":["https://openalex.org/I4654613"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5027227036","display_name":"Panagiotis Alexiou","orcid":"https://orcid.org/0000-0003-3437-7482"},"institutions":[{"id":"https://openalex.org/I197854408","display_name":"University of Malta","ror":"https://ror.org/03a62bv60","country_code":"MT","type":"education","lineage":["https://openalex.org/I197854408"]}],"countries":["MT"],"is_corresponding":false,"raw_author_name":"Alexiou, Panagiotis","raw_affiliation_strings":["Department of Applied Biomedical Science, Faculty of Health Sciences, University of Malta, Msida, Malta"],"raw_orcid":"https://orcid.org/0000-0003-3437-7482","affiliations":[{"raw_affiliation_string":"Department of Applied Biomedical Science, Faculty of Health Sciences, University of Malta, Msida, Malta","institution_ids":["https://openalex.org/I197854408"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":4,"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/T11269","display_name":"Algorithms and Data Compression","score":0.9997000098228455,"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"}},"topics":[{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9997000098228455,"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/T11309","display_name":"Music and Audio Processing","score":0.994700014591217,"subfield":{"id":"https://openalex.org/subfields/1711","display_name":"Signal Processing"},"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/T10320","display_name":"Neural Networks and Applications","score":0.9944999814033508,"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/differentiable-function","display_name":"Differentiable function","score":0.7324978113174438},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3978273868560791},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3695554733276367},{"id":"https://openalex.org/keywords/pure-mathematics","display_name":"Pure mathematics","score":0.22623595595359802}],"concepts":[{"id":"https://openalex.org/C202615002","wikidata":"https://www.wikidata.org/wiki/Q783507","display_name":"Differentiable function","level":2,"score":0.7324978113174438},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3978273868560791},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3695554733276367},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.22623595595359802}],"mesh":[],"locations_count":3,"locations":[{"id":"pmh:oai:arXiv.org:1904.12562","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1904.12562","pdf_url":"https://arxiv.org/pdf/1904.12562","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"doi:10.48550/arxiv.1904.12562","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.1904.12562","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"Preprint"},{"id":"doi:10.4230/lipics.wabi.2026.17","is_oa":true,"landing_page_url":"https://doi.org/10.4230/lipics.wabi.2026.17","pdf_url":null,"source":{"id":"https://openalex.org/S4393917817","display_name":"Leibniz international proceedings in informatics","issn_l":"1868-8969","issn":["1868-8969"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"ConferencePaper"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:1904.12562","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1904.12562","pdf_url":"https://arxiv.org/pdf/1904.12562","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"sustainable_development_goals":[{"display_name":"Quality Education","id":"https://metadata.un.org/sdg/4","score":0.6100000143051147}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":10,"referenced_works":["https://openalex.org/W1522301498","https://openalex.org/W1970026646","https://openalex.org/W2022349790","https://openalex.org/W2110340112","https://openalex.org/W2119149496","https://openalex.org/W2127141656","https://openalex.org/W2142838865","https://openalex.org/W2151501021","https://openalex.org/W2187089797","https://openalex.org/W2737931494"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W4391375266","https://openalex.org/W4285277090","https://openalex.org/W4327738859","https://openalex.org/W1979597421","https://openalex.org/W2007980826","https://openalex.org/W2061531152","https://openalex.org/W3002753104","https://openalex.org/W2077600819","https://openalex.org/W2348722996"],"abstract_inverted_index":{"Edit":[0],"distance,":[1,6,120],"also":[2],"known":[3,40],"as":[4,58,61,122,124],"Levenshtein":[5],"is":[7,34,39,95,103,108],"an":[8],"essential":[9],"way":[10],"to":[11,17,41,44,64,110,117],"compare":[12],"two":[13],"strings":[14],"that":[15,38],"proved":[16],"be":[18,42,128],"particularly":[19],"useful":[20],"in":[21,54],"the":[22,49,140],"analysis":[23],"of":[24,51,68,76,99,139,148],"genetic":[25],"sequences":[26,69],"and":[27,79,105,146],"natural":[28],"language":[29],"processing.":[30],"However,":[31],"edit":[32,71,91,100,119],"distance":[33,72,92],"a":[35,66,86,96],"discrete":[36],"function":[37],"hard":[43],"optimize.":[45],"This":[46],"fact":[47],"hampers":[48],"use":[50],"this":[52,82],"metric":[53,88,142],"Machine":[55],"Learning.":[56],"Even":[57],"simple":[59],"algorithm":[60],"K-means":[62],"fails":[63],"cluster":[65],"set":[67],"using":[70],"if":[73],"they":[74],"are":[75],"variable":[77],"length":[78],"abundance.":[80],"In":[81],"paper":[83],"we":[84],"propose":[85],"novel":[87],"-":[89],"soft":[90],"(SED),":[93],"which":[94],"smooth":[97],"approximation":[98],"distance.":[101],"It":[102],"differentiable":[104],"therefore":[106],"it":[107,112],"possible":[109],"optimize":[111],"with":[113,130],"gradient":[114],"methods.":[115],"Similar":[116],"original":[118],"SED":[121],"well":[123],"its":[125],"derivatives":[126],"can":[127],"calculated":[129],"recurrent":[131],"formulas":[132],"at":[133],"polynomial":[134],"time.":[135],"We":[136],"prove":[137],"usefulness":[138],"proposed":[141],"on":[143],"synthetic":[144],"datasets":[145],"clustering":[147],"biological":[149],"sequences.":[150]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1}],"updated_date":"2026-08-28T12:50:07.497085","created_date":"2025-10-10T00:00:00"}
