{"id":"https://openalex.org/W4405489103","doi":"https://doi.org/10.1109/embc53108.2024.10781891","title":"On the optimization of GWFA algorithm: enabling real-case applications supporting alignment backtracking","display_name":"On the optimization of GWFA algorithm: enabling real-case applications supporting alignment backtracking","publication_year":2024,"publication_date":"2024-07-15","ids":{"openalex":"https://openalex.org/W4405489103","doi":"https://doi.org/10.1109/embc53108.2024.10781891","pmid":"https://pubmed.ncbi.nlm.nih.gov/40039311"},"language":"en","primary_location":{"id":"doi:10.1109/embc53108.2024.10781891","is_oa":false,"landing_page_url":"https://doi.org/10.1109/embc53108.2024.10781891","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 46th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://hdl.handle.net/11311/1287281","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5115513400","display_name":"Mirko Coggi","orcid":"https://orcid.org/0009-0001-8263-7114"},"institutions":[{"id":"https://openalex.org/I93860229","display_name":"Politecnico di Milano","ror":"https://ror.org/01nffqt88","country_code":"IT","type":"education","lineage":["https://openalex.org/I93860229"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Mirko Coggi","raw_affiliation_strings":["Informatica e Bioingegneria Politecnico di Milano,Dipartimento di Elettronica,Milan,Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Informatica e Bioingegneria Politecnico di Milano,Dipartimento di Elettronica,Milan,Italy","institution_ids":["https://openalex.org/I93860229"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5115513401","display_name":"Antonio Sgarlata","orcid":null},"institutions":[{"id":"https://openalex.org/I93860229","display_name":"Politecnico di Milano","ror":"https://ror.org/01nffqt88","country_code":"IT","type":"education","lineage":["https://openalex.org/I93860229"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Antonio Sgarlata","raw_affiliation_strings":["Informatica e Bioingegneria Politecnico di Milano,Dipartimento di Elettronica,Milan,Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Informatica e Bioingegneria Politecnico di Milano,Dipartimento di Elettronica,Milan,Italy","institution_ids":["https://openalex.org/I93860229"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063408697","display_name":"Guido Walter Di Donato","orcid":"https://orcid.org/0000-0003-2026-9755"},"institutions":[{"id":"https://openalex.org/I93860229","display_name":"Politecnico di Milano","ror":"https://ror.org/01nffqt88","country_code":"IT","type":"education","lineage":["https://openalex.org/I93860229"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Guido Walter Di Donato","raw_affiliation_strings":["Informatica e Bioingegneria Politecnico di Milano,Dipartimento di Elettronica,Milan,Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Informatica e Bioingegneria Politecnico di Milano,Dipartimento di Elettronica,Milan,Italy","institution_ids":["https://openalex.org/I93860229"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5010543929","display_name":"Marco D. Santambrogio","orcid":"https://orcid.org/0000-0002-9883-9693"},"institutions":[{"id":"https://openalex.org/I93860229","display_name":"Politecnico di Milano","ror":"https://ror.org/01nffqt88","country_code":"IT","type":"education","lineage":["https://openalex.org/I93860229"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Marco Domenico Santambrogio","raw_affiliation_strings":["Informatica e Bioingegneria Politecnico di Milano,Dipartimento di Elettronica,Milan,Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Informatica e Bioingegneria Politecnico di Milano,Dipartimento di Elettronica,Milan,Italy","institution_ids":["https://openalex.org/I93860229"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I93860229"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":"2024","issue":null,"first_page":"1","last_page":"4"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9925000071525574,"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":0.9925000071525574,"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":0.9725000262260437,"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/T11975","display_name":"Evolutionary Algorithms and Applications","score":0.9675999879837036,"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/backtracking","display_name":"Backtracking","score":0.9123344421386719},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7102922201156616},{"id":"https://openalex.org/keywords/optimization-algorithm","display_name":"Optimization algorithm","score":0.49385958909988403},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.46397122740745544},{"id":"https://openalex.org/keywords/algorithm-design","display_name":"Algorithm design","score":0.4115140438079834},{"id":"https://openalex.org/keywords/mathematical-optimization","display_name":"Mathematical optimization","score":0.29598453640937805},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.12063655257225037}],"concepts":[{"id":"https://openalex.org/C156884757","wikidata":"https://www.wikidata.org/wiki/Q798554","display_name":"Backtracking","level":2,"score":0.9123344421386719},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7102922201156616},{"id":"https://openalex.org/C2987595161","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Optimization algorithm","level":2,"score":0.49385958909988403},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.46397122740745544},{"id":"https://openalex.org/C106516650","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm design","level":2,"score":0.4115140438079834},{"id":"https://openalex.org/C126255220","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Mathematical optimization","level":1,"score":0.29598453640937805},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.12063655257225037}],"mesh":[{"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","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":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1109/embc53108.2024.10781891","is_oa":false,"landing_page_url":"https://doi.org/10.1109/embc53108.2024.10781891","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 46th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)","raw_type":"proceedings-article"},{"id":"pmid:40039311","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40039311","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":"Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference","raw_type":null},{"id":"pmh:oai:re.public.polimi.it:11311/1287281","is_oa":true,"landing_page_url":"https://hdl.handle.net/11311/1287281","pdf_url":null,"source":{"id":"https://openalex.org/S4306400312","display_name":"Virtual Community of Pathological Anatomy (University of Castilla La Mancha)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I79189158","host_organization_name":"University of Castilla-La Mancha","host_organization_lineage":["https://openalex.org/I79189158"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/conferenceObject"}],"best_oa_location":{"id":"pmh:oai:re.public.polimi.it:11311/1287281","is_oa":true,"landing_page_url":"https://hdl.handle.net/11311/1287281","pdf_url":null,"source":{"id":"https://openalex.org/S4306400312","display_name":"Virtual Community of Pathological Anatomy (University of Castilla La Mancha)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I79189158","host_organization_name":"University of Castilla-La Mancha","host_organization_lineage":["https://openalex.org/I79189158"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/conferenceObject"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":13,"referenced_works":["https://openalex.org/W2766525247","https://openalex.org/W2888300707","https://openalex.org/W2952366981","https://openalex.org/W3018787322","https://openalex.org/W3086678357","https://openalex.org/W3088400220","https://openalex.org/W4220680041","https://openalex.org/W4224278121","https://openalex.org/W4283734026","https://openalex.org/W4285226269","https://openalex.org/W4308878077","https://openalex.org/W4312613469","https://openalex.org/W6839675312"],"related_works":["https://openalex.org/W4366549320","https://openalex.org/W4287863136","https://openalex.org/W3006015132","https://openalex.org/W160089862","https://openalex.org/W2965078190","https://openalex.org/W3040644038","https://openalex.org/W4311207076","https://openalex.org/W4407317978","https://openalex.org/W2393888177","https://openalex.org/W2140656843"],"abstract_inverted_index":{"The":[0],"Human":[1],"Pangenome":[2],"Reference":[3],"Consortium":[4],"(HPRC)":[5],"proved":[6],"that":[7,135],"pangenome":[8],"graphs":[9],"represent":[10],"a":[11,31,114,125,150],"population\u2019s":[12],"genetic":[13],"variability":[14],"more":[15],"efficiently":[16],"and":[17,52,80,137,162],"accurately":[18],"than":[19],"linear":[20],"references.":[21],"Graphs":[22],"can":[23],"intrinsically":[24],"encode":[25],"variations":[26,79],"as":[27,93],"alternative":[28],"paths":[29],"inside":[30],"directed":[32],"set":[33],"of":[34,71,131],"sequence":[35],"nodes":[36],"connected":[37],"by":[38],"edges.":[39],"Despite":[40],"their":[41],"higher":[42],"complexity,":[43],"graph-based":[44],"genome":[45],"analysis":[46],"pipelines":[47],"are":[48],"gaining":[49],"significant":[50],"interest,":[51],"the":[53,68,86,94,105,132,139,143,158],"first":[54],"sequence-to-graph":[55],"aligners":[56],"have":[57],"already":[58],"shown":[59],"improvements":[60],"in":[61,65,117,142,153],"semi-global":[62],"alignment.":[63],"However,":[64,104],"pangenomics":[66],"studies,":[67],"global":[69],"alignment":[70,112],"long":[72,99],"reads":[73,100],"is":[74],"fundamental":[75],"for":[76,97],"identifying":[77],"structural":[78],"haplotype":[81],"phasing.":[82],"In":[83,120],"this":[84,121],"context,":[85],"Graph":[87],"Wavefront":[88],"Alignment":[89],"(GWFA)":[90],"algorithm":[91,134],"emerged":[92],"fastest":[95],"strategy":[96],"aligning":[98],"to":[101,157],"genomic":[102],"graphs.":[103],"available":[106],"GWFA":[107,133],"implementation":[108,130],"does":[109],"not":[110],"support":[111],"backtracking,":[113],"crucial":[115],"feature":[116],"real-case":[118],"studies.":[119],"paper,":[122],"we":[123],"propose":[124],"new":[126],"open-source<sup":[127],"xmlns:mml=\"http://www.w3.org/1998/Math/MathML\"":[128],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">1</sup>":[129],"computes":[136],"reports":[138],"complete":[140],"traceback":[141],"standard":[144],"GAF":[145],"format.":[146],"Our":[147],"work":[148],"achieves":[149],"20\u00d7":[151],"speedup":[152],"execution":[154],"time":[155],"compared":[156],"state-of-the-art":[159],"tool":[160],"GraphAligner":[161],"competitive":[163],"memory":[164],"usage.":[165]},"counts_by_year":[],"updated_date":"2026-07-15T18:14:33.161393","created_date":"2025-10-10T00:00:00"}
