{"id":"https://openalex.org/W4413966911","doi":"https://doi.org/10.1109/access.2025.3605681","title":"Phylogeny Reconstruction Using Multi-Agent Surface Area Pressure Features","display_name":"Phylogeny Reconstruction Using Multi-Agent Surface Area Pressure Features","publication_year":2025,"publication_date":"2025-01-01","ids":{"openalex":"https://openalex.org/W4413966911","doi":"https://doi.org/10.1109/access.2025.3605681"},"language":"en","primary_location":{"id":"doi:10.1109/access.2025.3605681","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2025.3605681","pdf_url":null,"source":{"id":"https://openalex.org/S2485537415","display_name":"IEEE Access","issn_l":"2169-3536","issn":["2169-3536"],"is_oa":true,"is_in_doaj":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Access","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1109/access.2025.3605681","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5027571861","display_name":"Md. Sayeed Iftekhar Yousuf","orcid":"https://orcid.org/0000-0003-0918-8532"},"institutions":[{"id":"https://openalex.org/I894293524","display_name":"University of Chittagong","ror":"https://ror.org/01173vs27","country_code":"BD","type":"education","lineage":["https://openalex.org/I894293524"]}],"countries":["BD"],"is_corresponding":true,"raw_author_name":"Md Sayeed Iftekhar Yousuf","raw_affiliation_strings":["Department of Computer Science and Engineering, University of Chittagong, Chittagong, Bangladesh"],"raw_orcid":"https://orcid.org/0000-0003-0918-8532","affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, University of Chittagong, Chittagong, Bangladesh","institution_ids":["https://openalex.org/I894293524"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101860722","display_name":"Machbah Uddin","orcid":"https://orcid.org/0000-0002-1572-8606"},"institutions":[{"id":"https://openalex.org/I24057909","display_name":"Bangladesh Agricultural University","ror":"https://ror.org/03k5zb271","country_code":"BD","type":"education","lineage":["https://openalex.org/I24057909"]}],"countries":["BD"],"is_corresponding":false,"raw_author_name":"Machbah Uddin","raw_affiliation_strings":["Department of Computer Science and Mathematics, Bangladesh Agricultural University, Mymensingh, Bangladesh"],"raw_orcid":"https://orcid.org/0000-0002-1572-8606","affiliations":[{"raw_affiliation_string":"Department of Computer Science and Mathematics, Bangladesh Agricultural University, Mymensingh, Bangladesh","institution_ids":["https://openalex.org/I24057909"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060130297","display_name":"Mohammad Khairul Islam","orcid":"https://orcid.org/0000-0001-5432-1406"},"institutions":[{"id":"https://openalex.org/I894293524","display_name":"University of Chittagong","ror":"https://ror.org/01173vs27","country_code":"BD","type":"education","lineage":["https://openalex.org/I894293524"]}],"countries":["BD"],"is_corresponding":false,"raw_author_name":"Mohammad Khairul Islam","raw_affiliation_strings":["Department of Computer Science and Engineering, University of Chittagong, Chittagong, Bangladesh"],"raw_orcid":"https://orcid.org/0000-0001-5432-1406","affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, University of Chittagong, Chittagong, Bangladesh","institution_ids":["https://openalex.org/I894293524"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050445420","display_name":"Md. Rakib Hassan","orcid":"https://orcid.org/0000-0001-9368-6942"},"institutions":[{"id":"https://openalex.org/I24057909","display_name":"Bangladesh Agricultural University","ror":"https://ror.org/03k5zb271","country_code":"BD","type":"education","lineage":["https://openalex.org/I24057909"]}],"countries":["BD"],"is_corresponding":false,"raw_author_name":"Md Rakib Hasan","raw_affiliation_strings":["Department of Computer Science and Mathematics, Bangladesh Agricultural University, Mymensingh, Bangladesh"],"raw_orcid":"https://orcid.org/0000-0001-9368-6942","affiliations":[{"raw_affiliation_string":"Department of Computer Science and Mathematics, Bangladesh Agricultural University, Mymensingh, Bangladesh","institution_ids":["https://openalex.org/I24057909"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5004785444","display_name":"Farah Jahan","orcid":"https://orcid.org/0000-0001-9991-9575"},"institutions":[{"id":"https://openalex.org/I894293524","display_name":"University of Chittagong","ror":"https://ror.org/01173vs27","country_code":"BD","type":"education","lineage":["https://openalex.org/I894293524"]}],"countries":["BD"],"is_corresponding":false,"raw_author_name":"Farah Jahan","raw_affiliation_strings":["Department of Computer Science and Engineering, University of Chittagong, Chittagong, Bangladesh"],"raw_orcid":"https://orcid.org/0000-0001-9991-9575","affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, University of Chittagong, Chittagong, Bangladesh","institution_ids":["https://openalex.org/I894293524"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5027571861"],"corresponding_institution_ids":["https://openalex.org/I894293524"],"apc_list":{"value":1850,"currency":"USD","value_usd":1850},"apc_paid":{"value":1850,"currency":"USD","value_usd":1850},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.19477828,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"13","issue":null,"first_page":"156188","last_page":"156202"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9714999794960022,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9714999794960022,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9671000242233276,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T10591","display_name":"Theoretical and Computational Physics","score":0.9560999870300293,"subfield":{"id":"https://openalex.org/subfields/3104","display_name":"Condensed Matter Physics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/surface-reconstruction","display_name":"Surface reconstruction","score":0.5946351289749146},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.591340959072113},{"id":"https://openalex.org/keywords/surface","display_name":"Surface (topology)","score":0.3421633541584015},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.12659534811973572},{"id":"https://openalex.org/keywords/geometry","display_name":"Geometry","score":0.08799928426742554}],"concepts":[{"id":"https://openalex.org/C20885615","wikidata":"https://www.wikidata.org/wiki/Q825595","display_name":"Surface reconstruction","level":3,"score":0.5946351289749146},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.591340959072113},{"id":"https://openalex.org/C2776799497","wikidata":"https://www.wikidata.org/wiki/Q484298","display_name":"Surface (topology)","level":2,"score":0.3421633541584015},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.12659534811973572},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.08799928426742554}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/access.2025.3605681","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2025.3605681","pdf_url":null,"source":{"id":"https://openalex.org/S2485537415","display_name":"IEEE Access","issn_l":"2169-3536","issn":["2169-3536"],"is_oa":true,"is_in_doaj":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Access","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:839d887f8c74410881b80ed25bce9b54","is_oa":true,"landing_page_url":"https://doaj.org/article/839d887f8c74410881b80ed25bce9b54","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"IEEE Access, Vol 13, Pp 156188-156202 (2025)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1109/access.2025.3605681","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2025.3605681","pdf_url":null,"source":{"id":"https://openalex.org/S2485537415","display_name":"IEEE Access","issn_l":"2169-3536","issn":["2169-3536"],"is_oa":true,"is_in_doaj":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Access","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320316035","display_name":"University Grants Commission of Bangladesh","ror":"https://ror.org/04jtt0w10"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":66,"referenced_works":["https://openalex.org/W364444290","https://openalex.org/W608159890","https://openalex.org/W2003297364","https://openalex.org/W2006075770","https://openalex.org/W2009896347","https://openalex.org/W2022677086","https://openalex.org/W2102502076","https://openalex.org/W2117484859","https://openalex.org/W2125121305","https://openalex.org/W2132926880","https://openalex.org/W2149792928","https://openalex.org/W2568830712","https://openalex.org/W2754950010","https://openalex.org/W2756169797","https://openalex.org/W2761430568","https://openalex.org/W2781617831","https://openalex.org/W2809852815","https://openalex.org/W2815392379","https://openalex.org/W2891646971","https://openalex.org/W2891675266","https://openalex.org/W2919121574","https://openalex.org/W2950996529","https://openalex.org/W2962807110","https://openalex.org/W2963607348","https://openalex.org/W2977620381","https://openalex.org/W2999125722","https://openalex.org/W3000394202","https://openalex.org/W3008164819","https://openalex.org/W3008730728","https://openalex.org/W3021969064","https://openalex.org/W3025857586","https://openalex.org/W3033870872","https://openalex.org/W3047758698","https://openalex.org/W3094775423","https://openalex.org/W3104455460","https://openalex.org/W3111995113","https://openalex.org/W3157823684","https://openalex.org/W3164066860","https://openalex.org/W3194665116","https://openalex.org/W3196731440","https://openalex.org/W3202942824","https://openalex.org/W3204148984","https://openalex.org/W3208025896","https://openalex.org/W4206311651","https://openalex.org/W4221107627","https://openalex.org/W4221128536","https://openalex.org/W4226066396","https://openalex.org/W4229000355","https://openalex.org/W4281253663","https://openalex.org/W4285740661","https://openalex.org/W4286110908","https://openalex.org/W4292136218","https://openalex.org/W4292553223","https://openalex.org/W4293255502","https://openalex.org/W4297493168","https://openalex.org/W4307236031","https://openalex.org/W4308921565","https://openalex.org/W4312875106","https://openalex.org/W4313256701","https://openalex.org/W4318071537","https://openalex.org/W4323060104","https://openalex.org/W4360908940","https://openalex.org/W4384080192","https://openalex.org/W4385483417","https://openalex.org/W4386025199","https://openalex.org/W4393312730"],"related_works":["https://openalex.org/W2064026934","https://openalex.org/W2083481614","https://openalex.org/W3095081273","https://openalex.org/W2090665771","https://openalex.org/W2169427544","https://openalex.org/W1984855422","https://openalex.org/W122154308","https://openalex.org/W33542082","https://openalex.org/W2391505850","https://openalex.org/W2384105963"],"abstract_inverted_index":{"Phylogenetic":[0],"analysis":[1],"of":[2,12,64,76,159,168,182,247],"species":[3],"is":[4,146,149,200,210,214],"essential":[5],"for":[6,105,178,216],"understanding":[7],"the":[8,61,73,156,166,169,179,197,207,233,264],"various":[9],"biological":[10],"activities":[11],"an":[13],"organism,":[14],"including":[15,110],"gene":[16],"editing,":[17],"drug":[18],"design,":[19],"and":[20,68,112,152,173,212,220,232,270],"vaccine":[21],"development.":[22],"Traditional":[23],"alignment-based":[24],"(AB)":[25],"methods,":[26,254],"however,":[27,95],"face":[28],"significant":[29,79],"computational":[30,65,248],"challenges,":[31],"becoming":[32],"<italic":[33,170,183,193],"xmlns:mml=\"http://www.w3.org/1998/Math/MathML\"":[34,171,184,194],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">NP</i>-hard":[35],"when":[36],"applied":[37],"to":[38,59,72,126,134,190,258],"large":[39],"or":[40],"medium-sized":[41],"sequences.":[42,131],"As":[43],"a":[44,137,160,175,191],"result,":[45],"alignment-free":[46],"(AF)":[47],"approaches":[48,91],"have":[49,88,115],"gained":[50],"attraction.":[51],"Despite":[52],"their":[53],"growing":[54],"popularity,":[55],"AF":[56,77],"methods":[57,121],"struggle":[58],"optimize":[60],"critical":[62],"aspects":[63],"time,":[66,249],"accuracy,":[67],"memory":[69],"usage.":[70],"Due":[71],"time":[74],"inefficiency":[75],"approaches,":[78,109],"man-hours":[80],"are":[81,97,122,272],"wasted":[82],"in":[83,129,154,245],"laboratories.":[84],"Consequently,":[85],"different":[86],"studies":[87],"employed":[89],"statistical":[90],"on":[92,229],"entire":[93],"sequences;":[94],"these":[96,135],"less":[98],"efficient":[99,153],"because":[100],"they":[101],"lose":[102],"positional":[103,180,198],"information,":[104],"which":[106,148,206],"relative":[107,157,203],"information-based":[108],"entropy":[111],"joint":[113],"probability,":[114],"achieved":[116,238],"higher":[117],"performance.":[118],"However,":[119],"entropy-based":[120],"not":[123],"highly":[124,150],"sensitive":[125,151],"small":[127],"changes":[128],"DNA":[130,161],"In":[132],"response":[133],"limitations,":[136],"novel":[138],"multi-agent":[139],"surface":[140],"area":[141],"pressure":[142],"(MASAP)":[143],"feature-based":[144],"method":[145,236],"proposed,":[147],"representing":[155],"information":[158,181],"sequence.":[162],"First,":[163],"it":[164],"selects":[165],"length":[167],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">k</i>-mer":[172],"constructs":[174],"2D":[176],"list":[177],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">k</i>-mers,":[185],"where":[186],"each":[187],"row":[188],"corresponds":[189],"specific":[192],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">k</i>-mer.":[195],"Subsequently,":[196],"data":[199,204],"converted":[201],"into":[202],"from":[205],"MASAP":[208,235,250],"feature":[209,217],"derived,":[211],"this":[213],"used":[215],"descriptor":[218],"generation":[219],"phylogenetic":[221],"tree":[222],"reconstruction.":[223],"Extensive":[224],"experiments":[225],"were":[226],"carried":[227],"out":[228],"benchmark":[230],"datasets,":[231],"proposed":[234],"consistently":[237],"top-ranked":[239],"accuracy":[240],"across":[241],"all":[242],"datasets.":[243],"Furthermore,":[244],"terms":[246],"significantly":[251],"outperforms":[252],"existing":[253],"being":[255],"5,":[256],"151":[257],"8,":[259],"162":[260],"times":[261],"faster":[262],"than":[263],"MEGA":[265],"tool.":[266],"The":[267],"source":[268],"code":[269],"datasets":[271],"available":[273],"at":[274],"https://github.com/machbah/MASP.":[275]},"counts_by_year":[],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}
