{"id":"https://openalex.org/W4385789905","doi":"https://doi.org/10.3233/jifs-231897","title":"Classifying the bacterial taxonomy with its metagenomic data using the deep neural network model","display_name":"Classifying the bacterial taxonomy with its metagenomic data using the deep neural network model","publication_year":2023,"publication_date":"2023-08-13","ids":{"openalex":"https://openalex.org/W4385789905","doi":"https://doi.org/10.3233/jifs-231897"},"language":"en","primary_location":{"id":"doi:10.3233/jifs-231897","is_oa":false,"landing_page_url":"https://doi.org/10.3233/jifs-231897","pdf_url":null,"source":{"id":"https://openalex.org/S179157397","display_name":"Journal of Intelligent & Fuzzy Systems","issn_l":"1064-1246","issn":["1064-1246","1875-8967"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310318577","host_organization_name":"IOS Press","host_organization_lineage":["https://openalex.org/P4310318577"],"host_organization_lineage_names":["IOS Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Intelligent &amp; Fuzzy Systems","raw_type":"journal-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/A5072261829","display_name":"Ramakrishnan Raman","orcid":"https://orcid.org/0000-0003-3642-6989"},"institutions":[{"id":"https://openalex.org/I244572783","display_name":"Symbiosis International University","ror":"https://ror.org/005r2ww51","country_code":"IN","type":"education","lineage":["https://openalex.org/I244572783"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"Ramakrishnan Raman","raw_affiliation_strings":["Symbiosis Institute of Business Management, Pune & Symbiosis International (Deemed) University, Pune, India"],"affiliations":[{"raw_affiliation_string":"Symbiosis Institute of Business Management, Pune & Symbiosis International (Deemed) University, Pune, India","institution_ids":["https://openalex.org/I244572783"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077705857","display_name":"Amit Barve","orcid":null},"institutions":[{"id":"https://openalex.org/I9694494","display_name":"Parul University","ror":"https://ror.org/024v3fg07","country_code":"IN","type":"education","lineage":["https://openalex.org/I9694494"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Amit Barve","raw_affiliation_strings":["Department of Computer Science and Engineering, Parul Institute of Technology, Faculty of Engineering and Technology, Parul University, P.O. Limda, Gujarat, India"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Parul Institute of Technology, Faculty of Engineering and Technology, Parul University, P.O. Limda, Gujarat, India","institution_ids":["https://openalex.org/I9694494"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051558117","display_name":"R. Meenakshi","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"R. Meenakshi","raw_affiliation_strings":["Department of Computer Science and Engineering, Chennai Institute of Technology, Kundrathur, Tamil Nadu, India"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Chennai Institute of Technology, Kundrathur, Tamil Nadu, India","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060546076","display_name":"G. M. Jayaseelan","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"G.M. Jayaseelan","raw_affiliation_strings":["Skillsmith India, Ayapakkam, Chennai, Tamil Nadu, India"],"affiliations":[{"raw_affiliation_string":"Skillsmith India, Ayapakkam, Chennai, Tamil Nadu, India","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049515073","display_name":"P. Ganeshan","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"P. Ganeshan","raw_affiliation_strings":["Department of Mechanical Engineering, Sri Eshwar Engineering College, Coimbatore, Tamilnadu, India"],"affiliations":[{"raw_affiliation_string":"Department of Mechanical Engineering, Sri Eshwar Engineering College, Coimbatore, Tamilnadu, India","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038631452","display_name":"Syed Noeman Taqui","orcid":"https://orcid.org/0000-0002-3546-7212"},"institutions":[{"id":"https://openalex.org/I85461943","display_name":"Saveetha University","ror":"https://ror.org/0034me914","country_code":"IN","type":"education","lineage":["https://openalex.org/I85461943"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Syed Noeman Taqui","raw_affiliation_strings":["Department of VLSI Microelectronics, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai, Tamil Nadu, India"],"affiliations":[{"raw_affiliation_string":"Department of VLSI Microelectronics, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai, Tamil Nadu, India","institution_ids":["https://openalex.org/I85461943"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084805819","display_name":"Hesham S. Almoallim","orcid":null},"institutions":[{"id":"https://openalex.org/I28022161","display_name":"King Saud University","ror":"https://ror.org/02f81g417","country_code":"SA","type":"education","lineage":["https://openalex.org/I28022161"]}],"countries":["SA"],"is_corresponding":false,"raw_author_name":"Hesham S. Almoallim","raw_affiliation_strings":["Department of Oral and Maxillofacial Surgery, College of Dentistry, King Saud University, Riyadh, Saudi Arabia"],"affiliations":[{"raw_affiliation_string":"Department of Oral and Maxillofacial Surgery, College of Dentistry, King Saud University, Riyadh, Saudi Arabia","institution_ids":["https://openalex.org/I28022161"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012969367","display_name":"Sulaiman Ali Alharbi","orcid":"https://orcid.org/0000-0002-4196-2746"},"institutions":[{"id":"https://openalex.org/I28022161","display_name":"King Saud University","ror":"https://ror.org/02f81g417","country_code":"SA","type":"education","lineage":["https://openalex.org/I28022161"]}],"countries":["SA"],"is_corresponding":false,"raw_author_name":"Sulaiman Ali Alharbi","raw_affiliation_strings":["Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia"],"affiliations":[{"raw_affiliation_string":"Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia","institution_ids":["https://openalex.org/I28022161"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5079889129","display_name":"Shyam S. Raghavan","orcid":"https://orcid.org/0000-0002-3816-1542"},"institutions":[{"id":"https://openalex.org/I160606119","display_name":"University of Tennessee Health Science Center","ror":"https://ror.org/0011qv509","country_code":"US","type":"education","lineage":["https://openalex.org/I160606119"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"S.S. Raghavan","raw_affiliation_strings":["Department of Biology, University of Tennessee Health Science center, Memphis, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biology, University of Tennessee Health Science center, Memphis, USA","institution_ids":["https://openalex.org/I160606119"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5072261829"],"corresponding_institution_ids":["https://openalex.org/I244572783"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.27571256,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"45","issue":"5","first_page":"7603","last_page":"7618"},"is_retracted":true,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","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/T10015","display_name":"Genomics and Phylogenetic Studies","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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9901999831199646,"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":0.9724000096321106,"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/artificial-intelligence","display_name":"Artificial intelligence","score":0.7915722727775574},{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.6934307813644409},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6878527998924255},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.6386532783508301},{"id":"https://openalex.org/keywords/classifier","display_name":"Classifier (UML)","score":0.6023144721984863},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.5707330107688904},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.5391348600387573},{"id":"https://openalex.org/keywords/deep-belief-network","display_name":"Deep belief network","score":0.5372832417488098},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5104286074638367},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.4650932848453522},{"id":"https://openalex.org/keywords/categorization","display_name":"Categorization","score":0.43125343322753906},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.35158106684684753},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.15069124102592468}],"concepts":[{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.7915722727775574},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.6934307813644409},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6878527998924255},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.6386532783508301},{"id":"https://openalex.org/C95623464","wikidata":"https://www.wikidata.org/wiki/Q1096149","display_name":"Classifier (UML)","level":2,"score":0.6023144721984863},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.5707330107688904},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.5391348600387573},{"id":"https://openalex.org/C97385483","wikidata":"https://www.wikidata.org/wiki/Q16954980","display_name":"Deep belief network","level":3,"score":0.5372832417488098},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5104286074638367},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.4650932848453522},{"id":"https://openalex.org/C94124525","wikidata":"https://www.wikidata.org/wiki/Q912550","display_name":"Categorization","level":2,"score":0.43125343322753906},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.35158106684684753},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.15069124102592468},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.3233/jifs-231897","is_oa":false,"landing_page_url":"https://doi.org/10.3233/jifs-231897","pdf_url":null,"source":{"id":"https://openalex.org/S179157397","display_name":"Journal of Intelligent & Fuzzy Systems","issn_l":"1064-1246","issn":["1064-1246","1875-8967"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310318577","host_organization_name":"IOS Press","host_organization_lineage":["https://openalex.org/P4310318577"],"host_organization_lineage_names":["IOS Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Intelligent &amp; Fuzzy Systems","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":30,"referenced_works":["https://openalex.org/W1501213224","https://openalex.org/W1504967947","https://openalex.org/W1985657529","https://openalex.org/W1990116189","https://openalex.org/W2008528231","https://openalex.org/W2095648296","https://openalex.org/W2116410071","https://openalex.org/W2138785419","https://openalex.org/W2159008215","https://openalex.org/W2178155017","https://openalex.org/W2193346577","https://openalex.org/W2210461468","https://openalex.org/W2257287664","https://openalex.org/W2260894375","https://openalex.org/W2418536394","https://openalex.org/W2464743969","https://openalex.org/W2562468253","https://openalex.org/W2610577962","https://openalex.org/W2611595334","https://openalex.org/W2728183739","https://openalex.org/W2855293443","https://openalex.org/W2941555836","https://openalex.org/W2945285105","https://openalex.org/W2951160681","https://openalex.org/W2956023148","https://openalex.org/W2979348177","https://openalex.org/W3008594856","https://openalex.org/W3013482090","https://openalex.org/W3113074526","https://openalex.org/W6630052595"],"related_works":["https://openalex.org/W2165912799","https://openalex.org/W638577851","https://openalex.org/W2968354375","https://openalex.org/W2359440920","https://openalex.org/W2889550857","https://openalex.org/W3013372948","https://openalex.org/W3135997498","https://openalex.org/W4242417330","https://openalex.org/W2735662278","https://openalex.org/W3198631238"],"abstract_inverted_index":{"Because":[0],"of":[1,25,74,89,116],"the":[2,26,37,75,148,153,162,167,188,204,210,244,258,264,270,275],"two":[3,131],"sequenced":[4],"methods":[5],"stated":[6],"above,":[7],"SG":[8,53,285],"and":[9,91,108,111,141,158,195,228],"AMP,":[10],"are":[11],"being":[12],"used":[13,49,68,267],"in":[14,263],"different":[15],"ways,":[16],"present":[17],"a":[18,41,65,69,121,170,216,229,237,248,256],"deep":[19,133,137,230],"learning":[20,107,134,231],"methodology":[21,150],"for":[22,33,105,113,124,173,191,219,251,269],"taxonomic":[23,184],"categorization":[24],"metagenomic":[27,118,271],"information":[28],"which":[29],"could":[30,278],"be":[31,261,279],"utilized":[32,280],"either.":[34],"To":[35,98],"place":[36],"suggested":[38,215,245],"pipeline":[39],"to":[40,50,58,84,151,161,274,281],"trial,":[42],"1000":[43],"16":[44,220],"S":[45,221],"full-length":[46],"genomes":[47],"were":[48],"generate":[51],"either":[52,284],"or":[54,286],"AMP":[55,201,287],"short-reads.":[56],"Then,":[57],"map":[59],"sequencing":[60],"as":[61,247,255],"matrices":[62],"into":[63],"such":[64],"number":[66],"space,":[67],"k-mer":[70,226],"model.":[71],"Our":[72],"analysis":[73],"existing":[76],"approaches":[77],"revealed":[78],"several":[79],"drawbacks,":[80],"including":[81],"limited":[82],"ability":[83],"handle":[85],"complex":[86],"hierarchical":[87],"representations":[88,227],"data":[90],"suboptimal":[92],"feature":[93,106],"extraction":[94],"from":[95],"grid-like":[96,117],"structures.":[97],"overcome":[99],"these":[100],"limitations,":[101],"we":[102],"introduce":[103],"DBNs":[104],"dimensionality":[109],"reduction,":[110],"CNNs":[112],"efficient":[114],"processing":[115],"data.":[119],"Finally,":[120],"training":[122,130],"set":[123],"every":[125,183,234],"taxon":[126,235],"was":[127],"obtained":[128],"by":[129,166],"distinct":[132],"constructions,":[135],"specifically":[136],"belief":[138],"network":[139,144],"(DBN)":[140],"convolutional":[142],"neural":[143],"(CNN).":[145],"This":[146,213],"examined":[147],"proposed":[149],"determine":[152],"best":[154],"factor":[155],"that":[156,233],"determines":[157],"compared":[159],"findings":[160,242],"classification":[163,217,238],"abilities":[164],"offered":[165],"RDP":[168,180,205],"classifier,":[169],"standard":[171],"classifier":[172,206],"bacterium":[174,253],"identification.":[175],"These":[176],"designs":[177],"outperform":[178],"using":[179,200],"classifiers":[181],"at":[182,187],"level.":[185],"So,":[186],"genetic":[189],"level,":[190],"example,":[192],"both":[193],"CNN":[194],"DBN":[196],"achieved":[197,207],"91.4%":[198],"accuracy":[199],"short-reads,":[202],"but":[203],"83.9%":[208],"with":[209],"same":[211],"information.":[212,288],"paper,":[214],"method":[218],"short-read":[222],"sequences":[223],"created":[224],"on":[225],"structure,":[232],"creates":[236],"method.":[239],"The":[240],"experimental":[241],"validate":[243],"pipelines":[246],"realistic":[249],"strategy":[250],"classifying":[252],"samples;":[254],"result,":[257],"technique":[259],"might":[260],"included":[262],"most":[265],"commonly":[266],"tools":[268],"research.":[272],"According":[273],"outcomes,":[276],"it":[277],"effectively":[282],"classify":[283]},"counts_by_year":[],"updated_date":"2026-01-30T23:17:42.513302","created_date":"2025-10-10T00:00:00"}
