{"id":"https://openalex.org/W7126056066","doi":"https://doi.org/10.1109/bibm66473.2025.11356246","title":"An Effective VAE-Based Framework with Triple-Stage Training Strategy for Generating Antibiotics Treating Salmonella","display_name":"An Effective VAE-Based Framework with Triple-Stage Training Strategy for Generating Antibiotics Treating Salmonella","publication_year":2025,"publication_date":"2025-12-15","ids":{"openalex":"https://openalex.org/W7126056066","doi":"https://doi.org/10.1109/bibm66473.2025.11356246"},"language":null,"primary_location":{"id":"doi:10.1109/bibm66473.2025.11356246","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm66473.2025.11356246","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2025 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-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/A5124151577","display_name":"Yanwei Ma","orcid":null},"institutions":[{"id":"https://openalex.org/I40963666","display_name":"Central China Normal University","ror":"https://ror.org/03x1jna21","country_code":"CN","type":"education","lineage":["https://openalex.org/I40963666"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yanwei Ma","raw_affiliation_strings":["Central China Normal University,Hubei Provincial Key Laboratory of Artificial Intelligence and Smart Learning,Wuhan,Hubei,PR China,430079"],"affiliations":[{"raw_affiliation_string":"Central China Normal University,Hubei Provincial Key Laboratory of Artificial Intelligence and Smart Learning,Wuhan,Hubei,PR China,430079","institution_ids":["https://openalex.org/I40963666"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124259547","display_name":"Yue Gou","orcid":null},"institutions":[{"id":"https://openalex.org/I40963666","display_name":"Central China Normal University","ror":"https://ror.org/03x1jna21","country_code":"CN","type":"education","lineage":["https://openalex.org/I40963666"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yue Gou","raw_affiliation_strings":["Central China Normal University,Hubei Provincial Key Laboratory of Artificial Intelligence and Smart Learning,Wuhan,Hubei,PR China,430079"],"affiliations":[{"raw_affiliation_string":"Central China Normal University,Hubei Provincial Key Laboratory of Artificial Intelligence and Smart Learning,Wuhan,Hubei,PR China,430079","institution_ids":["https://openalex.org/I40963666"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5121481513","display_name":"Yiting Shen","orcid":null},"institutions":[{"id":"https://openalex.org/I74525822","display_name":"Hubei University of Technology","ror":"https://ror.org/02d3fj342","country_code":"CN","type":"education","lineage":["https://openalex.org/I74525822"]},{"id":"https://openalex.org/I91125648","display_name":"Wuhan Institute of Technology","ror":"https://ror.org/04jcykh16","country_code":"CN","type":"education","lineage":["https://openalex.org/I91125648"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yiting Shen","raw_affiliation_strings":["Detroit Green Technology Institute, Hubei University of Technology,Wuhan,Hubei,PR China,430079"],"affiliations":[{"raw_affiliation_string":"Detroit Green Technology Institute, Hubei University of Technology,Wuhan,Hubei,PR China,430079","institution_ids":["https://openalex.org/I74525822","https://openalex.org/I91125648"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5121420414","display_name":"Weizhong Zhao","orcid":null},"institutions":[{"id":"https://openalex.org/I40963666","display_name":"Central China Normal University","ror":"https://ror.org/03x1jna21","country_code":"CN","type":"education","lineage":["https://openalex.org/I40963666"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Weizhong Zhao","raw_affiliation_strings":["Central China Normal University,Hubei Provincial Key Laboratory of Artificial Intelligence and Smart Learning,Wuhan,Hubei,PR China,430079"],"affiliations":[{"raw_affiliation_string":"Central China Normal University,Hubei Provincial Key Laboratory of Artificial Intelligence and Smart Learning,Wuhan,Hubei,PR China,430079","institution_ids":["https://openalex.org/I40963666"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5124151577"],"corresponding_institution_ids":["https://openalex.org/I40963666"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.75522243,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"681","last_page":"686"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.8555999994277954,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.8555999994277954,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.05510000139474869,"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":0.024000000208616257,"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/antibiotics","display_name":"Antibiotics","score":0.7265999913215637},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.545199990272522},{"id":"https://openalex.org/keywords/salmonella","display_name":"Salmonella","score":0.4345000088214874},{"id":"https://openalex.org/keywords/autoencoder","display_name":"Autoencoder","score":0.35929998755455017},{"id":"https://openalex.org/keywords/antibiotic-resistance","display_name":"Antibiotic resistance","score":0.31139999628067017}],"concepts":[{"id":"https://openalex.org/C501593827","wikidata":"https://www.wikidata.org/wiki/Q12187","display_name":"Antibiotics","level":2,"score":0.7265999913215637},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.545199990272522},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.46639999747276306},{"id":"https://openalex.org/C2781065037","wikidata":"https://www.wikidata.org/wiki/Q150839","display_name":"Salmonella","level":3,"score":0.4345000088214874},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.41830000281333923},{"id":"https://openalex.org/C101738243","wikidata":"https://www.wikidata.org/wiki/Q786435","display_name":"Autoencoder","level":3,"score":0.35929998755455017},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.34880000352859497},{"id":"https://openalex.org/C94665300","wikidata":"https://www.wikidata.org/wiki/Q63391344","display_name":"Antibiotic resistance","level":3,"score":0.31139999628067017},{"id":"https://openalex.org/C184337299","wikidata":"https://www.wikidata.org/wiki/Q1437428","display_name":"Semantics (computer science)","level":2,"score":0.2957000136375427},{"id":"https://openalex.org/C177713679","wikidata":"https://www.wikidata.org/wiki/Q679690","display_name":"Intensive care medicine","level":1,"score":0.2854999899864197},{"id":"https://openalex.org/C161624437","wikidata":"https://www.wikidata.org/wiki/Q1988322","display_name":"Small molecule","level":2,"score":0.27410000562667847},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2736999988555908},{"id":"https://openalex.org/C138816342","wikidata":"https://www.wikidata.org/wiki/Q189603","display_name":"Public health","level":2,"score":0.2734000086784363},{"id":"https://openalex.org/C150903083","wikidata":"https://www.wikidata.org/wiki/Q7108","display_name":"Biotechnology","level":1,"score":0.27300000190734863},{"id":"https://openalex.org/C112930515","wikidata":"https://www.wikidata.org/wiki/Q4389547","display_name":"Risk analysis (engineering)","level":1,"score":0.26080000400543213}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm66473.2025.11356246","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm66473.2025.11356246","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2025 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"No poverty","id":"https://metadata.un.org/sdg/1","score":0.6525356769561768}],"awards":[{"id":"https://openalex.org/G3221909189","display_name":null,"funder_award_id":"62472192,62372205","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":19,"referenced_works":["https://openalex.org/W116732074","https://openalex.org/W2059787259","https://openalex.org/W2101997581","https://openalex.org/W2786822213","https://openalex.org/W3011719258","https://openalex.org/W3209056694","https://openalex.org/W4207082850","https://openalex.org/W4220819798","https://openalex.org/W4243575454","https://openalex.org/W4251010148","https://openalex.org/W4291020097","https://openalex.org/W4311219784","https://openalex.org/W4387541094","https://openalex.org/W4392775277","https://openalex.org/W4393190824","https://openalex.org/W4399138888","https://openalex.org/W4400389945","https://openalex.org/W4408149544","https://openalex.org/W4409726076"],"related_works":[],"abstract_inverted_index":{"Salmonella":[0,96,183,254],"infections":[1],"pose":[2],"a":[3,22,100,123,152,176,244],"significant":[4],"global":[5,38],"public":[6],"health":[7],"threat,":[8],"and":[9,35,40,72,113,219,237],"the":[10,27,37,108,136,141,163,169,190,210,228,248],"emergence":[11],"of":[12,24,29,42,110,125,148,155,179,223,250],"multi-drug":[13],"resistant":[14],"strains":[15],"has":[16,45],"left":[17],"traditional":[18,30],"antibiotic":[19,31,93,157,173],"agents":[20],"in":[21,61,98,145],"predicament":[23],"ineffectiveness.":[25],"Since":[26],"development":[28,41,249],"drugs":[32,130],"is":[33,104,131,159,185,231],"costly":[34],"time-consuming,":[36],"research":[39],"novel":[43],"antibiotics":[44,63,181,251],"nearly":[46],"stagnated":[47],"at":[48],"present.":[49],"Although":[50],"several":[51,200],"generative":[52],"molecular":[53,202],"design":[54],"models":[55],"have":[56],"been":[57],"proposed,":[58],"their":[59],"application":[60],"generating":[62,92],"targeting":[64,95],"specific":[65,194],"pathogens":[66,184],"suffers":[67],"from":[68],"undesirable":[69],"antibacterial":[70,240],"efficacy":[71,112],"poor":[73,111],"diversity":[74,115],"due":[75],"to":[76,106,134,139,161,167,187,213,233,247],"limited":[77],"training":[78,102],"data.":[79],"In":[80,197],"this":[81],"paper,":[82],"we":[83],"propose":[84],"an":[85],"effective":[86,236],"Variational":[87],"AutoEncoder":[88],"(VAE)":[89],"framework":[90,138,166,230],"for":[91,116],"molecules":[94,158,192,215],"bacteria,":[97],"which":[99],"triple-stage":[101],"strategy":[103],"utilized":[105,186],"address":[107],"issues":[109],"low":[114],"existing":[117],"molecule":[118,129],"generation":[119],"models.":[120],"More":[121],"specifically,":[122],"set":[124,154,178],"all":[126,156,180],"available":[127],"small":[128,149],"first":[132],"used":[133],"pre-train":[135],"VAE-based":[137],"capture":[140],"general":[142],"semantics":[143,171],"contained":[144],"various":[146],"types":[147],"molecules.":[150],"Then,":[151],"mediumsize":[153],"employed":[160],"fine-tune":[162],"pre-trained":[164],"VAE":[165,211],"learn":[168],"fine-grained":[170],"among":[172],"agents.":[174],"Finally,":[175],"small-size":[177],"treating":[182],"optimize":[188],"further":[189],"generated":[191],"with":[193,216],"anti-Salmonella":[195],"activity.":[196],"addition,":[198],"introducing":[199],"key":[201],"properties":[203],"as":[204],"conditional":[205],"input":[206],"can":[207],"effectively":[208],"guide":[209],"model":[212],"generate":[214,234],"ideal":[217],"absorption":[218],"metabolic":[220],"properties.":[221],"Results":[222],"comprehensive":[224],"experiments":[225],"show":[226],"that":[227],"proposed":[229],"able":[232],"highly":[235],"structurally":[238],"diverse":[239],"candidate":[241],"molecules,":[242],"providing":[243],"feasible":[245],"solution":[246],"against":[252],"drug-resistant":[253],"pathogens.":[255]},"counts_by_year":[],"updated_date":"2026-04-09T08:11:56.329763","created_date":"2026-01-30T00:00:00"}
