{"id":"https://openalex.org/W7126059752","doi":"https://doi.org/10.1109/bibm66473.2025.11357153","title":"SyAGram: Dual-Component Framework for Anti-Gram-Negative AMP Classification and Generation","display_name":"SyAGram: Dual-Component Framework for Anti-Gram-Negative AMP Classification and Generation","publication_year":2025,"publication_date":"2025-12-15","ids":{"openalex":"https://openalex.org/W7126059752","doi":"https://doi.org/10.1109/bibm66473.2025.11357153"},"language":null,"primary_location":{"id":"doi:10.1109/bibm66473.2025.11357153","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm66473.2025.11357153","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":"conference-paper","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/A5124215435","display_name":"Xinxiang Wang","orcid":null},"institutions":[{"id":"https://openalex.org/I12615008","display_name":"Beijing Normal-Hong Kong Baptist University","ror":"https://ror.org/04snvc712","country_code":"CN","type":"education","lineage":["https://openalex.org/I12615008"]},{"id":"https://openalex.org/I141568987","display_name":"Hong Kong Baptist University","ror":"https://ror.org/0145fw131","country_code":"HK","type":"education","lineage":["https://openalex.org/I141568987"]}],"countries":["CN","HK"],"is_corresponding":false,"raw_author_name":"Xinxiang Wang","raw_affiliation_strings":["Beijing Normal-Hong Kong Baptist University,*Guangdong Provincial/Zhuhai Key Laboratory IRADS,Zhuhai,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beijing Normal-Hong Kong Baptist University,*Guangdong Provincial/Zhuhai Key Laboratory IRADS,Zhuhai,China","institution_ids":["https://openalex.org/I12615008","https://openalex.org/I141568987"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083202487","display_name":"Xinze Li","orcid":"https://orcid.org/0009-0005-0035-6802"},"institutions":[{"id":"https://openalex.org/I12615008","display_name":"Beijing Normal-Hong Kong Baptist University","ror":"https://ror.org/04snvc712","country_code":"CN","type":"education","lineage":["https://openalex.org/I12615008"]},{"id":"https://openalex.org/I141568987","display_name":"Hong Kong Baptist University","ror":"https://ror.org/0145fw131","country_code":"HK","type":"education","lineage":["https://openalex.org/I141568987"]}],"countries":["CN","HK"],"is_corresponding":false,"raw_author_name":"Xinze Li","raw_affiliation_strings":["Beijing Normal-Hong Kong Baptist University,*Guangdong Provincial/Zhuhai Key Laboratory IRADS,Zhuhai,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beijing Normal-Hong Kong Baptist University,*Guangdong Provincial/Zhuhai Key Laboratory IRADS,Zhuhai,China","institution_ids":["https://openalex.org/I12615008","https://openalex.org/I141568987"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124178105","display_name":"Yue Guan","orcid":null},"institutions":[{"id":"https://openalex.org/I12615008","display_name":"Beijing Normal-Hong Kong Baptist University","ror":"https://ror.org/04snvc712","country_code":"CN","type":"education","lineage":["https://openalex.org/I12615008"]},{"id":"https://openalex.org/I141568987","display_name":"Hong Kong Baptist University","ror":"https://ror.org/0145fw131","country_code":"HK","type":"education","lineage":["https://openalex.org/I141568987"]}],"countries":["CN","HK"],"is_corresponding":false,"raw_author_name":"Yue Guan","raw_affiliation_strings":["Beijing Normal-Hong Kong Baptist University,*Guangdong Provincial/Zhuhai Key Laboratory IRADS,Zhuhai,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beijing Normal-Hong Kong Baptist University,*Guangdong Provincial/Zhuhai Key Laboratory IRADS,Zhuhai,China","institution_ids":["https://openalex.org/I12615008","https://openalex.org/I141568987"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124219328","display_name":"Feiyang Chen","orcid":null},"institutions":[{"id":"https://openalex.org/I12615008","display_name":"Beijing Normal-Hong Kong Baptist University","ror":"https://ror.org/04snvc712","country_code":"CN","type":"education","lineage":["https://openalex.org/I12615008"]},{"id":"https://openalex.org/I141568987","display_name":"Hong Kong Baptist University","ror":"https://ror.org/0145fw131","country_code":"HK","type":"education","lineage":["https://openalex.org/I141568987"]}],"countries":["CN","HK"],"is_corresponding":false,"raw_author_name":"Feiyang Chen","raw_affiliation_strings":["Beijing Normal-Hong Kong Baptist University,*Guangdong Provincial/Zhuhai Key Laboratory IRADS,Zhuhai,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beijing Normal-Hong Kong Baptist University,*Guangdong Provincial/Zhuhai Key Laboratory IRADS,Zhuhai,China","institution_ids":["https://openalex.org/I12615008","https://openalex.org/I141568987"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5120954443","display_name":"Pengxu Chen","orcid":null},"institutions":[{"id":"https://openalex.org/I194450716","display_name":"Jilin University","ror":"https://ror.org/00js3aw79","country_code":"CN","type":"education","lineage":["https://openalex.org/I194450716"]},{"id":"https://openalex.org/I4210134929","display_name":"Jilin Province Science and Technology Department","ror":"https://ror.org/049x38272","country_code":"CN","type":"government","lineage":["https://openalex.org/I4210134929"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Pengxu Chen","raw_affiliation_strings":["College of Computer Science and Technology, Jilin University,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Jilin University,China","institution_ids":["https://openalex.org/I194450716","https://openalex.org/I4210134929"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124250048","display_name":"Feng Yang","orcid":null},"institutions":[{"id":"https://openalex.org/I196699116","display_name":"Wuhan University of Technology","ror":"https://ror.org/03fe7t173","country_code":"CN","type":"education","lineage":["https://openalex.org/I196699116"]},{"id":"https://openalex.org/I43922553","display_name":"Wuhan University of Science and Technology","ror":"https://ror.org/00e4hrk88","country_code":"CN","type":"education","lineage":["https://openalex.org/I43922553"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Feng Yang","raw_affiliation_strings":["College of Computer Science and Technology, Wuhan University,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Wuhan University,China","institution_ids":["https://openalex.org/I196699116","https://openalex.org/I43922553"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100685937","display_name":"Jiaxing Chen","orcid":"https://orcid.org/0000-0003-4518-0941"},"institutions":[{"id":"https://openalex.org/I12615008","display_name":"Beijing Normal-Hong Kong Baptist University","ror":"https://ror.org/04snvc712","country_code":"CN","type":"education","lineage":["https://openalex.org/I12615008"]},{"id":"https://openalex.org/I141568987","display_name":"Hong Kong Baptist University","ror":"https://ror.org/0145fw131","country_code":"HK","type":"education","lineage":["https://openalex.org/I141568987"]}],"countries":["CN","HK"],"is_corresponding":false,"raw_author_name":"Jiaxing Chen","raw_affiliation_strings":["Beijing Normal-Hong Kong Baptist University,*Guangdong Provincial/Zhuhai Key Laboratory IRADS,Zhuhai,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beijing Normal-Hong Kong Baptist University,*Guangdong Provincial/Zhuhai Key Laboratory IRADS,Zhuhai,China","institution_ids":["https://openalex.org/I12615008","https://openalex.org/I141568987"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":[],"corresponding_institution_ids":[],"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":null,"issue":null,"first_page":"202","last_page":"207"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11103","display_name":"Antimicrobial Peptides and Activities","score":0.8393999934196472,"subfield":{"id":"https://openalex.org/subfields/2404","display_name":"Microbiology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11103","display_name":"Antimicrobial Peptides and Activities","score":0.8393999934196472,"subfield":{"id":"https://openalex.org/subfields/2404","display_name":"Microbiology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.10760000348091125,"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.013000000268220901,"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/classifier","display_name":"Classifier (UML)","score":0.5898000001907349},{"id":"https://openalex.org/keywords/peptide","display_name":"Peptide","score":0.4830999970436096},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.44029998779296875},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.4172999858856201},{"id":"https://openalex.org/keywords/encoder","display_name":"Encoder","score":0.39879998564720154}],"concepts":[{"id":"https://openalex.org/C95623464","wikidata":"https://www.wikidata.org/wiki/Q1096149","display_name":"Classifier (UML)","level":2,"score":0.5898000001907349},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5461000204086304},{"id":"https://openalex.org/C2779281246","wikidata":"https://www.wikidata.org/wiki/Q172847","display_name":"Peptide","level":2,"score":0.4830999970436096},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.44029998779296875},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4212000072002411},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.4172999858856201},{"id":"https://openalex.org/C118505674","wikidata":"https://www.wikidata.org/wiki/Q42586063","display_name":"Encoder","level":2,"score":0.39879998564720154},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.364300012588501},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3625999987125397},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.335999995470047},{"id":"https://openalex.org/C2780992000","wikidata":"https://www.wikidata.org/wiki/Q17016113","display_name":"Generator (circuit theory)","level":3,"score":0.3278999924659729},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.28049999475479126},{"id":"https://openalex.org/C34146451","wikidata":"https://www.wikidata.org/wiki/Q5048094","display_name":"Cascade","level":2,"score":0.27489998936653137},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.260699987411499},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.2524999976158142}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm66473.2025.11357153","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm66473.2025.11357153","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":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":23,"referenced_works":["https://openalex.org/W1978444624","https://openalex.org/W2588467130","https://openalex.org/W3145130117","https://openalex.org/W3154086429","https://openalex.org/W3206629920","https://openalex.org/W4226148785","https://openalex.org/W4226320060","https://openalex.org/W4310641985","https://openalex.org/W4322580799","https://openalex.org/W4324344300","https://openalex.org/W4327550249","https://openalex.org/W4382198814","https://openalex.org/W4389450648","https://openalex.org/W4390126076","https://openalex.org/W4390838129","https://openalex.org/W4391652414","https://openalex.org/W4392571650","https://openalex.org/W4402557213","https://openalex.org/W4403242149","https://openalex.org/W4407360649","https://openalex.org/W4408221130","https://openalex.org/W4408433527","https://openalex.org/W4409430637"],"related_works":[],"abstract_inverted_index":{"Gram-negative":[0],"bacteria":[1],"are":[2,14],"a":[3,29,39,46,60,96,135,145],"major":[4],"driver":[5],"of":[6,101,105],"antimicrobial":[7],"resistance,":[8],"yet":[9],"most":[10],"computational":[11],"AMP":[12],"methods":[13],"trained":[15],"for":[16,33,79,139],"broad-spectrum":[17],"performance":[18],"and":[19,54,75,91,113],"do":[20],"not":[21],"capture":[22],"outer-membrane":[23],"specific":[24],"constraints.":[25],"We":[26],"present":[27],"SyAGram,":[28],"dual-component":[30],"framework":[31],"specialized":[32],"anti-Gram-negative":[34],"peptide":[35,140],"discovery.":[36],"SyAGram-Synth":[37,94],"is":[38,59,148],"discrete":[40],"diffusion":[41],"generator":[42],"(D3PM)":[43],"guided":[44],"by":[45],"task-adapted":[47],"ESM-2":[48],"encoder":[49],"via":[50],"crossattention,":[51],"providing":[52],"stable":[53],"controllable":[55],"sequence":[56,66],"synthesis.":[57],"SyAGram-Pred":[58,85],"hybrid":[61],"classifier":[62],"that":[63],"fuses":[64],"BiLSTM-based":[65],"features":[67],"with":[68,103,129],"global":[69],"physicochemical":[70,126],"descriptors":[71],"to":[72],"reflect":[73],"charge":[74],"amphipathicity":[76],"patterns":[77],"critical":[78],"Gramnegative":[80,143],"activity.":[81],"On":[82],"curated":[83],"datasets,":[84],"attains":[86],"89.12%":[87],"accuracy,":[88],"91.53%":[89],"AUC,":[90],"90.06%":[92],"F1.":[93],"yields":[95],"mean":[97],"predicted":[98,107],"activity":[99],"score":[100],"0.856,":[102],"92%":[104],"sequences":[106],"active":[108],"(<tex":[109,119],"xmlns:mml=\"http://www.w3.org/1998/Math/MathML\"":[110,120],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">$\\geq":[111,121],"0.5$</tex>)":[112],"62.3":[114],"%":[115],"at":[116,150],"high":[117],"confidence":[118],"0.9$</tex>).":[122],"Generated":[123],"peptides":[124],"exhibit":[125],"profiles":[127],"consistent":[128],"natural":[130],"AMPs.":[131],"SyAGram":[132],"thus":[133],"offers":[134],"practical,":[136],"targeted":[137],"pipeline":[138],"design":[141],"against":[142],"pathogens;":[144],"web":[146],"demo":[147],"available":[149],"https://synergyg":[151],"ram-4lsud.ondigitalocean.app/.":[152]},"counts_by_year":[],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2026-01-30T00:00:00"}
