{"id":"https://openalex.org/W4411599976","doi":"https://doi.org/10.1109/jbhi.2025.3582652","title":"Phage Host Prediction Using Deep Neural Network With Multi-Source Protein Language Models and Squeeze-and-Excitation Attention Mechanism","display_name":"Phage Host Prediction Using Deep Neural Network With Multi-Source Protein Language Models and Squeeze-and-Excitation Attention Mechanism","publication_year":2025,"publication_date":"2025-06-24","ids":{"openalex":"https://openalex.org/W4411599976","doi":"https://doi.org/10.1109/jbhi.2025.3582652","pmid":"https://pubmed.ncbi.nlm.nih.gov/40553681"},"language":"en","primary_location":{"id":"doi:10.1109/jbhi.2025.3582652","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2025.3582652","pdf_url":null,"source":{"id":"https://openalex.org/S2495854775","display_name":"IEEE Journal of Biomedical and Health Informatics","issn_l":"2168-2194","issn":["2168-2194","2168-2208"],"is_oa":false,"is_in_doaj":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Journal of Biomedical and Health Informatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"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/A5007566560","display_name":"Peng Gao","orcid":"https://orcid.org/0000-0002-4963-2282"},"institutions":[{"id":"https://openalex.org/I180726961","display_name":"Shenzhen University","ror":"https://ror.org/01vy4gh70","country_code":"CN","type":"education","lineage":["https://openalex.org/I180726961"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Peng Gao","raw_affiliation_strings":["College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China","institution_ids":["https://openalex.org/I180726961"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102818415","display_name":"Long Xu","orcid":"https://orcid.org/0000-0003-2869-8474"},"institutions":[{"id":"https://openalex.org/I180726961","display_name":"Shenzhen University","ror":"https://ror.org/01vy4gh70","country_code":"CN","type":"education","lineage":["https://openalex.org/I180726961"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Long Xu","raw_affiliation_strings":["College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China","institution_ids":["https://openalex.org/I180726961"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101854884","display_name":"Yuan Bai","orcid":"https://orcid.org/0000-0002-8468-8118"},"institutions":[{"id":"https://openalex.org/I889458895","display_name":"University of Hong Kong","ror":"https://ror.org/02zhqgq86","country_code":"HK","type":"education","lineage":["https://openalex.org/I889458895"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Yuan Bai","raw_affiliation_strings":["School of Public Health, The University of Hong Kong, Hong Kong SAR, China","University of Hong Kong, Hong Kong, China"],"affiliations":[{"raw_affiliation_string":"School of Public Health, The University of Hong Kong, Hong Kong SAR, China","institution_ids":["https://openalex.org/I889458895"]},{"raw_affiliation_string":"University of Hong Kong, Hong Kong, China","institution_ids":["https://openalex.org/I889458895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066935890","display_name":"Qiuzhen Lin","orcid":"https://orcid.org/0000-0003-2415-0401"},"institutions":[{"id":"https://openalex.org/I180726961","display_name":"Shenzhen University","ror":"https://ror.org/01vy4gh70","country_code":"CN","type":"education","lineage":["https://openalex.org/I180726961"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qiuzhen Lin","raw_affiliation_strings":["College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China","institution_ids":["https://openalex.org/I180726961"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046906366","display_name":"Junkai Ji","orcid":"https://orcid.org/0000-0002-1985-938X"},"institutions":[{"id":"https://openalex.org/I180726961","display_name":"Shenzhen University","ror":"https://ror.org/01vy4gh70","country_code":"CN","type":"education","lineage":["https://openalex.org/I180726961"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Junkai Ji","raw_affiliation_strings":["National Engineering Laboratory for Big Data System Computing Technology, Shenzhen University, Shenzhen, China"],"affiliations":[{"raw_affiliation_string":"National Engineering Laboratory for Big Data System Computing Technology, Shenzhen University, Shenzhen, China","institution_ids":["https://openalex.org/I180726961"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5103127486","display_name":"Lijia Ma","orcid":"https://orcid.org/0000-0002-1201-8051"},"institutions":[{"id":"https://openalex.org/I180726961","display_name":"Shenzhen University","ror":"https://ror.org/01vy4gh70","country_code":"CN","type":"education","lineage":["https://openalex.org/I180726961"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lijia Ma","raw_affiliation_strings":["College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China","institution_ids":["https://openalex.org/I180726961"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5007566560"],"corresponding_institution_ids":["https://openalex.org/I180726961"],"apc_list":null,"apc_paid":null,"fwci":5.1578,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.94792609,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":91,"max":99},"biblio":{"volume":"30","issue":"2","first_page":"1759","last_page":"1771"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11048","display_name":"Bacteriophages and microbial interactions","score":0.9983000159263611,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11048","display_name":"Bacteriophages and microbial interactions","score":0.9983000159263611,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9980000257492065,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9736999869346619,"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/computer-science","display_name":"Computer science","score":0.7081822156906128},{"id":"https://openalex.org/keywords/mechanism","display_name":"Mechanism (biology)","score":0.6471782922744751},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.5980274677276611},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5243968367576599},{"id":"https://openalex.org/keywords/host","display_name":"Host (biology)","score":0.514821469783783},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.10972067713737488},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.10166352987289429}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7081822156906128},{"id":"https://openalex.org/C89611455","wikidata":"https://www.wikidata.org/wiki/Q6804646","display_name":"Mechanism (biology)","level":2,"score":0.6471782922744751},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.5980274677276611},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5243968367576599},{"id":"https://openalex.org/C126831891","wikidata":"https://www.wikidata.org/wiki/Q221673","display_name":"Host (biology)","level":2,"score":0.514821469783783},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.10972067713737488},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.10166352987289429},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001435","descriptor_name":"Bacteriophages","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001435","descriptor_name":"Bacteriophages","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001435","descriptor_name":"Bacteriophages","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"descriptor_ui":"D001435","descriptor_name":"Bacteriophages","qualifier_ui":"Q000502","qualifier_name":"physiology","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":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1109/jbhi.2025.3582652","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2025.3582652","pdf_url":null,"source":{"id":"https://openalex.org/S2495854775","display_name":"IEEE Journal of Biomedical and Health Informatics","issn_l":"2168-2194","issn":["2168-2194","2168-2208"],"is_oa":false,"is_in_doaj":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Journal of Biomedical and Health Informatics","raw_type":"journal-article"},{"id":"pmid:40553681","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40553681","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":"IEEE journal of biomedical and health informatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":56,"referenced_works":["https://openalex.org/W2076048958","https://openalex.org/W2104933073","https://openalex.org/W2112796928","https://openalex.org/W2119168155","https://openalex.org/W2122111042","https://openalex.org/W2132791018","https://openalex.org/W2148143831","https://openalex.org/W2153635508","https://openalex.org/W2168508521","https://openalex.org/W2194775991","https://openalex.org/W2295598076","https://openalex.org/W2345960958","https://openalex.org/W2514983714","https://openalex.org/W2734399491","https://openalex.org/W2752782242","https://openalex.org/W2767759966","https://openalex.org/W2808071711","https://openalex.org/W2896457183","https://openalex.org/W2911844640","https://openalex.org/W2951692438","https://openalex.org/W2995514860","https://openalex.org/W3051688178","https://openalex.org/W3082096568","https://openalex.org/W3121345102","https://openalex.org/W3122809531","https://openalex.org/W3133773931","https://openalex.org/W3146944767","https://openalex.org/W3147885797","https://openalex.org/W3171187312","https://openalex.org/W3177500196","https://openalex.org/W3196522895","https://openalex.org/W3200765011","https://openalex.org/W3215755691","https://openalex.org/W4205954540","https://openalex.org/W4206677002","https://openalex.org/W4220964139","https://openalex.org/W4226147938","https://openalex.org/W4226426165","https://openalex.org/W4287887523","https://openalex.org/W4310012181","https://openalex.org/W4327550249","https://openalex.org/W4360994011","https://openalex.org/W4384643940","https://openalex.org/W4385212722","https://openalex.org/W4385245566","https://openalex.org/W4386980190","https://openalex.org/W4387447837","https://openalex.org/W4389235782","https://openalex.org/W4390905493","https://openalex.org/W4391766310","https://openalex.org/W4392693790","https://openalex.org/W4392811737","https://openalex.org/W4393641017","https://openalex.org/W4400762160","https://openalex.org/W4403210286","https://openalex.org/W4406308609"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"Phage":[0],"therapy":[1],"(PT)":[2],"has":[3],"become":[4],"a":[5,40,91,151,158,169,181],"promising":[6],"alternative":[7],"for":[8,98,187],"treating":[9],"infections":[10],"with":[11],"the":[12,44,66,77,119,144,175,196],"increase":[13],"of":[14,35,84,177],"antimicrobial":[15],"resistance.":[16],"PT":[17],"utilizes":[18],"phages":[19,54],"to":[20,22,51,55,117,138,162,173],"bind":[21],"specific":[23],"receptors":[24],"on":[25,101],"bacterial":[26],"surfaces":[27],"via":[28],"receptor-binding":[29],"proteins":[30],"(RBPs),":[31],"enabling":[32],"precise":[33],"destruction":[34],"targeted":[36],"hosts.":[37,57],"In":[38,86,104],"PT,":[39],"key":[41],"issue":[42],"is":[43,185],"phage":[45,102],"host":[46,188,199],"prediction":[47,200],"(PHP),":[48],"which":[49,156],"tries":[50],"match":[52],"therapeutic":[53],"pathogenic":[56],"However,":[58],"traditional":[59],"PHP":[60,99],"methods":[61,75],"are":[62],"often":[63],"hindered":[64],"by":[65],"time-consuming":[67],"and":[68,80,115,128,167,204],"expensive":[69],"wet-lab":[70],"experiments,":[71],"while":[72],"recent":[73],"computational":[74],"neglect":[76],"evolutionary":[78],"diversity":[79],"local":[81,164],"feature":[82],"patterns":[83],"RBPs.":[85,103],"this":[87],"article,":[88],"we":[89,106,132,149],"propose":[90],"novel":[92],"deep":[93,152],"neural":[94,153,160],"network":[95,154,161,184],"(called":[96],"PHPRBP)":[97],"based":[100],"PHPRBP,":[105],"first":[107],"utilize":[108],"pre-trained":[109],"protein":[110],"language":[111],"models":[112],"(i.e.,":[113],"ESM2":[114],"ProtT5)":[116],"learn":[118],"multi-source":[120],"embedding":[121],"representations":[122],"from":[123],"these":[124],"RBPs,":[125],"revealing":[126],"diverse":[127],"complementary":[129],"features.":[130,179],"Then,":[131],"employ":[133],"an":[134],"adaptive":[135],"synthetic":[136],"technique":[137],"augment":[139],"minority":[140],"class":[141],"samples,":[142],"addressing":[143],"data":[145],"scarcity":[146],"issue.":[147],"Subsequently,":[148],"design":[150],"architecture,":[155],"uses":[157],"convolutional":[159],"capture":[163],"sequence":[165],"features,":[166],"applies":[168],"squeeze-and-excitation":[170],"attention":[171],"mechanism":[172],"enhance":[174],"contribution":[176],"important":[178],"Finally,":[180],"fully":[182],"connected":[183],"used":[186],"prediction.":[189],"Experimental":[190],"results":[191],"show":[192],"that":[193],"PHPRBP":[194],"outperforms":[195],"state-of-the-arts":[197],"in":[198],"at":[201],"both":[202],"genus":[203],"species":[205],"levels.":[206]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":1}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
