{"id":"https://openalex.org/W4384643940","doi":"https://doi.org/10.1093/bib/bbad239","title":"Zero-shot-capable identification of phage\u2013host relationships with whole-genome sequence representation by contrastive learning","display_name":"Zero-shot-capable identification of phage\u2013host relationships with whole-genome sequence representation by contrastive learning","publication_year":2023,"publication_date":"2023-07-18","ids":{"openalex":"https://openalex.org/W4384643940","doi":"https://doi.org/10.1093/bib/bbad239","pmid":"https://pubmed.ncbi.nlm.nih.gov/37466138"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbad239","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad239","pdf_url":"https://academic.oup.com/bib/advance-article-pdf/doi/10.1093/bib/bbad239/50907173/bbad239.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bib/advance-article-pdf/doi/10.1093/bib/bbad239/50907173/bbad239.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101711221","display_name":"Yaozhong Zhang","orcid":"https://orcid.org/0000-0001-5598-2521"},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Yao-zhong Zhang","raw_affiliation_strings":["The Institute of Medical Science, The University of Tokyo Division of Health Medical Intelligence, Human Genome Center, , Shirokanedai 4-6-1, Minato-ku, 108-8639 Tokyo , Japan"],"raw_orcid":"https://orcid.org/0000-0001-5598-2521","affiliations":[{"raw_affiliation_string":"The Institute of Medical Science, The University of Tokyo Division of Health Medical Intelligence, Human Genome Center, , Shirokanedai 4-6-1, Minato-ku, 108-8639 Tokyo , Japan","institution_ids":["https://openalex.org/I74801974"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042861050","display_name":"Yunjie Liu","orcid":"https://orcid.org/0000-0001-9454-5666"},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yunjie Liu","raw_affiliation_strings":["The Institute of Medical Science, The University of Tokyo Division of Health Medical Intelligence, Human Genome Center, , Shirokanedai 4-6-1, Minato-ku, 108-8639 Tokyo , Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Institute of Medical Science, The University of Tokyo Division of Health Medical Intelligence, Human Genome Center, , Shirokanedai 4-6-1, Minato-ku, 108-8639 Tokyo , Japan","institution_ids":["https://openalex.org/I74801974"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087847911","display_name":"Zeheng Bai","orcid":"https://orcid.org/0000-0002-4921-0936"},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Zeheng Bai","raw_affiliation_strings":["The Institute of Medical Science, The University of Tokyo Division of Health Medical Intelligence, Human Genome Center, , Shirokanedai 4-6-1, Minato-ku, 108-8639 Tokyo , Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Institute of Medical Science, The University of Tokyo Division of Health Medical Intelligence, Human Genome Center, , Shirokanedai 4-6-1, Minato-ku, 108-8639 Tokyo , Japan","institution_ids":["https://openalex.org/I74801974"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071346389","display_name":"Kosuke Fujimoto","orcid":"https://orcid.org/0000-0002-2948-549X"},"institutions":[{"id":"https://openalex.org/I4387152983","display_name":"Osaka Metropolitan University","ror":"https://ror.org/01hvx5h04","country_code":"JP","type":"education","lineage":["https://openalex.org/I4387152983"]},{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Kosuke Fujimoto","raw_affiliation_strings":["Department of Immunology and Genomics, Graduate School of Medicine, Osaka Metropolitan University , Asahi-machi 1-4-3, Abeno-ku, 545-8585 Osaka , Japan","Division of Metagenome Medicine, Human Genome Center, The Institute of Medical Science, The University of Tokyo , Shirokanedai 4-6-1, Minato-ku, 108-8639 Tokyo , Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Immunology and Genomics, Graduate School of Medicine, Osaka Metropolitan University , Asahi-machi 1-4-3, Abeno-ku, 545-8585 Osaka , Japan","institution_ids":["https://openalex.org/I4387152983"]},{"raw_affiliation_string":"Division of Metagenome Medicine, Human Genome Center, The Institute of Medical Science, The University of Tokyo , Shirokanedai 4-6-1, Minato-ku, 108-8639 Tokyo , Japan","institution_ids":["https://openalex.org/I74801974"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051593432","display_name":"Satoshi Uematsu","orcid":"https://orcid.org/0000-0002-5347-6737"},"institutions":[{"id":"https://openalex.org/I4387152983","display_name":"Osaka Metropolitan University","ror":"https://ror.org/01hvx5h04","country_code":"JP","type":"education","lineage":["https://openalex.org/I4387152983"]},{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Satoshi Uematsu","raw_affiliation_strings":["Department of Immunology and Genomics, Graduate School of Medicine, Osaka Metropolitan University , Asahi-machi 1-4-3, Abeno-ku, 545-8585 Osaka , Japan","Division of Metagenome Medicine, Human Genome Center, The Institute of Medical Science, The University of Tokyo , Shirokanedai 4-6-1, Minato-ku, 108-8639 Tokyo , Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Immunology and Genomics, Graduate School of Medicine, Osaka Metropolitan University , Asahi-machi 1-4-3, Abeno-ku, 545-8585 Osaka , Japan","institution_ids":["https://openalex.org/I4387152983"]},{"raw_affiliation_string":"Division of Metagenome Medicine, Human Genome Center, The Institute of Medical Science, The University of Tokyo , Shirokanedai 4-6-1, Minato-ku, 108-8639 Tokyo , Japan","institution_ids":["https://openalex.org/I74801974"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5090788230","display_name":"Seiya Imoto","orcid":"https://orcid.org/0000-0002-2989-308X"},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Seiya Imoto","raw_affiliation_strings":["The Institute of Medical Science, The University of Tokyo Division of Health Medical Intelligence, Human Genome Center, , Shirokanedai 4-6-1, Minato-ku, 108-8639 Tokyo , Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Institute of Medical Science, The University of Tokyo Division of Health Medical Intelligence, Human Genome Center, , Shirokanedai 4-6-1, Minato-ku, 108-8639 Tokyo , Japan","institution_ids":["https://openalex.org/I74801974"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5090788230","https://openalex.org/A5101711221"],"corresponding_institution_ids":["https://openalex.org/I74801974"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":3.8471,"has_fulltext":true,"cited_by_count":17,"citation_normalized_percentile":{"value":0.93191682,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"24","issue":"5","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11048","display_name":"Bacteriophages and microbial interactions","score":0.9997000098228455,"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":0.9997000098228455,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9994000196456909,"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/T10494","display_name":"Plant Virus Research Studies","score":0.9979000091552734,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.7098758220672607},{"id":"https://openalex.org/keywords/host","display_name":"Host (biology)","score":0.6441603899002075},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.5757068395614624},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5068450570106506},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.4705767035484314},{"id":"https://openalex.org/keywords/whole-genome-sequencing","display_name":"Whole genome sequencing","score":0.4701792299747467},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.45340389013290405},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.4472367763519287},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.44212955236434937},{"id":"https://openalex.org/keywords/feature-learning","display_name":"Feature learning","score":0.426756888628006},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.40233755111694336},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3719489872455597},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.252738356590271},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.15135273337364197}],"concepts":[{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.7098758220672607},{"id":"https://openalex.org/C126831891","wikidata":"https://www.wikidata.org/wiki/Q221673","display_name":"Host (biology)","level":2,"score":0.6441603899002075},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.5757068395614624},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5068450570106506},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.4705767035484314},{"id":"https://openalex.org/C24432333","wikidata":"https://www.wikidata.org/wiki/Q2068526","display_name":"Whole genome sequencing","level":4,"score":0.4701792299747467},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.45340389013290405},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.4472367763519287},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.44212955236434937},{"id":"https://openalex.org/C59404180","wikidata":"https://www.wikidata.org/wiki/Q17013334","display_name":"Feature learning","level":2,"score":0.426756888628006},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.40233755111694336},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3719489872455597},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.252738356590271},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.15135273337364197},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000073336","descriptor_name":"Whole Genome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000073336","descriptor_name":"Whole Genome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000073336","descriptor_name":"Whole Genome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbad239","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad239","pdf_url":"https://academic.oup.com/bib/advance-article-pdf/doi/10.1093/bib/bbad239/50907173/bbad239.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37466138","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37466138","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10516345","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10516345","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10516345/pdf/bbad239.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbad239","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad239","pdf_url":"https://academic.oup.com/bib/advance-article-pdf/doi/10.1093/bib/bbad239/50907173/bbad239.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2337946962","display_name":"Fundamental research for the development of phage therapies targeting intestinal pathobiont","funder_award_id":"22H00477","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G3837059165","display_name":null,"funder_award_id":"JP21K12104","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G8295330643","display_name":"Development of Information Base Technology for Evaluation of Organ Functions of Intestinal Microbiota by Disease Metagenomics","funder_award_id":"21H03538","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"}],"funders":[{"id":"https://openalex.org/F4320310760","display_name":"Uehara Memorial Foundation","ror":"https://ror.org/00gc20a07"},{"id":"https://openalex.org/F4320311405","display_name":"Japan Agency for Medical Research and Development","ror":"https://ror.org/004rtk039"},{"id":"https://openalex.org/F4320322832","display_name":"University of Tokyo","ror":"https://ror.org/057zh3y96"},{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"},{"id":"https://openalex.org/F4320336716","display_name":"Institute of Medical Science, University of Tokyo","ror":null}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4384643940.pdf"},"referenced_works_count":26,"referenced_works":["https://openalex.org/W176296285","https://openalex.org/W1508259457","https://openalex.org/W1966912927","https://openalex.org/W2068308871","https://openalex.org/W2119859604","https://openalex.org/W2129103781","https://openalex.org/W2142678478","https://openalex.org/W2148630429","https://openalex.org/W2158406706","https://openalex.org/W2559100382","https://openalex.org/W2597507805","https://openalex.org/W2732139758","https://openalex.org/W2734399491","https://openalex.org/W3042057078","https://openalex.org/W3097355569","https://openalex.org/W3107997545","https://openalex.org/W3112043731","https://openalex.org/W3118981004","https://openalex.org/W3173126360","https://openalex.org/W3191098167","https://openalex.org/W3200765011","https://openalex.org/W3213133098","https://openalex.org/W4226147938","https://openalex.org/W4285389023","https://openalex.org/W4293456291","https://openalex.org/W6683390034"],"related_works":["https://openalex.org/W2378211422","https://openalex.org/W2745001401","https://openalex.org/W4321353415","https://openalex.org/W2130974462","https://openalex.org/W972276598","https://openalex.org/W4246352526","https://openalex.org/W2028665553","https://openalex.org/W4230315250","https://openalex.org/W2086519370","https://openalex.org/W2087343574"],"abstract_inverted_index":{"Accurately":[0],"identifying":[1,26,201],"phage-host":[2,28,53,202,228,244],"relationships":[3,29,96,229],"from":[4],"their":[5,141],"genome":[6,180,231],"sequences":[7,80,217],"is":[8,58,207],"still":[9],"challenging,":[10],"especially":[11],"for":[12,200,230,254],"those":[13],"phages":[14,62,93,219],"and":[15,33,87,94,124,162,220,223,246],"hosts":[16,66,123,126,161,222],"with":[17,81,133],"less":[18],"homologous":[19],"sequences.":[20],"In":[21,171],"this":[22,211],"work,":[23],"focusing":[24],"on":[25,106,111,140,159,168],"the":[27,31,64,72,107,112,149,156,176,241,249],"at":[30],"species":[32,184],"genus":[34],"level,":[35],"we":[36,77],"propose":[37],"a":[38,115,164,188],"contrastive":[39,98,101,153],"learning":[40,57,102,154],"based":[41],"approach":[42,206,235],"to":[43,60,68,209,227,239],"learn":[44,88],"whole-genome":[45,79,192,216],"sequence":[46,232],"embeddings":[47,90],"that":[48,91,148,195],"can":[49,120,236],"take":[50],"account":[51],"of":[52,173,179,191,218,243,251],"interactions":[54,245],"(PHIs).":[55],"Contrastive":[56],"used":[59,238],"make":[61],"infecting":[63],"same":[65],"close":[67],"each":[69],"other":[70],"in":[71,127,187,248],"new":[73],"representation":[74,85],"space.":[75],"Specifically,":[76],"rephrase":[78],"frequency":[82],"chaos":[83],"game":[84],"(FCGR)":[86],"latent":[89],"'encapsulate'":[92],"host":[95],"through":[97],"learning.":[99],"The":[100,144,204],"method":[103,132,151],"works":[104],"well":[105],"imbalanced":[108],"dataset.":[109],"Based":[110],"learned":[113],"embeddings,":[114],"proposed":[116,136,150,205],"pipeline":[117],"named":[118],"CL4PHI":[119],"predict":[121],"known":[122,160],"unseen":[125,169],"training.":[128],"We":[129],"compare":[130],"our":[131],"two":[134],"recently":[135],"state-of-the-art":[137],"learning-based":[138],"methods":[139,199],"benchmark":[142],"datasets.":[143],"experiment":[145],"results":[146],"demonstrate":[147],"using":[152],"improves":[155],"prediction":[157,166],"accuracy":[158],"demonstrates":[163],"zero-shot":[165],"capability":[167],"hosts.":[170],"terms":[172],"potential":[174],"applications,":[175],"rapid":[177],"pace":[178],"sequencing":[181,193],"across":[182],"different":[183],"has":[185],"resulted":[186],"vast":[189],"amount":[190],"data":[194],"require":[196],"efficient":[197],"computational":[198],"interactions.":[203],"expected":[208],"address":[210],"need":[212],"by":[213],"efficiently":[214],"processing":[215],"prokaryotic":[221],"capturing":[224],"features":[225],"related":[226],"representation.":[233],"This":[234],"be":[237],"accelerate":[240],"discovery":[242],"aid":[247],"development":[250],"phage-based":[252],"therapies":[253],"infectious":[255],"diseases.":[256]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":1}],"updated_date":"2026-06-22T08:00:12.763002","created_date":"2025-10-10T00:00:00"}