{"doi":"10.1371/journal.pcbi.1011671","title":"Prokaryotic virus host prediction with graph contrastive augmentaion","abstract":"<jats:p>Prokaryotic viruses, also known as bacteriophages, play crucial roles in regulating microbial communities and have the potential for phage therapy applications. Accurate prediction of phage-host interactions is essential for understanding the dynamics of these viruses and their impacts on bacterial populations. Numerous computational methods have been developed to tackle this challenging task. However, most existing prediction models can be constrained due to the substantial number of unknown interactions in comparison to the constrained diversity of available training data. To solve the problem, we introduce a model for <jats:bold>p</jats:bold>rokaryotic virus <jats:bold>h</jats:bold>ost <jats:bold>p</jats:bold>rediction with <jats:bold>g</jats:bold>raph <jats:bold>c</jats:bold>ontrastive <jats:bold>a</jats:bold>ugmentation (PHPGCA). Specifically, we construct a comprehensive heterogeneous graph by integrating virus-virus protein similarity and virus-host DNA sequence similarity information. As the backbone encoder for learning node representations in the virus-prokaryote graph, we employ LGCN, a state-of-the-art graph embedding technique. Additionally, we apply graph contrastive learning to augment the node representations without the need for additional labels. We further conducted two case studies aimed at predicting the host range of multi-species phages, helping to understand the phage ecology and evolution.</jats:p>","journal":"PLOS Computational Biology","year":2023,"id":640989,"datarank":0.3453877639491069,"base_score":2.302585092994046,"endowment":2.302585092994046,"self_citation_contribution":0.3453877639491069,"citation_network_contribution":0.0,"self_endowment_contribution":0.3453877639491069,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":9,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1666235,"name":"Jun-Peng Zhong","orcid":null,"position":1,"is_corresponding":false},{"id":342119,"name":"Yun Liu","orcid":"0000-0002-9916-6646","position":2,"is_corresponding":false},{"id":1666236,"name":"Jian-Qiang Li","orcid":null,"position":3,"is_corresponding":false},{"id":537701,"name":"Zhihua Du","orcid":"0000-0002-7213-2198","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Prokaryotic virus host prediction with graph contrastive augmentaion","abstract":"<jats:p>Prokaryotic viruses, also known as bacteriophages, play crucial roles in regulating microbial communities and have the potential for phage therapy applications. Accurate prediction of phage-host interactions is essential for understanding the dynamics of these viruses and their impacts on bacterial populations. Numerous computational methods have been developed to tackle this challenging task. However, most existing prediction models can be constrained due to the substantial number of unknown interactions in comparison to the constrained diversity of available training data. To solve the problem, we introduce a model for <jats:bold>p</jats:bold>rokaryotic virus <jats:bold>h</jats:bold>ost <jats:bold>p</jats:bold>rediction with <jats:bold>g</jats:bold>raph <jats:bold>c</jats:bold>ontrastive <jats:bold>a</jats:bold>ugmentation (PHPGCA). Specifically, we construct a comprehensive heterogeneous graph by integrating virus-virus protein similarity and virus-host DNA sequence similarity information. As the backbone encoder for learning node representations in the virus-prokaryote graph, we employ LGCN, a state-of-the-art graph embedding technique. Additionally, we apply graph contrastive learning to augment the node representations without the need for additional labels. We further conducted two case studies aimed at predicting the host range of multi-species phages, helping to understand the phage ecology and evolution.</jats:p>","is_dataset_classified":null,"base_score":2.302585092994046,"endowment":2.302585092994046,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"38039280","pmcid":"PMC10691718","openalex_id":"https://openalex.org/W4389235782","authors":[],"funders":[{"funder_name":"National Key R&D Program of China under Grant","grant_id":"2020YFA0908700","title":null},{"funder_name":"National Nature Science Foundation of China under Grant","grant_id":"62176164","title":null},{"funder_name":"Natural Science Foundation of Guangdong Province under Grant","grant_id":"2023A1515010992","title":null},{"funder_name":"Science and Technology Innovation Committee Foundation of Shenzhen City under Grant","grant_id":"JCYJ20220531101217039","title":null},{"funder_name":"Science and Technology Innovation Committee Foundation of Shenzhen City under Grant","grant_id":"JCYJ20190808144207651","title":null}],"total_grants":5,"fwci":1.7351,"citation_percentile":0.84019577,"influential_citations":0,"citation_trend":[{"year":2025,"count":4},{"year":2026,"count":5}],"oa_status":"gold","license":"cc-by","oa_locations":[{"url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011671&type=printable","host_type":"journal"},{"url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011671&type=printable","host_type":"publisher"},{"url":"https://dx.plos.org/10.1371/journal.pcbi.1011671","host_type":"publisher"},{"url":"https://doi.org/10.1371/journal.pcbi.1011671","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/38039280","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10691718","host_type":"repository"},{"url":"https://doaj.org/article/72b5f009357940b1a37eb68bcbbff818","host_type":"repository"},{"url":"https://doaj.org/article/8ec3fbe3118b4b208a0dbb8ef6bf230b","host_type":"repository"},{"url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10691718/pdf/pcbi.1011671.pdf","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC10691718","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC10691718?pdf=render","host_type":"Europe_PMC"}],"fields_of_study":["Bacteriophages and microbial interactions","Genomics and Phylogenetic Studies","RNA and protein synthesis mechanisms","Prokaryotic Cells","Bacteriophages","Ecology","Host Specificity","Learning"],"mesh_terms":["Bacteriophages","Ecology","Learning","Prokaryotic Cells","Host Specificity"],"keywords":["Host (biology)","Computational biology","Computer science","Biology","Genetics"],"sdg_mappings":[{"sdg_number":0,"sdg_label":"Life in Land"}],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-07T15:09:12.526885Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}