{"id":"https://openalex.org/W2911844640","doi":"https://doi.org/10.1109/bibm.2018.8621433","title":"Exploration of multiclass and one-class learning methods for prediction of phage-bacteria interaction at strain level","display_name":"Exploration of multiclass and one-class learning methods for prediction of phage-bacteria interaction at strain level","publication_year":2018,"publication_date":"2018-12-01","ids":{"openalex":"https://openalex.org/W2911844640","doi":"https://doi.org/10.1109/bibm.2018.8621433","mag":"2911844640"},"language":"en","primary_location":{"id":"doi:10.1109/bibm.2018.8621433","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2018.8621433","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2018 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/A5108508159","display_name":"Diogo Manuel Carvalho Leite","orcid":null},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"funder","lineage":["https://openalex.org/I12708293"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Diogo Manuel Carvalho Leite","raw_affiliation_strings":["SIB - Swiss Institute of Bio-informatics"],"affiliations":[{"raw_affiliation_string":"SIB - Swiss Institute of Bio-informatics","institution_ids":["https://openalex.org/I12708293"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111400866","display_name":"J.F. del Ca\u00f1izo L\u00f3pez","orcid":null},"institutions":[{"id":"https://openalex.org/I47726972","display_name":"Universidad Aut\u00f3noma de Occidente","ror":"https://ror.org/02drkkh02","country_code":"CO","type":"education","lineage":["https://openalex.org/I47726972"]}],"countries":["CO"],"is_corresponding":false,"raw_author_name":"Juan Fernando Lopez","raw_affiliation_strings":["Faculty of engineering, Universidad Aut\u00d3noma de Occidente, Cali, Colombia"],"affiliations":[{"raw_affiliation_string":"Faculty of engineering, Universidad Aut\u00d3noma de Occidente, Cali, Colombia","institution_ids":["https://openalex.org/I47726972"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011962412","display_name":"Xavier Brochet","orcid":null},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"funder","lineage":["https://openalex.org/I12708293"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Xavier Brochet","raw_affiliation_strings":["SIB - Swiss Institute of Bio-informatics"],"affiliations":[{"raw_affiliation_string":"SIB - Swiss Institute of Bio-informatics","institution_ids":["https://openalex.org/I12708293"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054464987","display_name":"Miguel Arturo Barreto-Sanz","orcid":null},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"funder","lineage":["https://openalex.org/I12708293"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Miguel Barreto-Sanz","raw_affiliation_strings":["SIB - Swiss Institute of Bio-informatics"],"affiliations":[{"raw_affiliation_string":"SIB - Swiss Institute of Bio-informatics","institution_ids":["https://openalex.org/I12708293"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040119306","display_name":"Yok\u2010Ai Que","orcid":"https://orcid.org/0000-0001-9443-6101"},"institutions":[{"id":"https://openalex.org/I2801112126","display_name":"University Hospital of Bern","ror":"https://ror.org/01q9sj412","country_code":"CH","type":"healthcare","lineage":["https://openalex.org/I2801112126"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Yok-Ai Que","raw_affiliation_strings":["Department of Intensive Care medicine, Bern University Hospital (Inselspital), Bern, Freiburgstrasse"],"affiliations":[{"raw_affiliation_string":"Department of Intensive Care medicine, Bern University Hospital (Inselspital), Bern, Freiburgstrasse","institution_ids":["https://openalex.org/I2801112126"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048044374","display_name":"Gr\u00e9gory Resch","orcid":"https://orcid.org/0000-0003-2341-4591"},"institutions":[{"id":"https://openalex.org/I97565354","display_name":"University of Lausanne","ror":"https://ror.org/019whta54","country_code":"CH","type":"education","lineage":["https://openalex.org/I97565354"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Gregory Resch","raw_affiliation_strings":["Department of Fundamental Microbiology, University of Lausanne, Lausanne"],"affiliations":[{"raw_affiliation_string":"Department of Fundamental Microbiology, University of Lausanne, Lausanne","institution_ids":["https://openalex.org/I97565354"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5050923109","display_name":"Carlos Andr\u00e9s Pe\u00f1a-Reyes","orcid":"https://orcid.org/0000-0002-2113-6498"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"funder","lineage":["https://openalex.org/I12708293"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Carlos Pena-Reyes","raw_affiliation_strings":["SIB - Swiss Institute of Bio-informatics"],"affiliations":[{"raw_affiliation_string":"SIB - Swiss Institute of Bio-informatics","institution_ids":["https://openalex.org/I12708293"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5108508159"],"corresponding_institution_ids":["https://openalex.org/I12708293"],"apc_list":null,"apc_paid":null,"fwci":0.7777,"has_fulltext":false,"cited_by_count":14,"citation_normalized_percentile":{"value":0.75768549,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":null,"issue":null,"first_page":"1818","last_page":"1825"},"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/T11688","display_name":"Microbial infections and disease research","score":0.9914000034332275,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9901000261306763,"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/in-silico","display_name":"In silico","score":0.6282844543457031},{"id":"https://openalex.org/keywords/bacteria","display_name":"Bacteria","score":0.5977748036384583},{"id":"https://openalex.org/keywords/phage-therapy","display_name":"Phage therapy","score":0.5327140688896179},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5266138315200806},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4989442825317383},{"id":"https://openalex.org/keywords/class","display_name":"Class (philosophy)","score":0.4682392179965973},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.45697247982025146},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.43310248851776123},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4168599545955658},{"id":"https://openalex.org/keywords/strain","display_name":"Strain (injury)","score":0.4126822352409363},{"id":"https://openalex.org/keywords/bacteriophage","display_name":"Bacteriophage","score":0.20543813705444336},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.186163067817688},{"id":"https://openalex.org/keywords/escherichia-coli","display_name":"Escherichia coli","score":0.15037807822227478}],"concepts":[{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.6282844543457031},{"id":"https://openalex.org/C523546767","wikidata":"https://www.wikidata.org/wiki/Q10876","display_name":"Bacteria","level":2,"score":0.5977748036384583},{"id":"https://openalex.org/C2779256223","wikidata":"https://www.wikidata.org/wiki/Q611870","display_name":"Phage therapy","level":5,"score":0.5327140688896179},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5266138315200806},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4989442825317383},{"id":"https://openalex.org/C2777212361","wikidata":"https://www.wikidata.org/wiki/Q5127848","display_name":"Class (philosophy)","level":2,"score":0.4682392179965973},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.45697247982025146},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.43310248851776123},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4168599545955658},{"id":"https://openalex.org/C2778022156","wikidata":"https://www.wikidata.org/wiki/Q576145","display_name":"Strain (injury)","level":2,"score":0.4126822352409363},{"id":"https://openalex.org/C2776441376","wikidata":"https://www.wikidata.org/wiki/Q165028","display_name":"Bacteriophage","level":4,"score":0.20543813705444336},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.186163067817688},{"id":"https://openalex.org/C547475151","wikidata":"https://www.wikidata.org/wiki/Q25419","display_name":"Escherichia coli","level":3,"score":0.15037807822227478},{"id":"https://openalex.org/C105702510","wikidata":"https://www.wikidata.org/wiki/Q514","display_name":"Anatomy","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1109/bibm.2018.8621433","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2018.8621433","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},{"id":"pmh:oai:hesso.tind.io:4350","is_oa":false,"landing_page_url":"https://arodes.hes-so.ch/record/4350/files/published%20version.pdf","pdf_url":null,"source":{"id":"https://openalex.org/S4306402432","display_name":"ArODES (HES-SO (https://www.hes-so.ch/))","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210088449","host_organization_name":"HES-SO Gen\u00e8ve","host_organization_lineage":["https://openalex.org/I4210088449"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://arodes.hes-so.ch/record/4350","raw_type":"Text"},{"id":"pmh:oai:iris.unil.ch:iris/176845","is_oa":false,"landing_page_url":"https://iris.unil.ch/handle/iris/176845","pdf_url":null,"source":{"id":"https://openalex.org/S7407055444","display_name":"IRIS","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"conference paper"},{"id":"pmh:oai:serval.unil.ch:BIB_9298EA1FE9D1","is_oa":false,"landing_page_url":"https://serval.unil.ch/notice/serval:BIB_9298EA1FE9D1","pdf_url":null,"source":{"id":"https://openalex.org/S4306401797","display_name":"SERVAL (Universit\u00e9 de Lausanne)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210093590","host_organization_name":"Swiss School of Archaeology in Greece","host_organization_lineage":["https://openalex.org/I4210093590"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp. 1818-1825","raw_type":"inproceedings"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.5400000214576721,"id":"https://metadata.un.org/sdg/12","display_name":"Responsible consumption and production"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":44,"referenced_works":["https://openalex.org/W349770100","https://openalex.org/W1497338499","https://openalex.org/W1570448133","https://openalex.org/W1728842521","https://openalex.org/W1977278302","https://openalex.org/W1980262437","https://openalex.org/W1985919127","https://openalex.org/W1998566510","https://openalex.org/W2031616673","https://openalex.org/W2032647857","https://openalex.org/W2036534399","https://openalex.org/W2040375736","https://openalex.org/W2043174271","https://openalex.org/W2080951458","https://openalex.org/W2085963663","https://openalex.org/W2087996087","https://openalex.org/W2088333086","https://openalex.org/W2100228443","https://openalex.org/W2106090237","https://openalex.org/W2108712612","https://openalex.org/W2111604015","https://openalex.org/W2118417130","https://openalex.org/W2122111042","https://openalex.org/W2131891835","https://openalex.org/W2151831732","https://openalex.org/W2153635508","https://openalex.org/W2154273408","https://openalex.org/W2189116376","https://openalex.org/W2245444176","https://openalex.org/W2296719434","https://openalex.org/W2345960958","https://openalex.org/W2515956436","https://openalex.org/W2527885430","https://openalex.org/W2599963923","https://openalex.org/W2753995775","https://openalex.org/W2769880685","https://openalex.org/W2808847099","https://openalex.org/W2911964244","https://openalex.org/W4243563432","https://openalex.org/W4254182148","https://openalex.org/W4256060553","https://openalex.org/W6611762666","https://openalex.org/W6637572315","https://openalex.org/W6686723365"],"related_works":["https://openalex.org/W2912862995","https://openalex.org/W3129816939","https://openalex.org/W2985427592","https://openalex.org/W2101501829","https://openalex.org/W2003194288","https://openalex.org/W2400569965","https://openalex.org/W2060263731","https://openalex.org/W391093122","https://openalex.org/W1521239975","https://openalex.org/W4387226540"],"abstract_inverted_index":{"The":[0,49],"emergence":[1],"and":[2,11,32,42,66,127,206,209],"rapid":[3],"dissemination":[4],"of":[5,19,27,51,77,89,105,121,124,157,196],"antibiotic":[6],"resistance":[7],"threatens":[8],"medical":[9],"progress":[10],"calls":[12,171],"for":[13,16,74,145,172],"innovative":[14],"approaches":[15,186],"the":[17,25,57,62,67,82,106,119,155,194],"management":[18],"multidrug":[20],"resistant":[21],"infections.":[22],"Phage-therapy,":[23],"i.e.,":[24],"use":[26,156,195,207],"viruses":[28],"that":[29],"specifically":[30],"infect":[31],"kill":[33],"bacteria":[34,65,103],"during":[35],"their":[36],"life":[37],"cycle,":[38],"is":[39,95,118,141],"a":[40,100],"re-emerging":[41],"promising":[43],"alternative":[44],"to":[45,98,109,114,166,174,187,212],"solve":[46],"this":[47,181,189],"problem.":[48,190],"success":[50],"phage":[52],"therapy":[53],"mainly":[54],"relies":[55],"on":[56],"exact":[58],"matching":[59],"between":[60],"both":[61,122],"target":[63,99],"pathogenic":[64,102],"therapeutic":[68],"phage.":[69],"Several":[70],"papers":[71],"propose":[72],"models":[73,112],"in-silico":[75],"prediction":[76,88],"phage-bacteria":[78,90,116,129,214],"interactions":[79,117],"but":[80],"at":[81,92,148,216],"species":[83,93],"level.":[84,150],"In":[85,180],"clinical":[86],"applications":[87],"interaction":[91,126,215],"level":[94],"not":[96],"enough":[97],"given":[101],"strain.One":[104],"main":[107],"challenges":[108],"train":[110],"classification":[111],"able":[113],"predict":[115,213],"need":[120,163],"types":[123],"samples:":[125],"non-interaction":[128,146],"couples.":[130],"Non-interactions":[131],"are":[132,183],"rarely":[133],"reported,":[134],"making":[135],"these":[136],"data":[137,147,205],"scarce.":[138],"This":[139],"problem":[140,170],"even":[142],"more":[143],"evident":[144],"strain":[149],"These":[151],"factors":[152],"make":[153],"difficult":[154],"classic":[158],"machine":[159],"learning":[160,198],"algorithms":[161],"which":[162],"relatively-balanced":[164],"classes":[165],"produce":[167],"accurate":[168],"predictions.This":[169],"solutions":[173],"deal":[175],"with":[176],"such":[177],"imbalanced":[178],"data.":[179],"paper":[182],"presented":[184],"two":[185],"tackle":[188],"1.":[191],"To":[192,201],"explore":[193],"One-Class":[197],"methods":[199],"2.":[200],"generate":[202],"putative":[203],"non-interacting":[204],"single":[208],"ensemble-learning":[210],"approaches,":[211],"strain-level.":[217]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":1}],"updated_date":"2026-03-06T13:50:29.536080","created_date":"2019-02-21T00:00:00"}
