{"id":"https://openalex.org/W4394759652","doi":"https://doi.org/10.1093/bioinformatics/btae180","title":"Causal-ARG: a causality-guided framework for annotating properties of antibiotic resistance genes","display_name":"Causal-ARG: a causality-guided framework for annotating properties of antibiotic resistance genes","publication_year":2024,"publication_date":"2024-03-29","ids":{"openalex":"https://openalex.org/W4394759652","doi":"https://doi.org/10.1093/bioinformatics/btae180","pmid":"https://pubmed.ncbi.nlm.nih.gov/38569882"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae180","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae180","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/40/4/btae180/57274997/btae180.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/40/4/btae180/57274997/btae180.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5079405950","display_name":"Weizhong Zhao","orcid":"https://orcid.org/0000-0001-8552-6084"},"institutions":[{"id":"https://openalex.org/I40963666","display_name":"Central China Normal University","ror":"https://ror.org/03x1jna21","country_code":"CN","type":"education","lineage":["https://openalex.org/I40963666"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Weizhong Zhao","raw_affiliation_strings":["Hubei Provincial Key Laboratory of Artificial Intelligence and Smart Learning, Central China Normal University , Wuhan, Hubei 430079, P.R. China","National Language Resources Monitoring & Research Center for Network Media, Central China Normal University , Wuhan, Hubei 430079, P.R. China","School of Computer, Central China Normal University , Wuhan, Hubei 430079, P.R. China"],"raw_orcid":"https://orcid.org/0000-0001-8552-6084","affiliations":[{"raw_affiliation_string":"Hubei Provincial Key Laboratory of Artificial Intelligence and Smart Learning, Central China Normal University , Wuhan, Hubei 430079, P.R. China","institution_ids":["https://openalex.org/I40963666"]},{"raw_affiliation_string":"National Language Resources Monitoring & Research Center for Network Media, Central China Normal University , Wuhan, Hubei 430079, P.R. China","institution_ids":["https://openalex.org/I40963666"]},{"raw_affiliation_string":"School of Computer, Central China Normal University , Wuhan, Hubei 430079, P.R. China","institution_ids":["https://openalex.org/I40963666"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013692094","display_name":"Junze Wu","orcid":null},"institutions":[{"id":"https://openalex.org/I40963666","display_name":"Central China Normal University","ror":"https://ror.org/03x1jna21","country_code":"CN","type":"education","lineage":["https://openalex.org/I40963666"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Junze Wu","raw_affiliation_strings":["Hubei Provincial Key Laboratory of Artificial Intelligence and Smart Learning, Central China Normal University , Wuhan, Hubei 430079, P.R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hubei Provincial Key Laboratory of Artificial Intelligence and Smart Learning, Central China Normal University , Wuhan, Hubei 430079, P.R. China","institution_ids":["https://openalex.org/I40963666"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003550654","display_name":"Xingpeng Jiang","orcid":"https://orcid.org/0000-0002-8848-9300"},"institutions":[{"id":"https://openalex.org/I40963666","display_name":"Central China Normal University","ror":"https://ror.org/03x1jna21","country_code":"CN","type":"education","lineage":["https://openalex.org/I40963666"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xingpeng Jiang","raw_affiliation_strings":["Hubei Provincial Key Laboratory of Artificial Intelligence and Smart Learning, Central China Normal University , Wuhan, Hubei 430079, P.R. China"],"raw_orcid":"https://orcid.org/0000-0002-8848-9300","affiliations":[{"raw_affiliation_string":"Hubei Provincial Key Laboratory of Artificial Intelligence and Smart Learning, Central China Normal University , Wuhan, Hubei 430079, P.R. China","institution_ids":["https://openalex.org/I40963666"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102010131","display_name":"Tingting He","orcid":"https://orcid.org/0000-0001-7523-6550"},"institutions":[{"id":"https://openalex.org/I40963666","display_name":"Central China Normal University","ror":"https://ror.org/03x1jna21","country_code":"CN","type":"education","lineage":["https://openalex.org/I40963666"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Tingting He","raw_affiliation_strings":["Hubei Provincial Key Laboratory of Artificial Intelligence and Smart Learning, Central China Normal University , Wuhan, Hubei 430079, P.R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hubei Provincial Key Laboratory of Artificial Intelligence and Smart Learning, Central China Normal University , Wuhan, Hubei 430079, P.R. China","institution_ids":["https://openalex.org/I40963666"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101569679","display_name":"Xiaohua Hu","orcid":"https://orcid.org/0000-0002-4777-3022"},"institutions":[{"id":"https://openalex.org/I72816309","display_name":"Drexel University","ror":"https://ror.org/04bdffz58","country_code":"US","type":"education","lineage":["https://openalex.org/I72816309"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xiaohua Hu","raw_affiliation_strings":["College of Computing & Informatics, Drexel University , Philadelphia, PA 19104, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computing & Informatics, Drexel University , Philadelphia, PA 19104, United States","institution_ids":["https://openalex.org/I72816309"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5003550654","https://openalex.org/A5079405950"],"corresponding_institution_ids":["https://openalex.org/I40963666"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.6332,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.6896013,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":98},"biblio":{"volume":"40","issue":"4","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.2766999900341034,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.2766999900341034,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.24220000207424164,"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/T11948","display_name":"Machine Learning in Materials Science","score":0.05909999832510948,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/causality","display_name":"Causality (physics)","score":0.743732750415802},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5628843307495117},{"id":"https://openalex.org/keywords/resistance","display_name":"Resistance (ecology)","score":0.529453694820404},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5149624943733215},{"id":"https://openalex.org/keywords/antibiotics","display_name":"Antibiotics","score":0.4931339621543884},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.44321301579475403},{"id":"https://openalex.org/keywords/antibiotic-resistance","display_name":"Antibiotic resistance","score":0.4417659044265747},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3962995111942291},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3960241377353668},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.08552184700965881},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.08299964666366577}],"concepts":[{"id":"https://openalex.org/C64357122","wikidata":"https://www.wikidata.org/wiki/Q1149766","display_name":"Causality (physics)","level":2,"score":0.743732750415802},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5628843307495117},{"id":"https://openalex.org/C57473165","wikidata":"https://www.wikidata.org/wiki/Q7315604","display_name":"Resistance (ecology)","level":2,"score":0.529453694820404},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5149624943733215},{"id":"https://openalex.org/C501593827","wikidata":"https://www.wikidata.org/wiki/Q12187","display_name":"Antibiotics","level":2,"score":0.4931339621543884},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.44321301579475403},{"id":"https://openalex.org/C94665300","wikidata":"https://www.wikidata.org/wiki/Q63391344","display_name":"Antibiotic resistance","level":3,"score":0.4417659044265747},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3962995111942291},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3960241377353668},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.08552184700965881},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.08299964666366577},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000900","descriptor_name":"Anti-Bacterial Agents","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D000900","descriptor_name":"Anti-Bacterial Agents","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D000900","descriptor_name":"Anti-Bacterial Agents","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D000900","descriptor_name":"Anti-Bacterial Agents","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D004352","descriptor_name":"Drug Resistance, Microbial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004352","descriptor_name":"Drug Resistance, Microbial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004352","descriptor_name":"Drug Resistance, Microbial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004352","descriptor_name":"Drug Resistance, Microbial","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005798","descriptor_name":"Genes, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005798","descriptor_name":"Genes, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005798","descriptor_name":"Genes, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005798","descriptor_name":"Genes, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btae180","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae180","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/40/4/btae180/57274997/btae180.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38569882","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38569882","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11026140","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11026140","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11026140/pdf/btae180.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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae180","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae180","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/40/4/btae180/57274997/btae180.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Good health and well-being","score":0.4300000071525574,"id":"https://metadata.un.org/sdg/3"}],"awards":[{"id":"https://openalex.org/G1307575636","display_name":"\u9762\u5411\u8111\u75be\u75c5\u7684\u4eba\u4f53\u80a0\u9053\u5fae\u751f\u7269\u7ec4\u5b66\u6570\u636e\u6316\u6398\u65b9\u6cd5\u7814\u7a76","funder_award_id":"61932008","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G1750061152","display_name":null,"funder_award_id":"2022CFB289","funder_id":"https://openalex.org/F4320322186","funder_display_name":"Natural Science Foundation of Hubei Province"},{"id":"https://openalex.org/G235156935","display_name":null,"funder_award_id":"62372205","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320322186","display_name":"Natural Science Foundation of Hubei Province","ror":null}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4394759652.pdf"},"referenced_works_count":26,"referenced_works":["https://openalex.org/W1987625100","https://openalex.org/W1989122238","https://openalex.org/W2017331448","https://openalex.org/W2171309014","https://openalex.org/W2305704688","https://openalex.org/W2542768043","https://openalex.org/W2805300175","https://openalex.org/W2921872415","https://openalex.org/W2951274106","https://openalex.org/W2952369555","https://openalex.org/W2966931150","https://openalex.org/W2982531601","https://openalex.org/W2994388045","https://openalex.org/W3007309629","https://openalex.org/W3128120098","https://openalex.org/W3205657162","https://openalex.org/W4206677002","https://openalex.org/W4207067711","https://openalex.org/W4211258437","https://openalex.org/W4226250938","https://openalex.org/W4300672471","https://openalex.org/W4309666648","https://openalex.org/W6754506371","https://openalex.org/W6760517126","https://openalex.org/W6769556952","https://openalex.org/W6807087183"],"related_works":["https://openalex.org/W2955020749","https://openalex.org/W2029063045","https://openalex.org/W2507683919","https://openalex.org/W2076505260","https://openalex.org/W4226193097","https://openalex.org/W4320037900","https://openalex.org/W4297123388","https://openalex.org/W3032187068","https://openalex.org/W4221083638","https://openalex.org/W3152803520"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1,179,204],"crisis":[2],"of":[3,22,32,55,68,79,107,127,138,166,174,177,189,196,199],"antibiotic":[4,33,62],"resistance,":[5],"which":[6,110,168],"causes":[7],"antibiotics":[8],"used":[9,143],"to":[10,14,26,41,82,144,159],"treat":[11],"bacterial":[12],"infections":[13],"become":[15],"less":[16],"effective,":[17],"has":[18],"emerged":[19],"as":[20],"one":[21],"the":[23,30,85,92,120,125,146,161,172,187,190,194],"foremost":[24],"challenges":[25],"public":[27],"health.":[28],"Identifying":[29],"properties":[31,67,78,106,126,156,165,176,198],"resistance":[34],"genes":[35],"(ARGs)":[36],"is":[37,113,142,157,169],"an":[38],"essential":[39],"way":[40],"mitigate":[42],"this":[43,52,97],"issue.":[44],"Although":[45],"numerous":[46],"methods":[47,73],"have":[48],"been":[49],"proposed":[50,191],"for":[51,74,84,104,115],"task,":[53],"most":[54],"these":[56,89],"approaches":[57],"concentrate":[58],"solely":[59],"on":[60,182,193],"predicting":[61,76],"class,":[63],"disregarding":[64],"other":[65],"important":[66],"ARGs.":[69,178,200],"In":[70,96,149],"addition,":[71,150],"existing":[72],"simultaneously":[75],"multiple":[77],"ARGs":[80,128],"fail":[81],"account":[83],"causal":[86,111,139,152,162],"relationships":[87,163],"among":[88,154,164],"properties,":[90],"limiting":[91],"predictive":[93],"performance.":[94],"RESULTS:":[95],"study,":[98],"we":[99],"propose":[100],"a":[101,132,151,183],"causality-guided":[102],"framework":[103,192],"annotating":[105,175,197],"ARGs,":[108,167],"in":[109,211],"inference":[112],"utilized":[114],"representation":[116,140],"learning.":[117],"More":[118],"specifically,":[119],"hidden":[121,147],"biological":[122],"patterns":[123],"determining":[124],"are":[129,209],"described":[130],"by":[131],"Gaussian":[133],"Mixture":[134],"Model,":[135],"and":[136,206],"procedure":[137],"learning":[141],"derive":[145],"features.":[148],"graph":[153],"different":[155],"constructed":[158],"capture":[160],"integrated":[170],"into":[171],"task":[173,195],"experimental":[180],"results":[181],"real-world":[184],"dataset":[185],"demonstrate":[186],"effectiveness":[188],"AVAILABILITY":[201],"AND":[202],"IMPLEMENTATION:":[203],"data":[205],"source":[207],"codes":[208],"available":[210],"GitHub":[212],"at":[213],"https://github.com/David-WZhao/CausalARG.":[214]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1}],"updated_date":"2026-06-16T07:32:37.131356","created_date":"2025-10-10T00:00:00"}
