{"id":"https://openalex.org/W4403197568","doi":"https://doi.org/10.1038/s42256-024-00908-5","title":"A multi-modal deep language model for contaminant removal from metagenome-assembled genomes","display_name":"A multi-modal deep language model for contaminant removal from metagenome-assembled genomes","publication_year":2024,"publication_date":"2024-10-07","ids":{"openalex":"https://openalex.org/W4403197568","doi":"https://doi.org/10.1038/s42256-024-00908-5"},"language":"en","primary_location":{"id":"doi:10.1038/s42256-024-00908-5","is_oa":false,"landing_page_url":"https://doi.org/10.1038/s42256-024-00908-5","pdf_url":null,"source":{"id":"https://openalex.org/S2912241403","display_name":"Nature Machine Intelligence","issn_l":"2522-5839","issn":["2522-5839"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Machine Intelligence","raw_type":"journal-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/A5070571727","display_name":"Bohao Zou","orcid":null},"institutions":[{"id":"https://openalex.org/I141568987","display_name":"Hong Kong Baptist University","ror":"https://ror.org/0145fw131","country_code":"HK","type":"education","lineage":["https://openalex.org/I141568987"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Bohao Zou","raw_affiliation_strings":["Department of Computer Science, Hong Kong Baptist University, Hong Kong, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Hong Kong Baptist University, Hong Kong, China","institution_ids":["https://openalex.org/I141568987"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100426869","display_name":"Jingjing Wang","orcid":"https://orcid.org/0000-0002-5202-9943"},"institutions":[{"id":"https://openalex.org/I141568987","display_name":"Hong Kong Baptist University","ror":"https://ror.org/0145fw131","country_code":"HK","type":"education","lineage":["https://openalex.org/I141568987"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Jingjing Wang","raw_affiliation_strings":["Department of Computer Science, Hong Kong Baptist University, Hong Kong, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Hong Kong Baptist University, Hong Kong, China","institution_ids":["https://openalex.org/I141568987"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101584884","display_name":"Yi Ding","orcid":"https://orcid.org/0000-0001-7525-7124"},"institutions":[{"id":"https://openalex.org/I141568987","display_name":"Hong Kong Baptist University","ror":"https://ror.org/0145fw131","country_code":"HK","type":"education","lineage":["https://openalex.org/I141568987"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Yi Ding","raw_affiliation_strings":["Department of Computer Science, Hong Kong Baptist University, Hong Kong, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Hong Kong Baptist University, Hong Kong, China","institution_ids":["https://openalex.org/I141568987"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024808861","display_name":"Zhenmiao Zhang","orcid":"https://orcid.org/0000-0003-3748-1664"},"institutions":[{"id":"https://openalex.org/I141568987","display_name":"Hong Kong Baptist University","ror":"https://ror.org/0145fw131","country_code":"HK","type":"education","lineage":["https://openalex.org/I141568987"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Zhenmiao Zhang","raw_affiliation_strings":["Department of Computer Science, Hong Kong Baptist University, Hong Kong, China"],"raw_orcid":"https://orcid.org/0000-0003-3748-1664","affiliations":[{"raw_affiliation_string":"Department of Computer Science, Hong Kong Baptist University, Hong Kong, China","institution_ids":["https://openalex.org/I141568987"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101698478","display_name":"Yufen Huang","orcid":"https://orcid.org/0000-0001-5939-1091"},"institutions":[{"id":"https://openalex.org/I100135526","display_name":"BGI Group (China)","ror":"https://ror.org/045pn2j94","country_code":"CN","type":"company","lineage":["https://openalex.org/I100135526"]},{"id":"https://openalex.org/I4387153646","display_name":"BGI Research","ror":"https://ror.org/05gsxrt27","country_code":"CN","type":"nonprofit","lineage":["https://openalex.org/I100135526","https://openalex.org/I4387153646"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yufen Huang","raw_affiliation_strings":["BGI Research, Shenzhen, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BGI Research, Shenzhen, China","institution_ids":["https://openalex.org/I100135526","https://openalex.org/I4387153646"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052083635","display_name":"Xiaodong Fang","orcid":"https://orcid.org/0000-0001-7061-3337"},"institutions":[{"id":"https://openalex.org/I100135526","display_name":"BGI Group (China)","ror":"https://ror.org/045pn2j94","country_code":"CN","type":"company","lineage":["https://openalex.org/I100135526"]},{"id":"https://openalex.org/I4387153646","display_name":"BGI Research","ror":"https://ror.org/05gsxrt27","country_code":"CN","type":"nonprofit","lineage":["https://openalex.org/I100135526","https://openalex.org/I4387153646"]},{"id":"https://openalex.org/I4405259006","display_name":"BGI Research, Sanya","ror":"https://ror.org/01j5pk676","country_code":"CN","type":"facility","lineage":["https://openalex.org/I100135526","https://openalex.org/I4387153646","https://openalex.org/I4405259006"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaodong Fang","raw_affiliation_strings":["BGI Research, Sanya, China","BGI Research, Shenzhen, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BGI Research, Sanya, China","institution_ids":["https://openalex.org/I4387153646","https://openalex.org/I4405259006"]},{"raw_affiliation_string":"BGI Research, Shenzhen, China","institution_ids":["https://openalex.org/I100135526","https://openalex.org/I4387153646"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084054549","display_name":"Ka Chun Cheung","orcid":"https://orcid.org/0000-0002-2939-4686"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ka Chun Cheung","raw_affiliation_strings":["NVIDIA AI Technology Center, NVIDIA, Hong Kong, China"],"raw_orcid":"https://orcid.org/0000-0002-2939-4686","affiliations":[{"raw_affiliation_string":"NVIDIA AI Technology Center, NVIDIA, Hong Kong, China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077539496","display_name":"Simon See","orcid":"https://orcid.org/0000-0002-4958-9237"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Simon See","raw_affiliation_strings":["NVIDIA AI Technology Center, NVIDIA, Hong Kong, China"],"raw_orcid":"https://orcid.org/0000-0002-4958-9237","affiliations":[{"raw_affiliation_string":"NVIDIA AI Technology Center, NVIDIA, Hong Kong, China","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100388624","display_name":"Lu Zhang","orcid":"https://orcid.org/0000-0002-2794-7371"},"institutions":[{"id":"https://openalex.org/I141568987","display_name":"Hong Kong Baptist University","ror":"https://ror.org/0145fw131","country_code":"HK","type":"education","lineage":["https://openalex.org/I141568987"]}],"countries":["HK"],"is_corresponding":true,"raw_author_name":"Lu Zhang","raw_affiliation_strings":["Department of Computer Science, Hong Kong Baptist University, Hong Kong, China","Institute for Research and Continuing Education, Hong Kong Baptist University, Hong Kong, China"],"raw_orcid":"https://orcid.org/0000-0002-2794-7371","affiliations":[{"raw_affiliation_string":"Department of Computer Science, Hong Kong Baptist University, Hong Kong, China","institution_ids":["https://openalex.org/I141568987"]},{"raw_affiliation_string":"Institute for Research and Continuing Education, Hong Kong Baptist University, Hong Kong, China","institution_ids":["https://openalex.org/I141568987"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5100388624"],"corresponding_institution_ids":["https://openalex.org/I141568987"],"apc_list":{"value":9750,"currency":"EUR","value_usd":11690},"apc_paid":null,"fwci":1.862,"has_fulltext":false,"cited_by_count":10,"citation_normalized_percentile":{"value":0.85814813,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"6","issue":"10","first_page":"1245","last_page":"1255"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.994700014591217,"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"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.994700014591217,"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/T11791","display_name":"Microbial Community Ecology and Physiology","score":0.9779000282287598,"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/T13157","display_name":"Cancer-related gene regulation","score":0.9229999780654907,"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/metagenomics","display_name":"Metagenomics","score":0.771033525466919},{"id":"https://openalex.org/keywords/modal","display_name":"Modal","score":0.6195358037948608},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.47420957684516907},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.36457252502441406},{"id":"https://openalex.org/keywords/environmental-science","display_name":"Environmental science","score":0.3524383306503296},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.341583788394928},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2821757197380066},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.16656893491744995},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.12144067883491516},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.11500906944274902}],"concepts":[{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.771033525466919},{"id":"https://openalex.org/C71139939","wikidata":"https://www.wikidata.org/wiki/Q910194","display_name":"Modal","level":2,"score":0.6195358037948608},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.47420957684516907},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.36457252502441406},{"id":"https://openalex.org/C39432304","wikidata":"https://www.wikidata.org/wiki/Q188847","display_name":"Environmental science","level":0,"score":0.3524383306503296},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.341583788394928},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2821757197380066},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.16656893491744995},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12144067883491516},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.11500906944274902},{"id":"https://openalex.org/C188027245","wikidata":"https://www.wikidata.org/wiki/Q750446","display_name":"Polymer chemistry","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1038/s42256-024-00908-5","is_oa":false,"landing_page_url":"https://doi.org/10.1038/s42256-024-00908-5","pdf_url":null,"source":{"id":"https://openalex.org/S2912241403","display_name":"Nature Machine Intelligence","issn_l":"2522-5839","issn":["2522-5839"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Machine Intelligence","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/2","display_name":"Zero hunger","score":0.5199999809265137}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":51,"referenced_works":["https://openalex.org/W2103901746","https://openalex.org/W2113679889","https://openalex.org/W2121291798","https://openalex.org/W2134089414","https://openalex.org/W2138863122","https://openalex.org/W2154680970","https://openalex.org/W2166123725","https://openalex.org/W2572263783","https://openalex.org/W2599417231","https://openalex.org/W2736920791","https://openalex.org/W2743473392","https://openalex.org/W2745006471","https://openalex.org/W2753961085","https://openalex.org/W2773939681","https://openalex.org/W2782371622","https://openalex.org/W2792809884","https://openalex.org/W2913972921","https://openalex.org/W2921815890","https://openalex.org/W2938868597","https://openalex.org/W2993103758","https://openalex.org/W3022735613","https://openalex.org/W3042742581","https://openalex.org/W3046066345","https://openalex.org/W3081371328","https://openalex.org/W3091506611","https://openalex.org/W3104596207","https://openalex.org/W3120084484","https://openalex.org/W3135367836","https://openalex.org/W3161138487","https://openalex.org/W3164173442","https://openalex.org/W3168040031","https://openalex.org/W3177828909","https://openalex.org/W3189549418","https://openalex.org/W4221166842","https://openalex.org/W4225002452","https://openalex.org/W4226404011","https://openalex.org/W4296412923","https://openalex.org/W4304481015","https://openalex.org/W4308999955","https://openalex.org/W4318034610","https://openalex.org/W4324308122","https://openalex.org/W4382537366","https://openalex.org/W4382631636","https://openalex.org/W4385302529","https://openalex.org/W4385346076","https://openalex.org/W4388592083","https://openalex.org/W4392846567","https://openalex.org/W4393469671","https://openalex.org/W4393624721","https://openalex.org/W4394698525","https://openalex.org/W6967992243"],"related_works":["https://openalex.org/W2210738511","https://openalex.org/W2487541429","https://openalex.org/W1910109602","https://openalex.org/W2080583581","https://openalex.org/W4297131566","https://openalex.org/W2017364432","https://openalex.org/W2329606903","https://openalex.org/W3156493549","https://openalex.org/W3195915274","https://openalex.org/W3158976456"],"abstract_inverted_index":null,"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":1}],"updated_date":"2026-07-14T08:27:34.040176","created_date":"2025-10-10T00:00:00"}
