{"id":"https://openalex.org/W4378804442","doi":"https://doi.org/10.1145/3592686.3592742","title":"Viabin: A novel method for Overlapped Binning of Metagenomic Contigs using ZINB-autodecoder and Assembly Graphs","display_name":"Viabin: A novel method for Overlapped Binning of Metagenomic Contigs using ZINB-autodecoder and Assembly Graphs","publication_year":2023,"publication_date":"2023-02-10","ids":{"openalex":"https://openalex.org/W4378804442","doi":"https://doi.org/10.1145/3592686.3592742"},"language":"en","primary_location":{"id":"doi:10.1145/3592686.3592742","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3592686.3592742","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2023 3rd International Conference on Bioinformatics and Intelligent Computing","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/A5059087261","display_name":"Fangyu Yu","orcid":"https://orcid.org/0000-0001-9113-3148"},"institutions":[{"id":"https://openalex.org/I194450716","display_name":"Jilin University","ror":"https://ror.org/00js3aw79","country_code":"CN","type":"education","lineage":["https://openalex.org/I194450716"]},{"id":"https://openalex.org/I4210100255","display_name":"Beijing Academy of Artificial Intelligence","ror":"https://ror.org/016a74861","country_code":"CN","type":"other","lineage":["https://openalex.org/I4210100255"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Fangyu Yu","raw_affiliation_strings":["School of Artificial Intelligence, Jilin University, China"],"raw_orcid":"https://orcid.org/0000-0001-9113-3148","affiliations":[{"raw_affiliation_string":"School of Artificial Intelligence, Jilin University, China","institution_ids":["https://openalex.org/I4210100255","https://openalex.org/I194450716"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070353791","display_name":"Ziming Yan","orcid":"https://orcid.org/0000-0002-6163-0845"},"institutions":[{"id":"https://openalex.org/I194450716","display_name":"Jilin University","ror":"https://ror.org/00js3aw79","country_code":"CN","type":"education","lineage":["https://openalex.org/I194450716"]},{"id":"https://openalex.org/I4210100255","display_name":"Beijing Academy of Artificial Intelligence","ror":"https://ror.org/016a74861","country_code":"CN","type":"other","lineage":["https://openalex.org/I4210100255"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ziming Yan","raw_affiliation_strings":["School of Artificial Intelligence, Jilin University, China"],"raw_orcid":"https://orcid.org/0000-0002-6163-0845","affiliations":[{"raw_affiliation_string":"School of Artificial Intelligence, Jilin University, China","institution_ids":["https://openalex.org/I4210100255","https://openalex.org/I194450716"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101683169","display_name":"Fu Liu","orcid":"https://orcid.org/0000-0003-4378-3140"},"institutions":[{"id":"https://openalex.org/I194450716","display_name":"Jilin University","ror":"https://ror.org/00js3aw79","country_code":"CN","type":"education","lineage":["https://openalex.org/I194450716"]},{"id":"https://openalex.org/I4210136497","display_name":"Jilin Medical University","ror":"https://ror.org/03mzw7781","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210136497"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fu Liu","raw_affiliation_strings":["College of Communication Engineering, Jilin University, China"],"raw_orcid":"https://orcid.org/0000-0003-4378-3140","affiliations":[{"raw_affiliation_string":"College of Communication Engineering, Jilin University, China","institution_ids":["https://openalex.org/I4210136497","https://openalex.org/I194450716"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5059087261"],"corresponding_institution_ids":["https://openalex.org/I194450716","https://openalex.org/I4210100255"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.2439606,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"310","last_page":"314"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998999834060669,"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":0.9998999834060669,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9977999925613403,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9936000108718872,"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/contig","display_name":"Contig","score":0.9704827070236206},{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.752007246017456},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5771521329879761},{"id":"https://openalex.org/keywords/autoencoder","display_name":"Autoencoder","score":0.4959937036037445},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.46925899386405945},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.44679924845695496},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.43134766817092896},{"id":"https://openalex.org/keywords/gaussian","display_name":"Gaussian","score":0.41927337646484375},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.32965701818466187},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3258594274520874},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.28574901819229126},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.13849389553070068},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.10548394918441772},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.07858571410179138}],"concepts":[{"id":"https://openalex.org/C59582021","wikidata":"https://www.wikidata.org/wiki/Q1128751","display_name":"Contig","level":4,"score":0.9704827070236206},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.752007246017456},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5771521329879761},{"id":"https://openalex.org/C101738243","wikidata":"https://www.wikidata.org/wiki/Q786435","display_name":"Autoencoder","level":3,"score":0.4959937036037445},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.46925899386405945},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.44679924845695496},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.43134766817092896},{"id":"https://openalex.org/C163716315","wikidata":"https://www.wikidata.org/wiki/Q901177","display_name":"Gaussian","level":2,"score":0.41927337646484375},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32965701818466187},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3258594274520874},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.28574901819229126},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.13849389553070068},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.10548394918441772},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.07858571410179138},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3592686.3592742","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3592686.3592742","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2023 3rd International Conference on Bioinformatics and Intelligent Computing","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.6800000071525574,"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":16,"referenced_works":["https://openalex.org/W1630959083","https://openalex.org/W1878521557","https://openalex.org/W2069689025","https://openalex.org/W2113679889","https://openalex.org/W2115026474","https://openalex.org/W2163352587","https://openalex.org/W2599417231","https://openalex.org/W2754579667","https://openalex.org/W2938868597","https://openalex.org/W2950954328","https://openalex.org/W3019706413","https://openalex.org/W3087455406","https://openalex.org/W3120084484","https://openalex.org/W3137047737","https://openalex.org/W4221065320","https://openalex.org/W4225007447"],"related_works":["https://openalex.org/W4313598112","https://openalex.org/W2097029864","https://openalex.org/W3128872455","https://openalex.org/W2078447778","https://openalex.org/W2973098646","https://openalex.org/W2337508844","https://openalex.org/W2926763004","https://openalex.org/W2996384775","https://openalex.org/W3005528502","https://openalex.org/W2200318732"],"abstract_inverted_index":{"Binning":[0],"the":[1,100,116,134,142,149],"metagenomic":[2],"contigs":[3,45,118,153,178],"into":[4],"potential":[5],"genomes":[6],"is":[7,87],"an":[8],"essential":[9],"step":[10],"to":[11,69,89,113,140,151,154,179],"investigate":[12],"and":[13,21,105,128],"characterize":[14],"various":[15],"genetic":[16],"materials":[17],"of":[18,34,43,137,169,177],"different":[19,54],"species":[20,55],"understand":[22],"microbial":[23],"populations.":[24],"Existing":[25],"tools":[26,76,139],"have":[27,57],"achieved":[28],"considerable":[29],"success":[30],"with":[31,133],"a":[32,50,63],"variety":[33],"datasets,":[35],"especially":[36],"in":[37,46,60],"long-length":[38],"sequences,":[39],"while":[40],"precise":[41],"classification":[42],"short":[44,170],"complex":[47],"metagenomics":[48],"remains":[49],"challenging":[51],"task.":[52],"Since":[53],"may":[56],"same":[58],"sequences":[59,172],"their":[61],"genomes,":[62],"contig":[64,74,86,171],"sequence":[65,129],"can":[66,98],"be":[67],"assigned":[68,88],"multiple":[70,180],"species.":[71,92],"However,":[72],"current":[73],"binning":[75,101,135,167],"merely":[77],"support":[78,175],"single":[79],"label":[80],"binning.":[81,144],"In":[82],"other":[83,138],"words,":[84],"each":[85],"just":[90],"one":[91],"This":[93],"article":[94],"introduced":[95],"Viabin":[96,108,162],"which":[97],"refine":[99],"results":[102,136],"using":[103],"ZINB-autoencoder":[104],"assembly":[106,126],"graphs.":[107],"used":[109],"Gaussian":[110],"mixture":[111],"model":[112],"preliminarily":[114],"classify":[115],"unclassified":[117],"encoded":[119],"by":[120],"autoencoder":[121],"based":[122],"on":[123],"ZINB.":[124],"Subsequently,":[125],"graph":[127],"feature":[130],"were":[131],"combined":[132],"complete":[141],"final":[143],"More":[145],"importantly,":[146],"it":[147],"had":[148],"capacity":[150],"assign":[152],"numerous":[155],"bins.":[156,181],"Experimental":[157],"3":[158],"datasets":[159],"demonstrated":[160],"that":[161],"could":[163],"not":[164],"only":[165],"improve":[166],"performance":[168],"but":[173],"also":[174],"assignment":[176]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
