Standardized Approaches for Assessing Metagenomic Contig Binning Performance from Barnes-Hut t-Stochastic Neighbor Embeddings

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dc.contributor.authorCeballos J.
dc.contributor.authorAriza-Jiménez L.
dc.contributor.authorPinel N.
dc.contributor.departmentUniversidad EAFIT. Departamento de Cienciasspa
dc.contributor.researchgroupModelado Matemáticospa
dc.creatorCeballos J.
dc.creatorAriza-Jiménez L.
dc.creatorPinel N.
dc.date.accessioned2021-04-12T14:11:50Z
dc.date.available2021-04-12T14:11:50Z
dc.date.issued2020-01-01
dc.description.abstractThe performance of unsupervised methods for metagenomic binning is often assessed using simulated microbial communities. The lack of well-characterized evaluation protocols and approaches to community construction cognizant of biological realities impedes the rigorous assessment and standardization of the binning process. This work attempted to standardize performance evaluation using benchmark communities constructed according to the genome similarity metric Average Amino Acid identity. This approach allowed us to extend and deepen our previous research on the unsupervised binning of metagenomic sequence fragments based on low-dimensional embeddings of pentamer frequency profiles. Experimental results evidenced our method’s potential for the binning of metagenomic contigs to become an alternative to state-of-the-art methods such as MetaCluster 3.0. © 2020, Springer Nature Switzerland AG.eng
dc.identifierhttps://eafit.fundanetsuite.com/Publicaciones/ProdCientif/PublicacionFrw.aspx?id=9839
dc.identifier.doi10.1007/978-3-030-30648-9_101
dc.identifier.issn16800737
dc.identifier.otherSCOPUS;2-s2.0-85075697730
dc.identifier.urihttp://hdl.handle.net/10784/27907
dc.language.isoengeng
dc.publisherSPRINGER
dc.relation.urihttps://www.scopus.com/inward/record.uri?eid=2-s2.0-85075697730&doi=10.1007%2f978-3-030-30648-9_101&partnerID=40&md5=59e77a6d6b78ed38968f21eb6346515d
dc.rightshttps://v2.sherpa.ac.uk/id/publication/issn/1680-0737
dc.sourceIfmbe Proceedings
dc.subject.keywordBiomedical engineeringeng
dc.subject.keywordBiophysicseng
dc.subject.keywordEmbeddingseng
dc.subject.keywordFuzzy clusteringeng
dc.subject.keywordPetroleum reservoir evaluationeng
dc.subject.keywordStochastic systemseng
dc.subject.keywordBinningeng
dc.subject.keywordCluster validity indiceseng
dc.subject.keywordCommunity constructionseng
dc.subject.keywordEvaluation protocoleng
dc.subject.keywordMetagenomicseng
dc.subject.keywordMicrobial communitieseng
dc.subject.keywordState-of-the-art methodseng
dc.subject.keywordUnsupervised methodeng
dc.subject.keywordBenchmarkingeng
dc.titleStandardized Approaches for Assessing Metagenomic Contig Binning Performance from Barnes-Hut t-Stochastic Neighbor Embeddingseng
dc.typeinfo:eu-repo/semantics/conferencePapereng
dc.typeconferencePapereng
dc.typeinfo:eu-repo/semantics/publishedVersioneng
dc.typepublishedVersioneng
dc.type.localDocumento de conferenciaspa

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