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On Clustering Validation in Metagenomics Sequence Binning

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Advances in Bioinformatics and Computational Biology (BSB 2019)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 11347))

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Abstract

In clustering, one of the most challenging aspects is the validation, whose objective is to evaluate how good a clustering solution is. Sequence binning is a clustering task on metagenomic data analysis. The sequence clustering challenge is essentially putting together sequences belonging to the same genome. As a clustering problem it requires proper use of validation criteria of the discovered partitions. In sequence binning, the concepts of precision and recall, and F-measure index (external validation) are normally used as benchmark. However, on practice, information about the (sub) optimal number of cluster is unknown, so these metrics might be biased to an overestimated “ground truth”. In the case of sequence binning analysis, where the reference information about genomes is not available, how to evaluate the quality of bins resulting from a clustering solution? To answer this question we empirically study both quantitative (internal indexes) and qualitative aspects (biological soundness) while evaluating clustering solutions on the sequence binning problem. Our experimental study indicates that the number of clusters, estimated by binning algorithms, do not have as much impact on the quality of bins by means of biological soundness of the discovered clusters. The quality of the sub-optimal bins (greater than 90%) were identified in both rich and poor clustering partitions. Qualitative validation is essential for proper evaluation of a sequence binning solution, generating bins with sub-optimal quality. Internal indexes can only be used in compliance with qualitative ones as a trade-off between the number of partitions and biological soundness of its respective bins.

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Authors and Affiliations

  1. Computer Science Graduate Program, Federal University of Pará, Belém, Brazil

    Paulo Oliveira, Kleber Padovani & Ronnie Alves

  2. Instituto Tecnológico Vale, Belém, Brazil

    Ronnie Alves

Authors
  1. Paulo Oliveira
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  2. Kleber Padovani
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  3. Ronnie Alves
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Corresponding author

Correspondence to Ronnie Alves .

Editor information

Editors and Affiliations

  1. Fluminense Federal University, Niterói, Brazil

    Luis Kowada

  2. Fluminense Federal University, Niterói, Brazil

    Daniel de Oliveira

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Oliveira, P., Padovani, K., Alves, R. (2020). On Clustering Validation in Metagenomics Sequence Binning. In: Kowada, L., de Oliveira, D. (eds) Advances in Bioinformatics and Computational Biology. BSB 2019. Lecture Notes in Computer Science(), vol 11347. Springer, Cham. https://doi.org/10.1007/978-3-030-46417-2_1

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  • DOI: https://doi.org/10.1007/978-3-030-46417-2_1

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-46416-5

  • Online ISBN: 978-3-030-46417-2

  • eBook Packages: Computer ScienceComputer Science (R0)

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