Genome feature exploration using hyperbolic Self-Organizing Maps

Martin C, Díaz Solórzano NN, Ontrup J, Nattkemper TW (2007)
In: Proceedings of the 6th International Workshop on Self-Organizing Maps (WSOM 2007). Bielefeld: Bielefeld University.

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Konferenzbeitrag | Veröffentlicht | Englisch
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Abstract / Bemerkung
The advent of sequencing technologies allows to reassess the relationship between species in the hierarchically organized tree of life. Self-Organizing Maps (SOM) in Euclidean and hyperbolic space are applied to genomic signatures of 350 different organisms of the two superkingdoms Bacteria and Archaea to link the sequence signature space to pre-defined taxonomic levels, i.e. the tree of life. In the hyperbolic space the SOMs are trained by either the standard algorithm (HSOM) or in a hierarchical manner (H²SOM). For evaluating the SOM performances, distances between organisms in the feature space, on the SOM grid and in the taxonomy tree are compared pair-wise. We show that the structure recovered using the different SOMs reflects the gold standard of current taxonomy. The distances between species are better preserved when using the HSOM or H²SOM which makes the hyperbolic space better suited for embedding the high dimensional genomic signatures.
Erscheinungsjahr
Titel des Konferenzbandes
Proceedings of the 6th International Workshop on Self-Organizing Maps (WSOM 2007)
Konferenz
WSOM 2007
Konferenzort
Bielefeld, Germany
Konferenzdatum
2007-09-03 – 2007-09-06
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Martin C, Díaz Solórzano NN, Ontrup J, Nattkemper TW. Genome feature exploration using hyperbolic Self-Organizing Maps. In: Proceedings of the 6th International Workshop on Self-Organizing Maps (WSOM 2007). Bielefeld: Bielefeld University; 2007.
Martin, C., Díaz Solórzano, N. N., Ontrup, J., & Nattkemper, T. W. (2007). Genome feature exploration using hyperbolic Self-Organizing Maps. Proceedings of the 6th International Workshop on Self-Organizing Maps (WSOM 2007) Bielefeld: Bielefeld University. doi:10.2390/biecoll-wsom2007-140
Martin, C., Díaz Solórzano, N. N., Ontrup, J., and Nattkemper, T. W. (2007). “Genome feature exploration using hyperbolic Self-Organizing Maps” in Proceedings of the 6th International Workshop on Self-Organizing Maps (WSOM 2007) (Bielefeld: Bielefeld University).
Martin, C., et al., 2007. Genome feature exploration using hyperbolic Self-Organizing Maps. In Proceedings of the 6th International Workshop on Self-Organizing Maps (WSOM 2007). Bielefeld: Bielefeld University.
C. Martin, et al., “Genome feature exploration using hyperbolic Self-Organizing Maps”, Proceedings of the 6th International Workshop on Self-Organizing Maps (WSOM 2007), Bielefeld: Bielefeld University, 2007.
Martin, C., Díaz Solórzano, N.N., Ontrup, J., Nattkemper, T.W.: Genome feature exploration using hyperbolic Self-Organizing Maps. Proceedings of the 6th International Workshop on Self-Organizing Maps (WSOM 2007). Bielefeld University, Bielefeld (2007).
Martin, Christian, Díaz Solórzano, Naryttza Namelly, Ontrup, Jörg, and Nattkemper, Tim Wilhelm. “Genome feature exploration using hyperbolic Self-Organizing Maps”. Proceedings of the 6th International Workshop on Self-Organizing Maps (WSOM 2007). Bielefeld: Bielefeld University, 2007.

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