Cargando…

Generalized EmbedSOM on quadtree-structured self-organizing maps

EmbedSOM is a simple and fast dimensionality reduction algorithm, originally developed for its applications in single-cell cytometry data analysis. We present an updated version of EmbedSOM, viewed as an algorithm for landmark-directed embedding enrichment, and demonstrate that it works well even wi...

Descripción completa

Detalles Bibliográficos
Autores principales: Kratochvíl, Miroslav, Koladiya, Abhishek, Vondrášek, Jiří
Formato: Online Artículo Texto
Lenguaje:English
Publicado: F1000 Research Limited 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7255855/
https://www.ncbi.nlm.nih.gov/pubmed/32518625
http://dx.doi.org/10.12688/f1000research.21642.2
_version_ 1783539805759471616
author Kratochvíl, Miroslav
Koladiya, Abhishek
Vondrášek, Jiří
author_facet Kratochvíl, Miroslav
Koladiya, Abhishek
Vondrášek, Jiří
author_sort Kratochvíl, Miroslav
collection PubMed
description EmbedSOM is a simple and fast dimensionality reduction algorithm, originally developed for its applications in single-cell cytometry data analysis. We present an updated version of EmbedSOM, viewed as an algorithm for landmark-directed embedding enrichment, and demonstrate that it works well even with manifold-learning techniques other than the self-organizing maps. Using this generalization, we introduce an inwards-growing variant of self-organizing maps that is designed to mitigate some earlier identified deficiencies of EmbedSOM output. Finally, we measure the performance of the generalized EmbedSOM, compare several variants of the algorithm that utilize different landmark-generating functions, and showcase the functionality on single-cell cytometry datasets from recent studies.
format Online
Article
Text
id pubmed-7255855
institution National Center for Biotechnology Information
language English
publishDate 2020
publisher F1000 Research Limited
record_format MEDLINE/PubMed
spelling pubmed-72558552020-06-08 Generalized EmbedSOM on quadtree-structured self-organizing maps Kratochvíl, Miroslav Koladiya, Abhishek Vondrášek, Jiří F1000Res Software Tool Article EmbedSOM is a simple and fast dimensionality reduction algorithm, originally developed for its applications in single-cell cytometry data analysis. We present an updated version of EmbedSOM, viewed as an algorithm for landmark-directed embedding enrichment, and demonstrate that it works well even with manifold-learning techniques other than the self-organizing maps. Using this generalization, we introduce an inwards-growing variant of self-organizing maps that is designed to mitigate some earlier identified deficiencies of EmbedSOM output. Finally, we measure the performance of the generalized EmbedSOM, compare several variants of the algorithm that utilize different landmark-generating functions, and showcase the functionality on single-cell cytometry datasets from recent studies. F1000 Research Limited 2020-05-19 /pmc/articles/PMC7255855/ /pubmed/32518625 http://dx.doi.org/10.12688/f1000research.21642.2 Text en Copyright: © 2020 Kratochvíl M et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Software Tool Article
Kratochvíl, Miroslav
Koladiya, Abhishek
Vondrášek, Jiří
Generalized EmbedSOM on quadtree-structured self-organizing maps
title Generalized EmbedSOM on quadtree-structured self-organizing maps
title_full Generalized EmbedSOM on quadtree-structured self-organizing maps
title_fullStr Generalized EmbedSOM on quadtree-structured self-organizing maps
title_full_unstemmed Generalized EmbedSOM on quadtree-structured self-organizing maps
title_short Generalized EmbedSOM on quadtree-structured self-organizing maps
title_sort generalized embedsom on quadtree-structured self-organizing maps
topic Software Tool Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7255855/
https://www.ncbi.nlm.nih.gov/pubmed/32518625
http://dx.doi.org/10.12688/f1000research.21642.2
work_keys_str_mv AT kratochvilmiroslav generalizedembedsomonquadtreestructuredselforganizingmaps
AT koladiyaabhishek generalizedembedsomonquadtreestructuredselforganizingmaps
AT vondrasekjiri generalizedembedsomonquadtreestructuredselforganizingmaps