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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...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
F1000 Research Limited
2020
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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 |
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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 |