UMAP-assisted $K$-means clustering of large-scale SARS-CoV-2 mutation datasets
Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has a worldwide devastating effect. The understanding of evolution and transmission of SARS-CoV-2 is of paramount importance for the COVID-19 control, combating, and prevention. Due to the rapid growth of both the number of SARS-CoV-2 genome sequences and the number of unique mutations, the phylogenetic analysis of SARS-CoV-2 genome isolates faces an emergent large-data challenge. We introduce a dimension-reduced $k$-means clustering strategy to tackle this challenge. We examine the performance and effectiveness of three dimension-reduction algorithms: principal component analysis (PCA), t-distributed stochastic neighbor embedding (t-SNE), and uniform manifold approximation and projection (UMAP). By using four benchmark datasets, we found that UMAP is the best-suited technique due to its stable, reliable, and efficient performance, its ability to improve clustering accuracy, especially for large Jaccard distanced-based datasets, and its superior clustering visualization. The UMAP-assisted $k$-means clustering enables us to shed light on increasingly large datasets from SARS-CoV-2 genome isolates..
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Preprint| Erscheinungsjahr: |
2020 |
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| Erschienen: |
2020 |
| Enthalten in: |
arXiv.org - (2020) vom: 30. Dez. Zur Gesamtaufnahme - year:2020 |
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| Sprache: |
Englisch |
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| Beteiligte Personen: |
Hozumi, Yuta [VerfasserIn] |
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| Links: |
Volltext [kostenfrei] |
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| PPN (Katalog-ID): |
XAR019650175 |
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| 520 | |a Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has a worldwide devastating effect. The understanding of evolution and transmission of SARS-CoV-2 is of paramount importance for the COVID-19 control, combating, and prevention. Due to the rapid growth of both the number of SARS-CoV-2 genome sequences and the number of unique mutations, the phylogenetic analysis of SARS-CoV-2 genome isolates faces an emergent large-data challenge. We introduce a dimension-reduced $k$-means clustering strategy to tackle this challenge. We examine the performance and effectiveness of three dimension-reduction algorithms: principal component analysis (PCA), t-distributed stochastic neighbor embedding (t-SNE), and uniform manifold approximation and projection (UMAP). By using four benchmark datasets, we found that UMAP is the best-suited technique due to its stable, reliable, and efficient performance, its ability to improve clustering accuracy, especially for large Jaccard distanced-based datasets, and its superior clustering visualization. The UMAP-assisted $k$-means clustering enables us to shed light on increasingly large datasets from SARS-CoV-2 genome isolates. | ||
| 700 | 1 | |a Wang, Rui |e verfasserin |4 aut | |
| 700 | 1 | |a Yin, Changchuan |e verfasserin |4 aut | |
| 700 | 1 | |a Wei, Guo-Wei |e verfasserin |4 aut | |
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