.png){kind=icon}
返回
Towards a comprehensive evaluation of dimension reduction methods for transcriptomic data visualization
.png){kind=icon}
OA
AI
DOI：10.1038/s42003-022-03628-x.png)
.png){kind=icon}
.png){kind=icon}
分享.png){kind=icon}
收藏
摘要
En 中文
The authors provide an evaluation framework for dimension reduction methods that illuminates the strengths and weaknesses of different algorithms, and applies this framework to evaluate the PCA, t-SNE, UMAP, TriMap, PaCMAP, ForceAtlas2, and PHATE algorithms. Dimension reduction (DR) algorithms project data from high dimensions to lower dimensions to enable visualization of interesting high-dimensional structure. DR algorithms are widely used for analysis of single-cell transcriptomic data. Despite widespread use of DR algorithms such as t-SNE and UMAP, these algorithms have characteristics that lead to lack of trust: they do not preserve important aspects of high-dimensional structure and are sensitive to arbitrary user choices. Given the importance of gaining insights from DR, DR methods should be evaluated carefully before trusting their results. In this paper, we introduce and perform a systematic evaluation of popular DR methods, including t-SNE, art-SNE, UMAP, PaCMAP, TriMap and ForceAtlas2. Our evaluation considers five components: preservation of local structure, preservation of global structure, sensitivity to parameter choices, sensitivity to preprocessing choices, and computational efficiency. This evaluation can help us to choose DR tools that align with the scientific goals of the user.
AI总结
对已上传原文的论文进行重点信息的提取，主要内容包括：简要概述、研究摘要、背景介绍、关键亮点、图文解析、展望与总结。
期刊
IF:
5.1
论文数:
1.1W
被引数:
3.2W
机构
引用论文
Task constraints modulate activation in right ventral lateral prefrontal cortex任务约束调节右腹外侧前额叶皮层的激活.png)
NeuroImage
NeuroImageIF0
PREAI
分享收藏Fast interpolation-based t-SNE for improved visualization of single-cell RNA-seq data基于快速插值的t-sne可改善单细胞rna-seq数据的可视化NATURE METHODSOAAI
NATURE METHODSIF32.1
OAAI分享收藏viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemiaNATURE BIOTECHNOLOGY
OAAI
NATURE BIOTECHNOLOGYIF41.7
OAAI分享收藏Multiplexed droplet single-cell RNA-sequencing using natural genetic variation使用自然遗传变异的多重液滴单细胞RNA测序NATURE BIOTECHNOLOGYOAAI
NATURE BIOTECHNOLOGYIF41.7
OAAI分享收藏Visual analysis of mass cytometry data by hierarchical stochastic neighbour embedding reveals rare cell typesNATURE COMMUNICATIONSOAAI
NATURE COMMUNICATIONSIF15.7
OAAI分享收藏Binding of a 4-Methyl-4-Aza-Steroid to 5α-Reductase of Rat Liver and Prostate Microsomes4-甲基-4-氮杂-类固醇与大鼠肝脏和前列腺微粒体的5 α-还原酶的结合
PREAI
分享收藏分享收藏Integrated single-cell analysis of multicellular immune dynamics during hyperacute HIV-1 infection超急性HIV-1感染过程中多细胞免疫动力学的集成单细胞分析NATURE MEDICINEOAAI
NATURE MEDICINEIF50
OAAI分享收藏
查看更多内容