将Aligned-UMAP应用于纵向生物医学研究
Anant Dadu1,2,3, Vipul K Satone4, Rachneet Kaur4
1Department of Computer Science, University of Illinois at Urbana-Champaign, Champaign, IL 61820, USA.
Patterns (New York, N.Y.)
|July 6, 2023
概括
对齐的UMAP可视化高维纵向数据,帮助生物发现. 仔细的参数调整对于最大限度地发挥其分析复杂生物医学数据集的潜力至关重要.
科学领域:
- 计算生物学 计算生物学
- 数据科学数据科学数据科学
- 生物信息学是一种生物信息学.
背景情况:
- 高维数据分析对于理解复杂的生物系统至关重要.
- 现有的缩小维度的方法往往仅限于横截面数据.
- 可视化纵向,高维数据集是一个重大挑战.
研究的目的:
- 引入和评估用于可视化高维纵向数据的Aligned-UMAP.
- 为了证明 Aligned-UMAP 在识别生物数据中的模式和轨迹方面的实用性.
- 提供有关参数调节的指导,以实现对齐-UMAP的最佳性能.
主要方法:
- 使用了Aligned-UMAP算法,这是统一的多元近似和投影 (UMAP) 的扩展.
- 在高维的纵向数据集上对算法的性能进行了基准测试.
- 实现代码为开源,以确保可重复性和广泛适用性.
主要成果:
- 对齐的UMAP有效地可视化高维的纵向数据集.
- 该算法可以识别生物数据中的重要模式和轨迹.
- 算法参数选择对可视化和分析的质量产生了重大影响.
结论:
- 对齐的UMAP是探索复杂,高维度纵向生物医学数据的宝贵工具.
- 需要仔细调整 Aligned-UMAP 的参数,才能充分发挥其潜力.
- 开源可用性提高了研究中对准UMAP的采用和推进.
相关概念视频
Longitudinal Studies
188
Longitudinal studies are also widely used in other medical and social science fields. For instance, in cardiovascular research, they can monitor patients' health over decades to identify risk factors for heart disease, such as high cholesterol or smoking, and evaluate the long-term effectiveness of preventive measures. Similarly, in mental health studies, researchers might follow individuals from adolescence into adulthood to understand the development and progression of conditions like...
188
Longitudinal Research
12.0K
Sometimes we want to see how people change over time, as in studies of human development and lifespan. When we test the same group of individuals repeatedly over an extended period of time, we are conducting longitudinal research. Longitudinal research is a research design in which data-gathering is administered repeatedly over an extended period of time. For example, we may survey a group of individuals about their dietary habits at age 20, retest them a decade later at age 30, and then again...
12.0K
Genome-wide Association Studies-GWAS
13.6K
Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
GWAS does not require the identification of the target gene involved in...
13.6K


