可扩展的格罗莫夫-瓦瑟斯坦基于生物时间序列的比较
Natalia Kravtsova1, Reginald L McGee Ii2, Adriana T Dawes3,4
1Department of Mathematics, The Ohio State University, 231 West 18th Avenue, Columbus, OH, 43210, USA.
Bulletin of mathematical biology
|July 6, 2023
概括
这项研究引入了一种新的最佳运输距离,用于比较生物时间序列轨迹,即使尺寸和数据点不同. 这种快速且可扩展的方法增强了对复杂生物数据的分析.
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
- 生物物理学的生物物理.
背景情况:
- 时间序列数据在生物研究中非常丰富.
- 将这些时间序列进行比较需要准确和高效的距离测量.
- 现有的方法面临着不同数据尺寸和间距的挑战.
研究的目的:
- 引入一种新的基于运输的最佳距离,用于比较生物时间序列.
- 为了应对不同尺寸,点数和轨迹间距所带来的挑战.
- 为生物学的时间序列分析提供快速,可扩展和准确的方法.
主要方法:
- 开发了一个修改后的格罗莫夫-瓦瑟斯坦距离优化程序.
- 为了计算效率,将问题缩小到一个一维的瓦瑟斯坦距离.
- 利用合格罗莫夫-瓦瑟斯坦重心来平均振荡时间序列.
主要成果:
- 拟议的距离提供了一个闭式解决方案,可以以高速计算.
- 经验评估表明,在各种生物数据集上表现强.
- 使用Fused Gromov-Wasserstein重心的平均值保留了比传统方法更多的轨迹特征.
结论:
- 新的距离测量器可以快速和有意义地比较生物时间序列.
- 它适用于广泛的生物数据分析任务.
- 该方法为分析复杂的生物动态提供了显著的优势.
相关概念视频
Evolutionary Relationships through Genome Comparisons
5.8K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
5.8K
Comparing the Survival Analysis of Two or More Groups
227
Survival analysis is a cornerstone of medical research, used to evaluate the time until an event of interest occurs, such as death, disease recurrence, or recovery. Unlike standard statistical methods, survival analysis is particularly adept at handling censored data—instances where the event has not occurred for some participants by the end of the study or remains unobserved. To address these unique challenges, specialized techniques like the Kaplan-Meier estimator, log-rank test, and...
227
Time-Series Graph
4.4K
A time-series graph is a line graph with repeated measurements taken at successive intervals of time. It is also called a time series chart. To construct a time-series graph, one must look at both pieces of a paired data set. The horizontal axis is used to plot the time increments, and the vertical axis is used to plot the values of the variable that one is measuring. By using the axes in this way, each point on the graph will correspond to time and a measured quantity. The points on the graph...
4.4K
Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes
12.6K
The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
12.6K
Gene Evolution - Fast or Slow?
7.2K
The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
In contrast, regions which code...
7.2K
Drug Concentration Versus Time Correlation
896
The plasma drug concentration-time curve is a crucial tool in pharmacokinetics, representing the drug's concentration in plasma at different time intervals post-administration. This curve illustrates the drug's journey from absorption into the systemic circulation, distribution to body tissues, and eventual elimination through excretion or biotransformation.
Two pivotal parameters are the minimum effective concentration (MEC) and the minimum toxic concentration (MTC). The MEC is the...
Two pivotal parameters are the minimum effective concentration (MEC) and the minimum toxic concentration (MTC). The MEC is the...
896


