在所有Lp规范下计算概括的cophenetic距离:一个近线性时间算法框架.
Paweł Górecki1, Alexey Markin2, Sriram Vijendran3
1Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Mazowieckie, Poland.
PLoS computational biology
|June 10, 2025
概括
我们介绍了一种新的算法,用于在所有Lp规范中有效计算通用共学距离. 这通过克服以前的计算局限性,推动了生物学中的大规模树木比较.
科学领域:
- 计算生物学 计算生物学
- 生物信息学是一种生物信息学.
- 算法科学 算法科学
背景情况:
- 哥芬尼距离是比较生物树木的关键指标.
- 现有的方法面临着大数据集的计算挑战.
- 以前的进步提供了近线性时间复杂性,但仅限于特定的矢量规范.
研究的目的:
- 开发一个近线性时间算法框架,用于所有Lp规范适用的通用共学距离.
- 提高大规模树木比较方法的可扩展性和多功能性.
- 解决先前框架在处理各种矢量规范方面的局限性.
主要方法:
- 开发了一种全新的算法框架,用于通用化的共学距离计算.
- 扩展框架以支持所有Lp向量规范.
- 进行了可扩展性研究以评估实际性能.
- 分析了跨越各种规范的距离元件的分布.
主要成果:
- 在所有 Lp 规范中实现了近线性时间复杂性,用于所有 Lp 规范中的通用化共学距离.
- 证明了新框架的实际性能和可扩展性.
- 提供了关于不同向量规范下的通用化共学距离行为的见解.
结论:
- 新的框架显著提高了大规模生物研究中通用共学距离的适用性.
- 这项工作克服了以前的局限性,使得这些指标可以更广泛地使用各种矢量规范.
- 这些发现有助于对大型生物数据集进行更具多样性和效率的比较分析.
更多相关视频
12:27Large-scale Reconstructions and Independent, Unbiased Clustering Based on Morphological Metrics to Classify Neurons in Selective Populations
Published on: February 15, 2017
6.9K
13:55Combined Immunofluorescence and DNA FISH on 3D-preserved Interphase Nuclei to Study Changes in 3D Nuclear Organization
Published on: February 3, 2013
18.3K
相关概念视频
Linear Approximation in Time Domain
69
Nonlinear systems often require sophisticated approaches for accurate modeling and analysis, with state-space representation being particularly effective. This method is especially useful for systems where variables and parameters vary with time or operating conditions, such as in a simple pendulum or a translational mechanical system with nonlinear springs.
For a simple pendulum with a mass evenly distributed along its length and the center of mass located at half the pendulum's length,...
For a simple pendulum with a mass evenly distributed along its length and the center of mass located at half the pendulum's length,...
69
Routh-Hurwitz Criterion II
199
In the application of the Routh-Hurwitz criterion, two specific scenarios can arise that complicate stability analysis.
The first scenario occurs when a singular zero appears in the first column of the Routh table. This situation creates a division by zero issues. To resolve this, a small positive or negative number, denoted as epsilon (∈), is substituted for the zero. The stability analysis proceeds by assuming a sign for ∈. If ∈ is positive, any sign change in the first...
The first scenario occurs when a singular zero appears in the first column of the Routh table. This situation creates a division by zero issues. To resolve this, a small positive or negative number, denoted as epsilon (∈), is substituted for the zero. The stability analysis proceeds by assuming a sign for ∈. If ∈ is positive, any sign change in the first...
199
Routh-Hurwitz Criterion I
184
Consider an electrical power grid, where stability is essential to prevent blackouts. The Routh-Hurwitz criterion is a valuable tool for assessing system stability under varying load conditions or faults. By analyzing the closed-loop transfer function, the Routh-Hurwitz criterion helps determine whether the system remains stable.
To apply the Routh-Hurwitz criterion, a Routh table is constructed. The table's rows are labeled with powers of the complex frequency variable s, starting from the...
To apply the Routh-Hurwitz criterion, a Routh table is constructed. The table's rows are labeled with powers of the complex frequency variable s, starting from the...
184
Linear Approximation in Frequency Domain
88
Linear systems are characterized by two main properties: superposition and homogeneity. Superposition allows the response to multiple inputs to be the sum of the responses to each individual input. Homogeneity ensures that scaling an input by a scalar results in the response being scaled by the same scalar.
In contrast, nonlinear systems do not inherently possess these properties. However, for small deviations around an operating point, a nonlinear system can often be approximated as linear....
In contrast, nonlinear systems do not inherently possess these properties. However, for small deviations around an operating point, a nonlinear system can often be approximated as linear....
88
Distance Corrections
26
To achieve precise distance measurements, especially in surveying and construction, certain corrections must be applied to account for potential sources of error like the standardization errors, temperature variations, and slope adjustments.Standardization error emerges when measurement equipment undergoes changes, such as wear, repairs, or weather impacts. To address this, surveyors compare the equipment’s readings to a standard. This process identifies any deviation that might lead to...
26
Central Limit Theorem
14.4K
The central limit theorem, abbreviated as clt, is one of the most powerful and useful ideas in all of statistics. The central limit theorem for sample means says that if you repeatedly draw samples of a given size and calculate their means, and create a histogram of those means, then the resulting histogram will tend to have an approximate normal bell shape. In other words, as sample sizes increase, the distribution of means follows the normal distribution more closely.
The sample size, n, that...
The sample size, n, that...
14.4K
