对基因表达数据集的非负矩阵因子化模型的最佳等级的决定使用单位不变膝盖方法:为等级选择开发和评估肘部方法
1Department of Biomedical Engineering, Düzce University, Düzce, Turkey.
JMIR bioinformatics and biotechnology
|June 27, 2024
概括
使用肘部方法的新单元不变膝盖 (UIK) 方法改善了对基因表达数据的非负矩阵因子化 (NMF) 排名选择. 这种更快,更高效的方法与现有指标相比,提供了优越的计算性能.
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.
- 数据分析 数据分析
背景情况:
- 基因表达数据分析需要强大的计算方法.
- 非负矩阵因子化 (NMF) 有效地从基因表达微阵列中提取见解.
- 在NMF中确定最佳排名 (r) 是一个重大挑战,在最佳技术上没有共识.
研究的目的:
- 根据肘法为NMF提出一种新的等级选择指标.
- 为了将拟议的度量与已建立的共性度量进行比较.
- 通过改进NMF等级确定来增强基因表达数据的分析.
主要方法:
- 在基因表达数据集上使用Unit Invariant Knee (UIK) 方法进行NMF排名选择.
- 在UIK方法中,通过在余平方和中检测曲率的第一个拐点来确定最佳排名.
- 这种方法使用极端距离估计器来准确识别膝盖点.
主要成果:
- 该UIK方法成功地应用于来自急性淋巴细胞白血病和急性髓性白血病样本的基因表达数据.
- 该UIK方法表现出易于执行,速度和独立于先验排序值输入或有影响力的初始参数.
- 在不同的算法中对NMF结果进行了比较,突出了UIK方法的效率.
结论:
- 肘部方法,特别是UIK实现,为基因表达和模拟突变数据提供可靠的排名预测.
- 在速度和计算效率方面,UIK方法超越了传统技术,消除了对曲线的视觉检查的需求.
- 基于肘部方法的提议的排名调整方法在基因表达数据分析中提供了理论上的优势,而不是基因表达数据分析的cophenetic测量.
更多相关视频
相关概念视频
01:29Mechanistic Models: Compartment Models in Algorithms for Numerical Problem Solving
48
Mechanistic models play a crucial role in algorithms for numerical problem-solving, particularly in nonlinear mixed effects modeling (NMEM). These models aim to minimize specific objective functions by evaluating various parameter estimates, leading to the development of systematic algorithms. In some cases, linearization techniques approximate the model using linear equations.
In individual population analyses, different algorithms are employed, such as Cauchy's method, which uses a...
In individual population analyses, different algorithms are employed, such as Cauchy's method, which uses a...
48
01:21Friedman Two-way Analysis of Variance by Ranks
180
Friedman's Two-Way Analysis of Variance by Ranks is a nonparametric test designed to identify differences across multiple test attempts when traditional assumptions of normality and equal variances do not apply. Unlike conventional ANOVA, which requires normally distributed data with equal variances, Friedman's test is ideal for ordinal or non-normally distributed data, making it particularly useful for analyzing dependent samples, such as matched subjects over time or repeated measures...
180
01:02Ranks
236
Unlike parametric methods, nonparametric statistics are ideal for nominal and ordinal data, requiring fewer assumptions about the population's nature or distribution. This makes nonparametric methods easier to apply and interpret, as they do not depend on parameters like mean or standard deviation. One common approach in nonparametric analysis is to sort data according to a specific criterion. For instance, we might arrange weather data from hottest to coldest days in a month or rank cities...
236
01:21Wilcoxon Rank-Sum Test
176
The Wilcoxon rank-sum test, also known as the Mann-Whitney U test, is a nonparametric test used to determine if there is a significant difference between the distributions of two independent samples. This test is designed specifically for two independent populations and has the following key requirements:
176
01:02Quantifying and Rejecting Outliers: The Grubbs Test
1.5K
Sometimes, a data set can have a recorded numerical observation that greatly deviates from the rest of the data. Assuming that the data is normally distributed, a statistical method called the Grubbs test can be used to determine whether the observation is truly an outlier. To perform a two-tailed Grubbs test, first, calculate the absolute difference between the outlier and the mean. Then, calculate the ratio between this difference and the standard deviation of the sample. This...
1.5K
01:14Wilcoxon Signed-Ranks Test for Median of Single Population
117
The Wilcoxon signed-rank test for the median of a single population is a nonparametric test used to evaluate whether the median of a population differs from a specified value. Unlike parametric tests, it does not require data to follow a normal distribution, making it suitable for non-normal or small samples. The test begins by calculating the difference (d) between each observation and the hypothesized median. The absolute values of these differences are ranked in ascending order, with ties...
117