由于节点程度而导致边缘存在的概率:基于网络的预测的基线
Michael Zietz1,2,3, Daniel S Himmelstein1,4, Kyle Kloster5,6
1Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA.
GigaScience
|February 7, 2024
概括
节点程度显著影响生物医学网络预测. 一个新的排列框架揭示了网络结构,而不仅仅是节点程度,往往只解释预测性能的一小部分.
科学领域:
- 计算生物学 计算生物学
- 网络科学 网络科学
- 生物信息学是一种生物信息学.
背景情况:
- 生物医学发现任务,如基因功能预测和药物重定位,依赖于网络边缘预测.
- 节点度分布在生物网络上有所不同,可能会影响预测.
研究的目的:
- 引入一个网络排列框架来量化节点度对边缘预测准确性的影响.
- 为了区分从节点级别到特定网络连接的性能贡献.
主要方法:
- 开发了一个网络变换框架,以隔离节点程度的影响.
- 为评估基线预测性能而生成仅度特征.
- 将整体性能分解为可归因度和网络特定的组件.
主要成果:
- 节点级通常占生物医学网络预测性能的很大一部分.
- 归因于特定网络连接的性能往往是一个次要的组成部分.
- 节点度的影响可能导致不特定或误导性预测.
结论:
- 研究人员在解释边缘预测结果时必须考虑节点度偏差.
- 拟议的排列方法为评估预测特异性提供了一个关键的基线.
- 开源的Python软件包"xswap"可用于实现这些方法.
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