利用内在连续性分析建立生物通路动力学模型
Building Models for Biopathway Dynamics Using Intrinsic Dimensionality Analysis
摘要：
对许多（如果不是所有）科学领域来说，一项重要任务是有效的知识整合、测试和编纂。它通常在可控的计算环境中通过模型构造来解决。尽管如此，基于计算机模拟的观测的吞吐量对于彻底的分析来说变得同样棘手。分子生物学尤其如此，这是本研究的一个主题。在这个项目中，我们的目标是测试一些方法来处理维数灾难。其中，我们发现降维技术特别吸引人。它们可用于识别不相关的可变性，并有助于理解高维数据集的关键过程。此外，我们对数据集进行了非线性时间序列分析，因为这些是比较结果的成熟方法。为了研究降维方法的有用性，我们决定基于一个具体的样本集进行研究。这个例子取自系统生物学领域，涉及亚细胞信号传导的动态进化。特别地，数据集涉及酵母信息素途径，并使用随机模型在计算机上进行研究。该模型重建了交配信息素刺激的信号传播。本文首先阐述了分子信号背景下多维分析问题产生的原因，然后介绍了模型的选择、仿真细节以及得到的时间序列动力学。对所用方法的描述，然后对结果及其生物学解释进行讨论，最后完成论文。
英文摘要：
An important task for many if not all the scientific domains is efficient knowledge integration, testing and codification. It is often solved with model construction in a controllable computational environment. In spite of that, the throughput of in-silico simulation-based observations become similarly intractable for thorough analysis. This is especially the case in molecular biology, which served as a subject for this study. In this project, we aimed to test some approaches developed to deal with the curse of dimensionality. Among these we found dimension reduction techniques especially appealing. They can be used to identify irrelevant variability and help to understand critical processes underlying high-dimensional datasets. Additionally, we subjected our data sets to nonlinear time series analysis, as those are well established methods for results comparison. To investigate the usefulness of dimension reduction methods, we decided to base our study on a concrete sample set. The example was taken from the domain of systems biology concerning dynamic evolution of sub-cellular signaling. Particularly, the dataset relates to the yeast pheromone pathway and is studied in-silico with a stochastic model. The model reconstructs signal propagation stimulated by a mating pheromone. In the paper, we elaborate on the reason of multidimensional analysis problem in the context of molecular signaling, and next, we introduce the model of choice, simulation details and obtained time series dynamics. A description of used methods followed by a discussion of results and their biological interpretation finalize the paper.
机构、总结、中文摘要均由AI分析而来，可能存在错误，请以论文正文为准。
