Building Models for Biopathway Dynamics Using Intrinsic Dimensionality Analysis

TL;DR

This paper explores the use of dimension reduction and nonlinear time series analysis to model and understand high-dimensional biological data, specifically focusing on yeast pheromone signaling pathways.

Contribution

It demonstrates the application of dimension reduction techniques to molecular signaling data and compares their effectiveness with nonlinear time series analysis methods.

Findings

Dimension reduction helps identify critical biological processes.

Nonlinear time series analysis provides insights into signal dynamics.

Methods improve understanding of high-dimensional biological datasets.

Abstract

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.