Inference and Validation of the Structure of Lotka-Volterra Models

Abstract

For close to a century, Lotka-Volterra (LV) models have been used to investigate interactions among populations of different species. For a few species, these investigations are straightforward. However, with the arrival of large and complex microbiomes, unprecedently rich data have become available and await analysis. In particular, these data require us to ask which microbial populations of a mixed community affect other populations, whether these influences are activating or inhibiting and how the interactions change over time. Here we present two new inference strategies for interaction parameters that are based on a new algebraic LV inference (ALVI) method. One strategy uses different survivor profiles of communities grown under similar conditions, while the other pertains to time series data. In addition, we address the question of whether observation data are compliant with the LV structure or require a richer modeling format. The code and data used in this manuscript are available at "https://github.com/LBSA-VoitLab/Inference_and_Validation_of_the_Structure_of_Lotka_Volterra_Models".