Exploring noise, degeneracy and determinism in biological networks with the einet package

Abstract

The functioning of biological systems depends heavily on the interaction of its constituents at various levels of organization, be it at the subcellular level or at the ecosystem scale. To understand the complexity of such interactions in a more abstract yet workable way, people have turned to networks as a useful representation (Gosak et al., 2018;Gysi & Nowick, 2020). The use of network science and its tools in biology has exploded in the past two decades, owing to the burst of high-resolution data and improved computational capabilities. The application of network science has improved our fundamental understanding of many biological systems and structures, such as food webs (

Fire and Rhizosphere Effects on Bacterial Co-Occurrence Patterns

“…Another class of alternative indices with an enhanced ability to distinguish between networks is based on considering the eigenvalues of the Laplacian and/or adjacency matrices [ 58 ]. In this paper, the natural connectivity of the networks was calculated as follows: where λ i is the i th eigenvalue of the adjacency matrix.…”

“…To assess the interplay between stochasticity and determinism in the network’s ties the effective information index ( EI ) was estimated according to Klein et al [ 58 ]. First, the tie strengths of each variable i were averaged separately for each one, and the Shannon entropy (uncertainty) associated with averages were calculated (determinism component; ).…”

Interactions and information: Exploring task allocation in ant colonies using network analysis

“…We used Effective Information and its normalised measure, Effectiveness , to measure colony-level noisiness in the system, with respect to its underlying mechanisms (Hoel et al, 2020; Klein et al, 2022). Since we are considering the mechanism of communication and information flow among ants, Effective Information measures the level of predictability, or degeneracy, in ant-to-ant interactions.…”

“…For comparison, this is akin to the normalisation of Shannon diversity to Shannon equitability in ecological studies. Effectiveness was calculated for each observed network (i.e., for each day, for every colony), using the R package einet (Byrum et al, 2020; Klein et al, 2022).…”

“…Klein et al, 2022). Since we are considering the mechanism of communication and information flow among ants, Effective Information measures the level of predictability, or degeneracy, in ant-to-ant interactions.…”