Related papers: What Makes a Bacterial Model a Good Reservoir Comp…
Biological neural networks can perform complex computations to predict their environment, far above the limited predictive capabilities of individual neurons. While conventional approaches to understanding these computations often focus on…
Despite major environmental and genetic differences, microbial metabolic networks are known to generate consistent physiological outcomes across vastly different organisms. This remarkable robustness suggests that, at least in bacteria,…
Bacteria are easily characterizable model organisms with an impressively complicated set of capabilities. Among their capabilities is quorum sensing, a detailed cell-cell signaling system that may have a common origin with eukaryotic…
The identification of cellular objectives is one of the central topics in the research of microbial metabolic networks. In particular, the information about a cellular objective is needed in flux balance analysis which is a commonly used…
Physical reservoir computing is a computational framework that implements spatiotemporal information processing directly within physical systems. By exciting nonlinear dynamical systems and creating linear models from their state, we can…
Metagenomics has revealed hundreds of bacterial species in almost all microbiota. In a few well-studied cases, bacterial communities have been observed to coordinate their metabolic fluxes. In principle, bacteria can divide tasks to reap…
Microbial ecosystems are remarkably diverse, stable, and often consist of a balanced mixture of core and peripheral species. Here we propose a conceptual model exhibiting all these emergent properties in quantitative agreement with real…
In this paper, we present a biologically grounded approach to reservoir computing (RC), in which a network of cultured biological neurons serves as the reservoir substrate. This system, referred to as biological reservoir computing (BRC),…
Which properties of metabolic networks can be derived solely from stoichiometric information about the network's constituent reactions? Predictive results have been obtained by Flux Balance Analysis (FBA), by postulating that cells set…
The Reservoir Computing (RC) framework states that any non-linear, input-driven dynamical system (the reservoir) exhibiting properties such as a fading memory and input separability can be trained to perform computational tasks. This broad…
Reservoir computing is a machine learning paradigm that transforms the transient dynamics of high-dimensional nonlinear systems for processing time-series data. Although reservoir computing was initially proposed to model information…
Metagenomics has lowered the barrier to microbial discovery--enabling the identification of novel microbes without isolation--but cultures remain imperative for the deep study of microbes. Cultivation and isolation of non-model microbes…
Segregation of populations is a key question in evolution theory. One important aspect is the relation between spatial organization and the population's composition. Here we study a specific example -- sectors in expanding bacterial…
We propose an extended reservoir computer that shows the functional differentiation of neurons. The reservoir computer is developed to enable changing of the internal reservoir using evolutionary dynamics, and we call it an evolutionary…
In this paper, we introduce a paradigm for reservoir computing (RC) that leverages a pool of cultured biological neurons as the reservoir substrate, creating a biological reservoir computing (BRC). This system operates similarly to an echo…
As demand for computational resources reaches unprecedented levels, research is expanding into the use of complex material substrates for computing. In this study, we interface with a model of a hydrodynamic system, under development by a…
Reservoir computing has emerged as a powerful framework for time series modelling and forecasting including the prediction of discontinuous transitions. However, the mechanism behind its success is not yet fully understood. This letter…
Communication and coordination play a major role in the ability of bacterial cells to adapt to ever changing environments and conditions. Recent work has shown that such coordination underlies several aspects of bacterial responses…
One of the main properties of biological systems is modularity, which manifests itself at all levels of their organization, starting with the level of molecular genetics, ending with the level of whole organisms and their communities. In a…
The solution space of genome-scale models of cellular metabolism provides a map between physically viable flux configurations and cellular metabolic phenotypes described, at the most basic level, by the corresponding growth rates. By…