Related papers: The coherent feed-forward loop acts as an efficien…

While biological vision systems rely heavily on feedback connections to iteratively refine perception, most artificial neural networks remain purely feedforward, processing input in a single static pass. In this work, we propose a…

The activation/repression of a given gene is typically regulated by multiple transcription factors (TFs) that bind at the gene regulatory region and recruit RNA polymerase (RNAP). The interactions between the promoter region and TFs and…

Directed information transmission is paramount for many social, physical, and biological systems. For neural systems, scientists have studied this problem under the paradigm of feedforward networks for decades. In most models of feedforward…

A growing set of applications consider the process of network formation by using subgraphs as a tool for generating the network topology. One of the pressing research challenges is thus to be able to use these subgraphs to understand the…

We present a stochastic framework to study signal transmission in a generic two-step cascade $\text{S} \rightarrow \text{X} \rightarrow \text{Y}$. Starting from a set of Langevin equations obeying Gaussian noise processes we calculate the…

Biological systems encode function not primarily in steady states, but in the structure of transient responses elicited by time-varying stimuli. Overshoots, biphasic dynamics, adaptation kinetics, fold-change detection, entrainment, and…

We consider feed-forward networks, that is, networks where cells can be divided into layers, such that every edge targeting a layer, excluding the first one, starts in the prior layer. A feed-forward system is a dynamical system that…

Information spreading in complex networks is often modeled as diffusing information with certain probability from nodes that possess it to their neighbors that do not. Information cascades are triggered when the activation of a set of…

In studying primate vision, a large body of work focuses on the first feedforward sweep. During this initial time window, information is thought to pass through ventral stream regions in a stage-like fashion in an effort to extract…

Molecular communication is an expanding body of research. Recent advances in biology have encouraged using genetically engineered bacteria as the main component in the molecular communication. This has stimulated a new line of research that…

The propagation of noise through parallel regulatory pathways is a characteristic feature of feed-forward loops in genetic networks. Although the contributions of the direct and indirect regulatory pathways of feed-forward loops to output…

In this paper, we present a canonical structure for controlling information flow in neural networks with an efficient feedback routing mechanism based on a strategy of Distributed Iterative Gating (DIGNet). The structure of this mechanism…

Many studies have shown that cells use temporal dynamics of signalling molecules to encode information. One particular class of temporal dynamics is persistent and transient signals, i.e. signals of long and short durations respectively. It…

We present a stochastic formalism for signal transduction processes in bacterial two-component system. Using elementary mass action kinetics, the proposed model takes care of signal transduction in terms of phosphotransfer mechanism between…

Biologists rely heavily on the language of information, coding, and transmission that is commonplace in the field of information theory as developed by Claude Shannon, but there is open debate about whether such language is anything more…

Living systems are often described utilizing informational analogies. An important open question is whether information is merely a useful conceptual metaphor, or intrinsic to the operation of biological systems. To address this question,…

Community structure is an important factor in the behavior of real-world networks because it strongly affects the stability and thus the phase transition order of the spreading dynamics. We here propose a reversible social contagion model…

In this paper, a two-hop network in which information is transmitted from a source via a relay to a destination is considered. It is assumed that the channels are static fading with additive white Gaussian noise. All nodes are equipped with…

This paper proposes new framework of communication system leveraging promising generation capabilities of multi-modal generative models. Regarding nowadays smart applications, successful communication can be made by conveying the perceptual…

GTPases regulate a wide range of cellular processes, such as intracellular vesicular transport, signal transduction, and protein translation. These hydrolase enzymes operate as biochemical switches by toggling between an active guanosine…