Related papers: Identifying the phase diagram structure for optima…
Gene regulation is a series of processes that control gene expression and its extent. The connections among genes and their regulatory molecules, usually transcription factors, and a descriptive model of such connections, are known as gene…
In this paper, we consider the problem of optimal exogenous control of gene regulatory networks. Our approach consists in adapting an established reinforcement learning algorithm called the fitted Q iteration. This algorithm infers the…
The irreducible complexity of natural phenomena has led Graph Neural Networks to be employed as a standard model to perform representation learning tasks on graph-structured data. While their capacity to capture local and global patterns is…
This work clarifies the relation between network circuit (topology) and behavior (information transmission and synchronization) in active networks, e.g. neural networks. As an application, we show how to determine a network topology that is…
Networked systems display complex patterns of interactions between a large number of components. In physical networks, these interactions often occur along structural connections that link components in a hard-wired connection topology,…
Connectivity networks have recently become widely used in biology due to increasing amounts of information on the physical and functional links between individual proteins. This connectivity data provides valuable material for expanding our…
The human organism is an integrated network where complex physiologic systems, each with its own regulatory mechanisms, continuously interact, and where failure of one system can trigger a breakdown of the entire network. Identifying and…
The organization of interactions in complex systems can be described by networks connecting different units. These graphs are useful representations of the local and global complexity of the underlying systems. The origin of their…
Biological transport networks are highly optimized structures that ensure power-efficient distribution of fluids across various domains, including animal vasculature and plant venation. Theoretically, these networks can be described as…
Rapid advances in high-throughput technologies have led to considerable interest in analyzing genome-scale data in the context of biological pathways, with the goal of identifying functional systems that are involved in a given phenotype.…
Understanding the rules underlying organismal development is a major unsolved problem in biology. Each cell in a developing organism responds to signals in its local environment by dividing, excreting, consuming, or reorganizing, yet how…
The structure and dynamics of a typical biological system are complex due to strong and inhomogeneous interactions between its constituents. The investigation of such systems with classical mathematical tools, such as differential equations…
Transmission topology control is a tool used by system operators in the role of a control action taken into account as a preventive or corrective action relative to a specific outage or set of outages. However, their inclusion in most…
The two most fundamental processes describing change in biology, development and evolu-tion, occur over drastically different timescales, difficult to reconcile within a unified framework. Development involves temporal sequences of cell…
Based on a recently proposed non-equilibrium mechanism for spatial pattern formation [cond-mat/0312366] we study how morphogenesis can be controlled by locally coupled discrete dynamical networks, similar to gene regulation networks of…
A plethora of computational models have been developed in recent decades to account for the morphogenesis of complex biological fluid networks, such as capillary beds. Contemporary adaptation models are based on optimization schemes where…
Systems of networked mobile robots, such as unmanned aerial or ground vehicles, will play important roles in future military and commercial applications. The communications for such systems will typically be over wireless links and may…
We quantify the influence of the topology of a transcriptional regulatory network on its ability to process environmental signals. By posing the problem in terms of information theory, we may do this without specifying the function…
We show how any system with morphological degrees of freedom and locally limited free energy will, under the constraints of the free energy principle, evolve toward a neuromorphic morphology that supports hierarchical computations in which…
The Integrated Information Theory provides a quantitative approach to consciousness and can be applied to neural networks. An embodied agent controlled by such a network influences and is being influenced by its environment. This involves,…