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Networks are fundamental building blocks for representing data, and computations. Remarkable progress in learning in structurally defined (shallow or deep) networks has recently been achieved. Here we introduce evolutionary exploratory…
In physics of living systems, a search for relationships of a few macroscopic variables that emerge from many microscopic elements is a central issue. We evolved gene regulatory networks so that the expression of target genes (partial…
Robustness and evolvability are essential properties to the evolution of biological networks. To determine if a biological network is robust and/or evolvable, it is required to compare its functions before and after mutations. However, this…
Behavioral homogeneity is often critical for the functioning of network systems of interacting entities. In power grids, whose stable operation requires generator frequencies to be synchronized--and thus homogeneous--across the network,…
Learning-based methods for inverse problems, adapting to the data's inherent structure, have become ubiquitous in the last decade. Besides empirical investigations of their often remarkable performance, an increasing number of works…
Gene regulatory networks typically have low in-degrees, whereby any given gene is regulated by few of the genes in the network. What mechanisms might be responsible for these low in-degrees? Starting with an accepted framework of the…
Many natural, complex systems are remarkably stable thanks to an absence of feedback acting on their elements. When described as networks, these exhibit few or no cycles, and associated matrices have small leading eigenvalues. It has been…
Multicellular self-organization drives development in biological organisms, yet a comprehensive theory is lacking as basic properties of cells can complicate common approaches. Framing such properties by dynamic graphs led to new…
Switching of the direction of flagella rotations is the key control mechanism governing the chemotactic activity of E. coli and many other bacteria. Power-law distributions of switching times are most peculiar because their emergence cannot…
Failure, damage spread and recovery crucially underlie many spatially embedded networked systems ranging from transportation structures to the human body. Here we study the interplay between spontaneous damage, induced failure and recovery…
Modeling biological networks serves as both a major goal and an effective tool of systems biology in studying mechanisms that orchestrate the activities of gene products in cells. Biological networks are context specific and dynamic in…
Networks (graphs) in psychology are often restricted to settings without interventions. Here we consider a framework borrowed from biology that involves multiple interventions from different contexts (observations and experiments) in a…
A kinetic equation is derived for the phase density of a system of point particles, generating a system of integro-differential equations for distribution functions that have a deterministic meaning. The derivation took into account the…
The concept of network immunity, i.e., the robustness of the network connectivity after a random deletion of edges or vertices, has been investigated in biological or communication networks. We apply this concept to a self-assembling,…
A biological system achieve homeostasis when there is a regulated quantity that is maintained within a narrow range of values. Here we consider homeostasis as a phenomenon of network dynamics. In this context, we improve a general theory…
In many organisms the expression levels of each gene are controlled by the activation levels of known "Transcription Factors" (TF). A problem of considerable interest is that of estimating the "Transcription Regulation Networks" (TRN)…
We prove that complex networks of interactions have the capacity to regulate and buffer unpredictable fluctuations in production events. We show that non-bursty network-driven activation dynamics can effectively regulate the level of…
We introduce a quantitative measure of the capacity of a small biological network to evolve. We apply our measure to a stochastic description of the experimental setup of Guet et al. (Science 296:1466, 2002), treating chemical inducers as…
This work concerns the question of how two important dynamical properties, oscillations and bistability, emerge in an important biological signaling network. Specifically, we consider a model for dual-site phosphorylation and…
The possibility that evolutionary forces -- together with a few fundamental factors such as thermodynamic constraints, specific computational features enabling information processing, and ecological processes -- might constrain the logic of…