Related papers: It is useful to analyze correlation graphs

Graphs are structured data that models complex relations between real-world entities. Heterophilic graphs, where linked nodes are prone to be with different labels or dissimilar features, have recently attracted significant attention and…

Background: Acceleration of adaptation dynamics by stress-induced hypermutation has been found experimentally. Evolved evolvability is a prominent explanation. We investigate a more generally applicable explanation by a physical constraint.…

Large-scale perturbations in the microbiome constitution are strongly correlated, whether as a driver or a consequence, with the health and functioning of human physiology. However, understanding the difference in the microbiome profiles of…

The linear response to temperature changes is derived for systems with overdamped stochastic dynamics. Holding both in transient and steady state conditions, the results allow to compute nonequilibrium thermal susceptibilities from…

In this brief review, we critically examine the recent work done on correlation-based networks in financial systems. The structure of empirical correlation matrices constructed from the financial market data changes as the individual stock…

Biological sensory systems react to changes in their surroundings. They are characterized by fast response and slow adaptation to varying environmental cues. Insofar as sensory adaptive systems map environmental changes to changes of their…

Population structure affects the outcome of natural selection. Static population structures can be described by graphs, where individuals occupy the nodes, and interactions occur along the edges. General conditions for evolutionary success…

Temporal graphs represent the dynamic relationships among entities and occur in many real life application like social networks, e commerce, communication, road networks, biological systems, and many more. They necessitate research beyond…

Thermodynamic aspects of chemical reactions have a long history in the Physical Chemistry literature. In particular, biochemical cycles - the building-blocks of biochemical systems - require a source of energy to function. However, although…

We propose a new paradigm to design a network-based self-adaptive epidemic model that relies on the interplay between the network and its line graph. We implement this proposal on a Susceptible-Infected-Susceptible model in which both nodes…

Biological systems process information under noisy environment. Sensory adaptation model of E. coli is suitable for investigation because of its simplicity. To understand the adaptation processing quantitatively, stochastic thermodynamic…

Bond graphs can be used to build thermodynamically-compliant hierarchical models of biomolecular systems. As bond graphs have been widely used to model, analyse and synthesise engineering systems, this paper suggests that they can play the…

Whole-cell modelling is constrained by the laws of nature in general and the laws of thermodynamics in particular. This paper shows how one prolific source of information, stoichiometric models of biomolecular systems, can be integrated…

We propose a proof of convergence of an adaptive method used in molecular dynamics to compute free energy profiles. Mathematically, it amounts to studying the long-time behavior of a stochastic process which satisfies a non-linear…

Eukaryotic adaptation pathways operate within wide-ranging environmental conditions without stimulus saturation. Despite numerous differences in the adaptation mechanisms employed by bacteria and eukaryotes, all require energy consumption.…

Adaptive humoral immunity, from the physical perspective, can be regarded as the self-organization of the binding energy landscape of antibodies. In biological terms, the humoral immune system evolves and adapts its repertoire of antigen…

Sensory mechanisms in biology, from cells to humans, have the property of adaptivity, whereby the response produced by the sensor is adapted to the overall amplitude of the signal; reducing the sensitivity in the presence of strong…

The central nervous system is composed of many individual units -- from cells to areas -- that are connected with one another in a complex pattern of functional interactions that supports perception, action, and cognition. One natural and…

Systems with many interacting stochastic constituents are fully characterized by their free energy. Computing this quantity is therefore the objective of various approaches, notably perturbative expansions, which are applied in problems…

The paper examines the learning mechanism of adaptive agents over weakly-connected graphs and reveals an interesting behavior on how information flows through such topologies. The results clarify how asymmetries in the exchange of data can…