Related papers: Overcoming Problems in the Measurement of Biologic…
Social evolutionary theory seeks to explain increases in the scale and complexity of human societies, from origins to present. Over the course of the twentieth century, social evolutionary theory largely fell out of favor as a way of…
The word "complexity" is most often used as a meta--linguistic expression referring to certain intuitive characteristics of a natural system and/or its scientific description. These characteristics may include: sheer amount of data that…
Computers are deterministic dynamical systems (CHAOS 19:033124, 2009). Among other things, that implies that one should be able to use deterministic forecast rules to predict their behavior. That statement is sometimes-but not always-true.…
We apply formal measures of emergence, self-organization, homeostasis, autopoiesis and complexity to an aquatic ecosystem; in particular to the physiochemical component of an Arctic lake. These measures are based on information theory.…
Natural selection explains how life has evolved over millions of years from more primitive forms. The speed at which this happens, however, has sometimes defied formal explanations when based on random (uniformly distributed) mutations.…
Fluctuations in biochemical networks, e.g., in a living cell, have a complex origin that precludes a description of such systems in terms of bipartite or multipartite processes, as is usually done in the framework of stochastic and/or…
A central issue of the science of complex systems is the quantitative characterization of complexity. In the present work we address this issue by resorting to information geometry. Actually we propose a constructive way to associate to a -…
In an experimental study of single enzyme reactions, it has been proposed that the rate constants of the enzymatic reactions fluctuate randomly, according to a given distribution. To quantify the uncertainty arising from random rate…
I consider the many ways in which evolved information-flows are restricted and metabolic resources protected and hidden -- the thesis of living phenomena as evolutionary cryptosystems. I present the information theory of secrecy systems and…
In complex environments, there are costs to both ignorance and perception. An organism needs to track fitness-relevant information about its world, but the more information it tracks, the more resources it must devote to memory and…
Shannon Entropy is the preeminent tool for measuring the level of uncertainty (and conversely, information content) in a random variable. In the field of communications, entropy can be used to express the information content of given…
Boolean network models of strongly connected modules are capable of capturing the high regulatory complexity of many biological gene regulatory circuits. We study numerically the previously introduced basin entropy, a parameter for the…
The concept of entropy in nonequilibrium macroscopic systems is investigated in the light of an extended equation of motion for the density matrix obtained in a previous study. It is found that a time-dependent information entropy can be…
Phenotypes of individuals in a population of organisms are not fixed. Phenotypic fluctuations, which describe temporal variation of the phenotype of an individual or individual-to-individual variation across a population, are present in…
In many applications of evolutionary algorithms the computational cost of applying operators and storing populations is comparable to the cost of fitness evaluation. Furthermore, by knowing what exactly has changed in an individual by an…
This is a review of group entropy and its application to permutation complexity. Specifically we revisit a new approach to the notion of complexity in time serie analysis, based on both permutation entropy and group entropy. As a result,…
We consider the asymptotic behaviour of the fluctuation process for large stochastic systems of interacting particles driven by both idiosyncratic and common noise with an interaction kernel \(k \in L^2(\R^d) \cap L^\infty(\R^d)\). Our…
This work explores entropy analysis as a tool for probing information distribution within Transformer-based architectures. By quantifying token-level uncertainty and examining entropy patterns across different stages of processing, we aim…
We consider unitary dynamical evolutions on n qubits caused by time dependent pair-interaction Hamiltonians and show that the running time of a parallelized two-qubit gate network simulating the evolution is given by the time integral over…
Proteins are essential components of living systems, capable of performing a huge variety of tasks at the molecular level, such as recognition, signalling, copy, transport, ... The protein sequences realizing a given function may largely…