相关论文: Overcoming Problems in the Measurement of Biologic…

Genome assembly, the process of reconstructing a long genetic sequence by aligning and merging short fragments, or reads, is known to be NP-hard, either as a version of the shortest common superstring problem or in a Hamiltonian-cycle…

Here we deconstruct, and then in a reasoned way reconstruct, the concept of "entropy of a system," paying particular attention to where the randomness may be coming from. We start with the core concept of entropy as a COUNT associated with…

The issue of how to create open-ended evolution in an artificial system is one the open problems in artificial life. This paper examines two of the factors that have some bearing on this issue, using the Tierra artificial life system. {\em…

The paper makes the observation that all orders of information entropy are equal in signals composed of repeating units of distinct symbols where the units can be classified as a member of a symmetry group. This leads to an improved metric…

While Kolmogorov complexity is the accepted absolute measure of information content of an individual finite object, a similarly absolute notion is needed for the relation between an individual data sample and an individual model summarizing…

Noisy fluctuations are ubiquitous in complex systems. They play a crucial or delicate role in the dynamical evolution of gene regulation, signal transduction, biochemical reactions, among other systems. Therefore, it is essential to…

For many organisms, the number of sensory neurons is largely determined during development, before strong environmental cues are present. This is despite the fact that environments can fluctuate drastically both from generation to…

Fluctuations in the measured mRNA levels of unperturbed cells under fixed conditions have often been viewed as an impediment to the extraction of information from expression profiles. Here, we argue that such expression fluctuations should…

This article introduces the physics of information in the context of molecular biology and genomics. Entropy and information, the two central concepts of Shannon's theory of information and communication, are often confused with each other…

Computational problems can be classified according to their algorithmic complexity, which is defined based on how the resources needed to solve the problem, e.g. the execution time, scale with the problem size. Many problems in…

The computational complexity analysis of genetic programming (GP) has been started recently by analyzing simple (1+1) GP algorithms for the problems ORDER and MAJORITY. In this paper, we study how taking the complexity as an additional…

For a closed-loop control system with a digital channel between the sensor and the controller, the notion of invariance entropy quantifies the smallest average rate of information transmission above which a given compact subset of the state…

We propose to use the effect of measurements instead of their number to study the time evolution of quantum systems under monitoring. This time redefinition acts like a microscope which blows up the inner details of seemingly instantaneous…

Gathering the most information by picking the least amount of data is a common task in experimental design or when exploring an unknown environment in reinforcement learning and robotics. A widely used measure for quantifying the…

Understanding under which conditions the increase of systems complexity is evolutionary advantageous, and how this trend is related to the modulation of the intrinsic noise, are fascinating issues of utmost importance for synthetic and…

Maintenance of sexual reproduction and genetic recombination imposes physiological costs when compared to parthenogenic reproduction, most prominently: for maintaining the corresponding (molecular) machinery, for finding a mating partner,…

Environment plays a fundamental role in the competition for resources, and hence in the evolution of populations. Here, we study a well-mixed, finite population consisting of two strains competing for the limited resources provided by an…

An information theoretic measure is derived that quantifies the statistical coherence between systems evolving in time. The standard time delayed mutual information fails to distinguish information that is actually exchanged from shared…

Standard neutral population genetics theory with a strictly fixed population size has important limitations. An alternative model that allows independently fluctuating population sizes and reproduces the standard neutral evolution is…

Environmental changes greatly influence the evolution of populations. Here, we study the dynamics of a population of two strains, one growing slightly faster than the other, competing for resources in a time-varying binary environment…