Related papers: Information encoded in gene-frequency trajectories
The distribution of genetic polymorphisms in a population contains information about the mutation rate and the strength of natural selection at a locus. Here, we show that the Poisson Random Field (PRF) method of population-genetic…
Evolutionary forces shape patterns of genetic diversity within populations and contribute to phenotypic variation. In particular, recurrent positive selection has attracted significant interest in both theoretical and empirical studies.…
A measure called Physical Complexity is established and calculated for a population of sequences, based on statistical physics, automata theory, and information theory. It is a measure of the quantity of information in an organism's genome.…
The spreading of evolutionary novelties across populations is the central element of adaptation. Unless population are well-mixed (like bacteria in a shaken test tube), the spreading dynamics not only depends on fitness differences but also…
Rare trajectories of stochastic systems are important to understand -- because of their potential impact. However, their properties are by definition difficult to sample directly. Population dynamics provides a numerical tool allowing their…
Data driven methods for time series forecasting that quantify uncertainty open new important possibilities for robot tasks with hard real time constraints, allowing the robot system to make decisions that trade off between reaction time and…
Statistical systems are conceived from the standpoint of statistical mechanics, as made of a (generally large) number of identical units and exhibiting a (generally large) number of different configurations (microstates), among which only…
If a cultural feature is transmitted over generations and exposed to stochastic selection when spreading in a population, its evolution may be governed by statistical laws and be partly predictable, as in the case of genetic evolution.…
Hypergraphs have been a useful tool for analyzing population dynamics such as opinion formation and the public goods game occurring in overlapping groups of individuals. In the present study, we propose and analyze evolutionary dynamics on…
Mathematical models of gene regulatory networks are widely used to study cell fate changes and transcriptional regulation. When designing such models, it is important to accurately account for sources of stochasticity. However, doing so can…
We study the adaptation dynamics of an initially maladapted asexual population with genotypes represented by binary sequences of length $L$. The population evolves in a maximally rugged fitness landscape with a large number of local optima.…
Physical systems behave according to their underlying dynamical equations which, in turn, can be identified from experimental data. Explaining data requires selecting mathematical models that best capture the data regularities. Identifying…
We consider evolution of a large population, where fitness of each organism is defined by many phenotypical traits. These traits result from expression of many genes. We propose a new model of gene regulation, where gene expression is…
Gene expression programming is an evolutionary optimization algorithm with the potential to generate interpretable and easily implementable equations for regression problems. Despite knowledge gained from previous optimizations being…
When people pursue rewards in stochastic environments, they often match their choice frequencies to the observed target frequencies, even when this policy is demonstrably sub-optimal. We used a ``hide and seek'' task to evaluate this…
We study the trajectory optimization problem under chance constraints for continuous-time stochastic systems. To address chance constraints imposed on the entire stochastic trajectory, we propose a framework based on the set erosion…
This work addresses the problem of predicting the motion trajectories of dynamic objects in the environment. Recent advances in predicting motion patterns often rely on machine learning techniques to extrapolate motion patterns from…
Transposable elements, or transposons, are DNA sequences that can jump from site to site in the genome during the life cycle of a cell, usually encoding the very enzymes which perform their excision. However, some transposons are parasitic,…
The purpose of this Note is twofold: First, we introduce the general formalism of evolutionary genetics dynamics involving fitnesses, under both the deterministic and stochastic setups, and chiefly in discrete-time. In the process, we…
In this work, the dynamics of fluctuations in gene expression time series is investigated. By using collected data of gene expression from yeast and human organisms, we found that the fluctuations of gene expression level and its average…