Related papers: Simulating Genomes and Populations in the Mutation…
The genetic diversity of a species is shaped by its recent evolutionary history and can be used to infer demographic events or selective sweeps. Most inference methods are based on the null hypothesis that natural selection is a weak or…
When an advantageous mutation occurs in a population, the favorable allele may spread to the entire population in a short time, an event known as a selective sweep. As a result, when we sample $n$ individuals from a population and trace…
Immunological systems have been an abundant inspiration to contemporary computer scientists. Problem solving strategies, stemming from known immune system phenomena, have been successfully applied to challenging problems of modern computing…
We show that a simple evolutionary scheme, when applied to the minority game (MG), changes the phase structure of the game. In this scheme each agent evolves individually whenever his wealth reaches the specified bankruptcy level, in…
The evolution of many microbes and pathogens, including circulating viruses such as seasonal influenza, is driven by immune pressure from the host population. In turn, the immune systems of infected populations get updated, chasing viruses…
The evolutionary dynamics of a system of cancerous cells in a model of chronic myeloid leukemia (CML) is investigated by a statistical approach. Cancer progression is explored by applying a Monte Carlo method to simulate the stochastic…
Coalescent models are used to study the transmission dynamics of rapidly evolving pathogens from molecular sequence data obtained from infected individuals. However coalescent parameters, such as effective population size, offer limited…
Identifying drivers of complex traits from the noisy signals of genetic variation obtained from high throughput genome sequencing technologies is a central challenge faced by human geneticists today. We hypothesize that the variants…
We examine the feasibility of predicting and subsequently managing the future evolution of a Complex Adaptive System. Our archetypal system mimics a competitive population of mechanical, biological, informational or human objects. We show…
Studying how diverse human populations are related is of historical and anthropological interest, in addition to providing a realistic null model for testing for signatures of natural selection or disease associations. Furthermore,…
Many mathematical models of evolution assume that all individuals experience the same environment. Here, we study the Moran process in heterogeneous environments. The population is of finite size with two competing types, which are exposed…
Reliable estimation of spatio-temporal trends in population-level HIV incidence is becoming an increasingly critical component of HIV prevention policy-making. However, direct measurement is nearly impossible. Current, widely used models…
In nature, most microbial populations have complex spatial structures that can affect their evolution. Evolutionary graph theory predicts that some spatial structures modelled by placing individuals on the nodes of a graph affect the…
Recent improvements in high-throughput genotyping and sequencing technologies have afforded the collection of massive, genome-wide datasets of DNA information from hundreds of thousands of individuals. These datasets, in turn, provide…
Foundation models refer to architectures trained on vast datasets using autoregressive pre-training from natural language processing to capture intricate patterns and motifs. They were originally developed to transfer such learned knowledge…
Genomics are rapidly transforming medical practice and basic biomedical research, providing insights into disease mechanisms and improving therapeutic strategies, particularly in cancer. The ability to predict the future course of a…
Individual-based model (IBM) has been used to simulate and to design control strategies for dynamic systems that are subject to stochasticity and heterogeneity, such as infectious diseases. In the IBM, an individual is represented by a set…
The simple genetic algorithm is proposed for the simulation of quantum many body dynamics. It uses the selection of entangled quantum states and has the inbuilt absolute decoherence that comes from the limitation of classical memory. It…
Differential evolution (DE) is a well-known type of evolutionary algorithms (EA). Similarly to other EA variants it can suffer from small populations and loose diversity too quickly. This paper presents a new approach to mitigate this…
We developed two new alternatives to signature-based, spatial autoregressive models. In a simulation study, we found that the new models performed at least as well as existing approaches but presented shorter computation times. We then used…