Related papers: Modeling evolution in a Long Time Evolution Experi…
The development of a large non-coding fraction in eukaryotic DNA and the phenomenon of the code-bloat in the field of evolutionary computations show a striking similarity. This seems to suggest that (in the presence of mechanisms of code…
The design space of networked embedded systems is very large, posing challenges to the optimisation of such platforms when it comes to support applications with real-time guarantees. Recent research has shown that a number of inter-related…
We considered a {multi-block} molecular model of biological evolution, in which fitness is a function of the mean types of alleles located at different parts (blocks) of the genome. We formulated an infinite population model with selection…
Ecological and evolutionary dynamics have been historically regarded as unfolding at broadly separated timescales. However, these two types of processes are nowadays well documented to much more tightly than traditionally assumed,…
We introduce a system for experimental evolution consisting of populations of short oligonucleotides (Oli populations) evolving in a modified quantitative Polymerase Chain Reaction (qPCR). It is tractable at the genetic, genomic, phenotypic…
We introduce an Interaction and Trade-off based Eco-Evolutionary Model (ITEEM), in which species are competing for common resources in a well-mixed system, and their evolution in interaction trait space is subject to a life-history…
On-policy reinforcement learning (RL) algorithms are widely used for their strong asymptotic performance and training stability, but they struggle to scale with larger batch sizes, as additional parallel environments yield redundant data…
Arthur's (1988) model for competing technologies is discussed from the perspective of evolution theory. Using Arthur's own model for the simulation, we show that 'lock-ins' can be suppressed by adding reflexivity or uncertainty on the side…
Simulation of population dynamics is a central research theme in computational biology, which contributes to understanding the interactions between predators and preys. Conventional mathematical tools of this theme, however, are incapable…
Recent advancements have highlighted that large language models (LLMs), when given a small set of task-specific examples, demonstrate remarkable proficiency, a capability that extends to complex reasoning tasks. In particular, the…
Different types of evolutionary algorithms have been developed for constrained continuous optimization. We carry out a feature-based analysis of evolved constrained continuous optimization instances to understand the characteristics of…
Artificial life aims to understand the fundamental principles of biological life by creating computational models that exhibit life-like properties. Although artificial life systems show promise for simulating biological evolution,…
Bacteria evolve resistance to antibiotics by a multitude of mechanisms. A central, yet unsolved question is how resistance evolution affects cell growth at different drug levels. Here we develop a fitness model that predicts growth rates of…
The analysis of the evolutionary dynamics of a population with many polymorphic loci is challenging since a large number of possible genotypes needs to be tracked. In the absence of analytical solutions, forward computer simulations are an…
The evolution model with parallel mutation-selection scheme is solved for the case when selection is accompanied by base substitutions, insertions, and deletions. The fitness is assumed to be either a single-peak function (i.e., having one…
The outcomes of evolution are determined by which mutations occur and fix. In rapidly adapting microbial populations, this process is particularly hard to predict because lineages with different beneficial mutations often spread…
Biological evolution of a population is governed by the fitness landscape, which is a map from genotype to fitness. However, a fitness landscape depends on the organisms environment, and evolution in changing environments is still poorly…
Character evolution that affects ecological community interactions often occurs contemporaneously with temporal changes in population size, potentially altering the very nature of those dynamics. Such eco-evolutionary processes may be most…
To approximate convolutions which occur in evolution equations with memory terms, a variable-stepsize algorithm is presented for which advancing N steps requires only O(N log(N)) operations and O(log(N)) active memory, in place of O(N^2)…
Evolutionary agentic systems intensify the trade-off between computational efficiency and reasoning capability by repeatedly invoking large language models (LLMs) during inference. This setting raises a central question: how can an agent…