Related papers: Controlling uncertainty in aptamer selection
Gene selection plays a pivotal role in oncology research for improving outcome prediction accuracy and facilitating cost-effective genomic profiling for cancer patients. This paper introduces two gene selection strategies for deep…
Concomitant with the evolution of biological diversity must have been the evolution of mechanisms that facilitate evolution, due to the essentially infinite complexity of protein sequence space. We describe how evolvability can be an object…
Statistical detection of a rare class of objects in a two-class classification problem can pose several challenges. Because the class of interest is rare in the training data, there is relatively little information in the known class…
We study a continuous-time dynamical system that models the evolving distribution of genotypes in an infinite population where genomes may have infinitely many or even a continuum of loci, mutations accumulate along lineages without…
The alignment of biological sequences such as DNA, RNA, and proteins, is one of the basic tools that allow to detect evolutionary patterns, as well as functional/structural characterizations between homologous sequences in different…
The binding complexes formed by proteins and small molecule ligands are ubiquitous and critical to life. Despite recent advancements in protein structure prediction, existing algorithms are so far unable to systematically predict the…
The fitness contribution of an allele at one genetic site may depend on alleles at other sites, a phenomenon known as epistasis. Epistasis can profoundly influence the process of evolution in populations under selection, and can shape the…
We discuss stochastic dynamics of populations of individuals playing games. Our models possess two evolutionarily stable strategies: an efficient one, where a population is in a state with the maximal payoff (fitness) and a risk-dominant…
The modelling of evolutionary game dynamics in finite populations requires microscopic processes that determine how strategies spread. The exact details of these processes are often chosen without much further consideration. Different types…
We investigate a selection-mutation model for the dynamics of technological innovation,a special case of reaction-diffusion equations. Although mutations are assumed to increase the variety of technologies, not their average success…
The spatial structure of an evolving population affects which mutations become fixed. Some structures amplify selection, increasing the likelihood that beneficial mutations become fixed while deleterious mutations do not. Other structures…
Accurately predicting the survival rate of cancer patients is crucial for aiding clinicians in planning appropriate treatment, reducing cancer-related medical expenses, and significantly enhancing patients' quality of life. Multimodal…
In sexual populations, selection operates neither on the whole genome, which is repeatedly taken apart and reassembled by recombination, nor on individual alleles that are tightly linked to the chromosomal neighborhood. The resulting…
Adapting large language models (LLMs) to a targeted task efficiently and effectively remains a fundamental challenge. Such adaptation often requires iteratively improving the model toward a targeted task, yet collecting high-quality…
Large populations may contain numerous simultaneously segregating polymorphisms subject to natural selection. Since selection acts on individuals whose fitness depends on many loci, different loci affect each other's dynamics. This leads to…
Selective control in a population is the ability to control a member of the population while leaving the other members relatively unaffected. The concept of selective control is developed using cell death or apoptosis in heterogeneous cell…
Predicting the adaptation of populations to a changing environment is crucial to assess the impact of human activities on biodiversity. Many theoretical studies have tackled this issue by modeling the evolution of quantitative traits…
Gene-regulatory enhancers have been identified by many lines of evidence, including evolutionary conservation, regulatory protein binding, chromatin modifications, and DNA sequence motifs. To integrate these different approaches, we…
Evolutionary algorithms (EAs) are general-purpose optimisers that come with several parameters like the sizes of parent and offspring populations or the mutation rate. It is well known that the performance of EAs may depend drastically on…
Evolution by Natural Selection is a process by which progeny inherit some properties from their progenitors with small variation. These properties are subject to Natural Selection and are called adaptive traits and carriers of the latter…