Related papers: Gene-Environment Interaction: A Variable Selection…
Evolutionary game theory has been successfully used to investigate the dynamics of systems, in which many entities have competitive interactions. From a physics point of view, it is interesting to study conditions under which a coordination…
We study the conditions for the probing of an environment affecting one party of a bipartite system of interacting objects by measurements operated only on the other element. We show that entanglement plays no crucial role in such an…
Phylogenetic analyses of gene expression have great potential for addressing a wide range of questions. These analyses will, for example, identify genes that have evolutionary shifts in expression that are correlated with evolutionary…
In the genomic analysis, it is significant while challenging to identify markers associated with cancer outcomes or phenotypes. Based on the biological mechanisms of cancers and the characteristics of datasets as well, this paper proposes a…
This thesis investigates the use of problem-specific knowledge to enhance a genetic algorithm approach to multiple-choice optimisation problems.It shows that such information can significantly enhance performance, but that the choice of…
Phenotypical variability in the absence of genetic variation often reflects complex energetic landscapes associated with underlying gene regulatory networks (GRNs). In this view, different phenotypes are associated with alternative states…
Spatial environmental variation can either amplify or suppress the fixation of beneficial mutants in structured populations, yet the interplay of ecological factors and spatial structure in determining which outcome occurs remains…
Biological and social systems are structured at multiple scales, and the incentives of individuals who interact in a group may diverge from the collective incentive of the group as a whole. Mechanisms to resolve this tension are responsible…
The far-reaching consequences of ecological interactions in the dynamics of biological communities remain an intriguing subject. For decades, competition has been a cornerstone in ecological processes, but mounting evidence shows that…
Previous evolutionary studies demonstrated how evaluating evolving agents in variable environmental conditions enable them to develop solutions that are robust to environmental variation. We demonstrate how the robustness of the agents can…
In this paper we motivate and develop a model of gene expression for the purpose of studying the interaction between synthetic gene circuits and the chassis cell within which they are in- serted. This model focuses on the translational…
Variable selection, also known as feature selection in machine learning, plays an important role in modeling high dimensional data and is key to data-driven scientific discoveries. We consider here the problem of detecting influential…
Generative adversarial nets (GANs) have been successfully applied in many fields like image generation, inpainting, super-resolution and drug discovery, etc., by now, the inner process of GANs is far from been understood. To get deeper…
In computational biology, gene expression datasets are characterized by very few individual samples compared to a large number of measurements per sample. Thus, it is appealing to merge these datasets in order to increase the number of…
As the rapid proliferation of AI systems and harms spurs efforts in AI governance around the world, prioritizing among competing policy options has become increasingly challenging for policymakers and researchers. We introduce a methodology…
Gene regulatory networks typically have low in-degrees, whereby any given gene is regulated by few of the genes in the network. They also tend to have broad distributions for the out-degree. What mechanisms might be responsible for these…
Genetic interactions can strongly influence the fitness effects of individual mutations, yet the impact of these epistatic interactions on evolutionary dynamics remains poorly understood. Here we investigate the evolutionary role of…
Relations among species in ecosystems can be represented by complex networks where both negative (competition) and positive (mutualism) interactions are concurrently present. Recently, it has been shown that many ecosystems can be cast into…
Gene expression depends on thousands of factors and we usually only have access to tens or hundreds of observations of gene expression levels meaning we are in a high-dimensional setting. Additionally we don't always observe or care about…
This paper demonstrates that simple yet important characteristics of coevolution can occur in evolutionary algorithms when only a few conditions are met. We find that interaction-based fitness measurements such as fitness (linear) ranking…