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Evolutionary accumulation models (EvAMs) are an emerging class of machine learning methods designed to infer the evolutionary pathways by which features are acquired. Applications include cancer evolution (accumulation of mutations),…
Organisms have evolved immune systems that can counter pathogenic threats. The adaptive immune system in vertebrates consists of a diverse repertoire of immune receptors that can dynamically reorganize to specifically target the…
Current research on defending against adversarial examples focuses primarily on achieving robustness against a single attack type such as $\ell_2$ or $\ell_{\infty}$-bounded attacks. However, the space of possible perturbations is much…
Radical shifts in the genetic composition of large cell populations are rare events with quite low probabilities, which direct numerical simulations generally fail to evaluate accurately. In this paper, we develop a theoretical large…
Evolutionary game dynamics describes not only frequency dependent genetical evolution, but also cultural evolution in humans. In this context, successful strategies spread by imitation. It has been shown that the details of strategy update…
The emergence or adaptation of pathogens may lead to epidemics, highlighting the need for a thorough understanding of pathogen evolution. The tradeoff hypothesis suggests that virulence evolves to reach an optimal transmission intensity…
One of the main properties of biological systems is modularity, which manifests itself at all levels of their organization, starting with the level of molecular genetics, ending with the level of whole organisms and their communities. In a…
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…
Interest in the study of in-host microbial communities has increased in recent years due to our improved understanding of the communities' significant role in host health. As a result, the ability to model these communities using…
Understanding dynamics of an infectious disease helps in designing appropriate strategies for containing its spread in a population. Recent mathematical models are aimed at studying dynamics of some specific types of infectious diseases. In…
We study the evolution of preferences in multi-population settings that allow matches across distinct populations. Each individual has subjective preferences over potential outcomes, and chooses a best response based on his preferences and…
The design of protocols to suppress the propagation of viral infections is an enduring enterprise, especially hindered by limited knowledge of the mechanisms through which extinction of infection propagation comes about. We here report on a…
Aging is a fundamental aspect of living systems that undergo a progressive deterioration of physiological function with age and an increase of vulnerability to disease and death. Living systems, known as complex systems, require complexity…
During the ongoing COVID-19 pandemic, mathematical models of epidemic spreading have emerged as powerful tools to produce valuable predictions of the evolution of the pandemic, helping public health authorities decide which intervention…
It is known (see e.g. Weibull (1995)) that ESS is not robust against multiple mutations. In this article, we introduce robustness against multiple mutations and study some equivalent formulations and consequences.
Humans, domestic animals, orchard crops, and ornamental plants are commonly treated with antibiotics in response to bacterial infection. By curing infectious individuals, antibiotic therapy might limit the spread of contagious disease among…
Cooperation and competition between pathogens can alter the amount of individuals affected by a co-infection. Nonetheless, the evolution of the pathogens' behavior has been overlooked. Here, we consider a co-evolutionary model where the…
Practically, all chemotherapeutic agents lead to drug resistance. Clinically, it is a challenge to determine whether resistance arises prior to, or as a result of, cancer therapy. Further, a number of different intracellular and…
The study of microorganisms, or microbiology, has demonstrated significant development since its inception and is currently a key field of biological sciences that has a huge impact on modern society and scientific research. Over the…
Mixed microbial communities, usually composed of various bacterial and fungal species, are fundamental in a plethora of environments, from soil to human gut and skin. Their evolution is a paradigmatic example of intertwined dynamics, where…