Related papers: Simulating Evolution on Fitness Landscapes represe…
Much of the current theory of adaptation is based on Gillespie's mutational landscape model (MLM), which assumes that the fitness values of genotypes linked by single mutational steps are independent random variables. On the other hand, a…
We study the complexity of the valued constraint satisfaction problem (VCSP) for every valued structure with the domain ${\mathbb Q}$ that is preserved by all order-preserving bijections. Such VCSPs will be called temporal, in analogy to…
We have recently presented SAFE -- Solution And Fitness Evolution -- a commensalistic coevolutionary algorithm that maintains two coevolving populations: a population of candidate solutions and a population of candidate objective functions.…
The long-term sustainability of research software is a critical challenge, as it usually suffers from poor maintainability, lack of adaptability, and eventual obsolescence. This paper proposes a novel approach to addressing this issue by…
In this work, we integrate theoretical modeling, molecular simulation, and empirical analysis to identify and characterize evolutionary hysteresis. We first show how epistatic interactions create bistable fitness landscapes and structural…
Constraint satisfaction problems (CSPs) are an important formal framework for the uniform treatment of various prominent AI tasks, e.g., coloring or scheduling problems. Solving CSPs is, in general, known to be NP-complete and…
Finite valued constraint satisfaction problems are a formalism for describing many natural optimization problems, where constraints on the values that variables can take come with rational weights and the aim is to find an assignment of…
Realistic evolutionary fitness landscapes are notoriously difficult to construct. A recent cutting-edge model of virus assembly consists of a dodecahedral capsid with $12$ corresponding packaging signals in three affinity bands. This whole…
The constraint satisfaction problem asks to decide if a set of constraints over a relational structure $\mathcal{A}$ is satisfiable (CSP$(\mathcal{A})$). We consider CSP$(\mathcal{A} \cup \mathcal{B})$ where $\mathcal{A}$ is a structure and…
The sequence of a protein is not only constrained by its physical and biochemical properties under current selection, but also by features of its past evolutionary history. Understanding the extent and the form that these evolutionary…
In the constraint satisfaction problem (CSP) corresponding to a constraint language (i.e., a set of relations) $\Gamma$, the goal is to find an assignment of values to variables so that a given set of constraints specified by relations from…
The fitness level method is a widely used technique for estimating the mean hitting time of elitist evolutionary algorithms on level-based fitness functions. However, this paper identifies its main limitation: the linear lower bound derived…
Constraint satisfaction problems (CSPs) are a class of problems that are ubiquitous in science and engineering. It features a collection of constraints specified over subsets of variables. A CSP can be solved either directly or by reducing…
Functional effects of different mutations are known to combine to the total effect in highly nontrivial ways. For the trait under evolutionary selection (`fitness'), measured values over all possible combinations of a set of mutations yield…
The study of phase transition phenomenon of NP complete problems plays an important role in understanding the nature of hard problems. In this paper, we follow this line of research by considering the problem of counting solutions of…
The Constraint Satisfaction Problem (CSP) is a problem of computing a homomorphism $\mathbf{R}\to \mathbf{\Gamma}$ between two relational structures, where $\mathbf{R}$ is defined over a domain $V$ and $\mathbf{\Gamma}$ is defined over a…
The ability to engineer novel proteins with higher fitness for a desired property would be revolutionary for biotechnology and medicine. Modeling the combinatorially large space of sequences is infeasible; prior methods often constrain…
Intransitivity is supposed to be a main reason for deficits in coevolutionary progress and inheritable superiority. Besides, coevolutionary dynamics is characterized by interactions yielding subjective fitness, but aiming at solutions that…
The hardness of fitness functions is an important research topic in the field of evolutionary computation. In theory, the study can help understanding the ability of evolutionary algorithms. In practice, the study may provide a guideline to…
We consider the optimal dynamics in the infinite population evolution models with general symmetric fitness landscape. The search of optimal evolution trajectories are complicated due to sharp transitions (like shock waves) in evolution…