Related papers: Expected number of inversions after a sequence of …
In certain instances an electric network transforms in natural ways by the addition or removal of an edge. This can have interesting consequences for random walks, in light of the known relationships between electric resistance and random…
Combinatorial evolution - the creation of new things through the combination of existing things - can be a powerful way to evolve rather than design technical objects such as electronic circuits. Intriguingly, this seems to be an ongoing…
If one goes backward in time, the number of ancestors of an individual doubles at each generation. This exponential growth very quickly exceeds the population size, when this size is finite. As a consequence, the ancestors of a given…
Within the germinal center in follicles, B-cells proliferate, mutate and differentiate, while being submitted to a powerful selection~: a micro-evolutionary mechanism at the heart of adaptive immunity. A new foreign pathogen is confronted…
Quantum process tomography provides a means of measuring the evolution operator for a system at a fixed measurement time $t$. The problem of using that tomographic snapshot to predict the evolution operator at other times is generally…
This study proposes a data condensation method for multivariate kernel density estimation by genetic algorithm. First, our proposed algorithm generates multiple subsamples of a given size with replacement from the original sample. The…
The performance of different mutation operators is usually evaluated in conjunc-tion with specific parameter settings of genetic algorithms and target problems. Most studies focus on the classical genetic algorithm with different parameters…
Of the many modern approaches to calculating evolutionary distance via models of genome rearrangement, most are tied to a particular set of genomic modelling assumptions and to a restricted class of allowed rearrangements. The "position…
Rare transitions in stochastic processes can often be rigorously described via an underlying large deviation principle. Recent breakthroughs in the classification of reversible stochastic processes as gradient flows have led to a connection…
A connection is made between the random turns model of vicious walkers and random permutations indexed by their increasing subsequences. Consequently the scaled distribution of the maximum displacements in a particular asymmeteric version…
Biologists have long sought a way to explain how statistical properties of genetic sequences emerged and are maintained through evolution. On the one hand, non-random structures at different scales indicate a complex genome organisation. On…
A wide variety of transition-based algorithms are currently used for dependency parsers. Empirical studies have shown that performance varies across different treebanks in such a way that one algorithm outperforms another on one treebank…
Genetic algorithms are heuristic optimization techniques inspired by Darwinian evolution, which are characterized by successfully finding robust solutions for optimization problems. Here, we propose a subroutine-based quantum genetic…
We establish upper and lower bounds on the maximal number of steps needed to transform a cyclic permutation to the canonical cyclic permutation using conjugation by adjacent transpositions, and on the diameter of the underlying Schreier…
In the human genomes, recombination frequency between homologous chromosomes during meiosis is highly correlated with their physical length while it differs significantly when their coding density is considered. Furthermore, it has been…
Rearrangements of bacterial chromosomes can be studied mathematically at several levels, most prominently at a local, or sequence level, as well as at a topological level. The biological changes involved locally are inversions, deletions,…
The paper surveys the evolution of main algorithmic techniques to compare and search biological sequences. We highlight key algorithmic ideas emerged in response to several interconnected factors: shifts of biological analytical paradigm,…
We prove rapid mixing for certain Markov chains on the set $S_n$ of permutations on $1,2,\dots,n$ in which adjacent transpositions are made with probabilities that depend on the items being transposed. Typically, when in state $\sigma$, a…
We develop a diffusion approximation for systems subject to fast random resetting by small amplitudes. Equivalently, this describes systems with frequent but small catastrophes. We demonstrate the validity of the approximation by computing…
We have used the Monte Carlo based computer models to show that selection pressure could affect the distribution of recombination hotspots along the chromosome. Close to critical crossover rate, where genomes may switch between the…