Related papers: Perfect Edge-Transmitting Recombination of Permuta…
At the core of high throughput DNA sequencing platforms lies a bio-physical surface process that results in a random geometry of clusters of homogenous short DNA fragments typically hundreds of base pairs long - bridge amplification. The…
Recent work has proven the existence of extreme inbreeding in a European ancestry sample taken from the contemporary UK population \cite{nature_01}. This result brings our attention again to a math problem related to inbreeding family trees…
Crossover is a powerful mechanism for generating new solutions from a given population of solutions. Crossover comes with a discrepancy in itself: on the one hand, crossover usually works best if there is enough diversity in the population;…
A permutation is said to be a square if it can be obtained by shuffling two order-isomorphic patterns. The definition is intended to be the natural counterpart to the ordinary shuffle of words and languages. In this paper, we tackle the…
The time evolution of a simple model for crossover is discussed. A variant of this model with an improved exploration behavior in phase space is derived as a subset of standard one- and multi-point crossover operations. This model is solved…
The generation of random graphs using edge swaps provides a reliable method to draw uniformly random samples of sets of graphs respecting some simple constraints, e.g. degree distributions. However, in general, it is not necessarily…
A simple but empirically efficient heuristic algorithm for the edge-coloring of graphs is presented. Its basic idea is the displacement of "conflicts" (repeated colors in the edges incident to a vertex) along paths of adjacent vertices…
Intragenomic recombination (crossover) is a very important evolutionary mechanism. The crossover events are not evenly distributed along the natural chromosomes. Monte Carlo simulations revealed that frequency of recombinations decides…
Reconciling a gene tree with a species tree is an important task that reveals much about the evolution of genes, genomes, and species, as well as about the molecular function of genes. A wide array of computational tools have been devised…
Edge-matching problems, also called edge matching puzzles, are abstractions of placement problems with neighborhood conditions. Pieces with colored edges have to be placed on a board such that adjacent edges have the same color. The problem…
Genome rearrangement has been an active area of research in computational comparative genomics for the last three decades. While initially mostly an interesting algorithmic endeavor, now the practical application by applying rearrangement…
Tuning tensor program generation involves searching for various possible program transformation combinations for a given program on target hardware to optimize the tensor program execution. It is already a complex process because of the…
This paper studies non-crossing geometric perfect matchings. Two such perfect matchings are \emph{compatible} if they have the same vertex set and their union is also non-crossing. Our first result states that for any two perfect matchings…
Population diversity is crucial in evolutionary algorithms as it helps with global exploration and facilitates the use of crossover. Despite many runtime analyses showing advantages of population diversity, we have no clear picture of how…
In extension problems of partial graph drawings one is given an incomplete drawing of an input graph $G$ and is asked to complete the drawing while maintaining certain properties. A prominent area where such problems arise is that of…
A genetic algorithm is suitable for exploring large search spaces as it finds an approximate solution. Because of this advantage, genetic algorithm is effective in exploring vast and unknown space such as molecular search space. Though the…
Horizontal gene transfer is an important contributor to evolution. According to Walter M.\ Fitch, two genes are xenologs if they are separated by at least one HGT. More formally, the directed Fitch graph has a set of genes is its vertices,…
The Exact Circular Pattern Matching (ECPM) problem consists of reporting every occurrence of a rotation of a pattern $P$ in a text $T$. In many real-world applications, specifically in computational biology, circular rotations are of…
An evolutionary algorithm (EA) is developed as an alternative to the EM algorithm for parameter estimation in model-based clustering. This EA facilitates a different search of the fitness landscape, i.e., the likelihood surface, utilizing…
Parent selection methods are widely used in evolutionary computation to accelerate the optimization process, yet their theoretical benefits are still poorly understood. In this paper, we address this gap by proposing a parent selection…