Related papers: Perfect Edge-Transmitting Recombination of Permuta…
Horizontal gene transfer inference approaches are usually based on gene sequences: parametric methods search for patterns that deviate from a particular genomic signature, while phylogenetic methods use sequences to reconstruct the gene and…
We propose a genetic algorithm (GA) for hyperparameter optimization of artificial neural networks which includes chromosomal crossover as well as a decoupling of parameters (i.e., weights and biases) from hyperparameters (e.g., learning…
In phylogenetics, tree-based networks are used to model and visualize the evolutionary history of species where reticulate events such as horizontal gene transfer have occurred. Formally, a tree-based network $N$ consists of a phylogenetic…
We look at the evolution through rewiring of the degree distribution of a network so the number edges is constant. This is exactly equivalent to the evolution of probability distributions in models of cultural transmission with drift and…
Genetic algorithms are high-level heuristic optimization methods which enjoy great popularity thanks to their intuitive description, flexibility, and, of course, effectiveness. The optimization procedure is based on the evolution of…
This study introduces an innovative crossover operator named Particle Swarm Optimization-inspired Crossover (PSOX), which is specifically developed for real-coded genetic algorithms. Departing from conventional crossover approaches that…
Evolving networks with a constant number of edges may be modelled using a rewiring process. These models are used to describe many real-world processes including the evolution of cultural artifacts such as family names, the evolution of…
The deterministic selection-recombination equation describes the evolution of the genetic type composition of a population under selection and recombination in a law of large numbers regime. So far, an explicit solution has seemed out of…
A permutation may be represented by a collection of paths in the plane. We consider a natural class of such representations, which we call tangles, in which the paths consist of straight segments at 45 degree angles, and the permutation is…
The genetic algorithm (GA) is an optimization and search technique based on the principles of genetics and natural selection. A GA allows a population composed of many individuals to evolve under specified selection rules to a state that…
In this paper I present a conjecture for a recursive algorithm that finds each permutation of combining two sets of objects (AKA the Shuffle Product). This algorithm provides an efficient way to navigate this problem, as each atomic…
Given a graph, we associate each edge with the transposition which exchanges the endvertices. Fixing a linear order on the edge set, we obtain a permutation of the vertices. D\'enes proved that the permutation is a full cyclic permutation…
Graph Crossing Number is a fundamental problem with various applications. In this problem, the goal is to draw an input graph $G$ in the plane so as to minimize the number of crossings between the images of its edges. Despite extensive…
Pedigrees are directed acyclic graphs that represent ancestral relationships between individuals in a population. Based on a schematic recombination process, we describe two simple Markov models for sequences evolving on pedigrees - Model R…
Genetic algorithms are modeled after the biological evolutionary processes that use natural selection to select the best species to survive. They are heuristics based and low cost to compute. Genetic algorithms use selection, crossover, and…
Ancestral sequence reconstruction is a key task in computational biology. It consists in inferring a molecular sequence at an ancestral species of a known phylogeny, given descendant sequences at the tip of the tree. In addition to its many…
Genome assembly, the process of reconstructing a long genetic sequence by aligning and merging short fragments, or reads, is known to be NP-hard, either as a version of the shortest common superstring problem or in a Hamiltonian-cycle…
We study the problem of edge partitioning, where the goal is to partition the edge set of a graph into several parts. The replication factor of a vertex $v$ is the number of parts that contain edges incident to $v$. The goal is to minimize…
Solving the recombination equation has been a long-standing challenge of \emph{deterministic} population genetics. We review recent progress obtained by introducing ancestral processes, as traditionally used in the context of…
Reconstruction of family trees, or pedigree reconstruction, for a group of individuals is a fundamental problem in genetics. The problem is known to be NP-hard even for datasets known to only contain siblings. Some recent methods have been…