相关论文: Minimizing the number of episodes and Gallai's the…
A common problem in phylogenetics is to try to infer a species phylogeny from gene trees. We consider different variants of this problem. The first variant, called Unrestricted Minimal Episodes Inference, aims at inferring a species tree…
We consider the following problem: from a given set of gene families trees on a set of genomes, find a first speciation, that splits these genomes into two subsets, that minimizes the number of gene duplications that happened before this…
Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families…
We studied how to obtain a distribution for the number of ancestors in species of sexual reproduction. Present models concentrate on the estimation of distributions repetitions of ancestors in genealogical trees. It has been shown that is…
Many applications in machine learning can be framed as minimization problems and solved efficiently using gradient-based techniques. However, recent applications of generative models, particularly GANs, have triggered interest in solving…
Min-SEIS-Cluster is an optimization problem which aims at minimizing the infection spreading in networks. In this problem, nodes can be susceptible to an infection, exposed to an infection, or infectious. One of the main features of this…
Pedigrees, or family trees, are graphs of family relationships that are used to study inheritance. A fundamental problem in computational biology is to find, for a pedigree with $n$ individuals genotyped at every site, a set of…
The reconstruction of the history of evolutionary genome-wide events among a set of related organisms is of great biological interest. A simplified model that captures only content modifying operations was introduced recently. It allows the…
The study of genetic map linearization leads to a combinatorial hard problem, called the {\em minimum breakpoint linearization} (MBL) problem. It is aimed at finding a linearization of a partial order which attains the minimum breakpoint…
Understanding the evolution of a set of genes or species is a fundamental problem in evolutionary biology. The problem we study here takes as input a set of trees describing {possibly discordant} evolutionary scenarios for a given set of…
For a finite group $G$, the size of a minimum generating set of $G$ is denoted by $d(G)$. Given a finite group $G$ and an integer $k$, deciding if $d(G)\leq k$ is known as the minimum generating set (MIN-GEN) problem. A group $G$ of order…
The supertree problem asking for a tree displaying a set of consistent input trees has been largely considered for the reconstruction of species trees. Here, we rather explore this framework for the sake of reconstructing a gene tree from a…
In the classical interval scheduling type of problems, a set of $n$ jobs, characterized by their start and end time, need to be executed by a set of machines, under various constraints. In this paper we study a new variant in which the jobs…
We demonstrate how a genetic algorithm solves the problem of minimizing the resources used for network coding, subject to a throughput constraint, in a multicast scenario. A genetic algorithm avoids the computational complexity that makes…
Given an elementary chain of vertex set V, seen as a labelling of V by the set {1, ...,n=|V|}, and another discrete structure over $V$, say a graph G, the problem of common intervals is to compute the induced subgraphs G[I], such that $I$…
Genomes and genes diversify during evolution; however, it is unclear to what extent genes still retain the relationship among species. Model species for molecular phylogenetic studies include yeasts and viruses whose genomes were sequenced…
Over a quarter of century after the invention of genetic algorithms and miriads of their modifications, as well as successful implementations, we are still lacking many essential details of thorough analysis of it's inner working. One of…
Gene tree/species tree reconciliation is a recent decisive progress in phylo-genetic methods, accounting for the possible differences between gene histories and species histories. Reconciliation consists in explaining these differences by…
Understanding how the time-complexity of evolutionary algorithms (EAs) depend on their parameter settings and characteristics of fitness landscapes is a fundamental problem in evolutionary computation. Most rigorous results were derived…
In the small phylogeny problem we, are given a phylogenetic tree and gene orders of the extant species and our goal is to reconstruct all of the ancestral genomes so that the number of evolutionary operations is minimized. Algorithms for…