Related papers: The Power of Many: A Physarum Swarm Steiner Tree A…
We consider in this paper the problem of discovering, via a traceroute algorithm, the topology of a network, whose graph is spanned by an infinite branching process. A subset of nodes is selected according to some criterion. As a measure of…
A fundamental problem in the study of phylogenetic networks is to determine whether or not a given phylogenetic network contains a given phylogenetic tree. We develop a quadratic-time algorithm for this problem for binary nearly-stable…
Phylogenetic trees are widely used to display estimates of how groups of species evolved. Each phylogenetic tree can be seen as a collection of clusters, subgroups of the species that evolved from a common ancestor. When phylogenetic trees…
This work focuses on clustering populations with a hierarchical dependency structure that can be described by a tree. A particular example that is the focus of our work is the phylogenetic tree, with nodes often representing biological…
We introduce a fully written programmed code with a supervised method for generating Steiner trees. Our choice of the programming language, and the use of well-known theorems from Geometry and Complex Analysis, allowed this method to be…
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…
The paper tackles the problem of clustering multiple networks, directed or not, that do not share the same set of vertices, into groups of networks with similar topology. A statistical model-based approach based on a finite mixture of…
Probabilistic graphical models (PGMs) are powerful tools for solving systems of complex relationships over a variety of probability distributions. However, while tree-structured PGMs always result in efficient and exact solutions, inference…
This paper presents the development of a distributed application that facilitates the understanding and application of swarm intelligence in solving optimization problems. The platform comprises a search space of customizable random…
Complex systems are usually represented as an intricate set of relations between their components forming a complex graph or network. The understanding of their functioning and emergent properties are strongly related to their structural…
We consider the problem of uniformly generating a spanning tree, of a connected undirected graph. This process is useful to compute statistics, namely for phylogenetic trees. We describe a Markov chain for producing these trees. For cycle…
We present a new exact algorithm for the Steiner tree problem in edge-weighted graphs. Our algorithm improves the classical dynamic programming approach by Dreyfus and Wagner. We achieve a significantly better practical performance via…
As researchers collect increasingly large molecular data sets to reconstruct the Tree of Life, the heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. A class of phylogenetic…
The particle swarm approach provides a low complexity solution to the optimization problem among various existing heuristic algorithms. Recent advances in the algorithm resulted in improved performance at the cost of increased computational…
In this paper, a new meta-heuristic algorithm, called beetle swarm optimization algorithm, is proposed by enhancing the performance of swarm optimization through beetle foraging principles. The performance of 23 benchmark functions is…
The Steiner Tree Problem (STP) in graphs is an important problem with various applications in many areas such as design of integrated circuits, evolution theory, networking, etc. In this paper, we propose an algorithm to solve the STP. The…
Network design under uncertainty arises in countless real-world settings and can be captured by the Stochastic Steiner Tree Problem (SSTP). Although there are a few approaches specifically tailored to this stochastic optimization problem,…
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…
We introduce the Pitman Yor Diffusion Tree (PYDT) for hierarchical clustering, a generalization of the Dirichlet Diffusion Tree (Neal, 2001) which removes the restriction to binary branching structure. The generative process is described…
Swarm robots, inspired by the emergence of animal herds, are robots that assemble a large number of modules and self-organize themselves to form specific morphologies and exhibit specific functions. These modular robots perform relatively…