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Modelling the substitution of nucleotides along a phylogenetic tree is usually done by a hidden Markov process. This allows to define a distribution of characters at the leaves of the trees and one might be able to obtain polynomial…
Classification of gene trees is an important task both in the analysis of multi-locus phylogenetic data, and assessment of the convergence of Markov Chain Monte Carlo (MCMC) analyses used in Bayesian phylogenetic tree reconstruction. The…
An algorithm on weighted graphs is called universally optimal if it is optimal for every input graph, in the worst case taken over all weight assignments. Informally, this means the algorithm is competitive even with algorithms that are…
For a set of red and blue points in the plane, a minimum bichromatic spanning tree (MinBST) is a shortest spanning tree of the points such that every edge has a red and a blue endpoint. A MinBST can be computed in $O(n\log n)$ time where…
We introduce a graph partitioning problem motivated by computational topology and propose two algorithms that produce approximate solutions. Specifically, given a weighted, undirected graph $G$ and a positive integer $k$, we desire to find…
The statistical shape analysis called Procrustes analysis minimizes the distance between matrices by similarity transformations. The method returns a set of optimal orthogonal matrices, which project each matrix into a common space. This…
The tree edit distance is a natural dissimilarity measure between rooted ordered trees whose nodes are labeled over an alphabet $\Sigma$. It is defined as the minimum number of node edits (insertions, deletions, and relabelings) required to…
The Metric Traveling Salesman Problem (TSP) is a classical NP-hard optimization problem. The double-tree shortcutting method for Metric TSP yields an exponentially-sized space of TSP tours, each of which approximates the optimal solution…
A distance-based method to reconstruct a phylogenetic tree with $n$ leaves takes a distance matrix, $n \times n$ symmetric matrix with $0$s in the diagonal, as its input and reconstructs a tree with $n$ leaves using tools in combinatorics.…
In this paper, we prove that the self-dual morphological hierarchical structure computed on a n-D gray-level wellcomposed image u by the algorithm of G{\'e}raud et al. [1] is exactly the mathematical structure defined to be the tree of…
How can heuristic strategies emerge from smaller building blocks? We propose Approximate Bayesian Computation as a computational solution to this problem. As a first proof of concept, we demonstrate how a heuristic decision strategy such as…
In this paper, we consider the Uniform Cost-Distance Steiner Tree Problem in metric spaces, a generalization of the well-known Steiner tree problem. Cost-distance Steiner trees minimize the sum of the total length and the weighted path…
Background: The reconstruction of the phylogenetic tree topology of four taxa is, still nowadays, one of the main challenges in phylogenetics. Its difficulties lie in considering not too restrictive evolutionary models, and correctly…
We present four novel approximation algorithms for finding triangulation of minimum treewidth. Two of the algorithms improve on the running times of algorithms by Robertson and Seymour, and Becker and Geiger that approximate the optimum by…
Randomized Greedy Algorithms (RGAs) are interesting approaches to solve problems whose structures are not well understood as well as problems in combinatorial optimization which incorporate the random processes and the greedy algorithms.…
$\newcommand{\eps}{\varepsilon}$ In this paper, we consider two important problems defined on finite metric spaces, and provide efficient new algorithms and approximation schemes for these problems on inputs given as graph shortest path…
This work considers the problem of computing distances between structured objects such as undirected graphs, seen as probability distributions in a specific metric space. We consider a new transportation distance (i.e. that minimizes a…
Bounded-angle (minimum) spanning trees were first introduced in the context of wireless networks with directional antennas. They are reminiscent of bounded-degree spanning trees, which have received significant attention. Let $P =…
Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of non-treelike evolutionary events, like recombination, hybridization, or lateral gene transfer. In this paper, we present and study a new…
Cartesian tree pattern matching consists of finding all the factors of a text that have the same Cartesian tree than a given pattern. There already exist theoretical and practical solutions for the exact case. In this paper, we propose the…