Related papers: A polynomial time algorithm for calculating the pr…

A normal network is uniquely determined by the set of phylogenetic trees that it displays. Given a set $\mathcal{P}$ of rooted binary phylogenetic trees, this paper presents a polynomial-time algorithm that reconstructs the unique binary…

We propose a reinforcement-learning algorithm to tackle the challenge of reconstructing phylogenetic trees. The search for the tree that best describes the data is algorithmically challenging, thus all current algorithms for phylogeny…

The method for analyzing algorithmic runtime complexity using decision trees is discussed using the sorting algorithm. This method is then extended to optimal algorithms which may find all cliques of size q in network N, or simply the first…

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 calculate the probability distribution of repetitions of ancestors in a genealogical tree for simple neutral models of a closed population with sexual reproduction and non-overlapping generations. Each ancestor at generation g in the…

Phylogenetic networks are often constructed by merging multiple conflicting phylogenetic signals into a directed acyclic graph. It is interesting to explore whether a network constructed in this way induces biologically-relevant…

Background: Tree reconciliation problems have long been studied in phylogenetics. A particular variant of the reconciliation problem for a gene tree T and a species tree S assumes that for each interior vertex x of T it is known whether x…

The Hausdorff distance is a relatively new measure of similarity of graphs. The notion of the Hausdorff distance considers a special kind of a common subgraph of the compared graphs and depends on the structural properties outside of the…

In this paper, we present a distributed algorithm to compute various parameters of a tree such as the process number, the edge search number or the node search number and so the pathwidth. This algorithm requires n steps, an overall…

The graph isomorphism problem is theoretically interesting and also has many practical applications. The best known classical algorithms for graph isomorphism all run in time super-polynomial in the size of the graph in the worst case. An…

Suppose $P$ is a symmetric convex polygon in the plane. We give a polynomial time algorithm that decides if $P$ can tile the plane by transations at some level (not necessarily at level one; this is multiple tiling). The main technical…

Tree search is a fundamental tool for planning, as many sequential decision-making problems can be framed as searching over tree-structured spaces. We propose an uncertainty-guided tree search algorithm for settings where the reward…

Reconstructing the tree of life from molecular sequences is a fundamental problem in computational biology. Modern data sets often contain a large number of genes, which can complicate the reconstruction problem due to the fact that…

This paper studies the relationship between undirected (unrooted) and directed (rooted) phylogenetic networks. We describe a polynomial-time algorithm for deciding whether an undirected nonbinary phylogenetic network, given the locations of…

In recent years, a number of methods have been developed to infer complex demographic histories, especially historical population size changes, from genomic sequence data. Coalescent Hidden Markov Models have proven to be particularly…

We give a greedy learning algorithm for reconstructing an evolutionary tree based on a certain harmonic average on triplets of terminal taxa. After the pairwise distances between terminal taxa are estimated from sequence data, the algorithm…

We investigate the complexity of several fundamental polynomial-time solvable problems on graphs and on matrices, when the given instance has low treewidth; in the case of matrices, we consider the treewidth of the graph formed by non-zero…

Gene gain-loss-duplication models are commonly based on continuous-time birth-death processes. Employed in a phylogenetic context, such models have been increasingly popular in studies of gene content evolution across multiple genomes.…

The MULTICUT IN TREES problem consists in deciding, given a tree, a set of requests (i.e. paths in the tree) and an integer k, whether there exists a set of k edges cutting all the requests. This problem was shown to be FPT by Guo and…

We consider the problem of inferring the topology of a network using the measurements available at the end nodes, without cooperation from the internal nodes. To this end, we provide a simple method to obtain path interference which…