Related papers: On Two Measures of Distance between Fully-Labelled…

Each gene has its own evolutionary history which can substantially differ from the evolutionary histories of other genes. For example, some individual genes or operons can be affected by specific horizontal gene transfer and recombination…

Riemannian optimization uses local methods to solve optimization problems whose constraint set is a smooth manifold. A linear step along some descent direction usually leaves the constraints, and hence retraction maps are used to…

We introduce a semiparametric approach to neighbor-based classification. We build off the recently proposed Boundary Trees algorithm by Mathy et al.(2015) which enables fast neighbor-based classification, regression and retrieval in large…

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…

In this paper, we explore the theory and expand upon the practice of fitness landscape analysis for optimization problems over the space of permutations. Many of the computational and analytical tools for fitness landscape analysis, such as…

Many different metrics exist for evaluating parsing results, including Viterbi, Crossing Brackets Rate, Zero Crossing Brackets Rate, and several others. However, most parsing algorithms, including the Viterbi algorithm, attempt to optimize…

This paper introduces constNJ, the first algorithm for phylogenetic reconstruction of sets of trees with constrained pairwise rooted subtree-prune regraft (rSPR) distance. We are motivated by the problem of constructing sets of trees which…

Contemporary accelerator designs exhibit a high degree of spatial localization, wherein two-dimensional physical distance determines communication costs between processing elements. This situation presents considerable algorithmic…

In this paper we present a simple framework to study various distance problems of permutations, including the transposition and block-interchange distance of permutations as well as the reversal distance of signed permutations. These…

Following Poupard's study of strictly ordered binary trees with respect to two parameters, namely, "end of minimal chain" and "parent of maximum leaf" a true Tree Calculus is being developed to solve a partial difference equation system and…

We present a new approximation algorithm for the treewidth problem which finds an upper bound on the treewidth and constructs a corresponding tree decomposition as well. Our algorithm is a faster variation of Reed's classical algorithm. For…

The tree inclusion problem is, given two node-labeled trees $P$ and $T$ (the ``pattern tree'' and the ``target tree''), to locate every minimal subtree in $T$ (if any) that can be obtained by applying a sequence of node insertion operations…

We develop the complex-analytic viewpoint on the tree convolutions studied by the second author and Weihua Liu in "An operad of non-commutative independences defined by trees" (Dissertationes Mathematicae, 2020, doi:10.4064/dm797-6-2020),…

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…

The structure of an evolving network contains information about its past. Extracting this information efficiently, however, is, in general, a difficult challenge. We formulate a fast and efficient method to estimate the most likely history…

We observe $n$ sequences at each of $m$ sites, and assume that they have evolved from an ancestral sequence that forms the root of a binary tree of known topology and branch lengths, but the sequence states at internal nodes are unknown.…

We provide time- and sample-efficient algorithms for learning and testing latent-tree Ising models, i.e. Ising models that may only be observed at their leaf nodes. On the learning side, we obtain efficient algorithms for learning a…

We show that the problem of constructing tree-structured descriptions of data layouts that are optimal with respect to space or other criteria from given sequences of displacements, can be solved in polynomial time. The problem is relevant…

In this study, we investigate the problem of comparing gene trees reconciled with the same species tree using a novel semi-metric, called the Path-Label Reconciliation (PLR) dissimilarity measure. This approach not only quantifies…

We present an unusual algorithm involving classification trees where two trees are grown in opposite directions so that they are matched at their leaves. This approach finds application in a new data mining task we formulate, called…