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For a metric graph $G=(V,E)$ and $R\subset V$, the internal Steiner minimum tree problem asks for a minimum weight Steiner tree spanning $R$ such that every vertex in $R$ is not a leaf. This note shows a simple polynomial-time…
Distance-based phylogenetic algorithms attempt to solve the NP-hard least squares phylogeny problem by mapping an arbitrary dissimilarity map representing biological data to a tree metric. The set of all dissimilarity maps is a Euclidean…
Edit distance between trees is a natural generalization of the classical edit distance between strings, in which the allowed elementary operations are contraction, uncontraction and relabeling of an edge. Demaine et al. [ACM Trans. on…
In evolutionary biology, phylogenetic networks are constructed to represent the evolution of species in which reticulate events are thought to have occurred, such as recombination and hybridization. It is therefore useful to have…
Given a graph G, the {\em maximum internal spanning tree problem} (MIST for short) asks for computing a spanning tree T of G such that the number of internal vertices in T is maximized. MIST has possible applications in the design of…
Comparative analyses of phylogenetic trees typically require identical taxon sets, however, in practice, trees often include distinct but overlapping taxa. Pruning non-shared leaves discards phylogenetic signal, whereas tree completion can…
Computing the rotation distance between two binary trees with $n$ internal nodes efficiently (in $poly(n)$ time) is a long standing open question in the study of height balancing in tree data structures. In this paper, we initiate the study…
We present a new approximation algorithm for the minimum 2-edge-connected spanning subgraph problem. Its approximation ratio is $\frac{4}{3}$, which matches the current best ratio. The approximation ratio of the algorithm is $\frac{6}{5}$…
We describe the first strongly subquadratic time algorithm with subexponential approximation ratio for approximately computing the Fr\'echet distance between two polygonal chains. Specifically, let $P$ and $Q$ be two polygonal chains with…
Self-nested trees present a systematic form of redundancy in their subtrees and thus achieve optimal compression rates by DAG compression. A method for quantifying the degree of self-similarity of plants through self-nested trees has been…
Prediction suffix trees (PST) provide an effective tool for sequence modelling and prediction. Current prediction techniques for PSTs rely on exact matching between the suffix of the current sequence and the previously observed sequence. We…
The problem of finding the shortest path for a vehicle visiting a given sequence of target points subject to the motion constraints of the vehicle is an important problem that arises in several monitoring and surveillance applications…
There are several tools available to infer phylogenetic trees, which depict the evolutionary relationships among biological entities such as viral and bacterial strains in infectious outbreaks, or cancerous cells in tumor progression trees.…
We design new approximation algorithms for the Multiway Cut problem, improving the previously known factor of 1.32388 [Buchbinder et al., 2013]. We proceed in three steps. First, we analyze the rounding scheme of Buchbinder et al., 2013 and…
Sparse residual tree (SRT) is an adaptive exploration method for multivariate scattered data approximation. It leads to sparse and stable approximations in areas where the data is sufficient or redundant, and points out the possible local…
Rotation distances measure the differences in structure between rooted ordered binary trees. The one-dimensional skeleta of associahedra are rotation graphs, where two vertices representing trees are connected by an edge if they differ by a…
We consider the classical tree edit distance between ordered labeled trees, which is defined as the minimum-cost sequence of node edit operations that transform one tree into another. The state-of-the-art solutions for the tree edit…
We present new and improved fixed-parameter algorithms for computing maximum agreement forests (MAFs) of pairs of rooted binary phylogenetic trees. The size of such a forest for two trees corresponds to their subtree prune-and-regraft…
Tree rotations (left and right) are basic local deformations allowing to transform between two unlabeled binary trees of the same size. Hence, there is a natural problem of practically finding such transformation path with low number of…
We propose an algorithm named best-scored random forest for binary classification problems. The terminology "best-scored" means to select the one with the best empirical performance out of a certain number of purely random tree candidates…