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Dynamic programming over tree decompositions is a common technique in parameterized algorithms. In this paper, we study whether this technique can also be applied to compute Pareto sets of multiobjective optimization problems. We first…
Agreement forests continue to play a central role in the comparison of phylogenetic trees since their introduction more than 25 years ago. More specifically, they are used to characterise several distances that are based on tree…
In this work we study the interleaving distance between merge trees from a combinatorial point of view. We use a particular type of matching between trees to obtain a novel formulation of the distance. With such formulation, we tackle the…
Evolution is a process that is influenced by various environmental factors, e.g. the interactions between different species, genes, and biogeographical properties. Hence, it is interesting to study the combined evolutionary history of…
The basic goal of survivable network design is to build cheap networks that guarantee the connectivity of certain pairs of nodes despite the failure of a few edges or nodes. A celebrated result by Jain [Combinatorica'01] provides a…
Several algorithms build on the perfect phylogeny model to infer evolutionary trees. This problem is particularly hard when evolutionary trees are inferred from the fraction of genomes that have mutations in different positions, across…
The Forest Augmentation Problem (FAP) asks for a minimum set of additional edges (links) that make a given forest 2-edge-connected while spanning all vertices. A key special case is the Path Augmentation Problem (PAP), where the input…
The Mutliagent Path Finding (MAPF) problem consists of identifying the trajectories that a set of agents should follow inside a given network in order to reach their desired destinations as soon as possible, but without colliding with each…
Different sources of information might tell different stories about the evolutionary history of a given set of species. This leads to (rooted) phylogenetic trees that "disagree" on triples of species, which we call "conflict triples". An…
We present the first sub-quadratic time algorithm that with high probability correctly reconstructs phylogenetic trees for short sequences generated by a Markov model of evolution. Due to rapid expansion in sequence databases, such very…
We define a search problem on trees that closely captures the backtracking behavior of all current practical graph isomorphism algorithms. Given two trees with colored leaves, the goal is to find two leaves of matching color, one in each of…
We study approximation algorithms for the forest cover and bounded forest cover problems. A probabilistic $2+\epsilon$ approximation algorithm for the forest cover problem is given using the method of dual fitting. A deterministic algorithm…
A \emph{binary tanglegram} is a drawing of a pair of rooted binary trees whose leaf sets are in one-to-one correspondence; matching leaves are connected by inter-tree edges. For applications, for example, in phylogenetics, it is essential…
A merge tree is a fundamental topological structure used to capture the sub-level set (and similarly, super-level set) topology in scalar data analysis. The interleaving distance is a theoretically sound, stable metric for comparing merge…
The problem of constructing optimal factoring automata arises in the context of unification factoring for the efficient execution of logic programs. Given an ordered set of $n$ strings of length $m$, the problem is to construct a trie-like…
The subtree prune-and-regraft (SPR) distance metric is a fundamental way of comparing evolutionary trees. It has wide-ranging applications, such as to study lateral genetic transfer, viral recombination, and Markov chain Monte Carlo…
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…
In the longest plane spanning tree problem, we are given a finite planar point set $\mathcal{P}$, and our task is to find a plane (i.e., noncrossing) spanning tree for $\mathcal{P}$ with maximum total Euclidean edge length. Despite more…
Random Forests (RF) and Extreme Gradient Boosting (XGBoost) are two of the most widely used and highly performing classification and regression models. They aggregate equally weighted CART trees, generated randomly in RF or sequentially in…
Recently, a new vector encoding, Ordered Leaf Attachment (OLA), was introduced that represents $n$-leaf phylogenetic trees as $n-1$ length integer vectors by recording the placement location of each leaf. Both encoding and decoding of trees…