Related papers: Reduction rules for the maximum parsimony distance…
In many interesting cases the reconstruction of a correct phylogeny is blurred by high mutation rates and/or horizontal transfer events. As a consequence a divergence arises between the true evolutionary distances and the differences…
Brambles were introduced as the dual notion to treewidth, one of the most central concepts of the graph minor theory of Robertson and Seymour. Recently, Grohe and Marx showed that there are graphs G, in which every bramble of order larger…
The subtrees and BC-subtrees (subtrees where any two leaves are at even distance apart) have been extensively studied in recent years. Such structures, under special constraints on degrees, have applications in many fields. Through an…
In this paper we introduce and study three new measures for efficient discriminative comparison of phylogenetic trees. The NNI navigation dissimilarity $d_{nav}$ counts the steps along a "combing" of the Nearest Neighbor Interchange (NNI)…
The problem of comparing trees representing the evolutionary histories of cancerous tumors has turned out to be crucial, since there is a variety of different methods which typically infer multiple possible trees. A departure from the…
Motivated by comparative genomics, Chen et al. [9] introduced the Maximum Duo-preservation String Mapping (MDSM) problem in which we are given two strings $s_1$ and $s_2$ from the same alphabet and the goal is to find a mapping $\pi$…
With applications in distribution systems and communication networks, the minimum stretch spanning tree problem is to find a spanning tree T of a graph G such that the maximum distance in T between two adjacent vertices is minimized. 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…
In phylogenetics, a central problem is to infer the evolutionary relationships between a set of species $X$; these relationships are often depicted via a phylogenetic tree -- a tree having its leaves univocally labeled by elements of $X$…
Geodesic distance, sometimes called shortest path length, has proven useful in a great variety of applications, such as information retrieval on networks including treelike networked models. Here, our goal is to analytically determine the…
In phylogenetic networks, it is desirable to estimate edge lengths in substitutions per site or calendar time. Yet, there is a lack of scalable methods that provide such estimates. Here we consider the problem of obtaining edge length…
The full strong branching (FSB) rule is well known to produce extremely small branch-and-bound trees. This rule guides branching decisions based exclusively on the information regarding local gains in the linear programming (LP) bounds. We…
We identify a sufficient condition, treewidth-pliability, that gives a polynomial-time algorithm for an arbitrarily good approximation of the optimal value in a large class of Max-2-CSPs parameterised by the class of allowed constraint…
In the laminar-constrained spanning tree problem, the goal is to find a minimum-cost spanning tree which respects upper bounds on the number of times each cut in a given laminar family is crossed. This generalizes the well-studied…
Fitting distances to tree metrics and ultrametrics are two widely used methods in hierarchical clustering, primarily explored within the context of numerical taxonomy. Given a positive distance function…
The maximum parsimony phylogenetic tree reconstruction problem is NP-hard, presenting a computational bottleneck for classical computing and motivating the exploration of emerging paradigms like quantum computing. To this end, we design…
Merge trees are a type of graph-based topological summary that tracks the evolution of connected components in the sublevel sets of scalar functions. They enjoy widespread applications in data analysis and scientific visualization. In this…
Given a rooted point set $P$, the rooted $y-$Monotone Minimum Spanning Tree (rooted $y-$MMST) of $P$ is the spanning geometric graph of $P$ in which all the vertices are connected to the root by some $y-$monotone path and the sum of the…
Recently, $p$-presentation distances for $p\in [1,\infty]$ were introduced for merge trees and multiparameter persistence modules as more sensitive variations of the respective interleaving distances ($p=\infty)$. It is well-known that…
Many popular algorithms for searching the space of leaf-labelled trees are based on tree rearrangement operations. Under any such operation, the problem is reduced to searching a graph where vertices are trees and (undirected) edges are…