Related papers: Parameterized Algorithms for the Maximum Agreement…
We study the crossing-minimization problem in a layered graph drawing of planar-embedded rooted trees whose leaves have a given total order on the first layer, which adheres to the embedding of each individual tree. The task is then to…
This paper presents an efficient algorithm for retrieving from a database of trees, all trees that match a given query tree approximately, that is, within a certain error tolerance. It has natural language processing applications in…
Random forests are among the most popular classification and regression methods used in industrial applications. To be effective, the parameters of random forests must be carefully tuned. This is usually done by choosing values that…
The Persistent-Phylogeny Model is an extension of the widely studied Perfect-Phylogeny Model, encompassing a broader range of evolutionary phenomena. Biological and algorithmic questions concerning persistent phylogeny have been intensely…
Given two graphs $H$ and $G$, the Subgraph Isomorphism problem asks if $H$ is isomorphic to a subgraph of $G$. While NP-hard in general, algorithms exist for various parameterized versions of the problem: for example, the problem can be…
The input to the agreement problem is a collection $P = \{T_1, T_2, \dots , T_k\}$ of phylogenetic trees, called input trees, over partially overlapping sets of taxa. The question is whether there exists a tree $T$, called an agreement…
Network Phylogenetic Diversity (Network-PD) is a measure for the diversity of a set of species based on a rooted phylogenetic network (with branch lengths and inheritance probabilities on the reticulation edges) describing the evolution of…
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…
Random forests and, more generally, (decision\nobreakdash-)tree ensembles are widely used methods for classification and regression. Recent algorithmic advances allow to compute decision trees that are optimal for various measures such as…
With the development of connected filters for the last decade, many algorithms have been proposed to compute the max-tree. Max-tree allows to compute the most advanced connected operators in a simple way. However, no fair comparison of…
Treewidth and hypertree width have proven to be highly successful structural parameters in the context of the Constraint Satisfaction Problem (CSP). When either of these parameters is bounded by a constant, then CSP becomes solvable in…
The amount of completely sequenced chloroplast genomes increases rapidly every day, leading to the possibility to build large-scale phylogenetic trees of plant species. Considering a subset of close plant species defined according to their…
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…
We investigate the parameterized complexity of the Isometric Path Partition problem when parameterized by the treewidth ($\mathrm{tw}$) of the input graph, arguably one of the most widely studied parameters. Courcelle's theorem shows that…
Construction of phylogenetic trees and networks for extant species from their characters represents one of the key problems in phylogenomics. While solution to this problem is not always uniquely defined and there exist multiple methods for…
Phylogenetic networks are a flexible model of evolution that can represent reticulate evolution and handle complex data. Tree-based networks, which are phylogenetic networks that have a spanning tree with the same root and leaf-set as the…
In the PATH COVER problem, one asks to cover the vertices of a graph using the smallest possible number of (not necessarily disjoint) paths. While the variant where the paths need to be pairwise vertex-disjoint, which we call PATH…
Most of major algorithms for phylogenetic tree reconstruction assume that sequences in the analyzed set either do not have any offspring, or that parent sequences can maximally mutate into just two descendants. The graph resulting from such…
In the \textsc{Maximum Degree Contraction} problem, input is a graph $G$ on $n$ vertices, and integers $k, d$, and the objective is to check whether $G$ can be transformed into a graph of maximum degree at most $d$, using at most $k$ edge…
We initiate the study of tree structures in the context of scenario-based robust optimization. Specifically, we study Binary Search Trees (BSTs) and Huffman coding, two fundamental techniques for efficiently managing and encoding data based…