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Tree ensembles such as random forests (RFs) and gradient boosting machines (GBMs) are among the most widely used supervised learners, yet their theoretical properties remain incompletely understood. We adopt a spectral perspective on these…
Pairwise compatibility graphs (PCGs) with non-negative integer edge weights recently have been used to describe rare evolutionary events and scenarios with horizontal gene transfer. Here we consider the case that vertices are separated by…
Graph matching, also known as network alignment, refers to finding a bijection between the vertex sets of two given graphs so as to maximally align their edges. This fundamental computational problem arises frequently in multiple fields…
In 1998, B\"{o}cker and Dress gave a 1-to-1 correspondence between symbolically dated rooted trees and symbolic ultrametrics. We consider the corresponding problem for unrooted trees. More precisely, given a tree $T$ with leaf set $X$ and a…
The modular decomposition of a symmetric map $\delta\colon X\times X \to \Upsilon$ (or, equivalently, a set of symmetric binary relations, a 2-structure, or an edge-colored undirected graph) is a natural construction to capture key features…
We consider the problem of finding a maximum size triangle-free $2$-matching in a graph $G=(V,E)$. A (simple) $2$-matching is any subset of the edges such that each vertex is incident to at most two edges from the subset. The first…
Given a graph $G=(V,E)$, a $\beta$-ruling set is a subset $S\subseteq V$ that is i) independent, and ii) every node $v\in V$ has a node of $S$ within distance $\beta$. In this paper we present almost optimal distributed algorithms for…
A chief problem in phylogenetics and database theory is the computation of a maximum consistent tree from a set of rooted or unrooted trees. A standard input are triplets, rooted binary trees on three leaves, or quartets, unrooted binary…
The problems studied in this paper originate from Graph Motif, a problem introduced in 2006 in the context of biological networks. Informally speaking, it consists in deciding if a multiset of colors occurs in a connected subgraph of a…
Shortest-path roadmaps, also known as reduced visibility graphs, provides a highly efficient multi-query method for computing optimal paths in two-dimensional environments. Combined with Minkowski sum computations, shortest-path roadmaps…
Evolutionary scenarios displaying reticulation events are often represented by rooted phylogenetic networks. Due to biological reasons, those events occur very rarely, and, thus, networks containing a minimum number of such events,…
Binary jumbled pattern matching asks to preprocess a binary string $S$ in order to answer queries $(i,j)$ which ask for a substring of $S$ that is of length $i$ and has exactly $j$ 1-bits. This problem naturally generalizes to…
Given a connected, undirected graph whose edges are labelled (or coloured), the minimum labelling spanning tree (MLST) problem seeks a spanning tree whose edges have the smallest number of distinct labels (or colours). In recent work, the…
The quest for colorful components (connected components where each color is associated with at most one vertex) inside a vertex-colored graph has been widely considered in the last ten years. Here we consider two variants, Minimum Colorful…
Ecologists have long suspected that species are more likely to interact if their traits match in a particular way. For example, a pollination interaction may be more likely if the proportions of a bee's tongue fit a plant's flower shape.…
Subgraph complementation is an operation that toggles all adjacencies inside a selected vertex set. Given a graph \(G\) and a target class \(\mathcal{C}\), the Minimum Subgraph Complementation problem asks for a minimum-size vertex set…
The popular neighbor-joining (NJ) algorithm used in phylogenetics is a greedy algorithm for finding the balanced minimum evolution (BME) tree associated to a dissimilarity map. From this point of view, NJ is ``optimal'' when the algorithm…
We describe and analyse a simple greedy algorithm \2G\ that finds a good 2-matching $M$ in the random graph $G=G_{n,cn}^{\d\geq 3}$ when $c\geq 15$. A 2-matching is a spanning subgraph of maximum degree two and $G$ is drawn uniformly from…
There are multiple factors which can cause the phylogenetic inference process to produce two or more conflicting hypotheses of the evolutionary history of a set X of biological entities. That is: phylogenetic trees with the same set of leaf…
Binary relations derived from labeled rooted trees play an import role in mathematical biology as formal models of evolutionary relationships. The (symmetrized) Fitch relation formalizes xenology as the pairs of genes separated by at least…