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Bayesian networks faithfully represent the symmetric conditional independences existing between the components of a random vector. Staged trees are an extension of Bayesian networks for categorical random vectors whose graph represents…
Phylogenetic trees are leaf-labelled trees, where the leaves correspond to extant species (taxa), and the internal vertices represent ancestral species. The evolutionary history of a set of species can be explained by more than one…
The mode of a collection of values (i.e., the most frequent value in the collection) is a key summary statistic. Finding the mode in a given range of an array of values is thus of great importance, and constructing a data structure to solve…
The identification of cancer genes is a critical yet challenging problem in cancer genomics research. Existing computational methods, including deep graph neural networks, fail to exploit the multilayered gene-gene interactions or provide…
In this paper, we show that any $B_2$-VPG graph (i.e., an intersection graph of orthogonal curves with at most 2 bends) can be decomposed into $O(\log n)$ outerstring graphs or $O(\log^3 n)$ permutation graphs. This leads to better…
We present a deterministic distributed algorithm that computes a $(2\Delta-1)$-edge-coloring, or even list-edge-coloring, in any $n$-node graph with maximum degree $\Delta$, in $O(\log^7 \Delta \log n)$ rounds. This answers one of the…
We consider the problem of exact and inexact matching of weighted undirected graphs, in which a bijective correspondence is sought to minimize a quadratic weight disagreement. This computationally challenging problem is often relaxed as a…
LRM-Trees are an elegant way to partition a sequence of values into sorted consecutive blocks, and to express the relative position of the first element of each block within a previous block. They were used to encode ordinal trees and to…
We present a simple linear-time algorithm that finds a spanning tree $T$ of a given $2$-edge-connected graph $G$ such that each vertex $v$ of $T$ has degree at most $\lceil \frac{\deg_G(v)}{2}\rceil + 1$.
In a graph G, a dissociation set is a subset of vertices which induces a subgraph with vertex degree at most 1. Finding a dissociation set of maximum cardinality in a graph is NP-hard even for bipartite graphs and is called the maximum…
Motivated by applications in cancer genomics and following the work of Hajirasouliha and Raphael (WABI 2014), Hujdurovi\'c et al. (IEEE TCBB, to appear) introduced the minimum conflict-free row split (MCRS) problem: split each row of a…
The minimum height of vertex and edge partition trees are well-studied graph parameters known as, for instance, vertex and edge ranking number. While they are NP-hard to determine in general, linear-time algorithms exist for trees.…
Phylogenetic networks generalise phylogenetic trees and allow for the accurate representation of the evolutionary history of a set of present-day species whose past includes reticulate events such as hybridisation and lateral gene transfer.…
In the Minimum Bisection problem, input is a graph $G$ and the goal is to partition the vertex set into two parts $A$ and $B$, such that $||A|-|B|| \le 1$ and the number $k$ of edges between $A$ and $B$ is minimized. This problem can be…
Let c denote a non-negative constant. Suppose that we are given an edge-weighted bipartite graph G=(V,E) with its 2-layered drawing and a family X of intersecting edge pairs. We consider the problem of finding a maximum weighted matching M*…
We describe approximation algorithms in Linial's classic LOCAL model of distributed computing to find maximum-weight matchings in a hypergraph of rank $r$. Our main result is a deterministic algorithm to generate a matching which is an…
Lateral gene transfer (LGT) is a common mechanism of non-vertical evolution where genetic material is transferred between two more or less distantly related organisms. It is particularly common in bacteria where it contributes to adaptive…
We consider the problem of graph matching, or learning vertex correspondence, between two correlated stochastic block models (SBMs). The graph matching problem arises in various fields, including computer vision, natural language processing…
A phylogenetic tree is a graphical representation of an evolutionary history of taxa in which the leaves correspond to the taxa and the non-leaves correspond to speciations. One of important problems in phylogenetic analysis is to assemble…
The ancestral maximum-likelihood and phylogeography problems are two fundamental problems involving evolutionary studies. The ancestral maximum-likelihood problem involves identifying a rooted tree alongside internal node sequences that…