Related papers: Constructing minimal phylogenetic networks from so…

Recently, so-called treebased phylogenetic networks have gained considerable interest in the literature, where a treebased network is a network that can be constructed from a phylogenetic tree, called the base tree, by adding additional…

Connectivity problems like k-Path and k-Disjoint Paths relate to many important milestones in parameterized complexity, namely the Graph Minors Project, color coding, and the recent development of techniques for obtaining kernelization…

Phylogenetic network is an evolutionary model that uses a rooted directed acyclic graph (instead of a tree) to model an evolutionary history of species in which reticulate events (e.g., hybrid speciation or horizontal gene transfer)…

Let $\mathcal{T}$ be an unrooted binary tree with $n$ distinctly labelled leaves. Deriving its name from the field of phylogenetics, a convex character on $\mathcal{T}$ is simply a partition of the leaves such that the minimal spanning…

It is commonly believed that real networks are scale-free and fraction of nodes $P(k)$ with degree $k$ satisfies the power law $P(k) \propto k^{-\gamma} \text{ for } k > k_{min} > 0$. Preferential attachment is the mechanism that has been…

We study the problem of explainable clustering in the setting first formalized by Dasgupta, Frost, Moshkovitz, and Rashtchian (ICML 2020). A $k$-clustering is said to be explainable if it is given by a decision tree where each internal node…

The inference of phylogenetic networks, which model complex evolutionary processes including hybridization and gene flow, remains a central challenge in evolutionary biology. Until now, statistically consistent inference methods have been…

Evolutionary histories for species that cross with one another or exchange genetic material can be represented by leaf-labelled, directed graphs called phylogenetic networks. A major challenge in the burgeoning area of phylogenetic networks…

We consider the NP-hard Tree Containment problem that has important applications in phylogenetics. The problem asks if a given leaf-labeled network contains a subdivision of a given leaf-labeled tree. We develop a fast algorithm for the…

In temporal ordered clustering, given a single snapshot of a dynamic network in which nodes arrive at distinct time instants, we aim at partitioning its nodes into $K$ ordered clusters $\mathcal{C}_1 \prec \cdots \prec \mathcal{C}_K$ such…

Given a static vertex-selection problem (e.g. independent set, dominating set) on a graph, we can define a corresponding temporally satisfying reconfiguration problem on a temporal graph which asks for a sequence of solutions to the…

A graph is a $k$-leaf power of a tree $T$ if its vertices are leaves of $T$ and two vertices are adjacent in $T$ if and only if their distance in $T$ is at most $k$. Then $T$ is a $k$-leaf root of $G$. This notion was introduced by…

We construct a fixed parameter algorithm parameterized by d and k that takes as an input a graph G' obtained from a d-degenerate graph G by complementing on at most k arbitrary subsets of the vertex set of G and outputs a graph H such that…

In this work we employ machine learning to understand structured mathematical data involving finite groups and derive a theorem about necessary properties of generators of finite simple groups. We create a database of all 2-generated…

A temporal network is a dynamic graph where every edge is assigned an integer time label that indicates at which discrete time step the edge is available. We consider the problem of hierarchically decomposing the network and introduce an…

Phylogenetic networks are used to represent evolutionary scenarios in biology and linguistics. To find the most probable scenario, it may be necessary to compare candidate networks, to distinguish different networks, and to see when one…

For a family of graphs $\mathcal{G}$, the $\mathcal{G}$-\textsc{Contraction} problem takes as an input a graph $G$ and an integer $k$, and the goal is to decide if there exists $F \subseteq E(G)$ of size at most $k$ such that $G/F$ belongs…

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…

In phylogenetics, it is important for the phylogenetic network model parameters to be identifiable so that the evolutionary histories of a group of species can be consistently inferred. However, as the complexity of the phylogenetic network…

For a finite collection of graphs ${\cal F}$, the \textsc{${\cal F}$-TM-Deletion} problem has as input an $n$-vertex graph $G$ and an integer $k$ and asks whether there exists a set $S \subseteq V(G)$ with $|S| \leq k$ such that $G…