Related papers: Parameterized Algorithms for Diversity of Networks…

Given a graph $G=(V,E)$, a set $\mathcal{F}$ of forbidden subgraphs, we study $\mathcal{F}$-Free Edge Deletion, where the goal is to remove minimum number of edges such that the resulting graph does not contain any $F\in \mathcal{F}$ as a…

Highly dynamic networks are characterized by frequent changes in the availability of communication links. These networks are often partitioned into several components, which split and merge unpredictably. We present a distributed algorithm…

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…

Driven by the need for better models that allow one to shed light into the question how life's diversity has evolved, phylogenetic networks have now joined phylogenetic trees in the center of phylogenetics research. Like phylogenetic trees,…

Tree-based networks are a class of phylogenetic networks that attempt to formally capture what is meant by "tree-like" evolution. A given non-tree-based phylogenetic network, however, might appear to be very close to being tree-based, or…

Invariants for complicated objects such as those arising in phylogenetics, whether they are invariants as matrices, polynomials, or other mathematical structures, are important tools for distinguishing and working with such objects. In this…

In recent years, graph neural networks (GNNs) have gained increasing attention, as they possess the excellent capability of processing graph-related problems. In practice, hyperparameter optimisation (HPO) is critical for GNNs to achieve…

Food webs have been found to exhibit remarkable motif profiles, patterns in the relative prevalences of all possible three-species sub-graphs, and this has been related to ecosystem properties such as stability and robustness. Analysing 46…

A phylogenetic tree is a way to organize a finite set of species, individuals or other sources of related data. The species for which we have existing DNA data make up the set of leaves of the tree. The balanced minimal evolution method of…

The k-CO-PATH SET problem asks, given a graph G and a positive integer k, whether one can delete k edges from G so that the remainder is a collection of disjoint paths. We give a linear-time fpt algorithm with complexity O^*(1.588^k) for…

Genomes and genes diversify during evolution; however, it is unclear to what extent genes still retain the relationship among species. Model species for molecular phylogenetic studies include yeasts and viruses whose genomes were sequenced…

Finding a globally optimal Bayesian Network using exhaustive search is a problem with super-exponential complexity, which severely restricts the number of variables that it can work for. We implement a dynamic programming based algorithm…

We present linear-time algorithms for partitioning a path or a tree with weights on the vertices by removing $k$ edges to maximize the minimum-weight component. We also use the same framework to partition a path with weight on the vertices,…

A decision problem is called parameterized if its input is a pair of strings. One of these strings is referred to as a parameter. The problem: given a propositional logic program P and a non-negative integer k, decide whether P has a stable…

The notion of $\mathcal{H}$-treewidth, where $\mathcal{H}$ is a hereditary graph class, was recently introduced as a generalization of the treewidth of an undirected graph. Roughly speaking, a graph of $\mathcal{H}$-treewidth at most $k$…

We propose a reinforcement-learning algorithm to tackle the challenge of reconstructing phylogenetic trees. The search for the tree that best describes the data is algorithmically challenging, thus all current algorithms for phylogeny…

In the first paper (part I) of this series of two, we introduce four novel definitions of the ODT problems: three for size-constrained trees and one for depth-constrained trees. These definitions are stated unambiguously through executable…

Phylogenetic diversity is a measure for describing how much of an evolutionary tree is spanned by a subset of species. If one applies this to the (unknown) subset of current species that will still be present at some future time, then this…

In this paper we study the fixed-parameter tractability of the problem of deciding whether a given temporal graph admits a temporal walk that visits all vertices (temporal exploration) or, in some problem variants, a certain subset of the…

Phylogenetic networks are generalizations of phylogenetic trees that allow the representation of reticulation events such as horizontal gene transfer or hybridization, and can also represent uncertainty in inference. A subclass of these,…