Related papers: On Computing the Maximum Parsimony Score of a Phyl…
We consider hypergraph network design problems where the goal is to construct a hypergraph that satisfies certain connectivity requirements. For graph network design problems where the goal is to construct a graph that satisfies certain…
Causal Bayesian networks are widely used tools for summarising the dependencies between variables and elucidating their putative causal relationships. By restricting the search to trees, for example, learning the optimum from data is…
One of the main aims in phylogenetics is the estimation of ancestral sequences based on present-day data like, for instance, DNA alignments. One way to estimate the data of the last common ancestor of a given set of species is to first…
Phylogenetic networks are a generalization of phylogenetic trees to leaf-labeled directed acyclic graphs that represent ancestral relationships between species whose past includes non-tree-like events such as hybridization and horizontal…
Phylogenetic trees canonically arise as embeddings of phylogenetic networks. We recently showed that the problem of deciding if two phylogenetic networks embed the same sets of phylogenetic trees is computationally hard, \blue{in…
We study augmenting a plane Euclidean network with a segment, called a shortcut, to minimize the largest distance between any two points along the edges of the resulting network. Problems of this type have received considerable attention…
Reticulate evolution gives rise to complex phylogenetic networks, making their interpretation challenging. A typical approach is to extract trees within such networks. Since Francis and Steel's seminal paper, "Which Phylogenetic Networks…
In this paper we investigate mathematical questions concerning the reliability (reconstruction accuracy) of Fitch's maximum parsimony algorithm for reconstructing the ancestral state given a phylogenetic tree and a character. In particular,…
Phylogenetic networks are increasingly being considered as better suited to represent the complexity of the evolutionary relationships between species. One class of phylogenetic networks that has received a lot of attention recently is the…
Accurate reconstruction of phylogenies remains a key challenge in evolutionary biology. Most biologically plausible formulations of the problem are formally NP-hard, with no known efficient solution. The standard in practice are fast…
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,…
In biodiversity conservation it is often necessary to prioritize the species to conserve. Existing approaches to prioritization, e.g. the Fair Proportion Index and the Shapley Value, are based on phylogenetic trees and rank species…
One of the main aims of phylogenetics is to reconstruct the \enquote{Tree of Life}. In this respect, different methods and criteria are used to analyze DNA sequences of different species and to compare them in order to derive the…
The maximum common subtree isomorphism problem asks for the largest possible isomorphism between subtrees of two given input trees. This problem is a natural restriction of the maximum common subgraph problem, which is ${\sf NP}$-hard in…
Given an edge-weighted graph $G$ on $n$ nodes, the NP-hard Max-Cut problem asks for a node bipartition such that the sum of edge weights joining the different partitions is maximized. We propose a fixed-parameter tractable algorithm…
It is a known fact that, given two rooted binary phylogenetic trees, the concept of maximum acyclic agreement forests is sufficient to compute hybridization networks with minimum hybridization number. In this work, we demonstrate by first…
Modeling the behavior of coupled networks is challenging due to their intricate dynamics. For example in neuroscience, it is of critical importance to understand the relationship between the functional neural processes and anatomical…
Given a graph G, the {\em maximum internal spanning tree problem} (MIST for short) asks for computing a spanning tree T of G such that the number of internal vertices in T is maximized. MIST has possible applications in the design of…
A useful approach to the mathematical analysis of large-scale biological networks is based upon their decompositions into monotone dynamical systems. This paper deals with two computational problems associated to finding decompositions…
Reticulate evolution can be modelled using phylogenetic networks. Tree-based networks, which are one of the more general classes of phylogenetic networks, have recently gained eminence for its ability to represent evolutionary histories…