Related papers: On Determining if Tree-based Networks Contain Fixe…
Orthology and paralogy relations are often inferred by methods based on gene similarity, which usually yield a graph depicting the relationships between gene pairs. Such relation graphs are known to frequently contain errors, as they cannot…
Phylogenetic networks have gained prominence over the years due to their ability to represent complex non-treelike evolutionary events such as recombination or hybridization. Popular combinatorial objects used to construct them are triplet…
The search for similarity and dissimilarity measures on phylogenetic trees has been motivated by the computation of consensus trees, the search by similarity in phylogenetic databases, and the assessment of clustering results in…
Deep neural networks (DNNs) and decision trees (DTs) are both state-of-the-art classifiers. DNNs perform well due to their representational learning capabilities, while DTs are computationally efficient as they perform inference along one…
We systematically study the computational complexity of a broad class of computational problems in phylogenetic reconstruction. The class contains for example the rooted triple consistency problem, forbidden subtree problems, the quartet…
We consider the message complexity of verifying whether a given subgraph of the communication network forms a tree with specific properties both in the KT-$\rho$ (nodes know their $\rho$-hop neighborhood, including node IDs) and the KT-$0$…
Semidirected networks have received interest in evolutionary biology as the appropriate generalization of unrooted trees to networks, in which some but not all edges are directed. Yet these networks lack proper theoretical study. We define…
Reconciling a gene tree with a species tree is an important task that reveals much about the evolution of genes, genomes, and species, as well as about the molecular function of genes. A wide array of computational tools have been devised…
An $\alpha$-thin tree $T$ of a graph $G$ is a spanning tree such that every cut of $G$ has at most an $\alpha$ proportion of its edges in $T$. The Thin Tree Conjecture proposes that there exists a function $f$ such that for any $\alpha >…
Random forests on the one hand, and neural networks on the other hand, have met great success in the machine learning community for their predictive performance. Combinations of both have been proposed in the literature, notably leading to…
In evolutionary studies it is common to use phylogenetic trees to represent the evolutionary history of a set of species. However, in case the transfer of genes or other genetic information between the species or their ancestors has…
Galled trees are studied as a recombination model in population genetics. This class of phylogenetic networks is generalized into tree-child, galled and reticulation-visible network classes by relaxing a structural condition imposed on…
Phylogenetic networks are rooted directed acyclic graphs that represent evolutionary relationships between species whose past includes reticulation events such as hybridisation and horizontal gene transfer. To search the space of…
The contraction cost of a tensor network depends on the contraction order. However, the optimal contraction ordering problem is known to be NP-hard. We show that the linear contraction ordering problem for tree tensor networks admits a…
We perform a refined complexity-theoretic analysis of three classical problems in the context of Hierarchical Task Network Planning: the verification of a provided plan, whether an executable plan exists, and whether a given state can be…
In the Maximize Phylogenetic Diversity problem, we are given a phylogenetic tree that represents the genetic proximity of species, and we are asked to select a subset of species of maximum phylogenetic diversity to be preserved through…
A neural network with fixed topology can be regarded as a parametrization of functions, which decides on the correlations between functional variations when parameters are adapted. We propose an analysis, based on a differential geometry…
A tree $t$-spanner of a graph $G$ is a spanning tree of $G$ such that the distance between pairs of vertices in the tree is at most $t$ times their distance in $G$. Deciding tree $t$-spanner admissible graphs has been proved to be tractable…
A tree-based network $\mathcal N$ on $X$ is universal if every rooted binary phylogenetic $X$-tree is a base tree for $\mathcal N$. Hayamizu and, independently, Zhang constructively showed that, for all positive integers $n$, there exists…
We investigate parameterized algorithms for computing the average-tree phylogenetic diversity (APD) in rooted phylogenetic networks, studying the problem under different structural parameters that capture the deviation of a network from a…