Related papers: Using the tangle: a consistent construction of phy…
We demonstrate the use of computational phylogenetic techniques to solve a central problem in inferential network monitoring. More precisely, we design a novel algorithm for multicast-based delay inference, i.e. the problem of…
Phylogenetic inference can potentially result in a more accurate tree using data from multiple loci. However, if the loci are incongruent--due to events such as incomplete lineage sorting or horizontal gene transfer--it can be misleading to…
Phylogenetic reconstruction aims at finding plausible hypotheses of the evolutionary history of genes or species based on genomic sequence information. The distinction of orthologous genes (genes that having a common ancestry and diverged…
Historical linguistics aims at inferring the most likely language phylogenetic tree starting from information concerning the evolutionary relatedness of languages. The available information are typically lists of homologous (lexical,…
Background: The reconstruction of the phylogenetic tree topology of four taxa is, still nowadays, one of the main challenges in phylogenetics. Its difficulties lie in considering not too restrictive evolutionary models, and correctly…
Learning the distance metric between pairs of examples is of great importance for learning and visual recognition. With the remarkable success from the state of the art convolutional neural networks, recent works have shown promising…
Phylogenetic networks are used to represent the evolutionary history of species. Recently, the new class of orchard networks was introduced, which were later shown to be interpretable as trees with additional horizontal arcs. This makes the…
Agreement forests continue to play a central role in the comparison of phylogenetic trees since their introduction more than 25 years ago. More specifically, they are used to characterise several distances that are based on tree…
Let $T$ be an arbitrary phylogenetic tree with $n$ leaves. It is well-known that the average quartet distance between two assignments of taxa to the leaves of $T$ is $\frac 23 \binom{n}{4}$. However, a longstanding conjecture of Bandelt and…
Complex networks can be used for modeling street meshes and urban agglomerates. With such a model, many aspects of a city can be investigated to promote a better quality of life to its citizens. Along these lines, this paper proposes a set…
This paper relates parameter distance to gradient breakdown for a broad class of nonlinear compositional functions. The analysis leads to a new distance function called deep relative trust and a descent lemma for neural networks. Since the…
Galled trees, directed acyclic graphs that model evolutionary histories with isolated hybridization events, have become very popular due to both their biological significance and the existence of polynomial time algorithms for their…
A phylogenetic network is a directed acyclic graph that visualises an evolutionary history containing so-called reticulations such as recombinations, hybridisations or lateral gene transfers. Here we consider the construction of a simplest…
Merge trees are fundamental structures in topological data analysis. Interleaving distance is a widely accepted metric for comparing merge trees, with applications in visualization and scientific computing. While a greedy algorithm exists…
Phylogenetic networks which are, as opposed to trees, suitable to describe processes like hybridization and horizontal gene transfer, play a substantial role in evolutionary research. However, while non-treelike events need to be taken into…
Understanding the emergence of biodiversity patterns in nature is a central problem in biology. Theoretical models of speciation have addressed this question in the macroecological scale, but little has been investigated in the…
Dissimilarity measures for (possibly weighted) phylogenetic trees based on the comparison of their vectors of path lengths between pairs of taxa, have been present in the systematics literature since the early seventies. But, as far as…
Clustering is an important part of many modern data analysis pipelines, including network analysis and data retrieval. There are many different clustering algorithms developed by various communities, and it is often not clear which…
Evolutionary mechanism in a self-organized system cause some functional changes that force to adapt new conformation of the interaction pattern between the components of that system. Measuring the structural differences one can retrace the…
Protein structural alignment is an important problem in computational biology. In this paper, we present first successes on provably optimal pairwise alignment of protein inter-residue distance matrices, using the popular Dali scoring…