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Typing methods are widely used in the surveillance of infectious diseases, outbreaks investigation and studies of the natural history of an infection. And their use is becoming standard, in particular with the introduction of High…
A graph G is a k-leaf power, for an integer k >= 2, if there is a tree T with leaf set V(G) such that, for all vertices x, y in V(G), the edge xy exists in G if and only if the distance between x and y in T is at most k. Such a tree T is…
This paper introduces constNJ, the first algorithm for phylogenetic reconstruction of sets of trees with constrained pairwise rooted subtree-prune regraft (rSPR) distance. We are motivated by the problem of constructing sets of trees which…
For a model of molecular evolution to be useful for phylogenetic inference, the topology of evolutionary trees must be identifiable. That is, from a joint distribution the model predicts, it must be possible to recover the tree parameter.…
Merge trees are a type of graph-based topological summary that tracks the evolution of connected components in the sublevel sets of scalar functions. They enjoy widespread applications in data analysis and scientific visualization. In this…
Graphs are interesting structures: extremely useful to depict real-life problems, extremely easy to understand given a sketch, extremely complicated to represent formally, extremely complicated to compare. Phylogeny is the study of the…
Consider a population that is expanding in two-dimensional space. Suppose we collect data from a sample of individuals taken at random either from the entire population, or from near the outer boundary of the population. A quantity of…
Phylogenetic trees are leaf-labelled trees used to model the evolution of species. In practice it is not uncommon to obtain two topologically distinct trees for the same set of species, and this motivates the use of distance measures to…
Relying on recent advances in statistical estimation of covariance distances based on random matrix theory, this article proposes an improved covariance and precision matrix estimation for a wide family of metrics. The method is shown to…
Reachability and shortest path problems are NL-complete for general graphs. They are known to be in L for graphs of tree-width 2 [JT07]. However, for graphs of tree-width larger than 2, no bound better than NL is known. In this paper, we…
Phylogenetic networks extend phylogenetic trees to model non-vertical inheritance, by which a lineage inherits material from multiple parents. The computational complexity of estimating phylogenetic networks from genome-wide data with…
Inference of network-like evolutionary relationships between species from genomic data must address the interwoven signals from both gene flow and incomplete lineage sorting. The heavy computational demands of standard approaches to this…
Ecological spatial patterns reflect the underlying processes that shape the structure of species and communities. Mechanisms like inter and intra species competition, dispersal and host-pathogen interactions are believed to act over a wide…
The reconstruction of phylogenies from DNA or protein sequences is a major task of computational evolutionary biology. Common phenomena, notably variations in mutation rates across genomes and incongruences between gene lineage histories,…
A variety of algorithms have been proposed for reconstructing trees that show the evolutionary relationships between species by comparing differences in genetic data across present-day taxa. If the leaf-to-leaf distances in a tree can be…
We study a fundamental issue in cosmology: Whether we can rely on a cosmological model to understand the real history of the Universe. This fundamental, still unresolved issue is often called the ``model-fitting problem (or averaging…
This paper explores hierarchical clustering in the case where pairs of points have dissimilarity scores (e.g. distances) as a part of the input. The recently introduced objective for points with dissimilarity scores results in every tree…
This paper presents the Cascaded Metric Tree (CMT) for efficient satisfaction of metric search queries over a dataset of N objects. It provides extra information that permits query algorithms to exploit all distance calculations performed…
Survival trees are popular alternatives to Cox or Aalen regression models that offer both modelling flexibility and graphical interpretability. This paper introduces a new algorithm for survival trees that relaxes the assumption of…
We begin with an interpretation of the L1-distance between two power spectral densities and then, following an analogous rationale, we develop a natural metric for quantifying distance between respective covariance matrices.